Query 040220
Match_columns 370
No_of_seqs 150 out of 1592
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 06:16:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040220.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040220hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1054 Glutamate-gated AMPA-t 100.0 3.2E-49 6.8E-54 382.7 10.0 319 6-347 427-841 (897)
2 KOG4440 NMDA selective glutama 100.0 4.6E-42 1E-46 334.4 14.4 304 21-341 461-839 (993)
3 KOG1052 Glutamate-gated kainat 100.0 1.7E-40 3.6E-45 348.3 25.4 321 5-351 225-624 (656)
4 KOG1053 Glutamate-gated NMDA-t 100.0 5.9E-41 1.3E-45 336.9 20.4 299 21-341 464-838 (1258)
5 PRK10797 glutamate and asparta 99.8 2.3E-19 5E-24 171.4 16.8 197 2-323 47-275 (302)
6 PF00497 SBP_bac_3: Bacterial 99.8 1.5E-19 3.2E-24 162.7 13.3 198 3-320 7-225 (225)
7 PRK09495 glnH glutamine ABC tr 99.8 8.2E-19 1.8E-23 162.4 16.7 194 3-322 33-246 (247)
8 PRK15007 putative ABC transpor 99.8 5.1E-18 1.1E-22 156.3 16.4 192 2-320 28-243 (243)
9 PRK15010 ABC transporter lysin 99.8 6.8E-18 1.5E-22 157.6 16.8 194 3-320 34-255 (260)
10 PRK11917 bifunctional adhesin/ 99.8 7.6E-18 1.6E-22 157.5 16.1 191 2-318 45-258 (259)
11 PRK11260 cystine transporter s 99.8 1.3E-17 2.9E-22 156.1 16.6 197 2-321 48-263 (266)
12 PRK15437 histidine ABC transpo 99.7 5E-17 1.1E-21 151.6 16.4 195 3-321 34-256 (259)
13 TIGR01096 3A0103s03R lysine-ar 99.7 1.6E-16 3.4E-21 146.8 16.5 193 2-318 31-250 (250)
14 TIGR02995 ectoine_ehuB ectoine 99.7 8.1E-16 1.7E-20 144.8 15.3 195 3-319 40-261 (275)
15 PRK10859 membrane-bound lytic 99.7 6.5E-16 1.4E-20 156.7 13.6 193 4-321 50-268 (482)
16 COG0834 HisJ ABC-type amino ac 99.6 1.7E-14 3.7E-19 134.5 15.5 197 3-321 43-266 (275)
17 TIGR03870 ABC_MoxJ methanol ox 99.6 1.3E-14 2.8E-19 134.5 14.1 80 2-99 7-91 (246)
18 PRK09959 hybrid sensory histid 99.6 1.9E-14 4.2E-19 160.9 16.6 192 2-321 309-522 (1197)
19 TIGR02285 conserved hypothetic 99.6 3.2E-14 7E-19 133.4 12.8 87 2-99 24-114 (268)
20 PF00060 Lig_chan: Ligand-gate 99.6 5.7E-16 1.2E-20 132.0 0.1 95 111-222 1-102 (148)
21 PRK09959 hybrid sensory histid 99.5 8.3E-14 1.8E-18 155.8 13.7 194 2-320 63-278 (1197)
22 cd00134 PBPb Bacterial peripla 99.5 1.1E-12 2.4E-17 115.9 16.4 191 2-318 6-218 (218)
23 TIGR03871 ABC_peri_MoxJ_2 quin 99.5 1.4E-12 3.1E-17 119.1 14.6 80 2-99 7-90 (232)
24 smart00062 PBPb Bacterial peri 99.4 3.8E-12 8.2E-17 112.1 15.1 192 2-318 7-219 (219)
25 smart00079 PBPe Eukaryotic hom 99.0 3.1E-09 6.7E-14 88.7 9.4 94 225-320 14-134 (134)
26 COG4623 Predicted soluble lyti 98.8 3.2E-08 7E-13 94.0 10.0 182 20-321 41-249 (473)
27 PRK00489 hisG ATP phosphoribos 98.0 1.5E-05 3.2E-10 75.7 8.4 46 49-99 56-103 (287)
28 PF10613 Lig_chan-Glu_bd: Liga 97.9 6.8E-06 1.5E-10 59.7 2.1 37 7-43 1-40 (65)
29 TIGR01098 3A0109s03R phosphate 97.6 0.00061 1.3E-08 62.9 10.9 75 21-100 46-132 (254)
30 TIGR03431 PhnD phosphonate ABC 96.4 0.04 8.6E-07 52.0 11.3 71 244-314 176-259 (288)
31 PF07885 Ion_trans_2: Ion chan 95.0 0.073 1.6E-06 40.0 5.8 55 145-216 22-77 (79)
32 PRK11553 alkanesulfonate trans 93.6 0.51 1.1E-05 45.0 9.8 46 48-99 68-119 (314)
33 KOG1419 Voltage-gated K+ chann 92.6 0.22 4.8E-06 50.4 5.7 88 114-218 236-324 (654)
34 KOG3713 Voltage-gated K+ chann 85.2 1.3 2.8E-05 44.4 4.8 64 122-206 356-420 (477)
35 TIGR01729 taurine_ABC_bnd taur 84.5 2.6 5.5E-05 39.8 6.4 63 32-99 20-90 (300)
36 PF14503 YhfZ_C: YhfZ C-termin 82.7 2.2 4.7E-05 39.1 4.8 78 19-99 23-107 (232)
37 PF12974 Phosphonate-bd: ABC t 81.7 2.6 5.6E-05 38.5 5.0 74 243-316 144-229 (243)
38 PLN03192 Voltage-dependent pot 73.8 4.3 9.4E-05 44.3 4.7 52 149-217 252-304 (823)
39 PF09084 NMT1: NMT1/THI5 like; 73.8 9.8 0.00021 33.6 6.4 47 48-99 33-83 (216)
40 PRK10537 voltage-gated potassi 70.2 8.3 0.00018 38.4 5.4 53 144-213 165-218 (393)
41 PF12273 RCR: Chitin synthesis 58.7 5.4 0.00012 33.0 1.4 28 111-138 1-28 (130)
42 cd05466 PBP2_LTTR_substrate Th 56.3 29 0.00063 28.4 5.6 65 25-99 14-82 (197)
43 TIGR01728 SsuA_fam ABC transpo 56.0 83 0.0018 28.7 9.1 16 244-259 136-151 (288)
44 PF03466 LysR_substrate: LysR 50.3 41 0.00089 28.5 5.7 64 26-99 21-88 (209)
45 cd08468 PBP2_Pa0477 The C-term 46.1 66 0.0014 27.2 6.4 69 24-99 13-85 (202)
46 TIGR02122 TRAP_TAXI TRAP trans 45.9 28 0.0006 32.8 4.2 68 27-100 48-132 (320)
47 KOG0498 K+-channel ERG and rel 41.5 32 0.00069 36.9 4.1 53 148-217 295-348 (727)
48 cd08415 PBP2_LysR_opines_like 40.4 80 0.0017 26.1 6.0 67 23-99 12-82 (196)
49 cd08438 PBP2_CidR The C-termin 39.6 85 0.0018 25.9 6.0 66 24-99 13-82 (197)
50 PF03180 Lipoprotein_9: NLPA l 38.1 68 0.0015 29.5 5.3 68 241-311 32-123 (237)
51 cd08463 PBP2_DntR_like_4 The C 37.0 1.2E+02 0.0026 25.8 6.6 66 24-99 13-83 (203)
52 cd08436 PBP2_LTTR_like_3 The C 36.7 97 0.0021 25.5 5.9 66 25-99 14-83 (194)
53 cd08442 PBP2_YofA_SoxR_like Th 35.9 1.1E+02 0.0024 25.2 6.1 67 23-99 12-82 (193)
54 cd08462 PBP2_NodD The C-termin 35.9 1E+02 0.0022 25.9 6.0 63 27-99 16-81 (200)
55 cd08414 PBP2_LTTR_aromatics_li 35.9 1E+02 0.0022 25.5 5.8 64 26-99 15-82 (197)
56 cd08437 PBP2_MleR The substrat 35.3 1.1E+02 0.0023 25.5 6.0 67 25-99 14-84 (198)
57 cd08453 PBP2_IlvR The C-termin 35.1 1.2E+02 0.0027 25.2 6.3 68 25-99 14-85 (200)
58 cd08466 PBP2_LeuO The C-termin 35.0 1.2E+02 0.0025 25.3 6.2 65 25-99 14-82 (200)
59 cd08461 PBP2_DntR_like_3 The C 34.9 93 0.002 25.9 5.5 66 24-99 13-82 (198)
60 cd08425 PBP2_CynR The C-termin 34.8 1.1E+02 0.0024 25.4 5.9 65 25-99 15-83 (197)
61 cd08434 PBP2_GltC_like The sub 34.7 1.1E+02 0.0024 25.1 5.9 65 25-99 14-82 (195)
62 cd08426 PBP2_LTTR_like_5 The C 34.5 1.1E+02 0.0024 25.4 5.9 64 26-99 15-82 (199)
63 cd08448 PBP2_LTTR_aromatics_li 34.4 1.1E+02 0.0024 25.2 5.9 65 25-99 14-82 (197)
64 cd08420 PBP2_CysL_like C-termi 34.1 1.2E+02 0.0026 24.9 6.0 66 24-99 13-82 (201)
65 cd08465 PBP2_ToxR The C-termin 33.9 92 0.002 26.3 5.3 66 24-99 13-82 (200)
66 cd08445 PBP2_BenM_CatM_CatR Th 33.8 1.4E+02 0.003 25.1 6.5 66 24-99 14-83 (203)
67 cd08419 PBP2_CbbR_RubisCO_like 32.8 1.1E+02 0.0024 25.2 5.6 65 25-99 13-81 (197)
68 cd08440 PBP2_LTTR_like_4 TThe 32.2 1.4E+02 0.0029 24.5 6.0 66 24-99 13-82 (197)
69 cd08423 PBP2_LTTR_like_6 The C 32.0 1.4E+02 0.003 24.7 6.1 68 25-99 14-87 (200)
70 cd08456 PBP2_LysR The C-termin 31.8 1.1E+02 0.0025 25.2 5.6 66 24-99 13-82 (196)
71 cd08435 PBP2_GbpR The C-termin 31.5 1.7E+02 0.0037 24.1 6.6 66 26-99 15-84 (201)
72 cd08411 PBP2_OxyR The C-termin 31.0 1.2E+02 0.0026 25.2 5.6 65 25-99 15-83 (200)
73 cd08451 PBP2_BudR The C-termin 30.9 1.4E+02 0.003 24.7 5.9 66 25-99 15-84 (199)
74 cd08459 PBP2_DntR_NahR_LinR_li 30.7 1.5E+02 0.0032 24.7 6.1 65 25-99 14-82 (201)
75 cd08469 PBP2_PnbR The C-termin 30.6 1.5E+02 0.0033 25.3 6.2 65 25-99 14-82 (221)
76 cd08450 PBP2_HcaR The C-termin 30.2 1.5E+02 0.0032 24.5 6.0 65 25-99 14-82 (196)
77 PF13379 NMT1_2: NMT1-like fam 30.1 4.1E+02 0.009 23.9 9.9 61 33-98 29-99 (252)
78 PRK11480 tauA taurine transpor 30.1 2.2E+02 0.0047 27.0 7.7 15 245-259 158-172 (320)
79 cd08486 PBP2_CbnR The C-termin 30.1 1.2E+02 0.0027 25.5 5.5 64 26-99 16-83 (198)
80 cd08421 PBP2_LTTR_like_1 The C 30.0 1.5E+02 0.0032 24.6 5.9 65 25-99 14-82 (198)
81 PRK03601 transcriptional regul 29.7 1.1E+02 0.0023 28.3 5.3 64 26-99 104-171 (275)
82 cd08418 PBP2_TdcA The C-termin 29.6 1.7E+02 0.0036 24.2 6.2 67 25-99 14-84 (201)
83 cd08429 PBP2_NhaR The C-termin 29.5 1.4E+02 0.0031 25.5 5.8 68 24-98 13-84 (204)
84 PRK09791 putative DNA-binding 29.0 1.5E+02 0.0033 27.5 6.3 67 25-99 109-179 (302)
85 cd08416 PBP2_MdcR The C-termin 29.0 1.7E+02 0.0038 24.1 6.2 68 24-99 13-84 (199)
86 cd08413 PBP2_CysB_like The C-t 28.8 1.5E+02 0.0032 24.9 5.8 67 24-99 13-83 (198)
87 PRK11242 DNA-binding transcrip 28.7 1.3E+02 0.0029 27.6 5.8 65 25-99 105-173 (296)
88 cd08446 PBP2_Chlorocatechol Th 28.3 1.6E+02 0.0035 24.3 5.9 64 26-99 16-83 (198)
89 cd08417 PBP2_Nitroaromatics_li 28.0 1.3E+02 0.0029 24.9 5.3 65 25-99 14-82 (200)
90 cd08452 PBP2_AlsR The C-termin 27.6 1.7E+02 0.0036 24.5 5.9 64 26-99 15-82 (197)
91 TIGR02424 TF_pcaQ pca operon t 27.5 1.6E+02 0.0035 27.2 6.2 65 27-99 109-177 (300)
92 COG4905 Predicted membrane pro 27.1 90 0.0019 27.7 3.8 33 107-139 57-93 (243)
93 cd08412 PBP2_PAO1_like The C-t 26.8 1.6E+02 0.0035 24.3 5.6 67 23-99 12-82 (198)
94 cd08467 PBP2_SyrM The C-termin 26.8 1.7E+02 0.0038 24.5 5.9 65 25-99 14-82 (200)
95 PRK11151 DNA-binding transcrip 26.6 1.7E+02 0.0036 27.3 6.1 63 27-99 107-173 (305)
96 cd08478 PBP2_CrgA The C-termin 26.1 1.3E+02 0.0029 25.0 5.0 62 27-98 19-81 (199)
97 PF10853 DUF2650: Protein of u 26.1 45 0.00098 21.4 1.4 16 110-125 22-37 (38)
98 cd08447 PBP2_LTTR_aromatics_li 26.0 2.3E+02 0.005 23.3 6.4 66 24-99 13-82 (198)
99 CHL00180 rbcR LysR transcripti 25.7 1.8E+02 0.0039 27.2 6.1 66 27-99 111-180 (305)
100 PRK10341 DNA-binding transcrip 25.6 1.8E+02 0.0038 27.3 6.1 65 27-99 113-181 (312)
101 PF10661 EssA: WXG100 protein 25.5 63 0.0014 27.4 2.6 58 75-135 85-142 (145)
102 cd08430 PBP2_IlvY The C-termin 25.2 2.3E+02 0.005 23.3 6.3 68 23-99 12-83 (199)
103 KOG1418 Tandem pore domain K+ 25.0 38 0.00083 33.0 1.5 54 147-217 115-169 (433)
104 cd01324 cbb3_Oxidase_CcoQ Cyto 25.0 1E+02 0.0022 20.8 3.1 27 113-139 12-38 (48)
105 cd08443 PBP2_CysB The C-termin 24.7 2.2E+02 0.0047 23.9 6.1 68 23-99 12-83 (198)
106 cd08457 PBP2_OccR The C-termin 24.4 2E+02 0.0043 23.8 5.8 66 23-98 12-81 (196)
107 cd08444 PBP2_Cbl The C-termina 23.9 1.9E+02 0.0041 24.2 5.6 68 23-99 12-83 (198)
108 cd08449 PBP2_XapR The C-termin 23.8 2.2E+02 0.0048 23.3 5.9 67 25-99 14-84 (197)
109 PRK09906 DNA-binding transcrip 23.1 2.2E+02 0.0047 26.3 6.2 62 28-99 107-172 (296)
110 TIGR02136 ptsS_2 phosphate bin 23.0 88 0.0019 29.3 3.4 46 48-99 75-127 (287)
111 cd08441 PBP2_MetR The C-termin 22.7 2.9E+02 0.0063 22.8 6.5 64 26-99 15-82 (198)
112 PF13396 PLDc_N: Phospholipase 22.5 93 0.002 20.3 2.5 28 108-135 18-45 (46)
113 cd08432 PBP2_GcdR_TrpI_HvrB_Am 22.4 1.6E+02 0.0035 24.2 4.7 62 27-98 16-78 (194)
114 cd08433 PBP2_Nac The C-teminal 22.4 2.3E+02 0.005 23.4 5.7 66 24-99 13-82 (198)
115 PF11446 DUF2897: Protein of u 22.3 1.2E+02 0.0025 21.2 3.0 24 111-134 2-25 (55)
116 cd08439 PBP2_LrhA_like The C-t 22.2 1.9E+02 0.0042 23.8 5.2 62 26-99 15-80 (185)
117 cd08485 PBP2_ClcR The C-termin 22.0 2E+02 0.0043 24.1 5.3 65 25-99 15-83 (198)
118 cd08464 PBP2_DntR_like_2 The C 21.7 2.5E+02 0.0055 23.1 5.9 65 25-99 14-82 (200)
119 cd08427 PBP2_LTTR_like_2 The C 21.5 2.5E+02 0.0054 23.0 5.7 68 24-99 13-84 (195)
120 cd08460 PBP2_DntR_like_1 The C 21.4 2.4E+02 0.0052 23.5 5.7 67 23-99 12-81 (200)
121 PRK12682 transcriptional regul 20.5 2.4E+02 0.0051 26.3 5.9 65 26-99 108-176 (309)
122 KOG1545 Voltage-gated shaker-l 20.4 42 0.00091 32.8 0.6 34 146-196 392-426 (507)
No 1
>KOG1054 consensus Glutamate-gated AMPA-type ion channel receptor subunit GluR2 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=3.2e-49 Score=382.72 Aligned_cols=319 Identities=18% Similarity=0.290 Sum_probs=264.1
Q ss_pred ccceEEeecCC--CCCCceEEeeHHHHHHHHh-cCCceEEEEe----hhh----------hhhhhccccccCCceeEEEe
Q 040220 6 GKFVKVKFSDN--PYENEYDGFCIELYYESQL-ACKGISILFF----FLQ----------LMMRIRHEENFLRNYDSVVG 68 (370)
Q Consensus 6 ~Pfv~~~~~~~--~~~~~~~G~~idl~~~la~-lg~~~~i~~~----~~~----------li~~~~~~~L~~g~~Diai~ 68 (370)
-|||++|.+-. .++++|.||+|||+.+||+ .|.+|++.+. |.. |+|+ |..|++|+|++
T Consensus 427 spyvm~kkn~~~~egn~ryEGyCvdLa~~iAkhi~~~Y~l~iv~dgkyGardaD~k~WnGMvGe-----Lv~grAdiavA 501 (897)
T KOG1054|consen 427 SPYVMLKKNHEQLEGNERYEGYCVDLAAEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMVGE-----LVYGRADIAVA 501 (897)
T ss_pred CchhHHHhhHHHhcCCcccceeHHHHHHHHHHhcCceEEEEEecCCcccccCCCcccccchhHH-----HhcCccceEEe
Confidence 48999965544 4568999999999999999 9888886543 221 7777 99999999999
Q ss_pred cccccccccceeeecccccccceEEEEeCCCC--cCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCC----
Q 040220 69 DATILADRAKIVEFTQPCAESRLSMIVPAKTE--ESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNG---- 142 (370)
Q Consensus 69 ~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~~--~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~---- 142 (370)
++|||.+|++++|||.|++..|++|++++|+. .+.++|+.|+..++|+|++.+.+.++.++++..|+++.+++.
T Consensus 502 pLTIt~~REeviDFSKPfMslGISIMIKKPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~Ee~~ 581 (897)
T KOG1054|consen 502 PLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFE 581 (897)
T ss_pred eeeeehhhhhhhccccchhhcCeEEEEeCcccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEeccCchheeccccc
Confidence 99999999999999999999999999999974 569999999999999999999999999999999998866431
Q ss_pred --C-----C--CCCccchHHHHHHHhHhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCc
Q 040220 143 --P-----R--KDQIGTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPS 213 (370)
Q Consensus 143 --~-----~--~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~ 213 (370)
+ + ..++.+++||+++++++|+. | ..||+.+||++.++||||++|++++|||||+
T Consensus 582 rg~~t~~~~~NeFgifNsLWFsLgAFMQQG~--------------D---I~PRslSGRIvggvWWFFTlIIiSSYTANLA 644 (897)
T KOG1054|consen 582 RGRFTPSDPPNEFGIFNSLWFSLGAFMQQGC--------------D---ISPRSLSGRIVGGVWWFFTLIIISSYTANLA 644 (897)
T ss_pred cCCCCCCCCCccchhhHHHHHHHHHHHhcCC--------------C---CCccccccceeccchhhhhhhhhhhhhhHHH
Confidence 1 1 13477999999999997653 3 4589999999999999999999999999999
Q ss_pred cccccccCCC------------CCeEeeeCChhHHHHHH-----hc----------------CChHHHHHHhh--ccccc
Q 040220 214 PMLTVQPLRP------------NPKVACDRDSFVRNYLQ-----NF----------------GSDYNYQGEFG--SNHIA 258 (370)
Q Consensus 214 s~Lt~~~~~~------------~~~vg~~~~s~~~~~l~-----~~----------------~~~~~~~~~l~--~g~~~ 258 (370)
|+||++++.+ ...+|+..+....++++ .| .+..|++++++ +|+++
T Consensus 645 AFLTvErMvsPIESaEDLAkQteIaYGt~~~GSTkeFFr~Skiavy~kMW~yM~SaepsVFv~t~aeGv~rVRksKGkyA 724 (897)
T KOG1054|consen 645 AFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMKSAEPSVFVRTTAEGVARVRKSKGKYA 724 (897)
T ss_pred HHHhHHhhcCcchhHHHHhhcceeeeeecCCCchHHHHhhhhHHHHHHHHHHHhcCCcceeeehhhhHHHHHHhcCCceE
Confidence 9999998877 45677776665555554 22 34667777775 56777
Q ss_pred c---cchhHHHHh-hcccceEEcCCCCCccceeee---CCcchHHHHHHHHHhhhcCchhHHHHhhcCCC----------
Q 040220 259 G---PPYEKVFVS-QYCRIYAATTPTYGFGGLGFL---SSPIAADFSEAILKLSENKKLKSLEYNEKELE---------- 321 (370)
Q Consensus 259 a---~~~~~~~~~-~~c~~~~~~~~~~~~~~~~~a---~spl~~~in~~i~~l~e~G~~~~l~~~w~~~~---------- 321 (370)
+ ....+|..+ ++|+ -..+|..+...+||+| +|.|++.+|.++++|.|.|.+++|++|||=+.
T Consensus 725 fLLEsTmNey~eqRkPCD-TMKVGgNLds~GYGiATp~Gsslr~~vNLAvLkL~E~G~LdKLkNKWWYDkGeC~sg~~ds 803 (897)
T KOG1054|consen 725 FLLESTMNEYIEQRKPCD-TMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGSGGGDS 803 (897)
T ss_pred eehHhhhhhhhhccCCcc-ceecccccCCcceeecCCCCcccccchhhhhhhhcccchHHHhhhhhcccccccCCCCCCC
Confidence 7 234455554 4698 6677788899999999 99999999999999999999999999998443
Q ss_pred ----CCcceeccchhHHhHhhhh--------heeeeec
Q 040220 322 ----PPGELYRLLGLLMYMSGAL--------SRWEYVD 347 (370)
Q Consensus 322 ----~~l~l~~l~G~f~~l~~g~--------~~~~~~~ 347 (370)
.+|++.+++|+|++|.+|+ .||.|..
T Consensus 804 ~~ktsaLsLSnVAGvFYIL~gGl~laMlvALiEF~yks 841 (897)
T KOG1054|consen 804 KDKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKS 841 (897)
T ss_pred CcchhhcchhhccceeeeehhhHHHHHHHHHHHHHHHh
Confidence 2499999999999987775 4788763
No 2
>KOG4440 consensus NMDA selective glutamate-gated ion channel receptor subunit GRIN1 [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=4.6e-42 Score=334.37 Aligned_cols=304 Identities=19% Similarity=0.282 Sum_probs=255.6
Q ss_pred ceEEeeHHHHHHHHh-cCCceEEEEeh----hh---------hhhhhc---cccccCCceeEEEecccccccccceeeec
Q 040220 21 EYDGFCIELYYESQL-ACKGISILFFF----LQ---------LMMRIR---HEENFLRNYDSVVGDATILADRAKIVEFT 83 (370)
Q Consensus 21 ~~~G~~idl~~~la~-lg~~~~i~~~~----~~---------li~~~~---~~~L~~g~~Diai~~~tit~eR~~~vdFS 83 (370)
...||+|||+-.|++ +||.|.+.+.. .. ..+.+| ++||..+++||+++++||++||++.++||
T Consensus 461 CC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMivaplTINpERa~yieFs 540 (993)
T KOG4440|consen 461 CCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMIVAPLTINPERAQYIEFS 540 (993)
T ss_pred hhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeecccccccceehhhhhhhhCCccceEeeceeeChhhhhheecc
Confidence 347999999999999 98777654432 11 111122 44499999999999999999999999999
Q ss_pred ccccccceEEEEeCCCC-cCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCC-CCCC-------CCCCccchHHH
Q 040220 84 QPCAESRLSMIVPAKTE-ESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSE-FNGP-------RKDQIGTALWF 154 (370)
Q Consensus 84 ~P~~~~~~~ilv~~~~~-~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~-~~~~-------~~~~~~~~~w~ 154 (370)
.|+-..|++|+.+++.. +++-+|++||+.++|+++.++..++++++|++.|+++-+ |... ..-.+++.+||
T Consensus 541 kPfkYqGitILeKk~~r~Stl~SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPFgRFk~~ds~~~ee~alnlssAmWF 620 (993)
T KOG4440|consen 541 KPFKYQGITILEKKEIRRSTLDSFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPFGRFKVNDSEEEEEDALNLSSAMWF 620 (993)
T ss_pred CcccccceEEEeeCCCCCchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccceeeccCccchhhhcchhhhHHH
Confidence 99999999999998865 568899999999999999999999999999999988743 3211 12248899999
Q ss_pred HHHHhHhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCC-----------
Q 040220 155 NFSSILFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRP----------- 223 (370)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~----------- 223 (370)
++|.++..+-. ...||+.++|++..+|+=|++|++++|||||+|+|-+++.+.
T Consensus 621 ~WGVLLNSGig----------------EgtPRSfSARvLGmVWaGFaMIiVASYTANLAAFLVLdrPe~~ltGinDpRLR 684 (993)
T KOG4440|consen 621 SWGVLLNSGIG----------------EGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLDRPEERLTGINDPRLR 684 (993)
T ss_pred HhHhhhccccC----------------CCCCcchhHHHHHHHHhhhheeeehhhhhhhhhheeecCccccccCCCCcccc
Confidence 99999965431 255999999999999999999999999999999998766554
Q ss_pred ----CCeEeeeCChhHHHHHH---------------hcCChHHHHHHhhcccccc----cchhHHHHhhcccceEEcCCC
Q 040220 224 ----NPKVACDRDSFVRNYLQ---------------NFGSDYNYQGEFGSNHIAG----PPYEKVFVSQYCRIYAATTPT 280 (370)
Q Consensus 224 ----~~~vg~~~~s~~~~~l~---------------~~~~~~~~~~~l~~g~~~a----~~~~~~~~~~~c~~~~~~~~~ 280 (370)
+..+|+..+|...-|++ +|.+.++++.++++|+.+| ..-++|...++|+ +...|+.
T Consensus 685 Nps~nf~~aTVk~SsVd~YFrRqVELS~MyR~ME~hNy~~A~eAiq~v~~gkL~AFIWDS~rLEfEAs~~Ce-LvT~GeL 763 (993)
T KOG4440|consen 685 NPSDNFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDGKLHAFIWDSARLEFEASQKCE-LVTTGEL 763 (993)
T ss_pred CcccceeEEEecCccHHHHHHHHhHHHHHHHhhhhcchhhHHHHHHHHHcCceeEEEeecceeeehhhcccc-eEecccc
Confidence 56777777776666655 6888899999999999999 3445677889999 8889999
Q ss_pred CCccceeee---CCcchHHHHHHHHHhhhcCchhHHHHhhcCCC------------CCcceeccchhHHhHhhhhh
Q 040220 281 YGFGGLGFL---SSPIAADFSEAILKLSENKKLKSLEYNEKELE------------PPGELYRLLGLLMYMSGALS 341 (370)
Q Consensus 281 ~~~~~~~~a---~spl~~~in~~i~~l~e~G~~~~l~~~w~~~~------------~~l~l~~l~G~f~~l~~g~~ 341 (370)
|...+||+. +|||++.+..+|+++.|+|.+++|.++|.... ..|++++.+|+|++.++|++
T Consensus 764 FgRSgyGIGlqK~SPWt~~vtlaIL~~hEsGfMEkLDk~Wi~~Ggpq~c~~~~k~PatLgl~NMagvFiLV~~Gia 839 (993)
T KOG4440|consen 764 FGRSGYGIGLQKDSPWTQNVTLAILKSHESGFMEKLDKTWIRYGGPQECDSRSKAPATLGLENMAGVFILVAGGIA 839 (993)
T ss_pred ccccccccccccCCCCcchhhHHHHHhhhcchHHHHHHHHHhcCCcchhhhhccCcccccccccccEEEEEecchh
Confidence 999999998 99999999999999999999999999997652 12999999999999888875
No 3
>KOG1052 consensus Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1.7e-40 Score=348.26 Aligned_cols=321 Identities=26% Similarity=0.344 Sum_probs=266.3
Q ss_pred CccceEEeec--CCCCCCceEEeeHHHHHHHHh-cCCceEEEEe------------hhhhhhhhccccccCCceeEEEec
Q 040220 5 FGKFVKVKFS--DNPYENEYDGFCIELYYESQL-ACKGISILFF------------FLQLMMRIRHEENFLRNYDSVVGD 69 (370)
Q Consensus 5 ~~Pfv~~~~~--~~~~~~~~~G~~idl~~~la~-lg~~~~i~~~------------~~~li~~~~~~~L~~g~~Diai~~ 69 (370)
-+||+...++ ....++.+.|+++||++++++ |||++++... |..++++ |.+|++|++ ++
T Consensus 225 ~~P~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~g~~~~~g~~~g~v~~-----l~~~~advg-~~ 298 (656)
T KOG1052|consen 225 EPPFVDLVEDLAILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGSGSRDPNGNWDGLVGQ-----LVDGEADVG-AD 298 (656)
T ss_pred cCCceeeeecccccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCCCCCCCCCChhHHHHH-----HhcCccccc-cc
Confidence 4678888555 223456899999999999999 9888775432 1226777 999999999 99
Q ss_pred ccccccccceeeecccccccceEEEEeCCCCcC-cceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCC---C
Q 040220 70 ATILADRAKIVEFTQPCAESRLSMIVPAKTEES-AWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPR---K 145 (370)
Q Consensus 70 ~tit~eR~~~vdFS~P~~~~~~~ilv~~~~~~~-~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~---~ 145 (370)
++++++|.+.+|||.||+..+.++++++++... .|.|++||+++||++++++++++++++|+++|..+.++ .+. .
T Consensus 299 ~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~~~~fl~Pf~~~vW~~i~~~~l~~~~~~~~~~~~~~~~~-~~~~~~~ 377 (656)
T KOG1052|consen 299 ITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSKLWNFLAPFSPEVWLLILASLLLVGLLLWILERLSPYEL-PPRQIVT 377 (656)
T ss_pred eEEeecccccEEeccceEeccEEEEEEecCCcccceEEecCCcHHHHHHHHHHHHHHHHHHHHHhccccccC-Cccccce
Confidence 999999999999999999999999999987643 79999999999999999999999999999999888777 222 1
Q ss_pred C--CccchHHHHHHHhHhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCC
Q 040220 146 D--QIGTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRP 223 (370)
Q Consensus 146 ~--~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~ 223 (370)
. ...+++|+++++++.|++ +..|++.++|++.++||+++++++++|||+|+|+||++++.+
T Consensus 378 ~~~~~~~~~~~~~~~~~~q~~-----------------~~~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~~~~~ 440 (656)
T KOG1052|consen 378 SLFSLLNCLWLTVGSLLQQGS-----------------DEIPRSLSTRLLLGAWWLFVLILISSYTANLTAFLTVPRLRS 440 (656)
T ss_pred eEeecccchhhhhHHHhccCC-----------------CccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcccccCC
Confidence 1 134578999999998765 166999999999999999999999999999999999999855
Q ss_pred ------------CCeEeeeCChhHHHHHH---------------hcCChHHHHHHhhccc---ccc---cchhHHHHhhc
Q 040220 224 ------------NPKVACDRDSFVRNYLQ---------------NFGSDYNYQGEFGSNH---IAG---PPYEKVFVSQY 270 (370)
Q Consensus 224 ------------~~~vg~~~~s~~~~~l~---------------~~~~~~~~~~~l~~g~---~~a---~~~~~~~~~~~ 270 (370)
+.++|...++....+++ .+.+.+++++++++|. +++ ..+..+...++
T Consensus 441 ~i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~~~~~~~~~~~~~~~~~~~~ 520 (656)
T KOG1052|consen 441 PIDSLDDLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQRSVPLASPEEGVERVRKGPSGGYAFASDELYLAYLFLRD 520 (656)
T ss_pred cccCHHHHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccCCCccCCCHHHHHHHHHcCCCCceEEEeccHHHHHHHhhc
Confidence 56888888887776653 3567899999999994 666 22333444443
Q ss_pred --ccceEEcCCCCCccceeee---CCcchHHHHHHHHHhhhcCchhHHHHhhcCCC------------CCcceeccchhH
Q 040220 271 --CRIYAATTPTYGFGGLGFL---SSPIAADFSEAILKLSENKKLKSLEYNEKELE------------PPGELYRLLGLL 333 (370)
Q Consensus 271 --c~~~~~~~~~~~~~~~~~a---~spl~~~in~~i~~l~e~G~~~~l~~~w~~~~------------~~l~l~~l~G~f 333 (370)
|+ ++++++.+...+|| + +|||++.+|.+|+++.|+|.+++++++|+.+. ..++++++.|+|
T Consensus 521 ~~c~-~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e~g~l~~~~~kw~~~~~~~~~~~~~~~~~~l~~~~~~g~F 598 (656)
T KOG1052|consen 521 EICD-LTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQETGILQKLKRKWFSKKPCLPKCSQTEKTKALDLESFWGLF 598 (656)
T ss_pred CCCc-eEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhccccHHHHHHHHhccCCCCCCCCCCcccccccchhhHHHHH
Confidence 77 99999999999999 6 99999999999999999999999999999864 129999999999
Q ss_pred HhHhhhhh--------eeeeecCCCC
Q 040220 334 MYMSGALS--------RWEYVDPSNA 351 (370)
Q Consensus 334 ~~l~~g~~--------~~~~~~~~~~ 351 (370)
+++++|+. |++|..++..
T Consensus 599 ~i~~~g~~lal~vfi~E~~~~~~~~~ 624 (656)
T KOG1052|consen 599 LILLVGYLLALLVFILELLYSRRRTL 624 (656)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 99988854 6666655554
No 4
>KOG1053 consensus Glutamate-gated NMDA-type ion channel receptor subunit GRIN2A and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=5.9e-41 Score=336.91 Aligned_cols=299 Identities=17% Similarity=0.303 Sum_probs=246.9
Q ss_pred ceEEeeHHHHHHHHh-cCCceEEEEe----hh--------hhhhhhccccccCCceeEEEecccccccccceeeeccccc
Q 040220 21 EYDGFCIELYYESQL-ACKGISILFF----FL--------QLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCA 87 (370)
Q Consensus 21 ~~~G~~idl~~~la~-lg~~~~i~~~----~~--------~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~ 87 (370)
+..||+|||++.||+ +||.|.+-.. +. -|||+ |..+++|||+++++|++||.++||||.|+.
T Consensus 464 CCkGfCIDiLkKlA~~v~FtYDLYlVtnGKhGkk~ng~WnGmIGe-----v~~~rA~MAVgSltINeeRSevVDFSvPFv 538 (1258)
T KOG1053|consen 464 CCKGFCIDILKKLARDVKFTYDLYLVTNGKHGKKINGVWNGMIGE-----VVYQRADMAVGSLTINEERSEVVDFSVPFV 538 (1258)
T ss_pred hhhhhhHHHHHHHHhhcCcceEEEEecCCcccceecCcchhhHHH-----HHhhhhheeeeeeEechhhhcccccccccc
Confidence 458999999999999 9999886221 11 18888 999999999999999999999999999999
Q ss_pred ccceEEEEeCCCC-cCcceecccCchHHHHHHHHHHHHH-HHHHHhccccCCCCCC---------CCCCCCccchHHHHH
Q 040220 88 ESRLSMIVPAKTE-ESAWRFMKPCTWEMWVVTDAILVNT-RFVVWFPEHQRNSEFN---------GPRKDQIGTALWFNF 156 (370)
Q Consensus 88 ~~~~~ilv~~~~~-~~~~~~l~PF~~~vW~~il~~~~~~-~~~~~~~~r~~~~~~~---------~~~~~~~~~~~w~~~ 156 (370)
.++++++|++.+. .+.-+|+.||++.||++++++++++ ++.+++.|..++..+. +.+...++.++|..+
T Consensus 539 eTgIsVmV~rsngtvspsAFLePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~l~~gkkpggp~Ftigkaiwllw 618 (1258)
T KOG1053|consen 539 ETGISVMVARSNGTVSPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGPSFTIGKAIWLLW 618 (1258)
T ss_pred ccceEEEEEecCCccCchhhcCCcchHHHHHHHHHHHHHHHHHHHHHhhcCcccccccccCCCCCCCcceehhhHHHHHH
Confidence 9999999998765 6789999999999999998887655 6667788888765432 234566899999999
Q ss_pred HHhHhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCC-------------
Q 040220 157 SSILFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRP------------- 223 (370)
Q Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~------------- 223 (370)
+.++...- ++ ++||.+-+|+++.+|-||+++..++|||||+|+|--+.+-.
T Consensus 619 aLvFnnsV--------------pv--~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d~vSGlsD~KfqrP 682 (1258)
T KOG1053|consen 619 ALVFNNSV--------------PV--ENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYDTVSGLSDPKFQRP 682 (1258)
T ss_pred HHHhCCCc--------------CC--CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccCcccccCc
Confidence 98885432 12 67999999999999999999999999999999995322211
Q ss_pred -----CCeEeeeCChhHHHHHH-----------hc--CChHHHHHHhhcccccccchhH----HHHh--hcccceEEcC-
Q 040220 224 -----NPKVACDRDSFVRNYLQ-----------NF--GSDYNYQGEFGSNHIAGPPYEK----VFVS--QYCRIYAATT- 278 (370)
Q Consensus 224 -----~~~vg~~~~s~~~~~l~-----------~~--~~~~~~~~~l~~g~~~a~~~~~----~~~~--~~c~~~~~~~- 278 (370)
..+.|+..++..+++++ .| ...+++++.|++|+.||..|+. |... +.|. +..+|
T Consensus 683 ~dq~PpFRFGTVpngSTE~niR~Nyp~MHeYM~kyNq~~v~dal~sLK~gKLDAFIyDaAVLnY~agkDegCK-LvTIGs 761 (1258)
T KOG1053|consen 683 HDQYPPFRFGTVPNGSTERNIRSNYPEMHEYMVKYNQPGVEDALESLKNGKLDAFIYDAAVLNYMAGKDEGCK-LVTIGS 761 (1258)
T ss_pred cccCCCcccccCCCCchhhhHHhccHHHHHHHHHhccCchHHHHHHHhcccchhHHHHHHHHHHhhccCCCce-EEEecC
Confidence 57888876655555444 33 4578899999999999966654 4443 4588 66666
Q ss_pred -CCCCccceeee---CCcchHHHHHHHHHhhhcCchhHHHHhhcCCCC----------CcceeccchhHHhHhhhhh
Q 040220 279 -PTYGFGGLGFL---SSPIAADFSEAILKLSENKKLKSLEYNEKELEP----------PGELYRLLGLLMYMSGALS 341 (370)
Q Consensus 279 -~~~~~~~~~~a---~spl~~~in~~i~~l~e~G~~~~l~~~w~~~~~----------~l~l~~l~G~f~~l~~g~~ 341 (370)
+.|...+||++ |||++..||.+|++++.+|.++.|++.|+...| +|++++++|+|+.|++|++
T Consensus 762 gKvFAttGYGIal~k~Spwkr~IdlallQy~gdGeme~Le~~Wltgic~n~k~evmSsqLdIdnmaGvFymL~~amg 838 (1258)
T KOG1053|consen 762 GKVFATTGYGIALPKNSPWKRQIDLALLQYLGDGEMEMLETLWLTGICHNSKNEVMSSQLDIDNMAGVFYMLAVAMG 838 (1258)
T ss_pred CceeeecceeeecCCCCcchhhHHHHHHHHhccchHHHHHHHHhhcccccchhhhhhcccChhhhhhHHHHHHHHHH
Confidence 88999999999 999999999999999999999999999997753 4999999999999988875
No 5
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.82 E-value=2.3e-19 Score=171.40 Aligned_cols=197 Identities=9% Similarity=0.001 Sum_probs=146.1
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-----cCC-ceEEEEe---hhhhhhhhccccccCCceeEEEecccc
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-----ACK-GISILFF---FLQLMMRIRHEENFLRNYDSVVGDATI 72 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-----lg~-~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~ti 72 (370)
.++||||.+. +.++ +++||++||+++|++ ||. +.++++. +..++.. |.+|++|++++++++
T Consensus 47 ~~~~pP~~f~--~~~g---~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~~~~~~i~~-----L~~G~~Di~~~~~~~ 116 (302)
T PRK10797 47 RESSVPFSYY--DNQQ---KVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPL-----LQNGTFDFECGSTTN 116 (302)
T ss_pred cCCCCCcceE--CCCC---CEeeecHHHHHHHHHHHHHhhCCCCceEEEEEcChHhHHHH-----HHCCCccEEecCCcc
Confidence 4679999998 6433 799999997776654 542 2233232 2336677 999999999999999
Q ss_pred cccccceeeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchH
Q 040220 73 LADRAKIVEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTAL 152 (370)
Q Consensus 73 t~eR~~~vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~ 152 (370)
|++|.+.++||.||+.++.++++++++...
T Consensus 117 t~eR~~~~~fS~Py~~~~~~lv~r~~~~i~-------------------------------------------------- 146 (302)
T PRK10797 117 NLERQKQAAFSDTIFVVGTRLLTKKGGDIK-------------------------------------------------- 146 (302)
T ss_pred CcchhhcceecccEeeccEEEEEECCCCCC--------------------------------------------------
Confidence 999999999999999999999999754210
Q ss_pred HHHHHHhHhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCC
Q 040220 153 WFNFSSILFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRD 232 (370)
Q Consensus 153 w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~ 232 (370)
+...+. +.++|+..|
T Consensus 147 ----------------------------------------------------------------sl~dL~-Gk~V~v~~g 161 (302)
T PRK10797 147 ----------------------------------------------------------------DFADLK-GKAVVVTSG 161 (302)
T ss_pred ----------------------------------------------------------------ChHHcC-CCEEEEeCC
Confidence 011122 677888887
Q ss_pred hhHHHHHH-------------hcCChHHHHHHhhcccccccchhH----HHHhh--cccceEEcCCCCCccceeee----
Q 040220 233 SFVRNYLQ-------------NFGSDYNYQGEFGSNHIAGPPYEK----VFVSQ--YCRIYAATTPTYGFGGLGFL---- 289 (370)
Q Consensus 233 s~~~~~l~-------------~~~~~~~~~~~l~~g~~~a~~~~~----~~~~~--~c~~~~~~~~~~~~~~~~~a---- 289 (370)
+...++++ .+.+.++++++|.+|++|+..... +...+ ..+.+.++++.+...+|+++
T Consensus 162 s~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~d~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~~a~~k~ 241 (302)
T PRK10797 162 TTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKD 241 (302)
T ss_pred CcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEccHHHHHHHHHcCCCCcceEECCccCCcCceeEEEeCC
Confidence 76655543 346788999999999999943322 22222 23447777777777778877
Q ss_pred CCcchHHHHHHHHHhhhcCchhHHHHhhcCCCCC
Q 040220 290 SSPIAADFSEAILKLSENKKLKSLEYNEKELEPP 323 (370)
Q Consensus 290 ~spl~~~in~~i~~l~e~G~~~~l~~~w~~~~~~ 323 (370)
++.+++.+|.+|.+++++|.+++|.++|++...|
T Consensus 242 ~~~L~~~in~~L~~l~~~G~l~~i~~kw~~~~~~ 275 (302)
T PRK10797 242 DPQFKKLMDDTIAQAQTSGEAEKWFDKWFKNPIP 275 (302)
T ss_pred CHHHHHHHHHHHHHHHhCchHHHHHHHHcCCCCC
Confidence 3469999999999999999999999999998643
No 6
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=99.82 E-value=1.5e-19 Score=162.74 Aligned_cols=198 Identities=16% Similarity=0.193 Sum_probs=149.8
Q ss_pred CCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEEE-EehhhhhhhhccccccCCceeEEEeccccccccccee
Q 040220 3 TSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISIL-FFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKIV 80 (370)
Q Consensus 3 ~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i~-~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~v 80 (370)
.++|||.+. +.++ ++.|+++|+++++++ +|+++++. +.+..++.+ |.+|++|+++++++.+++|.+.+
T Consensus 7 ~~~~P~~~~--~~~~---~~~G~~~dl~~~i~~~~g~~~~~~~~~~~~~~~~-----l~~g~~D~~~~~~~~~~~r~~~~ 76 (225)
T PF00497_consen 7 EDYPPFSYI--DEDG---EPSGIDVDLLRAIAKRLGIKIEFVPMPWSRLLEM-----LENGKADIIIGGLSITPERAKKF 76 (225)
T ss_dssp SEBTTTBEE--ETTS---EEESHHHHHHHHHHHHHTCEEEEEEEEGGGHHHH-----HHTTSSSEEESSEB-BHHHHTTE
T ss_pred CCCCCeEEE--CCCC---CEEEEhHHHHHHHHhhcccccceeeccccccccc-----ccccccccccccccccccccccc
Confidence 579999999 6644 799999999999999 98887733 346668888 99999999999999999999999
Q ss_pred eecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHhH
Q 040220 81 EFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSIL 160 (370)
Q Consensus 81 dFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~~ 160 (370)
+||.|++....++++++++....
T Consensus 77 ~~s~p~~~~~~~~~~~~~~~~~~--------------------------------------------------------- 99 (225)
T PF00497_consen 77 DFSDPYYSSPYVLVVRKGDAPPI--------------------------------------------------------- 99 (225)
T ss_dssp EEESESEEEEEEEEEETTSTCST---------------------------------------------------------
T ss_pred cccccccchhheeeecccccccc---------------------------------------------------------
Confidence 99999999999999997531100
Q ss_pred hccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHHH
Q 040220 161 FAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYLQ 240 (370)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l~ 240 (370)
...+ ++..+. +.++|+..++...++++
T Consensus 100 ----------------------~~~~------------------------------~~~dl~-~~~i~~~~g~~~~~~l~ 126 (225)
T PF00497_consen 100 ----------------------KTIK------------------------------SLDDLK-GKRIGVVRGSSYADYLK 126 (225)
T ss_dssp ----------------------SSHS------------------------------SGGGGT-TSEEEEETTSHHHHHHH
T ss_pred ----------------------cccc------------------------------chhhhc-CcccccccchhHHHHhh
Confidence 0000 122233 77899998887766654
Q ss_pred ----------hcCChHHHHHHhhccccccc----chhHHHHhhccc-ceEEcCCCCCccceeee----CCcchHHHHHHH
Q 040220 241 ----------NFGSDYNYQGEFGSNHIAGP----PYEKVFVSQYCR-IYAATTPTYGFGGLGFL----SSPIAADFSEAI 301 (370)
Q Consensus 241 ----------~~~~~~~~~~~l~~g~~~a~----~~~~~~~~~~c~-~~~~~~~~~~~~~~~~a----~spl~~~in~~i 301 (370)
.+.+.++++++|.+|++|+. ....+.+++... ............+++++ ++++++.||++|
T Consensus 127 ~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~i 206 (225)
T PF00497_consen 127 QQYPSNINIVEVDSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRKKNPELLEIFNKAI 206 (225)
T ss_dssp HHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEETTTHHHHHHHHHHH
T ss_pred hhccchhhhcccccHHHHHHHHhcCCeeeeeccchhhhhhhhhcccccccccccccccceeEEeecccccHHHHHHHHHH
Confidence 35789999999999999993 334455555432 22222233334445554 778999999999
Q ss_pred HHhhhcCchhHHHHhhcCC
Q 040220 302 LKLSENKKLKSLEYNEKEL 320 (370)
Q Consensus 302 ~~l~e~G~~~~l~~~w~~~ 320 (370)
.+|.++|.++++.+||+++
T Consensus 207 ~~l~~~G~~~~i~~ky~g~ 225 (225)
T PF00497_consen 207 RELKQSGEIQKILKKYLGD 225 (225)
T ss_dssp HHHHHTTHHHHHHHHHHSS
T ss_pred HHHHhCcHHHHHHHHHcCC
Confidence 9999999999999999975
No 7
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.81 E-value=8.2e-19 Score=162.36 Aligned_cols=194 Identities=20% Similarity=0.203 Sum_probs=148.8
Q ss_pred CCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEE-EEehhhhhhhhccccccCCceeEEEeccccccccccee
Q 040220 3 TSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISI-LFFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKIV 80 (370)
Q Consensus 3 ~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i-~~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~v 80 (370)
+++|||.+. + ++ ++.|+++||++++++ +|.++++ .+.+..++.. |.+|++|+++++++.+++|++.+
T Consensus 33 ~~~~P~~~~--~-~g---~~~G~~vdl~~~ia~~lg~~~~~~~~~~~~~~~~-----l~~G~vDi~~~~~~~t~~R~~~~ 101 (247)
T PRK09495 33 TAFVPFEFK--Q-GD---KYVGFDIDLWAAIAKELKLDYTLKPMDFSGIIPA-----LQTKNVDLALAGITITDERKKAI 101 (247)
T ss_pred CCCCCeeec--C-CC---ceEEEeHHHHHHHHHHhCCceEEEeCCHHHHHHH-----HhCCCcCEEEecCccCHHHHhhc
Confidence 579999876 3 33 689999999999999 9877664 2346668888 99999999999999999999999
Q ss_pred eecccccccceEEEEeCCCC-cCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHh
Q 040220 81 EFTQPCAESRLSMIVPAKTE-ESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSI 159 (370)
Q Consensus 81 dFS~P~~~~~~~ilv~~~~~-~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~ 159 (370)
+||.||+.++..+++++++. ..
T Consensus 102 ~fs~p~~~~~~~~~~~~~~~~~~--------------------------------------------------------- 124 (247)
T PRK09495 102 DFSDGYYKSGLLVMVKANNNDIK--------------------------------------------------------- 124 (247)
T ss_pred cccchheecceEEEEECCCCCCC---------------------------------------------------------
Confidence 99999999999999986542 00
Q ss_pred HhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHH
Q 040220 160 LFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYL 239 (370)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l 239 (370)
+.+.+. +.++|+..|+...+++
T Consensus 125 ---------------------------------------------------------~~~dL~-g~~I~v~~g~~~~~~l 146 (247)
T PRK09495 125 ---------------------------------------------------------SVKDLD-GKVVAVKSGTGSVDYA 146 (247)
T ss_pred ---------------------------------------------------------ChHHhC-CCEEEEecCchHHHHH
Confidence 011122 6677777776655555
Q ss_pred H---------hcCChHHHHHHhhcccccccch----hHHHHhhc-ccceEEcCCCCCccceeee---CCcchHHHHHHHH
Q 040220 240 Q---------NFGSDYNYQGEFGSNHIAGPPY----EKVFVSQY-CRIYAATTPTYGFGGLGFL---SSPIAADFSEAIL 302 (370)
Q Consensus 240 ~---------~~~~~~~~~~~l~~g~~~a~~~----~~~~~~~~-c~~~~~~~~~~~~~~~~~a---~spl~~~in~~i~ 302 (370)
. .+.+..+++++|.+|++|+... ..+++++. .+.+..++.......++++ ++++++.+|++|.
T Consensus 147 ~~~~~~~~i~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~n~al~ 226 (247)
T PRK09495 147 KANIKTKDLRQFPNIDNAYLELGTGRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSELREKVNGALK 226 (247)
T ss_pred HhcCCCCceEEcCCHHHHHHHHHcCceeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEEEcCcHHHHHHHHHHHH
Confidence 4 3567788999999999999332 33444433 3346666665555666666 5699999999999
Q ss_pred HhhhcCchhHHHHhhcCCCC
Q 040220 303 KLSENKKLKSLEYNEKELEP 322 (370)
Q Consensus 303 ~l~e~G~~~~l~~~w~~~~~ 322 (370)
++.++|.++++.++|++..+
T Consensus 227 ~~~~~g~~~~i~~k~~~~~~ 246 (247)
T PRK09495 227 TLKENGTYAEIYKKWFGTEP 246 (247)
T ss_pred HHHHCCcHHHHHHHHcCCCC
Confidence 99999999999999998754
No 8
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.78 E-value=5.1e-18 Score=156.26 Aligned_cols=192 Identities=16% Similarity=0.181 Sum_probs=143.3
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEEE-EehhhhhhhhccccccCCceeEEEecccccccccce
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISIL-FFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKI 79 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i~-~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~ 79 (370)
.+++|||.+. +.++ ++.|+++|+++++++ +|+++++. ..+..++.. +.+|++|+++++++.+++|++.
T Consensus 28 ~~~~~P~~~~--~~~g---~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~-----l~~g~~D~~~~~~~~~~~r~~~ 97 (243)
T PRK15007 28 EASYPPFESI--DANN---QIVGFDVDLAQALCKEIDATCTFSNQAFDSLIPS-----LKFRRVEAVMAGMDITPEREKQ 97 (243)
T ss_pred CCCCCCceee--CCCC---CEEeeeHHHHHHHHHHhCCcEEEEeCCHHHHhHH-----HhCCCcCEEEEcCccCHHHhcc
Confidence 3589999999 6544 799999999999999 99887742 345568888 9999999999899999999999
Q ss_pred eeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHh
Q 040220 80 VEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSI 159 (370)
Q Consensus 80 vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~ 159 (370)
++||.||+..+..++.++....
T Consensus 98 ~~fs~p~~~~~~~~v~~~~~~~---------------------------------------------------------- 119 (243)
T PRK15007 98 VLFTTPYYDNSALFVGQQGKYT---------------------------------------------------------- 119 (243)
T ss_pred cceecCccccceEEEEeCCCCC----------------------------------------------------------
Confidence 9999999998877776643210
Q ss_pred HhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHH
Q 040220 160 LFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYL 239 (370)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l 239 (370)
+.+.+. +.++|+.+|+...+++
T Consensus 120 ---------------------------------------------------------~~~dL~-g~~Igv~~g~~~~~~l 141 (243)
T PRK15007 120 ---------------------------------------------------------SVDQLK-GKKVGVQNGTTHQKFI 141 (243)
T ss_pred ---------------------------------------------------------CHHHhC-CCeEEEecCcHHHHHH
Confidence 011122 6688888887766655
Q ss_pred H---------hcCChHHHHHHhhcccccccc----hhHHHHhhcccceEEcCCCC-----Cccceeee----CCcchHHH
Q 040220 240 Q---------NFGSDYNYQGEFGSNHIAGPP----YEKVFVSQYCRIYAATTPTY-----GFGGLGFL----SSPIAADF 297 (370)
Q Consensus 240 ~---------~~~~~~~~~~~l~~g~~~a~~----~~~~~~~~~c~~~~~~~~~~-----~~~~~~~a----~spl~~~i 297 (370)
. .+.+.++++++|.+|++|+.. ...+++.+..+ +..++... ...+.+++ +.++++.+
T Consensus 142 ~~~~~~~~~~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l 220 (243)
T PRK15007 142 MDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTEWLKDNPK-LAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKL 220 (243)
T ss_pred HHhCCCCeEEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHhcCCC-ceeecCcccccccCCcceEEEEeCCCHHHHHHH
Confidence 4 356788999999999999932 22344444443 43433222 12235565 45799999
Q ss_pred HHHHHHhhhcCchhHHHHhhcCC
Q 040220 298 SEAILKLSENKKLKSLEYNEKEL 320 (370)
Q Consensus 298 n~~i~~l~e~G~~~~l~~~w~~~ 320 (370)
|++|.++.++|.++++.++|+.+
T Consensus 221 n~~l~~l~~~g~~~~i~~~w~~~ 243 (243)
T PRK15007 221 NTALEKVKKDGTYETIYNKWFQK 243 (243)
T ss_pred HHHHHHHHhCCcHHHHHHHhcCC
Confidence 99999999999999999999863
No 9
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.78 E-value=6.8e-18 Score=157.57 Aligned_cols=194 Identities=15% Similarity=0.203 Sum_probs=144.1
Q ss_pred CCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEE-EEehhhhhhhhccccccCCceeEEEeccccccccccee
Q 040220 3 TSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISI-LFFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKIV 80 (370)
Q Consensus 3 ~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i-~~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~v 80 (370)
+++|||.+. +.++ +++|+++||++++++ +|.++++ ...+..++.. +.+|++|+++++++.|++|++.+
T Consensus 34 ~~~pPf~~~--~~~g---~~~G~~vdl~~~ia~~lg~~~~~~~~~~~~~~~~-----l~~g~~Di~~~~~~~t~eR~~~~ 103 (260)
T PRK15010 34 TTYAPFSSK--DAKG---DFVGFDIDLGNEMCKRMQVKCTWVASDFDALIPS-----LKAKKIDAIISSLSITDKRQQEI 103 (260)
T ss_pred CCcCCceeE--CCCC---CEEeeeHHHHHHHHHHhCCceEEEeCCHHHHHHH-----HHCCCCCEEEecCcCCHHHHhhc
Confidence 479999998 6544 799999999999999 9888763 2335568888 99999999999999999999999
Q ss_pred eecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHhH
Q 040220 81 EFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSIL 160 (370)
Q Consensus 81 dFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~~ 160 (370)
+||.|++.+...++++++.....
T Consensus 104 ~fs~p~~~~~~~~~~~~~~~~~~--------------------------------------------------------- 126 (260)
T PRK15010 104 AFSDKLYAADSRLIAAKGSPIQP--------------------------------------------------------- 126 (260)
T ss_pred ccccceEeccEEEEEECCCCCCC---------------------------------------------------------
Confidence 99999999999999987652100
Q ss_pred hccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHHH
Q 040220 161 FAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYLQ 240 (370)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l~ 240 (370)
+...+. +.++|+.+|+....++.
T Consensus 127 --------------------------------------------------------~~~dl~-g~~Igv~~gs~~~~~~~ 149 (260)
T PRK15010 127 --------------------------------------------------------TLDSLK-GKHVGVLQGSTQEAYAN 149 (260)
T ss_pred --------------------------------------------------------ChhHcC-CCEEEEecCchHHHHHH
Confidence 011122 67888888886655542
Q ss_pred -----------hcCChHHHHHHhhcccccccch----hHH-HHhh-cccceEEcCCCCCcc-----ceeee----CCcch
Q 040220 241 -----------NFGSDYNYQGEFGSNHIAGPPY----EKV-FVSQ-YCRIYAATTPTYGFG-----GLGFL----SSPIA 294 (370)
Q Consensus 241 -----------~~~~~~~~~~~l~~g~~~a~~~----~~~-~~~~-~c~~~~~~~~~~~~~-----~~~~a----~spl~ 294 (370)
.+.+.++++++|.+|++|+... ..+ +.++ ..+.+...++..... +++++ +.+++
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~L~ 229 (260)
T PRK15010 150 ETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVGLRKDDAELT 229 (260)
T ss_pred HhcccCCceEEecCCHHHHHHHHHcCCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEEEEeCCCHHHH
Confidence 3567788899999999999332 222 2222 233344444332222 23454 56799
Q ss_pred HHHHHHHHHhhhcCchhHHHHhhcCC
Q 040220 295 ADFSEAILKLSENKKLKSLEYNEKEL 320 (370)
Q Consensus 295 ~~in~~i~~l~e~G~~~~l~~~w~~~ 320 (370)
+.+|++|.+++++|.++++.+||++.
T Consensus 230 ~~ln~~l~~l~~~G~~~~i~~ky~~~ 255 (260)
T PRK15010 230 AAFNKALGELRQDGTYDKMAKKYFDF 255 (260)
T ss_pred HHHHHHHHHHHhCCcHHHHHHHhcCC
Confidence 99999999999999999999999864
No 10
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.77 E-value=7.6e-18 Score=157.45 Aligned_cols=191 Identities=10% Similarity=0.154 Sum_probs=141.2
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-c-CCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccc
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-A-CKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADR 76 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-l-g~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR 76 (370)
.+++|||.+. +.++ +++.||++||++++++ | |.+.++++. +.....+ |.+|++|++++++++|+||
T Consensus 45 ~~~~pP~~~~--~~~~--g~~~G~~vdl~~~ia~~llg~~~~~~~~~~~~~~~~~~-----l~~g~~D~~~~~~~~t~eR 115 (259)
T PRK11917 45 KNDVPHYALL--DQAT--GEIKGFEIDVAKLLAKSILGDDKKIKLVAVNAKTRGPL-----LDNGSVDAVIATFTITPER 115 (259)
T ss_pred CCCCCCceee--eCCC--CceeEeeHHHHHHHHHHhcCCCccEEEEEcChhhHHHH-----HHCCCccEEEecccCChhh
Confidence 4689999988 5322 3799999999999999 7 755444444 2335677 9999999999999999999
Q ss_pred cceeeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHH
Q 040220 77 AKIVEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNF 156 (370)
Q Consensus 77 ~~~vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~ 156 (370)
.+.++||.||+.++..+++++++..+
T Consensus 116 ~~~~~fs~py~~~~~~lvv~~~~~~~------------------------------------------------------ 141 (259)
T PRK11917 116 KRIYNFSEPYYQDAIGLLVLKEKNYK------------------------------------------------------ 141 (259)
T ss_pred hheeeeccCceeeceEEEEECCCCCC------------------------------------------------------
Confidence 99999999999999999999764210
Q ss_pred HHhHhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHH
Q 040220 157 SSILFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVR 236 (370)
Q Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~ 236 (370)
+.+.+. +.++|+..|+...
T Consensus 142 ------------------------------------------------------------s~~dL~-g~~V~v~~gs~~~ 160 (259)
T PRK11917 142 ------------------------------------------------------------SLADMK-GANIGVAQAATTK 160 (259)
T ss_pred ------------------------------------------------------------CHHHhC-CCeEEEecCCcHH
Confidence 012222 6778887776554
Q ss_pred HHHH-------------hcCChHHHHHHhhcccccccchhHHHHhhc-ccceEEcCCCCCccceeee----CCcchHHHH
Q 040220 237 NYLQ-------------NFGSDYNYQGEFGSNHIAGPPYEKVFVSQY-CRIYAATTPTYGFGGLGFL----SSPIAADFS 298 (370)
Q Consensus 237 ~~l~-------------~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~-c~~~~~~~~~~~~~~~~~a----~spl~~~in 298 (370)
+.+. .+++..+.+++|.+|++|+.......+..+ -+...+++..+...+|+++ +..+++.+|
T Consensus 161 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~k~~~~l~~~ln 240 (259)
T PRK11917 161 KAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVDKSILLGYVDDKSEILPDSFEPQSYGIVTKKDDPAFAKYVD 240 (259)
T ss_pred HHHHHhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEecHHHHHHhhhcCCeecCCcCCCCceEEEEeCCCHHHHHHHH
Confidence 4322 256778899999999999943333222111 1124566667777788887 456999999
Q ss_pred HHHHHhhhcCchhHHHHhhc
Q 040220 299 EAILKLSENKKLKSLEYNEK 318 (370)
Q Consensus 299 ~~i~~l~e~G~~~~l~~~w~ 318 (370)
+.|.++.. .+++|.+||-
T Consensus 241 ~~l~~~~~--~~~~i~~kw~ 258 (259)
T PRK11917 241 DFVKEHKN--EIDALAKKWG 258 (259)
T ss_pred HHHHHHHH--HHHHHHHHhC
Confidence 99999864 8999999994
No 11
>PRK11260 cystine transporter subunit; Provisional
Probab=99.76 E-value=1.3e-17 Score=156.11 Aligned_cols=197 Identities=16% Similarity=0.183 Sum_probs=149.3
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEEE-EehhhhhhhhccccccCCceeEEEecccccccccce
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISIL-FFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKI 79 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i~-~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~ 79 (370)
..++|||.+. +.++ ++.|+.+|+++++++ +|.++++. ..+..+..+ |.+|++|+++++++.+++|.+.
T Consensus 48 ~~~~~P~~~~--~~~g---~~~G~~~dl~~~i~~~lg~~~e~~~~~~~~~~~~-----l~~G~~D~~~~~~~~~~~r~~~ 117 (266)
T PRK11260 48 EGTYPPFSFQ--GEDG---KLTGFEVEFAEALAKHLGVKASLKPTKWDGMLAS-----LDSKRIDVVINQVTISDERKKK 117 (266)
T ss_pred CCCcCCceEE--CCCC---CEEEehHHHHHHHHHHHCCeEEEEeCCHHHHHHH-----HhcCCCCEEEeccccCHHHHhc
Confidence 3478999887 5444 799999999999999 98876632 235558888 9999999999999999999999
Q ss_pred eeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHh
Q 040220 80 VEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSI 159 (370)
Q Consensus 80 vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~ 159 (370)
+.||.|++..+.++++++.+..+.
T Consensus 118 ~~fs~p~~~~~~~~~~~~~~~~~~-------------------------------------------------------- 141 (266)
T PRK11260 118 YDFSTPYTVSGIQALVKKGNEGTI-------------------------------------------------------- 141 (266)
T ss_pred cccCCceeecceEEEEEcCCcCCC--------------------------------------------------------
Confidence 999999999999999887542100
Q ss_pred HhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHH
Q 040220 160 LFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYL 239 (370)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l 239 (370)
+ ....+. +.++|+..|+....++
T Consensus 142 --------------------------~------------------------------~~~dL~-g~~Igv~~G~~~~~~l 164 (266)
T PRK11260 142 --------------------------K------------------------------TAADLK-GKKVGVGLGTNYEQWL 164 (266)
T ss_pred --------------------------C------------------------------CHHHcC-CCEEEEecCCcHHHHH
Confidence 0 011122 6678887777666655
Q ss_pred H---------hcCChHHHHHHhhcccccccch----hHHHHhhcccceEEcCCCCCccceeee----CCcchHHHHHHHH
Q 040220 240 Q---------NFGSDYNYQGEFGSNHIAGPPY----EKVFVSQYCRIYAATTPTYGFGGLGFL----SSPIAADFSEAIL 302 (370)
Q Consensus 240 ~---------~~~~~~~~~~~l~~g~~~a~~~----~~~~~~~~c~~~~~~~~~~~~~~~~~a----~spl~~~in~~i~ 302 (370)
. .+++..+++++|.+|++|+... ..+++++..+.+.+....+...+++++ ++.+++.+|++|.
T Consensus 165 ~~~~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~~ln~~l~ 244 (266)
T PRK11260 165 RQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGVALRKGNPDLLKAVNQAIA 244 (266)
T ss_pred HHhCCCCceEecCCHHHHHHHHHcCCCCEEEechHHHHHHHHhCCCcceecCCccccCceEEEEeCCCHHHHHHHHHHHH
Confidence 4 3667889999999999999322 234455544434555555656666666 5579999999999
Q ss_pred HhhhcCchhHHHHhhcCCC
Q 040220 303 KLSENKKLKSLEYNEKELE 321 (370)
Q Consensus 303 ~l~e~G~~~~l~~~w~~~~ 321 (370)
+++++|.++++.++|++.+
T Consensus 245 ~~~~~g~~~~i~~k~~~~~ 263 (266)
T PRK11260 245 EMQKDGTLKALSEKWFGAD 263 (266)
T ss_pred HHHhCCcHHHHHHHhcCCc
Confidence 9999999999999999865
No 12
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.74 E-value=5e-17 Score=151.60 Aligned_cols=195 Identities=15% Similarity=0.199 Sum_probs=143.1
Q ss_pred CCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEE-EEehhhhhhhhccccccCCceeEEEeccccccccccee
Q 040220 3 TSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISI-LFFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKIV 80 (370)
Q Consensus 3 ~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i-~~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~v 80 (370)
+++|||.+. ++++ ++.|+++|+++++++ +|.++++ .+.+..++.. +.+|++|+++++++.|++|++.+
T Consensus 34 ~~~~P~~~~--~~~g---~~~G~~vdi~~~ia~~lg~~i~~~~~pw~~~~~~-----l~~g~~D~~~~~~~~t~eR~~~~ 103 (259)
T PRK15437 34 PTYAPFESK--NSQG---ELVGFDIDLAKELCKRINTQCTFVENPLDALIPS-----LKAKKIDAIMSSLSITEKRQQEI 103 (259)
T ss_pred CCCCCccee--CCCC---CEEeeeHHHHHHHHHHcCCceEEEeCCHHHHHHH-----HHCCCCCEEEecCCCCHHHhhhc
Confidence 469999998 6554 799999999999999 9877663 2345558888 99999999999999999999999
Q ss_pred eecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHhH
Q 040220 81 EFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSIL 160 (370)
Q Consensus 81 dFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~~ 160 (370)
+||.|++.++..++++++++...
T Consensus 104 ~fs~p~~~~~~~~~~~~~~~~~~--------------------------------------------------------- 126 (259)
T PRK15437 104 AFTDKLYAADSRLVVAKNSDIQP--------------------------------------------------------- 126 (259)
T ss_pred cccchhhcCceEEEEECCCCCCC---------------------------------------------------------
Confidence 99999999999999988652100
Q ss_pred hccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHHH
Q 040220 161 FAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYLQ 240 (370)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l~ 240 (370)
++.++. +.++|+.+|+....+++
T Consensus 127 --------------------------------------------------------~~~dl~-g~~Igv~~g~~~~~~~~ 149 (259)
T PRK15437 127 --------------------------------------------------------TVESLK-GKRVGVLQGTTQETFGN 149 (259)
T ss_pred --------------------------------------------------------ChHHhC-CCEEEEecCcHHHHHHH
Confidence 011122 67888888876554433
Q ss_pred -----------hcCChHHHHHHhhcccccccchhHH-----HHhhc-ccceEEcCCCC-----Cccceeee----CCcch
Q 040220 241 -----------NFGSDYNYQGEFGSNHIAGPPYEKV-----FVSQY-CRIYAATTPTY-----GFGGLGFL----SSPIA 294 (370)
Q Consensus 241 -----------~~~~~~~~~~~l~~g~~~a~~~~~~-----~~~~~-c~~~~~~~~~~-----~~~~~~~a----~spl~ 294 (370)
.+.+.++++++|.+|++|+...... +.++. -+.+.+.+..+ ....++++ +.+++
T Consensus 150 ~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ia~~~~~~~l~ 229 (259)
T PRK15437 150 EHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELR 229 (259)
T ss_pred hhccccCceEEecCCHHHHHHHHHcCCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEEEEeCCCHHHH
Confidence 3456788999999999999433221 22221 11233322222 12234455 67899
Q ss_pred HHHHHHHHHhhhcCchhHHHHhhcCCC
Q 040220 295 ADFSEAILKLSENKKLKSLEYNEKELE 321 (370)
Q Consensus 295 ~~in~~i~~l~e~G~~~~l~~~w~~~~ 321 (370)
+.+|++|.++.++|.++++.+||++..
T Consensus 230 ~~~n~~l~~~~~~G~~~~i~~k~~~~~ 256 (259)
T PRK15437 230 EALNKAFAEMRADGTYEKLAKKYFDFD 256 (259)
T ss_pred HHHHHHHHHHHHCCcHHHHHHHhcCCc
Confidence 999999999999999999999999754
No 13
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.72 E-value=1.6e-16 Score=146.75 Aligned_cols=193 Identities=15% Similarity=0.167 Sum_probs=142.5
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEE-EEehhhhhhhhccccccCCceeEEEecccccccccce
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISI-LFFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKI 79 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i-~~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~ 79 (370)
.++++||.+. +.++ +++|+++|+++.+++ +|.++++ ...+.+++.. |.+|++|+++++++.+++|.+.
T Consensus 31 ~~~~~P~~~~--~~~g---~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~-----l~~G~~D~~~~~~~~~~~r~~~ 100 (250)
T TIGR01096 31 ETGYPPFESK--DANG---KLVGFDVDLAKALCKRMKAKCKFVEQNFDGLIPS-----LKAKKVDAIMATMSITPKRQKQ 100 (250)
T ss_pred CCCCCCceEE--CCCC---CEEeehHHHHHHHHHHhCCeEEEEeCCHHHHHHH-----HhCCCcCEEEecCccCHHHhhc
Confidence 3579999998 5544 799999999999999 9877663 2345558888 9999999999889999999999
Q ss_pred eeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHh
Q 040220 80 VEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSI 159 (370)
Q Consensus 80 vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~ 159 (370)
+.||.|++.++..+++++++...
T Consensus 101 ~~~s~p~~~~~~~~~~~~~~~~~--------------------------------------------------------- 123 (250)
T TIGR01096 101 IDFSDPYYATGQGFVVKKGSDLA--------------------------------------------------------- 123 (250)
T ss_pred cccccchhcCCeEEEEECCCCcC---------------------------------------------------------
Confidence 99999999999999998755210
Q ss_pred HhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHH
Q 040220 160 LFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYL 239 (370)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l 239 (370)
. +.+.+. +.++|+..|+....++
T Consensus 124 ---~-----------------------------------------------------~~~dl~-g~~i~~~~g~~~~~~l 146 (250)
T TIGR01096 124 ---K-----------------------------------------------------TLEDLD-GKTVGVQSGTTHEQYL 146 (250)
T ss_pred ---C-----------------------------------------------------ChHHcC-CCEEEEecCchHHHHH
Confidence 0 011122 5567776666544443
Q ss_pred H----------hcCChHHHHHHhhcccccccc----hhHHHHhhcc--cceEEcCCCCCcc-----ceeee----CCcch
Q 040220 240 Q----------NFGSDYNYQGEFGSNHIAGPP----YEKVFVSQYC--RIYAATTPTYGFG-----GLGFL----SSPIA 294 (370)
Q Consensus 240 ~----------~~~~~~~~~~~l~~g~~~a~~----~~~~~~~~~c--~~~~~~~~~~~~~-----~~~~a----~spl~ 294 (370)
. .+.+.++++++|.+|++|+.. ...+.+.+.. +.+.+++..+... .++++ +..++
T Consensus 147 ~~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 226 (250)
T TIGR01096 147 KDYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKGDTELK 226 (250)
T ss_pred HHhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccCCceEEEEeCCCHHHH
Confidence 3 356789999999999999932 2333444332 2365665443321 25555 45699
Q ss_pred HHHHHHHHHhhhcCchhHHHHhhc
Q 040220 295 ADFSEAILKLSENKKLKSLEYNEK 318 (370)
Q Consensus 295 ~~in~~i~~l~e~G~~~~l~~~w~ 318 (370)
+.+|++|.+|.++|.++++.+||+
T Consensus 227 ~~ln~~l~~l~~~g~~~~i~~kw~ 250 (250)
T TIGR01096 227 AAFNKALAAIRADGTYQKISKKWF 250 (250)
T ss_pred HHHHHHHHHHHHCCcHHHHHHhhC
Confidence 999999999999999999999996
No 14
>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=99.68 E-value=8.1e-16 Score=144.84 Aligned_cols=195 Identities=12% Similarity=0.047 Sum_probs=141.7
Q ss_pred CCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCc-eEEE-EehhhhhhhhccccccCCceeEEEecccccccccce
Q 040220 3 TSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKG-ISIL-FFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKI 79 (370)
Q Consensus 3 ~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~-~~i~-~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~ 79 (370)
+++|||.+. +.++ ++.|+++||++++++ +|.+ +++. ..+..++.. +.+|++|++++++++|++|++.
T Consensus 40 ~~~pP~~~~--~~~g---~~~G~~~dl~~~i~~~lg~~~~~~~~~~w~~~~~~-----l~~G~~Di~~~~~~~t~eR~~~ 109 (275)
T TIGR02995 40 ANEPPFTYV--GADG---KVSGAAPDVARAIFKRLGIADVNASITEYGALIPG-----LQAGRFDAIAAGLFIKPERCKQ 109 (275)
T ss_pred cCCCCceeE--CCCC---ceecchHHHHHHHHHHhCCCceeeccCCHHHHHHH-----HHCCCcCEEeecccCCHHHHhc
Confidence 468999998 6554 789999999999999 9875 3322 235558888 9999999999999999999999
Q ss_pred eeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHh
Q 040220 80 VEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSI 159 (370)
Q Consensus 80 vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~ 159 (370)
++||.||+.+..++++++++..+..
T Consensus 110 ~~fs~py~~~~~~~~~~~~~~~~i~------------------------------------------------------- 134 (275)
T TIGR02995 110 VAFTQPILCDAEALLVKKGNPKGLK------------------------------------------------------- 134 (275)
T ss_pred cccccceeecceeEEEECCCCCCCC-------------------------------------------------------
Confidence 9999999999999999886521100
Q ss_pred HhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCC--CCCeEeeeCChhHHH
Q 040220 160 LFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLR--PNPKVACDRDSFVRN 237 (370)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~--~~~~vg~~~~s~~~~ 237 (370)
+.+.+. ++.++|+..|+...+
T Consensus 135 ---------------------------------------------------------~~~dl~~~~g~~Igv~~g~~~~~ 157 (275)
T TIGR02995 135 ---------------------------------------------------------SYKDIAKNPDAKIAAPGGGTEEK 157 (275)
T ss_pred ---------------------------------------------------------CHHHhccCCCceEEEeCCcHHHH
Confidence 011111 156888888887776
Q ss_pred HHH----------hcCChHHHHHHhhcccccccc----hhHHHHhhcc-cceEEcCCCC-Cc--cceeee----CCcchH
Q 040220 238 YLQ----------NFGSDYNYQGEFGSNHIAGPP----YEKVFVSQYC-RIYAATTPTY-GF--GGLGFL----SSPIAA 295 (370)
Q Consensus 238 ~l~----------~~~~~~~~~~~l~~g~~~a~~----~~~~~~~~~c-~~~~~~~~~~-~~--~~~~~a----~spl~~ 295 (370)
+++ .+.+.++++++|.+|++|+.. ...+.+++.- ..+..+.+.- .+ ..++++ +..+++
T Consensus 158 ~l~~~~~~~~~i~~~~~~~~~i~~L~~grvDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 237 (275)
T TIGR02995 158 LAREAGVKREQIIVVPDGQSGLKMVQDGRADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPVRYYGGAAFRPEDKELRD 237 (275)
T ss_pred HHHHcCCChhhEEEeCCHHHHHHHHHcCCCCEEecChHHHHHHHHhCCCCCceeecCccCCccccceeEEECCCCHHHHH
Confidence 665 246778999999999999932 2334443321 1233332211 11 122554 567999
Q ss_pred HHHHHHHHhhhcCchhHHHHhhcC
Q 040220 296 DFSEAILKLSENKKLKSLEYNEKE 319 (370)
Q Consensus 296 ~in~~i~~l~e~G~~~~l~~~w~~ 319 (370)
.+|++|.++.++|.++++.++|--
T Consensus 238 ~~n~~l~~~~~sG~~~~i~~ky~~ 261 (275)
T TIGR02995 238 AFNVELAKLKESGEFAKIIAPYGF 261 (275)
T ss_pred HHHHHHHHHHhChHHHHHHHHhCC
Confidence 999999999999999999999943
No 15
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.66 E-value=6.5e-16 Score=156.73 Aligned_cols=193 Identities=13% Similarity=0.009 Sum_probs=142.4
Q ss_pred CCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEEE-E-ehhhhhhhhccccccCCceeEEEeccccccccccee
Q 040220 4 SFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISIL-F-FFLQLMMRIRHEENFLRNYDSVVGDATILADRAKIV 80 (370)
Q Consensus 4 ~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i~-~-~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~v 80 (370)
..+|+.+. +.++ ...||++||++++++ +|+++++. + .+.+++.+ |.+|++|++++++++|++|.+.+
T Consensus 50 ~~~P~~~~--~~~~---~~~G~~~DLl~~ia~~LGv~~e~v~~~~~~~ll~a-----L~~G~iDi~~~~lt~T~eR~~~~ 119 (482)
T PRK10859 50 INSPLTYY--IGND---GPTGFEYELAKRFADYLGVKLEIKVRDNISQLFDA-----LDKGKADLAAAGLTYTPERLKQF 119 (482)
T ss_pred ecCCCeeE--ecCC---CcccHHHHHHHHHHHHhCCcEEEEecCCHHHHHHH-----HhCCCCCEEeccCcCChhhhccC
Confidence 34677776 4443 349999999999999 99887754 2 35668999 99999999999999999999999
Q ss_pred eecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHhH
Q 040220 81 EFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSIL 160 (370)
Q Consensus 81 dFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~~ 160 (370)
+||.||+.....+++++.+.. .
T Consensus 120 ~FS~Py~~~~~~lv~r~~~~~-i--------------------------------------------------------- 141 (482)
T PRK10859 120 RFGPPYYSVSQQLVYRKGQPR-P--------------------------------------------------------- 141 (482)
T ss_pred cccCCceeeeEEEEEeCCCCC-C---------------------------------------------------------
Confidence 999999999999999875410 0
Q ss_pred hccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHHH
Q 040220 161 FAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYLQ 240 (370)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l~ 240 (370)
+ +++.+. +.++|+..|+...+.++
T Consensus 142 -------------------------~------------------------------~l~dL~-Gk~I~V~~gS~~~~~L~ 165 (482)
T PRK10859 142 -------------------------R------------------------------SLGDLK-GGTLTVAAGSSHVETLQ 165 (482)
T ss_pred -------------------------C------------------------------CHHHhC-CCeEEEECCCcHHHHHH
Confidence 0 011222 67788887776655442
Q ss_pred --------------hcCChHHHHHHhhcccccccchhH----HHHhhcccceEEcCCCCCccceeee-----CCcchHHH
Q 040220 241 --------------NFGSDYNYQGEFGSNHIAGPPYEK----VFVSQYCRIYAATTPTYGFGGLGFL-----SSPIAADF 297 (370)
Q Consensus 241 --------------~~~~~~~~~~~l~~g~~~a~~~~~----~~~~~~c~~~~~~~~~~~~~~~~~a-----~spl~~~i 297 (370)
.+.+.++++++|.+|++|+..... +....+.+ +.+........+++++ +..|++.+
T Consensus 166 ~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d~~~~~~~~~~~p~-l~v~~~l~~~~~~~~av~k~~~~~L~~~l 244 (482)
T PRK10859 166 ELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPE-LAVAFDLTDEQPVAWALPPSGDDSLYAAL 244 (482)
T ss_pred HHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEECcHHHHHHHHhCCC-ceeeeecCCCceeEEEEeCCCCHHHHHHH
Confidence 235788999999999999933222 22223334 5554444344556665 23599999
Q ss_pred HHHHHHhhhcCchhHHHHhhcCCC
Q 040220 298 SEAILKLSENKKLKSLEYNEKELE 321 (370)
Q Consensus 298 n~~i~~l~e~G~~~~l~~~w~~~~ 321 (370)
|++|.++.++|.++++.+|||+..
T Consensus 245 n~~L~~i~~~G~l~~L~~kyfg~~ 268 (482)
T PRK10859 245 LDFFNQIKEDGTLARLEEKYFGHV 268 (482)
T ss_pred HHHHHHhhcCCHHHHHHHHHhhhh
Confidence 999999999999999999999885
No 16
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.60 E-value=1.7e-14 Score=134.52 Aligned_cols=197 Identities=13% Similarity=0.104 Sum_probs=144.7
Q ss_pred CCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCce--EEE-EehhhhhhhhccccccCCceeEEEecccccccccc
Q 040220 3 TSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGI--SIL-FFFLQLMMRIRHEENFLRNYDSVVGDATILADRAK 78 (370)
Q Consensus 3 ~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~--~i~-~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~ 78 (370)
...+||.+. +... +++.||++|+++++++ ++..- .+. ..+..++.. |..|++|++++++++|++|.+
T Consensus 43 ~~~~p~~~~--~~~~--~~~~G~dvdl~~~ia~~l~~~~~~~~~~~~~~~~~~~-----l~~g~~D~~~~~~~~t~er~~ 113 (275)
T COG0834 43 TYAPPFEFL--DAKG--GKLVGFDVDLAKAIAKRLGGDKKVEFVPVAWDGLIPA-----LKAGKVDIIIAGMTITPERKK 113 (275)
T ss_pred CCCCCcccc--cCCC--CeEEeeeHHHHHHHHHHhCCcceeEEeccchhhhhHH-----HhcCCcCEEEeccccCHHHhc
Confidence 345699999 6553 3899999999999999 87542 222 245668888 999999999999999999999
Q ss_pred eeeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHH
Q 040220 79 IVEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSS 158 (370)
Q Consensus 79 ~vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~ 158 (370)
.++||.||+..+..+++++++....
T Consensus 114 ~~~fs~py~~~~~~~~~~~~~~~~~------------------------------------------------------- 138 (275)
T COG0834 114 KVDFSDPYYYSGQVLLVKKDSDIGI------------------------------------------------------- 138 (275)
T ss_pred cccccccccccCeEEEEECCCCcCc-------------------------------------------------------
Confidence 9999999999999999998763110
Q ss_pred hHhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChh--HH
Q 040220 159 ILFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSF--VR 236 (370)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~--~~ 236 (370)
.+...+. +.++|+..|+. ..
T Consensus 139 ---------------------------------------------------------~~~~DL~-gk~v~v~~gt~~~~~ 160 (275)
T COG0834 139 ---------------------------------------------------------KSLEDLK-GKKVGVQLGTTDEAE 160 (275)
T ss_pred ---------------------------------------------------------CCHHHhC-CCEEEEEcCcchhHH
Confidence 0012222 67888888877 44
Q ss_pred HHHH---------hcCChHHHHHHhhcccccccch----hHH--HHhhcccceEEcCCCCCc-cceeee---C--CcchH
Q 040220 237 NYLQ---------NFGSDYNYQGEFGSNHIAGPPY----EKV--FVSQYCRIYAATTPTYGF-GGLGFL---S--SPIAA 295 (370)
Q Consensus 237 ~~l~---------~~~~~~~~~~~l~~g~~~a~~~----~~~--~~~~~c~~~~~~~~~~~~-~~~~~a---~--spl~~ 295 (370)
.... .|++..+.+.++++|++|+... ..+ ...+..+........... .+++++ + .++++
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 240 (275)
T COG0834 161 EKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIALRKGDDPELLE 240 (275)
T ss_pred HHHhhccCCceEEeeCCHHHHHHHHHcCCccEEEcchHhhhhhhhhhcCCCCceeeeccCCCcceeEEEeccCCcHHHHH
Confidence 4332 5677888999999999999332 222 122222212223223333 577777 5 37999
Q ss_pred HHHHHHHHhhhcCchhHHHHhhcCCC
Q 040220 296 DFSEAILKLSENKKLKSLEYNEKELE 321 (370)
Q Consensus 296 ~in~~i~~l~e~G~~~~l~~~w~~~~ 321 (370)
.+|++|.++.++|.++++.++|+...
T Consensus 241 ~in~~l~~l~~~G~~~~i~~kw~~~~ 266 (275)
T COG0834 241 AVNKALKELKADGTLQKISDKWFGPD 266 (275)
T ss_pred HHHHHHHHHHhCccHHHHHHHhcCcc
Confidence 99999999999999999999999854
No 17
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=99.60 E-value=1.3e-14 Score=134.52 Aligned_cols=80 Identities=13% Similarity=0.031 Sum_probs=66.4
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEE-EEehhhhh---hhhccccccCCceeEEEecccccccc
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISI-LFFFLQLM---MRIRHEENFLRNYDSVVGDATILADR 76 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i-~~~~~~li---~~~~~~~L~~g~~Diai~~~tit~eR 76 (370)
.++||||.+. + + .||++||+++|++ ||+++++ ...|..++ .. |.+|++|+++ +++++++|
T Consensus 7 ~~~~pPf~~~--~--~-----~Gfdvdl~~~ia~~lg~~~~~~~~~~~~~~~~~~~-----L~~g~~Dii~-~~~~t~~r 71 (246)
T TIGR03870 7 ATKEAPYSTK--D--G-----SGFENKIAAALAAAMGRKVVFVWLAKPAIYLVRDG-----LDKKLCDVVL-GLDTGDPR 71 (246)
T ss_pred CCCCCCCccC--C--C-----CcchHHHHHHHHHHhCCCeEEEEeccchhhHHHHH-----HhcCCccEEE-eCCCChHH
Confidence 4789999997 4 2 6999999999999 9988763 33444444 57 9999999998 58998888
Q ss_pred cceeeecccccccceEEEEeCCC
Q 040220 77 AKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 77 ~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
++||.||+.++.++++++++
T Consensus 72 ---~~fS~PY~~~~~~~v~~k~~ 91 (246)
T TIGR03870 72 ---VLTTKPYYRSSYVFLTRKDR 91 (246)
T ss_pred ---HhcccCcEEeeeEEEEeCCC
Confidence 67999999999999999865
No 18
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.59 E-value=1.9e-14 Score=160.88 Aligned_cols=192 Identities=12% Similarity=0.110 Sum_probs=143.9
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceE-EEEe-hhhhhhhhccccccCCceeEEEecccccccccc
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGIS-ILFF-FLQLMMRIRHEENFLRNYDSVVGDATILADRAK 78 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~-i~~~-~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~ 78 (370)
.++||||.+. |.++ +++||++|++++|++ +|++++ +... +.+.... |.+|++|++ .+++.|++|.+
T Consensus 309 ~~~~pP~~~~--d~~g---~~~G~~~Dll~~i~~~~g~~~~~v~~~~~~~~~~~-----l~~g~~D~i-~~~~~t~~r~~ 377 (1197)
T PRK09959 309 NPYSPPYSMT--DENG---SVRGVMGDILNIITLQTGLNFSPITVSHNIHAGTQ-----LNPGGWDII-PGAIYSEDREN 377 (1197)
T ss_pred CCCCCCeeEE--CCCC---cEeeehHHHHHHHHHHHCCeEEEEecCCHHHHHHH-----HHCCCceEe-ecccCCccccc
Confidence 5689999999 7554 799999999999999 997766 2222 3346777 999999976 45678999999
Q ss_pred eeeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHH
Q 040220 79 IVEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSS 158 (370)
Q Consensus 79 ~vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~ 158 (370)
.++||.||+.++.++++++.... .
T Consensus 378 ~~~fs~py~~~~~~~v~~~~~~~-~------------------------------------------------------- 401 (1197)
T PRK09959 378 NVLFAEAFITTPYVFVMQKAPDS-E------------------------------------------------------- 401 (1197)
T ss_pred cceeccccccCCEEEEEecCCCC-c-------------------------------------------------------
Confidence 99999999999999998764310 0
Q ss_pred hHhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHH
Q 040220 159 ILFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNY 238 (370)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~ 238 (370)
. +.. .+.++|+..++...++
T Consensus 402 ------------------------~---------------------------------~~~---~g~~vav~~g~~~~~~ 421 (1197)
T PRK09959 402 ------------------------Q---------------------------------TLK---KGMKVAIPYYYELHSQ 421 (1197)
T ss_pred ------------------------c---------------------------------ccc---cCCEEEEeCCcchHHH
Confidence 0 000 1678888888766666
Q ss_pred HH---------hcCChHHHHHHhhccccccc----chhHHHHhhcc-c-ceEEcCCCCCccceeee----CCcchHHHHH
Q 040220 239 LQ---------NFGSDYNYQGEFGSNHIAGP----PYEKVFVSQYC-R-IYAATTPTYGFGGLGFL----SSPIAADFSE 299 (370)
Q Consensus 239 l~---------~~~~~~~~~~~l~~g~~~a~----~~~~~~~~~~c-~-~~~~~~~~~~~~~~~~a----~spl~~~in~ 299 (370)
+. .|++.++++++|.+|++|+. ....|+++++- + ...+..+.+....++++ +.+|++.+|+
T Consensus 422 ~~~~~p~~~~~~~~~~~~~l~av~~G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~av~k~~~~L~~~lnk 501 (1197)
T PRK09959 422 LKEMYPEVEWIKVDNASAAFHKVKEGELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGEPELKDIINK 501 (1197)
T ss_pred HHHHCCCcEEEEcCCHHHHHHHHHcCCCCEEehhhHHHHHHHHhcccccceeeecCCCCchheEEeeCCCCHHHHHHHHH
Confidence 54 47789999999999999992 34556665532 2 12333333444566666 5679999999
Q ss_pred HHHHhhhcCchhHHHHhhcCCC
Q 040220 300 AILKLSENKKLKSLEYNEKELE 321 (370)
Q Consensus 300 ~i~~l~e~G~~~~l~~~w~~~~ 321 (370)
+|..+.++ .++++.+||++..
T Consensus 502 ~l~~i~~~-~~~~i~~kW~~~~ 522 (1197)
T PRK09959 502 ALNAIPPS-EVLRLTEKWIKMP 522 (1197)
T ss_pred HHHhCCHH-HHHHHHhhcccCC
Confidence 99999998 8999999999764
No 19
>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=99.56 E-value=3.2e-14 Score=133.38 Aligned_cols=87 Identities=11% Similarity=0.072 Sum_probs=70.1
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-c-CCceEE-EEehhhhhhhhccccccCCceeEEEecccccccccc
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-A-CKGISI-LFFFLQLMMRIRHEENFLRNYDSVVGDATILADRAK 78 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-l-g~~~~i-~~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~ 78 (370)
.++||||.+. +.++ ..+|+.+++++++++ + |.++++ .+.|..++.. | +|+.|.++.++++|+||++
T Consensus 24 ~~~~pPf~~~--~~~~---~~~G~~~~i~~~i~~~~~~~~~~~~~~pw~r~l~~-----l-~~~~d~~~~~~~~t~eR~~ 92 (268)
T TIGR02285 24 VNDFPPFFIF--SGPS---KGRGVFDVILQEIRRALPQYEHRFVRVSFARSLKE-----L-QGKGGVCTVNLLRTPEREK 92 (268)
T ss_pred ecccCCeeEe--CCCC---CCCChHHHHHHHHHHHcCCCceeEEECCHHHHHHH-----H-hcCCCeEEeeccCCcchhh
Confidence 3579999988 5433 679999999999999 7 666553 2346668888 8 7888888888999999999
Q ss_pred eeeecccccc-cceEEEEeCCC
Q 040220 79 IVEFTQPCAE-SRLSMIVPAKT 99 (370)
Q Consensus 79 ~vdFS~P~~~-~~~~ilv~~~~ 99 (370)
.++||.||+. ....+++++.+
T Consensus 93 ~~~Fs~P~~~~~~~~~~~~~~~ 114 (268)
T TIGR02285 93 FLIFSDPTLRALPVGLVLRKEL 114 (268)
T ss_pred ceeecCCccccCCceEEEccch
Confidence 9999999985 57888888754
No 20
>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=99.55 E-value=5.7e-16 Score=131.99 Aligned_cols=95 Identities=24% Similarity=0.503 Sum_probs=69.3
Q ss_pred chHHHHHHHHHHHHHHHHHHhccccCCCCCCC-------CCCCCccchHHHHHHHhHhccCccceeeeeeccccCccccC
Q 040220 111 TWEMWVVTDAILVNTRFVVWFPEHQRNSEFNG-------PRKDQIGTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFGG 183 (370)
Q Consensus 111 ~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~-------~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 183 (370)
+|+||++++++++++++++|++++..+.+++. +....+.+++|++++++++|+.. .
T Consensus 1 s~~vW~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~-----------------~ 63 (148)
T PF00060_consen 1 SWSVWLLILLSILLVSLVLWLFERFSPYEWRKNQSSPPRRWRFSLSNSFWYTFGTLLQQGSS-----------------I 63 (148)
T ss_dssp -HHHHHHHHHHHHHHHTTGGGT------------------HHHHHHHHHHHCCCCCHHHHH-------------------
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccccccCcccHHHHHHHHHHhhcccccc-----------------c
Confidence 58999999999999999999999977665543 12234778899999999975541 6
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCC
Q 040220 184 RIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLR 222 (370)
Q Consensus 184 ~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~ 222 (370)
+|++.++|++.+.|++++++++++|+|+|+|+||.++.+
T Consensus 64 ~~~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~~~ 102 (148)
T PF00060_consen 64 RPRSWSGRILLAFWWLFSLILIASYTANLTSFLTVPKYE 102 (148)
T ss_dssp ----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcC
Confidence 699999999999999999999999999999999998755
No 21
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.52 E-value=8.3e-14 Score=155.79 Aligned_cols=194 Identities=9% Similarity=-0.009 Sum_probs=141.5
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEE-EE-ehhhhhhhhccccccCCceeEEEecccccccccc
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISI-LF-FFLQLMMRIRHEENFLRNYDSVVGDATILADRAK 78 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i-~~-~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~ 78 (370)
.++++||.+.. +.+ ++++||++|+++.|++ +|+++++ .+ .|.+++.+ |.+|++|+++++++.+++|.+
T Consensus 63 ~~~~~p~~~~~-~~~---g~~~G~~~D~l~~ia~~lG~~~e~v~~~~~~~~l~~-----l~~g~iDl~~~~~~~~~~r~~ 133 (1197)
T PRK09959 63 HKSQTATLLHT-DSQ---QRVRGINADYLNLLKRALNIKLTLREYADHQKAMDA-----LEEGEVDIVLSHLVASPPLND 133 (1197)
T ss_pred cCCCCCCceee-cCC---CccceecHHHHHHHHHhcCCceEEEeCCCHHHHHHH-----HHcCCCcEecCcccccccccc
Confidence 35565655540 333 3899999999999999 9998884 45 57789999 999999999999999999999
Q ss_pred eeeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHH
Q 040220 79 IVEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSS 158 (370)
Q Consensus 79 ~vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~ 158 (370)
.++||.||+.+...++++++.....
T Consensus 134 ~~~fs~py~~~~~~~v~~~~~~~~~------------------------------------------------------- 158 (1197)
T PRK09959 134 DIAATKPLIITFPALVTTLHDSMRP------------------------------------------------------- 158 (1197)
T ss_pred chhcCCCccCCCceEEEeCCCCCCC-------------------------------------------------------
Confidence 9999999999999999987542100
Q ss_pred hHhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHH
Q 040220 159 ILFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNY 238 (370)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~ 238 (370)
...+. +.++|+.+|+...++
T Consensus 159 -----------------------------------------------------------~~~l~-~~~i~~~~g~~~~~~ 178 (1197)
T PRK09959 159 -----------------------------------------------------------LTSSK-PVNIARVANYPPDEV 178 (1197)
T ss_pred -----------------------------------------------------------ccccc-CeEEEEeCCCCCHHH
Confidence 00111 556676666655555
Q ss_pred HH---------hcCChHHHHHHhhccccccc----chhHHHHhhcc-cceEEcCCCCCc-cceeee---CC-cchHHHHH
Q 040220 239 LQ---------NFGSDYNYQGEFGSNHIAGP----PYEKVFVSQYC-RIYAATTPTYGF-GGLGFL---SS-PIAADFSE 299 (370)
Q Consensus 239 l~---------~~~~~~~~~~~l~~g~~~a~----~~~~~~~~~~c-~~~~~~~~~~~~-~~~~~a---~s-pl~~~in~ 299 (370)
++ .|++..+++++|.+|++|+. ....++++++. ..+.+.+....+ ....++ +. .+.+.+|+
T Consensus 179 ~~~~~p~~~i~~~~s~~~al~av~~G~~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~lnk 258 (1197)
T PRK09959 179 IHQSFPKATIISFTNLYQALASVSAGQNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKESVILNEVLNR 258 (1197)
T ss_pred HHHhCCCCEEEeCCCHHHHHHHHHcCCCCEEEccHHHHHHHHhcccccceEEEeeccCCCCceeEEEcCCcHHHHHHHHH
Confidence 44 57889999999999999992 33455555432 224444322122 223343 44 48999999
Q ss_pred HHHHhhhcCchhHHHHhhcCC
Q 040220 300 AILKLSENKKLKSLEYNEKEL 320 (370)
Q Consensus 300 ~i~~l~e~G~~~~l~~~w~~~ 320 (370)
+|..+.++|.. .+.+||++.
T Consensus 259 al~~i~~~~~~-~i~~kW~~~ 278 (1197)
T PRK09959 259 FVDALTNEVRY-EVSQNWLDT 278 (1197)
T ss_pred HHHhCCHHHHH-HHHHhccCC
Confidence 99999999998 999999864
No 22
>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=99.49 E-value=1.1e-12 Score=115.87 Aligned_cols=191 Identities=17% Similarity=0.218 Sum_probs=138.6
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEEE-EehhhhhhhhccccccCCceeEEEecccccccccce
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISIL-FFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKI 79 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i~-~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~ 79 (370)
.+.+|||.+. +.++ ++.|+..|+++.+++ +|.++++. .....++.+ |.+|++|+++++...+++|.+.
T Consensus 6 ~~~~~p~~~~--~~~g---~~~G~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~-----l~~g~~D~~~~~~~~~~~~~~~ 75 (218)
T cd00134 6 AGTYPPFSFR--DANG---ELTGFDVDLAKAIAKELGVKVKFVEVDWDGLITA-----LKSGKVDLIAAGMTITPERAKQ 75 (218)
T ss_pred CCCCCCeeEE--CCCC---CEEeeeHHHHHHHHHHhCCeEEEEeCCHHHHHHH-----HhcCCcCEEeecCcCCHHHHhh
Confidence 5678999988 5444 799999999999999 98665522 223447777 9999999999988889999999
Q ss_pred eeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHh
Q 040220 80 VEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSI 159 (370)
Q Consensus 80 vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~ 159 (370)
+.|+.|+......+++++++....
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------------------------------- 99 (218)
T cd00134 76 VDFSDPYYKSGQVILVKKGSPIKS-------------------------------------------------------- 99 (218)
T ss_pred ccCcccceeccEEEEEECCCCCCC--------------------------------------------------------
Confidence 999999999999999998653110
Q ss_pred HhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHH
Q 040220 160 LFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYL 239 (370)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l 239 (370)
...+. +.++++..++....++
T Consensus 100 ----------------------------------------------------------~~dl~-g~~i~~~~~~~~~~~~ 120 (218)
T cd00134 100 ----------------------------------------------------------VKDLK-GKKVAVQKGSTAEKYL 120 (218)
T ss_pred ----------------------------------------------------------hHHhC-CCEEEEEcCchHHHHH
Confidence 11111 4455555444433333
Q ss_pred H---------hcCChHHHHHHhhccccccc----chhHHHHhhc-ccceEEcCCC--CCccceeee---CC-cchHHHHH
Q 040220 240 Q---------NFGSDYNYQGEFGSNHIAGP----PYEKVFVSQY-CRIYAATTPT--YGFGGLGFL---SS-PIAADFSE 299 (370)
Q Consensus 240 ~---------~~~~~~~~~~~l~~g~~~a~----~~~~~~~~~~-c~~~~~~~~~--~~~~~~~~a---~s-pl~~~in~ 299 (370)
. .+.+.++.++++.+|++|+. +...+..++. ++ +.++... ..+..++++ ++ .+.+.+|+
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 199 (218)
T cd00134 121 KKALPEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPE-LKIVGPSIDLEPLGFGVAVGKDNKELLDAVNK 199 (218)
T ss_pred HHhCCcccEEEeCCHHHHHHHHHcCCccEEEeccHHHHHHHHhcCCC-cEEeccccCCCccceEEEEcCCCHHHHHHHHH
Confidence 2 35678899999999999992 2333344443 44 6666543 233345665 33 68999999
Q ss_pred HHHHhhhcCchhHHHHhhc
Q 040220 300 AILKLSENKKLKSLEYNEK 318 (370)
Q Consensus 300 ~i~~l~e~G~~~~l~~~w~ 318 (370)
+|.+++++|.++.+.++|+
T Consensus 200 ~l~~~~~~g~~~~i~~~~~ 218 (218)
T cd00134 200 ALKELRADGELKKISKKWF 218 (218)
T ss_pred HHHHHHhCccHHHHHHhhC
Confidence 9999999999999999996
No 23
>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=99.46 E-value=1.4e-12 Score=119.10 Aligned_cols=80 Identities=13% Similarity=0.014 Sum_probs=63.5
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEEEE-e--hhhhhhhhccccccCCceeEEEeccccccccc
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISILF-F--FLQLMMRIRHEENFLRNYDSVVGDATILADRA 77 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i~~-~--~~~li~~~~~~~L~~g~~Diai~~~tit~eR~ 77 (370)
.++||||.+. +..||++||++++++ +|.++++.+ . ...++.. +.+|++|++++ +++|.
T Consensus 7 ~~~~~P~~~~---------~~~G~~~el~~~i~~~~g~~i~~~~~~~~~~~~~~~-----l~~g~~Di~~~----~~~r~ 68 (232)
T TIGR03871 7 DPNNLPFSNE---------KGEGFENKIAQLLADDLGLPLEYTWFPQRRGFVRNT-----LNAGRCDVVIG----VPAGY 68 (232)
T ss_pred CCCCCCccCC---------CCCchHHHHHHHHHHHcCCceEEEecCcchhhHHHH-----HhcCCccEEEe----ccCcc
Confidence 4678998864 236999999999999 987765332 1 1224567 89999999876 57899
Q ss_pred ceeeecccccccceEEEEeCCC
Q 040220 78 KIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 78 ~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+.++||.||+..+.++++++++
T Consensus 69 ~~~~fs~py~~~~~~lv~~~~~ 90 (232)
T TIGR03871 69 EMVLTTRPYYRSTYVFVTRKDS 90 (232)
T ss_pred ccccccCCcEeeeEEEEEeCCC
Confidence 9999999999999999999864
No 24
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.43 E-value=3.8e-12 Score=112.11 Aligned_cols=192 Identities=18% Similarity=0.204 Sum_probs=138.3
Q ss_pred CCCCccceEEeecCCCCCCceEEeeHHHHHHHHh-cCCceEEEE-ehhhhhhhhccccccCCceeEEEecccccccccce
Q 040220 2 GTSFGKFVKVKFSDNPYENEYDGFCIELYYESQL-ACKGISILF-FFLQLMMRIRHEENFLRNYDSVVGDATILADRAKI 79 (370)
Q Consensus 2 ~~~~~Pfv~~~~~~~~~~~~~~G~~idl~~~la~-lg~~~~i~~-~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~ 79 (370)
.++++||... +.++ ++.|+.+|+++.+.+ +|+++++.. .+..++.. +.+|++|+++++...+.+|.+.
T Consensus 7 ~~~~~p~~~~--~~~g---~~~G~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~-----l~~g~~D~~~~~~~~~~~~~~~ 76 (219)
T smart00062 7 NGDYPPFSFA--DEDG---ELTGFDVDLAKAIAKELGLKVEFVEVSFDNLLTA-----LKSGKIDVVAAGMTITPERAKQ 76 (219)
T ss_pred cCCCCCcEEE--CCCC---CcccchHHHHHHHHHHhCCeEEEEeccHHHHHHH-----HHCCcccEEeccccCCHHHHhh
Confidence 3678999998 6454 699999999999999 987766322 23448888 9999999999988888999999
Q ss_pred eeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHh
Q 040220 80 VEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSI 159 (370)
Q Consensus 80 vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~ 159 (370)
+.|+.|+...+..++++++.+...
T Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------------------------------- 100 (219)
T smart00062 77 VDFSDPYYKSGQVILVRKDSPIKS-------------------------------------------------------- 100 (219)
T ss_pred eeeccceeeceeEEEEecCCCCCC--------------------------------------------------------
Confidence 999999999999999987653110
Q ss_pred HhccCccceeeeeeccccCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHH
Q 040220 160 LFAYGKEHVLHFIIMVNWKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYL 239 (370)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l 239 (370)
.+.+. +.++++..++....++
T Consensus 101 ----------------------------------------------------------~~dL~-g~~i~~~~g~~~~~~~ 121 (219)
T smart00062 101 ----------------------------------------------------------LEDLK-GKKVAVVAGTTGEELL 121 (219)
T ss_pred ----------------------------------------------------------hHHhC-CCEEEEecCccHHHHH
Confidence 11111 4455555444444333
Q ss_pred H---------hcCChHHHHHHhhccccccc----chhHHHHhhcc-cceEEcCCCCCc-cceeee---CC-cchHHHHHH
Q 040220 240 Q---------NFGSDYNYQGEFGSNHIAGP----PYEKVFVSQYC-RIYAATTPTYGF-GGLGFL---SS-PIAADFSEA 300 (370)
Q Consensus 240 ~---------~~~~~~~~~~~l~~g~~~a~----~~~~~~~~~~c-~~~~~~~~~~~~-~~~~~a---~s-pl~~~in~~ 300 (370)
. .+.+..+.+++|.+|++|+. +...+...+.. ..+.++.+.... ..++++ ++ .+++.+++.
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (219)
T smart00062 122 KKLYPEAKIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFAVRKGDPELLDKINKA 201 (219)
T ss_pred HHhCCCceEEEcCCHHHHHHHhhcCcccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEEEECCCHHHHHHHHHH
Confidence 2 34567889999999999992 22333343331 236666554443 556665 55 589999999
Q ss_pred HHHhhhcCchhHHHHhhc
Q 040220 301 ILKLSENKKLKSLEYNEK 318 (370)
Q Consensus 301 i~~l~e~G~~~~l~~~w~ 318 (370)
|.++.++|.++++.++|+
T Consensus 202 l~~~~~~~~~~~i~~~~~ 219 (219)
T smart00062 202 LKELKADGTLKKIYEKWF 219 (219)
T ss_pred HHHHHhCchHHHHHhccC
Confidence 999999999999999996
No 25
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=98.97 E-value=3.1e-09 Score=88.71 Aligned_cols=94 Identities=26% Similarity=0.286 Sum_probs=80.2
Q ss_pred CeEeeeCChhHHHHHHh--------------------cCChHHHHHHhhcccccc----cchhHHHHhhcccceEEcCCC
Q 040220 225 PKVACDRDSFVRNYLQN--------------------FGSDYNYQGEFGSNHIAG----PPYEKVFVSQYCRIYAATTPT 280 (370)
Q Consensus 225 ~~vg~~~~s~~~~~l~~--------------------~~~~~~~~~~l~~g~~~a----~~~~~~~~~~~c~~~~~~~~~ 280 (370)
.++|+..|+....+++. |++..+++.+|++|+ |+ .+.+.++.++.|+ +.+++..
T Consensus 14 ~~vgv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~v~d~~~~~~~~~~~~~-~~~~~~~ 91 (134)
T smart00079 14 IEYGTIRGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLMESTYLDYELSQNCD-LMTVGEN 91 (134)
T ss_pred ccceEecCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-CEEEeehHhHHHHHhCCCC-eEEcCcc
Confidence 78999999888777651 567889999999999 99 3556666666787 8888888
Q ss_pred CCccceeee---CCcchHHHHHHHHHhhhcCchhHHHHhhcCC
Q 040220 281 YGFGGLGFL---SSPIAADFSEAILKLSENKKLKSLEYNEKEL 320 (370)
Q Consensus 281 ~~~~~~~~a---~spl~~~in~~i~~l~e~G~~~~l~~~w~~~ 320 (370)
+...+||++ +++|++.+|.+|.+|.++|.++++.++|+++
T Consensus 92 ~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~G~~~~l~~kw~~~ 134 (134)
T smart00079 92 FGRKGYGIAFPKGSPLRDDLSRAILKLSESGELQKLENKWWKK 134 (134)
T ss_pred cCCCceEEEecCCCHHHHHHHHHHHHHHhcCcHHHHHHhhccC
Confidence 888889888 8899999999999999999999999999874
No 26
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=98.78 E-value=3.2e-08 Score=94.02 Aligned_cols=182 Identities=13% Similarity=-0.005 Sum_probs=126.5
Q ss_pred CceEEeeHHHHHHHHh-cCCceEEEE--ehhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEe
Q 040220 20 NEYDGFCIELYYESQL-ACKGISILF--FFLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVP 96 (370)
Q Consensus 20 ~~~~G~~idl~~~la~-lg~~~~i~~--~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~ 96 (370)
+...|++.|+.++.|+ ||.+.++.. ...++..+ |.+|++|++.+++...++|.+.+.....|+..+..++.+
T Consensus 41 ~~p~G~eYelak~Fa~yLgV~Lki~~~~n~dqLf~a-----L~ng~~DL~Aagl~~~~~~l~~~~~gP~y~svs~qlVyR 115 (473)
T COG4623 41 GGPTGLEYELAKAFADYLGVKLKIIPADNIDQLFDA-----LDNGNADLAAAGLLYNSERLKNFQPGPTYYSVSQQLVYR 115 (473)
T ss_pred CCccchhHHHHHHHHHHhCCeEEEEecCCHHHHHHH-----HhCCCcceecccccCChhHhcccCCCCceecccHHHHhh
Confidence 3568999999999999 986655432 24559999 999999999999999999999999998888888888888
Q ss_pred CCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHhHhccCccceeeeeeccc
Q 040220 97 AKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSILFAYGKEHVLHFIIMVN 176 (370)
Q Consensus 97 ~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~ 176 (370)
+++.
T Consensus 116 kG~~---------------------------------------------------------------------------- 119 (473)
T COG4623 116 KGQY---------------------------------------------------------------------------- 119 (473)
T ss_pred cCCC----------------------------------------------------------------------------
Confidence 7752
Q ss_pred cCccccCcccchhhHHHHHHHHHHHHHHHHHhhcCCccccccccCCCCCeEeeeCChhHHHHHH-----hc---------
Q 040220 177 WKPIFGGRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLTVQPLRPNPKVACDRDSFVRNYLQ-----NF--------- 242 (370)
Q Consensus 177 ~~~~~~~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~~~vg~~~~s~~~~~l~-----~~--------- 242 (370)
+|++ ..++. +..+-+.+|+....-++ .|
T Consensus 120 -------Rp~~------------------------------l~~L~-g~~i~v~~gs~~~~~l~~lk~~kyP~l~~k~d~ 161 (473)
T COG4623 120 -------RPRS------------------------------LGQLK-GRQITVAKGSAHVEDLKLLKETKYPELIWKVDD 161 (473)
T ss_pred -------CCCC------------------------------HHHcc-CceeeccCCcHHHHHHHHHHHhhcchhhhhhcc
Confidence 1111 11111 33333444443322222 11
Q ss_pred -CChHHHHHHhhcccccccchhHHH---Hhh-cccceEEcCCCCCccceee--e---CCcchHHHHHHHHHhhhcCchhH
Q 040220 243 -GSDYNYQGEFGSNHIAGPPYEKVF---VSQ-YCRIYAATTPTYGFGGLGF--L---SSPIAADFSEAILKLSENKKLKS 312 (370)
Q Consensus 243 -~~~~~~~~~l~~g~~~a~~~~~~~---~~~-~c~~~~~~~~~~~~~~~~~--a---~spl~~~in~~i~~l~e~G~~~~ 312 (370)
...++.++.+..|++++....... .++ +++ +.+.-+.-...+.+. . ++.+...++..+..+.|+|.++.
T Consensus 162 ~~~~~dLle~v~~Gkldytiads~~is~~q~i~P~-laVafd~tde~~v~Wy~~~~dd~tL~a~ll~F~~~~~e~g~lar 240 (473)
T COG4623 162 KLGVEDLLEMVAEGKLDYTIADSVEISLFQRVHPE-LAVAFDLTDEQPVAWYLPRDDDSTLSAALLDFLNEAKEDGLLAR 240 (473)
T ss_pred cccHHHHHHHHhcCCcceeeeccHHHHHHHHhCcc-ceeeeecccccCceeeccCCchHHHHHHHHHHHHHhhcchHHHH
Confidence 246788999999999994333221 222 344 555544333344444 3 57899999999999999999999
Q ss_pred HHHhhcCCC
Q 040220 313 LEYNEKELE 321 (370)
Q Consensus 313 l~~~w~~~~ 321 (370)
+++||++.-
T Consensus 241 leeky~gH~ 249 (473)
T COG4623 241 LEEKYLGHG 249 (473)
T ss_pred HHHHHhccc
Confidence 999999654
No 27
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.05 E-value=1.5e-05 Score=75.72 Aligned_cols=46 Identities=17% Similarity=0.093 Sum_probs=40.6
Q ss_pred hhhhhccccccCCceeEEEecccccccccceeeeccc--ccccceEEEEeCCC
Q 040220 49 LMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQP--CAESRLSMIVPAKT 99 (370)
Q Consensus 49 li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P--~~~~~~~ilv~~~~ 99 (370)
++.. |.+|++|+++++.+++.||.+.++|+.| |....+.+++|+..
T Consensus 56 i~~~-----L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~ 103 (287)
T PRK00489 56 IPGY-----VADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDS 103 (287)
T ss_pred HHHH-----HHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCC
Confidence 7777 9999999999999999999999999998 66777888888754
No 28
>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=97.88 E-value=6.8e-06 Score=59.74 Aligned_cols=37 Identities=27% Similarity=0.407 Sum_probs=28.6
Q ss_pred cceEEeec--CCCCCCceEEeeHHHHHHHHh-cCCceEEE
Q 040220 7 KFVKVKFS--DNPYENEYDGFCIELYYESQL-ACKGISIL 43 (370)
Q Consensus 7 Pfv~~~~~--~~~~~~~~~G~~idl~~~la~-lg~~~~i~ 43 (370)
||++.+.+ ...++.++.||+|||+++||+ |||+|++.
T Consensus 1 Pfvm~~~~~~~~~g~~~~eGyciDll~~la~~l~F~y~i~ 40 (65)
T PF10613_consen 1 PFVMLKEDGENLTGNDRYEGYCIDLLEELAEELNFTYEIY 40 (65)
T ss_dssp TTBEE-TTSSGSBGGGGEESHHHHHHHHHHHHHT-EEEEE
T ss_pred CeEEEecCCcccCCCccEEEEHHHHHHHHHHHcCCeEEEE
Confidence 89999544 114457999999999999999 99998864
No 29
>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=97.59 E-value=0.00061 Score=62.86 Aligned_cols=75 Identities=11% Similarity=-0.017 Sum_probs=53.2
Q ss_pred ceEEeeHHHHHHHHh-cCCceEEEE--ehhhhhhhhccccccCCceeEEEecccccc---cccceeeeccccccc-----
Q 040220 21 EYDGFCIELYYESQL-ACKGISILF--FFLQLMMRIRHEENFLRNYDSVVGDATILA---DRAKIVEFTQPCAES----- 89 (370)
Q Consensus 21 ~~~G~~idl~~~la~-lg~~~~i~~--~~~~li~~~~~~~L~~g~~Diai~~~tit~---eR~~~vdFS~P~~~~----- 89 (370)
.+.+...++.+.+++ +|.++++.. .+.+++.. +.+|++|+++.+..... +|.+..+|+.|+...
T Consensus 46 ~~~~~~~~l~~~l~~~~g~~v~~~~~~~~~~~~~~-----l~~g~~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 (254)
T TIGR01098 46 NLTRRWEPLADYLEKKLGIKVQLFVATDYSAVIEA-----MRFGRVDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPG 120 (254)
T ss_pred HHHHHHHHHHHHHHHHhCCcEEEEeCCCHHHHHHH-----HHcCCccEEEECcHHHHHHHHhcCCceEEeeccccCCCCc
Confidence 344556789999999 987766432 24458888 99999999997765443 677778899886643
Q ss_pred -ceEEEEeCCCC
Q 040220 90 -RLSMIVPAKTE 100 (370)
Q Consensus 90 -~~~ilv~~~~~ 100 (370)
...++++++++
T Consensus 121 ~~~~lvv~~d~~ 132 (254)
T TIGR01098 121 YYSVIIVKADSP 132 (254)
T ss_pred eEEEEEEECCCC
Confidence 24677777553
No 30
>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=96.36 E-value=0.04 Score=51.97 Aligned_cols=71 Identities=8% Similarity=-0.029 Sum_probs=43.7
Q ss_pred ChHHHHHHhhcccccccch----hHHHHh-hcc---cceEEcCC--CCCccceeee-C--CcchHHHHHHHHHhhhcCch
Q 040220 244 SDYNYQGEFGSNHIAGPPY----EKVFVS-QYC---RIYAATTP--TYGFGGLGFL-S--SPIAADFSEAILKLSENKKL 310 (370)
Q Consensus 244 ~~~~~~~~l~~g~~~a~~~----~~~~~~-~~c---~~~~~~~~--~~~~~~~~~a-~--spl~~~in~~i~~l~e~G~~ 310 (370)
+..+.+.+|.+|++|+... ...+.+ ... ..+.++.. .+...++++. + ..+++.+++++.++.+++..
T Consensus 176 ~~~~~~~al~~G~vDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~ 255 (288)
T TIGR03431 176 SHEAAILAVANGTVDAATTNDENLDRMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKTDKA 255 (288)
T ss_pred chHHHHHHHHcCCCCeEeccHHHHHHHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCCcHH
Confidence 5788999999999999322 222232 111 11343322 2333344444 4 35999999999999999776
Q ss_pred hHHH
Q 040220 311 KSLE 314 (370)
Q Consensus 311 ~~l~ 314 (370)
++..
T Consensus 256 ~~~~ 259 (288)
T TIGR03431 256 CFEK 259 (288)
T ss_pred HHHh
Confidence 6543
No 31
>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=94.97 E-value=0.073 Score=40.01 Aligned_cols=55 Identities=18% Similarity=0.361 Sum_probs=44.0
Q ss_pred CCCccchHHHHHHHhHhccCccceeeeeeccccCccccC-cccchhhHHHHHHHHHHHHHHHHHhhcCCcccc
Q 040220 145 KDQIGTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFGG-RIDSNLTRLVVVVWLFVVLILTSSYTASPSPML 216 (370)
Q Consensus 145 ~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~L 216 (370)
..++.+++|+++.++.+.| ||+ .|.+..+|++...+.+.++.+.+...+.+++.+
T Consensus 22 ~~~~~da~yfs~~t~tTvG-----------------yGDi~p~t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l 77 (79)
T PF07885_consen 22 KWSFIDALYFSFVTITTVG-----------------YGDIVPQTPAGRIFTIIYMLIGIFLFALFLSVLASVL 77 (79)
T ss_dssp TTSHHHHHHHHHHHHTT--------------------SSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhccc-----------------CCCccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3467899999999999875 233 488999999999999999999998888777654
No 32
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=93.63 E-value=0.51 Score=44.99 Aligned_cols=46 Identities=13% Similarity=0.031 Sum_probs=29.2
Q ss_pred hhhhhhccccccCCceeEEEecccccccccc------eeeecccccccceEEEEeCCC
Q 040220 48 QLMMRIRHEENFLRNYDSVVGDATILADRAK------IVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 48 ~li~~~~~~~L~~g~~Diai~~~tit~eR~~------~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+++.+ |.+|++|+++.+ .....+.+ .+..+.|+......+++++++
T Consensus 68 ~~~~a-----L~~G~iDia~~~-~~~~~~~~~~g~~~~~v~~~~~~~~~~~lvv~~~s 119 (314)
T PRK11553 68 QMLEA-----LNVGSIDLGSTG-DIPPIFAQAAGADLVYVGVEPPKPKAEVILVAENS 119 (314)
T ss_pred HHHHH-----HHcCCCCEEccC-CHHHHHHHhCCCCEEEEEEecCCCcceEEEEeCCC
Confidence 47888 999999999875 33333221 122245666666778887654
No 33
>KOG1419 consensus Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism]
Probab=92.63 E-value=0.22 Score=50.38 Aligned_cols=88 Identities=15% Similarity=0.286 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHhHhccCccceeeeeeccccCccccC-cccchhhHH
Q 040220 114 MWVVTDAILVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFGG-RIDSNLTRL 192 (370)
Q Consensus 114 vW~~il~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~R~ 192 (370)
.|-+-++.+++.++++|+.|.....+-.+..-....+++||..-++++.+ ||+ .|.+|.||+
T Consensus 236 t~YIGFL~LIfsSflVYLaEKd~~~e~~n~~F~TyADALWWG~ITltTIG-----------------YGDk~P~TWlGr~ 298 (654)
T KOG1419|consen 236 TWYIGFLVLIFSSFLVYLAEKDAQGEGTNDEFPTYADALWWGVITLTTIG-----------------YGDKTPQTWLGRL 298 (654)
T ss_pred HHHHHHHHHHHHHHHHHHhhcccccccccccchhHHHHHHhhheeEEeec-----------------cCCcCcccchhHH
Confidence 46666777888899999999874443333333457899999999998775 444 499999999
Q ss_pred HHHHHHHHHHHHHHHhhcCCcccccc
Q 040220 193 VVVVWLFVVLILTSSYTASPSPMLTV 218 (370)
Q Consensus 193 l~~~w~~~~lil~~~Yta~L~s~Lt~ 218 (370)
+.++.-++++-.-+.=.+.|.|=+++
T Consensus 299 laa~fsligiSFFALPAGILGSGfAL 324 (654)
T KOG1419|consen 299 LAACFSLIGISFFALPAGILGSGFAL 324 (654)
T ss_pred HHHHHHHHHHHHHhcccccccchhhh
Confidence 99998888888887777777776664
No 34
>KOG3713 consensus Voltage-gated K+ channel KCNB/KCNC [Inorganic ion transport and metabolism]
Probab=85.19 E-value=1.3 Score=44.43 Aligned_cols=64 Identities=16% Similarity=0.331 Sum_probs=47.7
Q ss_pred HHHHHHHHHhccccCCCCCCCCCCCCccchHHHHHHHhHhccCccceeeeeeccccCccccCc-ccchhhHHHHHHHHHH
Q 040220 122 LVNTRFVVWFPEHQRNSEFNGPRKDQIGTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFGGR-IDSNLTRLVVVVWLFV 200 (370)
Q Consensus 122 ~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~R~l~~~w~~~ 200 (370)
+++.+.++|.+|+-.+.. .-..+--++||++.+|++.| ||+. |++++||++...=.++
T Consensus 356 I~iFStlvY~~Ek~~~~~----~FtSIPa~~WWaiVTMTTVG-----------------YGDm~P~T~~Gklvas~cil~ 414 (477)
T KOG3713|consen 356 IVIFSTLVYFAEKDEPDT----KFTSIPAGFWWAVVTMTTVG-----------------YGDMVPVTVLGKLVASLCILC 414 (477)
T ss_pred HHHHHHHHHHhhhcCCCC----CCccccchhheeeEEEeeec-----------------ccCccccccchHHHHHHHHHH
Confidence 344577889999864332 12346678999999999875 4555 8999999999988888
Q ss_pred HHHHHH
Q 040220 201 VLILTS 206 (370)
Q Consensus 201 ~lil~~ 206 (370)
++++.+
T Consensus 415 GVLvlA 420 (477)
T KOG3713|consen 415 GVLVLA 420 (477)
T ss_pred hHHHhh
Confidence 877776
No 35
>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=84.55 E-value=2.6 Score=39.84 Aligned_cols=63 Identities=13% Similarity=-0.029 Sum_probs=34.4
Q ss_pred HHHh-cCCceEE-EEeh-hhhhhhhccccccCCceeEEEeccccc-ccccceee----ecccccccceEEEEeCCC
Q 040220 32 ESQL-ACKGISI-LFFF-LQLMMRIRHEENFLRNYDSVVGDATIL-ADRAKIVE----FTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 32 ~la~-lg~~~~i-~~~~-~~li~~~~~~~L~~g~~Diai~~~tit-~eR~~~vd----FS~P~~~~~~~ilv~~~~ 99 (370)
.+++ +|++.++ .+.. .+++.+ |.+|++|+++.+.+.. ..+.+..+ +..++......+++++++
T Consensus 20 ~~~k~~Gl~Ve~~~~~~~~~~~~a-----l~~G~iD~~~~~~~~~~~a~~~g~~~~~v~~~~~~~~~~~lv~~~~s 90 (300)
T TIGR01729 20 AAAKEAGATIDWRKFDSGADISTA-----LASGNVPIGVIGSSPLAAAASRGVPIELFWILDNIGKSEALVAREGS 90 (300)
T ss_pred chHHhcCCeeEEEecCcHHHHHHH-----HHcCCCCEeccCCCHHHHHHHCCCCeEEEEEeccCCccceEEecCCC
Confidence 4566 7766553 2222 248888 9999999998654432 22222222 222333334566666544
No 36
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=82.70 E-value=2.2 Score=39.11 Aligned_cols=78 Identities=18% Similarity=0.144 Sum_probs=42.0
Q ss_pred CCceEEeeHHHHHHHHhcCCceEEEEehhhhhhhhccccccCCceeEEEec-------ccccccccceeeecccccccce
Q 040220 19 ENEYDGFCIELYYESQLACKGISILFFFLQLMMRIRHEENFLRNYDSVVGD-------ATILADRAKIVEFTQPCAESRL 91 (370)
Q Consensus 19 ~~~~~G~~idl~~~la~lg~~~~i~~~~~~li~~~~~~~L~~g~~Diai~~-------~tit~eR~~~vdFS~P~~~~~~ 91 (370)
+.+|.|+.=-|...+.+.|+++.+.|-.+. .+|++.|.+|++|+|+.+ +.-..+..-+++|-.--|.+..
T Consensus 23 Sr~YEGLATGl~~~f~~~~ip~~~aymRGa---~~Rie~l~~g~yDfaVvS~lAA~~~i~~~~~l~i~~~fG~~sYvs~H 99 (232)
T PF14503_consen 23 SRRYEGLATGLYEQFEESGIPLNFAYMRGA---ENRIEALKNGRYDFAVVSKLAAEHYIEEGEDLEIVLEFGPGSYVSEH 99 (232)
T ss_dssp SHHHHHHHHHHHCTTT--TS-EEEEE-S-H---HHHHHHHHTTS-SEEEEEHHHHCCCCCC-SSEEEEEE--TTSSS--E
T ss_pred hhhhHHHHHHHHHHhccCCCceEEEeeccc---hHHHHHHHhCCcceEeehHHHHHHHHhhccCeEEEEeeCCCCcccce
Confidence 345667666666555554445554343332 033444999999999987 2223444557888887788888
Q ss_pred EEEEeCCC
Q 040220 92 SMIVPAKT 99 (370)
Q Consensus 92 ~ilv~~~~ 99 (370)
+++.+++.
T Consensus 100 vli~~~~~ 107 (232)
T PF14503_consen 100 VLIFRDGE 107 (232)
T ss_dssp EEEEETT-
T ss_pred EEEEecCC
Confidence 88888765
No 37
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=81.65 E-value=2.6 Score=38.49 Aligned_cols=74 Identities=9% Similarity=0.083 Sum_probs=42.2
Q ss_pred CChHHHHHHhhcccccccchhH--H--HHhh---cccceEEcCCCCCccceeee-----CCcchHHHHHHHHHhhhcCch
Q 040220 243 GSDYNYQGEFGSNHIAGPPYEK--V--FVSQ---YCRIYAATTPTYGFGGLGFL-----SSPIAADFSEAILKLSENKKL 310 (370)
Q Consensus 243 ~~~~~~~~~l~~g~~~a~~~~~--~--~~~~---~c~~~~~~~~~~~~~~~~~a-----~spl~~~in~~i~~l~e~G~~ 310 (370)
.+.+..+++|.+|++|+..... + +... ..+.++++...-....+.++ ....++.+-.++..+..+-.-
T Consensus 144 ~~~~~~~~~l~~G~~Da~~~~~~~~~~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~~~~ 223 (243)
T PF12974_consen 144 GSHDAVLEALLNGKADAAAIPSDAFERLEAEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKDPEG 223 (243)
T ss_dssp E-HHHHHHHHHTTSSSEEEEEHHHHHHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSSHHH
T ss_pred CCHHHHHHHHHcCCccEEEEechhHHHHHHccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCChhh
Confidence 4677889999999999922111 1 1111 23346676543223344444 334788999999998876444
Q ss_pred hHHHHh
Q 040220 311 KSLEYN 316 (370)
Q Consensus 311 ~~l~~~ 316 (370)
.++.+.
T Consensus 224 ~~~l~~ 229 (243)
T PF12974_consen 224 KAILDA 229 (243)
T ss_dssp HHHHHH
T ss_pred HHHHHh
Confidence 444443
No 38
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=73.84 E-value=4.3 Score=44.35 Aligned_cols=52 Identities=10% Similarity=0.295 Sum_probs=43.8
Q ss_pred cchHHHHHHHhHhccCccceeeeeeccccCccccC-cccchhhHHHHHHHHHHHHHHHHHhhcCCccccc
Q 040220 149 GTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFGG-RIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLT 217 (370)
Q Consensus 149 ~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt 217 (370)
..++||++.++++.| ||+ .|.+...|++.++++++++.+.++..+++++.+.
T Consensus 252 i~slYwai~TmtTVG-----------------YGDi~p~t~~E~i~~i~~ml~g~~~~a~~ig~i~~li~ 304 (823)
T PLN03192 252 ISAIYWSITTMTTVG-----------------YGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVV 304 (823)
T ss_pred HHHHHHHHHHHhhcc-----------------CCCcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 347999999998765 233 4899999999999999999999999999998764
No 39
>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=73.82 E-value=9.8 Score=33.64 Aligned_cols=47 Identities=15% Similarity=0.138 Sum_probs=28.2
Q ss_pred hhhhhhccccccCCceeEEEecccccc-cccceee---ecccccccceEEEEeCCC
Q 040220 48 QLMMRIRHEENFLRNYDSVVGDATILA-DRAKIVE---FTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 48 ~li~~~~~~~L~~g~~Diai~~~tit~-eR~~~vd---FS~P~~~~~~~ilv~~~~ 99 (370)
+.+.+ |.+|++|++++....-. .|.+-.+ +-..+......+++++.+
T Consensus 33 ~~~~~-----l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s 83 (216)
T PF09084_consen 33 DVLEA-----LASGKADIAVAGPDAVLFARAKGADIKIIAASYQSSPNALVVRKDS 83 (216)
T ss_dssp HHHHH-----HHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEECCEEEEEETTT
T ss_pred HHHHH-----HhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCCceEEEEeccC
Confidence 37788 99999999998776443 3433332 222333345556666543
No 40
>PRK10537 voltage-gated potassium channel; Provisional
Probab=70.19 E-value=8.3 Score=38.36 Aligned_cols=53 Identities=13% Similarity=0.207 Sum_probs=39.9
Q ss_pred CCCCccchHHHHHHHhHhccCccceeeeeeccccCccccCc-ccchhhHHHHHHHHHHHHHHHHHhhcCCc
Q 040220 144 RKDQIGTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFGGR-IDSNLTRLVVVVWLFVVLILTSSYTASPS 213 (370)
Q Consensus 144 ~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~R~l~~~w~~~~lil~~~Yta~L~ 213 (370)
...++.+++|+++.++.+.+ ||+. |.+..+|++...+.++++.+..+..+.++
T Consensus 165 ~~~s~~dA~y~svvt~tTvG-----------------yGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~ 218 (393)
T PRK10537 165 PIESLSTAFYFSIVTMSTVG-----------------YGDIVPVSESARLFTISVIILGITVFATSISAIF 218 (393)
T ss_pred CCCCHHHHHHhhheeeeccc-----------------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34578899999999888764 2333 78999999999999988877655444443
No 41
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=58.72 E-value=5.4 Score=33.05 Aligned_cols=28 Identities=11% Similarity=0.390 Sum_probs=18.6
Q ss_pred chHHHHHHHHHHHHHHHHHHhccccCCC
Q 040220 111 TWEMWVVTDAILVNTRFVVWFPEHQRNS 138 (370)
Q Consensus 111 ~~~vW~~il~~~~~~~~~~~~~~r~~~~ 138 (370)
+|-+|++++++++++.++++++.+++..
T Consensus 1 RW~l~~iii~~i~l~~~~~~~~~rRR~r 28 (130)
T PF12273_consen 1 RWVLFAIIIVAILLFLFLFYCHNRRRRR 28 (130)
T ss_pred CeeeHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3667888777777777766666655433
No 42
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=56.29 E-value=29 Score=28.41 Aligned_cols=65 Identities=15% Similarity=0.135 Sum_probs=40.9
Q ss_pred eeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.++++.+.+ .. +.++++.. ..++.. |.+|++|++++..... .+.+++ .++....+.++++++.
T Consensus 14 ~l~~~i~~~~~~~p-~i~i~~~~~~~~~~~~~-----l~~g~~D~~i~~~~~~---~~~~~~-~~l~~~~~~~~~~~~~ 82 (197)
T cd05466 14 LLPPLLAAFRQRYP-GVELSLVEGGSSELLEA-----LLEGELDLAIVALPVD---DPGLES-EPLFEEPLVLVVPPDH 82 (197)
T ss_pred HhHHHHHHHHHHCC-CCEEEEEECChHHHHHH-----HHcCCceEEEEcCCCC---CCcceE-eeeeccceEEEecCCC
Confidence 34556666666 43 33343332 237778 9999999999765543 333443 3777888888887664
No 43
>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=56.00 E-value=83 Score=28.68 Aligned_cols=16 Identities=6% Similarity=0.279 Sum_probs=13.5
Q ss_pred ChHHHHHHhhcccccc
Q 040220 244 SDYNYQGEFGSNHIAG 259 (370)
Q Consensus 244 ~~~~~~~~l~~g~~~a 259 (370)
+..+..+++.+|++|+
T Consensus 136 ~~~~~~~al~~g~vda 151 (288)
T TIGR01728 136 GPSDARAAFAAGQVDA 151 (288)
T ss_pred CcHHHHHHHHCCCCCE
Confidence 4567789999999999
No 44
>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=50.31 E-value=41 Score=28.47 Aligned_cols=64 Identities=17% Similarity=0.033 Sum_probs=43.2
Q ss_pred eHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.+++..+.+ .. +.++++. ...++.. |.+|++|++++.... ....+.+ .|+....+.+++++..
T Consensus 21 l~~~l~~~~~~~P-~i~i~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~~---~~~~~~~-~~l~~~~~~~~~~~~~ 88 (209)
T PF03466_consen 21 LPPLLAEFRERHP-NIRIEIREGDSDELIEA-----LRSGELDLAITFGPP---PPPGLES-EPLGEEPLVLVVSPDH 88 (209)
T ss_dssp HHHHHHHHHHHST-TEEEEEEEESHHHHHHH-----HHTTSSSEEEESSSS---SSTTEEE-EEEEEEEEEEEEETTS
T ss_pred HHHHHHHHHHHCC-CcEEEEEeccchhhhHH-----HhcccccEEEEEeec---ccccccc-ccccceeeeeeeeccc
Confidence 3466667766 43 4444333 2348888 999999999886666 3333433 3888999999998765
No 45
>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=46.06 E-value=66 Score=27.18 Aligned_cols=69 Identities=10% Similarity=0.017 Sum_probs=43.0
Q ss_pred EeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+-.+++..+.+ .. +.+++.. ...++.. |.+|++|+++........-.+.+.. .|.......++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~h 85 (202)
T cd08468 13 AVMPRLMARLEELAP-SVRLNLVHAEQKLPLDA-----LLAGEIDFALGYSHDDGAEPRLIEE-RDWWEDTYVVIASRDH 85 (202)
T ss_pred HHhHHHHHHHHhhCC-CCEEEEEECChHhHHHH-----HHCCCccEEEecccccccCCCCEEE-EEEecCcEEEEEeCCC
Confidence 345677777777 53 3344333 2338888 9999999999754322111233444 4778888888887654
No 46
>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=45.86 E-value=28 Score=32.79 Aligned_cols=68 Identities=3% Similarity=-0.098 Sum_probs=40.4
Q ss_pred HHHHHHHHh-cCCceEEEEeh----hhhhhhhccccccCCceeEEEecccccc------------cccceeeeccccccc
Q 040220 27 IELYYESQL-ACKGISILFFF----LQLMMRIRHEENFLRNYDSVVGDATILA------------DRAKIVEFTQPCAES 89 (370)
Q Consensus 27 idl~~~la~-lg~~~~i~~~~----~~li~~~~~~~L~~g~~Diai~~~tit~------------eR~~~vdFS~P~~~~ 89 (370)
.++.+.+++ +| +.+++... ...+.. |.+|++|+++....... .+.+.+....+++..
T Consensus 48 ~~la~~~~~~~~-~i~v~~~~~~~~~~~~~~-----l~~G~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~ 121 (320)
T TIGR02122 48 GAIAQLINKKSG-KLRVRVQSTGGSVENVNL-----LEAGEADLAIVQSDVAYYAYEGDGEFEFEGPVEKLRALASLYPE 121 (320)
T ss_pred HHHHHHHhccCC-CeeEEEEeCcchHHHHHH-----HhCCCCcEEEEcchhHHHHhcCcCccccCCCCccHHhHHHhccc
Confidence 456677777 76 23433332 237778 99999999998743311 112223323355666
Q ss_pred ceEEEEeCCCC
Q 040220 90 RLSMIVPAKTE 100 (370)
Q Consensus 90 ~~~ilv~~~~~ 100 (370)
...+++++..+
T Consensus 122 ~~~lvv~~d~~ 132 (320)
T TIGR02122 122 YIQIVVRKDSG 132 (320)
T ss_pred cEEEEEECCCC
Confidence 77788887654
No 47
>KOG0498 consensus K+-channel ERG and related proteins, contain PAS/PAC sensor domain [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=41.53 E-value=32 Score=36.93 Aligned_cols=53 Identities=13% Similarity=0.170 Sum_probs=44.7
Q ss_pred ccchHHHHHHHhHhccCccceeeeeeccccCcccc-CcccchhhHHHHHHHHHHHHHHHHHhhcCCccccc
Q 040220 148 IGTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFG-GRIDSNLTRLVVVVWLFVVLILTSSYTASPSPMLT 217 (370)
Q Consensus 148 ~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt 217 (370)
...++||++.++.+.|. | ..+...+-.++.++.+++++++.+..-+|+++++.
T Consensus 295 Y~~aLyw~l~tLstvG~-----------------g~~~s~~~~E~iFsi~~mi~GllL~A~lIGNmt~~iq 348 (727)
T KOG0498|consen 295 YVYALYWGLSTLSTVGY-----------------GLVHANNMGEKIFSIFIMLFGLLLFAYLIGNMTALLQ 348 (727)
T ss_pred HHHHHHHHhhHhhhccC-----------------CccCCCCcHHHHHHHHHHHHhHHHHHHHHhhHHHhHH
Confidence 34678999999986643 2 44788888999999999999999999999999985
No 48
>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=40.41 E-value=80 Score=26.13 Aligned_cols=67 Identities=9% Similarity=0.003 Sum_probs=44.0
Q ss_pred EEeeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 23 DGFCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 23 ~G~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
..+-.++++.+.+ .. +.+++... .++... |.+|++|+++...... ...+ -+.|+....+.+++++.
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~~ 81 (196)
T cd08415 12 LSLLPRAIARFRARHP-DVRISLHTLSSSTVVEA-----VLSGQADLGLASLPLD---HPGL-ESEPLASGRAVCVLPPG 81 (196)
T ss_pred ccccHHHHHHHHHHCC-CcEEEEEecchHHHHHH-----HHcCCccEEEEeCCCC---CCcc-eeeeecccceEEEEcCC
Confidence 4556788888887 53 44444332 247777 9999999999754332 2233 35588888888888765
Q ss_pred C
Q 040220 99 T 99 (370)
Q Consensus 99 ~ 99 (370)
.
T Consensus 82 ~ 82 (196)
T cd08415 82 H 82 (196)
T ss_pred C
Confidence 3
No 49
>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=39.61 E-value=85 Score=25.92 Aligned_cols=66 Identities=9% Similarity=0.005 Sum_probs=42.9
Q ss_pred EeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+-.++++.+.+ .. +.++++. ...+... |.+|++|+++..-... .+.+.+. |+....+.++++++.
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~~~~~~~~~~-----L~~~~~Dl~i~~~~~~---~~~~~~~-~l~~~~~~~v~~~~~ 82 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVEYGGKKVEQA-----VLNGELDVGITVLPVD---EEEFDSQ-PLCNEPLVAVLPRGH 82 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEEcCcHHHHHH-----HHcCCCCEEEEecccc---cCCceeE-EeccccEEEEecCCC
Confidence 455677788877 53 4444443 2337788 9999999999754332 2334444 777888888887654
No 50
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=38.05 E-value=68 Score=29.52 Aligned_cols=68 Identities=19% Similarity=0.322 Sum_probs=46.1
Q ss_pred hcCChHHHHHHhhcccccc-----cchhHHHHhhcccceEEcCCCCCccceeee-------------------CCcchHH
Q 040220 241 NFGSDYNYQGEFGSNHIAG-----PPYEKVFVSQYCRIYAATTPTYGFGGLGFL-------------------SSPIAAD 296 (370)
Q Consensus 241 ~~~~~~~~~~~l~~g~~~a-----~~~~~~~~~~~c~~~~~~~~~~~~~~~~~a-------------------~spl~~~ 296 (370)
.|.+..+.-++|.+|.+|+ .+|++-+.+++-.++..+++.+ ..++|+. +.| ..
T Consensus 32 ~f~D~~~~N~AL~~G~iDaN~fQh~~yl~~~n~~~~~~L~~v~~~~-~~p~glYS~k~~sl~~lp~Ga~VaIpnD~--sN 108 (237)
T PF03180_consen 32 EFSDYVQPNEALADGEIDANFFQHIPYLEQFNKENGYNLVPVGPTY-IEPMGLYSKKYKSLDDLPDGATVAIPNDP--SN 108 (237)
T ss_dssp EESSTTHHHHHHHTTSSSEEEEEEHHHHHHHHHHHT--EEEEEEEE-E---EEEESSSSSGGGS-TTEEEEEESSH--HH
T ss_pred EecchhhcChHHHCCCcceeccCCHHHHHHHHHHCCCcEEEeccee-EEeEEEeecccCchhhcCCCCEEEEeCCc--cc
Confidence 5778888899999999999 5666666655554576666543 3445554 222 36
Q ss_pred HHHHHHHhhhcCchh
Q 040220 297 FSEAILKLSENKKLK 311 (370)
Q Consensus 297 in~~i~~l~e~G~~~ 311 (370)
..++|.-|++.|++.
T Consensus 109 ~~RaL~lLq~aGLI~ 123 (237)
T PF03180_consen 109 QARALKLLQEAGLIT 123 (237)
T ss_dssp HHHHHHHHHHTTSEE
T ss_pred hhHHHHHHHhCCeEE
Confidence 778999999999885
No 51
>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=37.02 E-value=1.2e+02 Score=25.79 Aligned_cols=66 Identities=15% Similarity=0.099 Sum_probs=43.3
Q ss_pred EeeHHHHHHHHh-cCCceEEEEeh----hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 24 GFCIELYYESQL-ACKGISILFFF----LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~~----~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
.+-.+++..+.+ .. +.+++..- ..+... |.+|++|+++..-.. ..+.+++ .|+......++++++
T Consensus 13 ~~~~~~l~~~~~~~P-~~~v~~~~~~~~~~l~~~-----L~~g~lDl~i~~~~~---~~~~l~~-~~l~~~~~~lv~~~~ 82 (203)
T cd08463 13 LFLPELVARFRREAP-GARLEIHPLGPDFDYERA-----LASGELDLVIGNWPE---PPEHLHL-SPLFSDEIVCLMRAD 82 (203)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEeCCcchhHHHH-----HhcCCeeEEEecccc---CCCCcEE-eEeecCceEEEEeCC
Confidence 455677777777 53 34444431 347888 999999999974222 1233555 478888999888876
Q ss_pred C
Q 040220 99 T 99 (370)
Q Consensus 99 ~ 99 (370)
.
T Consensus 83 h 83 (203)
T cd08463 83 H 83 (203)
T ss_pred C
Confidence 4
No 52
>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=36.71 E-value=97 Score=25.50 Aligned_cols=66 Identities=15% Similarity=-0.014 Sum_probs=40.8
Q ss_pred eeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.++++.+.+ .. +.++++.. .++... |.+|++|+++..... +..+.+.+ .+.....+.++++.+.
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~i~~~~~~~~~~~-----l~~~~~Dl~i~~~~~--~~~~~~~~-~~l~~~~~~~~~~~~~ 83 (194)
T cd08436 14 DLPELLARFHRRHP-GVDIRLRQAGSDDLLAA-----VREGRLDLAFVGLPE--RRPPGLAS-RELAREPLVAVVAPDH 83 (194)
T ss_pred HHHHHHHHHHHHCC-CcEEEEecCCHHHHHHH-----HHcCCccEEEEecCC--CCCCCcEE-EEeecceEEEEecCCC
Confidence 34556666666 43 33444432 237778 999999999975433 23333444 4777888888877654
No 53
>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=35.90 E-value=1.1e+02 Score=25.21 Aligned_cols=67 Identities=10% Similarity=0.011 Sum_probs=42.3
Q ss_pred EEeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 23 DGFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 23 ~G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
..+-.+++..+.+ .. +.+++.. ..++... |.+|++|+++..-. .....+.. .+.....+.+++++.
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~g~~Dl~i~~~~---~~~~~~~~-~~l~~~~~~~v~~~~ 81 (193)
T cd08442 12 AVRLPPLLAAYHARYP-KVDLSLSTGTTGALIQA-----VLEGRLDGAFVAGP---VEHPRLEQ-EPVFQEELVLVSPKG 81 (193)
T ss_pred hhhhHHHHHHHHHHCC-CceEEEEeCCcHHHHHH-----HHCCCccEEEEeCC---CCCCCcEE-EEeecCcEEEEecCC
Confidence 3445677788777 53 3333333 2347788 99999999986432 22333433 377788888888765
Q ss_pred C
Q 040220 99 T 99 (370)
Q Consensus 99 ~ 99 (370)
.
T Consensus 82 ~ 82 (193)
T cd08442 82 H 82 (193)
T ss_pred C
Confidence 4
No 54
>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=35.90 E-value=1e+02 Score=25.87 Aligned_cols=63 Identities=13% Similarity=-0.011 Sum_probs=39.1
Q ss_pred HHHHHHHHh-cCCceEEEEeh--hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 27 IELYYESQL-ACKGISILFFF--LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 27 idl~~~la~-lg~~~~i~~~~--~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+++..+.+ .. +.+++..- .+++.. |.+|++|+++..-.... ..+.. .|+....+.++++++.
T Consensus 16 ~~~i~~~~~~~P-~i~l~i~~~~~~~~~~-----l~~g~~D~~i~~~~~~~---~~~~~-~~l~~~~~~~v~~~~h 81 (200)
T cd08462 16 PPVIERVAREAP-GVRFELLPPDDQPHEL-----LERGEVDLLIAPERFMS---DGHPS-EPLFEEEFVCVVWADN 81 (200)
T ss_pred HHHHHHHHHHCC-CCEEEEecCChhHHHH-----HhcCCeeEEEecCCCCC---CCcee-eeeeccceEEEEcCCC
Confidence 456666666 43 33333321 257888 99999999997432222 23443 3788888888887654
No 55
>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=35.88 E-value=1e+02 Score=25.47 Aligned_cols=64 Identities=9% Similarity=-0.055 Sum_probs=40.3
Q ss_pred eHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.+++..+.+ .. +.++++. ..++... |.+|++|+++...... .+.+.+ .|+....+.+++++..
T Consensus 15 l~~~l~~~~~~~p-~i~i~i~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~~v~~~~~ 82 (197)
T cd08414 15 LPRLLRRFRARYP-DVELELREMTTAEQLEA-----LRAGRLDVGFVRPPPD---PPGLAS-RPLLREPLVVALPADH 82 (197)
T ss_pred HHHHHHHHHHHCC-CcEEEEecCChHHHHHH-----HHcCCccEEEEcCCCC---CCCeeE-EEEeeccEEEEecCCC
Confidence 3456666666 43 3444443 2347788 9999999999753322 233433 4788888888887654
No 56
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=35.25 E-value=1.1e+02 Score=25.53 Aligned_cols=67 Identities=10% Similarity=0.039 Sum_probs=42.3
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.++++. ..++... |.+|++|+++.... ...+.+.+++ .+.....+.++++.+.
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~-~~~~~~~l~~-~~l~~~~~~~~~~~~h 84 (198)
T cd08437 14 YFPKLAKDLIKTGL-MIQIDTYEGGSAELLEQ-----LLQGDLDIALLGSL-TPLENSALHS-KIIKTQHFMIIVSKDH 84 (198)
T ss_pred HhHHHHHHHHHhCC-ceEEEEEEcCHHHHHHH-----HHcCCCCEEEecCC-CCCCcccceE-EEeecceEEEEecCCC
Confidence 34566777777 43 4444443 2337888 99999999996421 1122344554 4788888888887654
No 57
>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=35.08 E-value=1.2e+02 Score=25.24 Aligned_cols=68 Identities=13% Similarity=-0.018 Sum_probs=40.5
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++.. ..++... |.+|++|+++..-....+....++ +.|.....+.+++++..
T Consensus 14 ~l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~g~~D~~i~~~~~~~~~~~~~~-~~~l~~~~~~~v~~~~h 85 (200)
T cd08453 14 VLPELVRRFREAYP-DVELQLREATSDVQLEA-----LLAGEIDAGIVIPPPGASAPPALA-YRPLLSEPLVLAVPAAW 85 (200)
T ss_pred HHHHHHHHHHHhCC-CceEEEEeCCHHHHHHH-----HHcCCCCEEEEecCcccCCCccee-EEEeeeCceEEEEECCC
Confidence 34566667766 43 3333333 2337788 999999999864322211123343 34777888888887654
No 58
>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=34.97 E-value=1.2e+02 Score=25.30 Aligned_cols=65 Identities=17% Similarity=0.011 Sum_probs=40.2
Q ss_pred eeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++... .++... |.+|++|+++.... .....+.. .|+....+.++++++.
T Consensus 14 ~l~~~l~~f~~~~P-~v~l~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~---~~~~~~~~-~~l~~~~~~lv~~~~~ 82 (200)
T cd08466 14 LLPRLLARLKQLAP-NISLRESPSSEEDLFED-----LRLQEVDLVIDYVP---FRDPSFKS-ELLFEDELVCVARKDH 82 (200)
T ss_pred HHHHHHHHHHHHCC-CCEEEEecCchHhHHHH-----HHcCCccEEEeccc---CCCCCcee-eeecccceEEEEeCCC
Confidence 34566666666 43 33333332 247788 99999999996422 22233433 4788889999888654
No 59
>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=34.93 E-value=93 Score=25.88 Aligned_cols=66 Identities=12% Similarity=0.023 Sum_probs=41.1
Q ss_pred EeeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
++-.+++..+.+ .. +.+++... ..+... |.+|++|+++..... ....+. +.++....+.++++.+.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~i~~~~~~~~~~~-----l~~~~~Di~i~~~~~---~~~~~~-~~~l~~~~~~lv~~~~~ 82 (198)
T cd08461 13 AILPPLLAALRQEAP-GVRVAIRDLESDNLEAQ-----LERGEVDLALTTPEY---APDGLR-SRPLFEERYVCVTRRGH 82 (198)
T ss_pred HHhHHHHHHHHHHCC-CcEEEEeeCCcccHHHH-----HhcCCCcEEEecCcc---CCccce-eeeeecCcEEEEEcCCC
Confidence 344667777777 43 33444432 237777 999999999864322 222333 45788888888887654
No 60
>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=34.85 E-value=1.1e+02 Score=25.44 Aligned_cols=65 Identities=18% Similarity=0.126 Sum_probs=40.7
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.++++. ...+... |.+|++|+++..... ....+++ .++....+.++++++.
T Consensus 15 ~l~~~l~~~~~~~P-~v~i~i~~~~~~~~~~~-----l~~g~~Dl~i~~~~~---~~~~~~~-~~l~~~~~~~v~~~~~ 83 (197)
T cd08425 15 LIGPLIDRFHARYP-GIALSLREMPQERIEAA-----LADDRLDLGIAFAPV---RSPDIDA-QPLFDERLALVVGATH 83 (197)
T ss_pred hhHHHHHHHHHHCC-CcEEEEEECcHHHHHHH-----HHcCCccEEEEecCC---CCCCcEE-EEeccccEEEEecCCC
Confidence 34567777776 43 3333332 2337778 999999999964332 2233433 4788888888887654
No 61
>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=34.70 E-value=1.1e+02 Score=25.11 Aligned_cols=65 Identities=12% Similarity=0.090 Sum_probs=40.0
Q ss_pred eeHHHHHHHHh-cCCceEEEEehh---hhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFFFL---QLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~~---~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-..++..+.+ .. +.+++.... .+..+ +.+|++|+++..... ..+.+++ .++....+.+++++..
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~i~~~~~~~~~~~-----l~~~~~Dl~i~~~~~---~~~~l~~-~~l~~~~~~~v~~~~~ 82 (195)
T cd08434 14 LVPDLIRAFRKEYP-NVTFELHQGSTDELLDD-----LKNGELDLALCSPVP---DEPDIEW-IPLFTEELVLVVPKDH 82 (195)
T ss_pred hhHHHHHHHHHhCC-CeEEEEecCcHHHHHHH-----HHcCCccEEEEccCC---CCCCeeE-EEeecceEEEEecCCC
Confidence 34456666666 42 333433322 26777 999999999865332 2344444 3788888888887654
No 62
>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=34.53 E-value=1.1e+02 Score=25.37 Aligned_cols=64 Identities=8% Similarity=-0.034 Sum_probs=40.3
Q ss_pred eHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.+++..+.+ .. +.+++.. ..++... |.+|++|+++....... ..++ +.+.....+.++++++.
T Consensus 15 l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~~~~D~~i~~~~~~~---~~~~-~~~l~~~~~~~v~~~~h 82 (199)
T cd08426 15 LPSLIARFRQRYP-GVFFTVDVASTADVLEA-----VLSGEADIGLAFSPPPE---PGIR-VHSRQPAPIGAVVPPGH 82 (199)
T ss_pred HHHHHHHHHHhCC-CeEEEEEeCCcHHHHHH-----HHCCCccEEEecCCCCC---CCeE-EEeeccCcEEEEecCCC
Confidence 3456666666 43 4444443 2337788 99999999997433322 2344 35788888888887654
No 63
>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=34.43 E-value=1.1e+02 Score=25.22 Aligned_cols=65 Identities=8% Similarity=-0.061 Sum_probs=41.2
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++.. ..++... +.+|++|+++..-. .....+++ .++....+.+++++..
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~i~~~~~~~~~~~-----l~~~~~Di~i~~~~---~~~~~~~~-~~l~~~~~~~~~~~~h 82 (197)
T cd08448 14 GLPRILRAFRAEYP-GIEVALHEMSSAEQIEA-----LLRGELDLGFVHSR---RLPAGLSA-RLLHREPFVCCLPAGH 82 (197)
T ss_pred HHHHHHHHHHHHCC-CCeEEEEeCCHHHHHHH-----HHcCCcceEEEeCC---CCCcCceE-EEEecCcEEEEeeCCC
Confidence 44567777777 53 3344433 3337777 99999999986432 22333444 4788888888877654
No 64
>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=34.05 E-value=1.2e+02 Score=24.94 Aligned_cols=66 Identities=14% Similarity=0.089 Sum_probs=42.2
Q ss_pred EeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+-.+++..+.+ .. +.+++.. ..++... |.+|++|+++...... .+.+.+ .|.....+.++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~~~l~~~~~~~~~~~~~-----l~~g~~D~~i~~~~~~---~~~~~~-~~l~~~~~~~v~~~~~ 82 (201)
T cd08420 13 YLLPRLLARFRKRYP-EVRVSLTIGNTEEIAER-----VLDGEIDLGLVEGPVD---HPDLIV-EPFAEDELVLVVPPDH 82 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEeCCcHHHHHH-----HHCCCccEEEecCCCC---CcceEE-EeecCccEEEEecCCC
Confidence 445677777777 43 3333333 2337788 9999999999754332 233433 4788888888887654
No 65
>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=33.89 E-value=92 Score=26.32 Aligned_cols=66 Identities=15% Similarity=0.044 Sum_probs=41.6
Q ss_pred EeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
++-.+++..+.+ .. +.+++.. ...++.. |.+|++|+++...... ...++.. |.....+.++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~i~l~i~~~~~~~~~~~-----L~~g~~Dl~i~~~~~~---~~~~~~~-~l~~~~~~lv~~~~h 82 (200)
T cd08465 13 LVLPALMRQLRAEAP-GIDLAVSQASREAMLAQ-----VADGEIDLALGVFPEL---PEELHAE-TLFEERFVCLADRAT 82 (200)
T ss_pred HhhhHHHHHHHHHCC-CcEEEEecCChHhHHHH-----HHCCCccEEEeccccC---CcCeeEE-EeeeccEEEEEeCCC
Confidence 344566777766 43 4444433 3348888 9999999999643322 2334443 677788888887654
No 66
>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=33.82 E-value=1.4e+02 Score=25.10 Aligned_cols=66 Identities=20% Similarity=0.106 Sum_probs=41.4
Q ss_pred EeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
++-.+++..+.+ .. +.+++.. ..+++.. |.+|++|++++..... ...+.. .|+....+.++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~~v~~~~h 83 (203)
T cd08445 14 GLLPELIRRFRQAAP-DVEIELIEMTTVQQIEA-----LKEGRIDVGFGRLRIE---DPAIRR-IVLREEPLVVALPAGH 83 (203)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEeCChHHHHHH-----HHcCCCcEEEecCCCC---CCCcee-EEEEeccEEEEeeCCC
Confidence 345566777776 43 4444443 2347788 9999999999643222 223433 3778888888887654
No 67
>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=32.77 E-value=1.1e+02 Score=25.19 Aligned_cols=65 Identities=15% Similarity=0.086 Sum_probs=40.2
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++.. ...+..+ |.+|++|+++....... ..+ -+.++....+.++++.+.
T Consensus 13 ~l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~~~~~~~ 81 (197)
T cd08419 13 FAPRLLGAFCRRHP-GVEVSLRVGNREQVLER-----LADNEDDLAIMGRPPED---LDL-VAEPFLDNPLVVIAPPDH 81 (197)
T ss_pred HhhHHHHHHHHHCC-CceEEEEECCHHHHHHH-----HhcCCccEEEecCCCCC---CCe-EEEEeccCCEEEEecCCC
Confidence 44566666666 43 3334333 2237778 99999999996433221 223 345788888888887654
No 68
>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=32.20 E-value=1.4e+02 Score=24.52 Aligned_cols=66 Identities=14% Similarity=0.120 Sum_probs=42.3
Q ss_pred EeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+-.++++.+.+ .. +.+++.. ..++... |.+|++|+++..... ....+.. .++....+.+++++..
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~~~~~~~~~~-----l~~g~~D~~i~~~~~---~~~~~~~-~~l~~~~~~~~~~~~~ 82 (197)
T cd08440 13 TLLPPVLAAFRRRHP-GIRVRLRDVSAEQVIEA-----VRSGEVDFGIGSEPE---ADPDLEF-EPLLRDPFVLVCPKDH 82 (197)
T ss_pred hHHHHHHHHHHHhCC-CcEEEEEeCChHHHHHH-----HHcCCccEEEEeCCC---CCCCeeE-EEeecccEEEEecCCC
Confidence 445677777777 53 4444333 3347788 999999999975332 2233433 4778888888887654
No 69
>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=32.00 E-value=1.4e+02 Score=24.65 Aligned_cols=68 Identities=10% Similarity=0.010 Sum_probs=41.4
Q ss_pred eeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEeccccc--ccccceeeecccccccceEEEEeCC
Q 040220 25 FCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATIL--ADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit--~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
+-.+++..+.+ .. +.+++... ..+... |.+|++|+++..-... ....+.+. +.+.......+++++.
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~~~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~ 86 (200)
T cd08423 14 LLPPALAALRARHP-GLEVRLREAEPPESLDA-----LRAGELDLAVVFDYPVTPPPDDPGLT-RVPLLDDPLDLVLPAD 86 (200)
T ss_pred hhhHHHHHHHHhCC-CCeEEEEeCCHHHHHHH-----HhcCCccEEEEeccccccCCCCCCcE-EEEeccCcEEEEecCC
Confidence 34566677776 43 33444432 237788 9999999999642211 12233443 4578888888888765
Q ss_pred C
Q 040220 99 T 99 (370)
Q Consensus 99 ~ 99 (370)
.
T Consensus 87 ~ 87 (200)
T cd08423 87 H 87 (200)
T ss_pred C
Confidence 4
No 70
>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=31.84 E-value=1.1e+02 Score=25.20 Aligned_cols=66 Identities=8% Similarity=-0.096 Sum_probs=40.2
Q ss_pred EeeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+-.+++..+.+ .. +.+++... ..+..+ |.+|++|+++...... ...+. +.+.....+.++++...
T Consensus 13 ~~l~~~l~~~~~~~P-~i~~~i~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~~~~~ 82 (196)
T cd08456 13 SFLPRAIKAFLQRHP-DVTISIHTRDSPTVEQW-----LSAQQCDLGLVSTLHE---PPGIE-RERLLRIDGVCVLPPGH 82 (196)
T ss_pred hhHHHHHHHHHHHCC-CcEEEEEeCCHHHHHHH-----HHcCCccEEEEecCCC---CCCee-EEEeeccCeEEEecCCC
Confidence 344567777777 53 33443432 226777 9999999999643222 22333 44777788888776543
No 71
>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=31.48 E-value=1.7e+02 Score=24.11 Aligned_cols=66 Identities=8% Similarity=-0.042 Sum_probs=40.3
Q ss_pred eHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.+++..+.+ .. +.+++.. ..++... |.+|++|+++...... .+.+.+.+ .|+....+.++++++.
T Consensus 15 l~~~l~~~~~~~P-~v~i~i~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~-~~~~~~~~-~~l~~~~~~~~~~~~~ 84 (201)
T cd08435 15 LPPAIARLLARHP-RLTVRVVEGTSDELLEG-----LRAGELDLAIGRLADD-EQPPDLAS-EELADEPLVVVARPGH 84 (201)
T ss_pred HHHHHHHHHHHCC-CeEEEEEeCCHHHHHHH-----HHcCCccEEEEecCcc-cCCCCcEE-EEcccCcEEEEEeCCC
Confidence 3556666666 43 3344333 2337777 9999999998643211 12333444 4888888998887654
No 72
>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=30.97 E-value=1.2e+02 Score=25.20 Aligned_cols=65 Identities=11% Similarity=0.034 Sum_probs=40.4
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++.. ...++.. |.+|++|+++..-... ...+.+. ++....+.++++++.
T Consensus 15 ~l~~~l~~~~~~~P-~i~i~i~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~---~~~~~~~-~l~~~~~~~v~~~~~ 83 (200)
T cd08411 15 LLPRLLPALRQAYP-KLRLYLREDQTERLLEK-----LRSGELDAALLALPVD---EPGLEEE-PLFDEPFLLAVPKDH 83 (200)
T ss_pred hhHHHHHHHHHHCC-CcEEEEEeCcHHHHHHH-----HHcCCccEEEEeccCC---CCCceEE-EeeccceEEEecCCC
Confidence 44566667766 53 4444443 2347788 9999999999643222 2334333 677888888887654
No 73
>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=30.90 E-value=1.4e+02 Score=24.68 Aligned_cols=66 Identities=11% Similarity=0.022 Sum_probs=41.4
Q ss_pred eeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.++++.+.+ .. +.+++... ..+... |.+|++|+++...... ....+ -+.|.+...+.++++.+.
T Consensus 15 ~l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~~~~ 84 (199)
T cd08451 15 LVPGLIRRFREAYP-DVELTLEEANTAELLEA-----LREGRLDAAFVRPPVA--RSDGL-VLELLLEEPMLVALPAGH 84 (199)
T ss_pred ccHHHHHHHHHHCC-CcEEEEecCChHHHHHH-----HHCCCccEEEEecCCC--CCCce-eEEEeecccEEEEecCCC
Confidence 55677788777 43 33444432 236778 9999999999643322 12223 335788888888886543
No 74
>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=30.74 E-value=1.5e+02 Score=24.74 Aligned_cols=65 Identities=18% Similarity=0.006 Sum_probs=41.4
Q ss_pred eeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.++++.. .++... |.+|++|+++...... ...+. +.|.....+.++++++.
T Consensus 14 ~l~~~l~~~~~~~P-~v~v~i~~~~~~~~~~~-----l~~g~~D~~i~~~~~~---~~~l~-~~~l~~~~~~~v~~~~~ 82 (201)
T cd08459 14 FLPRLLAALREVAP-GVRIETVRLPVDELEEA-----LESGEIDLAIGYLPDL---GAGFF-QQRLFRERYVCLVRKDH 82 (201)
T ss_pred HHHHHHHHHHHHCC-CCeEEEEecCccCHHHH-----hhCCCceEEEEcCCCC---cccce-EEEeecCceEEEEcCCC
Confidence 34566777776 43 33443332 237778 9999999999754322 23344 45888888888887654
No 75
>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=30.64 E-value=1.5e+02 Score=25.33 Aligned_cols=65 Identities=15% Similarity=0.043 Sum_probs=40.8
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.++++. ...+... |.+|++|++++... ...+.+.+ .|.....+.++++++.
T Consensus 14 ~l~~~l~~f~~~~P-~v~l~i~~~~~~~~~~~-----l~~g~~Di~i~~~~---~~~~~l~~-~~l~~~~~~~v~~~~~ 82 (221)
T cd08469 14 LLPALVRRLETEAP-GIDLRIRPVTRLDLAEQ-----LDLGRIDLVIGIFE---QIPPRFRR-RTLFDEDEVWVMRKDH 82 (221)
T ss_pred HHHHHHHHHHHHCC-CcEEEEeeCChhhHHHH-----HHCCCccEEEecCC---CCCcccee-eeeeccceEEEEeCCC
Confidence 34556666666 43 3334333 2237778 99999999997432 22234544 4888888888887654
No 76
>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=30.22 E-value=1.5e+02 Score=24.47 Aligned_cols=65 Identities=14% Similarity=0.054 Sum_probs=40.4
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.++++.+.+ .. +.+++.. ..++... |.+|++|+++...... ...++ +.+.....+.++++.+.
T Consensus 14 ~l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~~~~~ 82 (196)
T cd08450 14 WLPEVLPILREEHP-DLDVELSSLFSPQLAEA-----LMRGKLDVAFMRPEIQ---SDGID-YQLLLKEPLIVVLPADH 82 (196)
T ss_pred hHHHHHHHHHhhCC-CcEEEEEecChHHHHHH-----HhcCCccEEEEeCCCC---CCCcE-EEEEEccceEEEecCCC
Confidence 44566677776 43 4444433 2237778 9999999999643222 23343 34778888888887654
No 77
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=30.13 E-value=4.1e+02 Score=23.93 Aligned_cols=61 Identities=8% Similarity=-0.032 Sum_probs=35.5
Q ss_pred HHh-cCCceEEE-Ee-hhhhhhhhccccccCCceeEEEe--cccccccccc-----eeeecccccccceEEEEeCC
Q 040220 33 SQL-ACKGISIL-FF-FLQLMMRIRHEENFLRNYDSVVG--DATILADRAK-----IVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 33 la~-lg~~~~i~-~~-~~~li~~~~~~~L~~g~~Diai~--~~tit~eR~~-----~vdFS~P~~~~~~~ilv~~~ 98 (370)
+-+ .|++.++. +. -.+++.+ |.+|++|++.. ++..-..+-. .+.........+..++++.+
T Consensus 29 ~f~~~G~~ve~~~~~~g~~~~~a-----l~~G~iD~a~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~g~~lvv~~~ 99 (252)
T PF13379_consen 29 LFEKEGLDVEWVQFASGADILEA-----LAAGEIDIAFVLAPALIAIAKGAGGPDVDIVVLAGLSQNGNALVVRND 99 (252)
T ss_dssp HHHHTTSCEEEEEESSHHHHHHH-----HHCTSSSEEEECTHHHHHHHTTTTT----EEEEEECSBSSEEEEECGG
T ss_pred hHHHcCCEEEEEEcCCHHHHHHH-----HHcCCCCEEEechHHHHHHHcCCCCcccceEEeeccCCCceEEEEcCc
Confidence 444 66665421 22 2338888 99999999988 2222233333 23333345667788888864
No 78
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=30.12 E-value=2.2e+02 Score=27.02 Aligned_cols=15 Identities=13% Similarity=0.164 Sum_probs=13.2
Q ss_pred hHHHHHHhhcccccc
Q 040220 245 DYNYQGEFGSNHIAG 259 (370)
Q Consensus 245 ~~~~~~~l~~g~~~a 259 (370)
..+...++.+|++|+
T Consensus 158 ~~~~~~Al~~G~VDA 172 (320)
T PRK11480 158 PPAIIAAWQRGDIDG 172 (320)
T ss_pred cHHHHHHHHcCCcCE
Confidence 567889999999998
No 79
>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=30.09 E-value=1.2e+02 Score=25.52 Aligned_cols=64 Identities=9% Similarity=-0.107 Sum_probs=38.9
Q ss_pred eHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.+++..+.+ .. +.+++.. ...++.. |.+|++|+++..-. . ....++ +.|.....+.++++++.
T Consensus 16 l~~~l~~f~~~~P-~v~i~i~~~~~~~l~~~-----l~~g~~D~~~~~~~--~-~~~~~~-~~~l~~~~~~lv~~~~h 83 (198)
T cd08486 16 LPLLLRAFLTSTP-TATVSLTHMTKDEQVEG-----LLAGTIHVGFSRFF--P-RHPGIE-IVNIAQEDLYLAVHRSQ 83 (198)
T ss_pred HHHHHHHHHHhCC-CeEEEEEECCHHHHHHH-----HHcCCceEEEecCC--C-CCCceE-EEEEeeccEEEEecCCC
Confidence 3455666665 43 3333333 2338888 99999999996422 1 223344 34677788888887654
No 80
>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=29.96 E-value=1.5e+02 Score=24.58 Aligned_cols=65 Identities=17% Similarity=0.082 Sum_probs=41.9
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++.. ..+++.. |.+|++|+++..-.. ..+.+.+ .|.....+.++++++.
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~~~~~~~~~~~~~-----l~~~~~D~~i~~~~~---~~~~~~~-~~l~~~~~~~v~~~~~ 82 (198)
T cd08421 14 FLPEDLASFLAAHP-DVRIDLEERLSADIVRA-----VAEGRADLGIVAGNV---DAAGLET-RPYRTDRLVVVVPRDH 82 (198)
T ss_pred hhHHHHHHHHHHCC-CceEEEEecCcHHHHHH-----HhcCCceEEEEecCC---CCCCcEE-EEeecCcEEEEeCCCC
Confidence 34567777777 43 3333332 2347788 999999999974332 3344544 5788888888887654
No 81
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=29.75 E-value=1.1e+02 Score=28.29 Aligned_cols=64 Identities=9% Similarity=-0.045 Sum_probs=39.7
Q ss_pred eHHHHHHHHh-cCCceEEEE---ehhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILF---FFLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~---~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.+++..+.+ .. +.+++. ...+++.. |.+|++|++++...... ..+. ..|+....+.++++.+.
T Consensus 104 l~~~l~~f~~~~P-~v~v~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~~---~~l~-~~~l~~~~~~~v~~~~~ 171 (275)
T PRK03601 104 LTPWLGRLYQNQE-ALQFEARIAQRQSLVKQ-----LHERQLDLLITTEAPKM---DEFS-SQLLGHFTLALYTSAPS 171 (275)
T ss_pred HHHHHHHHHHhCC-CcEEEEEECChHHHHHH-----HHcCCCCEEEEcCCCcc---CCcc-EEEecceeEEEEecCch
Confidence 3445555555 21 333333 23348888 99999999997544332 2343 44888999988887654
No 82
>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=29.61 E-value=1.7e+02 Score=24.23 Aligned_cols=67 Identities=12% Similarity=0.027 Sum_probs=40.9
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.++++. ..++... |.+|++|++++..... .....+.+ .|.....+.++++.+.
T Consensus 14 ~l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~-~~~~~~~~-~~l~~~~~~~v~~~~~ 84 (201)
T cd08418 14 LMPAVINRFKEQFP-DVQISIYEGQLSSLLPE-----LRDGRLDFAIGTLPDE-MYLKELIS-EPLFESDFVVVARKDH 84 (201)
T ss_pred hhHHHHHHHHHHCC-CceEEEEeCcHHHHHHH-----HHcCCCcEEEEecCCC-CCCcceeE-EeecCCceEEEeCCCC
Confidence 34566666666 43 3334333 2347788 9999999999743221 11233444 4778888888887654
No 83
>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=29.48 E-value=1.4e+02 Score=25.52 Aligned_cols=68 Identities=15% Similarity=0.089 Sum_probs=38.6
Q ss_pred EeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 24 GFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
.+-.++++.+.+ .. +.+++.. ..+++.. |.+|++|+++.......+-...+. +.|.....+.++++.+
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~~~~~~~~~~-----L~~~~~D~~i~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~ 84 (204)
T cd08429 13 SIAYRLLEPAMDLHE-PIRLVCREGKLEQLLAD-----LALHRLDMVLADRPMPSSLDVKGY-SHRLGECGVSFFAAPP 84 (204)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEeCCHHHHHHH-----HHcCCccEEEecCCCccccchhee-eccccccceEEEecCC
Confidence 344566677666 43 3333332 2338888 999999999964332211011222 3477777777776543
No 84
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=29.00 E-value=1.5e+02 Score=27.47 Aligned_cols=67 Identities=4% Similarity=-0.023 Sum_probs=42.0
Q ss_pred eeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ -. +.++++.. .++... |.+|++|+++....-. .....+.+ .|+....+.++++++.
T Consensus 109 ~l~~~l~~~~~~~p-~i~~~~~~~~~~~~~~~-----l~~g~~Di~i~~~~~~-~~~~~~~~-~~l~~~~~~l~~~~~~ 179 (302)
T PRK09791 109 LMPAVISRFHQQHP-QVKVRIMEGQLVSMINE-----LRQGELDFTINTYYQG-PYDHEFTF-EKLLEKQFAVFCRPGH 179 (302)
T ss_pred hhHHHHHHHHHHCC-CeEEEEEeCChHHHHHH-----HHCCCccEEEEecCCc-ccccceeE-EEeccceEEEEEcCCC
Confidence 44566666666 43 44444443 348888 9999999998732111 11233555 5888999999987654
No 85
>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=28.97 E-value=1.7e+02 Score=24.13 Aligned_cols=68 Identities=15% Similarity=0.065 Sum_probs=41.7
Q ss_pred EeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
++-.+++..+.+ .. +.+++.. ..++... |.+|++|+++...... .....++ +.++....+.+++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~-~~~~~l~-~~~l~~~~~~~v~~~~h 84 (199)
T cd08416 13 NTVPRIIMGLKLRRP-ELDIELTLGSNKDLLKK-----LKDGELDAILVATPEG-LNDPDFE-VVPLFEDDIFLAVPATS 84 (199)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEEEcCcHHHHHH-----HhCCCCCEEEEecCCc-CCCCCeE-EEEeecceEEEEECCCC
Confidence 345667777777 53 4444443 2236777 9999999999753321 1222233 44778888888887654
No 86
>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=28.84 E-value=1.5e+02 Score=24.92 Aligned_cols=67 Identities=10% Similarity=0.016 Sum_probs=42.5
Q ss_pred EeeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+-.+++..+.+ .. +.+++... ..+... |.+|++|+++..-... ....+.+ .+.....+.++++.+.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~~~~~~~~~~-----l~~g~~D~~i~~~~~~--~~~~~~~-~~l~~~~~~~v~~~~h 83 (198)
T cd08413 13 YVLPPVIAAFRKRYP-KVKLSLHQGTPSQIAEM-----VLKGEADIAIATEALD--DHPDLVT-LPCYRWNHCVIVPPGH 83 (198)
T ss_pred hhccHHHHHHHHhCC-ceEEEEEeCCHHHHHHH-----HHcCCCCEEEEccCCC--CCCCcEE-EEeeeeeEEEEecCCC
Confidence 345677788877 53 43444432 237788 9999999999643221 1223443 5788888888887654
No 87
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=28.67 E-value=1.3e+02 Score=27.65 Aligned_cols=65 Identities=15% Similarity=0.078 Sum_probs=41.2
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++.. ...++.. |.+|++|+++..... +.+.+. +.++....+.++++++.
T Consensus 105 ~l~~~l~~~~~~~p-~~~i~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~~---~~~~l~-~~~l~~~~~~~~~~~~~ 173 (296)
T PRK11242 105 LIGPLIDAFHARYP-GITLTIREMSQERIEAL-----LADDELDVGIAFAPV---HSPEIE-AQPLFTETLALVVGRHH 173 (296)
T ss_pred hhHHHHHHHHHHCC-CCEEEEEeCCHHHHHHH-----HHCCCCcEEEEecCC---CCccee-EEEeeeccEEEEEcCCC
Confidence 34566666666 43 4344332 2337788 999999999964332 233343 35788888888888754
No 88
>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=28.30 E-value=1.6e+02 Score=24.33 Aligned_cols=64 Identities=11% Similarity=0.012 Sum_probs=38.9
Q ss_pred eHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.+++..+.+ .. +.+++.. ..++... |.+|++|+++...... ...+. +.++....+.++++...
T Consensus 16 l~~~i~~~~~~~P-~v~l~i~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~~ 83 (198)
T cd08446 16 VPRLLRAFLTARP-DVTVSLHNMTKDEQIEA-----LRAGRIHIGFGRFYPV---EPDIA-VENVAQERLYLAVPKSH 83 (198)
T ss_pred HHHHHHHHHHHCC-CeEEEEeeCCHHHHHHH-----HHCCCccEEEEecCCC---CCCce-eEEeeeccEEEEEeCCC
Confidence 3456666666 43 3344333 2337778 9999999999643222 22232 34777888888877654
No 89
>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=27.99 E-value=1.3e+02 Score=24.92 Aligned_cols=65 Identities=17% Similarity=0.081 Sum_probs=40.3
Q ss_pred eeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++... ..+... |.+|++|+++..... ..+.+. +.|+....+.++++...
T Consensus 14 ~~~~~i~~~~~~~P-~i~l~~~~~~~~~~~~~-----l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~~ 82 (200)
T cd08417 14 LLPPLLARLRQEAP-GVRLRFVPLDRDDLEEA-----LESGEIDLAIGVFPE---LPPGLR-SQPLFEDRFVCVARKDH 82 (200)
T ss_pred HHHHHHHHHHhhCC-CeEEEeccCCHHHHHHH-----HHcCCCCEEEeeccc---CCCccc-hhhhhcCceEEEecCCC
Confidence 34456666666 43 33343332 236778 999999999975332 233333 35888888888887654
No 90
>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=27.60 E-value=1.7e+02 Score=24.48 Aligned_cols=64 Identities=6% Similarity=-0.040 Sum_probs=39.4
Q ss_pred eHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.+++..+.+ .. +.+++.. ..++... |.+|++|+++..- +.....+.. .++....+.++++...
T Consensus 15 l~~~l~~~~~~~P-~v~i~i~~~~~~~~~~~-----l~~~~~Dl~i~~~---~~~~~~~~~-~~l~~~~~~lv~~~~h 82 (197)
T cd08452 15 LPPIVREYRKKFP-SVKVELRELSSPDQVEE-----LLKGRIDIGFLHP---PIQHTALHI-ETVQSSPCVLALPKQH 82 (197)
T ss_pred HHHHHHHHHHHCC-CcEEEEEecChHHHHHH-----HHCCCccEEEeeC---CCCCCCeeE-EEeeeccEEEEEeCCC
Confidence 3566677766 43 3333332 3347888 9999999999632 222233443 4777788888877643
No 91
>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=27.52 E-value=1.6e+02 Score=27.21 Aligned_cols=65 Identities=15% Similarity=0.083 Sum_probs=39.8
Q ss_pred HHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 27 IELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 27 idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+++..+.+ .. +.++++.. .+++.+ |.+|++|++++..... .....+.+. |.....+.+++++..
T Consensus 109 ~~~l~~~~~~~P-~~~i~~~~~~~~~~~~~-----l~~g~~D~~i~~~~~~-~~~~~~~~~-~l~~~~~~~~~~~~h 177 (300)
T TIGR02424 109 PEVVKRFLARAP-RLRVRIMTGPNAYLLDQ-----LRVGALDLVVGRLGAP-ETMQGLSFE-HLYNEPVVFVVRAGH 177 (300)
T ss_pred HHHHHHHHHhCC-CcEEEEEeCchHHHHHH-----HHCCCCCEEEEecCCc-ccccceeee-eecCCceEEEEcCCC
Confidence 455555555 43 33333332 227778 9999999999754332 222334444 888888988887654
No 92
>COG4905 Predicted membrane protein [Function unknown]
Probab=27.10 E-value=90 Score=27.68 Aligned_cols=33 Identities=9% Similarity=-0.029 Sum_probs=24.5
Q ss_pred cccCchHHHHHHHHHHHHHHHHH----HhccccCCCC
Q 040220 107 MKPCTWEMWVVTDAILVNTRFVV----WFPEHQRNSE 139 (370)
Q Consensus 107 l~PF~~~vW~~il~~~~~~~~~~----~~~~r~~~~~ 139 (370)
..||+..+|..++.++++++++- |.+|...+..
T Consensus 57 ~lpf~nnl~sL~ifsi~ivTv~Eyvt~~ILEa~Fn~k 93 (243)
T COG4905 57 GLPFKNNLISLIIFSIFIVTVLEYVTGFILEAIFNCK 93 (243)
T ss_pred EecCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 45889999999999988887764 5566655543
No 93
>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=26.83 E-value=1.6e+02 Score=24.26 Aligned_cols=67 Identities=12% Similarity=-0.030 Sum_probs=42.7
Q ss_pred EEeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 23 DGFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 23 ~G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
.++-.+++..+.+ .. +.++++. ..++... |.+|++|+++..... ..+.+. +.|+......++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~~~~~~~~~~-----l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~ 81 (198)
T cd08412 12 PYYLPGLLRRFREAYP-GVEVRVVEGNQEELEEG-----LRSGELDLALTYDLD---LPEDIA-FEPLARLPPYVWLPAD 81 (198)
T ss_pred hhhhHHHHHHHHHHCC-CcEEEEEECCHHHHHHH-----HHcCCCcEEEEcCCC---CCcccc-eeeeeccceEEEecCC
Confidence 3455677777777 53 4444443 2237778 999999999974322 223343 3588888888888765
Q ss_pred C
Q 040220 99 T 99 (370)
Q Consensus 99 ~ 99 (370)
.
T Consensus 82 ~ 82 (198)
T cd08412 82 H 82 (198)
T ss_pred C
Confidence 4
No 94
>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=26.76 E-value=1.7e+02 Score=24.49 Aligned_cols=65 Identities=11% Similarity=-0.029 Sum_probs=40.0
Q ss_pred eeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++... ..+... |.+|++|+++..... . ...+.. .+.....+.+++++..
T Consensus 14 ~l~~~l~~~~~~~P-~i~l~~~~~~~~~~~~~-----l~~g~~D~~i~~~~~--~-~~~~~~-~~l~~~~~~~v~~~~h 82 (200)
T cd08467 14 LLPRLAPRLRERAP-GLDLRLCPIGDDLAERG-----LEQGTIDLAVGRFAV--P-PDGLVV-RRLYDDGFACLVRHGH 82 (200)
T ss_pred HHHHHHHHHHhhCC-CCEEEEecCCcccHHHH-----hhCCCcCEEEecCCC--C-Ccccee-EEeeeccEEEEEcCCC
Confidence 44566777776 43 33333332 237788 999999999964222 2 233443 4788888888887653
No 95
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=26.57 E-value=1.7e+02 Score=27.28 Aligned_cols=63 Identities=8% Similarity=-0.007 Sum_probs=39.3
Q ss_pred HHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 27 IELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 27 idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
..++..+.+ -. +.+++.. ...++.. |.+|++|+++.......+ .+ .+.|+....+.+++++..
T Consensus 107 ~~~l~~~~~~~P-~v~i~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~~~---~l-~~~~l~~~~~~~~~~~~h 173 (305)
T PRK11151 107 PHIIPMLHQTFP-KLEMYLHEAQTHQLLAQ-----LDSGKLDCAILALVKESE---AF-IEVPLFDEPMLLAVYEDH 173 (305)
T ss_pred HHHHHHHHHHCC-CcEEEEEeCCHHHHHHH-----HHcCCccEEEEecCCCCC---Ce-EEEEeccCcEEEEecCCC
Confidence 344445555 32 3333333 2338888 999999999975433322 23 456889999999987654
No 96
>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene wh
Probab=26.11 E-value=1.3e+02 Score=24.96 Aligned_cols=62 Identities=13% Similarity=0.130 Sum_probs=36.5
Q ss_pred HHHHHHHHh-cCCceEEEEehhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 27 IELYYESQL-ACKGISILFFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 27 idl~~~la~-lg~~~~i~~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
.+++..+.+ .. +.+++..-...+.+ +.+|++|+++..... ....+.+ .|+....+.++++++
T Consensus 19 ~~~l~~f~~~~P-~v~i~~~~~~~~~~-----l~~~~~D~~i~~~~~---~~~~l~~-~~l~~~~~~~v~~~~ 81 (199)
T cd08478 19 APLIAKFRERYP-DIELELVSNEGIID-----LIERKTDVAIRIGEL---TDSTLHA-RPLGKSRLRILASPD 81 (199)
T ss_pred HHHHHHHHHHCC-CeEEEEEecccccc-----chhccccEEEEecCC---CCCCceE-EEcccccEEEEECHH
Confidence 455566665 43 33443332234445 778999999964322 2233433 488888888888754
No 97
>PF10853 DUF2650: Protein of unknown function (DUF2650); InterPro: IPR022559 This region is found in proteins with unknown function in metazoa.
Probab=26.07 E-value=45 Score=21.45 Aligned_cols=16 Identities=13% Similarity=0.443 Sum_probs=12.1
Q ss_pred CchHHHHHHHHHHHHH
Q 040220 110 CTWEMWVVTDAILVNT 125 (370)
Q Consensus 110 F~~~vW~~il~~~~~~ 125 (370)
|..+.|+.++++++++
T Consensus 22 f~lq~Wv~v~l~v~~v 37 (38)
T PF10853_consen 22 FRLQIWVIVLLAVLGV 37 (38)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 5678999988777653
No 98
>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=25.98 E-value=2.3e+02 Score=23.32 Aligned_cols=66 Identities=14% Similarity=0.028 Sum_probs=41.1
Q ss_pred EeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+-.+++..+.+ .. +.+++.. ..++... |.+|++|+++..-. ...+.+.. .+.....+.++++...
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~~~~~~~~~~-----l~~g~~D~~i~~~~---~~~~~~~~-~~l~~~~~~~v~~~~~ 82 (198)
T cd08447 13 SFLPRLLAAARAALP-DVDLVLREMVTTDQIEA-----LESGRIDLGLLRPP---FARPGLET-RPLVREPLVAAVPAGH 82 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEeCCHHHHHHH-----HHcCCceEEEecCC---CCCCCeeE-EEeecCceEEEecCCC
Confidence 344567777777 54 4444443 3347788 99999999996422 22233333 4777888888876643
No 99
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=25.67 E-value=1.8e+02 Score=27.15 Aligned_cols=66 Identities=15% Similarity=0.123 Sum_probs=39.6
Q ss_pred HHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 27 IELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 27 idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+++..+.+ .. +.++++. ...++.. |.+|++|+++..-....+..+.+ .+.|+....+.++++...
T Consensus 111 ~~~l~~~~~~~P-~v~i~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~~~~~ 180 (305)
T CHL00180 111 PRLIGLFRQRYP-QINVQLQVHSTRRIAWN-----VANGQIDIAIVGGEVPTELKKIL-EITPYVEDELALIIPKSH 180 (305)
T ss_pred HHHHHHHHHHCC-CceEEEEeCCHHHHHHH-----HHcCCccEEEEcCccCcccccce-eEEEeccCcEEEEECCCC
Confidence 455555555 32 3333333 2337778 99999999997433222211223 345888889999987754
No 100
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=25.61 E-value=1.8e+02 Score=27.33 Aligned_cols=65 Identities=8% Similarity=0.075 Sum_probs=39.6
Q ss_pred HHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 27 IELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 27 idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+++..+.+ .. +.+++.. ...++.. |.+|++|+++.......+ .+.+.+ .|+....+.+++++..
T Consensus 113 ~~~l~~~~~~~p-~v~i~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~~~-~~~l~~-~~l~~~~~~lv~~~~~ 181 (312)
T PRK10341 113 SDMINKFKEVFP-KAQVSMYEAQLSSFLPA-----IRDGRLDFAIGTLSNEMK-LQDLHV-EPLFESEFVLVASKSR 181 (312)
T ss_pred HHHHHHHHHhCC-CCEEEEEeCCHHHHHHH-----HHcCCCcEEEecCCcccc-cCCeeE-EEEecccEEEEEcCCC
Confidence 355555555 32 3333333 3348888 999999999964332211 233433 4888889999987654
No 101
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=25.46 E-value=63 Score=27.40 Aligned_cols=58 Identities=10% Similarity=0.043 Sum_probs=32.9
Q ss_pred cccceeeecccccccceEEEEeCCCCcCcceecccCchHHHHHHHHHHHHHHHHHHhcccc
Q 040220 75 DRAKIVEFTQPCAESRLSMIVPAKTEESAWRFMKPCTWEMWVVTDAILVNTRFVVWFPEHQ 135 (370)
Q Consensus 75 eR~~~vdFS~P~~~~~~~ilv~~~~~~~~~~~l~PF~~~vW~~il~~~~~~~~~~~~~~r~ 135 (370)
++.+..-|+..|....-..... +. .--.--.|.++.+|++++++++++++.+|...|.
T Consensus 85 ~~~k~~LFs~~y~~~~~~~~~s-~~--~~~~~~~~~~~~i~~~i~g~ll~i~~giy~~~r~ 142 (145)
T PF10661_consen 85 KETKDSLFSSDYQVKADEVASS-PN--TENKTKKPISPTILLSIGGILLAICGGIYVVLRK 142 (145)
T ss_pred HHHHHHhhccccccchhhhhcc-hh--hhhhhccchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446677888775544111111 00 0011134666777777888888888888876653
No 102
>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=25.22 E-value=2.3e+02 Score=23.27 Aligned_cols=68 Identities=15% Similarity=0.096 Sum_probs=42.0
Q ss_pred EEeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 23 DGFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 23 ~G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
..+-.+++..+.+ .. +.+++.. ..++..+ |.+|++|+++..-.... ...+.+ .++....+.++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~l~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~~--~~~l~~-~~l~~~~~~~~~~~~ 82 (199)
T cd08430 12 YSFLPPILERFRAQHP-QVEIKLHTGDPADAIDK-----VLNGEADIAIAARPDKL--PARLAF-LPLATSPLVFIAPNI 82 (199)
T ss_pred eeeccHHHHHHHHHCC-CceEEEEeCCHHHHHHH-----HHCCCCCEEEEecCCCC--CcccEE-EeeccceEEEEEeCC
Confidence 3455778888888 53 3344333 2337788 99999999996432211 122333 467777888887765
Q ss_pred C
Q 040220 99 T 99 (370)
Q Consensus 99 ~ 99 (370)
.
T Consensus 83 ~ 83 (199)
T cd08430 83 A 83 (199)
T ss_pred c
Confidence 3
No 103
>KOG1418 consensus Tandem pore domain K+ channel [Inorganic ion transport and metabolism]
Probab=25.03 E-value=38 Score=33.02 Aligned_cols=54 Identities=20% Similarity=0.276 Sum_probs=42.9
Q ss_pred CccchHHHHHHHhHhccCccceeeeeeccccCccccCc-ccchhhHHHHHHHHHHHHHHHHHhhcCCccccc
Q 040220 147 QIGTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFGGR-IDSNLTRLVVVVWLFVVLILTSSYTASPSPMLT 217 (370)
Q Consensus 147 ~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt 217 (370)
.+.+++.|++.++++.| ||.- |++..||++++.|.++++-++-..-+++.-+++
T Consensus 115 ~f~~al~fs~tv~TTIG-----------------YG~i~P~T~~Gr~~~i~YaliGIPl~li~l~~~g~~l~ 169 (433)
T KOG1418|consen 115 SFSSALLFSITVITTIG-----------------YGNIAPRTDAGRLFTILYALVGIPLMLLILADIGKFLA 169 (433)
T ss_pred ecchhHhhhhheeeecc-----------------CCcccCCcCcchhHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 46788889888888764 4444 899999999999999999888777776666654
No 104
>cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322
Probab=25.02 E-value=1e+02 Score=20.81 Aligned_cols=27 Identities=22% Similarity=0.316 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHhccccCCCC
Q 040220 113 EMWVVTDAILVNTRFVVWFPEHQRNSE 139 (370)
Q Consensus 113 ~vW~~il~~~~~~~~~~~~~~r~~~~~ 139 (370)
++|..+...++.++.++|.....+.+.
T Consensus 12 ~~~~l~~~~~~Figiv~wa~~p~~k~~ 38 (48)
T cd01324 12 DSWGLLYLALFFLGVVVWAFRPGRKKA 38 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCcchh
Confidence 578888888888899999887665443
No 105
>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=24.69 E-value=2.2e+02 Score=23.86 Aligned_cols=68 Identities=10% Similarity=-0.039 Sum_probs=43.5
Q ss_pred EEeeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 23 DGFCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 23 ~G~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
..+-.+++..+.+ .. +.+++... ..+... |.+|++|+++..-.. .....+. +.++....+.++++++
T Consensus 12 ~~~l~~~l~~f~~~~P-~~~i~i~~~~~~~~~~~-----l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~~~ 82 (198)
T cd08443 12 RYVLPPVIKGFIERYP-RVSLQMHQGSPTQIAEM-----VSKGLVDFAIATEAL--HDYDDLI-TLPCYHWNRCVVVKRD 82 (198)
T ss_pred eeECcHHHHHHHHHCC-CeEEEEEeCCHHHHHHH-----HHCCCccEEEEeccc--cccCCce-EeeeeeceEEEEEcCC
Confidence 4566788888887 53 44444432 347778 999999999963221 1222343 3577888888887765
Q ss_pred C
Q 040220 99 T 99 (370)
Q Consensus 99 ~ 99 (370)
.
T Consensus 83 h 83 (198)
T cd08443 83 H 83 (198)
T ss_pred C
Confidence 4
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=24.44 E-value=2e+02 Score=23.84 Aligned_cols=66 Identities=11% Similarity=0.013 Sum_probs=41.2
Q ss_pred EEeeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 23 DGFCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 23 ~G~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
..+-.+++..+.+ .. +.+++... ..+... |.+|++|+++...... .+.+.. .++....+.+++++.
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~~~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~~~~~~~ 81 (196)
T cd08457 12 NGFLPRFLAAFLRLRP-NLHLSLMGLSSSQVLEA-----VASGRADLGIADGPLE---ERQGFL-IETRSLPAVVAVPMG 81 (196)
T ss_pred ccccHHHHHHHHHHCC-CeEEEEEecCcHHHHHH-----HHcCCccEEEeccCCC---CCCcEE-EEeccCCeEEEeeCC
Confidence 3455677888877 53 44444432 336777 8999999999653322 223333 467777888777764
No 107
>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=23.92 E-value=1.9e+02 Score=24.18 Aligned_cols=68 Identities=7% Similarity=-0.063 Sum_probs=42.8
Q ss_pred EEeeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 23 DGFCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 23 ~G~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
.++-.+++..+.+ .. +.+++... .+++.. |.+|++|+++..-... ....+. +.|+......++++..
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~l~i~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~--~~~~~~-~~~l~~~~~~~~~~~~ 82 (198)
T cd08444 12 RYALPWVVQAFKEQFP-NVHLVLHQGSPEEIASM-----LANGQADIGIATEALE--NHPELV-SFPYYDWHHHIIVPVG 82 (198)
T ss_pred hhhhhHHHHHHHHHCC-CeEEEEEeCCHHHHHHH-----HHCCCccEEEeccccC--CCcCcE-EeeccccceeEEecCC
Confidence 3456677777777 54 44444432 237788 9999999999642211 122233 4578888888888765
Q ss_pred C
Q 040220 99 T 99 (370)
Q Consensus 99 ~ 99 (370)
.
T Consensus 83 h 83 (198)
T cd08444 83 H 83 (198)
T ss_pred C
Confidence 4
No 108
>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=23.83 E-value=2.2e+02 Score=23.34 Aligned_cols=67 Identities=4% Similarity=-0.155 Sum_probs=40.6
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-..++..+.+ .. +.+++.. ...++.. |.+|++|+++....... +...+.+ .|+....+.++++...
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~~~~~~~~~~~~~-----l~~~~~Dl~i~~~~~~~-~~~~~~~-~~l~~~~~~~v~~~~~ 84 (197)
T cd08449 14 GLGPALRRFKRQYP-NVTVRFHELSPEAQKAA-----LLSKRIDLGFVRFADTL-NDPPLAS-ELLWREPMVVALPEEH 84 (197)
T ss_pred hHHHHHHHHHHHCC-CeEEEEEECCHHHHHHH-----HhCCCccEEEecccccC-CCCCceE-EEEEEeeEEEEecCCC
Confidence 44566677776 43 3444443 2337788 99999999996433221 1233433 4778888888887653
No 109
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=23.12 E-value=2.2e+02 Score=26.26 Aligned_cols=62 Identities=10% Similarity=0.036 Sum_probs=39.8
Q ss_pred HHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 28 ELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 28 dl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+++..+.+ .. +.++++.. ..++.. |.+|++|+++..... ..+.+++ .|.....+.+++++..
T Consensus 107 ~~~~~~~~~~p-~v~i~~~~~~~~~~~~~-----l~~~~~D~~i~~~~~---~~~~l~~-~~l~~~~~~~v~~~~~ 172 (296)
T PRK09906 107 KVLPMFRLRHP-DTLIELVSLITTQQEEK-----LRRGELDVGFMRHPV---YSDEIDY-LELLDEPLVVVLPVDH 172 (296)
T ss_pred HHHHHHHHHCC-CeEEEEEeCCcHHHHHH-----HHcCCeeEEEecCCC---CCCCceE-EEEecccEEEEecCCC
Confidence 44455555 32 33333332 237788 999999999975443 3344554 5899999999988654
No 110
>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=22.97 E-value=88 Score=29.32 Aligned_cols=46 Identities=13% Similarity=0.000 Sum_probs=30.9
Q ss_pred hhhhhhccccccCCceeEEEecccccccc-------cceeeecccccccceEEEEeCCC
Q 040220 48 QLMMRIRHEENFLRNYDSVVGDATILADR-------AKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 48 ~li~~~~~~~L~~g~~Diai~~~tit~eR-------~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+++.. |.+|++|+++..-...++. ...+.+ .|+....+.++++++.
T Consensus 75 ~l~~~-----L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~~-~~l~~~~l~lvv~~~h 127 (287)
T TIGR02136 75 TGIKA-----LINGTVDIGNSSRPIKDEELQKDKQKGIKLIE-HKVAVDGLAVVVNKKN 127 (287)
T ss_pred HHHHH-----HHcCCCchhhccCCCCHHHHHHHhhcCCCceE-EEEEEeeEEEEECCCC
Confidence 38888 9999999998643333322 111333 3888899999987654
No 111
>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=22.71 E-value=2.9e+02 Score=22.78 Aligned_cols=64 Identities=6% Similarity=0.098 Sum_probs=39.1
Q ss_pred eHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.+++..+.+ .. +.+++.. ..++... |.+|++|+++..-.. ....+.. .++....+.++++.+.
T Consensus 15 ~~~~l~~~~~~~P-~i~i~i~~~~~~~~~~~-----l~~g~~Dl~i~~~~~---~~~~~~~-~~l~~~~~~~~~~~~~ 82 (198)
T cd08441 15 LMPVLDQFRERWP-DVELDLSSGFHFDPLPA-----LLRGELDLVITSDPL---PLPGIAY-EPLFDYEVVLVVAPDH 82 (198)
T ss_pred hHHHHHHHHHhCC-CeEEEEEeCCchhHHHH-----HHcCCceEEEecCCc---CCCCcEE-EEccCCcEEEEEcCCC
Confidence 3466666666 43 3334333 2347788 999999999964322 2233433 3777888888877654
No 112
>PF13396 PLDc_N: Phospholipase_D-nuclease N-terminal
Probab=22.55 E-value=93 Score=20.31 Aligned_cols=28 Identities=7% Similarity=0.211 Sum_probs=22.2
Q ss_pred ccCchHHHHHHHHHHHHHHHHHHhcccc
Q 040220 108 KPCTWEMWVVTDAILVNTRFVVWFPEHQ 135 (370)
Q Consensus 108 ~PF~~~vW~~il~~~~~~~~~~~~~~r~ 135 (370)
+|-..-.|+.+++.+-+.+.++|++-++
T Consensus 18 ~~~~k~~W~~~i~~~P~iG~i~Yl~~gr 45 (46)
T PF13396_consen 18 SPSSKILWLIVILFFPIIGPILYLIFGR 45 (46)
T ss_pred CCchhhHHHHHHHHHHHHHHhheEEEeC
Confidence 3445668999999999999999987654
No 113
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. 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 can interact with a cognate membrane transport complex compris
Probab=22.39 E-value=1.6e+02 Score=24.18 Aligned_cols=62 Identities=10% Similarity=-0.048 Sum_probs=36.1
Q ss_pred HHHHHHHHh-cCCceEEEEehhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCC
Q 040220 27 IELYYESQL-ACKGISILFFFLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAK 98 (370)
Q Consensus 27 idl~~~la~-lg~~~~i~~~~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~ 98 (370)
.+++..+.+ .. +.+++......+.. |.+|++|+++..... ....+. +.+.....+.++++++
T Consensus 16 ~~~l~~~~~~~P-~v~i~~~~~~~~~~-----l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~ 78 (194)
T cd08432 16 IPRLARFQARHP-DIDLRLSTSDRLVD-----FAREGIDLAIRYGDG---DWPGLE-AERLMDEELVPVCSPA 78 (194)
T ss_pred HHHhHHHHHHCC-CeEEEEEecCCccc-----cccccccEEEEecCC---CCCCcc-eEEccCCcEEEecCHH
Confidence 444555555 43 33444433334556 899999999964322 122232 4577888888887753
No 114
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=22.37 E-value=2.3e+02 Score=23.39 Aligned_cols=66 Identities=17% Similarity=0.080 Sum_probs=41.2
Q ss_pred EeeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+-.+++..+.+ .. +.+++..- ..+... |.+|++|+++..... ....+ -+.|.....+.++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~~~~~~~~~~-----l~~~~~D~~i~~~~~---~~~~~-~~~~l~~~~~~~~~~~~~ 82 (198)
T cd08433 13 VLAVPLLRAVRRRYP-GIRLRIVEGLSGHLLEW-----LLNGRLDLALLYGPP---PIPGL-STEPLLEEDLFLVGPADA 82 (198)
T ss_pred hcchHHHHHHHHHCC-CcEEEEEecCcHHHHHH-----HhCCCCcEEEEeCCC---CCCCe-eEEEeccccEEEEecCCC
Confidence 345677777777 53 33443332 337778 999999999964322 22223 234788888888887654
No 115
>PF11446 DUF2897: Protein of unknown function (DUF2897); InterPro: IPR021550 This is a bacterial family of uncharacterised proteins.
Probab=22.35 E-value=1.2e+02 Score=21.24 Aligned_cols=24 Identities=17% Similarity=0.211 Sum_probs=14.8
Q ss_pred chHHHHHHHHHHHHHHHHHHhccc
Q 040220 111 TWEMWVVTDAILVNTRFVVWFPEH 134 (370)
Q Consensus 111 ~~~vW~~il~~~~~~~~~~~~~~r 134 (370)
.|.+|+++++++-++..=+.++..
T Consensus 2 ~~~~wlIIviVlgvIigNia~LK~ 25 (55)
T PF11446_consen 2 TWNPWLIIVIVLGVIIGNIAALKY 25 (55)
T ss_pred cchhhHHHHHHHHHHHhHHHHHHH
Confidence 467898887776555444444443
No 116
>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=22.22 E-value=1.9e+02 Score=23.75 Aligned_cols=62 Identities=11% Similarity=-0.176 Sum_probs=37.2
Q ss_pred eHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.+++..+.+ .. +.++++.. .++..+ |.+|++|+++.... . ... -+.+.....+.+++++..
T Consensus 15 l~~~l~~~~~~~P-~v~i~~~~~~~~~~~~~-----l~~~~~Dl~i~~~~--~---~~~-~~~~l~~~~~~~v~~~~~ 80 (185)
T cd08439 15 LPFLLNRFASVYP-RLAIEVVCKRTPRLMEM-----LERGEVDLALITHP--P---PGA-SATILRRSPTVWYCAAGY 80 (185)
T ss_pred HHHHHHHHHHHCC-CeEEEEEECChHHHHHH-----HHCCCCcEEEEecc--C---CCC-CceEEEEecCEEEECCCC
Confidence 3456666666 32 33344332 237778 99999999987421 1 112 245677778887776653
No 117
>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=22.04 E-value=2e+02 Score=24.14 Aligned_cols=65 Identities=11% Similarity=-0.115 Sum_probs=38.9
Q ss_pred eeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++.. ...++.+ |.+|++|+++...... ...+.. .++....+.++++++.
T Consensus 15 ~l~~~l~~~~~~~P-~i~l~~~~~~~~~~~~~-----l~~~~~D~~i~~~~~~---~~~l~~-~~l~~~~~~~~~~~~~ 83 (198)
T cd08485 15 TLPLLLRQLLSVAP-SATVSLTQMSKNRQIEA-----LDAGTIDIGFGRFYPY---QEGVVV-RNVTNERLFLGAQKSR 83 (198)
T ss_pred HHHHHHHHHHHhCC-CcEEEEEECCHHHHHHH-----HHcCCccEEEecCCCC---CCCeEE-EEeeccceEEEeCCCC
Confidence 34566666666 43 4444433 2337888 9999999999743221 223433 4677777777776543
No 118
>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=21.66 E-value=2.5e+02 Score=23.09 Aligned_cols=65 Identities=11% Similarity=0.026 Sum_probs=38.8
Q ss_pred eeHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 25 FCIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 25 ~~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
+-.+++..+.+ .. +.+++... ..+... |.+|++|+++..-... ...+.. .+.....+.++++...
T Consensus 14 ~l~~~l~~~~~~~P-~v~l~i~~~~~~~~~~~-----l~~g~~D~~i~~~~~~---~~~~~~-~~l~~~~~~~v~~~~~ 82 (200)
T cd08464 14 LAPPLLAALRAEAP-GVRLVFRQVDPFNVGDM-----LDRGEIDLAIGVFGEL---PAWLKR-EVLYTEGYACLFDPQQ 82 (200)
T ss_pred HHHHHHHHHHHHCC-CcEEEEecCCcccHHHH-----HhcCcccEEEecCCCC---ccccee-eeecccceEEEEeCCC
Confidence 34556666666 43 33333332 226777 9999999999643221 233433 4788888888876543
No 119
>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=21.50 E-value=2.5e+02 Score=22.98 Aligned_cols=68 Identities=15% Similarity=0.111 Sum_probs=41.3
Q ss_pred EeeHHHHHHHHh-cCCceEEEEe---hhhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 24 GFCIELYYESQL-ACKGISILFF---FLQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 24 G~~idl~~~la~-lg~~~~i~~~---~~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
.+-.+++..+.+ .. +.+++.. ...+... |.+|++|+++..-... ...+.+. +.+.....+.++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~~~~~~~~~~-----l~~g~~Dl~i~~~~~~-~~~~~~~-~~~l~~~~~~~v~~~~~ 84 (195)
T cd08427 13 GLLPRALARLRRRHP-DLEVHIVPGLSAELLAR-----VDAGELDAAIVVEPPF-PLPKDLV-WTPLVREPLVLIAPAEL 84 (195)
T ss_pred HHhHHHHHHHHHHCC-CceEEEEeCCcHHHHHH-----HHCCCCCEEEEcCCCC-ccccCce-EEEcccCcEEEEECCCC
Confidence 344567777776 43 3334333 2337788 9999999999743221 1123343 34778888888887654
No 120
>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=21.38 E-value=2.4e+02 Score=23.49 Aligned_cols=67 Identities=16% Similarity=0.041 Sum_probs=41.8
Q ss_pred EEeeHHHHHHHHh-cCCceEEEEeh--hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 23 DGFCIELYYESQL-ACKGISILFFF--LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 23 ~G~~idl~~~la~-lg~~~~i~~~~--~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
..+-.+++..+.+ .. +.+++... ..++.. |.+|++|+++..... ....+++ .|.....+.++++.+.
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~v~l~~~~~~~~~~-----l~~g~~D~~i~~~~~---~~~~~~~-~~l~~~~~~~v~~~~h 81 (200)
T cd08460 12 AAFGPALLAAVAAEAP-GVRLRFVPESDKDVDA-----LREGRIDLEIGVLGP---TGPEIRV-QTLFRDRFVGVVRAGH 81 (200)
T ss_pred HHHHHHHHHHHHHHCC-CCEEEEecCchhHHHH-----HHCCCccEEEecCCC---CCcchhe-eeeeccceEEEEeCCC
Confidence 3455667777777 43 33333321 246777 999999999974322 1223444 5788888888887654
No 121
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=20.46 E-value=2.4e+02 Score=26.34 Aligned_cols=65 Identities=9% Similarity=0.070 Sum_probs=39.4
Q ss_pred eHHHHHHHHh-cCCceEEEEeh---hhhhhhhccccccCCceeEEEecccccccccceeeecccccccceEEEEeCCC
Q 040220 26 CIELYYESQL-ACKGISILFFF---LQLMMRIRHEENFLRNYDSVVGDATILADRAKIVEFTQPCAESRLSMIVPAKT 99 (370)
Q Consensus 26 ~idl~~~la~-lg~~~~i~~~~---~~li~~~~~~~L~~g~~Diai~~~tit~eR~~~vdFS~P~~~~~~~ilv~~~~ 99 (370)
-.++++.+.+ .. +.++++.. ..++.. |.+|++|++++.-... ....++. .|+......++++.+.
T Consensus 108 l~~~l~~~~~~~P-~i~i~i~~~~~~~~~~~-----l~~g~~D~~i~~~~~~--~~~~l~~-~~l~~~~~~~~~~~~~ 176 (309)
T PRK12682 108 LPRVVAAFRKRYP-KVNLSLHQGSPDEIARM-----VISGEADIGIATESLA--DDPDLAT-LPCYDWQHAVIVPPDH 176 (309)
T ss_pred HHHHHHHHHHhCC-CeEEEEecCCHHHHHHH-----HHcCCccEEEecCccc--CCCcceE-EEeeeeeEEEEecCCC
Confidence 3455555555 43 34444432 237778 9999999999743221 1223443 4788888888887654
No 122
>KOG1545 consensus Voltage-gated shaker-like K+ channel KCNA [Inorganic ion transport and metabolism]
Probab=20.37 E-value=42 Score=32.81 Aligned_cols=34 Identities=15% Similarity=0.252 Sum_probs=25.5
Q ss_pred CCccchHHHHHHHhHhccCccceeeeeeccccCccccCc-ccchhhHHHHHH
Q 040220 146 DQIGTALWFNFSSILFAYGKEHVLHFIIMVNWKPIFGGR-IDSNLTRLVVVV 196 (370)
Q Consensus 146 ~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~R~l~~~ 196 (370)
..+-+++||...++++.+ ||+. |-+..|+++...
T Consensus 392 ~SIPdaFWwavVTMTTVG-----------------YGDm~P~TvgGKIVGsl 426 (507)
T KOG1545|consen 392 SSIPDAFWWAVVTMTTVG-----------------YGDMVPVTVGGKIVGSL 426 (507)
T ss_pred CcCcccceEEEEEEEeec-----------------cccceecccCceehhhH
Confidence 357789999999998765 3444 788888887653
Done!