Query psy13439
Match_columns 261
No_of_seqs 196 out of 2132
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 19:26:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13439.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13439hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1054|consensus 100.0 4.4E-42 9.6E-47 316.8 3.2 206 8-259 454-662 (897)
2 KOG1053|consensus 100.0 1.2E-34 2.5E-39 277.0 14.0 201 13-261 479-679 (1258)
3 KOG4440|consensus 100.0 1.2E-33 2.5E-38 262.4 10.8 202 10-261 473-683 (993)
4 KOG1052|consensus 100.0 9.6E-31 2.1E-35 256.9 9.4 194 10-260 255-449 (656)
5 PF00060 Lig_chan: Ligand-gate 99.7 1.1E-18 2.4E-23 139.8 -5.9 73 187-260 40-112 (148)
6 PRK10797 glutamate and asparta 98.3 1.2E-06 2.5E-11 78.8 5.7 80 31-119 90-169 (302)
7 PRK11917 bifunctional adhesin/ 98.2 2.5E-06 5.3E-11 74.9 5.1 80 32-120 86-165 (259)
8 COG0834 HisJ ABC-type amino ac 98.0 9.4E-06 2E-10 70.6 5.4 57 30-86 80-136 (275)
9 PF10613 Lig_chan-Glu_bd: Liga 98.0 7.4E-06 1.6E-10 56.6 3.7 40 6-45 24-65 (65)
10 PF00497 SBP_bac_3: Bacterial 97.9 1.8E-05 3.8E-10 66.1 5.4 62 11-83 33-94 (225)
11 PRK15437 histidine ABC transpo 97.9 2.2E-05 4.8E-10 68.5 5.9 56 31-86 69-124 (259)
12 PRK09495 glnH glutamine ABC tr 97.9 2.2E-05 4.8E-10 67.8 5.7 60 32-91 68-128 (247)
13 PRK15010 ABC transporter lysin 97.8 3.5E-05 7.6E-10 67.2 6.0 83 31-122 69-152 (260)
14 TIGR03870 ABC_MoxJ methanol ox 97.7 6E-05 1.3E-09 65.4 5.9 79 31-120 39-123 (246)
15 TIGR02995 ectoine_ehuB ectoine 97.7 5.1E-05 1.1E-09 66.9 5.3 55 31-85 76-130 (275)
16 PRK15007 putative ABC transpor 97.6 0.00015 3.2E-09 62.2 6.9 53 31-83 64-116 (243)
17 PRK10859 membrane-bound lytic 97.6 9.1E-05 2E-09 70.8 5.6 52 33-84 87-138 (482)
18 PRK00489 hisG ATP phosphoribos 97.3 0.00027 5.8E-09 63.1 5.0 87 5-91 17-110 (287)
19 PRK11260 cystine transporter s 97.3 0.00042 9.1E-09 60.6 5.8 54 31-84 84-137 (266)
20 TIGR02285 conserved hypothetic 97.3 0.00031 6.6E-09 61.6 4.6 53 31-84 61-114 (268)
21 TIGR01096 3A0103s03R lysine-ar 97.3 0.0005 1.1E-08 59.1 5.6 55 31-85 67-121 (250)
22 PRK09959 hybrid sensory histid 97.2 0.00038 8.2E-09 73.3 5.4 58 31-88 100-158 (1197)
23 cd00134 PBPb Bacterial peripla 96.6 0.0049 1.1E-07 50.1 6.1 60 32-91 43-102 (218)
24 TIGR03871 ABC_peri_MoxJ_2 quin 96.5 0.0049 1.1E-07 52.3 5.6 45 36-84 46-90 (232)
25 smart00062 PBPb Bacterial peri 96.5 0.0061 1.3E-07 49.4 5.7 60 33-92 45-104 (219)
26 PF07885 Ion_trans_2: Ion chan 95.8 0.021 4.6E-07 40.6 4.8 57 189-245 22-78 (79)
27 PRK09959 hybrid sensory histid 95.4 0.019 4.2E-07 60.6 4.9 51 33-84 348-398 (1197)
28 KOG1053|consensus 94.6 0.031 6.7E-07 56.1 3.4 67 143-235 559-625 (1258)
29 COG4623 Predicted soluble lyti 94.2 0.063 1.4E-06 49.4 4.4 83 4-86 12-120 (473)
30 TIGR01098 3A0109s03R phosphate 93.4 0.09 2E-06 45.2 3.8 60 33-92 71-139 (254)
31 TIGR03431 PhnD phosphonate ABC 89.5 0.37 8E-06 42.5 3.5 58 32-92 65-133 (288)
32 KOG1419|consensus 88.1 0.53 1.1E-05 45.3 3.6 87 153-246 238-324 (654)
33 PRK11553 alkanesulfonate trans 80.9 2.9 6.2E-05 37.3 4.9 55 36-91 66-126 (314)
34 PLN03192 Voltage-dependent pot 69.2 5.2 0.00011 41.0 3.8 53 194-246 253-305 (823)
35 TIGR02122 TRAP_TAXI TRAP trans 64.6 6.9 0.00015 34.6 3.3 59 34-92 69-139 (320)
36 KOG0498|consensus 63.7 9.1 0.0002 38.7 4.1 54 193-246 296-349 (727)
37 cd05466 PBP2_LTTR_substrate Th 62.2 18 0.00038 27.8 4.9 49 33-85 35-83 (197)
38 TIGR01729 taurine_ABC_bnd taur 61.4 9.1 0.0002 33.8 3.4 57 35-91 36-97 (300)
39 KOG3713|consensus 58.2 9.2 0.0002 36.5 2.9 47 189-235 375-421 (477)
40 PRK10537 voltage-gated potassi 58.1 9.2 0.0002 35.8 2.9 53 190-242 167-219 (393)
41 cd08468 PBP2_Pa0477 The C-term 53.1 31 0.00068 27.4 5.1 53 32-85 34-86 (202)
42 PF09084 NMT1: NMT1/THI5 like; 52.5 23 0.0005 29.2 4.3 66 34-106 29-98 (216)
43 cd08415 PBP2_LysR_opines_like 47.7 48 0.001 25.7 5.3 50 31-84 33-82 (196)
44 KOG1418|consensus 46.4 16 0.00035 33.3 2.6 59 187-245 111-169 (433)
45 cd08463 PBP2_DntR_like_4 The C 45.9 40 0.00086 27.0 4.7 47 35-85 38-84 (203)
46 PF03466 LysR_substrate: LysR 45.8 41 0.00089 26.6 4.7 49 32-84 40-88 (209)
47 cd08465 PBP2_ToxR The C-termin 45.1 46 0.00099 26.4 4.9 49 32-84 34-82 (200)
48 TIGR01728 SsuA_fam ABC transpo 43.6 20 0.00043 30.8 2.6 57 35-91 38-98 (288)
49 cd08451 PBP2_BudR The C-termin 42.6 71 0.0015 24.8 5.6 50 32-84 35-84 (199)
50 cd08466 PBP2_LeuO The C-termin 42.5 85 0.0018 24.5 6.0 51 31-85 33-83 (200)
51 cd08459 PBP2_DntR_NahR_LinR_li 40.9 66 0.0014 25.2 5.2 50 32-85 34-83 (201)
52 cd08429 PBP2_NhaR The C-termin 40.3 68 0.0015 25.8 5.2 53 30-83 32-84 (204)
53 cd08462 PBP2_NodD The C-termin 40.2 75 0.0016 25.0 5.4 48 33-85 35-82 (200)
54 cd08446 PBP2_Chlorocatechol Th 39.8 68 0.0015 25.0 5.1 50 31-84 34-83 (198)
55 cd08461 PBP2_DntR_like_3 The C 39.1 67 0.0014 25.0 4.9 48 33-84 35-82 (198)
56 cd08453 PBP2_IlvR The C-termin 37.9 98 0.0021 24.2 5.7 53 32-85 34-86 (200)
57 PRK11151 DNA-binding transcrip 37.8 78 0.0017 27.7 5.5 49 32-84 125-173 (305)
58 cd08445 PBP2_BenM_CatM_CatR Th 37.8 95 0.0021 24.4 5.7 48 33-84 36-83 (203)
59 cd08440 PBP2_LTTR_like_4 TThe 37.8 95 0.002 23.8 5.6 49 32-84 34-82 (197)
60 cd08412 PBP2_PAO1_like The C-t 37.7 60 0.0013 25.2 4.4 49 32-84 34-82 (198)
61 cd08486 PBP2_CbnR The C-termin 37.1 75 0.0016 25.1 5.0 49 32-84 35-83 (198)
62 cd08419 PBP2_CbbR_RubisCO_like 37.1 96 0.0021 23.9 5.5 49 32-84 33-81 (197)
63 cd08426 PBP2_LTTR_like_5 The C 36.3 90 0.0019 24.2 5.3 48 33-84 35-82 (199)
64 cd08417 PBP2_Nitroaromatics_li 36.0 64 0.0014 25.1 4.4 49 32-84 34-82 (200)
65 cd08460 PBP2_DntR_like_1 The C 35.8 1.2E+02 0.0026 23.7 6.0 48 33-85 35-82 (200)
66 cd08448 PBP2_LTTR_aromatics_li 35.6 90 0.0019 24.1 5.1 49 32-84 34-82 (197)
67 PRK03601 transcriptional regul 35.5 71 0.0015 27.6 4.8 50 32-85 123-172 (275)
68 cd08449 PBP2_XapR The C-termin 35.4 89 0.0019 24.1 5.1 51 32-84 34-84 (197)
69 cd08452 PBP2_AlsR The C-termin 35.2 95 0.0021 24.3 5.3 49 32-84 34-82 (197)
70 cd08420 PBP2_CysL_like C-termi 35.1 1.1E+02 0.0024 23.5 5.6 49 33-85 35-83 (201)
71 cd08421 PBP2_LTTR_like_1 The C 34.9 83 0.0018 24.4 4.8 49 32-84 34-82 (198)
72 cd08450 PBP2_HcaR The C-termin 34.8 1E+02 0.0022 23.9 5.3 49 32-84 34-82 (196)
73 cd08438 PBP2_CidR The C-termin 34.5 73 0.0016 24.6 4.4 49 32-84 34-82 (197)
74 cd08467 PBP2_SyrM The C-termin 34.2 1E+02 0.0022 24.3 5.3 51 31-85 33-83 (200)
75 cd08434 PBP2_GltC_like The sub 34.1 1E+02 0.0022 23.6 5.2 49 32-84 34-82 (195)
76 cd08456 PBP2_LysR The C-termin 33.7 89 0.0019 24.2 4.8 49 32-84 34-82 (196)
77 TIGR02136 ptsS_2 phosphate bin 33.4 61 0.0013 28.5 4.1 54 31-84 68-127 (287)
78 cd08436 PBP2_LTTR_like_3 The C 33.0 1.2E+02 0.0027 23.2 5.6 50 32-84 34-83 (194)
79 cd08418 PBP2_TdcA The C-termin 32.6 1.2E+02 0.0025 23.5 5.4 51 32-84 34-84 (201)
80 cd08425 PBP2_CynR The C-termin 32.0 1.1E+02 0.0023 23.8 5.1 49 32-84 35-83 (197)
81 PRK11242 DNA-binding transcrip 32.0 1.1E+02 0.0023 26.5 5.4 50 32-85 125-174 (296)
82 PRK09906 DNA-binding transcrip 32.0 1.1E+02 0.0024 26.5 5.5 50 32-85 124-173 (296)
83 cd08414 PBP2_LTTR_aromatics_li 31.7 1.2E+02 0.0027 23.2 5.4 49 32-84 34-82 (197)
84 CHL00180 rbcR LysR transcripti 31.4 1.1E+02 0.0024 26.8 5.4 53 32-85 129-181 (305)
85 PRK10918 phosphate ABC transpo 30.7 71 0.0015 29.3 4.1 51 32-83 60-111 (346)
86 cd08427 PBP2_LTTR_like_2 The C 30.3 96 0.0021 23.9 4.5 52 32-85 34-85 (195)
87 cd08469 PBP2_PnbR The C-termin 29.8 1.5E+02 0.0033 23.6 5.7 50 32-85 34-83 (221)
88 cd08413 PBP2_CysB_like The C-t 29.2 1.3E+02 0.0027 23.7 5.1 51 32-85 34-84 (198)
89 cd08442 PBP2_YofA_SoxR_like Th 29.2 1.2E+02 0.0027 23.2 5.0 50 32-85 34-83 (193)
90 cd08430 PBP2_IlvY The C-termin 29.1 1.3E+02 0.0028 23.2 5.1 50 32-84 34-83 (199)
91 PF13379 NMT1_2: NMT1-like fam 28.7 38 0.00081 29.0 1.9 60 33-93 42-113 (252)
92 TIGR03339 phn_lysR aminoethylp 28.7 92 0.002 26.5 4.4 50 32-85 118-167 (279)
93 PRK10341 DNA-binding transcrip 28.5 97 0.0021 27.3 4.6 52 32-85 131-182 (312)
94 PF01007 IRK: Inward rectifier 28.3 92 0.002 28.5 4.4 62 189-250 82-145 (336)
95 cd08441 PBP2_MetR The C-termin 28.2 1.5E+02 0.0033 23.0 5.3 49 32-84 34-82 (198)
96 TIGR02424 TF_pcaQ pca operon t 27.4 1.2E+02 0.0025 26.4 4.9 52 32-85 127-178 (300)
97 cd08444 PBP2_Cbl The C-termina 26.1 1.6E+02 0.0035 23.1 5.1 51 32-85 34-84 (198)
98 PRK12683 transcriptional regul 26.0 1.6E+02 0.0035 25.9 5.5 52 31-85 126-177 (309)
99 cd08485 PBP2_ClcR The C-termin 25.6 1.3E+02 0.0029 23.6 4.6 49 32-84 35-83 (198)
100 cd08437 PBP2_MleR The substrat 25.3 1.6E+02 0.0035 22.8 5.0 51 32-84 34-84 (198)
101 TIGR00975 3a0107s03 phosphate 25.3 96 0.0021 27.9 4.0 50 33-83 34-86 (314)
102 cd01423 MGS_CPS_I_III Methylgl 25.1 67 0.0015 24.1 2.5 37 37-73 61-106 (116)
103 cd08464 PBP2_DntR_like_2 The C 25.0 1.7E+02 0.0037 22.6 5.1 49 32-84 34-82 (200)
104 PRK09791 putative DNA-binding 24.7 1.5E+02 0.0032 25.8 5.0 53 32-86 129-181 (302)
105 cd08416 PBP2_MdcR The C-termin 24.0 1.7E+02 0.0037 22.6 4.9 51 32-84 34-84 (199)
106 cd08457 PBP2_OccR The C-termin 24.0 1.7E+02 0.0037 22.7 4.9 47 33-83 35-81 (196)
107 cd08439 PBP2_LrhA_like The C-t 23.7 1.5E+02 0.0034 22.8 4.6 47 32-84 34-80 (185)
108 cd08447 PBP2_LTTR_aromatics_li 23.6 1.9E+02 0.0041 22.3 5.1 49 32-84 34-82 (198)
109 cd03770 SR_TndX_transposase Se 23.5 1.2E+02 0.0026 23.6 3.8 75 6-83 22-107 (140)
110 cd08411 PBP2_OxyR The C-termin 23.5 1.8E+02 0.0039 22.5 5.0 49 32-84 35-83 (200)
111 cd08435 PBP2_GbpR The C-termin 23.2 2.5E+02 0.0054 21.5 5.7 51 33-85 35-85 (201)
112 cd08443 PBP2_CysB The C-termin 22.7 1.6E+02 0.0034 23.1 4.5 50 32-84 34-83 (198)
113 PF13531 SBP_bac_11: Bacterial 22.3 1.2E+02 0.0026 25.2 3.9 59 37-95 36-102 (230)
114 PRK13348 chromosome replicatio 22.1 1.4E+02 0.003 25.8 4.3 48 32-83 123-170 (294)
115 PRK11482 putative DNA-binding 22.1 1.2E+02 0.0027 26.8 4.1 48 34-85 151-198 (317)
116 cd08423 PBP2_LTTR_like_6 The C 21.6 2.4E+02 0.0051 21.6 5.3 51 33-84 35-87 (200)
117 cd08431 PBP2_HupR The C-termin 20.6 1.8E+02 0.0039 22.5 4.4 50 32-84 34-83 (195)
118 PRK12681 cysB transcriptional 20.4 1.9E+02 0.0041 25.8 4.9 52 31-85 126-177 (324)
119 cd08458 PBP2_NocR The C-termin 20.2 2.8E+02 0.0061 21.5 5.5 49 32-84 34-82 (196)
120 PRK12680 transcriptional regul 20.1 1.8E+02 0.004 25.9 4.8 50 32-84 127-176 (327)
No 1
>KOG1054|consensus
Probab=100.00 E-value=4.4e-42 Score=316.81 Aligned_cols=206 Identities=25% Similarity=0.519 Sum_probs=183.3
Q ss_pred hHhhhhcCcEEEEEEecCCceeEe-eCCc-hhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC-
Q psy13439 8 HESLKKKRKLLTVYLHSKNEVLSV-ENGK-WNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT- 84 (261)
Q Consensus 8 ~e~l~k~~~~~~~~~~~~~~~g~~-~~~~-~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~- 84 (261)
.|..|+-+.-|++....||++|.. .+++ |+||++.|..|++|+++++++||.+|.+.+|||.|++..++.+++++|.
T Consensus 454 ~~iAkhi~~~Y~l~iv~dgkyGardaD~k~WnGMvGeLv~grAdiavApLTIt~~REeviDFSKPfMslGISIMIKKPqK 533 (897)
T KOG1054|consen 454 AEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQK 533 (897)
T ss_pred HHHHHhcCceEEEEEecCCcccccCCCcccccchhHHHhcCccceEEeeeeeehhhhhhhccccchhhcCeEEEEeCccc
Confidence 344556667799999999999997 6777 9999999999999999999999999999999999999999999999996
Q ss_pred CCCCcccccCCCCcccccceehhhhHHHHHHHHHHHHhCCCCCcccccccCCCCCCCCCCCCCcchhhhhhhhhhhhcch
Q psy13439 85 GIISPTAFLEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPFDTASWMLVGVVAIQASAF 164 (261)
Q Consensus 85 ~~~~~~~~l~pF~~~vW~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (261)
+..+.++|++|+...+|++++... ++++.++++..|++|++
T Consensus 534 sk~gVFSFldPLa~eIWm~ivfaY-iGVSvvlFLVSrFSPYE-------------------------------------- 574 (897)
T KOG1054|consen 534 SKPGVFSFLDPLAYEIWMCIVFAY-IGVSVVLFLVSRFSPYE-------------------------------------- 574 (897)
T ss_pred CCCCeeeecchhHHHHHHHHHHHH-hcceEEEEEEeccCchh--------------------------------------
Confidence 567889999999999999998754 46667889999999854
Q ss_pred hhhhhhccCCCCCCCcccCCCCCCCCcchhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHhhcccceeee
Q psy13439 165 TIFFFEWLSPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFM 244 (261)
Q Consensus 165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~L 244 (261)
|+.....+++..+....+.|+++||+||++++++|||+++ +|++.|+||+.++||||++|++++|||||||||
T Consensus 575 ------wh~Ee~~rg~~t~~~~~NeFgifNsLWFsLgAFMQQG~DI-~PRslSGRIvggvWWFFTlIIiSSYTANLAAFL 647 (897)
T KOG1054|consen 575 ------WHTEEFERGRFTPSDPPNEFGIFNSLWFSLGAFMQQGCDI-SPRSLSGRIVGGVWWFFTLIIISSYTANLAAFL 647 (897)
T ss_pred ------eeccccccCCCCCCCCCccchhhHHHHHHHHHHHhcCCCC-CccccccceeccchhhhhhhhhhhhhhHHHHHH
Confidence 4444443444344467789999999999999999999999 999999999999999999999999999999999
Q ss_pred eccccccccCCccCC
Q psy13439 245 ITREEFHEFTGVDDV 259 (261)
Q Consensus 245 t~~~~~~~i~sl~Dl 259 (261)
|.++..+||.|.+||
T Consensus 648 TvErMvsPIESaEDL 662 (897)
T KOG1054|consen 648 TVERMVSPIESAEDL 662 (897)
T ss_pred hHHhhcCcchhHHHH
Confidence 999999999999998
No 2
>KOG1053|consensus
Probab=100.00 E-value=1.2e-34 Score=277.00 Aligned_cols=201 Identities=41% Similarity=0.794 Sum_probs=186.5
Q ss_pred hcCcEEEEEEecCCceeEeeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCCCCcccc
Q psy13439 13 KKRKLLTVYLHSKNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPTAF 92 (261)
Q Consensus 13 k~~~~~~~~~~~~~~~g~~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~~~~~~~ 92 (261)
.-+|+|+++++.+|++|+..|+.|+|||+.|..+++||++++++|+.||.+.+|||.|+.+.++.++|++.+...+...|
T Consensus 479 ~v~FtYDLYlVtnGKhGkk~ng~WnGmIGev~~~rA~MAVgSltINeeRSevVDFSvPFveTgIsVmV~rsngtvspsAF 558 (1258)
T KOG1053|consen 479 DVKFTYDLYLVTNGKHGKKINGVWNGMIGEVVYQRADMAVGSLTINEERSEVVDFSVPFVETGISVMVARSNGTVSPSAF 558 (1258)
T ss_pred hcCcceEEEEecCCcccceecCcchhhHHHHHhhhhheeeeeeEechhhhccccccccccccceEEEEEecCCccCchhh
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999888888999
Q ss_pred cCCCCcccccceehhhhHHHHHHHHHHHHhCCCCCcccccccCCCCCCCCCCCCCcchhhhhhhhhhhhcchhhhhhhcc
Q psy13439 93 LEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPFDTASWMLVGVVAIQASAFTIFFFEWL 172 (261)
Q Consensus 93 l~pF~~~vW~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 172 (261)
+.||++.+|+.+++++++++++..+++++++|.+++.+...
T Consensus 559 LePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~l~~--------------------------------------- 599 (1258)
T KOG1053|consen 559 LEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRNLAN--------------------------------------- 599 (1258)
T ss_pred cCCcchHHHHHHHHHHHHHHHHHHHHHhhcCcccccccccC---------------------------------------
Confidence 99999999999999999988888889999998887644311
Q ss_pred CCCCCCCcccCCCCCCCCcchhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHhhcccceeeeeccccccc
Q psy13439 173 SPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFMITREEFHE 252 (261)
Q Consensus 173 ~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~~~~~ 252 (261)
.+++-++.|++..++|..|+++++.+++.+.|++..+||++++|.+|++++.++|||||||+|..+++-.+
T Consensus 600 ---------gkkpggp~FtigkaiwllwaLvFnnsVpv~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d~ 670 (1258)
T KOG1053|consen 600 ---------GKKPGGPSFTIGKAIWLLWALVFNNSVPVENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYDT 670 (1258)
T ss_pred ---------CCCCCCcceehhhHHHHHHHHHhCCCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Confidence 13455788999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCccCCCC
Q psy13439 253 FTGVDDVRI 261 (261)
Q Consensus 253 i~sl~Dl~~ 261 (261)
++++.|-|+
T Consensus 671 vSGlsD~Kf 679 (1258)
T KOG1053|consen 671 VSGLSDPKF 679 (1258)
T ss_pred ccccCcccc
Confidence 999999764
No 3
>KOG4440|consensus
Probab=100.00 E-value=1.2e-33 Score=262.39 Aligned_cols=202 Identities=28% Similarity=0.568 Sum_probs=178.9
Q ss_pred hhhhcCcEEEEEEecCCceeEe---e------CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEE
Q psy13439 10 SLKKKRKLLTVYLHSKNEVLSV---E------NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVV 80 (261)
Q Consensus 10 ~l~k~~~~~~~~~~~~~~~g~~---~------~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv 80 (261)
.-+..||+|+..+..|+.+|.. . ..+|+|++|.|.+|++||++++++|++||.+.++||.|+...+++++.
T Consensus 473 Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMivaplTINpERa~yieFskPfkYqGitILe 552 (993)
T KOG4440|consen 473 LSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMIVAPLTINPERAQYIEFSKPFKYQGITILE 552 (993)
T ss_pred HHHhhcceEEEEEeecccccceeeeecccccccceehhhhhhhhCCccceEeeceeeChhhhhheeccCcccccceEEEe
Confidence 3447999999999999998863 2 235999999999999999999999999999999999999999999999
Q ss_pred EccCCCCCcccccCCCCcccccceehhhhHHHHHHHHHHHHhCCCCCcccccccCCCCCCCCCCCCCcchhhhhhhhhhh
Q psy13439 81 AKRTGIISPTAFLEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPFDTASWMLVGVVAIQ 160 (261)
Q Consensus 81 ~~~~~~~~~~~~l~pF~~~vW~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (261)
+++.+...+.+|++||+..+|+++++ .+.++++++|+.++++|++.....
T Consensus 553 Kk~~r~Stl~SFlQPfqstLW~lv~~-SVhvVal~lYlLDrfSPFgRFk~~----------------------------- 602 (993)
T KOG4440|consen 553 KKEIRRSTLDSFLQPFQSTLWLLVGL-SVHVVALMLYLLDRFSPFGRFKVN----------------------------- 602 (993)
T ss_pred eCCCCCchHHHHHhHHHHHHHHHHHH-HHHHHHHHHHHHHhcCcccceeec-----------------------------
Confidence 99988888999999999999999988 567788999999999997632111
Q ss_pred hcchhhhhhhccCCCCCCCcccCCCCCCCCcchhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHhhcccc
Q psy13439 161 ASAFTIFFFEWLSPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAIYTANL 240 (261)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L 240 (261)
. +.++.+...+++.++||+||.|++.|.+.+.|+|.|+|++..+|+-|++|++++|||||
T Consensus 603 -------------d-------s~~~ee~alnlssAmWF~WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTANL 662 (993)
T KOG4440|consen 603 -------------D-------SEEEEEDALNLSSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANL 662 (993)
T ss_pred -------------c-------CccchhhhcchhhhHHHHhHhhhccccCCCCCcchhHHHHHHHHhhhheeeehhhhhhh
Confidence 0 01233455689999999999999999999999999999999999999999999999999
Q ss_pred eeeeeccccccccCCccCCCC
Q psy13439 241 AAFMITREEFHEFTGVDDVRI 261 (261)
Q Consensus 241 ~s~Lt~~~~~~~i~sl~Dl~~ 261 (261)
||||...+++..++++.|=|+
T Consensus 663 AAFLVLdrPe~~ltGinDpRL 683 (993)
T KOG4440|consen 663 AAFLVLDRPEERLTGINDPRL 683 (993)
T ss_pred hhheeecCccccccCCCCccc
Confidence 999999999999999999775
No 4
>KOG1052|consensus
Probab=99.97 E-value=9.6e-31 Score=256.92 Aligned_cols=194 Identities=27% Similarity=0.524 Sum_probs=170.8
Q ss_pred hhhhcCcEEEEEEecCCceeEe-eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCCCC
Q psy13439 10 SLKKKRKLLTVYLHSKNEVLSV-ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIIS 88 (261)
Q Consensus 10 ~l~k~~~~~~~~~~~~~~~g~~-~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~~~ 88 (261)
..+.+|+.|+++...++. |.. ++|+|+|+++.|.+|++|++ ++++++++|.+.+|||.||+..+..+++++++....
T Consensus 255 l~~~l~f~~~~~~~~~~~-g~~~~~g~~~g~v~~l~~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~ 332 (656)
T KOG1052|consen 255 LAKRLNFSYEIIFVPDGS-GSRDPNGNWDGLVGQLVDGEADVG-ADITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSK 332 (656)
T ss_pred HHHhCCCceEEEEcCCCC-CCCCCCCChhHHHHHHhcCccccc-cceEEeecccccEEeccceEeccEEEEEEecCCccc
Confidence 345699999999999998 776 45999999999999999999 999999999999999999999999999999986655
Q ss_pred cccccCCCCcccccceehhhhHHHHHHHHHHHHhCCCCCcccccccCCCCCCCCCCCCCcchhhhhhhhhhhhcchhhhh
Q psy13439 89 PTAFLEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPFDTASWMLVGVVAIQASAFTIFF 168 (261)
Q Consensus 89 ~~~~l~pF~~~vW~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 168 (261)
.+.|++||++.+|++++++ +.++++++|+.+++.+++
T Consensus 333 ~~~fl~Pf~~~vW~~i~~~-~l~~~~~~~~~~~~~~~~------------------------------------------ 369 (656)
T KOG1052|consen 333 LWNFLAPFSPEVWLLILAS-LLLVGLLLWILERLSPYE------------------------------------------ 369 (656)
T ss_pred ceEEecCCcHHHHHHHHHH-HHHHHHHHHHHhcccccc------------------------------------------
Confidence 8899999999999999884 556678899999987743
Q ss_pred hhccCCCCCCCcccCCCCCCCCcchhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHhhcccceeeeeccc
Q psy13439 169 FEWLSPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFMITRE 248 (261)
Q Consensus 169 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~ 248 (261)
| |++ + .....+...+++|++++++++||+.. .|++.++|++.++||+++++++++|||||+|+||.++
T Consensus 370 --~--~~~-~------~~~~~~~~~~~~~~~~~~~~~q~~~~-~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~~ 437 (656)
T KOG1052|consen 370 --L--PPR-Q------IVTSLFSLLNCLWLTVGSLLQQGSDE-IPRSLSTRLLLGAWWLFVLILISSYTANLTAFLTVPR 437 (656)
T ss_pred --C--Ccc-c------cceeEeecccchhhhhHHHhccCCCc-cccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 2 111 0 12344567789999999999999986 9999999999999999999999999999999999999
Q ss_pred cccccCCccCCC
Q psy13439 249 EFHEFTGVDDVR 260 (261)
Q Consensus 249 ~~~~i~sl~Dl~ 260 (261)
...||++++||.
T Consensus 438 ~~~~i~~~~dL~ 449 (656)
T KOG1052|consen 438 LRSPIDSLDDLA 449 (656)
T ss_pred cCCcccCHHHHH
Confidence 999999999974
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=99.66 E-value=1.1e-18 Score=139.80 Aligned_cols=73 Identities=26% Similarity=0.643 Sum_probs=61.3
Q ss_pred CCCCcchhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHhhcccceeeeeccccccccCCccCCC
Q psy13439 187 SHRFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFMITREEFHEFTGVDDVR 260 (261)
Q Consensus 187 ~~~~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~Dl~ 260 (261)
+...++.+++|++++.+++|+... .|++.++|++.++||+++++++++|||+|+|+||.|+.+.+|+|++||.
T Consensus 40 ~~~~~~~~~~~~~~~~~~~q~~~~-~~~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~ 112 (148)
T PF00060_consen 40 RWRFSLSNSFWYTFGTLLQQGSSI-RPRSWSGRILLAFWWLFSLILIASYTANLTSFLTVPKYEPPIDSLEDLA 112 (148)
T ss_dssp -HHHHHHHHHHHCCCCCHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHTSS-SSHHHHH
T ss_pred cCcccHHHHHHHHHHhhccccccc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcCCCCCCHHHHH
Confidence 344578899999999999999987 9999999999999999999999999999999999999999999999973
No 6
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=98.28 E-value=1.2e-06 Score=78.75 Aligned_cols=80 Identities=18% Similarity=0.112 Sum_probs=62.4
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCCCCcccccCCCCcccccceehhhhH
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPTAFLEPFDTASWMLVGVVAIQ 110 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~~~~~~~l~pF~~~vW~~i~~~~l~ 110 (261)
+...+|++++.+|.+|++|++++++++|++|.+.++||.||+.++..++++++....++.+ +.+ ..+++ ..
T Consensus 90 ~v~~~~~~~i~~L~~G~~Di~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~~i~sl~d----L~G---k~V~v--~~ 160 (302)
T PRK10797 90 LIPITSQNRIPLLQNGTFDFECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGGDIKDFAD----LKG---KAVVV--TS 160 (302)
T ss_pred EEEcChHhHHHHHHCCCccEEecCCccCcchhhcceecccEeeccEEEEEECCCCCCChHH----cCC---CEEEE--eC
Confidence 4566788999999999999999999999999999999999999999999998765544444 445 34444 44
Q ss_pred HHHHHHHHH
Q psy13439 111 ASAFTIFFF 119 (261)
Q Consensus 111 ~~~~~~~l~ 119 (261)
++....++.
T Consensus 161 gs~~~~~l~ 169 (302)
T PRK10797 161 GTTSEVLLN 169 (302)
T ss_pred CCcHHHHHH
Confidence 554444443
No 7
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=98.16 E-value=2.5e-06 Score=74.87 Aligned_cols=80 Identities=20% Similarity=0.205 Sum_probs=61.5
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCCCCcccccCCCCcccccceehhhhHH
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPTAFLEPFDTASWMLVGVVAIQA 111 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~~~~~~~l~pF~~~vW~~i~~~~l~~ 111 (261)
...+|...+.+|.+|++|++++++++|+||.+.++||.||+.++..+++++++...++.+ +++ ..+++ ..+
T Consensus 86 ~~~~~~~~~~~l~~g~~D~~~~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~~~~s~~d----L~g---~~V~v--~~g 156 (259)
T PRK11917 86 VAVNAKTRGPLLDNGSVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEKNYKSLAD----MKG---ANIGV--AQA 156 (259)
T ss_pred EEcChhhHHHHHHCCCccEEEecccCChhhhheeeeccCceeeceEEEEECCCCCCCHHH----hCC---CeEEE--ecC
Confidence 455677888999999999999999999999999999999999999999998865544433 455 55554 444
Q ss_pred HHHHHHHHH
Q psy13439 112 SAFTIFFFE 120 (261)
Q Consensus 112 ~~~~~~l~~ 120 (261)
+.....+.+
T Consensus 157 s~~~~~l~~ 165 (259)
T PRK11917 157 ATTKKAIGE 165 (259)
T ss_pred CcHHHHHHH
Confidence 444444433
No 8
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=97.99 E-value=9.4e-06 Score=70.55 Aligned_cols=57 Identities=30% Similarity=0.537 Sum_probs=52.8
Q ss_pred EeeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCC
Q psy13439 30 SVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGI 86 (261)
Q Consensus 30 ~~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~ 86 (261)
.+....|++++++|.+|++|++++++++|+||.+.++||.||+.++..+++++.+..
T Consensus 80 ~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~er~~~~~fs~py~~~~~~~~~~~~~~~ 136 (275)
T COG0834 80 EFVPVAWDGLIPALKAGKVDIIIAGMTITPERKKKVDFSDPYYYSGQVLLVKKDSDI 136 (275)
T ss_pred EEeccchhhhhHHHhcCCcCEEEeccccCHHHhccccccccccccCeEEEEECCCCc
Confidence 346779999999999999999999999999999999999999999999999988654
No 9
>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=97.99 E-value=7.4e-06 Score=56.59 Aligned_cols=40 Identities=30% Similarity=0.527 Sum_probs=29.8
Q ss_pred hhhHhhh-hcCcEEEEEEecCCceeEe-eCCchhhHHHHHhc
Q psy13439 6 NQHESLK-KKRKLLTVYLHSKNEVLSV-ENGKWNGLIADLVN 45 (261)
Q Consensus 6 ~~~e~l~-k~~~~~~~~~~~~~~~g~~-~~~~~~gli~~L~~ 45 (261)
|.++.|+ +++|+|++..++|+.||.. .+++|+||+++|.+
T Consensus 24 Dll~~la~~l~F~y~i~~~~Dg~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 24 DLLEELAEELNFTYEIYLVPDGKYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp HHHHHHHHHHT-EEEEEE-TTS--EEBETTSEBEHHHHHHHT
T ss_pred HHHHHHHHHcCCeEEEEECCCCCCcCcCCCCcCcCHHHHhcC
Confidence 3445554 6999999999999999998 57999999999874
No 10
>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=97.91 E-value=1.8e-05 Score=66.15 Aligned_cols=62 Identities=26% Similarity=0.361 Sum_probs=53.0
Q ss_pred hhhcCcEEEEEEecCCceeEeeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEcc
Q psy13439 11 LKKKRKLLTVYLHSKNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKR 83 (261)
Q Consensus 11 l~k~~~~~~~~~~~~~~~g~~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~ 83 (261)
.+++|..++++. .+|+.++.+|.+|++|+++++++.|++|.+.++||.||+.....+++++.
T Consensus 33 ~~~~g~~~~~~~-----------~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~ 94 (225)
T PF00497_consen 33 AKRLGIKIEFVP-----------MPWSRLLEMLENGKADIIIGGLSITPERAKKFDFSDPYYSSPYVLVVRKG 94 (225)
T ss_dssp HHHHTCEEEEEE-----------EEGGGHHHHHHTTSSSEEESSEB-BHHHHTTEEEESESEEEEEEEEEETT
T ss_pred Hhhcccccceee-----------cccccccccccccccccccccccccccccccccccccccchhheeeeccc
Confidence 345565555554 37999999999999999999999999999999999999999999999975
No 11
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=97.89 E-value=2.2e-05 Score=68.49 Aligned_cols=56 Identities=29% Similarity=0.433 Sum_probs=51.2
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGI 86 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~ 86 (261)
+...+|+.++.++.+|++|+++++++.|++|.+.++||.||+.++..++++++...
T Consensus 69 ~~~~pw~~~~~~l~~g~~D~~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~ 124 (259)
T PRK15437 69 FVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDI 124 (259)
T ss_pred EEeCCHHHHHHHHHCCCCCEEEecCCCCHHHhhhccccchhhcCceEEEEECCCCC
Confidence 34567999999999999999999999999999999999999999999999987644
No 12
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=97.88 E-value=2.2e-05 Score=67.85 Aligned_cols=60 Identities=23% Similarity=0.464 Sum_probs=51.9
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC-CCCccc
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG-IISPTA 91 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~-~~~~~~ 91 (261)
...+|.+++.+|.+|++|+++++++.|++|.+.++||.||+.++..+++++... ..++.+
T Consensus 68 ~~~~~~~~~~~l~~G~vDi~~~~~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~d 128 (247)
T PRK09495 68 KPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDIKSVKD 128 (247)
T ss_pred EeCCHHHHHHHHhCCCcCEEEecCccCHHHHhhccccchheecceEEEEECCCCCCCChHH
Confidence 345799999999999999999999999999999999999999999999987653 444433
No 13
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=97.82 E-value=3.5e-05 Score=67.23 Aligned_cols=83 Identities=23% Similarity=0.335 Sum_probs=62.7
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCCC-CcccccCCCCcccccceehhhh
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGII-SPTAFLEPFDTASWMLVGVVAI 109 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~~-~~~~~l~pF~~~vW~~i~~~~l 109 (261)
+...+|+.++.++.+|++|++++++..|++|.+.++||.||+.++..++++++.... ++ ..+++ ..|++ .
T Consensus 69 ~~~~~~~~~~~~l~~g~~Di~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~----~dl~g---~~Igv--~ 139 (260)
T PRK15010 69 WVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTL----DSLKG---KHVGV--L 139 (260)
T ss_pred EEeCCHHHHHHHHHCCCCCEEEecCcCCHHHHhhcccccceEeccEEEEEECCCCCCCCh----hHcCC---CEEEE--e
Confidence 345679999999999999999999999999999999999999999999999876433 33 23455 44554 4
Q ss_pred HHHHHHHHHHHHh
Q psy13439 110 QASAFTIFFFEWL 122 (261)
Q Consensus 110 ~~~~~~~~l~~~~ 122 (261)
.++....++...+
T Consensus 140 ~gs~~~~~~~~~~ 152 (260)
T PRK15010 140 QGSTQEAYANETW 152 (260)
T ss_pred cCchHHHHHHHhc
Confidence 4554444454433
No 14
>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=97.73 E-value=6e-05 Score=65.43 Aligned_cols=79 Identities=19% Similarity=0.146 Sum_probs=55.9
Q ss_pred eeCCchhhHH---HHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC--CCCcccccCCCCccccc-ce
Q psy13439 31 VENGKWNGLI---ADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG--IISPTAFLEPFDTASWM-LV 104 (261)
Q Consensus 31 ~~~~~~~gli---~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~--~~~~~~~l~pF~~~vW~-~i 104 (261)
+...+|++++ .+|.+|++|+++ ++++|++| ++||.||+.++.++++++++. .+++.+ ..+.+ . .+
T Consensus 39 ~~~~~~~~~~~~~~~L~~g~~Dii~-~~~~t~~r---~~fS~PY~~~~~~~v~~k~~~~~~~~~~d--~~L~g---~~~v 109 (246)
T TIGR03870 39 FVWLAKPAIYLVRDGLDKKLCDVVL-GLDTGDPR---VLTTKPYYRSSYVFLTRKDRNLDIKSWND--PRLKK---VSKI 109 (246)
T ss_pred EEEeccchhhHHHHHHhcCCccEEE-eCCCChHH---HhcccCcEEeeeEEEEeCCCCCCCCCccc--hhhcc---CceE
Confidence 3456788876 699999999998 58999888 689999999999999998753 333221 11344 3 45
Q ss_pred ehhhhHHHHHHHHHHH
Q psy13439 105 GVVAIQASAFTIFFFE 120 (261)
Q Consensus 105 ~~~~l~~~~~~~~l~~ 120 (261)
++ ..++....++.+
T Consensus 110 gv--~~gs~~~~~l~~ 123 (246)
T TIGR03870 110 GV--IFGSPAETMLKQ 123 (246)
T ss_pred EE--ecCChHHHHHHh
Confidence 55 556666655544
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=97.71 E-value=5.1e-05 Score=66.90 Aligned_cols=55 Identities=27% Similarity=0.347 Sum_probs=50.8
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
+...+|+.++..|.+|++|+++++++.|++|.+.++||.||+.+...+++++++.
T Consensus 76 ~~~~~w~~~~~~l~~G~~Di~~~~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~ 130 (275)
T TIGR02995 76 ASITEYGALIPGLQAGRFDAIAAGLFIKPERCKQVAFTQPILCDAEALLVKKGNP 130 (275)
T ss_pred eccCCHHHHHHHHHCCCcCEEeecccCCHHHHhccccccceeecceeEEEECCCC
Confidence 4677899999999999999999999999999999999999999999999998753
No 16
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=97.63 E-value=0.00015 Score=62.22 Aligned_cols=53 Identities=25% Similarity=0.384 Sum_probs=47.2
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEcc
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKR 83 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~ 83 (261)
+...+|+.++.+|.+|++|+++++++.+++|.+.++||.||+..+..++.++.
T Consensus 64 ~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~~fs~p~~~~~~~~v~~~~ 116 (243)
T PRK15007 64 FSNQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQG 116 (243)
T ss_pred EEeCCHHHHhHHHhCCCcCEEEEcCccCHHHhcccceecCccccceEEEEeCC
Confidence 34567999999999999999999999999999999999999998877777654
No 17
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=97.60 E-value=9.1e-05 Score=70.84 Aligned_cols=52 Identities=21% Similarity=0.252 Sum_probs=49.0
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+|+.++.+|.+|++|++++++++|++|.+.++||.||+.....+++++..
T Consensus 87 ~~~~~~ll~aL~~G~iDi~~~~lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~ 138 (482)
T PRK10859 87 RDNISQLFDALDKGKADLAAAGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQ 138 (482)
T ss_pred cCCHHHHHHHHhCCCCCEEeccCcCChhhhccCcccCCceeeeEEEEEeCCC
Confidence 5679999999999999999999999999999999999999999999998865
No 18
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=97.35 E-value=0.00027 Score=63.10 Aligned_cols=87 Identities=8% Similarity=0.056 Sum_probs=64.5
Q ss_pred chhhHhhhhcCcEE-----EEEEecCCceeEeeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhcccccc--ccccceE
Q psy13439 5 DNQHESLKKKRKLL-----TVYLHSKNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVP--IMETGIA 77 (261)
Q Consensus 5 ~~~~e~l~k~~~~~-----~~~~~~~~~~g~~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~p--y~~~~~~ 77 (261)
++..+.+++.+..+ .+...-++.-.++...+|++++..|.+|++|+++++++.+.||.+.++|+.| |......
T Consensus 17 ~~~~~ll~~~g~~~~~~~r~~~~~~p~~~ie~~~~~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lv 96 (287)
T PRK00489 17 EPALELLAEAGLKIRRDSRSLIATDEDNPIEVLFLRPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLV 96 (287)
T ss_pred HHHHHHHHHcCCCCCCCCcceEeecCCCCEEEEEECcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEE
Confidence 34566666655432 2222223333456778899999999999999999999999999999999987 7777888
Q ss_pred EEEEccCCCCCccc
Q psy13439 78 IVVAKRTGIISPTA 91 (261)
Q Consensus 78 ~lv~~~~~~~~~~~ 91 (261)
++++++....++.+
T Consensus 97 vvvp~~~~i~sl~D 110 (287)
T PRK00489 97 LAVPEDSDWQGVED 110 (287)
T ss_pred EEEECCCCCCChHH
Confidence 88888776666444
No 19
>PRK11260 cystine transporter subunit; Provisional
Probab=97.32 E-value=0.00042 Score=60.62 Aligned_cols=54 Identities=28% Similarity=0.614 Sum_probs=49.1
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
+...+|..++.+|++|++|+++++++.+++|.+.+.||.||+..+..+++++.+
T Consensus 84 ~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~ 137 (266)
T PRK11260 84 LKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTVSGIQALVKKGN 137 (266)
T ss_pred EEeCCHHHHHHHHhcCCCCEEEeccccCHHHHhccccCCceeecceEEEEEcCC
Confidence 345679999999999999999999999999999999999999999999998764
No 20
>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=97.29 E-value=0.00031 Score=61.62 Aligned_cols=53 Identities=17% Similarity=0.288 Sum_probs=46.0
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccc-cceEEEEEccC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIME-TGIAIVVAKRT 84 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~-~~~~~lv~~~~ 84 (261)
+...+|+.++.+| +|+.|.++.++++|+||.+.++||.||+. ....+++++++
T Consensus 61 ~~~~pw~r~l~~l-~~~~d~~~~~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~ 114 (268)
T TIGR02285 61 FVRVSFARSLKEL-QGKGGVCTVNLLRTPEREKFLIFSDPTLRALPVGLVLRKEL 114 (268)
T ss_pred EEECCHHHHHHHH-hcCCCeEEeeccCCcchhhceeecCCccccCCceEEEccch
Confidence 4577899999999 78888888899999999999999999986 57888888764
No 21
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=97.27 E-value=0.0005 Score=59.07 Aligned_cols=55 Identities=29% Similarity=0.543 Sum_probs=50.2
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
+...+|+.++.+|.+|++|+++++++.+++|.+.+.||.||+.++..++++++..
T Consensus 67 ~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~ 121 (250)
T TIGR01096 67 FVEQNFDGLIPSLKAKKVDAIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSD 121 (250)
T ss_pred EEeCCHHHHHHHHhCCCcCEEEecCccCHHHhhccccccchhcCCeEEEEECCCC
Confidence 4456799999999999999999899999999999999999999999999988764
No 22
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.24 E-value=0.00038 Score=73.31 Aligned_cols=58 Identities=17% Similarity=0.217 Sum_probs=51.4
Q ss_pred eeC-CchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCCCC
Q psy13439 31 VEN-GKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIIS 88 (261)
Q Consensus 31 ~~~-~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~~~ 88 (261)
+.+ .+|++++.+|++|++|+++++++.|++|.+.++||.||+.+...++++++....+
T Consensus 100 ~v~~~~~~~~l~~l~~g~iDl~~~~~~~~~~r~~~~~fs~py~~~~~~~v~~~~~~~~~ 158 (1197)
T PRK09959 100 LREYADHQKAMDALEEGEVDIVLSHLVASPPLNDDIAATKPLIITFPALVTTLHDSMRP 158 (1197)
T ss_pred EEeCCCHHHHHHHHHcCCCcEecCccccccccccchhcCCCccCCCceEEEeCCCCCCC
Confidence 344 4899999999999999999999999999999999999999999999988654433
No 23
>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=96.63 E-value=0.0049 Score=50.15 Aligned_cols=60 Identities=32% Similarity=0.510 Sum_probs=52.4
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCCCCccc
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPTA 91 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~~~~~~ 91 (261)
....|..++.+|.+|++|+++++...+++|.+.+.|+.|+......+++++++...++.+
T Consensus 43 ~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d 102 (218)
T cd00134 43 VEVDWDGLITALKSGKVDLIAAGMTITPERAKQVDFSDPYYKSGQVILVKKGSPIKSVKD 102 (218)
T ss_pred EeCCHHHHHHHHhcCCcCEEeecCcCCHHHHhhccCcccceeccEEEEEECCCCCCChHH
Confidence 344489999999999999999988899999999999999999999999999876654444
No 24
>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=96.53 E-value=0.0049 Score=52.35 Aligned_cols=45 Identities=16% Similarity=0.091 Sum_probs=38.9
Q ss_pred hhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 36 WNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 36 ~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
+.-++..|++|++|++++ +++|.+.++||.||+..+.++++++++
T Consensus 46 ~~~~~~~l~~g~~Di~~~----~~~r~~~~~fs~py~~~~~~lv~~~~~ 90 (232)
T TIGR03871 46 RGFVRNTLNAGRCDVVIG----VPAGYEMVLTTRPYYRSTYVFVTRKDS 90 (232)
T ss_pred hhhHHHHHhcCCccEEEe----ccCccccccccCCcEeeeEEEEEeCCC
Confidence 344678899999999986 578999999999999999999998874
No 25
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=96.49 E-value=0.0061 Score=49.42 Aligned_cols=60 Identities=27% Similarity=0.424 Sum_probs=52.8
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCCCCcccc
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPTAF 92 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~~~~~~~ 92 (261)
..+|..++.+|.+|++|+++++...+++|.+.+.++.|++..+..++++++....++.++
T Consensus 45 ~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dL 104 (219)
T smart00062 45 EVSFDNLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYKSGQVILVRKDSPIKSLEDL 104 (219)
T ss_pred eccHHHHHHHHHCCcccEEeccccCCHHHHhheeeccceeeceeEEEEecCCCCCChHHh
Confidence 337899999999999999999888899999999999999999999999988776666554
No 26
>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=95.76 E-value=0.021 Score=40.57 Aligned_cols=57 Identities=11% Similarity=0.335 Sum_probs=47.7
Q ss_pred CCcchhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHhhcccceeeee
Q psy13439 189 RFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFMI 245 (261)
Q Consensus 189 ~~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt 245 (261)
..++.+++|+++..+...|.+.-.|.+..+|++...+.+.++.+.+...+.+++.++
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 447899999999999988876449999999999999999999999999998887664
No 27
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=95.39 E-value=0.019 Score=60.60 Aligned_cols=51 Identities=18% Similarity=0.089 Sum_probs=43.3
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
...|.....+|.+|++|++. +++.|++|.+.++||.||+.++.++++++..
T Consensus 348 ~~~~~~~~~~l~~g~~D~i~-~~~~t~~r~~~~~fs~py~~~~~~~v~~~~~ 398 (1197)
T PRK09959 348 VSHNIHAGTQLNPGGWDIIP-GAIYSEDRENNVLFAEAFITTPYVFVMQKAP 398 (1197)
T ss_pred cCCHHHHHHHHHCCCceEee-cccCCccccccceeccccccCCEEEEEecCC
Confidence 34466778889999999875 5568999999999999999999999998753
No 28
>KOG1053|consensus
Probab=94.55 E-value=0.031 Score=56.14 Aligned_cols=67 Identities=30% Similarity=0.669 Sum_probs=56.1
Q ss_pred CCCCCcchhhhhhhhhhhhcchhhhhhhccCCCCCCCcccCCCCCCCCcchhhHHHHHHHHHhcccCCCCCCchhhHHHH
Q psy13439 143 PEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMT 222 (261)
Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~ 222 (261)
-||+....|.++.|+++..++++||+|||.+|.+++++ . ..-+.|.+.+.-|--
T Consensus 559 LePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~---l-----------------------~~gkkpggp~Ftigk 612 (1258)
T KOG1053|consen 559 LEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRN---L-----------------------ANGKKPGGPSFTIGK 612 (1258)
T ss_pred cCCcchHHHHHHHHHHHHHHHHHHHHHhhcCccccccc---c-----------------------cCCCCCCCcceehhh
Confidence 57889999999999999999999999999999998754 1 111377888888888
Q ss_pred HHHHHHHHHHHHh
Q psy13439 223 NMWAMFAVVFLAI 235 (261)
Q Consensus 223 ~~w~l~~lil~~~ 235 (261)
..|+++++++.++
T Consensus 613 aiwllwaLvFnns 625 (1258)
T KOG1053|consen 613 AIWLLWALVFNNS 625 (1258)
T ss_pred HHHHHHHHHhCCC
Confidence 8999999998654
No 29
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=94.22 E-value=0.063 Score=49.37 Aligned_cols=83 Identities=18% Similarity=0.173 Sum_probs=65.9
Q ss_pred cchhhHhhhhcCcEEEEEEecCCceeE-------------------------e-eCCchhhHHHHHhcCceeEEEeCCCC
Q psy13439 4 EDNQHESLKKKRKLLTVYLHSKNEVLS-------------------------V-ENGKWNGLIADLVNRKTDMALTSLVI 57 (261)
Q Consensus 4 ~~~~~e~l~k~~~~~~~~~~~~~~~g~-------------------------~-~~~~~~gli~~L~~g~~Di~i~~i~i 57 (261)
+.+.++.|.+.|.++......+..++. + +-..-+.|+.+|.+|++|++++|+..
T Consensus 12 ee~~l~~Iq~rGvLrV~tinsp~sy~~~~~~p~G~eYelak~Fa~yLgV~Lki~~~~n~dqLf~aL~ng~~DL~Aagl~~ 91 (473)
T COG4623 12 EENDLAAIQARGVLRVSTINSPLSYFEDKGGPTGLEYELAKAFADYLGVKLKIIPADNIDQLFDALDNGNADLAAAGLLY 91 (473)
T ss_pred ccchHHHHHhcCeEEEEeecCccceeccCCCccchhHHHHHHHHHHhCCeEEEEecCCHHHHHHHHhCCCcceecccccC
Confidence 445677888888886666665544322 1 23345788999999999999999999
Q ss_pred ChhhhhhccccccccccceEEEEEccCCC
Q psy13439 58 NSRRESVVDFTVPIMETGIAIVVAKRTGI 86 (261)
Q Consensus 58 t~eR~~~vdfS~py~~~~~~~lv~~~~~~ 86 (261)
.++|.+.+.....|+....+++.+++...
T Consensus 92 ~~~~l~~~~~gP~y~svs~qlVyRkG~~R 120 (473)
T COG4623 92 NSERLKNFQPGPTYYSVSQQLVYRKGQYR 120 (473)
T ss_pred ChhHhcccCCCCceecccHHHHhhcCCCC
Confidence 99999999999999999999999988643
No 30
>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=93.39 E-value=0.09 Score=45.22 Aligned_cols=60 Identities=17% Similarity=0.160 Sum_probs=45.6
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCCh---hhhhhcccccccccc------ceEEEEEccCCCCCcccc
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINS---RRESVVDFTVPIMET------GIAIVVAKRTGIISPTAF 92 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~---eR~~~vdfS~py~~~------~~~~lv~~~~~~~~~~~~ 92 (261)
..+|+.++..+.+|++|+++++..... +|.+..+|+.||... ...++++++....++.++
T Consensus 71 ~~~~~~~~~~l~~g~~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~~i~~~~dL 139 (254)
T TIGR01098 71 ATDYSAVIEAMRFGRVDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADSPIKSLKDL 139 (254)
T ss_pred CCCHHHHHHHHHcCCccEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCCCCCChHHh
Confidence 456899999999999999998775544 566668888876643 357888887777776664
No 31
>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=89.47 E-value=0.37 Score=42.48 Aligned_cols=58 Identities=17% Similarity=0.150 Sum_probs=40.3
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCC---CChhhhhhc--------cccccccccceEEEEEccCCCCCcccc
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLV---INSRRESVV--------DFTVPIMETGIAIVVAKRTGIISPTAF 92 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~---it~eR~~~v--------dfS~py~~~~~~~lv~~~~~~~~~~~~ 92 (261)
...+|++++.+|.+|++|+++.+.. ...+|.+.. +++.||. ..+++++++...++.++
T Consensus 65 ~~~~~~~~~~al~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~---~~lvv~~ds~i~sl~DL 133 (288)
T TIGR03431 65 FATDYAGVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAFAIEVNADGSTGYY---SVLIVKKDSPIKSLEDL 133 (288)
T ss_pred eCCCHHHHHHHHHcCCccEEEEChHHHHHHHHhcCCeEEEEeccCCCCCceE---EEEEEeCCCCCCcHHHh
Confidence 4557999999999999999997642 222565553 3455554 57778877666666664
No 32
>KOG1419|consensus
Probab=88.11 E-value=0.53 Score=45.31 Aligned_cols=87 Identities=13% Similarity=0.209 Sum_probs=69.8
Q ss_pred hhhhhhhhhcchhhhhhhccCCCCCCCcccCCCCCCCCcchhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHH
Q psy13439 153 LVGVVAIQASAFTIFFFEWLSPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVF 232 (261)
Q Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil 232 (261)
-+|++++--..+.||..|.+-+... ......+..+++|+..-.+..-|.+.+.|+++.+|++++.+-++++-+
T Consensus 238 YIGFL~LIfsSflVYLaEKd~~~e~-------~n~~F~TyADALWWG~ITltTIGYGDk~P~TWlGr~laa~fsligiSF 310 (654)
T KOG1419|consen 238 YIGFLVLIFSSFLVYLAEKDAQGEG-------TNDEFPTYADALWWGVITLTTIGYGDKTPQTWLGRLLAACFSLIGISF 310 (654)
T ss_pred HHHHHHHHHHHHHHHHhhccccccc-------ccccchhHHHHHHhhheeEEeeccCCcCcccchhHHHHHHHHHHHHHH
Confidence 4677777777888888898866532 223444788999999888888888878999999999999999999998
Q ss_pred HHhhcccceeeeec
Q psy13439 233 LAIYTANLAAFMIT 246 (261)
Q Consensus 233 ~~~Yta~L~s~Lt~ 246 (261)
.+.=.+-|-|-++.
T Consensus 311 FALPAGILGSGfAL 324 (654)
T KOG1419|consen 311 FALPAGILGSGFAL 324 (654)
T ss_pred Hhcccccccchhhh
Confidence 88888878777764
No 33
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=80.91 E-value=2.9 Score=37.27 Aligned_cols=55 Identities=16% Similarity=0.085 Sum_probs=38.1
Q ss_pred hhhHHHHHhcCceeEEEeCCCCChhhhhhccc------cccccccceEEEEEccCCCCCccc
Q psy13439 36 WNGLIADLVNRKTDMALTSLVINSRRESVVDF------TVPIMETGIAIVVAKRTGIISPTA 91 (261)
Q Consensus 36 ~~gli~~L~~g~~Di~i~~i~it~eR~~~vdf------S~py~~~~~~~lv~~~~~~~~~~~ 91 (261)
...++.+|.+|++|+++.+ ..+..+.+...+ +.++......++++++....++.+
T Consensus 66 ~~~~~~aL~~G~iDia~~~-~~~~~~~~~~g~~~~~v~~~~~~~~~~~lvv~~~s~i~s~~d 126 (314)
T PRK11553 66 GPQMLEALNVGSIDLGSTG-DIPPIFAQAAGADLVYVGVEPPKPKAEVILVAENSPIKTVAD 126 (314)
T ss_pred cHHHHHHHHcCCCCEEccC-CHHHHHHHhCCCCEEEEEEecCCCcceEEEEeCCCCCCCHHH
Confidence 4689999999999999865 344444322222 456666677888988777766655
No 34
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=69.15 E-value=5.2 Score=41.00 Aligned_cols=53 Identities=6% Similarity=0.092 Sum_probs=46.1
Q ss_pred hhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHhhcccceeeeec
Q psy13439 194 RTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFMIT 246 (261)
Q Consensus 194 ~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~ 246 (261)
.|+|+++.++..-|.+.-.|.+...|++.+.+.++++.+.++..+++++.+..
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 38999999998877654489999999999999999999999999999987754
No 35
>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=64.64 E-value=6.9 Score=34.57 Aligned_cols=59 Identities=19% Similarity=0.151 Sum_probs=38.6
Q ss_pred CchhhHHHHHhcCceeEEEeCCCCCh------------hhhhhccccccccccceEEEEEccCCCCCcccc
Q psy13439 34 GKWNGLIADLVNRKTDMALTSLVINS------------RRESVVDFTVPIMETGIAIVVAKRTGIISPTAF 92 (261)
Q Consensus 34 ~~~~gli~~L~~g~~Di~i~~i~it~------------eR~~~vdfS~py~~~~~~~lv~~~~~~~~~~~~ 92 (261)
+.....+..|.+|++|+++.+..... .+.+.+....+++.....++++++....++.++
T Consensus 69 ~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~lvv~~d~~i~sl~dL 139 (320)
T TIGR02122 69 GGSVENVNLLEAGEADLAIVQSDVAYYAYEGDGEFEFEGPVEKLRALASLYPEYIQIVVRKDSGIKTVADL 139 (320)
T ss_pred cchHHHHHHHhCCCCcEEEEcchhHHHHhcCcCccccCCCCccHHhHHHhccccEEEEEECCCCCCcHHHc
Confidence 34457899999999999998753321 112233323356667778899888776666554
No 36
>KOG0498|consensus
Probab=63.74 E-value=9.1 Score=38.66 Aligned_cols=54 Identities=11% Similarity=0.233 Sum_probs=47.0
Q ss_pred hhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHhhcccceeeeec
Q psy13439 193 FRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFMIT 246 (261)
Q Consensus 193 ~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~ 246 (261)
.-|+|+++..|..-|.+...|...+-.++.+..+++.+++.+.--+|+++++..
T Consensus 296 ~~aLyw~l~tLstvG~g~~~s~~~~E~iFsi~~mi~GllL~A~lIGNmt~~iqs 349 (727)
T KOG0498|consen 296 VYALYWGLSTLSTVGYGLVHANNMGEKIFSIFIMLFGLLLFAYLIGNMTALLQS 349 (727)
T ss_pred HHHHHHHhhHhhhccCCccCCCCcHHHHHHHHHHHHhHHHHHHHHhhHHHhHHH
Confidence 359999999998666655578888999999999999999999999999999974
No 37
>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=62.18 E-value=18 Score=27.77 Aligned_cols=49 Identities=20% Similarity=0.424 Sum_probs=34.4
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
......++..|.+|++|+++....... +.++ ..++......+++++...
T Consensus 35 ~~~~~~~~~~l~~g~~D~~i~~~~~~~---~~~~-~~~l~~~~~~~~~~~~~~ 83 (197)
T cd05466 35 EGGSSELLEALLEGELDLAIVALPVDD---PGLE-SEPLFEEPLVLVVPPDHP 83 (197)
T ss_pred ECChHHHHHHHHcCCceEEEEcCCCCC---Ccce-EeeeeccceEEEecCCCC
Confidence 344568999999999999997655422 2233 456777888888877643
No 38
>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=61.40 E-value=9.1 Score=33.76 Aligned_cols=57 Identities=12% Similarity=0.117 Sum_probs=36.4
Q ss_pred chhhHHHHHhcCceeEEEeCCCCC-hhhhhhccc----cccccccceEEEEEccCCCCCccc
Q psy13439 35 KWNGLIADLVNRKTDMALTSLVIN-SRRESVVDF----TVPIMETGIAIVVAKRTGIISPTA 91 (261)
Q Consensus 35 ~~~gli~~L~~g~~Di~i~~i~it-~eR~~~vdf----S~py~~~~~~~lv~~~~~~~~~~~ 91 (261)
++..++.+|.+|++|++..+.+.. ..+.+..++ ...+......+++++++.+.++.+
T Consensus 36 ~~~~~~~al~~G~iD~~~~~~~~~~~a~~~g~~~~~v~~~~~~~~~~~lv~~~~s~I~s~~D 97 (300)
T TIGR01729 36 SGADISTALASGNVPIGVIGSSPLAAAASRGVPIELFWILDNIGKSEALVAREGSGIEKPED 97 (300)
T ss_pred cHHHHHHHHHcCCCCEeccCCCHHHHHHHCCCCeEEEEEeccCCccceEEecCCCCCCChhH
Confidence 467899999999999998765433 233333332 233333456788887766666554
No 39
>KOG3713|consensus
Probab=58.18 E-value=9.2 Score=36.47 Aligned_cols=47 Identities=15% Similarity=0.233 Sum_probs=38.6
Q ss_pred CCcchhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHh
Q psy13439 189 RFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAI 235 (261)
Q Consensus 189 ~~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~ 235 (261)
..++--++|++.-++..-|.+.-.|++.+||++++.-.+.++++++.
T Consensus 375 FtSIPa~~WWaiVTMTTVGYGDm~P~T~~Gklvas~cil~GVLvlAl 421 (477)
T KOG3713|consen 375 FTSIPAGFWWAVVTMTTVGYGDMVPVTVLGKLVASLCILCGVLVLAL 421 (477)
T ss_pred CccccchhheeeEEEeeecccCccccccchHHHHHHHHHHhHHHhhc
Confidence 44677899998888887777655999999999999988888877653
No 40
>PRK10537 voltage-gated potassium channel; Provisional
Probab=58.10 E-value=9.2 Score=35.80 Aligned_cols=53 Identities=11% Similarity=0.113 Sum_probs=42.2
Q ss_pred CcchhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHhhccccee
Q psy13439 190 FSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAIYTANLAA 242 (261)
Q Consensus 190 ~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s 242 (261)
.++.+++|+++-++..-|.+.-.|.+..+|++..++.++++.+..+..+.++.
T Consensus 167 ~s~~dA~y~svvt~tTvGyGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~~ 219 (393)
T PRK10537 167 ESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIFG 219 (393)
T ss_pred CCHHHHHHhhheeeecccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 37889999998888877765548999999999999999888776655555544
No 41
>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=53.10 E-value=31 Score=27.36 Aligned_cols=53 Identities=9% Similarity=0.073 Sum_probs=35.2
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
.++..+.++..|.+|++|+++........-.+.+.. .++......++++++..
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~hp 86 (202)
T cd08468 34 VHAEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEE-RDWWEDTYVVIASRDHP 86 (202)
T ss_pred EECChHhHHHHHHCCCccEEEecccccccCCCCEEE-EEEecCcEEEEEeCCCC
Confidence 455668999999999999999643221100123333 56778888888877654
No 42
>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=52.49 E-value=23 Score=29.22 Aligned_cols=66 Identities=26% Similarity=0.327 Sum_probs=44.9
Q ss_pred CchhhHHHHHhcCceeEEEeCCCCCh-hhhhhcccc---ccccccceEEEEEccCCCCCcccccCCCCcccccceeh
Q psy13439 34 GKWNGLIADLVNRKTDMALTSLVINS-RRESVVDFT---VPIMETGIAIVVAKRTGIISPTAFLEPFDTASWMLVGV 106 (261)
Q Consensus 34 ~~~~gli~~L~~g~~Di~i~~i~it~-eR~~~vdfS---~py~~~~~~~lv~~~~~~~~~~~~l~pF~~~vW~~i~~ 106 (261)
......+.+|.+|++|+++++...-. .|.+-.+.. ..+......++++++..++++.+ +++ ..+++
T Consensus 29 ~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~D----LkG---K~i~v 98 (216)
T PF09084_consen 29 GGGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSSPNALVVRKDSGIKSPAD----LKG---KKIGV 98 (216)
T ss_dssp SSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGG----GTT---SEEEE
T ss_pred cChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHH----hCC---CEEEE
Confidence 44578999999999999998885333 455545443 33445667888888877777766 455 55655
No 43
>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=47.75 E-value=48 Score=25.71 Aligned_cols=50 Identities=12% Similarity=0.213 Sum_probs=35.0
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
+..+..+.+...|.+|++|+++...... ...+ .+.++......+++++..
T Consensus 33 i~~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~~~ 82 (196)
T cd08415 33 LHTLSSSTVVEAVLSGQADLGLASLPLD---HPGL-ESEPLASGRAVCVLPPGH 82 (196)
T ss_pred EEecchHHHHHHHHcCCccEEEEeCCCC---CCcc-eeeeecccceEEEEcCCC
Confidence 3455667899999999999999643332 1222 356788888888887654
No 44
>KOG1418|consensus
Probab=46.35 E-value=16 Score=33.33 Aligned_cols=59 Identities=12% Similarity=0.287 Sum_probs=48.0
Q ss_pred CCCCcchhhHHHHHHHHHhcccCCCCCCchhhHHHHHHHHHHHHHHHHhhcccceeeee
Q psy13439 187 SHRFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFMI 245 (261)
Q Consensus 187 ~~~~~~~~s~~~~~~~l~~qg~~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt 245 (261)
...-+|.++++|++.++..-|.+.-.|++..||++++.|.++++=++-..-+++.-+|+
T Consensus 111 ~~~W~f~~al~fs~tv~TTIGYG~i~P~T~~Gr~~~i~YaliGIPl~li~l~~~g~~l~ 169 (433)
T KOG1418|consen 111 TQQWSFSSALLFSITVITTIGYGNIAPRTDAGRLFTILYALVGIPLMLLILADIGKFLA 169 (433)
T ss_pred CcceecchhHhhhhheeeeccCCcccCCcCcchhHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 33448899999999999977776559999999999999999988777776666666554
No 45
>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=45.92 E-value=40 Score=27.04 Aligned_cols=47 Identities=9% Similarity=0.081 Sum_probs=33.3
Q ss_pred chhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 35 KWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 35 ~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
+.+.++..|.+|++|+++..-.. ..+.+++ .++.+....++++++..
T Consensus 38 ~~~~l~~~L~~g~lDl~i~~~~~---~~~~l~~-~~l~~~~~~lv~~~~h~ 84 (203)
T cd08463 38 PDFDYERALASGELDLVIGNWPE---PPEHLHL-SPLFSDEIVCLMRADHP 84 (203)
T ss_pred cchhHHHHHhcCCeeEEEecccc---CCCCcEE-eEeecCceEEEEeCCCC
Confidence 45789999999999999964222 1222333 56788888888887754
No 46
>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=45.84 E-value=41 Score=26.57 Aligned_cols=49 Identities=22% Similarity=0.278 Sum_probs=36.5
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++.+.++..|.+|++|+++..... ....+. ..++......+++++..
T Consensus 40 ~~~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~~ 88 (209)
T PF03466_consen 40 REGDSDELIEALRSGELDLAITFGPP---PPPGLE-SEPLGEEPLVLVVSPDH 88 (209)
T ss_dssp EEESHHHHHHHHHTTSSSEEEESSSS---SSTTEE-EEEEEEEEEEEEEETTS
T ss_pred EeccchhhhHHHhcccccEEEEEeec---cccccc-cccccceeeeeeeeccc
Confidence 45556799999999999999976665 222222 46778889999998875
No 47
>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=45.09 E-value=46 Score=26.44 Aligned_cols=49 Identities=12% Similarity=0.201 Sum_probs=34.1
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++...++..|.+|++|+++...... ...+.. .+.......++++++.
T Consensus 34 ~~~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~lv~~~~h 82 (200)
T cd08465 34 SQASREAMLAQVADGEIDLALGVFPEL---PEELHA-ETLFEERFVCLADRAT 82 (200)
T ss_pred ecCChHhHHHHHHCCCccEEEeccccC---CcCeeE-EEeeeccEEEEEeCCC
Confidence 455678999999999999999643322 223333 4677788888887764
No 48
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=43.64 E-value=20 Score=30.77 Aligned_cols=57 Identities=16% Similarity=0.031 Sum_probs=34.7
Q ss_pred chhhHHHHHhcCceeEEEeCCCC-Chhhhhhccccc--cccc-cceEEEEEccCCCCCccc
Q psy13439 35 KWNGLIADLVNRKTDMALTSLVI-NSRRESVVDFTV--PIME-TGIAIVVAKRTGIISPTA 91 (261)
Q Consensus 35 ~~~gli~~L~~g~~Di~i~~i~i-t~eR~~~vdfS~--py~~-~~~~~lv~~~~~~~~~~~ 91 (261)
.+..++.+|.+|++|+++.+... -..+.+..++.. .+.. .+..++++++....++.+
T Consensus 38 ~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~~v~~~~~~i~s~~d 98 (288)
T TIGR01728 38 AGPPALEALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSDNKATAIVVIKGSPIRTVAD 98 (288)
T ss_pred CCcHHHHHHhcCCccccccCCcHHHHHHhcCCCEEEEEEecCCCceEEEECCCCCCCCHHH
Confidence 45688999999999998776642 122222223321 1122 467788877766666555
No 49
>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=42.58 E-value=71 Score=24.79 Aligned_cols=50 Identities=14% Similarity=0.194 Sum_probs=33.9
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++.+.+...|.+|++|+++...... ....+ -+.++......++++++.
T Consensus 35 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~~~~ 84 (199)
T cd08451 35 EEANTAELLEALREGRLDAAFVRPPVA--RSDGL-VLELLLEEPMLVALPAGH 84 (199)
T ss_pred ecCChHHHHHHHHCCCccEEEEecCCC--CCCce-eEEEeecccEEEEecCCC
Confidence 455567899999999999999643322 11122 346778888888887654
No 50
>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=42.48 E-value=85 Score=24.47 Aligned_cols=51 Identities=16% Similarity=0.191 Sum_probs=35.2
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
...++...+...|.+|++|+++..-. .....+. +.++......++++++..
T Consensus 33 ~~~~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~lv~~~~~~ 83 (200)
T cd08466 33 ESPSSEEDLFEDLRLQEVDLVIDYVP---FRDPSFK-SELLFEDELVCVARKDHP 83 (200)
T ss_pred EecCchHhHHHHHHcCCccEEEeccc---CCCCCce-eeeecccceEEEEeCCCC
Confidence 34556678999999999999995322 2222232 457888888888887643
No 51
>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=40.93 E-value=66 Score=25.19 Aligned_cols=50 Identities=14% Similarity=-0.006 Sum_probs=34.9
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..++.+.+...|.+|++|+++...... ...+. +.|+......++++++..
T Consensus 34 ~~~~~~~~~~~l~~g~~D~~i~~~~~~---~~~l~-~~~l~~~~~~~v~~~~~~ 83 (201)
T cd08459 34 VRLPVDELEEALESGEIDLAIGYLPDL---GAGFF-QQRLFRERYVCLVRKDHP 83 (201)
T ss_pred EecCccCHHHHhhCCCceEEEEcCCCC---cccce-EEEeecCceEEEEcCCCc
Confidence 444556889999999999999654322 22333 467888888888876643
No 52
>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=40.27 E-value=68 Score=25.79 Aligned_cols=53 Identities=25% Similarity=0.339 Sum_probs=33.5
Q ss_pred EeeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEcc
Q psy13439 30 SVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKR 83 (261)
Q Consensus 30 ~~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~ 83 (261)
+...+..+.++..|.+|++|+++......++-...+ ...|+......++++.+
T Consensus 32 ~i~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~ 84 (204)
T cd08429 32 VCREGKLEQLLADLALHRLDMVLADRPMPSSLDVKG-YSHRLGECGVSFFAAPP 84 (204)
T ss_pred EEEeCCHHHHHHHHHcCCccEEEecCCCccccchhe-eeccccccceEEEecCC
Confidence 345667789999999999999995433221100111 13577777777776544
No 53
>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=40.24 E-value=75 Score=25.03 Aligned_cols=48 Identities=15% Similarity=0.019 Sum_probs=32.4
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
+++- .++..|.+|++|+++..-.... ..+. ..|+......++++++..
T Consensus 35 ~~~~-~~~~~l~~g~~D~~i~~~~~~~---~~~~-~~~l~~~~~~~v~~~~hp 82 (200)
T cd08462 35 PPDD-QPHELLERGEVDLLIAPERFMS---DGHP-SEPLFEEEFVCVVWADNP 82 (200)
T ss_pred cCCh-hHHHHHhcCCeeEEEecCCCCC---CCce-eeeeeccceEEEEcCCCC
Confidence 3444 8999999999999996432221 2233 347778888888876654
No 54
>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=39.82 E-value=68 Score=24.99 Aligned_cols=50 Identities=12% Similarity=0.120 Sum_probs=34.3
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
...++.+.+...|.+|++|+++...... ...+ -+.++......+++++..
T Consensus 34 i~~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~~~ 83 (198)
T cd08446 34 LHNMTKDEQIEALRAGRIHIGFGRFYPV---EPDI-AVENVAQERLYLAVPKSH 83 (198)
T ss_pred EeeCCHHHHHHHHHCCCccEEEEecCCC---CCCc-eeEEeeeccEEEEEeCCC
Confidence 3456678899999999999999543221 1222 245677888888887754
No 55
>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=39.13 E-value=67 Score=25.05 Aligned_cols=48 Identities=21% Similarity=0.228 Sum_probs=32.5
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
.+..+.+...|.+|++|+++..... ..+.+. +.++......++++++.
T Consensus 35 ~~~~~~~~~~l~~~~~Di~i~~~~~---~~~~~~-~~~l~~~~~~lv~~~~~ 82 (198)
T cd08461 35 DLESDNLEAQLERGEVDLALTTPEY---APDGLR-SRPLFEERYVCVTRRGH 82 (198)
T ss_pred eCCcccHHHHHhcCCCcEEEecCcc---CCccce-eeeeecCcEEEEEcCCC
Confidence 3444678999999999999853222 122232 56778888888887654
No 56
>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=37.87 E-value=98 Score=24.16 Aligned_cols=53 Identities=8% Similarity=0.114 Sum_probs=34.3
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..+..+.+...|.+|++|+++..-....+....+. +.+.......+++++...
T Consensus 34 ~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~-~~~l~~~~~~~v~~~~hp 86 (200)
T cd08453 34 REATSDVQLEALLAGEIDAGIVIPPPGASAPPALA-YRPLLSEPLVLAVPAAWA 86 (200)
T ss_pred EeCCHHHHHHHHHcCCCCEEEEecCcccCCCccee-EEEeeeCceEEEEECCCc
Confidence 44556789999999999999864322111112222 466778888888877643
No 57
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=37.85 E-value=78 Score=27.66 Aligned_cols=49 Identities=24% Similarity=0.338 Sum_probs=35.7
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
.+.+-+.++.+|.+|++|+++.......+ . -.+.++...+..+++++..
T Consensus 125 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~---~-l~~~~l~~~~~~~~~~~~h 173 (305)
T PRK11151 125 HEAQTHQLLAQLDSGKLDCAILALVKESE---A-FIEVPLFDEPMLLAVYEDH 173 (305)
T ss_pred EeCCHHHHHHHHHcCCccEEEEecCCCCC---C-eEEEEeccCcEEEEecCCC
Confidence 45556889999999999999965433222 2 2357888899999987664
No 58
>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=37.82 E-value=95 Score=24.42 Aligned_cols=48 Identities=13% Similarity=0.183 Sum_probs=33.1
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
.+..+.++..|.+|++|++++...... ..+. +.++......++++++.
T Consensus 36 ~~~~~~~~~~l~~~~~Dl~i~~~~~~~---~~~~-~~~l~~~~~~~v~~~~h 83 (203)
T cd08445 36 EMTTVQQIEALKEGRIDVGFGRLRIED---PAIR-RIVLREEPLVVALPAGH 83 (203)
T ss_pred eCChHHHHHHHHcCCCcEEEecCCCCC---CCce-eEEEEeccEEEEeeCCC
Confidence 445678999999999999995432221 2232 45677888888887654
No 59
>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=37.76 E-value=95 Score=23.80 Aligned_cols=49 Identities=12% Similarity=0.190 Sum_probs=33.6
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++...+...|.+|++|+++..... ....+. +.++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~~ 82 (197)
T cd08440 34 RDVSAEQVIEAVRSGEVDFGIGSEPE---ADPDLE-FEPLLRDPFVLVCPKDH 82 (197)
T ss_pred EeCChHHHHHHHHcCCccEEEEeCCC---CCCCee-EEEeecccEEEEecCCC
Confidence 34456789999999999999964332 222222 35677888888887654
No 60
>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=37.72 E-value=60 Score=25.19 Aligned_cols=49 Identities=16% Similarity=0.089 Sum_probs=33.8
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++-..++..|.+|++|+++..... ....+. +.++......++++++.
T Consensus 34 ~~~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~~ 82 (198)
T cd08412 34 VEGNQEELEEGLRSGELDLALTYDLD---LPEDIA-FEPLARLPPYVWLPADH 82 (198)
T ss_pred EECCHHHHHHHHHcCCCcEEEEcCCC---CCcccc-eeeeeccceEEEecCCC
Confidence 34455788999999999999964322 122232 46788888888887654
No 61
>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=37.14 E-value=75 Score=25.15 Aligned_cols=49 Identities=10% Similarity=0.226 Sum_probs=33.4
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+..+.++..|.+|++|+++..-. + ....++ +.++......++++++.
T Consensus 35 ~~~~~~~l~~~l~~g~~D~~~~~~~--~-~~~~~~-~~~l~~~~~~lv~~~~h 83 (198)
T cd08486 35 THMTKDEQVEGLLAGTIHVGFSRFF--P-RHPGIE-IVNIAQEDLYLAVHRSQ 83 (198)
T ss_pred EECCHHHHHHHHHcCCceEEEecCC--C-CCCceE-EEEEeeccEEEEecCCC
Confidence 3456789999999999999995321 1 122233 35567778888887654
No 62
>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=37.08 E-value=96 Score=23.90 Aligned_cols=49 Identities=10% Similarity=0.275 Sum_probs=33.6
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+....++.+|.+|++|+++....... ..+ -..++......++++++.
T Consensus 33 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~~~~~~~ 81 (197)
T cd08419 33 RVGNREQVLERLADNEDDLAIMGRPPED---LDL-VAEPFLDNPLVVIAPPDH 81 (197)
T ss_pred EECCHHHHHHHHhcCCccEEEecCCCCC---CCe-EEEEeccCCEEEEecCCC
Confidence 3445678899999999999996433221 112 246778888888887654
No 63
>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=36.32 E-value=90 Score=24.24 Aligned_cols=48 Identities=10% Similarity=0.064 Sum_probs=33.3
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
.+.-+.++..|.+|++|+++....... ..+. +.++......+++++..
T Consensus 35 ~~~~~~~~~~l~~~~~D~~i~~~~~~~---~~~~-~~~l~~~~~~~v~~~~h 82 (199)
T cd08426 35 VASTADVLEAVLSGEADIGLAFSPPPE---PGIR-VHSRQPAPIGAVVPPGH 82 (199)
T ss_pred eCCcHHHHHHHHCCCccEEEecCCCCC---CCeE-EEeeccCcEEEEecCCC
Confidence 445578999999999999996433221 2222 46778888888887654
No 64
>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=36.03 E-value=64 Score=25.12 Aligned_cols=49 Identities=16% Similarity=0.171 Sum_probs=34.4
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
...+.+.+...|.+|++|+++.... .....+. ..++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~~~ 82 (200)
T cd08417 34 VPLDRDDLEEALESGEIDLAIGVFP---ELPPGLR-SQPLFEDRFVCVARKDH 82 (200)
T ss_pred ccCCHHHHHHHHHcCCCCEEEeecc---cCCCccc-hhhhhcCceEEEecCCC
Confidence 4555678999999999999996432 2222332 36778888888887664
No 65
>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=35.76 E-value=1.2e+02 Score=23.75 Aligned_cols=48 Identities=10% Similarity=0.029 Sum_probs=32.8
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
.++. .++..|.+|++|+++...... ...+. ..++......++++++..
T Consensus 35 ~~~~-~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~hp 82 (200)
T cd08460 35 PESD-KDVDALREGRIDLEIGVLGPT---GPEIR-VQTLFRDRFVGVVRAGHP 82 (200)
T ss_pred cCch-hHHHHHHCCCccEEEecCCCC---Ccchh-eeeeeccceEEEEeCCCC
Confidence 3444 688999999999999643221 22333 467788888888877653
No 66
>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=35.58 E-value=90 Score=24.07 Aligned_cols=49 Identities=6% Similarity=-0.010 Sum_probs=33.9
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+....+...|.+|++|+++..-.. ....+. +.++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~~~~Di~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~h 82 (197)
T cd08448 34 HEMSSAEQIEALLRGELDLGFVHSRR---LPAGLS-ARLLHREPFVCCLPAGH 82 (197)
T ss_pred EeCCHHHHHHHHHcCCcceEEEeCCC---CCcCce-EEEEecCcEEEEeeCCC
Confidence 34566889999999999999863322 222232 46778888888887654
No 67
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=35.53 E-value=71 Score=27.62 Aligned_cols=50 Identities=12% Similarity=0.127 Sum_probs=35.9
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..+....++..|.+|++|++++...... ..+ ...|+......++++++..
T Consensus 123 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~l-~~~~l~~~~~~~v~~~~~~ 172 (275)
T PRK03601 123 RIAQRQSLVKQLHERQLDLLITTEAPKM---DEF-SSQLLGHFTLALYTSAPSK 172 (275)
T ss_pred EECChHHHHHHHHcCCCCEEEEcCCCcc---CCc-cEEEecceeEEEEecCchh
Confidence 4566678999999999999997543322 223 3567888888888876543
No 68
>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=35.35 E-value=89 Score=24.13 Aligned_cols=51 Identities=6% Similarity=0.132 Sum_probs=33.6
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+..+.++..|.+|++|+++....... +...+. ..++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~-~~~l~~~~~~~v~~~~~ 84 (197)
T cd08449 34 HELSPEAQKAALLSKRIDLGFVRFADTL-NDPPLA-SELLWREPMVVALPEEH 84 (197)
T ss_pred EECCHHHHHHHHhCCCccEEEecccccC-CCCCce-EEEEEEeeEEEEecCCC
Confidence 4455678999999999999996432211 112222 35678888888887654
No 69
>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=35.19 E-value=95 Score=24.33 Aligned_cols=49 Identities=6% Similarity=0.141 Sum_probs=33.4
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+....+...|.+|++|+++..-. .....+. +.++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~lv~~~~h 82 (197)
T cd08452 34 RELSSPDQVEELLKGRIDIGFLHPP---IQHTALH-IETVQSSPCVLALPKQH 82 (197)
T ss_pred EecChHHHHHHHHCCCccEEEeeCC---CCCCCee-EEEeeeccEEEEEeCCC
Confidence 4456678999999999999996322 2222333 35677788888887654
No 70
>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=35.08 E-value=1.1e+02 Score=23.49 Aligned_cols=49 Identities=14% Similarity=0.235 Sum_probs=33.3
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
.++-..++.+|.+|++|+++...... .+.+. +.++......+++++...
T Consensus 35 ~~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~~~ 83 (201)
T cd08420 35 IGNTEEIAERVLDGEIDLGLVEGPVD---HPDLI-VEPFAEDELVLVVPPDHP 83 (201)
T ss_pred eCCcHHHHHHHHCCCccEEEecCCCC---CcceE-EEeecCccEEEEecCCCC
Confidence 34446789999999999999654332 22222 367788888888876543
No 71
>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=34.94 E-value=83 Score=24.41 Aligned_cols=49 Identities=12% Similarity=0.262 Sum_probs=34.3
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++...++..|.+|++|+++..... ..+.+. ..++......++++++.
T Consensus 34 ~~~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~~ 82 (198)
T cd08421 34 EERLSADIVRAVAEGRADLGIVAGNV---DAAGLE-TRPYRTDRLVVVVPRDH 82 (198)
T ss_pred EecCcHHHHHHHhcCCceEEEEecCC---CCCCcE-EEEeecCcEEEEeCCCC
Confidence 34455789999999999999964322 233333 36778888888887764
No 72
>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=34.80 E-value=1e+02 Score=23.88 Aligned_cols=49 Identities=16% Similarity=0.155 Sum_probs=33.4
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+....++..|.+|++|+++...... ...+. ..++......++++++.
T Consensus 34 ~~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~~~~~ 82 (196)
T cd08450 34 SSLFSPQLAEALMRGKLDVAFMRPEIQ---SDGID-YQLLLKEPLIVVLPADH 82 (196)
T ss_pred EecChHHHHHHHhcCCccEEEEeCCCC---CCCcE-EEEEEccceEEEecCCC
Confidence 444557899999999999998643222 12222 46677888888887654
No 73
>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=34.50 E-value=73 Score=24.59 Aligned_cols=49 Identities=16% Similarity=0.257 Sum_probs=33.4
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++-..++..|.+|++|+++..-... ...+. ..++......+++++..
T Consensus 34 ~~~~~~~~~~~L~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~~ 82 (197)
T cd08438 34 VEYGGKKVEQAVLNGELDVGITVLPVD---EEEFD-SQPLCNEPLVAVLPRGH 82 (197)
T ss_pred EEcCcHHHHHHHHcCCCCEEEEecccc---cCCce-eEEeccccEEEEecCCC
Confidence 344557889999999999999654332 22232 35677888888887664
No 74
>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=34.23 E-value=1e+02 Score=24.26 Aligned_cols=51 Identities=12% Similarity=0.040 Sum_probs=34.4
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
+..+....++..|.+|++|+++..... . ...+. ..+.......+++++...
T Consensus 33 ~~~~~~~~~~~~l~~g~~D~~i~~~~~--~-~~~~~-~~~l~~~~~~~v~~~~h~ 83 (200)
T cd08467 33 LCPIGDDLAERGLEQGTIDLAVGRFAV--P-PDGLV-VRRLYDDGFACLVRHGHP 83 (200)
T ss_pred EecCCcccHHHHhhCCCcCEEEecCCC--C-Cccce-eEEeeeccEEEEEcCCCc
Confidence 345555689999999999999953222 1 22333 357788888888876543
No 75
>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=34.07 E-value=1e+02 Score=23.61 Aligned_cols=49 Identities=31% Similarity=0.468 Sum_probs=33.7
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+....++..|.+|++|+++..... ..+.+. ..++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~~~ 82 (195)
T cd08434 34 HQGSTDELLDDLKNGELDLALCSPVP---DEPDIE-WIPLFTEELVLVVPKDH 82 (195)
T ss_pred ecCcHHHHHHHHHcCCccEEEEccCC---CCCCee-EEEeecceEEEEecCCC
Confidence 34455788999999999999864332 223333 35677888888887654
No 76
>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=33.66 E-value=89 Score=24.18 Aligned_cols=49 Identities=10% Similarity=0.073 Sum_probs=32.3
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+....++.+|.+|++|+++..-... ...+. +.+.......+++++..
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~~~~~ 82 (196)
T cd08456 34 HTRDSPTVEQWLSAQQCDLGLVSTLHE---PPGIE-RERLLRIDGVCVLPPGH 82 (196)
T ss_pred EeCCHHHHHHHHHcCCccEEEEecCCC---CCCee-EEEeeccCeEEEecCCC
Confidence 445556788999999999999643222 12222 45677778887776643
No 77
>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=33.40 E-value=61 Score=28.52 Aligned_cols=54 Identities=22% Similarity=0.282 Sum_probs=37.2
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhh-----hhccc-cccccccceEEEEEccC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRE-----SVVDF-TVPIMETGIAIVVAKRT 84 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~-----~~vdf-S~py~~~~~~~lv~~~~ 84 (261)
+..+..+.++..|.+|++|+++..-...++.. +..++ ..++......++++++.
T Consensus 68 i~~~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~~~~l~~~~l~lvv~~~h 127 (287)
T TIGR02136 68 VQGAGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKLIEHKVAVDGLAVVVNKKN 127 (287)
T ss_pred EccCCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCceEEEEEEeeEEEEECCCC
Confidence 34566789999999999999886543443331 12222 45888889998987664
No 78
>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=33.04 E-value=1.2e+02 Score=23.15 Aligned_cols=50 Identities=20% Similarity=0.260 Sum_probs=33.3
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++...+...|.+|++|+++..... +..+.+. ..++......++++++.
T Consensus 34 ~~~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~~~~~~~ 83 (194)
T cd08436 34 RQAGSDDLLAAVREGRLDLAFVGLPE--RRPPGLA-SRELAREPLVAVVAPDH 83 (194)
T ss_pred ecCCHHHHHHHHHcCCccEEEEecCC--CCCCCcE-EEEeecceEEEEecCCC
Confidence 34445788999999999999965332 1222232 35677778888877654
No 79
>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=32.59 E-value=1.2e+02 Score=23.55 Aligned_cols=51 Identities=20% Similarity=0.323 Sum_probs=33.8
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
.+.+.+.+...|.+|++|++++...... ....+. +.++......++++++.
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~-~~~~~~-~~~l~~~~~~~v~~~~~ 84 (201)
T cd08418 34 YEGQLSSLLPELRDGRLDFAIGTLPDEM-YLKELI-SEPLFESDFVVVARKDH 84 (201)
T ss_pred EeCcHHHHHHHHHcCCCcEEEEecCCCC-CCccee-EEeecCCceEEEeCCCC
Confidence 3455678999999999999996432211 112233 35677788888887654
No 80
>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=32.02 E-value=1.1e+02 Score=23.78 Aligned_cols=49 Identities=16% Similarity=0.312 Sum_probs=33.2
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
.+.....+...|.+|++|+++...... ...+. ..++......++++++.
T Consensus 35 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~~ 83 (197)
T cd08425 35 REMPQERIEAALADDRLDLGIAFAPVR---SPDID-AQPLFDERLALVVGATH 83 (197)
T ss_pred EECcHHHHHHHHHcCCccEEEEecCCC---CCCcE-EEEeccccEEEEecCCC
Confidence 344456889999999999999643322 22222 35677888888887664
No 81
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=31.97 E-value=1.1e+02 Score=26.47 Aligned_cols=50 Identities=14% Similarity=0.215 Sum_probs=34.8
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
.++.-..++..|.+|++|+++..... +.+.+ .+.++......++++++.+
T Consensus 125 ~~~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~l-~~~~l~~~~~~~~~~~~~p 174 (296)
T PRK11242 125 REMSQERIEALLADDELDVGIAFAPV---HSPEI-EAQPLFTETLALVVGRHHP 174 (296)
T ss_pred EeCCHHHHHHHHHCCCCcEEEEecCC---CCcce-eEEEeeeccEEEEEcCCCc
Confidence 35556788999999999999964332 22222 3467788888888887643
No 82
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=31.97 E-value=1.1e+02 Score=26.45 Aligned_cols=50 Identities=8% Similarity=0.127 Sum_probs=36.7
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
...+.++++..|.+|++|+++..... ..+.+.+ .|+......+++++...
T Consensus 124 ~~~~~~~~~~~l~~~~~D~~i~~~~~---~~~~l~~-~~l~~~~~~~v~~~~~p 173 (296)
T PRK09906 124 VSLITTQQEEKLRRGELDVGFMRHPV---YSDEIDY-LELLDEPLVVVLPVDHP 173 (296)
T ss_pred EeCCcHHHHHHHHcCCeeEEEecCCC---CCCCceE-EEEecccEEEEecCCCc
Confidence 45556789999999999999964433 2334444 68888899999887643
No 83
>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=31.66 E-value=1.2e+02 Score=23.22 Aligned_cols=49 Identities=6% Similarity=0.119 Sum_probs=33.8
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+.-+.+...|.+|++|+++...... .+.+. ..++......++++++.
T Consensus 34 ~~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~~ 82 (197)
T cd08414 34 REMTTAEQLEALRAGRLDVGFVRPPPD---PPGLA-SRPLLREPLVVALPADH 82 (197)
T ss_pred ecCChHHHHHHHHcCCccEEEEcCCCC---CCCee-EEEEeeccEEEEecCCC
Confidence 344557899999999999999643322 22232 36778888888887654
No 84
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=31.43 E-value=1.1e+02 Score=26.78 Aligned_cols=53 Identities=13% Similarity=0.236 Sum_probs=35.5
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..+..+.++..|.+|++|+++..-....+..+.+ ...++......+++++...
T Consensus 129 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~~~~~p 181 (305)
T CHL00180 129 QVHSTRRIAWNVANGQIDIAIVGGEVPTELKKIL-EITPYVEDELALIIPKSHP 181 (305)
T ss_pred EeCCHHHHHHHHHcCCccEEEEcCccCcccccce-eEEEeccCcEEEEECCCCc
Confidence 4555688999999999999996432222211222 2467788888888877643
No 85
>PRK10918 phosphate ABC transporter periplasmic substrate-binding protein PstS; Provisional
Probab=30.72 E-value=71 Score=29.35 Aligned_cols=51 Identities=14% Similarity=0.288 Sum_probs=38.8
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhc-cccccccccceEEEEEcc
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVV-DFTVPIMETGIAIVVAKR 83 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~v-dfS~py~~~~~~~lv~~~ 83 (261)
..|+-.| +.++.+|++|++.++-.++++..+.. -...|...+++++++..+
T Consensus 60 ~~GSG~G-i~~~~~g~vd~a~ssr~l~~~E~~~~~~~~~pva~daIaivvN~~ 111 (346)
T PRK10918 60 GIGSSGG-VKQIIANTVDFGASDAPLSDEKLAQEGLFQFPTVIGGVVLAVNIP 111 (346)
T ss_pred cCccHHH-HHHHHhCCCcEEecCccCCHHHHhhcCCeeeeEEEEEEEEEEeCC
Confidence 3566556 58889999999999999998755432 245678888999999755
No 86
>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=30.34 E-value=96 Score=23.90 Aligned_cols=52 Identities=12% Similarity=0.084 Sum_probs=34.4
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..+..+.++..|.+|++|+++..-... ...+.+ .+.++......+++++...
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~-~~~~l~~~~~~~v~~~~~p 85 (195)
T cd08427 34 VPGLSAELLARVDAGELDAAIVVEPPF-PLPKDL-VWTPLVREPLVLIAPAELA 85 (195)
T ss_pred EeCCcHHHHHHHHCCCCCEEEEcCCCC-ccccCc-eEEEcccCcEEEEECCCCC
Confidence 455668899999999999999643211 101223 2456778888888877643
No 87
>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=29.81 E-value=1.5e+02 Score=23.62 Aligned_cols=50 Identities=10% Similarity=0.017 Sum_probs=34.9
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
...+...+...|.+|++|+++..... ..+.+. ..|+......+++++...
T Consensus 34 ~~~~~~~~~~~l~~g~~Di~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~~~p 83 (221)
T cd08469 34 RPVTRLDLAEQLDLGRIDLVIGIFEQ---IPPRFR-RRTLFDEDEVWVMRKDHP 83 (221)
T ss_pred eeCChhhHHHHHHCCCccEEEecCCC---CCccce-eeeeeccceEEEEeCCCc
Confidence 34456789999999999999964322 223343 467888888888876643
No 88
>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=29.19 E-value=1.3e+02 Score=23.67 Aligned_cols=51 Identities=12% Similarity=0.216 Sum_probs=34.7
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..+....+..+|.+|++|+++...... ....+. +.+.......+++++...
T Consensus 34 ~~~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~~-~~~l~~~~~~~v~~~~hp 84 (198)
T cd08413 34 HQGTPSQIAEMVLKGEADIAIATEALD--DHPDLV-TLPCYRWNHCVIVPPGHP 84 (198)
T ss_pred EeCCHHHHHHHHHcCCCCEEEEccCCC--CCCCcE-EEEeeeeeEEEEecCCCc
Confidence 445567899999999999999533221 112233 467788888888877653
No 89
>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=29.15 E-value=1.2e+02 Score=23.18 Aligned_cols=50 Identities=16% Similarity=0.264 Sum_probs=34.0
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..+....+...|.+|++|+++..-. .....+. ..+.......+++++...
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~~~~ 83 (193)
T cd08442 34 STGTTGALIQAVLEGRLDGAFVAGP---VEHPRLE-QEPVFQEELVLVSPKGHP 83 (193)
T ss_pred EeCCcHHHHHHHHCCCccEEEEeCC---CCCCCcE-EEEeecCcEEEEecCCCc
Confidence 4555678999999999999986432 2222222 456778888888877643
No 90
>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=29.14 E-value=1.3e+02 Score=23.19 Aligned_cols=50 Identities=12% Similarity=0.232 Sum_probs=32.8
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++...++.+|.+|++|+++..-.... ...+. ..++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~--~~~l~-~~~l~~~~~~~~~~~~~ 83 (199)
T cd08430 34 HTGDPADAIDKVLNGEADIAIAARPDKL--PARLA-FLPLATSPLVFIAPNIA 83 (199)
T ss_pred EeCCHHHHHHHHHCCCCCEEEEecCCCC--CcccE-EEeeccceEEEEEeCCc
Confidence 4556678999999999999996422111 11222 35677777777777653
No 91
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=28.70 E-value=38 Score=29.02 Aligned_cols=60 Identities=17% Similarity=0.212 Sum_probs=38.4
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCC---Chhhhh-----hccccccccccceEEEEEcc----CCCCCccccc
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVI---NSRRES-----VVDFTVPIMETGIAIVVAKR----TGIISPTAFL 93 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~i---t~eR~~-----~vdfS~py~~~~~~~lv~~~----~~~~~~~~~l 93 (261)
-.++..++.+|.+|++|++.. ... -..+-. .+-........+..++++.+ ...+++.++.
T Consensus 42 ~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~~~~~~~~~~~~~~~~~g~~lvv~~~~~~~~~~~~~~dl~ 113 (252)
T PF13379_consen 42 FASGADILEALAAGEIDIAFV-LAPALIAIAKGAGGPDVDIVVLAGLSQNGNALVVRNDLKDASDIKSLADLI 113 (252)
T ss_dssp ESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTTTT----EEEEEECSBSSEEEEECGGGTTCSTTCCGHHHH
T ss_pred cCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCCCCcccceEEeeccCCCceEEEEcCccccCCCccCHHHHH
Confidence 345689999999999999987 321 122222 22333445667788888876 5566666653
No 92
>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=28.68 E-value=92 Score=26.48 Aligned_cols=50 Identities=20% Similarity=0.307 Sum_probs=34.5
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..+....++..|.+|++|+++..-..+. ..+. ..|+......++++++.+
T Consensus 118 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~~-~~~l~~~~~~lv~s~~~p 167 (279)
T TIGR03339 118 RIGNSQEVLQALQSYRVDVAVSSEVVDD---PRLD-RVVLGNDPLVAVVHRQHP 167 (279)
T ss_pred EECCHHHHHHHHHcCCCcEEEEecccCC---CceE-EEEcCCceEEEEECCCCc
Confidence 3455678899999999999996433322 2222 367778888888876653
No 93
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=28.54 E-value=97 Score=27.28 Aligned_cols=52 Identities=13% Similarity=0.284 Sum_probs=35.2
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..+..+.++.+|.+|++|+++....... ..+.+ -..|+......+++++..+
T Consensus 131 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~-~~~~l-~~~~l~~~~~~lv~~~~~p 182 (312)
T PRK10341 131 YEAQLSSFLPAIRDGRLDFAIGTLSNEM-KLQDL-HVEPLFESEFVLVASKSRT 182 (312)
T ss_pred EeCCHHHHHHHHHcCCCcEEEecCCccc-ccCCe-eEEEEecccEEEEEcCCCc
Confidence 4555678999999999999996432211 11222 3467888888888877643
No 94
>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=28.29 E-value=92 Score=28.53 Aligned_cols=62 Identities=13% Similarity=0.061 Sum_probs=49.8
Q ss_pred CCcchhhHHHHHHHHHhcccCC--CCCCchhhHHHHHHHHHHHHHHHHhhcccceeeeeccccc
Q psy13439 189 RFSLFRTYWLVWAVLFQAAVHI--DTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFMITREEF 250 (261)
Q Consensus 189 ~~~~~~s~~~~~~~l~~qg~~~--~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~~~ 250 (261)
..+|.++++|++.++..-|.+. ..|.+..+-+++..=.+.++++.+.-++-+.|-+++|+.+
T Consensus 82 ~~~f~~aF~FSveT~tTIGYG~~~~~~~c~~a~~l~~~q~~~g~l~~a~~~Glvfar~srP~~R 145 (336)
T PF01007_consen 82 VNSFTSAFLFSVETQTTIGYGSRYPTPECPYAIFLVTIQSLVGLLLDAFMTGLVFARFSRPKKR 145 (336)
T ss_dssp -TTHHHHHHHHHHHHTT---SSSEB-CSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCCG
T ss_pred ccchhhheeEEEEEEEEeccCCcccCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccc
Confidence 3478999999999998777654 2588888989988888999999999999999999998764
No 95
>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=28.24 E-value=1.5e+02 Score=22.97 Aligned_cols=49 Identities=18% Similarity=0.251 Sum_probs=32.6
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+....+...|.+|++|+++..-.. ....+. ..++......++++++.
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~~ 82 (198)
T cd08441 34 SSGFHFDPLPALLRGELDLVITSDPL---PLPGIA-YEPLFDYEVVLVVAPDH 82 (198)
T ss_pred EeCCchhHHHHHHcCCceEEEecCCc---CCCCcE-EEEccCCcEEEEEcCCC
Confidence 34556789999999999999953222 122222 35677778888877654
No 96
>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=27.43 E-value=1.2e+02 Score=26.38 Aligned_cols=52 Identities=13% Similarity=0.062 Sum_probs=35.4
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..++-+.++.+|.+|++|++++..... .....+. ..|+......+++++..+
T Consensus 127 ~~~~~~~~~~~l~~g~~D~~i~~~~~~-~~~~~~~-~~~l~~~~~~~~~~~~hp 178 (300)
T TIGR02424 127 MTGPNAYLLDQLRVGALDLVVGRLGAP-ETMQGLS-FEHLYNEPVVFVVRAGHP 178 (300)
T ss_pred EeCchHHHHHHHHCCCCCEEEEecCCc-cccccee-eeeecCCceEEEEcCCCc
Confidence 455667899999999999999644322 1222232 357888888888876643
No 97
>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=26.12 E-value=1.6e+02 Score=23.06 Aligned_cols=51 Identities=14% Similarity=0.237 Sum_probs=34.0
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
..++.+.++..|.+|++|+++..-... ....+ -+.++......+++++...
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~~~~~~hp 84 (198)
T cd08444 34 HQGSPEEIASMLANGQADIGIATEALE--NHPEL-VSFPYYDWHHHIIVPVGHP 84 (198)
T ss_pred EeCCHHHHHHHHHCCCccEEEeccccC--CCcCc-EEeeccccceeEEecCCCc
Confidence 455567899999999999999532211 11222 2467788888888876643
No 98
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=26.04 E-value=1.6e+02 Score=25.92 Aligned_cols=52 Identities=17% Similarity=0.234 Sum_probs=35.2
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
...+..+.++..|.+|++|+++....... ...+.+ .|+......++++++.+
T Consensus 126 ~~~~~~~~~~~~L~~~~~D~~i~~~~~~~--~~~l~~-~~l~~~~~~~v~~~~hp 177 (309)
T PRK12683 126 LRQGSPQEIAEMLLNGEADIGIATEALDR--EPDLVS-FPYYSWHHVVVVPKGHP 177 (309)
T ss_pred EEeCCHHHHHHHHHcCCccEEEecCCCCC--CCCceE-EEcccCeEEEEecCCCC
Confidence 35667889999999999999986322211 122333 46777788888876543
No 99
>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=25.56 E-value=1.3e+02 Score=23.58 Aligned_cols=49 Identities=12% Similarity=0.032 Sum_probs=31.5
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
.++.-+.++.+|.+|++|+++...... ...+. +.++......++++++.
T Consensus 35 ~~~~~~~~~~~l~~~~~D~~i~~~~~~---~~~l~-~~~l~~~~~~~~~~~~~ 83 (198)
T cd08485 35 TQMSKNRQIEALDAGTIDIGFGRFYPY---QEGVV-VRNVTNERLFLGAQKSR 83 (198)
T ss_pred EECCHHHHHHHHHcCCccEEEecCCCC---CCCeE-EEEeeccceEEEeCCCC
Confidence 344557899999999999998643221 12222 35677777777765543
No 100
>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=25.31 E-value=1.6e+02 Score=22.78 Aligned_cols=51 Identities=22% Similarity=0.272 Sum_probs=34.1
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+..+.+...|.+|++|+++.... .......+. ..++......++++++.
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~l~-~~~l~~~~~~~~~~~~h 84 (198)
T cd08437 34 YEGGSAELLEQLLQGDLDIALLGSL-TPLENSALH-SKIIKTQHFMIIVSKDH 84 (198)
T ss_pred EEcCHHHHHHHHHcCCCCEEEecCC-CCCCcccce-EEEeecceEEEEecCCC
Confidence 3445678999999999999995321 111223333 35778888888887654
No 101
>TIGR00975 3a0107s03 phosphate ABC transporter, phosphate-binding protein. This family represents one type of (periplasmic, in Gram-negative bacteria) phosphate-binding protein found in phosphate ABC (ATP-binding cassette) transporters. This protein is accompanied, generally in the same operon, by an ATP binding protein and (usually) two permease proteins.
Probab=25.29 E-value=96 Score=27.85 Aligned_cols=50 Identities=14% Similarity=0.186 Sum_probs=37.0
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhc--c-ccccccccceEEEEEcc
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVV--D-FTVPIMETGIAIVVAKR 83 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~v--d-fS~py~~~~~~~lv~~~ 83 (261)
.|+-.| +.+|.+|++|+++++-.++++..+.. . ...|+..+++++++..+
T Consensus 34 ~GSg~G-i~~l~~g~~dia~ssr~l~~~E~~~~~~~~~~~pva~dai~vivn~~ 86 (314)
T TIGR00975 34 IGSGAG-IAQFAAGTVDFGASDAPLSEADLASRGSGLLQFPTVIGAIVVTYNLP 86 (314)
T ss_pred CCCHHH-HHHHHcCCCCEEecCCCCCHHHHHhhcCCcEEeeEEeeeEEEEEeCC
Confidence 455444 68889999999999999997755432 2 24577888888888754
No 102
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=25.07 E-value=67 Score=24.07 Aligned_cols=37 Identities=24% Similarity=0.310 Sum_probs=25.6
Q ss_pred hhHHHHHhcCceeEEEeCCCC---------Chhhhhhccccccccc
Q psy13439 37 NGLIADLVNRKTDMALTSLVI---------NSRRESVVDFTVPIME 73 (261)
Q Consensus 37 ~gli~~L~~g~~Di~i~~i~i---------t~eR~~~vdfS~py~~ 73 (261)
..++..+.+|++|+++.-.+- ..-|+..+++-.|+.+
T Consensus 61 ~~i~~~i~~~~idlVIn~~~~~~~~~~~~~~~iRr~Av~~~ip~iT 106 (116)
T cd01423 61 PSLRELLAEGKIDLVINLPSNRGKRVLDNDYVMRRAADDFAVPLIT 106 (116)
T ss_pred hhHHHHHHcCCceEEEECCCCCCCccccCcEeeehhhHhhCCcccc
Confidence 468999999999999975332 1235556677666653
No 103
>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=25.03 E-value=1.7e+02 Score=22.59 Aligned_cols=49 Identities=10% Similarity=-0.013 Sum_probs=32.3
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+....++..|.+|++|+++..-... ...+. ..++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~~ 82 (200)
T cd08464 34 RQVDPFNVGDMLDRGEIDLAIGVFGEL---PAWLK-REVLYTEGYACLFDPQQ 82 (200)
T ss_pred ecCCcccHHHHHhcCcccEEEecCCCC---cccce-eeeecccceEEEEeCCC
Confidence 344556889999999999999643221 22232 35777778877776543
No 104
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=24.68 E-value=1.5e+02 Score=25.82 Aligned_cols=53 Identities=13% Similarity=0.242 Sum_probs=35.6
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCCC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGI 86 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~~ 86 (261)
..++...+..+|.+|++|+++....... ..+.+.+ .|+......+++++....
T Consensus 129 ~~~~~~~~~~~l~~g~~Di~i~~~~~~~-~~~~~~~-~~l~~~~~~l~~~~~~~~ 181 (302)
T PRK09791 129 MEGQLVSMINELRQGELDFTINTYYQGP-YDHEFTF-EKLLEKQFAVFCRPGHPA 181 (302)
T ss_pred EeCChHHHHHHHHCCCccEEEEecCCcc-cccceeE-EEeccceEEEEEcCCCCc
Confidence 3455678999999999999986321111 1223443 678888988888776543
No 105
>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=23.99 E-value=1.7e+02 Score=22.60 Aligned_cols=51 Identities=20% Similarity=0.243 Sum_probs=32.9
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+....+...|.+|++|+++...... .....+ -+.++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~~~~Dl~i~~~~~~-~~~~~l-~~~~l~~~~~~~v~~~~h 84 (199)
T cd08416 34 TLGSNKDLLKKLKDGELDAILVATPEG-LNDPDF-EVVPLFEDDIFLAVPATS 84 (199)
T ss_pred EEcCcHHHHHHHhCCCCCEEEEecCCc-CCCCCe-EEEEeecceEEEEECCCC
Confidence 344556789999999999999653221 011222 245677788888887654
No 106
>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=23.95 E-value=1.7e+02 Score=22.67 Aligned_cols=47 Identities=6% Similarity=0.043 Sum_probs=31.0
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEcc
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKR 83 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~ 83 (261)
.+.-+.+...|.+|++|+++...... ...+. ..++......+++++.
T Consensus 35 ~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~~~~ 81 (196)
T cd08457 35 GLSSSQVLEAVASGRADLGIADGPLE---ERQGF-LIETRSLPAVVAVPMG 81 (196)
T ss_pred ecCcHHHHHHHHcCCccEEEeccCCC---CCCcE-EEEeccCCeEEEeeCC
Confidence 33346888999999999999643322 22222 3567777877777764
No 107
>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=23.68 E-value=1.5e+02 Score=22.77 Aligned_cols=47 Identities=13% Similarity=-0.000 Sum_probs=31.6
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+.-+.+..+|.+|++|+++.... . ... -+.++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~~~~Dl~i~~~~--~---~~~-~~~~l~~~~~~~v~~~~~ 80 (185)
T cd08439 34 VCKRTPRLMEMLERGEVDLALITHP--P---PGA-SATILRRSPTVWYCAAGY 80 (185)
T ss_pred EECChHHHHHHHHCCCCcEEEEecc--C---CCC-CceEEEEecCEEEECCCC
Confidence 3444578899999999999986321 1 112 246677778887776654
No 108
>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=23.58 E-value=1.9e+02 Score=22.25 Aligned_cols=49 Identities=14% Similarity=0.089 Sum_probs=33.1
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+..+.+...|.+|++|+++.... .....+ .+.++......+++++..
T Consensus 34 ~~~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~~~ 82 (198)
T cd08447 34 REMVTTDQIEALESGRIDLGLLRPP---FARPGL-ETRPLVREPLVAAVPAGH 82 (198)
T ss_pred EeCCHHHHHHHHHcCCceEEEecCC---CCCCCe-eEEEeecCceEEEecCCC
Confidence 4556688999999999999996422 112222 235677888888876653
No 109
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=23.52 E-value=1.2e+02 Score=23.60 Aligned_cols=75 Identities=15% Similarity=0.166 Sum_probs=43.1
Q ss_pred hhhHhhh----hcCcEEEEEEecCCceeEe-eCCchhhHHHHHhcCceeEEEeCCCCChhhhh-----hcccccccccc-
Q psy13439 6 NQHESLK----KKRKLLTVYLHSKNEVLSV-ENGKWNGLIADLVNRKTDMALTSLVINSRRES-----VVDFTVPIMET- 74 (261)
Q Consensus 6 ~~~e~l~----k~~~~~~~~~~~~~~~g~~-~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~-----~vdfS~py~~~- 74 (261)
.|.+.++ +.|....-+...++.-|.. ....+..|+..+.+|++|.++.- ...|.. ...+..-+...
T Consensus 22 ~Q~~~l~~~a~~~g~~i~~~~~D~~~SG~~~~Rp~l~~ll~~~~~g~vd~vvv~---~ldRl~R~~~d~~~~~~~l~~~~ 98 (140)
T cd03770 22 NQKAILEEYAKENGLENIRHYIDDGFSGTTFDRPGFNRMIEDIEAGKIDIVIVK---DMSRLGRNYLKVGLYMEILFPKK 98 (140)
T ss_pred HHHHHHHHHHHHCCCEEEEEEEcCCCcCCcCCCHHHHHHHHHHHcCCCCEEEEe---ccchhccCHHHHHHHHHHHHhhc
Confidence 4555444 3465443344444444443 45568999999999999987742 233432 23343434444
Q ss_pred ceEEEEEcc
Q psy13439 75 GIAIVVAKR 83 (261)
Q Consensus 75 ~~~~lv~~~ 83 (261)
+..+++..+
T Consensus 99 gv~l~~~~~ 107 (140)
T cd03770 99 GVRFIAIND 107 (140)
T ss_pred CcEEEEecC
Confidence 777777654
No 110
>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=23.48 E-value=1.8e+02 Score=22.51 Aligned_cols=49 Identities=20% Similarity=0.350 Sum_probs=33.0
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
.+++...++..|.+|++|+++..-... ...+. ..++......++++++.
T Consensus 35 ~~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~~ 83 (200)
T cd08411 35 REDQTERLLEKLRSGELDAALLALPVD---EPGLE-EEPLFDEPFLLAVPKDH 83 (200)
T ss_pred EeCcHHHHHHHHHcCCccEEEEeccCC---CCCce-EEEeeccceEEEecCCC
Confidence 445567899999999999999643221 12222 34677788888887654
No 111
>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=23.19 E-value=2.5e+02 Score=21.53 Aligned_cols=51 Identities=14% Similarity=0.231 Sum_probs=34.0
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
.++-..+...|.+|++|+++...... .+.+.+. ..++......++++++..
T Consensus 35 ~~~~~~~~~~l~~~~~Dl~i~~~~~~-~~~~~~~-~~~l~~~~~~~~~~~~~~ 85 (201)
T cd08435 35 EGTSDELLEGLRAGELDLAIGRLADD-EQPPDLA-SEELADEPLVVVARPGHP 85 (201)
T ss_pred eCCHHHHHHHHHcCCccEEEEecCcc-cCCCCcE-EEEcccCcEEEEEeCCCc
Confidence 44557889999999999999643211 1122333 357788888888877643
No 112
>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=22.72 E-value=1.6e+02 Score=23.12 Aligned_cols=50 Identities=14% Similarity=0.164 Sum_probs=33.4
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++.+.+...|.+|++|+++..-.. .....+. +.++......++++++.
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~~~h 83 (198)
T cd08443 34 HQGSPTQIAEMVSKGLVDFAIATEAL--HDYDDLI-TLPCYHWNRCVVVKRDH 83 (198)
T ss_pred EeCCHHHHHHHHHCCCccEEEEeccc--cccCCce-EeeeeeceEEEEEcCCC
Confidence 45556789999999999999953221 1112233 46677888888877654
No 113
>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=22.31 E-value=1.2e+02 Score=25.18 Aligned_cols=59 Identities=24% Similarity=0.315 Sum_probs=42.3
Q ss_pred hhHHHHHhcC-ceeEEEeCCCCChhhhh---hcc--ccccccccceEEEEEccC--CCCCcccccCC
Q psy13439 37 NGLIADLVNR-KTDMALTSLVINSRRES---VVD--FTVPIMETGIAIVVAKRT--GIISPTAFLEP 95 (261)
Q Consensus 37 ~gli~~L~~g-~~Di~i~~i~it~eR~~---~vd--fS~py~~~~~~~lv~~~~--~~~~~~~~l~p 95 (261)
..+...|.+| ++|+.+.+-....++.. .++ -..|+..+..+++++++. ...+|.++.+|
T Consensus 36 ~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~vl~~~~~~~~~~~~~~dL~~~ 102 (230)
T PF13531_consen 36 GELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLARSPLVLAVPKGNPKGIRSWADLAQP 102 (230)
T ss_dssp HHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEEEEEEEEEETTSTTSTTCHHHHCST
T ss_pred HHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCcccccccCceEEEeccCcccccCCHHHHhhc
Confidence 5677777766 89999987654444442 344 567999999999999986 56678888877
No 114
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=22.11 E-value=1.4e+02 Score=25.81 Aligned_cols=48 Identities=8% Similarity=-0.119 Sum_probs=34.4
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEcc
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKR 83 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~ 83 (261)
..++.+.+...|.+|++|+++..... ..+.+. +.++......++++++
T Consensus 123 ~~~~~~~~~~~L~~~~~d~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~ 170 (294)
T PRK13348 123 IVDDQDHTFALLERGEVVGCVSTQPK---PMRGCL-AEPLGTMRYRCVASPA 170 (294)
T ss_pred EEcchHHHHHHHhcCCeEEEEecCCc---ccCCcc-cccccccceEEEEccc
Confidence 45556789999999999999854322 223444 5778888888888765
No 115
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=22.10 E-value=1.2e+02 Score=26.81 Aligned_cols=48 Identities=8% Similarity=0.106 Sum_probs=34.5
Q ss_pred CchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 34 GKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 34 ~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
...+.++..|.+|++|+++..... ..+.+.+ .++......++++++.+
T Consensus 151 ~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~~-~~l~~~~~~lv~~~~hp 198 (317)
T PRK11482 151 IPISDAENQLSQFQTDLIIDTHSC---SNRTIQH-HVLFTDNVVLVCRQGHP 198 (317)
T ss_pred ecchhHHHHHHCCCcCEEEeccCC---CCCceEE-EEEecCcEEEEEeCCCC
Confidence 455789999999999999965432 2233443 67888888888887654
No 116
>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=21.57 E-value=2.4e+02 Score=21.64 Aligned_cols=51 Identities=12% Similarity=0.143 Sum_probs=33.2
Q ss_pred CCchhhHHHHHhcCceeEEEeCCCCC--hhhhhhccccccccccceEEEEEccC
Q psy13439 33 NGKWNGLIADLVNRKTDMALTSLVIN--SRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 33 ~~~~~gli~~L~~g~~Di~i~~i~it--~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
.++-..+...|.+|++|+++..-... ....+.+ .+.++......+++++..
T Consensus 35 ~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~~ 87 (200)
T cd08423 35 EAEPPESLDALRAGELDLAVVFDYPVTPPPDDPGL-TRVPLLDDPLDLVLPADH 87 (200)
T ss_pred eCCHHHHHHHHhcCCccEEEEeccccccCCCCCCc-EEEEeccCcEEEEecCCC
Confidence 44446889999999999999532111 1122223 356778888888887654
No 117
>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=20.59 E-value=1.8e+02 Score=22.47 Aligned_cols=50 Identities=18% Similarity=0.149 Sum_probs=31.7
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
.+++.+.++.+|.+|++|+++...... -...+ -+.++......++++++.
T Consensus 34 ~~~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~~~h 83 (195)
T cd08431 34 SEEVLGGTWDALASGRADLVIGATGEL--PPGGV-KTRPLGEVEFVFAVAPNH 83 (195)
T ss_pred EEeccchHHHHHhCCCCCEEEEecCCC--CCCce-EEEecccceEEEEEcCCC
Confidence 344556889999999999999642211 11122 245666777777776653
No 118
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=20.45 E-value=1.9e+02 Score=25.76 Aligned_cols=52 Identities=12% Similarity=0.141 Sum_probs=34.7
Q ss_pred eeCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccCC
Q psy13439 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTG 85 (261)
Q Consensus 31 ~~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~~ 85 (261)
+..+..+.++..|.+|++|+++..-.. .....+. ..++......+++++..+
T Consensus 126 i~~~~~~~~~~~L~~g~iDl~i~~~~~--~~~~~l~-~~~l~~~~~~~v~~~~hp 177 (324)
T PRK12681 126 MHQGSPTQIAEAAAKGNADFAIATEAL--HLYDDLI-MLPCYHWNRSVVVPPDHP 177 (324)
T ss_pred EEeCCHHHHHHHHHcCCCCEEEecCcc--cCCCCeE-EEEeccceeEEEeCCCCh
Confidence 346677899999999999999963211 1122233 356777788888876543
No 119
>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=20.19 E-value=2.8e+02 Score=21.48 Aligned_cols=49 Identities=8% Similarity=0.053 Sum_probs=32.3
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..++-..+...|.+|++|+++....... ..+ -+.++......++++...
T Consensus 34 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~v~~~~h 82 (196)
T cd08458 34 DTVPSQTVLELVSLQHYDLGISILAGDY---PGL-TTEPVPSFRAVCLLPPGH 82 (196)
T ss_pred eccChHHHHHHHHcCCCCEEEEeccCCC---CCc-eEEEeccCceEEEecCCC
Confidence 3444567899999999999996433221 122 235677888888877653
No 120
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=20.08 E-value=1.8e+02 Score=25.90 Aligned_cols=50 Identities=18% Similarity=0.140 Sum_probs=34.6
Q ss_pred eCCchhhHHHHHhcCceeEEEeCCCCChhhhhhccccccccccceEEEEEccC
Q psy13439 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84 (261)
Q Consensus 32 ~~~~~~gli~~L~~g~~Di~i~~i~it~eR~~~vdfS~py~~~~~~~lv~~~~ 84 (261)
..+..+.++..|.+|++|+++..-.... ..... ..|++.....++++.+.
T Consensus 127 ~~~~~~~~~~~l~~g~~Dl~i~~~~~~~--~~~~~-~~~l~~~~~~l~~~~~h 176 (327)
T PRK12680 127 QQAAESAALDLLGQGDADIAIVSTAGGE--PSAGI-AVPLYRWRRLVVVPRGH 176 (327)
T ss_pred EeCChHHHHHHHHCCCCcEEEEecCCCC--CCcce-EEEeeccceEEEEeCCC
Confidence 4556688999999999999995422111 11222 47888888888887654
Done!