Query psy12229
Match_columns 444
No_of_seqs 130 out of 1653
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 22:05:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12229.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12229hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1054|consensus 100.0 7.5E-55 1.6E-59 425.5 20.5 359 5-419 417-799 (897)
2 KOG1053|consensus 100.0 3.8E-47 8.2E-52 385.4 22.0 352 5-409 411-807 (1258)
3 KOG1052|consensus 100.0 6.5E-44 1.4E-48 382.8 26.2 355 4-420 215-584 (656)
4 KOG4440|consensus 100.0 1.7E-43 3.8E-48 347.4 21.0 361 4-421 402-817 (993)
5 PF00497 SBP_bac_3: Bacterial 99.9 8.4E-21 1.8E-25 175.6 15.8 221 7-409 1-225 (225)
6 PRK09495 glnH glutamine ABC tr 99.9 2.3E-20 4.9E-25 176.8 17.2 220 4-411 24-246 (247)
7 PRK10797 glutamate and asparta 99.8 3.7E-20 8.1E-25 180.4 16.2 224 3-410 38-273 (302)
8 PRK11260 cystine transporter s 99.8 4.7E-19 1E-23 169.7 17.9 221 3-409 39-262 (266)
9 TIGR02995 ectoine_ehuB ectoine 99.8 1.2E-18 2.6E-23 167.7 16.5 224 3-408 31-261 (275)
10 PRK15007 putative ABC transpor 99.8 2.8E-18 6.2E-23 161.8 17.7 216 4-408 20-242 (243)
11 PRK15010 ABC transporter lysin 99.8 4.4E-18 9.5E-23 162.4 18.3 221 4-409 25-255 (260)
12 TIGR01096 3A0103s03R lysine-ar 99.8 8.5E-18 1.8E-22 159.1 18.2 217 5-407 24-250 (250)
13 PRK10859 membrane-bound lytic 99.8 6.4E-18 1.4E-22 174.9 16.1 225 4-410 42-268 (482)
14 PRK15437 histidine ABC transpo 99.8 2.1E-17 4.6E-22 157.6 17.4 220 5-409 26-255 (259)
15 PRK11917 bifunctional adhesin/ 99.7 2.6E-17 5.6E-22 157.0 15.2 217 3-407 36-258 (259)
16 TIGR02285 conserved hypothetic 99.7 6.2E-16 1.3E-20 148.3 12.9 235 5-410 18-263 (268)
17 TIGR03870 ABC_MoxJ methanol ox 99.7 1.1E-15 2.5E-20 144.6 13.8 220 6-406 1-241 (246)
18 PRK09959 hybrid sensory histid 99.6 5.8E-16 1.3E-20 177.7 11.1 245 3-435 54-306 (1197)
19 COG0834 HisJ ABC-type amino ac 99.6 1.6E-14 3.4E-19 138.3 16.2 222 4-410 33-266 (275)
20 smart00062 PBPb Bacterial peri 99.6 9.9E-14 2.2E-18 126.0 17.9 214 6-407 1-219 (219)
21 PRK09959 hybrid sensory histid 99.6 1.3E-14 2.8E-19 166.7 14.4 216 4-409 301-521 (1197)
22 cd00134 PBPb Bacterial peripla 99.6 1.5E-13 3.3E-18 125.0 17.6 213 7-407 1-218 (218)
23 TIGR03871 ABC_peri_MoxJ_2 quin 99.5 2.4E-13 5.2E-18 127.2 16.4 217 6-407 1-228 (232)
24 COG4623 Predicted soluble lyti 99.5 3.8E-13 8.3E-18 128.1 12.1 227 2-409 20-248 (473)
25 PF00060 Lig_chan: Ligand-gate 99.4 4.5E-14 9.6E-19 122.8 2.1 105 131-243 1-115 (148)
26 smart00079 PBPe Eukaryotic hom 99.4 8.6E-13 1.9E-17 112.6 10.0 131 232-408 1-133 (134)
27 PF10613 Lig_chan-Glu_bd: Liga 99.4 4.2E-13 9E-18 97.9 5.2 63 16-78 1-65 (65)
28 TIGR01098 3A0109s03R phosphate 98.5 3.2E-06 7E-11 80.0 14.4 69 314-386 180-254 (254)
29 PRK00489 hisG ATP phosphoribos 98.4 1.6E-06 3.5E-11 83.9 10.1 164 68-409 52-220 (287)
30 TIGR03431 PhnD phosphonate ABC 97.6 0.0018 3.8E-08 62.7 14.7 75 315-393 175-256 (288)
31 PRK11553 alkanesulfonate trans 95.9 0.21 4.7E-06 48.7 14.1 41 36-87 43-84 (314)
32 PF12974 Phosphonate-bd: ABC t 95.2 0.12 2.6E-06 48.4 9.4 73 313-389 142-220 (243)
33 PF03466 LysR_substrate: LysR 94.1 0.69 1.5E-05 41.0 11.1 67 34-117 20-87 (209)
34 TIGR01729 taurine_ABC_bnd taur 94.0 1.1 2.5E-05 43.2 13.2 37 41-88 20-56 (300)
35 COG3221 PhnD ABC-type phosphat 93.7 1.9 4.1E-05 41.9 13.7 73 312-388 181-260 (299)
36 cd05466 PBP2_LTTR_substrate Th 92.7 3.2 6.9E-05 35.5 12.9 68 33-117 13-81 (197)
37 PF07885 Ion_trans_2: Ion chan 92.5 0.53 1.1E-05 35.8 6.6 55 164-225 24-78 (79)
38 cd08468 PBP2_Pa0477 The C-term 91.8 3.6 7.8E-05 36.3 12.4 71 33-117 13-84 (202)
39 cd08421 PBP2_LTTR_like_1 The C 91.6 5.3 0.00011 34.7 13.1 68 33-117 13-81 (198)
40 cd08426 PBP2_LTTR_like_5 The C 91.2 7.4 0.00016 33.8 13.7 67 34-117 14-81 (199)
41 cd08459 PBP2_DntR_NahR_LinR_li 91.2 6.6 0.00014 34.3 13.4 68 33-117 13-81 (201)
42 cd08433 PBP2_Nac The C-teminal 90.5 8.6 0.00019 33.4 13.5 68 33-117 13-81 (198)
43 cd00918 Der-p2_like Several gr 90.2 0.24 5.2E-06 41.2 2.7 38 397-443 63-100 (120)
44 cd08412 PBP2_PAO1_like The C-t 90.2 11 0.00025 32.5 14.1 69 32-117 12-81 (198)
45 cd08417 PBP2_Nitroaromatics_li 90.0 7.9 0.00017 33.6 12.8 68 33-117 13-81 (200)
46 cd08462 PBP2_NodD The C-termin 90.0 5.4 0.00012 35.0 11.7 66 34-117 14-80 (200)
47 cd08467 PBP2_SyrM The C-termin 90.0 8.9 0.00019 33.7 13.1 68 33-117 13-81 (200)
48 cd08418 PBP2_TdcA The C-termin 90.0 8.6 0.00019 33.3 13.0 70 33-117 13-83 (201)
49 cd08460 PBP2_DntR_like_1 The C 89.8 4.8 0.0001 35.3 11.2 68 32-117 12-80 (200)
50 cd08419 PBP2_CbbR_RubisCO_like 89.7 9.7 0.00021 32.8 13.0 67 34-117 13-80 (197)
51 PRK11151 DNA-binding transcrip 89.6 9.2 0.0002 36.8 13.8 67 34-117 105-172 (305)
52 cd08442 PBP2_YofA_SoxR_like Th 89.2 11 0.00024 32.4 13.0 69 32-117 12-81 (193)
53 cd08438 PBP2_CidR The C-termin 89.1 10 0.00022 32.7 12.7 68 33-117 13-81 (197)
54 PF12727 PBP_like: PBP superfa 89.1 17 0.00036 32.9 14.2 112 230-385 80-191 (193)
55 KOG4063|consensus 89.0 0.45 9.7E-06 40.5 3.3 43 397-442 92-134 (158)
56 TIGR02122 TRAP_TAXI TRAP trans 88.9 2.7 5.8E-05 40.8 9.5 42 36-88 48-90 (320)
57 cd08466 PBP2_LeuO The C-termin 88.7 8.8 0.00019 33.4 12.1 68 33-117 13-81 (200)
58 cd08440 PBP2_LTTR_like_4 TThe 88.4 15 0.00033 31.5 13.5 69 32-117 12-81 (197)
59 PRK10837 putative DNA-binding 88.2 13 0.00028 35.3 13.7 67 34-117 103-170 (290)
60 cd08448 PBP2_LTTR_aromatics_li 88.1 16 0.00035 31.4 13.9 68 33-117 13-81 (197)
61 cd08420 PBP2_CysL_like C-termi 88.0 16 0.00035 31.4 13.3 69 32-117 12-81 (201)
62 cd08434 PBP2_GltC_like The sub 87.8 16 0.00036 31.2 13.3 68 33-117 13-81 (195)
63 cd08427 PBP2_LTTR_like_2 The C 87.2 12 0.00027 32.2 11.9 70 33-117 13-83 (195)
64 CHL00180 rbcR LysR transcripti 87.1 29 0.00064 33.3 17.1 70 34-117 109-179 (305)
65 cd08463 PBP2_DntR_like_4 The C 87.0 20 0.00044 31.6 13.4 70 32-117 12-82 (203)
66 cd08414 PBP2_LTTR_aromatics_li 86.4 20 0.00044 30.7 14.1 67 34-117 14-81 (197)
67 COG1910 Periplasmic molybdate- 86.4 13 0.00028 34.0 11.3 120 230-395 86-206 (223)
68 cd08461 PBP2_DntR_like_3 The C 86.3 15 0.00032 31.8 12.0 68 33-117 13-81 (198)
69 cd08415 PBP2_LysR_opines_like 86.3 14 0.00031 31.8 11.9 69 32-117 12-81 (196)
70 cd08413 PBP2_CysB_like The C-t 86.3 17 0.00037 31.7 12.5 69 33-117 13-82 (198)
71 cd08411 PBP2_OxyR The C-termin 85.9 19 0.00041 31.2 12.5 67 34-117 15-82 (200)
72 PRK11233 nitrogen assimilation 85.3 15 0.00033 35.4 12.5 67 34-117 106-173 (305)
73 PRK11242 DNA-binding transcrip 85.2 26 0.00056 33.3 14.0 68 33-117 104-172 (296)
74 TIGR01728 SsuA_fam ABC transpo 84.3 9 0.0002 36.2 10.2 37 42-89 21-59 (288)
75 cd08436 PBP2_LTTR_like_3 The C 84.2 26 0.00055 30.0 13.3 69 33-117 13-82 (194)
76 cd08423 PBP2_LTTR_like_6 The C 84.1 20 0.00044 30.8 11.9 70 34-117 14-86 (200)
77 cd08429 PBP2_NhaR The C-termin 83.9 29 0.00064 30.7 13.0 71 32-116 12-83 (204)
78 cd08464 PBP2_DntR_like_2 The C 83.6 28 0.00061 30.0 12.8 68 33-117 13-81 (200)
79 PRK12684 transcriptional regul 83.3 30 0.00064 33.5 13.6 68 34-117 107-175 (313)
80 cd08435 PBP2_GbpR The C-termin 83.2 29 0.00063 29.8 12.6 70 33-117 13-83 (201)
81 cd08456 PBP2_LysR The C-termin 83.1 28 0.00061 29.9 12.3 68 33-117 13-81 (196)
82 cd08441 PBP2_MetR The C-termin 82.9 30 0.00065 29.9 12.5 67 34-117 14-81 (198)
83 PRK12682 transcriptional regul 82.9 30 0.00065 33.3 13.4 69 33-117 106-175 (309)
84 PRK09791 putative DNA-binding 82.4 28 0.0006 33.4 12.9 69 34-117 109-178 (302)
85 cd08453 PBP2_IlvR The C-termin 82.0 33 0.00071 29.7 14.4 71 33-117 13-84 (200)
86 PF13379 NMT1_2: NMT1-like fam 82.0 17 0.00037 34.0 10.9 36 40-86 27-62 (252)
87 PRK12683 transcriptional regul 81.6 37 0.00081 32.8 13.5 67 35-117 108-175 (309)
88 cd08465 PBP2_ToxR The C-termin 80.7 28 0.0006 30.5 11.4 68 33-117 13-81 (200)
89 cd08451 PBP2_BudR The C-termin 80.7 36 0.00078 29.2 13.7 68 34-117 15-83 (199)
90 cd00916 Npc2_like Niemann-Pick 79.7 1.9 4E-05 36.0 3.1 39 398-443 66-104 (123)
91 PRK12681 cysB transcriptional 79.3 39 0.00085 33.0 12.9 67 35-117 108-175 (324)
92 cd08443 PBP2_CysB The C-termin 79.3 42 0.00091 29.2 12.8 70 32-117 12-82 (198)
93 PRK10341 DNA-binding transcrip 77.8 56 0.0012 31.5 13.4 67 36-117 113-180 (312)
94 cd08469 PBP2_PnbR The C-termin 77.6 50 0.0011 29.2 12.3 68 33-117 13-81 (221)
95 PRK11013 DNA-binding transcrip 77.4 59 0.0013 31.3 13.4 67 34-117 108-175 (309)
96 PRK12679 cbl transcriptional r 77.3 69 0.0015 31.0 13.9 75 314-395 224-300 (316)
97 cd08416 PBP2_MdcR The C-termin 77.1 47 0.001 28.5 12.4 71 32-117 12-83 (199)
98 TIGR03427 ABC_peri_uca ABC tra 76.1 30 0.00066 34.0 10.9 60 6-86 3-62 (328)
99 KOG3713|consensus 76.1 2.1 4.6E-05 43.6 2.8 44 165-215 378-421 (477)
100 PF09084 NMT1: NMT1/THI5 like; 75.9 12 0.00026 33.8 7.7 38 42-90 15-52 (216)
101 PRK09508 leuO leucine transcri 75.2 30 0.00066 33.4 10.8 68 33-117 125-193 (314)
102 COG1638 DctP TRAP-type C4-dica 75.2 6.1 0.00013 39.0 5.8 57 31-93 41-98 (332)
103 cd08444 PBP2_Cbl The C-termina 74.6 57 0.0012 28.3 12.4 70 32-117 12-82 (198)
104 cd00915 MD-1_MD-2 MD-1 and MD- 74.5 3.1 6.8E-05 34.9 3.0 40 397-442 69-110 (130)
105 TIGR03339 phn_lysR aminoethylp 71.5 88 0.0019 29.2 13.0 67 34-117 98-165 (279)
106 KOG0498|consensus 70.6 6 0.00013 43.0 4.8 68 167-241 297-369 (727)
107 PLN03192 Voltage-dependent pot 70.2 5.8 0.00013 44.3 4.8 68 168-242 254-326 (823)
108 cd08449 PBP2_XapR The C-termin 70.0 69 0.0015 27.3 13.4 70 33-117 13-83 (197)
109 cd08425 PBP2_CynR The C-termin 70.0 70 0.0015 27.4 12.7 67 34-117 15-82 (197)
110 TIGR02424 TF_pcaQ pca operon t 69.7 78 0.0017 30.1 12.1 68 35-117 108-176 (300)
111 PRK11482 putative DNA-binding 68.5 1.2E+02 0.0026 29.4 13.7 44 69-117 153-196 (317)
112 PRK15421 DNA-binding transcrip 64.9 1.4E+02 0.003 28.9 13.9 66 35-117 104-170 (317)
113 PRK11716 DNA-binding transcrip 64.1 1.2E+02 0.0026 28.0 12.2 68 34-117 81-149 (269)
114 cd08445 PBP2_BenM_CatM_CatR Th 63.7 98 0.0021 26.7 14.5 69 32-117 13-82 (203)
115 PRK12680 transcriptional regul 63.2 1.5E+02 0.0033 28.8 14.6 68 34-117 107-175 (327)
116 cd08457 PBP2_OccR The C-termin 62.5 1E+02 0.0022 26.5 13.0 69 32-117 12-81 (196)
117 cd08437 PBP2_MleR The substrat 62.5 1E+02 0.0022 26.5 13.7 69 34-117 14-83 (198)
118 cd08458 PBP2_NocR The C-termin 62.1 1E+02 0.0022 26.5 12.9 68 33-117 13-81 (196)
119 PRK07377 hypothetical protein; 58.9 24 0.00052 31.3 5.4 47 31-88 91-137 (184)
120 PRK09906 DNA-binding transcrip 57.6 1.7E+02 0.0037 27.6 13.6 66 35-117 105-171 (296)
121 KOG1419|consensus 54.7 17 0.00037 37.8 4.3 55 166-227 271-325 (654)
122 PRK10677 modA molybdate transp 54.6 1.9E+02 0.0041 27.2 15.3 72 33-117 39-116 (257)
123 cd08430 PBP2_IlvY The C-termin 52.1 45 0.00097 28.6 6.4 70 32-117 12-82 (199)
124 cd08447 PBP2_LTTR_aromatics_li 50.6 1.6E+02 0.0034 25.1 12.6 68 33-117 13-81 (198)
125 KOG1418|consensus 50.3 13 0.00029 37.3 3.0 55 165-226 116-170 (433)
126 PF13531 SBP_bac_11: Bacterial 49.3 2E+02 0.0044 26.0 16.0 74 31-117 9-88 (230)
127 PRK10918 phosphate ABC transpo 47.5 50 0.0011 32.9 6.4 68 38-118 44-112 (346)
128 cd00912 ML The ML (MD-2-relate 46.0 22 0.00049 29.5 3.2 41 398-442 66-107 (127)
129 cd08486 PBP2_CbnR The C-termin 46.0 63 0.0014 28.1 6.4 68 33-117 14-82 (198)
130 cd08446 PBP2_Chlorocatechol Th 45.4 75 0.0016 27.2 6.8 67 34-117 15-82 (198)
131 TIGR02136 ptsS_2 phosphate bin 43.9 40 0.00087 32.3 5.0 72 33-117 48-126 (287)
132 cd08452 PBP2_AlsR The C-termin 43.3 92 0.002 26.8 7.0 68 33-117 13-81 (197)
133 PRK11062 nhaR transcriptional 43.0 3E+02 0.0065 26.1 11.9 65 314-384 222-287 (296)
134 cd08450 PBP2_HcaR The C-termin 42.0 84 0.0018 26.8 6.5 68 33-117 13-81 (196)
135 cd08439 PBP2_LrhA_like The C-t 40.8 91 0.002 26.5 6.5 65 34-117 14-79 (185)
136 TIGR01256 modA molybdenum ABC 39.9 77 0.0017 28.6 6.1 72 33-117 6-83 (216)
137 PRK03601 transcriptional regul 39.3 77 0.0017 29.9 6.2 68 33-117 102-170 (275)
138 PF14034 Spore_YtrH: Sporulati 36.6 29 0.00063 27.7 2.2 41 199-242 2-42 (102)
139 PF12849 PBP_like_2: PBP super 36.2 55 0.0012 30.9 4.7 75 32-120 21-109 (281)
140 PF12916 DUF3834: Protein of u 36.0 44 0.00095 30.1 3.5 45 32-87 76-121 (201)
141 PRK10094 DNA-binding transcrip 34.0 4.3E+02 0.0092 25.3 14.4 69 34-117 107-176 (308)
142 TIGR00975 3a0107s03 phosphate 33.8 94 0.002 30.3 5.9 50 66-117 34-86 (314)
143 cd08485 PBP2_ClcR The C-termin 32.9 1.3E+02 0.0028 26.0 6.3 68 33-117 14-82 (198)
144 PF03480 SBP_bac_7: Bacterial 29.2 1.2E+02 0.0026 28.9 5.7 53 36-94 16-68 (286)
145 PRK10537 voltage-gated potassi 28.4 65 0.0014 32.6 3.8 52 164-222 168-219 (393)
146 cd08431 PBP2_HupR The C-termin 28.1 98 0.0021 26.4 4.6 70 32-117 12-82 (195)
147 cd03770 SR_TndX_transposase Se 26.3 1.6E+02 0.0034 24.8 5.3 50 37-86 25-74 (140)
148 COG4588 AcfC Accessory coloniz 25.7 3.3E+02 0.0072 24.9 7.2 44 32-88 32-75 (252)
149 cd08428 PBP2_IciA_ArgP The C-t 24.7 2.2E+02 0.0047 24.2 6.2 66 35-117 15-80 (195)
150 PF02879 PGM_PMM_II: Phosphogl 23.4 2.4E+02 0.0052 22.1 5.6 66 31-97 29-99 (104)
151 PRK11074 putative DNA-binding 22.7 2.2E+02 0.0047 27.1 6.2 69 35-118 107-176 (300)
152 smart00737 ML Domain involved 22.3 84 0.0018 25.5 2.8 37 399-442 62-98 (118)
153 PRK09986 DNA-binding transcrip 21.8 2.9E+02 0.0063 25.9 6.9 70 34-118 111-181 (294)
154 smart00857 Resolvase Resolvase 20.6 2.2E+02 0.0048 23.7 5.2 51 36-86 21-71 (148)
155 TIGR00787 dctP tripartite ATP- 20.3 1.9E+02 0.0042 27.0 5.2 106 230-388 125-232 (257)
No 1
>KOG1054|consensus
Probab=100.00 E-value=7.5e-55 Score=425.47 Aligned_cols=359 Identities=34% Similarity=0.607 Sum_probs=327.5
Q ss_pred eeeEEEeccCCCeEEEecCCC--CCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCc-cchhHHHHhcccc
Q psy12229 5 TNISDSRLKQEPFVMREESEG--GGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQ-WNGMIKELIEKRA 81 (444)
Q Consensus 5 ~~l~V~~~~~~Pf~~~~~~~~--~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~-~~g~i~~l~~g~~ 81 (444)
+++.|++---.||++...+-. .|+.++.|+++|++.++|+..+.+|++....+++||..++.++ |+||+|.|..|++
T Consensus 417 ~tvvvttiL~spyvm~kkn~~~~egn~ryEGyCvdLa~~iAkhi~~~Y~l~iv~dgkyGardaD~k~WnGMvGeLv~grA 496 (897)
T KOG1054|consen 417 RTVVVTTILESPYVMLKKNHEQLEGNERYEGYCVDLAAEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYGRA 496 (897)
T ss_pred ceEEEEEecCCchhHHHhhHHHhcCCcccceeHHHHHHHHHHhcCceEEEEEecCCcccccCCCcccccchhHHHhcCcc
Confidence 456667777778887766543 5777899999999999999999999999999999999999999 9999999999999
Q ss_pred cEEeecccccccccccccccccceecccEEEEEeCC-CCCCcccccccccchhHHHHHHHHHHHHh------cceecccc
Q psy12229 82 DIALGSLSVMAERENVVDFTVPYYDLVGITILMKKP-KTPTSLFKFLTVLETGVWLCILAAYCNLD------GEQMKYLI 154 (444)
Q Consensus 82 Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~-~~~~~~~~~l~pF~~~vWi~i~~~~~~~~------~~~~~~~~ 154 (444)
|++++++++|.+|.+.+|||.|++. .++.+|+++| ++.+..+.|+.|....+|+|++++++-++ .+|+|++|
T Consensus 497 diavApLTIt~~REeviDFSKPfMs-lGISIMIKKPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEw 575 (897)
T KOG1054|consen 497 DIAVAPLTITLVREEVIDFSKPFMS-LGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEW 575 (897)
T ss_pred ceEEeeeeeehhhhhhhccccchhh-cCeEEEEeCcccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEeccCchhe
Confidence 9999999999999999999999999 9999999999 57899999999999999999999998876 68899999
Q ss_pred ccCCC---CCCC-------cccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhh
Q psy12229 155 QVNPP---GDIL-------PEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFL 224 (444)
Q Consensus 155 ~~~~~---~~~~-------~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~L 224 (444)
+.... .+.. +..++.||.+++++.|| -+..|++.|+|++-++||+|.+|++++|+|+|+++|
T Consensus 576 h~Ee~~rg~~t~~~~~NeFgifNsLWFsLgAFMQQG--------~DI~PRslSGRIvggvWWFFTlIIiSSYTANLAAFL 647 (897)
T KOG1054|consen 576 HTEEFERGRFTPSDPPNEFGIFNSLWFSLGAFMQQG--------CDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFL 647 (897)
T ss_pred eccccccCCCCCCCCCccchhhHHHHHHHHHHHhcC--------CCCCccccccceeccchhhhhhhhhhhhhhHHHHHH
Confidence 88543 2221 12479999999999999 999999999999999999999999999999999999
Q ss_pred hcccCCCCCCChHHhhhCCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHH
Q psy12229 225 TVSRLDTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKM 304 (444)
Q Consensus 225 t~~~~~~~I~sl~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~ 304 (444)
|+.++.+||.|.+||++|+++.||+..+.++.+||+.+. + +.|.+|
T Consensus 648 TvErMvsPIESaEDLAkQteIaYGt~~~GSTkeFFr~Sk--------------------------i--------avy~kM 693 (897)
T KOG1054|consen 648 TVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSK--------------------------I--------AVYEKM 693 (897)
T ss_pred hHHhhcCcchhHHHHhhcceeeeeecCCCchHHHHhhhh--------------------------H--------HHHHHH
Confidence 999999999999999999999999999999999999763 2 678889
Q ss_pred HHHHHhcC---CCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhc-CCCccEEeCCcccccceEEEecCCCchhhhhH
Q psy12229 305 WQAMKEAK---LPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVM-TNCDLQMVGDEFSRKPYAIAVQQDRDARELFC 380 (444)
Q Consensus 305 ~~~~~~~~---~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~-~~c~l~~~~~~~~~~~~~~~~~k~sp~~~~in 380 (444)
|..|++.+ ++.+++|++++|++++ |+|||+.+..+-+|..+ ++|+-..++.++.+-+||++.||||.++..+|
T Consensus 694 W~yM~SaepsVFv~t~aeGv~rVRksK---GkyAfLLEsTmNey~eqRkPCDTMKVGgNLds~GYGiATp~Gsslr~~vN 770 (897)
T KOG1054|consen 694 WTYMKSAEPSVFVRTTAEGVARVRKSK---GKYAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVN 770 (897)
T ss_pred HHHHhcCCcceeeehhhhHHHHHHhcC---CceEeehHhhhhhhhhccCCccceecccccCCcceeecCCCCcccccchh
Confidence 99998874 6889999999999997 69999999999999998 78999999999999999999999999999999
Q ss_pred HHHHHHhcCCccccCCCCCcccccccccCCCCcccCCCC
Q psy12229 381 NVHANILSIPFPFIGVDGTSVCSSIFDTDGKTKVSCPLK 419 (444)
Q Consensus 381 ~~il~l~e~G~i~~~~~~~~~~~~kw~~~~~~~~~c~~~ 419 (444)
.+++.|.|.|+++|+ ++|||.|. ..|...
T Consensus 771 LAvLkL~E~G~LdKL-------kNKWWYDk---GeC~sg 799 (897)
T KOG1054|consen 771 LAVLKLNEQGLLDKL-------KNKWWYDK---GECGSG 799 (897)
T ss_pred hhhhhhcccchHHHh-------hhhhcccc---cccCCC
Confidence 999999999999999 99999984 488643
No 2
>KOG1053|consensus
Probab=100.00 E-value=3.8e-47 Score=385.39 Aligned_cols=352 Identities=24% Similarity=0.418 Sum_probs=317.3
Q ss_pred eeeEEEeccCCCeEEEecCCC----------------------------CCceeeeecHHHHHHHHHHHcCCeEEEEEcC
Q psy12229 5 TNISDSRLKQEPFVMREESEG----------------------------GGGVKYKGYCIDLIEEIRKLVGFEYEIFVAP 56 (444)
Q Consensus 5 ~~l~V~~~~~~Pf~~~~~~~~----------------------------~~~~~~~G~~~dil~~la~~lnft~~~~~~~ 56 (444)
.||+|+|.+-+||++...-+. +-+..++||++||++-||+-+||+|.++...
T Consensus 411 ~HL~VvTLeE~PFVive~vDP~t~~C~~ntvpc~s~~~~t~ss~~~~~~tvKkCCkGfCIDiLkKlA~~v~FtYDLYlVt 490 (1258)
T KOG1053|consen 411 LHLTVVTLEERPFVIVEDVDPLTQTCVRNTVPCRSQLNSTFSSGDEANRTVKKCCKGFCIDILKKLARDVKFTYDLYLVT 490 (1258)
T ss_pred ceeEEEEeccCCeEEEecCCCCcCcCCCCCCcchhhhhhccCCCccCCchHHhhhhhhhHHHHHHHHhhcCcceEEEEec
Confidence 489999999999999874221 1133578999999999999999999999999
Q ss_pred CCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHH
Q psy12229 57 DNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWL 136 (444)
Q Consensus 57 ~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi 136 (444)
+++||+.. ||.|+|||++|..+++||++++++++.||.+.+|||.||.+ +++.+||.+.+...+..+|+.||++.+|+
T Consensus 491 nGKhGkk~-ng~WnGmIGev~~~rA~MAVgSltINeeRSevVDFSvPFve-TgIsVmV~rsngtvspsAFLePfs~svWV 568 (1258)
T KOG1053|consen 491 NGKHGKKI-NGVWNGMIGEVVYQRADMAVGSLTINEERSEVVDFSVPFVE-TGISVMVARSNGTVSPSAFLEPFSPSVWV 568 (1258)
T ss_pred CCccccee-cCcchhhHHHHHhhhhheeeeeeEechhhhccccccccccc-cceEEEEEecCCccCchhhcCCcchHHHH
Confidence 99999985 88999999999999999999999999999999999999999 99999999999999999999999999999
Q ss_pred HHHHHHHHHh-------cceeccccccCCCCCCCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHH
Q psy12229 137 CILAAYCNLD-------GEQMKYLIQVNPPGDILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFG 209 (444)
Q Consensus 137 ~i~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~ 209 (444)
+++++++.++ .+++|+++.++....+...+..+-+.-+.++..+++|+.++ ..+.|+...+|+++.+|.+|+
T Consensus 569 mmFVm~livaai~vFlFEy~SPvgyn~~l~~gkkpggp~FtigkaiwllwaLvFnnsV-pv~nPKgtTskiMv~VWAfFa 647 (1258)
T KOG1053|consen 569 MMFVMCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGPSFTIGKAIWLLWALVFNNSV-PVENPKGTTSKIMVLVWAFFA 647 (1258)
T ss_pred HHHHHHHHHHHHHHHHHhhcCcccccccccCCCCCCCcceehhhHHHHHHHHHhCCCc-CCCCCCchHHHHHHHHHHHHH
Confidence 9998887755 78899998887776666667777788888888999999999 789999999999999999999
Q ss_pred HHHHHHhhhcchhhhhcccCCCCCCChHHhhhC------CceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCc
Q psy12229 210 FIIIASYTANLAAFLTVSRLDTPIESLDDLSKQ------YKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLS 283 (444)
Q Consensus 210 lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 283 (444)
++.-++|+|+|++++....+..++..+.|=.-| ...++|++.+++++++++
T Consensus 648 vifLAsYTANLAAfMIqE~~~d~vSGlsD~KfqrP~dq~PpFRFGTVpngSTE~niR----------------------- 704 (1258)
T KOG1053|consen 648 VIFLASYTANLAAFMIQEEYYDTVSGLSDPKFQRPHDQYPPFRFGTVPNGSTERNIR----------------------- 704 (1258)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhhccccCcccccCccccCCCcccccCCCCchhhhHH-----------------------
Confidence 999999999999999998888887777775443 156799999999998876
Q ss_pred HHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhc--CCCccEEeC--Cc
Q psy12229 284 DVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVM--TNCDLQMVG--DE 359 (444)
Q Consensus 284 ~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~--~~c~l~~~~--~~ 359 (444)
++|++|...|++-+ ....+++++.+++|+ -+|||+|...+.|.+. ++|+|..++ +.
T Consensus 705 ---------------~Nyp~MHeYM~kyN-q~~v~dal~sLK~gK----LDAFIyDaAVLnY~agkDegCKLvTIGsgKv 764 (1258)
T KOG1053|consen 705 ---------------SNYPEMHEYMVKYN-QPGVEDALESLKNGK----LDAFIYDAAVLNYMAGKDEGCKLVTIGSGKV 764 (1258)
T ss_pred ---------------hccHHHHHHHHHhc-cCchHHHHHHHhccc----chhHHHHHHHHHHhhccCCCceEEEecCCce
Confidence 56788888888744 568999999999998 8999999999999998 569999999 89
Q ss_pred ccccceEEEecCCCchhhhhHHHHHHHhcCCccccCCCCCcccccccccC
Q psy12229 360 FSRKPYAIAVQQDRDARELFCNVHANILSIPFPFIGVDGTSVCSSIFDTD 409 (444)
Q Consensus 360 ~~~~~~~~~~~k~sp~~~~in~~il~l~e~G~i~~~~~~~~~~~~kw~~~ 409 (444)
|...+||++++||||++..||.+|++.+.+|.++.+ +++|+..
T Consensus 765 FAttGYGIal~k~Spwkr~IdlallQy~gdGeme~L-------e~~Wltg 807 (1258)
T KOG1053|consen 765 FATTGYGIALPKNSPWKRQIDLALLQYLGDGEMEML-------ETLWLTG 807 (1258)
T ss_pred eeecceeeecCCCCcchhhHHHHHHHHhccchHHHH-------HHHHhhc
Confidence 999999999999999999999999999999999999 9999986
No 3
>KOG1052|consensus
Probab=100.00 E-value=6.5e-44 Score=382.79 Aligned_cols=355 Identities=32% Similarity=0.565 Sum_probs=309.5
Q ss_pred eeeeEEEeccCCCeEEEecC--CCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccc
Q psy12229 4 ITNISDSRLKQEPFVMREES--EGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRA 81 (444)
Q Consensus 4 ~~~l~V~~~~~~Pf~~~~~~--~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~ 81 (444)
..+++|.+...+||....++ ..++...+.|+++|+++++++++||+|+++.++++. |...++|+|+|++++|++|++
T Consensus 215 ~~~l~v~~~~~~P~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~-g~~~~~g~~~g~v~~l~~~~a 293 (656)
T KOG1052|consen 215 GKPLRVGVVTEPPFVDLVEDLAILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGS-GSRDPNGNWDGLVGQLVDGEA 293 (656)
T ss_pred CceEEEEEeccCCceeeeecccccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCC-CCCCCCCChhHHHHHHhcCcc
Confidence 67899999999999998887 444556899999999999999999999999999888 888888999999999999999
Q ss_pred cEEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHh------cceeccccc
Q psy12229 82 DIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLD------GEQMKYLIQ 155 (444)
Q Consensus 82 Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~------~~~~~~~~~ 155 (444)
|++ ++++++.+|...+|||.||+. .++++++++++..+..+.|++||++.+|+++++++++++ .++.+.++
T Consensus 294 dvg-~~~tit~~R~~~vdfT~p~~~-~~~~i~~~~~~~~~~~~~fl~Pf~~~vW~~i~~~~l~~~~~~~~~~~~~~~~~- 370 (656)
T KOG1052|consen 294 DVG-ADITITPERSKYVDFTIPYLQ-FGIVIIVRKPDSRSKLWNFLAPFSPEVWLLILASLLLVGLLLWILERLSPYEL- 370 (656)
T ss_pred ccc-cceEEeecccccEEeccceEe-ccEEEEEEecCCcccceEEecCCcHHHHHHHHHHHHHHHHHHHHHhccccccC-
Confidence 999 999999999999999999999 999999999987666999999999999999999999987 34444444
Q ss_pred cCCCCCCC---cccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCC
Q psy12229 156 VNPPGDIL---PEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTP 232 (444)
Q Consensus 156 ~~~~~~~~---~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~ 232 (444)
... .... ....+.|+++++++.|| ....|++.++|++.++||+++++++++|+|+|+|+||+++...+
T Consensus 371 ~~~-~~~~~~~~~~~~~~~~~~~~~~q~--------~~~~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~~~~~~ 441 (656)
T KOG1052|consen 371 PPR-QIVTSLFSLLNCLWLTVGSLLQQG--------SDEIPRSLSTRLLLGAWWLFVLILISSYTANLTAFLTVPRLRSP 441 (656)
T ss_pred Ccc-ccceeEeecccchhhhhHHHhccC--------CCccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCc
Confidence 111 1111 12346789999999999 88999999999999999999999999999999999999999999
Q ss_pred CCChHHhhhCCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHh--
Q psy12229 233 IESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKE-- 310 (444)
Q Consensus 233 I~sl~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~-- 310 (444)
|++++||+++.++.+|...++....+++++ .++| ..+.+
T Consensus 442 i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~-------~~~~--------------------------------~~~~~~~ 482 (656)
T KOG1052|consen 442 IDSLDDLADQSNIPYGTQRGSFTRIYLEES-------EDMW--------------------------------AFKVSQR 482 (656)
T ss_pred ccCHHHHHHhcCCeEEEEecchHHHHHHHH-------HHHH--------------------------------hhhccCC
Confidence 999999998778999999999999999875 1222 22222
Q ss_pred cCCCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcCC--CccEEeCCcccccceEEEecCCCchhhhhHHHHHHHhc
Q psy12229 311 AKLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTN--CDLQMVGDEFSRKPYAIAVQQDRDARELFCNVHANILS 388 (444)
Q Consensus 311 ~~~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~--c~l~~~~~~~~~~~~~~~~~k~sp~~~~in~~il~l~e 388 (444)
.....+.+|+++++++|.. +.++++.+...+.|....+ |+++.+++.+...+++ ++||||||++.++.+|++++|
T Consensus 483 ~~~~~~~~e~~~~v~~~~~--~~~~~~~~~~~~~~~~~~~~~c~~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e 559 (656)
T KOG1052|consen 483 SVPLASPEEGVERVRKGPS--GGYAFASDELYLAYLFLRDEICDLTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQE 559 (656)
T ss_pred CccCCCHHHHHHHHHcCCC--CceEEEeccHHHHHHHhhcCCCceEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhcc
Confidence 3357799999999999964 3699999999999888866 9999999999999999 999999999999999999999
Q ss_pred CCccccCCCCCcccccccccCCCCcccCCCCC
Q psy12229 389 IPFPFIGVDGTSVCSSIFDTDGKTKVSCPLKK 420 (444)
Q Consensus 389 ~G~i~~~~~~~~~~~~kw~~~~~~~~~c~~~~ 420 (444)
.|.+++| ++||+...+....|....
T Consensus 560 ~g~l~~~-------~~kw~~~~~~~~~~~~~~ 584 (656)
T KOG1052|consen 560 TGILQKL-------KRKWFSKKPCLPKCSQTE 584 (656)
T ss_pred ccHHHHH-------HHHhccCCCCCCCCCCcc
Confidence 9999999 999999864455676654
No 4
>KOG4440|consensus
Probab=100.00 E-value=1.7e-43 Score=347.42 Aligned_cols=361 Identities=26% Similarity=0.430 Sum_probs=306.9
Q ss_pred eeeeEEEeccCCCeEEEecCCC---------------------------------CCceeeeecHHHHHHHHHHHcCCeE
Q psy12229 4 ITNISDSRLKQEPFVMREESEG---------------------------------GGGVKYKGYCIDLIEEIRKLVGFEY 50 (444)
Q Consensus 4 ~~~l~V~~~~~~Pf~~~~~~~~---------------------------------~~~~~~~G~~~dil~~la~~lnft~ 50 (444)
-+||||.|.+.+||+|.+.... +..-...|+++|++-.+++.+||+|
T Consensus 402 pthLrivTi~~~PFVYv~p~~sd~~c~eef~~~~d~~~k~~c~gpn~s~p~s~~~t~~fCC~G~cIDLLi~Ls~~~Nfty 481 (993)
T KOG4440|consen 402 PTHLRIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDSSPGSPRHTVPFCCYGFCIDLLIKLSRTMNFTY 481 (993)
T ss_pred cceeEEEEeccCCeEEEecCCCCcchhhhccccCCcccceeecCCCCCCCCCcccCcchhhhHHHHHHHHHHHHhhcceE
Confidence 4799999999999999983111 0012467999999999999999999
Q ss_pred EEEEcCCCCCcccc--------CCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEEEEeCCCCCCc
Q psy12229 51 EIFVAPDNSFGNMD--------ENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTS 122 (444)
Q Consensus 51 ~~~~~~~~~~g~~~--------~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~ 122 (444)
+....+++++|... ..-.|+|+||.|.+|++||+++++++++||.++++||.|+.. .++.++.+++.+.+.
T Consensus 482 d~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMivaplTINpERa~yieFskPfkY-qGitILeKk~~r~St 560 (993)
T KOG4440|consen 482 DVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMIVAPLTINPERAQYIEFSKPFKY-QGITILEKKEIRRST 560 (993)
T ss_pred EEEEeecccccceeeeecccccccceehhhhhhhhCCccceEeeceeeChhhhhheeccCcccc-cceEEEeeCCCCCch
Confidence 99999999998643 122699999999999999999999999999999999999999 899999999999999
Q ss_pred ccccccccchhHHHHHHHHHHHHh------cceeccccccCCCCCCC-----cccchhhhhhhHhHhcccccccCCCCCC
Q psy12229 123 LFKFLTVLETGVWLCILAAYCNLD------GEQMKYLIQVNPPGDIL-----PEVIRAIILMQNITDAGILFDDSFSGGE 191 (444)
Q Consensus 123 ~~~~l~pF~~~vWi~i~~~~~~~~------~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~l~~~g~~~~~~~~~~~ 191 (444)
...|++||+..+|+++.++..+++ -+|+|++.-.....-.+ ......||.|+.++..| -+..
T Consensus 561 l~SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPFgRFk~~ds~~~ee~alnlssAmWF~WGVLLNSG-------igEg 633 (993)
T KOG4440|consen 561 LDSFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPFGRFKVNDSEEEEEDALNLSSAMWFSWGVLLNSG-------IGEG 633 (993)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccceeeccCccchhhhcchhhhHHHHhHhhhccc-------cCCC
Confidence 999999999999999998887766 56677654332111111 24678899999999887 3788
Q ss_pred CCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhC---CceeeEecCCChhhHHhhhhhhhhhH
Q psy12229 192 APKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQ---YKIQYAPLNGSAAMTYFQRMADIEGR 268 (444)
Q Consensus 192 ~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~ 268 (444)
.|++.|.|++-++|+=|++|++++|+|+|+++|.-.+.+..+..++|-.-. .+..++++.+++.+.||++.-
T Consensus 634 tPRSfSARvLGmVWaGFaMIiVASYTANLAAFLVLdrPe~~ltGinDpRLRNps~nf~~aTVk~SsVd~YFrRqV----- 708 (993)
T KOG4440|consen 634 TPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLDRPEERLTGINDPRLRNPSDNFIYATVKQSSVDIYFRRQV----- 708 (993)
T ss_pred CCcchhHHHHHHHHhhhheeeehhhhhhhhhheeecCccccccCCCCccccCcccceeEEEecCccHHHHHHHHh-----
Confidence 999999999999999999999999999999999998889888888886543 478899999999999999642
Q ss_pred HHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhc
Q psy12229 269 FYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVM 348 (444)
Q Consensus 269 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~ 348 (444)
| -..|+..|+.++ ..+-+|+++.|++|+ -.|||.|...++|.+.
T Consensus 709 --E-----------------------------LS~MyR~ME~hN-y~~A~eAiq~v~~gk----L~AFIWDS~rLEfEAs 752 (993)
T KOG4440|consen 709 --E-----------------------------LSTMYRHMEKHN-YESAAEAIQAVRDGK----LHAFIWDSARLEFEAS 752 (993)
T ss_pred --H-----------------------------HHHHHHhhhhcc-hhhHHHHHHHHHcCc----eeEEEeecceeeehhh
Confidence 1 123455565554 678999999999998 8999999999999999
Q ss_pred CCCccEEeCCcccccceEEEecCCCchhhhhHHHHHHHhcCCccccCCCCCcccccccccCCCCcccCCCCCC
Q psy12229 349 TNCDLQMVGDEFSRKPYAIAVQQDRDARELFCNVHANILSIPFPFIGVDGTSVCSSIFDTDGKTKVSCPLKKD 421 (444)
Q Consensus 349 ~~c~l~~~~~~~~~~~~~~~~~k~sp~~~~in~~il~l~e~G~i~~~~~~~~~~~~kw~~~~~~~~~c~~~~~ 421 (444)
++|.|...++.|....||+.++||||+.+.+..+|++++|+|+|+++ -++|..-+. .-.|...+.
T Consensus 753 ~~CeLvT~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~~hEsGfMEkL-------Dk~Wi~~Gg-pq~c~~~~k 817 (993)
T KOG4440|consen 753 QKCELVTTGELFGRSGYGIGLQKDSPWTQNVTLAILKSHESGFMEKL-------DKTWIRYGG-PQECDSRSK 817 (993)
T ss_pred cccceEeccccccccccccccccCCCCcchhhHHHHHhhhcchHHHH-------HHHHHhcCC-cchhhhhcc
Confidence 99999999999999999999999999999999999999999999999 999998752 334554433
No 5
>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=99.86 E-value=8.4e-21 Score=175.57 Aligned_cols=221 Identities=22% Similarity=0.332 Sum_probs=178.4
Q ss_pred eEEEe-ccCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEe
Q psy12229 7 ISDSR-LKQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIAL 85 (444)
Q Consensus 7 l~V~~-~~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~ 85 (444)
|||++ .++|||++.+.++ +..|+++|+++++++++|++++++.. +|..++.+|.+|++|+++
T Consensus 1 l~V~~~~~~~P~~~~~~~~-----~~~G~~~dl~~~i~~~~g~~~~~~~~------------~~~~~~~~l~~g~~D~~~ 63 (225)
T PF00497_consen 1 LRVGVDEDYPPFSYIDEDG-----EPSGIDVDLLRAIAKRLGIKIEFVPM------------PWSRLLEMLENGKADIII 63 (225)
T ss_dssp EEEEEESEBTTTBEEETTS-----EEESHHHHHHHHHHHHHTCEEEEEEE------------EGGGHHHHHHTTSSSEEE
T ss_pred CEEEEcCCCCCeEEECCCC-----CEEEEhHHHHHHHHhhcccccceeec------------cccccccccccccccccc
Confidence 68877 8999999999866 79999999999999999999999964 689999999999999999
Q ss_pred ecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCCCcc
Q psy12229 86 GSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDILPE 165 (444)
Q Consensus 86 ~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 (444)
+++..+.+|.+.++||.|++. ...++++++.+.
T Consensus 64 ~~~~~~~~r~~~~~~s~p~~~-~~~~~~~~~~~~---------------------------------------------- 96 (225)
T PF00497_consen 64 GGLSITPERAKKFDFSDPYYS-SPYVLVVRKGDA---------------------------------------------- 96 (225)
T ss_dssp SSEB-BHHHHTTEEEESESEE-EEEEEEEETTST----------------------------------------------
T ss_pred ccccccccccccccccccccc-hhheeeeccccc----------------------------------------------
Confidence 999999999999999999999 999999986420
Q ss_pred cchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhCCce
Q psy12229 166 VIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQYKI 245 (444)
Q Consensus 166 ~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~~~~ 245 (444)
+....+++++||.+ .
T Consensus 97 --------------------------------------------------------------~~~~~~~~~~dl~~---~ 111 (225)
T PF00497_consen 97 --------------------------------------------------------------PPIKTIKSLDDLKG---K 111 (225)
T ss_dssp --------------------------------------------------------------CSTSSHSSGGGGTT---S
T ss_pred --------------------------------------------------------------cccccccchhhhcC---c
Confidence 01345677888955 3
Q ss_pred eeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHHHHH
Q psy12229 246 QYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQRVR 325 (444)
Q Consensus 246 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~~v~ 325 (444)
++++..++...+++..... ...++ ....+.++++++|.
T Consensus 112 ~i~~~~g~~~~~~l~~~~~---------------------~~~~~---------------------~~~~~~~~~~~~l~ 149 (225)
T PF00497_consen 112 RIGVVRGSSYADYLKQQYP---------------------SNINI---------------------VEVDSPEEALEALL 149 (225)
T ss_dssp EEEEETTSHHHHHHHHHTH---------------------HTSEE---------------------EEESSHHHHHHHHH
T ss_pred ccccccchhHHHHhhhhcc---------------------chhhh---------------------cccccHHHHHHHHh
Confidence 7999999887777765210 00111 12469999999999
Q ss_pred hcCCCCCceEEEecccchhhhhcCCC--ccEEeCCcccccceEEEecC-CCchhhhhHHHHHHHhcCCccccCCCCCccc
Q psy12229 326 DSKSSSEGFGYLGDATDIRYLVMTNC--DLQMVGDEFSRKPYAIAVQQ-DRDARELFCNVHANILSIPFPFIGVDGTSVC 402 (444)
Q Consensus 326 ~~~~~~~~~a~i~d~~~~~y~~~~~c--~l~~~~~~~~~~~~~~~~~k-~sp~~~~in~~il~l~e~G~i~~~~~~~~~~ 402 (444)
+|+ .++++.+...+.|..++.. ............++++++++ ++.+.+.||++|.+|.++|.++++
T Consensus 150 ~g~----~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~i~~l~~~G~~~~i------- 218 (225)
T PF00497_consen 150 SGR----IDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRKKNPELLEIFNKAIRELKQSGEIQKI------- 218 (225)
T ss_dssp TTS----SSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEETTTHHHHHHHHHHHHHHHHTTHHHHH-------
T ss_pred cCC----eeeeeccchhhhhhhhhcccccccccccccccceeEEeecccccHHHHHHHHHHHHHHhCcHHHHH-------
Confidence 997 8999999999999988554 23332455556666667765 557999999999999999999999
Q ss_pred ccccccC
Q psy12229 403 SSIFDTD 409 (444)
Q Consensus 403 ~~kw~~~ 409 (444)
.+||+++
T Consensus 219 ~~ky~g~ 225 (225)
T PF00497_consen 219 LKKYLGD 225 (225)
T ss_dssp HHHHHSS
T ss_pred HHHHcCC
Confidence 9999975
No 6
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.85 E-value=2.3e-20 Score=176.79 Aligned_cols=220 Identities=21% Similarity=0.346 Sum_probs=180.0
Q ss_pred eeeeEEEec-cCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhccccc
Q psy12229 4 ITNISDSRL-KQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRAD 82 (444)
Q Consensus 4 ~~~l~V~~~-~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~D 82 (444)
-+.|+|++. ++|||.+.. ++ ++.|+++|+++++++++|.+++++.. +|.+++.++.+|++|
T Consensus 24 ~~~l~v~~~~~~~P~~~~~-~g-----~~~G~~vdl~~~ia~~lg~~~~~~~~------------~~~~~~~~l~~G~vD 85 (247)
T PRK09495 24 DKKLVVATDTAFVPFEFKQ-GD-----KYVGFDIDLWAAIAKELKLDYTLKPM------------DFSGIIPALQTKNVD 85 (247)
T ss_pred CCeEEEEeCCCCCCeeecC-CC-----ceEEEeHHHHHHHHHHhCCceEEEeC------------CHHHHHHHHhCCCcC
Confidence 357899876 799999864 34 58999999999999999999999854 689999999999999
Q ss_pred EEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCC
Q psy12229 83 IALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDI 162 (444)
Q Consensus 83 i~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~ 162 (444)
+++++++.+++|.+.++||.||+. +.+.+++++.
T Consensus 86 i~~~~~~~t~~R~~~~~fs~p~~~-~~~~~~~~~~--------------------------------------------- 119 (247)
T PRK09495 86 LALAGITITDERKKAIDFSDGYYK-SGLLVMVKAN--------------------------------------------- 119 (247)
T ss_pred EEEecCccCHHHHhhccccchhee-cceEEEEECC---------------------------------------------
Confidence 998889999999999999999999 8999999764
Q ss_pred CcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhC
Q psy12229 163 LPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQ 242 (444)
Q Consensus 163 ~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~ 242 (444)
..++++++||.++
T Consensus 120 -------------------------------------------------------------------~~~~~~~~dL~g~ 132 (247)
T PRK09495 120 -------------------------------------------------------------------NNDIKSVKDLDGK 132 (247)
T ss_pred -------------------------------------------------------------------CCCCCChHHhCCC
Confidence 2357899999663
Q ss_pred CceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHH
Q psy12229 243 YKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQ 322 (444)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~ 322 (444)
++++..++....+++.... ..+ .....+..++++
T Consensus 133 ---~I~v~~g~~~~~~l~~~~~----------------------~~~---------------------i~~~~~~~~~~~ 166 (247)
T PRK09495 133 ---VVAVKSGTGSVDYAKANIK----------------------TKD---------------------LRQFPNIDNAYL 166 (247)
T ss_pred ---EEEEecCchHHHHHHhcCC----------------------CCc---------------------eEEcCCHHHHHH
Confidence 7888888777766653210 000 112457889999
Q ss_pred HHHhcCCCCCceEEEecccchhhhhcCC--CccEEeCCcccccceEEEecCCCchhhhhHHHHHHHhcCCccccCCCCCc
Q psy12229 323 RVRDSKSSSEGFGYLGDATDIRYLVMTN--CDLQMVGDEFSRKPYAIAVQQDRDARELFCNVHANILSIPFPFIGVDGTS 400 (444)
Q Consensus 323 ~v~~~~~~~~~~a~i~d~~~~~y~~~~~--c~l~~~~~~~~~~~~~~~~~k~sp~~~~in~~il~l~e~G~i~~~~~~~~ 400 (444)
++.+|+ .+|++.+...+.|..++. .++..+.......+++++++|++.+.+.||++|.++.++|.++++
T Consensus 167 ~L~~gr----vDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~n~al~~~~~~g~~~~i----- 237 (247)
T PRK09495 167 ELGTGR----ADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSELREKVNGALKTLKENGTYAEI----- 237 (247)
T ss_pred HHHcCc----eeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEEEcCcHHHHHHHHHHHHHHHHCCcHHHH-----
Confidence 999998 999999988888776643 256666666666788899999999999999999999999999999
Q ss_pred ccccccccCCC
Q psy12229 401 VCSSIFDTDGK 411 (444)
Q Consensus 401 ~~~~kw~~~~~ 411 (444)
.+||+...|
T Consensus 238 --~~k~~~~~~ 246 (247)
T PRK09495 238 --YKKWFGTEP 246 (247)
T ss_pred --HHHHcCCCC
Confidence 999998653
No 7
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.84 E-value=3.7e-20 Score=180.37 Aligned_cols=224 Identities=15% Similarity=0.186 Sum_probs=176.8
Q ss_pred ceeeeEEEec-cCCCeEEEecCCCCCceeeeecHHHHHHHHHH----Hc---CCeEEEEEcCCCCCccccCCCccchhHH
Q psy12229 3 TITNISDSRL-KQEPFVMREESEGGGGVKYKGYCIDLIEEIRK----LV---GFEYEIFVAPDNSFGNMDENGQWNGMIK 74 (444)
Q Consensus 3 ~~~~l~V~~~-~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~----~l---nft~~~~~~~~~~~g~~~~ng~~~g~i~ 74 (444)
..+.|+|++. ++|||.+...++ +..|+++|++++|++ ++ +.++++++. +|.+++.
T Consensus 38 ~~g~L~Vg~~~~~pP~~f~~~~g-----~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~------------~~~~~i~ 100 (302)
T PRK10797 38 KNGVIVVGHRESSVPFSYYDNQQ-----KVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPI------------TSQNRIP 100 (302)
T ss_pred hCCeEEEEEcCCCCCcceECCCC-----CEeeecHHHHHHHHHHHHHhhCCCCceEEEEEc------------ChHhHHH
Confidence 3567899655 699999986544 699999998777766 55 478888855 5677899
Q ss_pred HHhcccccEEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceecccc
Q psy12229 75 ELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLI 154 (444)
Q Consensus 75 ~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~ 154 (444)
.|.+|++|++++++++|++|.+.++||.||+. ++..+++++.
T Consensus 101 ~L~~G~~Di~~~~~~~t~eR~~~~~fS~Py~~-~~~~lv~r~~------------------------------------- 142 (302)
T PRK10797 101 LLQNGTFDFECGSTTNNLERQKQAAFSDTIFV-VGTRLLTKKG------------------------------------- 142 (302)
T ss_pred HHHCCCccEEecCCccCcchhhcceecccEee-ccEEEEEECC-------------------------------------
Confidence 99999999999999999999999999999999 9999999764
Q ss_pred ccCCCCCCCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCC
Q psy12229 155 QVNPPGDILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIE 234 (444)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~ 234 (444)
. .|+
T Consensus 143 ---------------------------------------------------------------------------~-~i~ 146 (302)
T PRK10797 143 ---------------------------------------------------------------------------G-DIK 146 (302)
T ss_pred ---------------------------------------------------------------------------C-CCC
Confidence 1 367
Q ss_pred ChHHhhhCCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCC
Q psy12229 235 SLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLP 314 (444)
Q Consensus 235 sl~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~ 314 (444)
+++||.+ .++++..++....+++..... . .-+. +....
T Consensus 147 sl~dL~G---k~V~v~~gs~~~~~l~~~~~~---------------~-----~~~~-------------------~i~~~ 184 (302)
T PRK10797 147 DFADLKG---KAVVVTSGTTSEVLLNKLNEE---------------Q-----KMNM-------------------RIISA 184 (302)
T ss_pred ChHHcCC---CEEEEeCCCcHHHHHHHHhhh---------------c-----CCce-------------------EEEEe
Confidence 8899966 479999998888777542100 0 0000 11124
Q ss_pred CCHHHHHHHHHhcCCCCCceEEEecccchhhhhc--CC-CccEEeCCcccccceEEEecCCCc-hhhhhHHHHHHHhcCC
Q psy12229 315 NSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVM--TN-CDLQMVGDEFSRKPYAIAVQQDRD-ARELFCNVHANILSIP 390 (444)
Q Consensus 315 ~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~--~~-c~l~~~~~~~~~~~~~~~~~k~sp-~~~~in~~il~l~e~G 390 (444)
.+.+++++.|..|+ .+|++.|...+.+... .. ..++++++.+...+++++++|+++ +++.+|.+|.+++++|
T Consensus 185 ~~~~~~l~~L~~Gr----vDa~i~d~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~~a~~k~~~~L~~~in~~L~~l~~~G 260 (302)
T PRK10797 185 KDHGDSFRTLESGR----AVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQAQTSG 260 (302)
T ss_pred CCHHHHHHHHHcCC----ceEEEccHHHHHHHHHcCCCCcceEECCccCCcCceeEEEeCCCHHHHHHHHHHHHHHHhCc
Confidence 68999999999998 8999999776655332 22 257788877778889999999886 9999999999999999
Q ss_pred ccccCCCCCcccccccccCC
Q psy12229 391 FPFIGVDGTSVCSSIFDTDG 410 (444)
Q Consensus 391 ~i~~~~~~~~~~~~kw~~~~ 410 (444)
.++++ .+||++..
T Consensus 261 ~l~~i-------~~kw~~~~ 273 (302)
T PRK10797 261 EAEKW-------FDKWFKNP 273 (302)
T ss_pred hHHHH-------HHHHcCCC
Confidence 99999 99999964
No 8
>PRK11260 cystine transporter subunit; Provisional
Probab=99.82 E-value=4.7e-19 Score=169.69 Aligned_cols=221 Identities=20% Similarity=0.274 Sum_probs=179.6
Q ss_pred ceeeeEEEec-cCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccc
Q psy12229 3 TITNISDSRL-KQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRA 81 (444)
Q Consensus 3 ~~~~l~V~~~-~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~ 81 (444)
..+.|+|+.. ++|||.+.+.++ ++.|+.+|+++.+++++|.+++++.. +|..++.++++|++
T Consensus 39 ~~~~l~v~~~~~~~P~~~~~~~g-----~~~G~~~dl~~~i~~~lg~~~e~~~~------------~~~~~~~~l~~G~~ 101 (266)
T PRK11260 39 ERGTLLVGLEGTYPPFSFQGEDG-----KLTGFEVEFAEALAKHLGVKASLKPT------------KWDGMLASLDSKRI 101 (266)
T ss_pred cCCeEEEEeCCCcCCceEECCCC-----CEEEehHHHHHHHHHHHCCeEEEEeC------------CHHHHHHHHhcCCC
Confidence 4578999765 599999876555 68999999999999999999999864 58899999999999
Q ss_pred cEEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCC
Q psy12229 82 DIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGD 161 (444)
Q Consensus 82 Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~ 161 (444)
|+++++++.+.+|...+.||.|++. .+..+++++.+
T Consensus 102 D~~~~~~~~~~~r~~~~~fs~p~~~-~~~~~~~~~~~------------------------------------------- 137 (266)
T PRK11260 102 DVVINQVTISDERKKKYDFSTPYTV-SGIQALVKKGN------------------------------------------- 137 (266)
T ss_pred CEEEeccccCHHHHhccccCCceee-cceEEEEEcCC-------------------------------------------
Confidence 9999888999999999999999998 89999887642
Q ss_pred CCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhh
Q psy12229 162 ILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSK 241 (444)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~ 241 (444)
...+++++||.+
T Consensus 138 --------------------------------------------------------------------~~~~~~~~dL~g 149 (266)
T PRK11260 138 --------------------------------------------------------------------EGTIKTAADLKG 149 (266)
T ss_pred --------------------------------------------------------------------cCCCCCHHHcCC
Confidence 235788899855
Q ss_pred CCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHH
Q psy12229 242 QYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAV 321 (444)
Q Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~ 321 (444)
.++|+..|+....++++.. + .. +....++..+++
T Consensus 150 ---~~Igv~~G~~~~~~l~~~~---------------~-------~~---------------------~i~~~~~~~~~l 183 (266)
T PRK11260 150 ---KKVGVGLGTNYEQWLRQNV---------------Q-------GV---------------------DVRTYDDDPTKY 183 (266)
T ss_pred ---CEEEEecCCcHHHHHHHhC---------------C-------CC---------------------ceEecCCHHHHH
Confidence 4788888887776665321 0 00 011245788999
Q ss_pred HHHHhcCCCCCceEEEecccchhhhhcCCCc-cEEeCCcccccceEEEecCCCc-hhhhhHHHHHHHhcCCccccCCCCC
Q psy12229 322 QRVRDSKSSSEGFGYLGDATDIRYLVMTNCD-LQMVGDEFSRKPYAIAVQQDRD-ARELFCNVHANILSIPFPFIGVDGT 399 (444)
Q Consensus 322 ~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c~-l~~~~~~~~~~~~~~~~~k~sp-~~~~in~~il~l~e~G~i~~~~~~~ 399 (444)
+++.+|+ .++++.+.....++.++... +.+....+...+++++++|+++ +.+.+|++|.++.++|.++++
T Consensus 184 ~~L~~Gr----vD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~~ln~~l~~~~~~g~~~~i---- 255 (266)
T PRK11260 184 QDLRVGR----IDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGVALRKGNPDLLKAVNQAIAEMQKDGTLKAL---- 255 (266)
T ss_pred HHHHcCC----CCEEEechHHHHHHHHhCCCcceecCCccccCceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHH----
Confidence 9999998 89999998777777765443 5555666677888999999885 999999999999999999999
Q ss_pred cccccccccC
Q psy12229 400 SVCSSIFDTD 409 (444)
Q Consensus 400 ~~~~~kw~~~ 409 (444)
.+||+++
T Consensus 256 ---~~k~~~~ 262 (266)
T PRK11260 256 ---SEKWFGA 262 (266)
T ss_pred ---HHHhcCC
Confidence 9999986
No 9
>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=99.80 E-value=1.2e-18 Score=167.75 Aligned_cols=224 Identities=17% Similarity=0.140 Sum_probs=176.1
Q ss_pred ceeeeEEEeccCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCe-EEEEEcCCCCCccccCCCccchhHHHHhcccc
Q psy12229 3 TITNISDSRLKQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFE-YEIFVAPDNSFGNMDENGQWNGMIKELIEKRA 81 (444)
Q Consensus 3 ~~~~l~V~~~~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft-~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~ 81 (444)
..++|+|.+.++|||.+.+.++ ++.|+++|+++++++++|.+ +++... +|+.++..+.+|++
T Consensus 31 ~~~~l~v~~~~~pP~~~~~~~g-----~~~G~~~dl~~~i~~~lg~~~~~~~~~------------~w~~~~~~l~~G~~ 93 (275)
T TIGR02995 31 EQGFARIAIANEPPFTYVGADG-----KVSGAAPDVARAIFKRLGIADVNASIT------------EYGALIPGLQAGRF 93 (275)
T ss_pred hCCcEEEEccCCCCceeECCCC-----ceecchHHHHHHHHHHhCCCceeeccC------------CHHHHHHHHHCCCc
Confidence 3468999999999999987665 68999999999999999986 566543 79999999999999
Q ss_pred cEEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCC
Q psy12229 82 DIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGD 161 (444)
Q Consensus 82 Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~ 161 (444)
|+++++++.+++|...++||.||+. +...+++++.+
T Consensus 94 Di~~~~~~~t~eR~~~~~fs~py~~-~~~~~~~~~~~------------------------------------------- 129 (275)
T TIGR02995 94 DAIAAGLFIKPERCKQVAFTQPILC-DAEALLVKKGN------------------------------------------- 129 (275)
T ss_pred CEEeecccCCHHHHhccccccceee-cceeEEEECCC-------------------------------------------
Confidence 9988889999999999999999999 89999997752
Q ss_pred CCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhh
Q psy12229 162 ILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSK 241 (444)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~ 241 (444)
...+++++||.+
T Consensus 130 --------------------------------------------------------------------~~~i~~~~dl~~ 141 (275)
T TIGR02995 130 --------------------------------------------------------------------PKGLKSYKDIAK 141 (275)
T ss_pred --------------------------------------------------------------------CCCCCCHHHhcc
Confidence 234678888875
Q ss_pred CCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHH
Q psy12229 242 QYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAV 321 (444)
Q Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~ 321 (444)
..+.++|+..++...+++++.... .. +....++.++++
T Consensus 142 ~~g~~Igv~~g~~~~~~l~~~~~~---------------------~~---------------------~i~~~~~~~~~i 179 (275)
T TIGR02995 142 NPDAKIAAPGGGTEEKLAREAGVK---------------------RE---------------------QIIVVPDGQSGL 179 (275)
T ss_pred CCCceEEEeCCcHHHHHHHHcCCC---------------------hh---------------------hEEEeCCHHHHH
Confidence 445789999998887777642100 00 111246899999
Q ss_pred HHHHhcCCCCCceEEEecccchhhhhcCC--CccEEeCCc---ccccceEEEecCCC-chhhhhHHHHHHHhcCCccccC
Q psy12229 322 QRVRDSKSSSEGFGYLGDATDIRYLVMTN--CDLQMVGDE---FSRKPYAIAVQQDR-DARELFCNVHANILSIPFPFIG 395 (444)
Q Consensus 322 ~~v~~~~~~~~~~a~i~d~~~~~y~~~~~--c~l~~~~~~---~~~~~~~~~~~k~s-p~~~~in~~il~l~e~G~i~~~ 395 (444)
+.|.+|+ .++++.+...+.+..++. .++..+... ....+++++++++. .+.+.||+.|.++.++|.++++
T Consensus 180 ~~L~~gr----vDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~~sG~~~~i 255 (275)
T TIGR02995 180 KMVQDGR----ADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPVRYYGGAAFRPEDKELRDAFNVELAKLKESGEFAKI 255 (275)
T ss_pred HHHHcCC----CCEEecChHHHHHHHHhCCCCCceeecCccCCccccceeEEECCCCHHHHHHHHHHHHHHHhChHHHHH
Confidence 9999998 999999998888887642 244443321 11123378888766 5999999999999999999999
Q ss_pred CCCCccccccccc
Q psy12229 396 VDGTSVCSSIFDT 408 (444)
Q Consensus 396 ~~~~~~~~~kw~~ 408 (444)
.+||--
T Consensus 256 -------~~ky~~ 261 (275)
T TIGR02995 256 -------IAPYGF 261 (275)
T ss_pred -------HHHhCC
Confidence 999943
No 10
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.79 E-value=2.8e-18 Score=161.78 Aligned_cols=216 Identities=18% Similarity=0.223 Sum_probs=170.7
Q ss_pred eeeeEEEec-cCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhccccc
Q psy12229 4 ITNISDSRL-KQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRAD 82 (444)
Q Consensus 4 ~~~l~V~~~-~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~D 82 (444)
.+.|+|++. ++|||++...++ ++.|+++|+++++++++|.+++++.. +|..++.++.+|++|
T Consensus 20 ~~~l~v~~~~~~~P~~~~~~~g-----~~~G~~~dl~~~i~~~lg~~~~~~~~------------~~~~~~~~l~~g~~D 82 (243)
T PRK15007 20 AETIRFATEASYPPFESIDANN-----QIVGFDVDLAQALCKEIDATCTFSNQ------------AFDSLIPSLKFRRVE 82 (243)
T ss_pred CCcEEEEeCCCCCCceeeCCCC-----CEEeeeHHHHHHHHHHhCCcEEEEeC------------CHHHHhHHHhCCCcC
Confidence 357899876 899999987655 69999999999999999999999854 688999999999999
Q ss_pred EEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCC
Q psy12229 83 IALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDI 162 (444)
Q Consensus 83 i~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~ 162 (444)
++++++..+++|...++||.||+. .+..++.+..
T Consensus 83 ~~~~~~~~~~~r~~~~~fs~p~~~-~~~~~v~~~~--------------------------------------------- 116 (243)
T PRK15007 83 AVMAGMDITPEREKQVLFTTPYYD-NSALFVGQQG--------------------------------------------- 116 (243)
T ss_pred EEEEcCccCHHHhcccceecCccc-cceEEEEeCC---------------------------------------------
Confidence 988888899999999999999998 7766665422
Q ss_pred CcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhC
Q psy12229 163 LPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQ 242 (444)
Q Consensus 163 ~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~ 242 (444)
.+++++||.+
T Consensus 117 ---------------------------------------------------------------------~~~~~~dL~g- 126 (243)
T PRK15007 117 ---------------------------------------------------------------------KYTSVDQLKG- 126 (243)
T ss_pred ---------------------------------------------------------------------CCCCHHHhCC-
Confidence 2567888855
Q ss_pred CceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHH
Q psy12229 243 YKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQ 322 (444)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~ 322 (444)
.++|+..++...+++.+... +. +.....+.+++++
T Consensus 127 --~~Igv~~g~~~~~~l~~~~~----------------------~~---------------------~~~~~~~~~~~~~ 161 (243)
T PRK15007 127 --KKVGVQNGTTHQKFIMDKHP----------------------EI---------------------TTVPYDSYQNAKL 161 (243)
T ss_pred --CeEEEecCcHHHHHHHHhCC----------------------CC---------------------eEEEcCCHHHHHH
Confidence 47898888877776654210 00 0111357889999
Q ss_pred HHHhcCCCCCceEEEecccchhhhhcCCCccEEeCCc-----ccccceEEEecCCC-chhhhhHHHHHHHhcCCccccCC
Q psy12229 323 RVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGDE-----FSRKPYAIAVQQDR-DARELFCNVHANILSIPFPFIGV 396 (444)
Q Consensus 323 ~v~~~~~~~~~~a~i~d~~~~~y~~~~~c~l~~~~~~-----~~~~~~~~~~~k~s-p~~~~in~~il~l~e~G~i~~~~ 396 (444)
+|.+|+ .+|++.+...+.+..++...+..+... ....+.+++++++. ++.+.||+.|..+.++|.++++
T Consensus 162 ~L~~gr----vDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ln~~l~~l~~~g~~~~i- 236 (243)
T PRK15007 162 DLQNGR----IDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETI- 236 (243)
T ss_pred HHHcCC----CCEEEeCHHHHHHHHhcCCCceeecCcccccccCCcceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHH-
Confidence 999997 899999988877777665555554432 22335789998876 6999999999999999999999
Q ss_pred CCCccccccccc
Q psy12229 397 DGTSVCSSIFDT 408 (444)
Q Consensus 397 ~~~~~~~~kw~~ 408 (444)
.+||+.
T Consensus 237 ------~~~w~~ 242 (243)
T PRK15007 237 ------YNKWFQ 242 (243)
T ss_pred ------HHHhcC
Confidence 999985
No 11
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.79 E-value=4.4e-18 Score=162.41 Aligned_cols=221 Identities=14% Similarity=0.171 Sum_probs=170.0
Q ss_pred eeeeEEEec-cCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhccccc
Q psy12229 4 ITNISDSRL-KQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRAD 82 (444)
Q Consensus 4 ~~~l~V~~~-~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~D 82 (444)
-..|+|++. ++|||.+.++++ ++.|+++|++++++++++.+++++.. +|+.++.++..|++|
T Consensus 25 ~~~l~v~~~~~~pPf~~~~~~g-----~~~G~~vdl~~~ia~~lg~~~~~~~~------------~~~~~~~~l~~g~~D 87 (260)
T PRK15010 25 PETVRIGTDTTYAPFSSKDAKG-----DFVGFDIDLGNEMCKRMQVKCTWVAS------------DFDALIPSLKAKKID 87 (260)
T ss_pred CCeEEEEecCCcCCceeECCCC-----CEEeeeHHHHHHHHHHhCCceEEEeC------------CHHHHHHHHHCCCCC
Confidence 367899887 799999987655 68999999999999999999999854 689999999999999
Q ss_pred EEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCC
Q psy12229 83 IALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDI 162 (444)
Q Consensus 83 i~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~ 162 (444)
++++++..+++|.+.++||.||+. +..++++++..
T Consensus 88 i~~~~~~~t~eR~~~~~fs~p~~~-~~~~~~~~~~~-------------------------------------------- 122 (260)
T PRK15010 88 AIISSLSITDKRQQEIAFSDKLYA-ADSRLIAAKGS-------------------------------------------- 122 (260)
T ss_pred EEEecCcCCHHHHhhcccccceEe-ccEEEEEECCC--------------------------------------------
Confidence 999999999999999999999999 89999997752
Q ss_pred CcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhC
Q psy12229 163 LPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQ 242 (444)
Q Consensus 163 ~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~ 242 (444)
+...+++||.+
T Consensus 123 --------------------------------------------------------------------~~~~~~~dl~g- 133 (260)
T PRK15010 123 --------------------------------------------------------------------PIQPTLDSLKG- 133 (260)
T ss_pred --------------------------------------------------------------------CCCCChhHcCC-
Confidence 11135777855
Q ss_pred CceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHH
Q psy12229 243 YKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQ 322 (444)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~ 322 (444)
.++|+..++....++..... ..++ +.....+.+++++
T Consensus 134 --~~Igv~~gs~~~~~~~~~~~----------------------~~~~-------------------~~~~~~~~~~~~~ 170 (260)
T PRK15010 134 --KHVGVLQGSTQEAYANETWR----------------------SKGV-------------------DVVAYANQDLVYS 170 (260)
T ss_pred --CEEEEecCchHHHHHHHhcc----------------------cCCc-------------------eEEecCCHHHHHH
Confidence 47999988876666542100 0000 0112357889999
Q ss_pred HHHhcCCCCCceEEEecccchhh-hhcC-C-CccEEeCCcc-----cccceEEEecCCC-chhhhhHHHHHHHhcCCccc
Q psy12229 323 RVRDSKSSSEGFGYLGDATDIRY-LVMT-N-CDLQMVGDEF-----SRKPYAIAVQQDR-DARELFCNVHANILSIPFPF 393 (444)
Q Consensus 323 ~v~~~~~~~~~~a~i~d~~~~~y-~~~~-~-c~l~~~~~~~-----~~~~~~~~~~k~s-p~~~~in~~il~l~e~G~i~ 393 (444)
+|.+|+ .+|++.|...+.+ +.++ . .++.++...+ ....++++++++. .+.+.+|+.|.++.++|.++
T Consensus 171 ~l~~gr----iDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~L~~~ln~~l~~l~~~G~~~ 246 (260)
T PRK15010 171 DLAAGR----LDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELRQDGTYD 246 (260)
T ss_pred HHHcCC----ccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEEEEeCCCHHHHHHHHHHHHHHHhCCcHH
Confidence 999998 8999999776654 2222 1 2455554322 2234578898877 59999999999999999999
Q ss_pred cCCCCCcccccccccC
Q psy12229 394 IGVDGTSVCSSIFDTD 409 (444)
Q Consensus 394 ~~~~~~~~~~~kw~~~ 409 (444)
++ .+||++.
T Consensus 247 ~i-------~~ky~~~ 255 (260)
T PRK15010 247 KM-------AKKYFDF 255 (260)
T ss_pred HH-------HHHhcCC
Confidence 99 9999974
No 12
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.78 E-value=8.5e-18 Score=159.10 Aligned_cols=217 Identities=18% Similarity=0.282 Sum_probs=173.4
Q ss_pred eeeEEEec-cCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccE
Q psy12229 5 TNISDSRL-KQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADI 83 (444)
Q Consensus 5 ~~l~V~~~-~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di 83 (444)
++|+|... ++|||.+...++ +.+|+++|+++.+++.+|.+++++.. +|..++.++.+|++|+
T Consensus 24 ~~l~v~~~~~~~P~~~~~~~g-----~~~G~~~dl~~~i~~~lg~~~~~~~~------------~~~~~~~~l~~G~~D~ 86 (250)
T TIGR01096 24 GSVRIGTETGYPPFESKDANG-----KLVGFDVDLAKALCKRMKAKCKFVEQ------------NFDGLIPSLKAKKVDA 86 (250)
T ss_pred CeEEEEECCCCCCceEECCCC-----CEEeehHHHHHHHHHHhCCeEEEEeC------------CHHHHHHHHhCCCcCE
Confidence 57999765 799999987665 68999999999999999999999864 6889999999999999
Q ss_pred EeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCCC
Q psy12229 84 ALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDIL 163 (444)
Q Consensus 84 ~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (444)
+++++..+.+|.+.+.||.|++. ....+++++..
T Consensus 87 ~~~~~~~~~~r~~~~~~s~p~~~-~~~~~~~~~~~--------------------------------------------- 120 (250)
T TIGR01096 87 IMATMSITPKRQKQIDFSDPYYA-TGQGFVVKKGS--------------------------------------------- 120 (250)
T ss_pred EEecCccCHHHhhccccccchhc-CCeEEEEECCC---------------------------------------------
Confidence 98888889999999999999999 89999987652
Q ss_pred cccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhCC
Q psy12229 164 PEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQY 243 (444)
Q Consensus 164 ~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~~ 243 (444)
..+.+++||.+
T Consensus 121 -------------------------------------------------------------------~~~~~~~dl~g-- 131 (250)
T TIGR01096 121 -------------------------------------------------------------------DLAKTLEDLDG-- 131 (250)
T ss_pred -------------------------------------------------------------------CcCCChHHcCC--
Confidence 12356778854
Q ss_pred ceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHHH
Q psy12229 244 KIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQR 323 (444)
Q Consensus 244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~~ 323 (444)
.++++..++....++.+... .++ +.....+.++++++
T Consensus 132 -~~i~~~~g~~~~~~l~~~~~-----------------------~~~-------------------~~~~~~s~~~~~~~ 168 (250)
T TIGR01096 132 -KTVGVQSGTTHEQYLKDYFK-----------------------PGV-------------------DIVEYDSYDNANMD 168 (250)
T ss_pred -CEEEEecCchHHHHHHHhcc-----------------------CCc-------------------EEEEcCCHHHHHHH
Confidence 47888888887777764210 000 01124589999999
Q ss_pred HHhcCCCCCceEEEecccchhhhhcCCC---ccEEeCCcccc-----cceEEEecCCCc-hhhhhHHHHHHHhcCCcccc
Q psy12229 324 VRDSKSSSEGFGYLGDATDIRYLVMTNC---DLQMVGDEFSR-----KPYAIAVQQDRD-ARELFCNVHANILSIPFPFI 394 (444)
Q Consensus 324 v~~~~~~~~~~a~i~d~~~~~y~~~~~c---~l~~~~~~~~~-----~~~~~~~~k~sp-~~~~in~~il~l~e~G~i~~ 394 (444)
|.+|+ .++++.+...+.+..++.. ++.+++..+.. ..++++++++++ +...||+.|.+|.++|.++.
T Consensus 169 L~~g~----vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ln~~l~~l~~~g~~~~ 244 (250)
T TIGR01096 169 LKAGR----IDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKGDTELKAAFNKALAAIRADGTYQK 244 (250)
T ss_pred HHcCC----CCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccCCceEEEEeCCCHHHHHHHHHHHHHHHHCCcHHH
Confidence 99998 9999999888888776543 36666543332 237889999875 99999999999999999999
Q ss_pred CCCCCcccccccc
Q psy12229 395 GVDGTSVCSSIFD 407 (444)
Q Consensus 395 ~~~~~~~~~~kw~ 407 (444)
+ .+||+
T Consensus 245 i-------~~kw~ 250 (250)
T TIGR01096 245 I-------SKKWF 250 (250)
T ss_pred H-------HHhhC
Confidence 9 99995
No 13
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.77 E-value=6.4e-18 Score=174.91 Aligned_cols=225 Identities=19% Similarity=0.205 Sum_probs=176.6
Q ss_pred eeeeEEEeccCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccE
Q psy12229 4 ITNISDSRLKQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADI 83 (444)
Q Consensus 4 ~~~l~V~~~~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di 83 (444)
.+.|+|.+.. +|+.+...++ ...|+++|+++++++++|.+++++..+ +|+.++.+|.+|++|+
T Consensus 42 ~g~LrVg~~~-~P~~~~~~~~-----~~~G~~~DLl~~ia~~LGv~~e~v~~~-----------~~~~ll~aL~~G~iDi 104 (482)
T PRK10859 42 RGELRVGTIN-SPLTYYIGND-----GPTGFEYELAKRFADYLGVKLEIKVRD-----------NISQLFDALDKGKADL 104 (482)
T ss_pred CCEEEEEEec-CCCeeEecCC-----CcccHHHHHHHHHHHHhCCcEEEEecC-----------CHHHHHHHHhCCCCCE
Confidence 4679998876 4555554433 259999999999999999999998544 7999999999999999
Q ss_pred EeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCCC
Q psy12229 84 ALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDIL 163 (444)
Q Consensus 84 ~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (444)
+++++++|++|.+.++||.||+. ....+++++.
T Consensus 105 ~~~~lt~T~eR~~~~~FS~Py~~-~~~~lv~r~~---------------------------------------------- 137 (482)
T PRK10859 105 AAAGLTYTPERLKQFRFGPPYYS-VSQQLVYRKG---------------------------------------------- 137 (482)
T ss_pred EeccCcCChhhhccCcccCCcee-eeEEEEEeCC----------------------------------------------
Confidence 99999999999999999999999 8988888764
Q ss_pred cccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhCC
Q psy12229 164 PEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQY 243 (444)
Q Consensus 164 ~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~~ 243 (444)
...+++++||.+
T Consensus 138 ------------------------------------------------------------------~~~i~~l~dL~G-- 149 (482)
T PRK10859 138 ------------------------------------------------------------------QPRPRSLGDLKG-- 149 (482)
T ss_pred ------------------------------------------------------------------CCCCCCHHHhCC--
Confidence 235788999976
Q ss_pred ceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHHH
Q psy12229 244 KIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQR 323 (444)
Q Consensus 244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~~ 323 (444)
.++++..++...+.++.... .++.+. + ......+.++++++
T Consensus 150 -k~I~V~~gS~~~~~L~~l~~-----------------------------------~~p~i~--~-~~~~~~s~~e~l~a 190 (482)
T PRK10859 150 -GTLTVAAGSSHVETLQELKK-----------------------------------KYPELS--W-EESDDKDSEELLEQ 190 (482)
T ss_pred -CeEEEECCCcHHHHHHHHHH-----------------------------------hCCCce--E-EecCCCCHHHHHHH
Confidence 47898999888877764321 000000 0 00113589999999
Q ss_pred HHhcCCCCCceEEEecccchhhhhcCCCccEEeCCcccccceEEEecCC-C-chhhhhHHHHHHHhcCCccccCCCCCcc
Q psy12229 324 VRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQQD-R-DARELFCNVHANILSIPFPFIGVDGTSV 401 (444)
Q Consensus 324 v~~~~~~~~~~a~i~d~~~~~y~~~~~c~l~~~~~~~~~~~~~~~~~k~-s-p~~~~in~~il~l~e~G~i~~~~~~~~~ 401 (444)
|.+|+ .++++.|...+.+......++.+........+++++++|+ + .+...+|++|.++.++|.++++
T Consensus 191 L~~G~----iDa~v~d~~~~~~~~~~~p~l~v~~~l~~~~~~~~av~k~~~~~L~~~ln~~L~~i~~~G~l~~L------ 260 (482)
T PRK10859 191 VAEGK----IDYTIADSVEISLNQRYHPELAVAFDLTDEQPVAWALPPSGDDSLYAALLDFFNQIKEDGTLARL------ 260 (482)
T ss_pred HHCCC----CCEEEECcHHHHHHHHhCCCceeeeecCCCceeEEEEeCCCCHHHHHHHHHHHHHhhcCCHHHHH------
Confidence 99997 8999999877766555555666655444556789999994 4 4999999999999999999999
Q ss_pred cccccccCC
Q psy12229 402 CSSIFDTDG 410 (444)
Q Consensus 402 ~~~kw~~~~ 410 (444)
.+||++..
T Consensus 261 -~~kyfg~~ 268 (482)
T PRK10859 261 -EEKYFGHV 268 (482)
T ss_pred -HHHHhhhh
Confidence 99999864
No 14
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.76 E-value=2.1e-17 Score=157.62 Aligned_cols=220 Identities=15% Similarity=0.169 Sum_probs=169.2
Q ss_pred eeeEEEec-cCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccE
Q psy12229 5 TNISDSRL-KQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADI 83 (444)
Q Consensus 5 ~~l~V~~~-~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di 83 (444)
.+|+|.+. ++|||++.+.++ ++.|+++|++++++++++.+++++.. +|..++.++.+|++|+
T Consensus 26 ~~l~v~~~~~~~P~~~~~~~g-----~~~G~~vdi~~~ia~~lg~~i~~~~~------------pw~~~~~~l~~g~~D~ 88 (259)
T PRK15437 26 QNIRIGTDPTYAPFESKNSQG-----ELVGFDIDLAKELCKRINTQCTFVEN------------PLDALIPSLKAKKIDA 88 (259)
T ss_pred CeEEEEeCCCCCCcceeCCCC-----CEEeeeHHHHHHHHHHcCCceEEEeC------------CHHHHHHHHHCCCCCE
Confidence 57889877 599999987666 69999999999999999999999865 6899999999999999
Q ss_pred EeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCCC
Q psy12229 84 ALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDIL 163 (444)
Q Consensus 84 ~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (444)
++++++.+++|...++||.|++. ++..+++++..
T Consensus 89 ~~~~~~~t~eR~~~~~fs~p~~~-~~~~~~~~~~~--------------------------------------------- 122 (259)
T PRK15437 89 IMSSLSITEKRQQEIAFTDKLYA-ADSRLVVAKNS--------------------------------------------- 122 (259)
T ss_pred EEecCCCCHHHhhhccccchhhc-CceEEEEECCC---------------------------------------------
Confidence 99999999999999999999999 89999997652
Q ss_pred cccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhCC
Q psy12229 164 PEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQY 243 (444)
Q Consensus 164 ~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~~ 243 (444)
+...+++||.+
T Consensus 123 -------------------------------------------------------------------~~~~~~~dl~g-- 133 (259)
T PRK15437 123 -------------------------------------------------------------------DIQPTVESLKG-- 133 (259)
T ss_pred -------------------------------------------------------------------CCCCChHHhCC--
Confidence 11236778854
Q ss_pred ceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHHH
Q psy12229 244 KIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQR 323 (444)
Q Consensus 244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~~ 323 (444)
.++|+..++..+.+++..... .++ +.....+.++++++
T Consensus 134 -~~Igv~~g~~~~~~~~~~~~~----------------------~~~-------------------~~~~~~~~~~~i~~ 171 (259)
T PRK15437 134 -KRVGVLQGTTQETFGNEHWAP----------------------KGI-------------------EIVSYQGQDNIYSD 171 (259)
T ss_pred -CEEEEecCcHHHHHHHhhccc----------------------cCc-------------------eEEecCCHHHHHHH
Confidence 479999988877766542100 000 01124578899999
Q ss_pred HHhcCCCCCceEEEecccchhh--hhcC-CCccEEeC-----CcccccceEEEecCCC-chhhhhHHHHHHHhcCCcccc
Q psy12229 324 VRDSKSSSEGFGYLGDATDIRY--LVMT-NCDLQMVG-----DEFSRKPYAIAVQQDR-DARELFCNVHANILSIPFPFI 394 (444)
Q Consensus 324 v~~~~~~~~~~a~i~d~~~~~y--~~~~-~c~l~~~~-----~~~~~~~~~~~~~k~s-p~~~~in~~il~l~e~G~i~~ 394 (444)
|..|+ .++++.+.....+ ..+. ..++.+.+ +.+...+++++++++. .+.+.+|..+.++.++|.+++
T Consensus 172 L~~gr----vD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ia~~~~~~~l~~~~n~~l~~~~~~G~~~~ 247 (259)
T PRK15437 172 LTAGR----IDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEK 247 (259)
T ss_pred HHcCC----ccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEEEEeCCCHHHHHHHHHHHHHHHHCCcHHH
Confidence 99997 8999999866643 2221 12333322 2233344678887665 599999999999999999999
Q ss_pred CCCCCcccccccccC
Q psy12229 395 GVDGTSVCSSIFDTD 409 (444)
Q Consensus 395 ~~~~~~~~~~kw~~~ 409 (444)
+ .+||++-
T Consensus 248 i-------~~k~~~~ 255 (259)
T PRK15437 248 L-------AKKYFDF 255 (259)
T ss_pred H-------HHHhcCC
Confidence 9 9999975
No 15
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.74 E-value=2.6e-17 Score=157.03 Aligned_cols=217 Identities=13% Similarity=0.158 Sum_probs=167.1
Q ss_pred ceeeeEEEec-cCCCeEEEec-CCCCCceeeeecHHHHHHHHHHHc-CC--eEEEEEcCCCCCccccCCCccchhHHHHh
Q psy12229 3 TITNISDSRL-KQEPFVMREE-SEGGGGVKYKGYCIDLIEEIRKLV-GF--EYEIFVAPDNSFGNMDENGQWNGMIKELI 77 (444)
Q Consensus 3 ~~~~l~V~~~-~~~Pf~~~~~-~~~~~~~~~~G~~~dil~~la~~l-nf--t~~~~~~~~~~~g~~~~ng~~~g~i~~l~ 77 (444)
..++|+|++. ++|||.+.+. ++ ++.|+++|+++++|+++ +. +++++.. +|...+.+|.
T Consensus 36 ~~g~l~vg~~~~~pP~~~~~~~~g-----~~~G~~vdl~~~ia~~llg~~~~~~~~~~------------~~~~~~~~l~ 98 (259)
T PRK11917 36 SKGQLIVGVKNDVPHYALLDQATG-----EIKGFEIDVAKLLAKSILGDDKKIKLVAV------------NAKTRGPLLD 98 (259)
T ss_pred hCCEEEEEECCCCCCceeeeCCCC-----ceeEeeHHHHHHHHHHhcCCCccEEEEEc------------ChhhHHHHHH
Confidence 4578999665 6999999753 34 69999999999999995 64 5666544 4566678899
Q ss_pred cccccEEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccC
Q psy12229 78 EKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVN 157 (444)
Q Consensus 78 ~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~ 157 (444)
+|++|+++++++.|++|.+.++||.||+. ++..+++++.
T Consensus 99 ~g~~D~~~~~~~~t~eR~~~~~fs~py~~-~~~~lvv~~~---------------------------------------- 137 (259)
T PRK11917 99 NGSVDAVIATFTITPERKRIYNFSEPYYQ-DAIGLLVLKE---------------------------------------- 137 (259)
T ss_pred CCCccEEEecccCChhhhheeeeccCcee-eceEEEEECC----------------------------------------
Confidence 99999999999999999999999999999 9999999865
Q ss_pred CCCCCCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChH
Q psy12229 158 PPGDILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLD 237 (444)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~ 237 (444)
.++++++
T Consensus 138 -------------------------------------------------------------------------~~~~s~~ 144 (259)
T PRK11917 138 -------------------------------------------------------------------------KNYKSLA 144 (259)
T ss_pred -------------------------------------------------------------------------CCCCCHH
Confidence 1467899
Q ss_pred HhhhCCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCH
Q psy12229 238 DLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSL 317 (444)
Q Consensus 238 dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~ 317 (444)
||.+ ..+|+..++...+.+.+... . .++ . .+....++.
T Consensus 145 dL~g---~~V~v~~gs~~~~~l~~~~~----------~------------~~~------------~-----~~~~~~~~~ 182 (259)
T PRK11917 145 DMKG---ANIGVAQAATTKKAIGEAAK----------K------------IGI------------D-----VKFSEFPDY 182 (259)
T ss_pred HhCC---CeEEEecCCcHHHHHHHhhH----------h------------cCC------------c-----eeEEecCCH
Confidence 9966 47998888887766653210 0 000 0 001124588
Q ss_pred HHHHHHHHhcCCCCCceEEEecccchhhhhcCCCccEEeCCcccccceEEEecCCCc-hhhhhHHHHHHHhcCCccccCC
Q psy12229 318 EEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQQDRD-ARELFCNVHANILSIPFPFIGV 396 (444)
Q Consensus 318 ~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c~l~~~~~~~~~~~~~~~~~k~sp-~~~~in~~il~l~e~G~i~~~~ 396 (444)
.++++.+..|+ .+|++.+...+.++..+. ..++.+.+...+++++++|+++ +...+|+.|.++.. .++++
T Consensus 183 ~~~~~~l~~Gr----vDa~~~d~~~~~~~~~~~--~~~~~~~~~~~~~~~a~~k~~~~l~~~ln~~l~~~~~--~~~~i- 253 (259)
T PRK11917 183 PSIKAALDAKR----VDAFSVDKSILLGYVDDK--SEILPDSFEPQSYGIVTKKDDPAFAKYVDDFVKEHKN--EIDAL- 253 (259)
T ss_pred HHHHHHHHcCC----CcEEEecHHHHHHhhhcC--CeecCCcCCCCceEEEEeCCCHHHHHHHHHHHHHHHH--HHHHH-
Confidence 99999999997 899999987665544432 3566666777889999999886 99999999999864 79999
Q ss_pred CCCcccccccc
Q psy12229 397 DGTSVCSSIFD 407 (444)
Q Consensus 397 ~~~~~~~~kw~ 407 (444)
.+||-
T Consensus 254 ------~~kw~ 258 (259)
T PRK11917 254 ------AKKWG 258 (259)
T ss_pred ------HHHhC
Confidence 88883
No 16
>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=99.66 E-value=6.2e-16 Score=148.26 Aligned_cols=235 Identities=13% Similarity=0.112 Sum_probs=165.0
Q ss_pred eeeEEEeccCCCeEEEecCCCCCceeeeecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccE
Q psy12229 5 TNISDSRLKQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADI 83 (444)
Q Consensus 5 ~~l~V~~~~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di 83 (444)
.+|++++.+||||.+...++ +..|+..++++++++++ +++++++.. .|..++..+ .|+.|.
T Consensus 18 ~~l~~~~~~~pPf~~~~~~~-----~~~G~~~~i~~~i~~~~~~~~~~~~~~------------pw~r~l~~l-~~~~d~ 79 (268)
T TIGR02285 18 EAITWIVNDFPPFFIFSGPS-----KGRGVFDVILQEIRRALPQYEHRFVRV------------SFARSLKEL-QGKGGV 79 (268)
T ss_pred ceeEEEecccCCeeEeCCCC-----CCCChHHHHHHHHHHHcCCCceeEEEC------------CHHHHHHHH-hcCCCe
Confidence 47899999999999885444 57999999999999998 889888865 699999999 778888
Q ss_pred EeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCCC
Q psy12229 84 ALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDIL 163 (444)
Q Consensus 84 ~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (444)
++.++++|++|.+.++||.||+......+++++..... +.
T Consensus 80 ~~~~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~-~~--------------------------------------- 119 (268)
T TIGR02285 80 CTVNLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAG-VR--------------------------------------- 119 (268)
T ss_pred EEeeccCCcchhhceeecCCccccCCceEEEccchhhh-cc---------------------------------------
Confidence 88789999999999999999975146788887652100 00
Q ss_pred cccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCC-CCCChHHhhhC
Q psy12229 164 PEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDT-PIESLDDLSKQ 242 (444)
Q Consensus 164 ~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~-~I~sl~dL~~~ 242 (444)
..+. ++ ++.++.+.
T Consensus 120 ----------------------------------------------------------------~~~d~~~-~~~~l~~l 134 (268)
T TIGR02285 120 ----------------------------------------------------------------DEQDGDV-DLKKLLAS 134 (268)
T ss_pred ----------------------------------------------------------------ccCCCCc-cHHHHhcC
Confidence 0011 12 34444433
Q ss_pred CceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHH
Q psy12229 243 YKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQ 322 (444)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~ 322 (444)
.+.++|+..++.....+++... ... +. ...+.....+.+++++
T Consensus 135 ~g~~vgv~~g~~~~~~~~~~~~----------~~~-----------------------~~----~~~~~~~~~~~~~~~~ 177 (268)
T TIGR02285 135 KKKRLGVIASRSYGQQIDDILS----------DSG-----------------------YQ----HNTRIIGNAAMGNLFK 177 (268)
T ss_pred CCeEEEEecceeccHHHHHHHH----------hCC-----------------------cc----cceeeeccchHHHHHH
Confidence 3467888877655443332110 000 00 0000111346778999
Q ss_pred HHHhcCCCCCceEEEecccchhhhhcCC----CccEEeCCcc--cccceEEEecCCC---chhhhhHHHHHHHhcCCccc
Q psy12229 323 RVRDSKSSSEGFGYLGDATDIRYLVMTN----CDLQMVGDEF--SRKPYAIAVQQDR---DARELFCNVHANILSIPFPF 393 (444)
Q Consensus 323 ~v~~~~~~~~~~a~i~d~~~~~y~~~~~----c~l~~~~~~~--~~~~~~~~~~k~s---p~~~~in~~il~l~e~G~i~ 393 (444)
+|..|+ .++++.+...+.|+.++. ..+..+.... ...+++++++|+. .+.+.||++|.+|.++|.++
T Consensus 178 ~L~~Gr----vD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~k~~~~~~l~~~in~~L~~l~~dG~~~ 253 (268)
T TIGR02285 178 MLEKGR----VNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMPAHISVWVACPKTEWGRKVIADIDQALSELNVDPKYY 253 (268)
T ss_pred HHHcCC----ccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCccceEEEEEeCCCHHHHHHHHHHHHHHHHHhhCHHHH
Confidence 999998 999999998888887632 2344443222 2235688899864 59999999999999999999
Q ss_pred cCCCCCcccccccccCC
Q psy12229 394 IGVDGTSVCSSIFDTDG 410 (444)
Q Consensus 394 ~~~~~~~~~~~kw~~~~ 410 (444)
++ .+||++..
T Consensus 254 ~i-------~~k~~~~~ 263 (268)
T TIGR02285 254 KY-------FDRWLSPE 263 (268)
T ss_pred HH-------HHHhCCHh
Confidence 99 99999753
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=99.66 E-value=1.1e-15 Score=144.58 Aligned_cols=220 Identities=19% Similarity=0.204 Sum_probs=151.9
Q ss_pred eeEEEe-ccCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhH---HHHhcccc
Q psy12229 6 NISDSR-LKQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMI---KELIEKRA 81 (444)
Q Consensus 6 ~l~V~~-~~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i---~~l~~g~~ 81 (444)
+|+|++ .++|||++.+ + .|+++|+++++|+++|++++++.. +|.+++ ..|.+|++
T Consensus 1 ~l~vg~~~~~pPf~~~~--~-------~Gfdvdl~~~ia~~lg~~~~~~~~------------~~~~~~~~~~~L~~g~~ 59 (246)
T TIGR03870 1 TLRVCAATKEAPYSTKD--G-------SGFENKIAAALAAAMGRKVVFVWL------------AKPAIYLVRDGLDKKLC 59 (246)
T ss_pred CeEEEeCCCCCCCccCC--C-------CcchHHHHHHHHHHhCCCeEEEEe------------ccchhhHHHHHHhcCCc
Confidence 478866 5799999962 2 699999999999999999999965 577765 68999999
Q ss_pred cEEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCC
Q psy12229 82 DIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGD 161 (444)
Q Consensus 82 Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~ 161 (444)
|+++ +++++++| +.||.||+. ++.++++++.+
T Consensus 60 Dii~-~~~~t~~r---~~fS~PY~~-~~~~~v~~k~~------------------------------------------- 91 (246)
T TIGR03870 60 DVVL-GLDTGDPR---VLTTKPYYR-SSYVFLTRKDR------------------------------------------- 91 (246)
T ss_pred cEEE-eCCCChHH---HhcccCcEE-eeeEEEEeCCC-------------------------------------------
Confidence 9988 58888777 679999999 99999998762
Q ss_pred CCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHH--h
Q psy12229 162 ILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDD--L 239 (444)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~d--L 239 (444)
...+++++| |
T Consensus 92 --------------------------------------------------------------------~~~~~~~~d~~L 103 (246)
T TIGR03870 92 --------------------------------------------------------------------NLDIKSWNDPRL 103 (246)
T ss_pred --------------------------------------------------------------------CCCCCCccchhh
Confidence 123566654 5
Q ss_pred hhCCce-eeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCC-CCCH
Q psy12229 240 SKQYKI-QYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKL-PNSL 317 (444)
Q Consensus 240 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~-~~~~ 317 (444)
.+ . ++|+..++..+.+++...... +... ...++..++-+ ...+ ..+.
T Consensus 104 ~g---~~~vgv~~gs~~~~~l~~~~~~~-------------~~~~--~~~~~~~~~~~-------------~~~~~~~~~ 152 (246)
T TIGR03870 104 KK---VSKIGVIFGSPAETMLKQIGRYE-------------DNFA--YLYSLVNFKSP-------------RNQYTQIDP 152 (246)
T ss_pred cc---CceEEEecCChHHHHHHhcCccc-------------cccc--cccccccccCc-------------ccccccCCH
Confidence 43 3 789999999998877532000 0000 00000000000 0000 1146
Q ss_pred HHHHHHHHhcCCCCCceEEEecccchhhhhcC-CCccE--EeCCcc---------cccceEEEecCCCc-hhhhhHHHHH
Q psy12229 318 EEAVQRVRDSKSSSEGFGYLGDATDIRYLVMT-NCDLQ--MVGDEF---------SRKPYAIAVQQDRD-ARELFCNVHA 384 (444)
Q Consensus 318 ~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~-~c~l~--~~~~~~---------~~~~~~~~~~k~sp-~~~~in~~il 384 (444)
.++++.|..|+ .+|.+.+...+.++..+ ...+. .+.+.. ...+++++++|+.+ +++.||++|.
T Consensus 153 ~~~~~aL~~Gr----vDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~ 228 (246)
T TIGR03870 153 RKLVSEVATGK----ADLAVAFAPEVARYVKASPEPLRMTVIPDDATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALA 228 (246)
T ss_pred HHHHHHHHcCC----CCEEEeeHHhHHHHHHhCCCCceEEeccccccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHH
Confidence 88999999998 89999986666565553 22333 233221 11235899999986 9999999999
Q ss_pred HHhcCCccccCCCCCccccccc
Q psy12229 385 NILSIPFPFIGVDGTSVCSSIF 406 (444)
Q Consensus 385 ~l~e~G~i~~~~~~~~~~~~kw 406 (444)
+|. |.+++| ..+|
T Consensus 229 ~l~--~~~~~i-------~~~y 241 (246)
T TIGR03870 229 KAK--PRIDAI-------LKEE 241 (246)
T ss_pred HhH--HHHHHH-------HHHc
Confidence 999 488888 7777
No 18
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.64 E-value=5.8e-16 Score=177.71 Aligned_cols=245 Identities=11% Similarity=0.097 Sum_probs=187.1
Q ss_pred ceeeeEEEec-cCCCeEEE-ecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhccc
Q psy12229 3 TITNISDSRL-KQEPFVMR-EESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKR 80 (444)
Q Consensus 3 ~~~~l~V~~~-~~~Pf~~~-~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~ 80 (444)
..++|+|++. .++|+.+. ..++ ++.|+++|+++.+++++|.+++++..+ +|++++.++++|+
T Consensus 54 ~~~~l~vgv~~~~~p~~~~~~~~g-----~~~G~~~D~l~~ia~~lG~~~e~v~~~-----------~~~~~l~~l~~g~ 117 (1197)
T PRK09959 54 SKKNLVIAVHKSQTATLLHTDSQQ-----RVRGINADYLNLLKRALNIKLTLREYA-----------DHQKAMDALEEGE 117 (1197)
T ss_pred hCCeEEEEecCCCCCCceeecCCC-----ccceecHHHHHHHHHhcCCceEEEeCC-----------CHHHHHHHHHcCC
Confidence 3457899765 46555544 4555 699999999999999999999999654 8999999999999
Q ss_pred ccEEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCC
Q psy12229 81 ADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPG 160 (444)
Q Consensus 81 ~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~ 160 (444)
+|++++++..+++|.+.++||.||+. +...+++++..
T Consensus 118 iDl~~~~~~~~~~r~~~~~fs~py~~-~~~~~v~~~~~------------------------------------------ 154 (1197)
T PRK09959 118 VDIVLSHLVASPPLNDDIAATKPLII-TFPALVTTLHD------------------------------------------ 154 (1197)
T ss_pred CcEecCccccccccccchhcCCCccC-CCceEEEeCCC------------------------------------------
Confidence 99998889999999999999999998 88888887642
Q ss_pred CCCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhh
Q psy12229 161 DILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLS 240 (444)
Q Consensus 161 ~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~ 240 (444)
.+++++|+.
T Consensus 155 -----------------------------------------------------------------------~~~~~~~l~ 163 (1197)
T PRK09959 155 -----------------------------------------------------------------------SMRPLTSSK 163 (1197)
T ss_pred -----------------------------------------------------------------------CCCCccccc
Confidence 234555553
Q ss_pred hCCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHH
Q psy12229 241 KQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEA 320 (444)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~ 320 (444)
+ ..+++..+....+++++. |+++ +....++..++
T Consensus 164 ~---~~i~~~~g~~~~~~~~~~--------------------------------------~p~~-----~i~~~~s~~~a 197 (1197)
T PRK09959 164 P---VNIARVANYPPDEVIHQS--------------------------------------FPKA-----TIISFTNLYQA 197 (1197)
T ss_pred C---eEEEEeCCCCCHHHHHHh--------------------------------------CCCC-----EEEeCCCHHHH
Confidence 3 468888888777766542 1110 12246699999
Q ss_pred HHHHHhcCCCCCceEEEecccchhhhhcCCC--ccEEeCC-cccccceEEEecCCCc-hhhhhHHHHHHHhcCCccccCC
Q psy12229 321 VQRVRDSKSSSEGFGYLGDATDIRYLVMTNC--DLQMVGD-EFSRKPYAIAVQQDRD-ARELFCNVHANILSIPFPFIGV 396 (444)
Q Consensus 321 ~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c--~l~~~~~-~~~~~~~~~~~~k~sp-~~~~in~~il~l~e~G~i~~~~ 396 (444)
+++|..|+ .+|++.+...+.|+.+++. ++.++.. ........++++|+.+ +...+|++|..+.++|.. .+
T Consensus 198 l~av~~G~----~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~lnkal~~i~~~~~~-~i- 271 (1197)
T PRK09959 198 LASVSAGQ----NDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKESVILNEVLNRFVDALTNEVRY-EV- 271 (1197)
T ss_pred HHHHHcCC----CCEEEccHHHHHHHHhcccccceEEEeeccCCCCceeEEEcCCcHHHHHHHHHHHHhCCHHHHH-HH-
Confidence 99999998 9999999988988887542 4555542 2223445688899987 888999999999999987 88
Q ss_pred CCCcccccccccCCC-C-cccCCCCCCceeEeeeeeecccc
Q psy12229 397 DGTSVCSSIFDTDGK-T-KVSCPLKKDHVYRYINTFKILDR 435 (444)
Q Consensus 397 ~~~~~~~~kw~~~~~-~-~~~c~~~~~~~~~~~~~~~~l~~ 435 (444)
.+||+.... + ...-...+..++.|+.+++.+++
T Consensus 272 ------~~kW~~~~~~~~~~~~~~lt~~E~~wl~~~~~l~v 306 (1197)
T PRK09959 272 ------SQNWLDTGNLAFLNKPLELTEHEKQWIKQHPDLKV 306 (1197)
T ss_pred ------HHhccCCCCcccCCCCCCCCHHHHHHHHHCCceEE
Confidence 899997531 0 12223457788889988888765
No 19
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.61 E-value=1.6e-14 Score=138.31 Aligned_cols=222 Identities=21% Similarity=0.258 Sum_probs=170.5
Q ss_pred eeeeEEEec-c-CCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCe--EEEEEcCCCCCccccCCCccchhHHHHhcc
Q psy12229 4 ITNISDSRL-K-QEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFE--YEIFVAPDNSFGNMDENGQWNGMIKELIEK 79 (444)
Q Consensus 4 ~~~l~V~~~-~-~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft--~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g 79 (444)
...++|.+. . .+||.+....+ .+..|+++|+++++++.++.. .+++.. .|++++..+..|
T Consensus 33 ~~~~~v~~~~~~~~p~~~~~~~~----~~~~G~dvdl~~~ia~~l~~~~~~~~~~~------------~~~~~~~~l~~g 96 (275)
T COG0834 33 RGKLRVGTEATYAPPFEFLDAKG----GKLVGFDVDLAKAIAKRLGGDKKVEFVPV------------AWDGLIPALKAG 96 (275)
T ss_pred cCeEEEEecCCCCCCcccccCCC----CeEEeeeHHHHHHHHHHhCCcceeEEecc------------chhhhhHHHhcC
Confidence 355777555 4 45999998762 169999999999999999886 455533 799999999999
Q ss_pred cccEEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCC
Q psy12229 80 RADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPP 159 (444)
Q Consensus 80 ~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~ 159 (444)
++|++++++++|.+|.+.++||.||+. .+..+++++.+
T Consensus 97 ~~D~~~~~~~~t~er~~~~~fs~py~~-~~~~~~~~~~~----------------------------------------- 134 (275)
T COG0834 97 KVDIIIAGMTITPERKKKVDFSDPYYY-SGQVLLVKKDS----------------------------------------- 134 (275)
T ss_pred CcCEEEeccccCHHHhccccccccccc-cCeEEEEECCC-----------------------------------------
Confidence 999999999999999999999999999 99999998763
Q ss_pred CCCCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHh
Q psy12229 160 GDILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDL 239 (444)
Q Consensus 160 ~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL 239 (444)
...+.+.+||
T Consensus 135 ----------------------------------------------------------------------~~~~~~~~DL 144 (275)
T COG0834 135 ----------------------------------------------------------------------DIGIKSLEDL 144 (275)
T ss_pred ----------------------------------------------------------------------CcCcCCHHHh
Confidence 1127889999
Q ss_pred hhCCceeeEecCCCh--hhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCH
Q psy12229 240 SKQYKIQYAPLNGSA--AMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSL 317 (444)
Q Consensus 240 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~ 317 (444)
.+ ..+++..++. ......... .+. .....++.
T Consensus 145 ~g---k~v~v~~gt~~~~~~~~~~~~------------------------~~~-------------------~~~~~~~~ 178 (275)
T COG0834 145 KG---KKVGVQLGTTDEAEEKAKKPG------------------------PNA-------------------KIVAYDSN 178 (275)
T ss_pred CC---CEEEEEcCcchhHHHHHhhcc------------------------CCc-------------------eEEeeCCH
Confidence 77 4788888887 222221100 000 01124577
Q ss_pred HHHHHHHHhcCCCCCceEEEecccchhhh--hcCCCcc-EEeCCcccc-cceEEEecCC--CchhhhhHHHHHHHhcCCc
Q psy12229 318 EEAVQRVRDSKSSSEGFGYLGDATDIRYL--VMTNCDL-QMVGDEFSR-KPYAIAVQQD--RDARELFCNVHANILSIPF 391 (444)
Q Consensus 318 ~e~~~~v~~~~~~~~~~a~i~d~~~~~y~--~~~~c~l-~~~~~~~~~-~~~~~~~~k~--sp~~~~in~~il~l~e~G~ 391 (444)
.++++.+..|+ .+|++.|...+.+. ..+.... ......... .+++++++|+ ..+++.+|+.+.++.++|.
T Consensus 179 ~~~~~al~~Gr----~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~in~~l~~l~~~G~ 254 (275)
T COG0834 179 AEALLALKNGR----ADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIALRKGDDPELLEAVNKALKELKADGT 254 (275)
T ss_pred HHHHHHHHcCC----ccEEEcchHhhhhhhhhhcCCCCceeeeccCCCcceeEEEeccCCcHHHHHHHHHHHHHHHhCcc
Confidence 89999999998 99999999998883 3333322 222333333 6889999999 5799999999999999999
Q ss_pred cccCCCCCcccccccccCC
Q psy12229 392 PFIGVDGTSVCSSIFDTDG 410 (444)
Q Consensus 392 i~~~~~~~~~~~~kw~~~~ 410 (444)
++++ .+||+...
T Consensus 255 ~~~i-------~~kw~~~~ 266 (275)
T COG0834 255 LQKI-------SDKWFGPD 266 (275)
T ss_pred HHHH-------HHHhcCcc
Confidence 9999 99999853
No 20
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.58 E-value=9.9e-14 Score=125.98 Aligned_cols=214 Identities=22% Similarity=0.360 Sum_probs=170.4
Q ss_pred eeEEEe-ccCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEE
Q psy12229 6 NISDSR-LKQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIA 84 (444)
Q Consensus 6 ~l~V~~-~~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~ 84 (444)
+|+|++ .+++||.+...++ +..|+.+|+++.+.++++.+++++.. .|..++..+.+|++|++
T Consensus 1 ~l~v~~~~~~~p~~~~~~~g-----~~~G~~~~~~~~~~~~~g~~~~~~~~------------~~~~~~~~l~~g~~D~~ 63 (219)
T smart00062 1 TLRVGTNGDYPPFSFADEDG-----ELTGFDVDLAKAIAKELGLKVEFVEV------------SFDNLLTALKSGKIDVV 63 (219)
T ss_pred CEEEEecCCCCCcEEECCCC-----CcccchHHHHHHHHHHhCCeEEEEec------------cHHHHHHHHHCCcccEE
Confidence 478866 8899999988666 69999999999999999999999854 57889999999999999
Q ss_pred eecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCCCc
Q psy12229 85 LGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDILP 164 (444)
Q Consensus 85 ~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (444)
+++...+.+|...+.++.|+.. ....+++++.
T Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~----------------------------------------------- 95 (219)
T smart00062 64 AAGMTITPERAKQVDFSDPYYK-SGQVILVRKD----------------------------------------------- 95 (219)
T ss_pred eccccCCHHHHhheeeccceee-ceeEEEEecC-----------------------------------------------
Confidence 9887767888888899999998 8888888754
Q ss_pred ccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhCCc
Q psy12229 165 EVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQYK 244 (444)
Q Consensus 165 ~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~~~ 244 (444)
.++.+++||.+
T Consensus 96 ------------------------------------------------------------------~~~~~~~dL~g--- 106 (219)
T smart00062 96 ------------------------------------------------------------------SPIKSLEDLKG--- 106 (219)
T ss_pred ------------------------------------------------------------------CCCCChHHhCC---
Confidence 24788999955
Q ss_pred eeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHHHH
Q psy12229 245 IQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQRV 324 (444)
Q Consensus 245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~~v 324 (444)
.++++..++....++.... .++ +.....+..++++++
T Consensus 107 ~~i~~~~g~~~~~~~~~~~------------------------~~~-------------------~~~~~~~~~~~~~~l 143 (219)
T smart00062 107 KKVAVVAGTTGEELLKKLY------------------------PEA-------------------KIVSYDSQAEALAAL 143 (219)
T ss_pred CEEEEecCccHHHHHHHhC------------------------CCc-------------------eEEEcCCHHHHHHHh
Confidence 4788777766666655320 000 011245788999999
Q ss_pred HhcCCCCCceEEEecccchhhhhcCC--CccEEeCCcccc-cceEEEecCCCc-hhhhhHHHHHHHhcCCccccCCCCCc
Q psy12229 325 RDSKSSSEGFGYLGDATDIRYLVMTN--CDLQMVGDEFSR-KPYAIAVQQDRD-ARELFCNVHANILSIPFPFIGVDGTS 400 (444)
Q Consensus 325 ~~~~~~~~~~a~i~d~~~~~y~~~~~--c~l~~~~~~~~~-~~~~~~~~k~sp-~~~~in~~il~l~e~G~i~~~~~~~~ 400 (444)
..|+ .+|.+.+...+.+...+. +++.++...... .+++++++++++ +.+.+++.|..+.++|.++++
T Consensus 144 ~~g~----~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~i----- 214 (219)
T smart00062 144 KAGR----ADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFAVRKGDPELLDKINKALKELKADGTLKKI----- 214 (219)
T ss_pred hcCc----ccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEEEECCCHHHHHHHHHHHHHHHhCchHHHH-----
Confidence 9997 888888888777777644 567777665554 778899999985 999999999999999999999
Q ss_pred ccccccc
Q psy12229 401 VCSSIFD 407 (444)
Q Consensus 401 ~~~~kw~ 407 (444)
.++|+
T Consensus 215 --~~~~~ 219 (219)
T smart00062 215 --YEKWF 219 (219)
T ss_pred --HhccC
Confidence 88885
No 21
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.58 E-value=1.3e-14 Score=166.72 Aligned_cols=216 Identities=13% Similarity=0.135 Sum_probs=166.4
Q ss_pred eeeeEEEec-cCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhccccc
Q psy12229 4 ITNISDSRL-KQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRAD 82 (444)
Q Consensus 4 ~~~l~V~~~-~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~D 82 (444)
.+.|+|++. +||||.+.+.++ ++.|+++|+++++++++|.+++++..+ +|.....++.+|++|
T Consensus 301 ~~~l~v~~~~~~pP~~~~d~~g-----~~~G~~~Dll~~i~~~~g~~~~~v~~~-----------~~~~~~~~l~~g~~D 364 (1197)
T PRK09959 301 HPDLKVLENPYSPPYSMTDENG-----SVRGVMGDILNIITLQTGLNFSPITVS-----------HNIHAGTQLNPGGWD 364 (1197)
T ss_pred CCceEEEcCCCCCCeeEECCCC-----cEeeehHHHHHHHHHHHCCeEEEEecC-----------CHHHHHHHHHCCCce
Confidence 457888555 589999997666 799999999999999999999998654 567778889999999
Q ss_pred EEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCC
Q psy12229 83 IALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDI 162 (444)
Q Consensus 83 i~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~ 162 (444)
++. +...+++|.+.++||.||+. ..+++++++...
T Consensus 365 ~i~-~~~~t~~r~~~~~fs~py~~-~~~~~v~~~~~~------------------------------------------- 399 (1197)
T PRK09959 365 IIP-GAIYSEDRENNVLFAEAFIT-TPYVFVMQKAPD------------------------------------------- 399 (1197)
T ss_pred Eee-cccCCccccccceecccccc-CCEEEEEecCCC-------------------------------------------
Confidence 855 45578999999999999999 899998865410
Q ss_pred CcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhC
Q psy12229 163 LPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQ 242 (444)
Q Consensus 163 ~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~ 242 (444)
.+.++ .
T Consensus 400 ---------------------------------------------------------------------~~~~~---~-- 405 (1197)
T PRK09959 400 ---------------------------------------------------------------------SEQTL---K-- 405 (1197)
T ss_pred ---------------------------------------------------------------------Ccccc---c--
Confidence 11111 1
Q ss_pred CceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHH
Q psy12229 243 YKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQ 322 (444)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~ 322 (444)
.+.++|+..+....++++.. |+++ +....++.+++++
T Consensus 406 ~g~~vav~~g~~~~~~~~~~--------------------------------------~p~~-----~~~~~~~~~~~l~ 442 (1197)
T PRK09959 406 KGMKVAIPYYYELHSQLKEM--------------------------------------YPEV-----EWIKVDNASAAFH 442 (1197)
T ss_pred cCCEEEEeCCcchHHHHHHH--------------------------------------CCCc-----EEEEcCCHHHHHH
Confidence 13478888877766666532 1100 1123569999999
Q ss_pred HHHhcCCCCCceEEEecccchhhhhcCCC--ccE-EeCCcccccceEEEecCCCc-hhhhhHHHHHHHhcCCccccCCCC
Q psy12229 323 RVRDSKSSSEGFGYLGDATDIRYLVMTNC--DLQ-MVGDEFSRKPYAIAVQQDRD-ARELFCNVHANILSIPFPFIGVDG 398 (444)
Q Consensus 323 ~v~~~~~~~~~~a~i~d~~~~~y~~~~~c--~l~-~~~~~~~~~~~~~~~~k~sp-~~~~in~~il~l~e~G~i~~~~~~ 398 (444)
+|.+|+ .+|++.+...+.|+.++.. .+. .....+....++++++|+.| +...+|++|..+.++ ..+++
T Consensus 443 av~~G~----~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~av~k~~~~L~~~lnk~l~~i~~~-~~~~i--- 514 (1197)
T PRK09959 443 KVKEGE----LDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGEPELKDIINKALNAIPPS-EVLRL--- 514 (1197)
T ss_pred HHHcCC----CCEEehhhHHHHHHHHhcccccceeeecCCCCchheEEeeCCCCHHHHHHHHHHHHhCCHH-HHHHH---
Confidence 999998 9999999999999887532 333 33344556678999999986 999999999999998 78889
Q ss_pred CcccccccccC
Q psy12229 399 TSVCSSIFDTD 409 (444)
Q Consensus 399 ~~~~~~kw~~~ 409 (444)
.+||+..
T Consensus 515 ----~~kW~~~ 521 (1197)
T PRK09959 515 ----TEKWIKM 521 (1197)
T ss_pred ----HhhcccC
Confidence 9999874
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=99.56 E-value=1.5e-13 Score=124.96 Aligned_cols=213 Identities=23% Similarity=0.376 Sum_probs=167.7
Q ss_pred eEE-EeccCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEe
Q psy12229 7 ISD-SRLKQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIAL 85 (444)
Q Consensus 7 l~V-~~~~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~ 85 (444)
|+| +...+|||.+.+.++ +..|+..++++.++++++.+++++.. .|..++.++.+|++|+++
T Consensus 1 l~i~~~~~~~p~~~~~~~g-----~~~G~~~~~~~~~~~~~g~~~~~~~~------------~~~~~~~~l~~g~~D~~~ 63 (218)
T cd00134 1 LTVGTAGTYPPFSFRDANG-----ELTGFDVDLAKAIAKELGVKVKFVEV------------DWDGLITALKSGKVDLIA 63 (218)
T ss_pred CEEecCCCCCCeeEECCCC-----CEEeeeHHHHHHHHHHhCCeEEEEeC------------CHHHHHHHHhcCCcCEEe
Confidence 455 456699999997666 69999999999999999999999865 378899999999999999
Q ss_pred ecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCCCcc
Q psy12229 86 GSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDILPE 165 (444)
Q Consensus 86 ~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 (444)
.....+.+|...+.|+.|+.. ....+++++..
T Consensus 64 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~----------------------------------------------- 95 (218)
T cd00134 64 AGMTITPERAKQVDFSDPYYK-SGQVILVKKGS----------------------------------------------- 95 (218)
T ss_pred ecCcCCHHHHhhccCccccee-ccEEEEEECCC-----------------------------------------------
Confidence 887778888888999999999 89999998652
Q ss_pred cchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhCCce
Q psy12229 166 VIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQYKI 245 (444)
Q Consensus 166 ~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~~~~ 245 (444)
++.+++||.++
T Consensus 96 ------------------------------------------------------------------~~~~~~dl~g~--- 106 (218)
T cd00134 96 ------------------------------------------------------------------PIKSVKDLKGK--- 106 (218)
T ss_pred ------------------------------------------------------------------CCCChHHhCCC---
Confidence 34478888653
Q ss_pred eeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHHHHH
Q psy12229 246 QYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQRVR 325 (444)
Q Consensus 246 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~~v~ 325 (444)
++++..++....++.+... . .......+.+++++.|.
T Consensus 107 ~i~~~~~~~~~~~~~~~~~------------------------~-------------------~~~~~~~~~~~~~~~l~ 143 (218)
T cd00134 107 KVAVQKGSTAEKYLKKALP------------------------E-------------------AKVVSYDDNAEALAALE 143 (218)
T ss_pred EEEEEcCchHHHHHHHhCC------------------------c-------------------ccEEEeCCHHHHHHHHH
Confidence 6777766666666554210 0 01112457899999999
Q ss_pred hcCCCCCceEEEecccchhhhhcCC-CccEEeCCc--ccccceEEEecCCC-chhhhhHHHHHHHhcCCccccCCCCCcc
Q psy12229 326 DSKSSSEGFGYLGDATDIRYLVMTN-CDLQMVGDE--FSRKPYAIAVQQDR-DARELFCNVHANILSIPFPFIGVDGTSV 401 (444)
Q Consensus 326 ~~~~~~~~~a~i~d~~~~~y~~~~~-c~l~~~~~~--~~~~~~~~~~~k~s-p~~~~in~~il~l~e~G~i~~~~~~~~~ 401 (444)
+|+ .++++.+...+.+..++. +++.++... .....+++..++++ .+.+.+++++.+++++|..+.+
T Consensus 144 ~g~----~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~g~~~~i------ 213 (218)
T cd00134 144 NGR----ADAVIVDEIALAALLKKHPPELKIVGPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKI------ 213 (218)
T ss_pred cCC----ccEEEeccHHHHHHHHhcCCCcEEeccccCCCccceEEEEcCCCHHHHHHHHHHHHHHHhCccHHHH------
Confidence 997 889999888888776654 677777653 44455677777777 5999999999999999999999
Q ss_pred cccccc
Q psy12229 402 CSSIFD 407 (444)
Q Consensus 402 ~~~kw~ 407 (444)
.+||+
T Consensus 214 -~~~~~ 218 (218)
T cd00134 214 -SKKWF 218 (218)
T ss_pred -HHhhC
Confidence 88885
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=99.53 E-value=2.4e-13 Score=127.21 Aligned_cols=217 Identities=15% Similarity=0.133 Sum_probs=152.6
Q ss_pred eeEEEecc-CCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEE
Q psy12229 6 NISDSRLK-QEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIA 84 (444)
Q Consensus 6 ~l~V~~~~-~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~ 84 (444)
.|+|++.. +|||.+. ...|+++|++++++++++.+++++..+. .+..++..+.+|++|++
T Consensus 1 ~l~v~~~~~~~P~~~~---------~~~G~~~el~~~i~~~~g~~i~~~~~~~----------~~~~~~~~l~~g~~Di~ 61 (232)
T TIGR03871 1 ALRVCADPNNLPFSNE---------KGEGFENKIAQLLADDLGLPLEYTWFPQ----------RRGFVRNTLNAGRCDVV 61 (232)
T ss_pred CeEEEeCCCCCCccCC---------CCCchHHHHHHHHHHHcCCceEEEecCc----------chhhHHHHHhcCCccEE
Confidence 37786555 8999873 1369999999999999999999986531 23335678999999998
Q ss_pred eecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCCCCc
Q psy12229 85 LGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGDILP 164 (444)
Q Consensus 85 ~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (444)
++ +++|.+.++||.||+. .+.++++++.+
T Consensus 62 ~~----~~~r~~~~~fs~py~~-~~~~lv~~~~~---------------------------------------------- 90 (232)
T TIGR03871 62 IG----VPAGYEMVLTTRPYYR-STYVFVTRKDS---------------------------------------------- 90 (232)
T ss_pred Ee----ccCccccccccCCcEe-eeEEEEEeCCC----------------------------------------------
Confidence 76 4678888999999999 89999997762
Q ss_pred ccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHH--hhhC
Q psy12229 165 EVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDD--LSKQ 242 (444)
Q Consensus 165 ~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~d--L~~~ 242 (444)
...+++++| |.+
T Consensus 91 -----------------------------------------------------------------~~~~~~~~d~~l~g- 104 (232)
T TIGR03871 91 -----------------------------------------------------------------LLDVKSLDDPRLKK- 104 (232)
T ss_pred -----------------------------------------------------------------cccccchhhhhhcC-
Confidence 124667777 544
Q ss_pred CceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHHH
Q psy12229 243 YKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQ 322 (444)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~ 322 (444)
.++|+..++...+++.+..- . .++.. +. .. .......+..++++
T Consensus 105 --~~V~v~~g~~~~~~l~~~~~-~---------------------~~~~~--------~~-~~---~~~~~~~~~~~~~~ 148 (232)
T TIGR03871 105 --LRIGVFAGTPPAHWLARHGL-V---------------------ENVVG--------YS-LF---GDYRPESPPGRMVE 148 (232)
T ss_pred --CeEEEEcCChHHHHHHhcCc-c---------------------ccccc--------cc-cc---ccccccCCHHHHHH
Confidence 47888998888887764210 0 00000 00 00 00001237899999
Q ss_pred HHHhcCCCCCceEEEecccchhhhhcCC-CccEEeCCc------ccccceEEEecCCCc-hhhhhHHHHHHHhcCCcccc
Q psy12229 323 RVRDSKSSSEGFGYLGDATDIRYLVMTN-CDLQMVGDE------FSRKPYAIAVQQDRD-ARELFCNVHANILSIPFPFI 394 (444)
Q Consensus 323 ~v~~~~~~~~~~a~i~d~~~~~y~~~~~-c~l~~~~~~------~~~~~~~~~~~k~sp-~~~~in~~il~l~e~G~i~~ 394 (444)
.|..|+ .+|++.+...+.|+.++. .++.+.... ....+++++++++.+ +...||++|.++. |.+++
T Consensus 149 ~l~~G~----~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~--~~~~~ 222 (232)
T TIGR03871 149 DLAAGE----IDVAIVWGPIAGYFAKQAGPPLVVVPLLPEDGGIPFDYRIAMGVRKGDKAWKDELNAVLDRRQ--AEIDA 222 (232)
T ss_pred HHHcCC----cCEEEeccHHHHHHHHhCCCCceeeccccCCCCCCccceEEEEEecCCHHHHHHHHHHHHHHH--HHHHH
Confidence 999998 899999988888877643 244443321 123456888898774 9999999999986 47888
Q ss_pred CCCCCcccccccc
Q psy12229 395 GVDGTSVCSSIFD 407 (444)
Q Consensus 395 ~~~~~~~~~~kw~ 407 (444)
+ .+||.
T Consensus 223 i-------~~kyg 228 (232)
T TIGR03871 223 I-------LREYG 228 (232)
T ss_pred H-------HHHcC
Confidence 8 88884
No 24
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=99.47 E-value=3.8e-13 Score=128.05 Aligned_cols=227 Identities=16% Similarity=0.168 Sum_probs=180.0
Q ss_pred CceeeeEEEeccCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccc
Q psy12229 2 STITNISDSRLKQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRA 81 (444)
Q Consensus 2 ~~~~~l~V~~~~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~ 81 (444)
..++.|+|.|-+.|=-.+..+++ ..|+++++.+.+|+.||.++++.+.+ ..+.++.+|.+|++
T Consensus 20 q~rGvLrV~tinsp~sy~~~~~~------p~G~eYelak~Fa~yLgV~Lki~~~~-----------n~dqLf~aL~ng~~ 82 (473)
T COG4623 20 QARGVLRVSTINSPLSYFEDKGG------PTGLEYELAKAFADYLGVKLKIIPAD-----------NIDQLFDALDNGNA 82 (473)
T ss_pred HhcCeEEEEeecCccceeccCCC------ccchhHHHHHHHHHHhCCeEEEEecC-----------CHHHHHHHHhCCCc
Confidence 45788999887765444444444 68999999999999999999999764 45789999999999
Q ss_pred cEEeecccccccccccccccccceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHHhcceeccccccCCCCC
Q psy12229 82 DIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNLDGEQMKYLIQVNPPGD 161 (444)
Q Consensus 82 Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~~~~~~~~~~~~~~~~~ 161 (444)
|+++.++....+|.+.+....-|+. .++.++.++.
T Consensus 83 DL~Aagl~~~~~~l~~~~~gP~y~s-vs~qlVyRkG-------------------------------------------- 117 (473)
T COG4623 83 DLAAAGLLYNSERLKNFQPGPTYYS-VSQQLVYRKG-------------------------------------------- 117 (473)
T ss_pred ceecccccCChhHhcccCCCCceec-ccHHHHhhcC--------------------------------------------
Confidence 9999999999999999887777888 7878877765
Q ss_pred CCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhh
Q psy12229 162 ILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSK 241 (444)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~ 241 (444)
+...+++++|.+
T Consensus 118 --------------------------------------------------------------------~~Rp~~l~~L~g 129 (473)
T COG4623 118 --------------------------------------------------------------------QYRPRSLGQLKG 129 (473)
T ss_pred --------------------------------------------------------------------CCCCCCHHHccC
Confidence 223457778876
Q ss_pred CCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHHhcCCCCCHHHHH
Q psy12229 242 QYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAV 321 (444)
Q Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~ 321 (444)
+ ++.+..|+...+-++.... .+|+.+-..... ..+.+|.+
T Consensus 130 ~---~i~v~~gs~~~~~l~~lk~----------------------------------~kyP~l~~k~d~---~~~~~dLl 169 (473)
T COG4623 130 R---QITVAKGSAHVEDLKLLKE----------------------------------TKYPELIWKVDD---KLGVEDLL 169 (473)
T ss_pred c---eeeccCCcHHHHHHHHHHH----------------------------------hhcchhhhhhcc---cccHHHHH
Confidence 3 5777888876665554321 345544332222 34789999
Q ss_pred HHHHhcCCCCCceEEEecccchhhhhcCCCccEEeCCcccccceEEEecCCC--chhhhhHHHHHHHhcCCccccCCCCC
Q psy12229 322 QRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQQDR--DARELFCNVHANILSIPFPFIGVDGT 399 (444)
Q Consensus 322 ~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c~l~~~~~~~~~~~~~~~~~k~s--p~~~~in~~il~l~e~G~i~~~~~~~ 399 (444)
+.|..|+ -.-.+.|...+.-..+-+++|.+.-+.....++.+.+|.+. .+...++.++..+.|.|.++++
T Consensus 170 e~v~~Gk----ldytiads~~is~~q~i~P~laVafd~tde~~v~Wy~~~~dd~tL~a~ll~F~~~~~e~g~larl---- 241 (473)
T COG4623 170 EMVAEGK----LDYTIADSVEISLFQRVHPELAVAFDLTDEQPVAWYLPRDDDSTLSAALLDFLNEAKEDGLLARL---- 241 (473)
T ss_pred HHHhcCC----cceeeeccHHHHHHHHhCccceeeeecccccCceeeccCCchHHHHHHHHHHHHHhhcchHHHHH----
Confidence 9999997 77788888888888887888888887777789999999964 6999999999999999999999
Q ss_pred cccccccccC
Q psy12229 400 SVCSSIFDTD 409 (444)
Q Consensus 400 ~~~~~kw~~~ 409 (444)
.+|+++-
T Consensus 242 ---eeky~gH 248 (473)
T COG4623 242 ---EEKYLGH 248 (473)
T ss_pred ---HHHHhcc
Confidence 9999974
No 25
>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=99.42 E-value=4.5e-14 Score=122.79 Aligned_cols=105 Identities=34% Similarity=0.526 Sum_probs=74.2
Q ss_pred chhHHHHHHHHHHHHhc-c-----eeccccccCCC----CCCCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHH
Q psy12229 131 ETGVWLCILAAYCNLDG-E-----QMKYLIQVNPP----GDILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRL 200 (444)
Q Consensus 131 ~~~vWi~i~~~~~~~~~-~-----~~~~~~~~~~~----~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl 200 (444)
++.+|+++++++++++. . +.+.+++.... ..+......+++.++.++.|+ ....|++.++|+
T Consensus 1 s~~vW~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~--------~~~~~~s~s~Ri 72 (148)
T PF00060_consen 1 SWSVWLLILLSILLVSLVLWLFERFSPYEWRKNQSSPPRRWRFSLSNSFWYTFGTLLQQG--------SSIRPRSWSGRI 72 (148)
T ss_dssp -HHHHHHHHHHHHHHHTTGGGT------------------HHHHHHHHHHHCCCCCHHHH--------H------HHHHH
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccccccCcccHHHHHHHHHHhhcccc--------ccccccchHHHH
Confidence 57899999998888772 2 22222222000 011124567778999999999 999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhCC
Q psy12229 201 VAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQY 243 (444)
Q Consensus 201 ~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~~ 243 (444)
+.++|++++++++++|+|+|+|+||.|+++++|+|+|||.+++
T Consensus 73 l~~~w~l~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~ 115 (148)
T PF00060_consen 73 LLAFWWLFSLILIASYTANLTSFLTVPKYEPPIDSLEDLANSG 115 (148)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHCHHHTSS-SSHHHHHTHS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccCcCCCCCCHHHHHHCC
Confidence 9999999999999999999999999999999999999999964
No 26
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.42 E-value=8.6e-13 Score=112.64 Aligned_cols=131 Identities=32% Similarity=0.546 Sum_probs=107.7
Q ss_pred CCCChHHhhhCCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHH--H
Q psy12229 232 PIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAM--K 309 (444)
Q Consensus 232 ~I~sl~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~--~ 309 (444)
||++++||.++++.++|+..++..+.+++.... ..+.+++..+ .
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~~~~~~----------------------------------~~~~~~~~~~~~~ 46 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFFKRSGN----------------------------------PEYSRMWNYMSAS 46 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHHHhCCC----------------------------------hHHHHHHHHHHhC
Confidence 588999998754568999999999999986431 1122222222 1
Q ss_pred hcCCCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcCCCccEEeCCcccccceEEEecCCCchhhhhHHHHHHHhcC
Q psy12229 310 EAKLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQQDRDARELFCNVHANILSI 389 (444)
Q Consensus 310 ~~~~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c~l~~~~~~~~~~~~~~~~~k~sp~~~~in~~il~l~e~ 389 (444)
+....++..+++..|..| + +|++.|...+.|+.+++|++.++++.+...+++++++||+++++.+|..|.+|.++
T Consensus 47 ~~~~~~~~~~~~~~l~~g----~-da~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~ 121 (134)
T smart00079 47 PSVFVKSYAEGVQRVRVS----N-YAFLMESTYLDYELSQNCDLMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSES 121 (134)
T ss_pred CCCCCCCHHHHHHHHHcC----C-CEEEeehHhHHHHHhCCCCeEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhc
Confidence 233467899999999998 3 89999999999888878999999888888899999999999999999999999999
Q ss_pred CccccCCCCCccccccccc
Q psy12229 390 PFPFIGVDGTSVCSSIFDT 408 (444)
Q Consensus 390 G~i~~~~~~~~~~~~kw~~ 408 (444)
|.++++ .+||++
T Consensus 122 G~~~~l-------~~kw~~ 133 (134)
T smart00079 122 GELQKL-------ENKWWK 133 (134)
T ss_pred CcHHHH-------HHhhcc
Confidence 999999 999986
No 27
>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=99.39 E-value=4.2e-13 Score=97.88 Aligned_cols=63 Identities=51% Similarity=1.043 Sum_probs=53.3
Q ss_pred CeEEEecC--CCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhc
Q psy12229 16 PFVMREES--EGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIE 78 (444)
Q Consensus 16 Pf~~~~~~--~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~ 78 (444)
||++.+++ ..+|+.++.|+++|++++||+.+||+|+++.+++++||...+||+|+|++++|.+
T Consensus 1 Pfvm~~~~~~~~~g~~~~eGyciDll~~la~~l~F~y~i~~~~Dg~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 1 PFVMLKEDGENLTGNDRYEGYCIDLLEELAEELNFTYEIYLVPDGKYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp TTBEE-TTSSGSBGGGGEESHHHHHHHHHHHHHT-EEEEEE-TTS--EEBETTSEBEHHHHHHHT
T ss_pred CeEEEecCCcccCCCccEEEEHHHHHHHHHHHcCCeEEEEECCCCCCcCcCCCCcCcCHHHHhcC
Confidence 88888876 4467789999999999999999999999999999999999999999999999874
No 28
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=98.48 E-value=3.2e-06 Score=80.02 Aligned_cols=69 Identities=14% Similarity=0.097 Sum_probs=53.2
Q ss_pred CCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcCCC----ccEEeCCcccccceEEEecCC-Cc-hhhhhHHHHHHH
Q psy12229 314 PNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNC----DLQMVGDEFSRKPYAIAVQQD-RD-ARELFCNVHANI 386 (444)
Q Consensus 314 ~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c----~l~~~~~~~~~~~~~~~~~k~-sp-~~~~in~~il~l 386 (444)
..+..++++.|.+|+ .+|.+.+...+..+..++. ++.++.+.....+++++++|+ .+ +++.+|+.|..+
T Consensus 180 ~~~~~~~~~al~~G~----~Da~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 180 SGSHDASALAVANGK----VDAATNNSSAIGRLKKRGPSDMKKVRVIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred cCchHHHHHHHHcCC----CCeEEecHHHHHHHHHhCccchhheEEEEecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 346788999999997 8899998877766655432 577777655556679999999 54 999999998753
No 29
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.39 E-value=1.6e-06 Score=83.88 Aligned_cols=164 Identities=10% Similarity=0.076 Sum_probs=119.6
Q ss_pred ccchhHHHHhcccccEEeeccccccccccccccccc--ceecccEEEEEeCCCCCCcccccccccchhHHHHHHHHHHHH
Q psy12229 68 QWNGMIKELIEKRADIALGSLSVMAERENVVDFTVP--YYDLVGITILMKKPKTPTSLFKFLTVLETGVWLCILAAYCNL 145 (444)
Q Consensus 68 ~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p--~~~~~~~~ilvp~~~~~~~~~~~l~pF~~~vWi~i~~~~~~~ 145 (444)
.+.+++..|.+|++|+++++...+.+|.+.++|+.| |.. ..+++++|+.
T Consensus 52 ~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~-~~lvvvvp~~---------------------------- 102 (287)
T PRK00489 52 RPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGK-CRLVLAVPED---------------------------- 102 (287)
T ss_pred CcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCc-eEEEEEEECC----------------------------
Confidence 578999999999999999999999999888999987 666 7788888764
Q ss_pred hcceeccccccCCCCCCCcccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhh
Q psy12229 146 DGEQMKYLIQVNPPGDILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLT 225 (444)
Q Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt 225 (444)
T Consensus 103 -------------------------------------------------------------------------------- 102 (287)
T PRK00489 103 -------------------------------------------------------------------------------- 102 (287)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred cccCCCCCCChHHhhhCCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHH
Q psy12229 226 VSRLDTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMW 305 (444)
Q Consensus 226 ~~~~~~~I~sl~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~ 305 (444)
.+|.+++||.++ ++++..+....++|.... .+ .++
T Consensus 103 -----~~i~sl~DL~Gk---~ia~~~~~~~~~~l~~~g--------------i~--------~~i--------------- 137 (287)
T PRK00489 103 -----SDWQGVEDLAGK---RIATSYPNLTRRYLAEKG--------------ID--------AEV--------------- 137 (287)
T ss_pred -----CCCCChHHhCCC---EEEEcCcHHHHHHHHHcC--------------Cc--------eEE---------------
Confidence 357789999764 677766666666665421 00 000
Q ss_pred HHHHhcCCCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcCCCccEEeCCcccccceEEEecC--CCc-hhhhhHHH
Q psy12229 306 QAMKEAKLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQQ--DRD-ARELFCNV 382 (444)
Q Consensus 306 ~~~~~~~~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c~l~~~~~~~~~~~~~~~~~k--~sp-~~~~in~~ 382 (444)
....+..|+ .+..|. .+|++.+......+.+. ++.++ +.+.....+++.+| ++| .++.+|..
T Consensus 138 ------v~~~gs~ea--a~~~G~----aDaivd~~~~~~~l~~~--~L~~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~ 202 (287)
T PRK00489 138 ------VELSGAVEV--APRLGL----ADAIVDVVSTGTTLRAN--GLKIV-EVILRSEAVLIARKGWLDPEKQEKIDQL 202 (287)
T ss_pred ------EECCCchhh--hhcCCc----ccEEEeeHHHHHHHHHC--CCEEE-EeeeeeeEEEEEcccccChhHHHHHHHH
Confidence 112233333 345575 88887766666665553 57777 56667778999999 555 88889999
Q ss_pred HHHHhcCCccccCCCCCcccccccccC
Q psy12229 383 HANILSIPFPFIGVDGTSVCSSIFDTD 409 (444)
Q Consensus 383 il~l~e~G~i~~~~~~~~~~~~kw~~~ 409 (444)
+.++ .|.+... ..|||+.
T Consensus 203 l~~l--~g~l~a~-------~~k~~~~ 220 (287)
T PRK00489 203 LTRL--QGVLRAR-------ESKYLMM 220 (287)
T ss_pred HHHH--HHHHHhh-------ceEEEEE
Confidence 9999 4999999 9999985
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=97.59 E-value=0.0018 Score=62.65 Aligned_cols=75 Identities=13% Similarity=0.060 Sum_probs=51.4
Q ss_pred CCHHHHHHHHHhcCCCCCceEEEecccchhhhhc-CC----CccEEeCCcccccceEEEecCCC--chhhhhHHHHHHHh
Q psy12229 315 NSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVM-TN----CDLQMVGDEFSRKPYAIAVQQDR--DARELFCNVHANIL 387 (444)
Q Consensus 315 ~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~-~~----c~l~~~~~~~~~~~~~~~~~k~s--p~~~~in~~il~l~ 387 (444)
.+..++++.|..|+ .+|.+.+...+..+.+ .. .++.++...-.....+++++++- .+.+.+++.+.++.
T Consensus 175 ~~~~~~~~al~~G~----vDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~ 250 (288)
T TIGR03431 175 GSHEAAILAVANGT----VDAATTNDENLDRMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYH 250 (288)
T ss_pred CchHHHHHHHHcCC----CCeEeccHHHHHHHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcC
Confidence 36889999999997 8888888766655554 22 12444332111123468888884 49999999999999
Q ss_pred cCCccc
Q psy12229 388 SIPFPF 393 (444)
Q Consensus 388 e~G~i~ 393 (444)
+++.-+
T Consensus 251 ~~~~~~ 256 (288)
T TIGR03431 251 KTDKAC 256 (288)
T ss_pred CCcHHH
Confidence 985533
No 31
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=95.86 E-value=0.21 Score=48.69 Aligned_cols=41 Identities=12% Similarity=0.022 Sum_probs=29.6
Q ss_pred HHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeec
Q psy12229 36 IDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGS 87 (444)
Q Consensus 36 ~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~ 87 (444)
.+....+.+.. +.+++++..+ +...++.++.+|++|+++.+
T Consensus 43 ~~~~~~~~~~~p~v~ie~~~~~-----------~~~~~~~aL~~G~iDia~~~ 84 (314)
T PRK11553 43 AKSHQLLEKRFPQTKISWVEFP-----------AGPQMLEALNVGSIDLGSTG 84 (314)
T ss_pred HHhhCHHHHhCCCCeeEEEECC-----------CcHHHHHHHHcCCCCEEccC
Confidence 44455666655 6888887542 23578999999999998865
No 32
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=95.23 E-value=0.12 Score=48.45 Aligned_cols=73 Identities=8% Similarity=0.050 Sum_probs=47.5
Q ss_pred CCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcCC----CccEEeCCcccccceEEEecCCCc--hhhhhHHHHHHH
Q psy12229 313 LPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTN----CDLQMVGDEFSRKPYAIAVQQDRD--ARELFCNVHANI 386 (444)
Q Consensus 313 ~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~----c~l~~~~~~~~~~~~~~~~~k~sp--~~~~in~~il~l 386 (444)
+..+...+++.|.+|+ .+|.+.+...++-+.... .++.++...-..-...++.+++-| .++++-.+++.+
T Consensus 142 ~~~~~~~~~~~l~~G~----~Da~~~~~~~~~~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~ 217 (243)
T PF12974_consen 142 FVGSHDAVLEALLNGK----ADAAAIPSDAFERLEAEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSL 217 (243)
T ss_dssp EEE-HHHHHHHHHTTS----SSEEEEEHHHHHHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHT
T ss_pred EeCCHHHHHHHHHcCC----ccEEEEechhHHHHHHccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence 3458899999999997 777777766665554432 356666542222233566777654 899999999998
Q ss_pred hcC
Q psy12229 387 LSI 389 (444)
Q Consensus 387 ~e~ 389 (444)
..+
T Consensus 218 ~~~ 220 (243)
T PF12974_consen 218 SKD 220 (243)
T ss_dssp TSS
T ss_pred CCC
Confidence 864
No 33
>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=94.06 E-value=0.69 Score=41.01 Aligned_cols=67 Identities=15% Similarity=0.158 Sum_probs=46.6
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+..+++..+.++. +.++++... +...+++.|.+|++|+++..... ....+. ..+... ..+++
T Consensus 20 ~l~~~l~~~~~~~P~i~i~~~~~------------~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~-~~~~~ 82 (209)
T PF03466_consen 20 LLPPLLAEFRERHPNIRIEIREG------------DSDELIEALRSGELDLAITFGPP---PPPGLE-SEPLGE-EPLVL 82 (209)
T ss_dssp THHHHHHHHHHHSTTEEEEEEEE------------SHHHHHHHHHTTSSSEEEESSSS---SSTTEE-EEEEEE-EEEEE
T ss_pred HHHHHHHHHHHHCCCcEEEEEec------------cchhhhHHHhcccccEEEEEeec---cccccc-cccccc-eeeee
Confidence 4456666666655 456666633 45689999999999999987665 223332 456777 88999
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 83 ~~~~~ 87 (209)
T PF03466_consen 83 VVSPD 87 (209)
T ss_dssp EEETT
T ss_pred eeecc
Confidence 99876
No 34
>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=94.00 E-value=1.1 Score=43.25 Aligned_cols=37 Identities=11% Similarity=-0.047 Sum_probs=30.0
Q ss_pred HHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecc
Q psy12229 41 EIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSL 88 (444)
Q Consensus 41 ~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~ 88 (444)
.+++.+|.+++++..+ ++..++.++..|++|++..+.
T Consensus 20 ~~~k~~Gl~Ve~~~~~-----------~~~~~~~al~~G~iD~~~~~~ 56 (300)
T TIGR01729 20 AAAKEAGATIDWRKFD-----------SGADISTALASGNVPIGVIGS 56 (300)
T ss_pred chHHhcCCeeEEEecC-----------cHHHHHHHHHcCCCCEeccCC
Confidence 5777789999998664 456889999999999987544
No 35
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=93.68 E-value=1.9 Score=41.91 Aligned_cols=73 Identities=15% Similarity=0.078 Sum_probs=51.3
Q ss_pred CCCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcC--C---CccEEeCCcccccceEEEecCCC--chhhhhHHHHH
Q psy12229 312 KLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMT--N---CDLQMVGDEFSRKPYAIAVQQDR--DARELFCNVHA 384 (444)
Q Consensus 312 ~~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~--~---c~l~~~~~~~~~~~~~~~~~k~s--p~~~~in~~il 384 (444)
.+..+.+.++..|.+|+ .++-......+...... . .++.++.+.-......++++++- ..++++..+++
T Consensus 181 ~~~G~H~~a~~aV~nG~----vDva~~~~~~~~~~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~ 256 (299)
T COG3221 181 IFSGGHDAAVLAVANGQ----VDVAAVNSSARGLLKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFL 256 (299)
T ss_pred eccChHHHHHHHHHcCC----ceEEeccHHHHhhhhhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHH
Confidence 34556999999999997 77777776666555542 2 35677664333333457777776 49999999999
Q ss_pred HHhc
Q psy12229 385 NILS 388 (444)
Q Consensus 385 ~l~e 388 (444)
.+-+
T Consensus 257 ~l~~ 260 (299)
T COG3221 257 DLAK 260 (299)
T ss_pred hcCc
Confidence 9975
No 36
>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=92.71 E-value=3.2 Score=35.48 Aligned_cols=68 Identities=16% Similarity=0.318 Sum_probs=44.7
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.++++.+.++. +.++++... ....++..+.+|++|++++.... ....+. ..+... ..++
T Consensus 13 ~~l~~~i~~~~~~~p~i~i~~~~~------------~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~-~~~~ 75 (197)
T cd05466 13 YLLPPLLAAFRQRYPGVELSLVEG------------GSSELLEALLEGELDLAIVALPV---DDPGLE-SEPLFE-EPLV 75 (197)
T ss_pred HHhHHHHHHHHHHCCCCEEEEEEC------------ChHHHHHHHHcCCceEEEEcCCC---CCCcce-Eeeeec-cceE
Confidence 34556666666665 467777643 34578899999999999976543 223333 445666 6888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~~~~~~ 81 (197)
T cd05466 76 LVVPPD 81 (197)
T ss_pred EEecCC
Confidence 888765
No 37
>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=92.54 E-value=0.53 Score=35.75 Aligned_cols=55 Identities=25% Similarity=0.411 Sum_probs=47.5
Q ss_pred cccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhh
Q psy12229 164 PEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLT 225 (444)
Q Consensus 164 ~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt 225 (444)
....+.|+++.++...| +++..|.+..+|++.+.+.+.++.+.+...+.+.+.++
T Consensus 24 ~~~da~yfs~~t~tTvG-------yGDi~p~t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l~ 78 (79)
T PF07885_consen 24 SFIDALYFSFVTITTVG-------YGDIVPQTPAGRIFTIIYMLIGIFLFALFLSVLASVLT 78 (79)
T ss_dssp SHHHHHHHHHHHHTT----------SSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhccc-------CCCccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35678999999999999 68899999999999999999999999999999998875
No 38
>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=91.82 E-value=3.6 Score=36.27 Aligned_cols=71 Identities=11% Similarity=0.214 Sum_probs=47.2
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+..+++..+.++. +.+++++.. +...+++.|.+|++|++++...........+. +.+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~~~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~-~~~l~~-~~~~ 78 (202)
T cd08468 13 AVMPRLMARLEELAPSVRLNLVHA------------EQKLPLDALLAGEIDFALGYSHDDGAEPRLIE-ERDWWE-DTYV 78 (202)
T ss_pred HHhHHHHHHHHhhCCCCEEEEEEC------------ChHhHHHHHHCCCccEEEecccccccCCCCEE-EEEEec-CcEE
Confidence 45567888888877 578877732 45788999999999999875432100012333 345666 6778
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 79 ~~~~~~ 84 (202)
T cd08468 79 VIASRD 84 (202)
T ss_pred EEEeCC
Confidence 888665
No 39
>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=91.56 E-value=5.3 Score=34.71 Aligned_cols=68 Identities=12% Similarity=0.197 Sum_probs=45.5
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.++. +.++++... +...+++.+.+|++|+++..... ....+. ..+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~------------~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~-~~~~ 75 (198)
T cd08421 13 EFLPEDLASFLAAHPDVRIDLEER------------LSADIVRAVAEGRADLGIVAGNV---DAAGLE-TRPYRT-DRLV 75 (198)
T ss_pred hhhHHHHHHHHHHCCCceEEEEec------------CcHHHHHHHhcCCceEEEEecCC---CCCCcE-EEEeec-CcEE
Confidence 34456777777775 567777632 44678899999999999874432 223333 456667 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~v~~~~ 81 (198)
T cd08421 76 VVVPRD 81 (198)
T ss_pred EEeCCC
Confidence 887655
No 40
>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=91.23 E-value=7.4 Score=33.79 Aligned_cols=67 Identities=18% Similarity=0.162 Sum_probs=43.6
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-.+++..+.++. +.++++... ....+++.+.+|++|+++...... ...+. +.+... ..+++
T Consensus 14 ~l~~~l~~~~~~~P~i~l~i~~~------------~~~~~~~~l~~~~~D~~i~~~~~~---~~~~~-~~~l~~-~~~~~ 76 (199)
T cd08426 14 LLPSLIARFRQRYPGVFFTVDVA------------STADVLEAVLSGEADIGLAFSPPP---EPGIR-VHSRQP-APIGA 76 (199)
T ss_pred HHHHHHHHHHHhCCCeEEEEEeC------------CcHHHHHHHHCCCccEEEecCCCC---CCCeE-EEeecc-CcEEE
Confidence 4456677777664 566777632 446788999999999999743322 12332 455666 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 77 v~~~~ 81 (199)
T cd08426 77 VVPPG 81 (199)
T ss_pred EecCC
Confidence 88654
No 41
>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=91.22 E-value=6.6 Score=34.30 Aligned_cols=68 Identities=18% Similarity=0.262 Sum_probs=46.1
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.++. +.+++++.. +...+...+.+|++|+++...... ...+ .+.|... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~v~i~~~------------~~~~~~~~l~~g~~D~~i~~~~~~---~~~l-~~~~l~~-~~~~ 75 (201)
T cd08459 13 YFLPRLLAALREVAPGVRIETVRL------------PVDELEEALESGEIDLAIGYLPDL---GAGF-FQQRLFR-ERYV 75 (201)
T ss_pred HHHHHHHHHHHHHCCCCeEEEEec------------CccCHHHHhhCCCceEEEEcCCCC---cccc-eEEEeec-CceE
Confidence 34557777777776 467777632 445788999999999999754321 2334 3567777 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~v~~~~ 81 (201)
T cd08459 76 CLVRKD 81 (201)
T ss_pred EEEcCC
Confidence 888765
No 42
>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=90.55 E-value=8.6 Score=33.39 Aligned_cols=68 Identities=16% Similarity=0.161 Sum_probs=44.5
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.+.. +.++++... +...+...+.+|++|+++...... ...+ -+.+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~------------~~~~~~~~l~~~~~D~~i~~~~~~---~~~~-~~~~l~~-~~~~ 75 (198)
T cd08433 13 VLAVPLLRAVRRRYPGIRLRIVEG------------LSGHLLEWLLNGRLDLALLYGPPP---IPGL-STEPLLE-EDLF 75 (198)
T ss_pred hcchHHHHHHHHHCCCcEEEEEec------------CcHHHHHHHhCCCCcEEEEeCCCC---CCCe-eEEEecc-ccEE
Confidence 34456777777776 567777632 345788999999999998643221 2223 3456666 7778
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~~~~~~ 81 (198)
T cd08433 76 LVGPAD 81 (198)
T ss_pred EEecCC
Confidence 777654
No 43
>cd00918 Der-p2_like Several group 2 allergen proteins belong to the ML domain family. They include Dermatophagoides pteronyssinus, group 2 (Der p 2) and D. farinae, group 2 (Der f 2) allergens. These house dust mites cause heavy atopic diseases such as asthma and dermatitis. Although the allergenic properties of these proteins have been well characterized, their biological function in mites is unknown.
Probab=90.21 E-value=0.24 Score=41.16 Aligned_cols=38 Identities=26% Similarity=0.448 Sum_probs=32.5
Q ss_pred CCCcccccccccCCCCcccCCCCCCceeEeeeeeeccccCCCcccCC
Q psy12229 397 DGTSVCSSIFDTDGKTKVSCPLKKDHVYRYINTFKILDRYPKCSKDL 443 (444)
Q Consensus 397 ~~~~~~~~kw~~~~~~~~~c~~~~~~~~~~~~~~~~l~~~~~~~~~~ 443 (444)
++.|+| +|+ +||...++.+.|..+.+|.+.||.+++++
T Consensus 63 ~~~daC--~~l-------~CPl~~G~~~~y~~~~~V~~~~P~v~~~V 100 (120)
T cd00918 63 IETDGC--KYV-------KCPIKKGQHYDIKYTWNVPAILPKIKAVV 100 (120)
T ss_pred CCCCCc--ccE-------eCCCcCCcEEEEEEeeeccccCCCeEEEE
Confidence 458999 342 89999999999999999999999987753
No 44
>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=90.19 E-value=11 Score=32.46 Aligned_cols=69 Identities=14% Similarity=0.120 Sum_probs=47.2
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
.++-.+++..+.++. +.++++... +..+++..+.+|++|+++...... ...+ .+.++.. ..+
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~------------~~~~~~~~l~~~~~D~~i~~~~~~---~~~~-~~~~l~~-~~~ 74 (198)
T cd08412 12 PYYLPGLLRRFREAYPGVEVRVVEG------------NQEELEEGLRSGELDLALTYDLDL---PEDI-AFEPLAR-LPP 74 (198)
T ss_pred hhhhHHHHHHHHHHCCCcEEEEEEC------------CHHHHHHHHHcCCCcEEEEcCCCC---Cccc-ceeeeec-cce
Confidence 456677888887776 578888732 446788999999999998743221 2233 2466777 777
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 75 ~~~~~~~ 81 (198)
T cd08412 75 YVWLPAD 81 (198)
T ss_pred EEEecCC
Confidence 7777654
No 45
>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=90.05 E-value=7.9 Score=33.62 Aligned_cols=68 Identities=13% Similarity=0.187 Sum_probs=45.1
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+..+++..+.++. +.++++.. ++...+...+.+|++|+++..... ....+ -..+... ..++
T Consensus 13 ~~~~~~i~~~~~~~P~i~l~~~~------------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~-~~~~l~~-~~~~ 75 (200)
T cd08417 13 LLLPPLLARLRQEAPGVRLRFVP------------LDRDDLEEALESGEIDLAIGVFPE---LPPGL-RSQPLFE-DRFV 75 (200)
T ss_pred HHHHHHHHHHHhhCCCeEEEecc------------CCHHHHHHHHHcCCCCEEEeeccc---CCCcc-chhhhhc-CceE
Confidence 34456677777665 46666652 245678999999999999975432 22333 2456777 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~v~~~~ 81 (200)
T cd08417 76 CVARKD 81 (200)
T ss_pred EEecCC
Confidence 888765
No 46
>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=89.99 E-value=5.4 Score=35.04 Aligned_cols=66 Identities=12% Similarity=0.174 Sum_probs=43.4
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-..++..+.++. +.+++++. ++. .+++.+.+|++|+++....... ..+. ..|... ..+++
T Consensus 14 ~l~~~i~~~~~~~P~i~l~i~~------------~~~-~~~~~l~~g~~D~~i~~~~~~~---~~~~-~~~l~~-~~~~~ 75 (200)
T cd08462 14 LLPPVIERVAREAPGVRFELLP------------PDD-QPHELLERGEVDLLIAPERFMS---DGHP-SEPLFE-EEFVC 75 (200)
T ss_pred HHHHHHHHHHHHCCCCEEEEec------------CCh-hHHHHHhcCCeeEEEecCCCCC---CCce-eeeeec-cceEE
Confidence 4455667776666 47777763 233 7899999999999997433221 2232 446666 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 76 v~~~~ 80 (200)
T cd08462 76 VVWAD 80 (200)
T ss_pred EEcCC
Confidence 88655
No 47
>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=89.98 E-value=8.9 Score=33.66 Aligned_cols=68 Identities=18% Similarity=0.249 Sum_probs=44.6
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
++-.+++..+.++. +.++++... ....+++.+.+|++|+++..... . ...+. ..+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~~~~~------------~~~~~~~~l~~g~~D~~i~~~~~--~-~~~~~-~~~l~~-~~~~ 75 (200)
T cd08467 13 ALLPRLAPRLRERAPGLDLRLCPI------------GDDLAERGLEQGTIDLAVGRFAV--P-PDGLV-VRRLYD-DGFA 75 (200)
T ss_pred HHHHHHHHHHHhhCCCCEEEEecC------------CcccHHHHhhCCCcCEEEecCCC--C-Cccce-eEEeee-ccEE
Confidence 45566777777765 467777632 44578999999999999864321 1 12333 356667 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~v~~~~ 81 (200)
T cd08467 76 CLVRHG 81 (200)
T ss_pred EEEcCC
Confidence 888654
No 48
>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=89.97 E-value=8.6 Score=33.35 Aligned_cols=70 Identities=19% Similarity=0.348 Sum_probs=44.3
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-..++..+.++. +.++++.. ++...+...+.+|++|++++..... .....+. +.+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~------------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~~-~~~l~~-~~~~ 77 (201)
T cd08418 13 TLMPAVINRFKEQFPDVQISIYE------------GQLSSLLPELRDGRLDFAIGTLPDE-MYLKELI-SEPLFE-SDFV 77 (201)
T ss_pred hhhHHHHHHHHHHCCCceEEEEe------------CcHHHHHHHHHcCCCcEEEEecCCC-CCCccee-EEeecC-CceE
Confidence 34456667777665 56777763 2446789999999999999743221 1112332 355666 6777
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 78 ~v~~~~ 83 (201)
T cd08418 78 VVARKD 83 (201)
T ss_pred EEeCCC
Confidence 777654
No 49
>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=89.80 E-value=4.8 Score=35.31 Aligned_cols=68 Identities=12% Similarity=0.160 Sum_probs=45.1
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
.++..+++..+.++. +.++++.. ++. .+++.+.+|++|++++..... ...+. ..+... ..+
T Consensus 12 ~~~l~~~l~~~~~~~P~v~v~l~~------------~~~-~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~-~~~ 73 (200)
T cd08460 12 AAFGPALLAAVAAEAPGVRLRFVP------------ESD-KDVDALREGRIDLEIGVLGPT---GPEIR-VQTLFR-DRF 73 (200)
T ss_pred HHHHHHHHHHHHHHCCCCEEEEec------------Cch-hHHHHHHCCCccEEEecCCCC---Ccchh-eeeeec-cce
Confidence 355667777777776 46777752 233 678999999999998743221 12333 456667 788
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 74 ~~v~~~~ 80 (200)
T cd08460 74 VGVVRAG 80 (200)
T ss_pred EEEEeCC
Confidence 8888765
No 50
>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=89.74 E-value=9.7 Score=32.84 Aligned_cols=67 Identities=13% Similarity=0.244 Sum_probs=44.5
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+--+++..+.++. +.++++... ....+...+.+|++|+++....... ..+ .+.+... ..+++
T Consensus 13 ~l~~~l~~~~~~~P~i~l~i~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~-~~~~~ 75 (197)
T cd08419 13 FAPRLLGAFCRRHPGVEVSLRVG------------NREQVLERLADNEDDLAIMGRPPED---LDL-VAEPFLD-NPLVV 75 (197)
T ss_pred HhhHHHHHHHHHCCCceEEEEEC------------CHHHHHHHHhcCCccEEEecCCCCC---CCe-EEEEecc-CCEEE
Confidence 4556677777775 677777732 4467888999999999986433211 122 3456676 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 76 ~~~~~ 80 (197)
T cd08419 76 IAPPD 80 (197)
T ss_pred EecCC
Confidence 88654
No 51
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=89.63 E-value=9.2 Score=36.82 Aligned_cols=67 Identities=15% Similarity=0.212 Sum_probs=44.0
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-..++..+.+.. +.++++.. ++.+.+++++.+|++|+++....... ..+ .+.++.. ..+++
T Consensus 105 ~~~~~l~~~~~~~P~v~i~~~~------------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~l-~~~~l~~-~~~~~ 167 (305)
T PRK11151 105 LLPHIIPMLHQTFPKLEMYLHE------------AQTHQLLAQLDSGKLDCAILALVKES---EAF-IEVPLFD-EPMLL 167 (305)
T ss_pred HHHHHHHHHHHHCCCcEEEEEe------------CCHHHHHHHHHcCCccEEEEecCCCC---CCe-EEEEecc-CcEEE
Confidence 4445565666543 45666653 24478899999999999997543221 223 4567777 88888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 168 ~~~~~ 172 (305)
T PRK11151 168 AVYED 172 (305)
T ss_pred EecCC
Confidence 88765
No 52
>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=89.24 E-value=11 Score=32.41 Aligned_cols=69 Identities=13% Similarity=0.149 Sum_probs=45.7
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
..+..+++..+.++. +.++++... +...+...+.+|++|+++..... ....+. ..+... ..+
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~------------~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~-~~~ 74 (193)
T cd08442 12 AVRLPPLLAAYHARYPKVDLSLSTG------------TTGALIQAVLEGRLDGAFVAGPV---EHPRLE-QEPVFQ-EEL 74 (193)
T ss_pred hhhhHHHHHHHHHHCCCceEEEEeC------------CcHHHHHHHHCCCccEEEEeCCC---CCCCcE-EEEeec-CcE
Confidence 345567788887766 577887732 44678899999999999864322 122332 345566 677
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 75 ~~v~~~~ 81 (193)
T cd08442 75 VLVSPKG 81 (193)
T ss_pred EEEecCC
Confidence 7777654
No 53
>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=89.14 E-value=10 Score=32.73 Aligned_cols=68 Identities=15% Similarity=0.218 Sum_probs=44.6
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+..++++.+.+.. +.++++... +...+...|.+|++|+++...... ...+. ..+... ..++
T Consensus 13 ~~l~~~l~~~~~~~p~v~i~i~~~------------~~~~~~~~L~~~~~Dl~i~~~~~~---~~~~~-~~~l~~-~~~~ 75 (197)
T cd08438 13 LLFAPLLAAFRQRYPNIELELVEY------------GGKKVEQAVLNGELDVGITVLPVD---EEEFD-SQPLCN-EPLV 75 (197)
T ss_pred hhcHHHHHHHHHHCcCeEEEEEEc------------CcHHHHHHHHcCCCCEEEEecccc---cCCce-eEEecc-ccEE
Confidence 34567778887775 456666532 446788999999999998754321 22332 345666 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~v~~~~ 81 (197)
T cd08438 76 AVLPRG 81 (197)
T ss_pred EEecCC
Confidence 888665
No 54
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=89.12 E-value=17 Score=32.85 Aligned_cols=112 Identities=13% Similarity=0.135 Sum_probs=64.1
Q ss_pred CCCCCChHHhhhCCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHH
Q psy12229 230 DTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMK 309 (444)
Q Consensus 230 ~~~I~sl~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~ 309 (444)
...|.+++||.+.+-.-++-..++.+..+|+..- ...+++ ++.+.-|+
T Consensus 80 p~~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l----------~~~gi~-------~~~i~gy~--------------- 127 (193)
T PF12727_consen 80 PKGITSLEDLADPGLRFVNRQPGSGTRILFDQLL----------AEEGID-------PEDIPGYA--------------- 127 (193)
T ss_pred CccCCCHHHhccCCcEEEECCCCCHHHHHHHHHH----------HHcCCC-------hhhCCCcc---------------
Confidence 3479999999774433344457788888887642 111111 12222111
Q ss_pred hcCCCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcCCCccEEeCCcccccceEEEecCCCchhhhhHHHHHH
Q psy12229 310 EAKLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQQDRDARELFCNVHAN 385 (444)
Q Consensus 310 ~~~~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c~l~~~~~~~~~~~~~~~~~k~sp~~~~in~~il~ 385 (444)
....+..+....|..|+ .++-+.......-+ ..-++..+. .+.|-++++|..-..+.+.+.|.-
T Consensus 128 --~~~~th~~vA~aVa~G~----AD~G~g~~~~A~~~--~gL~Fvpl~----~E~~dlv~~~~~~~~~~vq~ll~~ 191 (193)
T PF12727_consen 128 --QEANTHLAVAAAVASGK----ADAGIGIRAAAEEF--YGLDFVPLA----EERYDLVIRREDLEDPAVQALLDF 191 (193)
T ss_pred --ccccChHHHHHHHHcCC----CCEEeehHHHHHhh--cCCCcEEcc----ccceEEEEEhhHcCCHHHHHHHHH
Confidence 12568899999999997 66666543222210 122333333 356789999887666666666543
No 55
>KOG4063|consensus
Probab=88.95 E-value=0.45 Score=40.45 Aligned_cols=43 Identities=28% Similarity=0.502 Sum_probs=36.0
Q ss_pred CCCcccccccccCCCCcccCCCCCCceeEeeeeeeccccCCCcccC
Q psy12229 397 DGTSVCSSIFDTDGKTKVSCPLKKDHVYRYINTFKILDRYPKCSKD 442 (444)
Q Consensus 397 ~~~~~~~~kw~~~~~~~~~c~~~~~~~~~~~~~~~~l~~~~~~~~~ 442 (444)
..+|+|..-.+.- .-.||...++.++|.+++||...||++.+.
T Consensus 92 ~~~dacv~~~l~~---gv~CPl~age~ytY~~slpI~~~yP~v~v~ 134 (158)
T KOG4063|consen 92 PASDACVCGNLLH---GVYCPLSAGEDYTYLNSLPITENYPEVSVI 134 (158)
T ss_pred CCCcccccccccc---cccCcccCCCceEEEEEeeccccCCceeEE
Confidence 3477787766553 459999999999999999999999999874
No 56
>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=88.89 E-value=2.7 Score=40.79 Aligned_cols=42 Identities=19% Similarity=0.142 Sum_probs=30.8
Q ss_pred HHHHHHHHHHcC-CeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecc
Q psy12229 36 IDLIEEIRKLVG-FEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSL 88 (444)
Q Consensus 36 ~dil~~la~~ln-ft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~ 88 (444)
..+.+.+++.++ .+++++.. +.....+..|.+|++|+++...
T Consensus 48 ~~la~~~~~~~~~i~v~~~~~-----------~~~~~~~~~l~~G~~D~~~~~~ 90 (320)
T TIGR02122 48 GAIAQLINKKSGKLRVRVQST-----------GGSVENVNLLEAGEADLAIVQS 90 (320)
T ss_pred HHHHHHHhccCCCeeEEEEeC-----------cchHHHHHHHhCCCCcEEEEcc
Confidence 456677777776 77777743 2345788999999999998764
No 57
>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=88.75 E-value=8.8 Score=33.38 Aligned_cols=68 Identities=9% Similarity=0.162 Sum_probs=46.3
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.+++ +.++++.. ++...+..++.+|++|+++..... ....+ -+.++.. ..++
T Consensus 13 ~~l~~~l~~f~~~~P~v~l~~~~------------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~-~~~~l~~-~~~~ 75 (200)
T cd08466 13 LLLPRLLARLKQLAPNISLRESP------------SSEEDLFEDLRLQEVDLVIDYVPF---RDPSF-KSELLFE-DELV 75 (200)
T ss_pred HHHHHHHHHHHHHCCCCEEEEec------------CchHhHHHHHHcCCccEEEecccC---CCCCc-eeeeecc-cceE
Confidence 45567777777776 57777773 345678999999999999864322 12333 2456677 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 lv~~~~ 81 (200)
T cd08466 76 CVARKD 81 (200)
T ss_pred EEEeCC
Confidence 888765
No 58
>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=88.45 E-value=15 Score=31.46 Aligned_cols=69 Identities=12% Similarity=0.118 Sum_probs=45.9
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
..+-.+++..+.++. +.++++... +...+.+.+.+|++|+++..... ....+ -+.+... ..+
T Consensus 12 ~~~l~~~l~~~~~~~p~v~i~i~~~------------~~~~~~~~l~~g~~D~~i~~~~~---~~~~~-~~~~l~~-~~~ 74 (197)
T cd08440 12 ATLLPPVLAAFRRRHPGIRVRLRDV------------SAEQVIEAVRSGEVDFGIGSEPE---ADPDL-EFEPLLR-DPF 74 (197)
T ss_pred hhHHHHHHHHHHHhCCCcEEEEEeC------------ChHHHHHHHHcCCccEEEEeCCC---CCCCe-eEEEeec-ccE
Confidence 345567777777765 567777632 44678899999999999875432 12223 2356666 788
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 75 ~~~~~~~ 81 (197)
T cd08440 75 VLVCPKD 81 (197)
T ss_pred EEEecCC
Confidence 8888765
No 59
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=88.22 E-value=13 Score=35.33 Aligned_cols=67 Identities=15% Similarity=0.224 Sum_probs=43.0
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+..+++..+.++. +.++++... ....++..+.+|++|+++...... ...+ ...+... ..+++
T Consensus 103 ~~~~~l~~~~~~~P~i~i~v~~~------------~~~~~~~~l~~g~~Di~i~~~~~~---~~~~-~~~~l~~-~~~~l 165 (290)
T PRK10837 103 ILPAMIARYRRDYPQLPLELSVG------------NSQDVINAVLDFRVDIGLIEGPCH---SPEL-ISEPWLE-DELVV 165 (290)
T ss_pred hhHHHHHHHHHHCCCceEEEEEC------------CHHHHHHHHHhCCceEEEecCCCC---CCce-eEEEeec-ceEEE
Confidence 3445666666665 567777632 446789999999999998643222 1223 2355666 67888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 166 v~~~~ 170 (290)
T PRK10837 166 FAAPD 170 (290)
T ss_pred EEcCC
Confidence 88765
No 60
>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=88.07 E-value=16 Score=31.38 Aligned_cols=68 Identities=9% Similarity=-0.024 Sum_probs=45.9
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.++. +.++++.. +...++...+.+|++|+++..... ....+ .+.+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~i~~------------~~~~~~~~~l~~~~~Di~i~~~~~---~~~~~-~~~~l~~-~~~~ 75 (197)
T cd08448 13 RGLPRILRAFRAEYPGIEVALHE------------MSSAEQIEALLRGELDLGFVHSRR---LPAGL-SARLLHR-EPFV 75 (197)
T ss_pred HHHHHHHHHHHHHCCCCeEEEEe------------CCHHHHHHHHHcCCcceEEEeCCC---CCcCc-eEEEEec-CcEE
Confidence 45567788887776 67888763 245678899999999999864321 12233 2456666 7788
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~~~~~~ 81 (197)
T cd08448 76 CCLPAG 81 (197)
T ss_pred EEeeCC
Confidence 777654
No 61
>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=88.03 E-value=16 Score=31.36 Aligned_cols=69 Identities=10% Similarity=0.145 Sum_probs=45.9
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
..+-.+++..+.++. +.++++... +...+..+|.+|++|+++...... ...+. +.+... ..+
T Consensus 12 ~~~l~~~l~~~~~~~P~~~l~~~~~------------~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~-~~~ 74 (201)
T cd08420 12 EYLLPRLLARFRKRYPEVRVSLTIG------------NTEEIAERVLDGEIDLGLVEGPVD---HPDLI-VEPFAE-DEL 74 (201)
T ss_pred hhhhHHHHHHHHHHCCCceEEEEeC------------CcHHHHHHHHCCCccEEEecCCCC---CcceE-EEeecC-ccE
Confidence 345667788888776 567777632 345778899999999998754322 22232 355666 777
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
.+++++.
T Consensus 75 ~~v~~~~ 81 (201)
T cd08420 75 VLVVPPD 81 (201)
T ss_pred EEEecCC
Confidence 8777654
No 62
>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=87.82 E-value=16 Score=31.20 Aligned_cols=68 Identities=22% Similarity=0.358 Sum_probs=44.4
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-..++..+.++. +.++++.. +....++.++.+|++|+++...... ...+. ..++.. ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~i~~------------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~l~-~~~l~~-~~~~ 75 (195)
T cd08434 13 SLVPDLIRAFRKEYPNVTFELHQ------------GSTDELLDDLKNGELDLALCSPVPD---EPDIE-WIPLFT-EELV 75 (195)
T ss_pred hhhHHHHHHHHHhCCCeEEEEec------------CcHHHHHHHHHcCCccEEEEccCCC---CCCee-EEEeec-ceEE
Confidence 44556777777776 56777763 2445778999999999998644322 22333 345666 6788
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~v~~~~ 81 (195)
T cd08434 76 LVVPKD 81 (195)
T ss_pred EEecCC
Confidence 887654
No 63
>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=87.15 E-value=12 Score=32.15 Aligned_cols=70 Identities=11% Similarity=0.116 Sum_probs=45.2
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.+.. +.++++.. ++.+.+++.+.+|++|+++..-... .....+ .+.+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~~~~------------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~-~~~~l~~-~~~~ 77 (195)
T cd08427 13 GLLPRALARLRRRHPDLEVHIVP------------GLSAELLARVDAGELDAAIVVEPPF-PLPKDL-VWTPLVR-EPLV 77 (195)
T ss_pred HHhHHHHHHHHHHCCCceEEEEe------------CCcHHHHHHHHCCCCCEEEEcCCCC-ccccCc-eEEEccc-CcEE
Confidence 34456777777766 66777763 2457788999999999998743211 102233 2455666 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 78 ~v~~~~ 83 (195)
T cd08427 78 LIAPAE 83 (195)
T ss_pred EEECCC
Confidence 888664
No 64
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=87.08 E-value=29 Score=33.32 Aligned_cols=70 Identities=17% Similarity=0.218 Sum_probs=44.2
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-.+++..+.++. +.++++... +...++..+.+|++|+++.......+....+ ...++.. ..+++
T Consensus 109 ~~~~~l~~~~~~~P~v~i~~~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~-~~~~l~~-~~~~~ 174 (305)
T CHL00180 109 LMPRLIGLFRQRYPQINVQLQVH------------STRRIAWNVANGQIDIAIVGGEVPTELKKIL-EITPYVE-DELAL 174 (305)
T ss_pred HHHHHHHHHHHHCCCceEEEEeC------------CHHHHHHHHHcCCccEEEEcCccCcccccce-eEEEecc-CcEEE
Confidence 3446666666654 456666532 4567889999999999997433222111223 3466777 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 175 v~~~~ 179 (305)
T CHL00180 175 IIPKS 179 (305)
T ss_pred EECCC
Confidence 88765
No 65
>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=86.96 E-value=20 Score=31.61 Aligned_cols=70 Identities=19% Similarity=0.269 Sum_probs=46.9
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
..+--+++..+.++. +.++++... ++...+.+.|.+|++|+++..... ....++ ..++.. ..+
T Consensus 12 ~~~~~~~l~~~~~~~P~~~v~~~~~-----------~~~~~l~~~L~~g~lDl~i~~~~~---~~~~l~-~~~l~~-~~~ 75 (203)
T cd08463 12 ALFLPELVARFRREAPGARLEIHPL-----------GPDFDYERALASGELDLVIGNWPE---PPEHLH-LSPLFS-DEI 75 (203)
T ss_pred HHHhHHHHHHHHHHCCCCEEEEEeC-----------CcchhHHHHHhcCCeeEEEecccc---CCCCcE-EeEeec-Cce
Confidence 345667788888776 467777731 134678999999999999974322 112333 355666 788
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 76 ~lv~~~~ 82 (203)
T cd08463 76 VCLMRAD 82 (203)
T ss_pred EEEEeCC
Confidence 8888766
No 66
>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=86.38 E-value=20 Score=30.74 Aligned_cols=67 Identities=12% Similarity=0.068 Sum_probs=43.9
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-.+++..+.+.. +.++++.. +....+...+.+|++|+++...... ...+ -..+... ..+++
T Consensus 14 ~l~~~l~~~~~~~p~i~i~i~~------------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~-~~~~~ 76 (197)
T cd08414 14 LLPRLLRRFRARYPDVELELRE------------MTTAEQLEALRAGRLDVGFVRPPPD---PPGL-ASRPLLR-EPLVV 76 (197)
T ss_pred HHHHHHHHHHHHCCCcEEEEec------------CChHHHHHHHHcCCccEEEEcCCCC---CCCe-eEEEEee-ccEEE
Confidence 4456666776665 46676663 2446788999999999999754322 2233 2456677 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 77 v~~~~ 81 (197)
T cd08414 77 ALPAD 81 (197)
T ss_pred EecCC
Confidence 88665
No 67
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=86.38 E-value=13 Score=33.97 Aligned_cols=120 Identities=13% Similarity=0.147 Sum_probs=69.5
Q ss_pred CCCCCChHHhhhCCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHH
Q psy12229 230 DTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMK 309 (444)
Q Consensus 230 ~~~I~sl~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~ 309 (444)
...|++++||.+..-.-+.-.+++.++.+|+..-. .. ...+.++.-|+.
T Consensus 86 pk~i~~~edl~~~d~~fVNR~rGSGTR~LlD~~L~----------~~-------~~~~~~I~GY~~-------------- 134 (223)
T COG1910 86 PKNISSLEDLLRKDLRFVNRNRGSGTRILLDELLG----------EL-------NILPDSIKGYSD-------------- 134 (223)
T ss_pred CCccccHHHHhhcCcEEEecCCCccHHHHHHHHHH----------Hc-------CcCchhcCCccc--------------
Confidence 34689999999964333444688888888875421 00 011122222211
Q ss_pred hcCCCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcCCC-ccEEeCCcccccceEEEecCCCchhhhhHHHHHHHhc
Q psy12229 310 EAKLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNC-DLQMVGDEFSRKPYAIAVQQDRDARELFCNVHANILS 388 (444)
Q Consensus 310 ~~~~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c-~l~~~~~~~~~~~~~~~~~k~sp~~~~in~~il~l~e 388 (444)
...+....-++|..|+ .+|=+. +++.+.++. ++..+ ..+.|-++.+|+.-=.+.+..++..|..
T Consensus 135 ---e~~th~avA~aVa~G~----AD~GvG----lr~~A~~~gL~Fipl----~~E~YD~virke~~~~~~vr~fi~~L~s 199 (223)
T COG1910 135 ---EATTHDAVASAVASGR----ADAGVG----LRHAAEKYGLDFIPL----GDEEYDFVIRKERLDKPVVRAFIKALKS 199 (223)
T ss_pred ---cccccHHHHHHHHcCC----CCcccc----HHHHHHHcCCceEEc----ccceEEEEEehhHccCHHHHHHHHHhcc
Confidence 2346677778899987 666665 345554443 44433 3346788999986555555556666666
Q ss_pred CCccccC
Q psy12229 389 IPFPFIG 395 (444)
Q Consensus 389 ~G~i~~~ 395 (444)
.|+-..+
T Consensus 200 ~~~~~~l 206 (223)
T COG1910 200 EGFAANL 206 (223)
T ss_pred ccccccC
Confidence 6664444
No 68
>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=86.32 E-value=15 Score=31.84 Aligned_cols=68 Identities=13% Similarity=0.183 Sum_probs=45.1
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
++-.+++..+.++. +.++++... ....+...+.+|++|+++..... ....+ -+.+... ..++
T Consensus 13 ~~l~~~l~~f~~~~P~v~i~i~~~------------~~~~~~~~l~~~~~Di~i~~~~~---~~~~~-~~~~l~~-~~~~ 75 (198)
T cd08461 13 AILPPLLAALRQEAPGVRVAIRDL------------ESDNLEAQLERGEVDLALTTPEY---APDGL-RSRPLFE-ERYV 75 (198)
T ss_pred HHhHHHHHHHHHHCCCcEEEEeeC------------CcccHHHHHhcCCCcEEEecCcc---CCccc-eeeeeec-CcEE
Confidence 44566777777776 577877632 33567899999999999864322 12233 2556777 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 lv~~~~ 81 (198)
T cd08461 76 CVTRRG 81 (198)
T ss_pred EEEcCC
Confidence 888664
No 69
>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=86.29 E-value=14 Score=31.76 Aligned_cols=69 Identities=12% Similarity=0.114 Sum_probs=47.0
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
..+-.+++..+.+.. +.++++... ...++...+.+|++|+++...... ...+ .+.++.. ...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~------------~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~-~~~ 74 (196)
T cd08415 12 LSLLPRAIARFRARHPDVRISLHTL------------SSSTVVEAVLSGQADLGLASLPLD---HPGL-ESEPLAS-GRA 74 (196)
T ss_pred ccccHHHHHHHHHHCCCcEEEEEec------------chHHHHHHHHcCCccEEEEeCCCC---CCcc-eeeeecc-cce
Confidence 345567888887765 667777632 446788999999999999754322 2223 3566777 788
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 75 ~~v~~~~ 81 (196)
T cd08415 75 VCVLPPG 81 (196)
T ss_pred EEEEcCC
Confidence 8888654
No 70
>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=86.26 E-value=17 Score=31.71 Aligned_cols=69 Identities=14% Similarity=0.165 Sum_probs=45.2
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+..+++..+.++. +.++++... ....+.+.+.+|++|+++...... ....+. +.+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~v~~~~~------------~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~~-~~~l~~-~~~~ 76 (198)
T cd08413 13 YVLPPVIAAFRKRYPKVKLSLHQG------------TPSQIAEMVLKGEADIAIATEALD--DHPDLV-TLPCYR-WNHC 76 (198)
T ss_pred hhccHHHHHHHHhCCceEEEEEeC------------CHHHHHHHHHcCCCCEEEEccCCC--CCCCcE-EEEeee-eeEE
Confidence 34566777777776 356777632 446788999999999999643221 122333 466677 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 77 ~v~~~~ 82 (198)
T cd08413 77 VIVPPG 82 (198)
T ss_pred EEecCC
Confidence 888765
No 71
>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=85.89 E-value=19 Score=31.24 Aligned_cols=67 Identities=19% Similarity=0.223 Sum_probs=43.1
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+--+++..+.++. +.++++.. ++...+++.+.+|++|+++...... ...+. ..+... ..+++
T Consensus 15 ~l~~~l~~~~~~~P~i~i~i~~------------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~-~~~~~ 77 (200)
T cd08411 15 LLPRLLPALRQAYPKLRLYLRE------------DQTERLLEKLRSGELDAALLALPVD---EPGLE-EEPLFD-EPFLL 77 (200)
T ss_pred hhHHHHHHHHHHCCCcEEEEEe------------CcHHHHHHHHHcCCccEEEEeccCC---CCCce-EEEeec-cceEE
Confidence 4456677777765 46777763 2456788999999999998643221 12232 344566 67777
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 78 v~~~~ 82 (200)
T cd08411 78 AVPKD 82 (200)
T ss_pred EecCC
Confidence 77654
No 72
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=85.31 E-value=15 Score=35.36 Aligned_cols=67 Identities=10% Similarity=0.116 Sum_probs=42.9
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+...++..+.++. +.++++... ....+...+.+|++|+++...... ...+ ...|+.. ..+++
T Consensus 106 ~~~~~l~~~~~~~p~i~l~~~~~------------~~~~~~~~l~~g~~Di~i~~~~~~---~~~~-~~~~l~~-~~~~l 168 (305)
T PRK11233 106 LTMPLLQAVRAEFPGIVLYLHEN------------SGATLNEKLMNGQLDMAVIYEHSP---VAGL-SSQPLLK-EDLFL 168 (305)
T ss_pred HHHHHHHHHHHHCCCcEEEEEEC------------CcHHHHHHHHCCCCCEEEEcCCcC---CCCc-EEEEEee-eeEEE
Confidence 3345677777765 667766632 335778899999999998643221 1223 3456777 77777
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 169 v~~~~ 173 (305)
T PRK11233 169 VGTQD 173 (305)
T ss_pred EEcCc
Confidence 77654
No 73
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=85.23 E-value=26 Score=33.34 Aligned_cols=68 Identities=12% Similarity=0.140 Sum_probs=45.2
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+..+++..+.++. +.++++.. +....++..+.+|++|+++..... ....+ .+.++.. +.++
T Consensus 104 ~~l~~~l~~~~~~~p~~~i~~~~------------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~l-~~~~l~~-~~~~ 166 (296)
T PRK11242 104 YLIGPLIDAFHARYPGITLTIRE------------MSQERIEALLADDELDVGIAFAPV---HSPEI-EAQPLFT-ETLA 166 (296)
T ss_pred hhhHHHHHHHHHHCCCCEEEEEe------------CCHHHHHHHHHCCCCcEEEEecCC---CCcce-eEEEeee-ccEE
Confidence 34566777777764 45566652 244678889999999999864432 22333 3566777 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 167 ~~~~~~ 172 (296)
T PRK11242 167 LVVGRH 172 (296)
T ss_pred EEEcCC
Confidence 888765
No 74
>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=84.26 E-value=9 Score=36.16 Aligned_cols=37 Identities=11% Similarity=-0.084 Sum_probs=26.0
Q ss_pred HHHHcC--CeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeeccc
Q psy12229 42 IRKLVG--FEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLS 89 (444)
Q Consensus 42 la~~ln--ft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~ 89 (444)
+-++.+ ++++++..+ +...++.+|.+|++|+++.+..
T Consensus 21 ~f~~~g~~l~v~~~~~~-----------~~~~~~~~l~~G~~D~~~~~~~ 59 (288)
T TIGR01728 21 LLEKELGKTKVEWVEFP-----------AGPPALEALGAGSLDFGYIGPG 59 (288)
T ss_pred HHHHhhCCceEEEEecC-----------CCcHHHHHHhcCCccccccCCc
Confidence 334445 778887543 3467899999999999876543
No 75
>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=84.16 E-value=26 Score=29.98 Aligned_cols=69 Identities=13% Similarity=0.128 Sum_probs=44.5
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.++. +.++++... +...+.+.+.+|++|+++..... +....+ ...+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~i~~~------------~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~-~~~~l~~-~~~~ 76 (194)
T cd08436 13 VDLPELLARFHRRHPGVDIRLRQA------------GSDDLLAAVREGRLDLAFVGLPE--RRPPGL-ASRELAR-EPLV 76 (194)
T ss_pred HHHHHHHHHHHHHCCCcEEEEecC------------CHHHHHHHHHcCCccEEEEecCC--CCCCCc-EEEEeec-ceEE
Confidence 45566777777766 567777632 34678899999999999875432 122233 2355566 6777
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 77 ~~~~~~ 82 (194)
T cd08436 77 AVVAPD 82 (194)
T ss_pred EEecCC
Confidence 777654
No 76
>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=84.14 E-value=20 Score=30.80 Aligned_cols=70 Identities=14% Similarity=0.119 Sum_probs=44.6
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeeccccc--ccccccccccccceecccE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVM--AERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t--~~r~~~~dfS~p~~~~~~~ 110 (444)
+-.+++..+.+.. +.++++... +...+...+.+|++|+++...... ......+ .+.+... ..+
T Consensus 14 ~l~~~l~~~~~~~P~i~i~~~~~------------~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~-~~~~l~~-~~~ 79 (200)
T cd08423 14 LLPPALAALRARHPGLEVRLREA------------EPPESLDALRAGELDLAVVFDYPVTPPPDDPGL-TRVPLLD-DPL 79 (200)
T ss_pred hhhHHHHHHHHhCCCCeEEEEeC------------CHHHHHHHHhcCCccEEEEeccccccCCCCCCc-EEEEecc-CcE
Confidence 4456677777775 567777632 345788999999999998643211 1122233 3556666 788
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 80 ~~~~~~~ 86 (200)
T cd08423 80 DLVLPAD 86 (200)
T ss_pred EEEecCC
Confidence 8887654
No 77
>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=83.86 E-value=29 Score=30.69 Aligned_cols=71 Identities=14% Similarity=0.203 Sum_probs=44.5
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
..+-.+++..+.+.. +.++++.. ++...++..|.+|++|+++........-...+ ...|... ..+
T Consensus 12 ~~~l~~~l~~f~~~~P~v~l~i~~------------~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~-~~~~l~~-~~~ 77 (204)
T cd08429 12 KSIAYRLLEPAMDLHEPIRLVCRE------------GKLEQLLADLALHRLDMVLADRPMPSSLDVKG-YSHRLGE-CGV 77 (204)
T ss_pred HHHHHHHHHHHHHhCCCcEEEEEe------------CCHHHHHHHHHcCCccEEEecCCCccccchhe-eeccccc-cce
Confidence 345567777777776 56777763 35678999999999999985432211100112 2446666 677
Q ss_pred EEEEeC
Q psy12229 111 TILMKK 116 (444)
Q Consensus 111 ~ilvp~ 116 (444)
+++++.
T Consensus 78 ~~~~~~ 83 (204)
T cd08429 78 SFFAAP 83 (204)
T ss_pred EEEecC
Confidence 776654
No 78
>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=83.61 E-value=28 Score=30.02 Aligned_cols=68 Identities=15% Similarity=0.116 Sum_probs=44.6
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
++-..++..+.++. +.++++... ....+...+.+|++|+++...... ...+ -+.+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~l~i~~~------------~~~~~~~~l~~g~~D~~i~~~~~~---~~~~-~~~~l~~-~~~~ 75 (200)
T cd08464 13 WLAPPLLAALRAEAPGVRLVFRQV------------DPFNVGDMLDRGEIDLAIGVFGEL---PAWL-KREVLYT-EGYA 75 (200)
T ss_pred HHHHHHHHHHHHHCCCcEEEEecC------------CcccHHHHHhcCcccEEEecCCCC---cccc-eeeeecc-cceE
Confidence 45566777777775 577777632 345778999999999998643321 2333 2456666 6777
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~v~~~~ 81 (200)
T cd08464 76 CLFDPQ 81 (200)
T ss_pred EEEeCC
Confidence 777654
No 79
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=83.30 E-value=30 Score=33.53 Aligned_cols=68 Identities=13% Similarity=0.220 Sum_probs=42.3
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-.+++..+.++. +.++++... +...++..+.+|++|+++..-.... ...+ -+.|+.. ..+++
T Consensus 107 ~l~~~l~~~~~~~p~i~l~~~~~------------~~~~~~~~L~~g~~D~~i~~~~~~~--~~~l-~~~~l~~-~~~~~ 170 (313)
T PRK12684 107 ALPAAIKEFKKRYPKVRLSILQG------------SPTQIAEMVLHGQADLAIATEAIAD--YKEL-VSLPCYQ-WNHCV 170 (313)
T ss_pred HhHHHHHHHHHHCCCceEEEEeC------------ChHHHHHHHHCCCcCEEEeecCCCC--CCCc-eEEEecc-ceEEE
Confidence 3445666666654 466666632 4567899999999999986432111 1223 2456666 77788
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 171 v~~~~ 175 (313)
T PRK12684 171 VVPPD 175 (313)
T ss_pred EeCCC
Confidence 87655
No 80
>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=83.18 E-value=29 Score=29.85 Aligned_cols=70 Identities=13% Similarity=0.132 Sum_probs=43.6
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.+.. +.++++.. ++...+.+.+.+|++|+++...... .+...+ ...+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~i~~------------~~~~~~~~~l~~~~~Dl~i~~~~~~-~~~~~~-~~~~l~~-~~~~ 77 (201)
T cd08435 13 VLLPPAIARLLARHPRLTVRVVE------------GTSDELLEGLRAGELDLAIGRLADD-EQPPDL-ASEELAD-EPLV 77 (201)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEe------------CCHHHHHHHHHcCCccEEEEecCcc-cCCCCc-EEEEccc-CcEE
Confidence 34456667776664 45666652 2446788899999999998643211 112233 2456667 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 78 ~~~~~~ 83 (201)
T cd08435 78 VVARPG 83 (201)
T ss_pred EEEeCC
Confidence 888765
No 81
>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=83.13 E-value=28 Score=29.91 Aligned_cols=68 Identities=9% Similarity=0.013 Sum_probs=44.9
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.++. +.++++... ....+++++.+|++|+++...... ...+. +.+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~~~i~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~-~~~~ 75 (196)
T cd08456 13 SFLPRAIKAFLQRHPDVTISIHTR------------DSPTVEQWLSAQQCDLGLVSTLHE---PPGIE-RERLLR-IDGV 75 (196)
T ss_pred hhHHHHHHHHHHHCCCcEEEEEeC------------CHHHHHHHHHcCCccEEEEecCCC---CCCee-EEEeec-cCeE
Confidence 45567788888876 577777632 445678899999999998643221 22232 455666 6777
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~~~~~~ 81 (196)
T cd08456 76 CVLPPG 81 (196)
T ss_pred EEecCC
Confidence 777654
No 82
>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=82.90 E-value=30 Score=29.89 Aligned_cols=67 Identities=10% Similarity=0.221 Sum_probs=43.0
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-..++..+.++. +.++++... ....+...|.+|++|+++..-.. ....+. ..+... ..+++
T Consensus 14 ~~~~~l~~~~~~~P~i~i~i~~~------------~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~-~~~~~ 76 (198)
T cd08441 14 WLMPVLDQFRERWPDVELDLSSG------------FHFDPLPALLRGELDLVITSDPL---PLPGIA-YEPLFD-YEVVL 76 (198)
T ss_pred hhHHHHHHHHHhCCCeEEEEEeC------------CchhHHHHHHcCCceEEEecCCc---CCCCcE-EEEccC-CcEEE
Confidence 4456777777776 467777632 44678899999999999864322 122332 344555 67777
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 77 ~~~~~ 81 (198)
T cd08441 77 VVAPD 81 (198)
T ss_pred EEcCC
Confidence 77654
No 83
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=82.89 E-value=30 Score=33.33 Aligned_cols=69 Identities=16% Similarity=0.236 Sum_probs=44.3
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+..+++..+.+.. +.++++... +...+...+.+|++|++++..... ....++ +.|+.. ...+
T Consensus 106 ~~l~~~l~~~~~~~P~i~i~i~~~------------~~~~~~~~l~~g~~D~~i~~~~~~--~~~~l~-~~~l~~-~~~~ 169 (309)
T PRK12682 106 YVLPRVVAAFRKRYPKVNLSLHQG------------SPDEIARMVISGEADIGIATESLA--DDPDLA-TLPCYD-WQHA 169 (309)
T ss_pred HHHHHHHHHHHHhCCCeEEEEecC------------CHHHHHHHHHcCCccEEEecCccc--CCCcce-EEEeee-eeEE
Confidence 34456666666664 456666532 346788999999999998743221 123343 456777 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 170 ~~~~~~ 175 (309)
T PRK12682 170 VIVPPD 175 (309)
T ss_pred EEecCC
Confidence 888765
No 84
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=82.43 E-value=28 Score=33.37 Aligned_cols=69 Identities=13% Similarity=0.157 Sum_probs=42.9
Q ss_pred cHHHHHHHHHHHcC-CeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLVG-FEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~ln-ft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-.+++..+.+... .++++.. ++..+++.+|.+|++|+++....... ....+. ..|+.. ..+++
T Consensus 109 ~l~~~l~~~~~~~p~i~~~~~~------------~~~~~~~~~l~~g~~Di~i~~~~~~~-~~~~~~-~~~l~~-~~~~l 173 (302)
T PRK09791 109 LMPAVISRFHQQHPQVKVRIME------------GQLVSMINELRQGELDFTINTYYQGP-YDHEFT-FEKLLE-KQFAV 173 (302)
T ss_pred hhHHHHHHHHHHCCCeEEEEEe------------CChHHHHHHHHCCCccEEEEecCCcc-ccccee-EEEecc-ceEEE
Confidence 34455666665553 4555552 24568899999999999987432111 122343 366777 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 174 ~~~~~ 178 (302)
T PRK09791 174 FCRPG 178 (302)
T ss_pred EEcCC
Confidence 88765
No 85
>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=82.02 E-value=33 Score=29.69 Aligned_cols=71 Identities=11% Similarity=0.101 Sum_probs=45.8
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-..++..+.++. +.++++... ....+...+.+|++|+++............+ -+.+... +.++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~------------~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~-~~~~l~~-~~~~ 78 (200)
T cd08453 13 SVLPELVRRFREAYPDVELQLREA------------TSDVQLEALLAGEIDAGIVIPPPGASAPPAL-AYRPLLS-EPLV 78 (200)
T ss_pred HHHHHHHHHHHHhCCCceEEEEeC------------CHHHHHHHHHcCCCCEEEEecCcccCCCcce-eEEEeee-CceE
Confidence 34567777787766 567777632 4457889999999999986432211112223 2456667 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 79 ~v~~~~ 84 (200)
T cd08453 79 LAVPAA 84 (200)
T ss_pred EEEECC
Confidence 888765
No 86
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=81.95 E-value=17 Score=34.01 Aligned_cols=36 Identities=17% Similarity=0.185 Sum_probs=29.8
Q ss_pred HHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEee
Q psy12229 40 EEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALG 86 (444)
Q Consensus 40 ~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~ 86 (444)
+-+-++.+++++++..+ ++..++.++..|++|++..
T Consensus 27 ~g~f~~~G~~ve~~~~~-----------~g~~~~~al~~G~iD~a~~ 62 (252)
T PF13379_consen 27 KGLFEKEGLDVEWVQFA-----------SGADILEALAAGEIDIAFV 62 (252)
T ss_dssp TTHHHHTTSCEEEEEES-----------SHHHHHHHHHCTSSSEEEE
T ss_pred cChHHHcCCEEEEEEcC-----------CHHHHHHHHHcCCCCEEEe
Confidence 34666779999998765 5678999999999999887
No 87
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=81.62 E-value=37 Score=32.80 Aligned_cols=67 Identities=15% Similarity=0.256 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEEE
Q psy12229 35 CIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITIL 113 (444)
Q Consensus 35 ~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~il 113 (444)
-..++..+.++. +.++++.. ++..+++..|.+|++|+++....... ...+.+ .|+.. ..++++
T Consensus 108 l~~~i~~f~~~~P~i~l~~~~------------~~~~~~~~~L~~~~~D~~i~~~~~~~--~~~l~~-~~l~~-~~~~~v 171 (309)
T PRK12683 108 LPKVVRQFKEVFPKVHLALRQ------------GSPQEIAEMLLNGEADIGIATEALDR--EPDLVS-FPYYS-WHHVVV 171 (309)
T ss_pred HHHHHHHHHHHCCCceEEEEe------------CCHHHHHHHHHcCCccEEEecCCCCC--CCCceE-EEccc-CeEEEE
Confidence 345666666665 56777763 35678999999999999986432211 123432 45666 677777
Q ss_pred EeCC
Q psy12229 114 MKKP 117 (444)
Q Consensus 114 vp~~ 117 (444)
+++.
T Consensus 172 ~~~~ 175 (309)
T PRK12683 172 VPKG 175 (309)
T ss_pred ecCC
Confidence 7755
No 88
>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=80.70 E-value=28 Score=30.47 Aligned_cols=68 Identities=13% Similarity=0.282 Sum_probs=44.2
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
++--+++..+.++. +.++++.. ++..++++.|.+|++|++++..... ...+. +.+... ..++
T Consensus 13 ~~l~~~l~~f~~~~P~i~l~i~~------------~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~-~~~l~~-~~~~ 75 (200)
T cd08465 13 LVLPALMRQLRAEAPGIDLAVSQ------------ASREAMLAQVADGEIDLALGVFPEL---PEELH-AETLFE-ERFV 75 (200)
T ss_pred HhhhHHHHHHHHHCCCcEEEEec------------CChHhHHHHHHCCCccEEEeccccC---CcCee-EEEeee-ccEE
Confidence 44556677776654 46777663 3557889999999999998643221 12333 345666 6788
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 lv~~~~ 81 (200)
T cd08465 76 CLADRA 81 (200)
T ss_pred EEEeCC
Confidence 888765
No 89
>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=80.67 E-value=36 Score=29.24 Aligned_cols=68 Identities=18% Similarity=0.163 Sum_probs=45.5
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+--++++.+.++. +.++++... +...+...+.+|++|+++...... ....+ .+.+... ..+++
T Consensus 15 ~l~~~l~~~~~~~P~i~l~i~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~-~~~~~ 78 (199)
T cd08451 15 LVPGLIRRFREAYPDVELTLEEA------------NTAELLEALREGRLDAAFVRPPVA--RSDGL-VLELLLE-EPMLV 78 (199)
T ss_pred ccHHHHHHHHHHCCCcEEEEecC------------ChHHHHHHHHCCCccEEEEecCCC--CCCce-eEEEeec-ccEEE
Confidence 5566788888776 567777732 446788999999999999643321 11223 3466677 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 79 v~~~~ 83 (199)
T cd08451 79 ALPAG 83 (199)
T ss_pred EecCC
Confidence 87654
No 90
>cd00916 Npc2_like Niemann-Pick type C2 (Npc2) is a lysosomal protein in which a mutation in the gene causes a rare form of Niemann-Pick type C disease, an autosomal recessive lipid storage disorder characterized by accumulation of low-density lipoprotein-derived cholesterol in lysosomes. Although Npc2 is known to bind cholesterol, the function of this protein is unknown. These proteins belong to the ML domain family.
Probab=79.69 E-value=1.9 Score=36.01 Aligned_cols=39 Identities=26% Similarity=0.509 Sum_probs=32.8
Q ss_pred CCcccccccccCCCCcccCCCCCCceeEeeeeeeccccCCCcccCC
Q psy12229 398 GTSVCSSIFDTDGKTKVSCPLKKDHVYRYINTFKILDRYPKCSKDL 443 (444)
Q Consensus 398 ~~~~~~~kw~~~~~~~~~c~~~~~~~~~~~~~~~~l~~~~~~~~~~ 443 (444)
+.|+|.. + + ..||...+..+.|..+.++.+.||.+++++
T Consensus 66 ~~daC~~--~-~----~~CPl~~G~~~~y~~~~~v~~~~P~i~~~v 104 (123)
T cd00916 66 NPDACKN--L-G----TSCPLSAGEDVTYTLSLPVLAPYPGISVTV 104 (123)
T ss_pred CCccccC--C-C----CCCCCcCCcEEEEEEeeeccccCCCeEEEE
Confidence 5789963 2 2 499999999999999999999999987753
No 91
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=79.34 E-value=39 Score=32.97 Aligned_cols=67 Identities=10% Similarity=0.138 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEEE
Q psy12229 35 CIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITIL 113 (444)
Q Consensus 35 ~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~il 113 (444)
--+++..+.++. +.++++.. ++...++..+.+|++|+++..... .....+. ..+... ..++++
T Consensus 108 l~~~l~~f~~~~P~i~i~i~~------------~~~~~~~~~L~~g~iDl~i~~~~~--~~~~~l~-~~~l~~-~~~~~v 171 (324)
T PRK12681 108 LPPVIKGFIERYPRVSLHMHQ------------GSPTQIAEAAAKGNADFAIATEAL--HLYDDLI-MLPCYH-WNRSVV 171 (324)
T ss_pred hHHHHHHHHHHCCCcEEEEEe------------CCHHHHHHHHHcCCCCEEEecCcc--cCCCCeE-EEEecc-ceeEEE
Confidence 344555555554 45566652 355788999999999999974211 1122232 345666 677777
Q ss_pred EeCC
Q psy12229 114 MKKP 117 (444)
Q Consensus 114 vp~~ 117 (444)
+++.
T Consensus 172 ~~~~ 175 (324)
T PRK12681 172 VPPD 175 (324)
T ss_pred eCCC
Confidence 7654
No 92
>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=79.33 E-value=42 Score=29.21 Aligned_cols=70 Identities=11% Similarity=0.152 Sum_probs=45.5
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
..+-.+++..+.++. +.++++.. ++...+...+.+|++|+++..... .....+. +.+... ..+
T Consensus 12 ~~~l~~~l~~f~~~~P~~~i~i~~------------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~-~~~ 75 (198)
T cd08443 12 RYVLPPVIKGFIERYPRVSLQMHQ------------GSPTQIAEMVSKGLVDFAIATEAL--HDYDDLI-TLPCYH-WNR 75 (198)
T ss_pred eeECcHHHHHHHHHCCCeEEEEEe------------CCHHHHHHHHHCCCccEEEEeccc--cccCCce-Eeeeee-ceE
Confidence 445667778877765 56777763 244678899999999999863221 1122332 456666 788
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 76 ~~v~~~~ 82 (198)
T cd08443 76 CVVVKRD 82 (198)
T ss_pred EEEEcCC
Confidence 8887655
No 93
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=77.79 E-value=56 Score=31.48 Aligned_cols=67 Identities=18% Similarity=0.376 Sum_probs=43.2
Q ss_pred HHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEEEE
Q psy12229 36 IDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILM 114 (444)
Q Consensus 36 ~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilv 114 (444)
.+++..+.+.. +.++++... ....++.+|.+|++|+++...... .....+ -..|... ..+++++
T Consensus 113 ~~~l~~~~~~~p~v~i~~~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~l-~~~~l~~-~~~~lv~ 177 (312)
T PRK10341 113 SDMINKFKEVFPKAQVSMYEA------------QLSSFLPAIRDGRLDFAIGTLSNE-MKLQDL-HVEPLFE-SEFVLVA 177 (312)
T ss_pred HHHHHHHHHhCCCCEEEEEeC------------CHHHHHHHHHcCCCcEEEecCCcc-cccCCe-eEEEEec-ccEEEEE
Confidence 45566666554 466666633 446889999999999999653221 111233 3566777 7888888
Q ss_pred eCC
Q psy12229 115 KKP 117 (444)
Q Consensus 115 p~~ 117 (444)
++.
T Consensus 178 ~~~ 180 (312)
T PRK10341 178 SKS 180 (312)
T ss_pred cCC
Confidence 765
No 94
>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=77.59 E-value=50 Score=29.23 Aligned_cols=68 Identities=15% Similarity=0.168 Sum_probs=45.3
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+..+++..+.++. +.++++... +...+.+.+.+|++|++++.... ....+. ..|... ..++
T Consensus 13 ~~l~~~l~~f~~~~P~v~l~i~~~------------~~~~~~~~l~~g~~Di~i~~~~~---~~~~l~-~~~l~~-~~~~ 75 (221)
T cd08469 13 VLLPALVRRLETEAPGIDLRIRPV------------TRLDLAEQLDLGRIDLVIGIFEQ---IPPRFR-RRTLFD-EDEV 75 (221)
T ss_pred HHHHHHHHHHHHHCCCcEEEEeeC------------ChhhHHHHHHCCCccEEEecCCC---CCccce-eeeeec-cceE
Confidence 34566777776665 467777632 44578899999999999975432 123343 456777 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~v~~~~ 81 (221)
T cd08469 76 WVMRKD 81 (221)
T ss_pred EEEeCC
Confidence 888765
No 95
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=77.37 E-value=59 Score=31.30 Aligned_cols=67 Identities=9% Similarity=-0.000 Sum_probs=41.2
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+..+++..+.+.. +.++++... +...+...+.+|++|+++...... ...+. ..+... ....+
T Consensus 108 ~l~~~l~~~~~~~P~v~i~i~~~------------~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~-~~~~~ 170 (309)
T PRK11013 108 LLPGLCQPFLARYPDVSLNIVPQ------------ESPLLEEWLSAQRHDLGLTETLHT---PAGTE-RTELLT-LDEVC 170 (309)
T ss_pred hHHHHHHHHHHHCCCCeEEEEeC------------CHHHHHHHHHcCCCCEEEEcCCCC---CCCce-eeeecc-eeEEE
Confidence 4456666666665 577777743 335678899999999998643321 12222 334555 56666
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 171 ~~~~~ 175 (309)
T PRK11013 171 VLPAG 175 (309)
T ss_pred EEcCC
Confidence 76654
No 96
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=77.26 E-value=69 Score=30.97 Aligned_cols=75 Identities=8% Similarity=-0.035 Sum_probs=46.7
Q ss_pred CCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcCCCccEEeC--CcccccceEEEecCCCchhhhhHHHHHHHhcCCc
Q psy12229 314 PNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVG--DEFSRKPYAIAVQQDRDARELFCNVHANILSIPF 391 (444)
Q Consensus 314 ~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c~l~~~~--~~~~~~~~~~~~~k~sp~~~~in~~il~l~e~G~ 391 (444)
..+.....+.+..|. +.+++-... .... +..++..+. +......+.++.+++.+....+..++.-+.+.=-
T Consensus 224 ~~s~~~~~~~v~~g~----Gi~~lp~~~-~~~~--~~~~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~ 296 (316)
T PRK12679 224 AQDSDVIKTYVALGL----GIGLVAEQS-SGEQ--EESNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLS 296 (316)
T ss_pred eccHHHHHHHHHcCC----cEEEecccc-cccc--cCCcEEEEECcccCCCceEEEEEeCCchhhHHHHHHHHHHhcccC
Confidence 457888889999985 777765532 3322 333455443 2334456788899998777777777765544443
Q ss_pred cccC
Q psy12229 392 PFIG 395 (444)
Q Consensus 392 i~~~ 395 (444)
++.+
T Consensus 297 ~~~~ 300 (316)
T PRK12679 297 VEDI 300 (316)
T ss_pred HHHH
Confidence 4444
No 97
>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=77.09 E-value=47 Score=28.54 Aligned_cols=71 Identities=13% Similarity=0.135 Sum_probs=45.8
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
.++-.+++..+.++. |.++++... ....+...+.+|++|+++...... .....+ -+.+... ..+
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~------------~~~~~~~~l~~~~~Dl~i~~~~~~-~~~~~l-~~~~l~~-~~~ 76 (199)
T cd08416 12 VNTVPRIIMGLKLRRPELDIELTLG------------SNKDLLKKLKDGELDAILVATPEG-LNDPDF-EVVPLFE-DDI 76 (199)
T ss_pred HhhhHHHHHHHHHhCCCeEEEEEEc------------CcHHHHHHHhCCCCCEEEEecCCc-CCCCCe-EEEEeec-ceE
Confidence 345567777777776 578887732 345678899999999999754320 012223 2455666 677
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
.+++++.
T Consensus 77 ~~v~~~~ 83 (199)
T cd08416 77 FLAVPAT 83 (199)
T ss_pred EEEECCC
Confidence 8877654
No 98
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=76.08 E-value=30 Score=34.04 Aligned_cols=60 Identities=8% Similarity=0.067 Sum_probs=36.4
Q ss_pred eeEEEeccCCCeEEEecCCCCCceeeeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEe
Q psy12229 6 NISDSRLKQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIAL 85 (444)
Q Consensus 6 ~l~V~~~~~~Pf~~~~~~~~~~~~~~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~ 85 (444)
.|||+...|+.|.-+.-. +-.| +++.-.+..|.+++++..+ +....+.++..|++|++.
T Consensus 3 ~~~i~~~~w~G~~p~~lA------~~~G----~fe~~l~~~Gl~Ve~~~f~-----------~~~~~l~Al~aG~iD~~~ 61 (328)
T TIGR03427 3 KFKVCWSIYAGWMPWGYA------AQQG----IVDKWADKYGITIEVVQIN-----------DYVESINQYTAGKFDGCT 61 (328)
T ss_pred ceEEEecCCccHHHHHHH------HHcC----chhhhHHHcCCeEEEEECC-----------ChHHHHHHHHcCCCCEEe
Confidence 466766666644433211 1133 2332335678899998664 345678888999999864
Q ss_pred e
Q psy12229 86 G 86 (444)
Q Consensus 86 ~ 86 (444)
.
T Consensus 62 ~ 62 (328)
T TIGR03427 62 M 62 (328)
T ss_pred e
Confidence 3
No 99
>KOG3713|consensus
Probab=76.07 E-value=2.1 Score=43.56 Aligned_cols=44 Identities=25% Similarity=0.326 Sum_probs=40.1
Q ss_pred ccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHH
Q psy12229 165 EVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIAS 215 (444)
Q Consensus 165 ~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~ 215 (444)
.+-+.||++-+|++.| |++..|++..+|++...-.+.|+++.+.
T Consensus 378 IPa~~WWaiVTMTTVG-------YGDm~P~T~~Gklvas~cil~GVLvlAl 421 (477)
T KOG3713|consen 378 IPAGFWWAVVTMTTVG-------YGDMVPVTVLGKLVASLCILCGVLVLAL 421 (477)
T ss_pred ccchhheeeEEEeeec-------ccCccccccchHHHHHHHHHHhHHHhhc
Confidence 5678999999999999 8999999999999999999998887765
No 100
>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=75.90 E-value=12 Score=33.83 Aligned_cols=38 Identities=24% Similarity=0.259 Sum_probs=29.5
Q ss_pred HHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccc
Q psy12229 42 IRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSV 90 (444)
Q Consensus 42 la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~ 90 (444)
+-++.|++++++... .....+.+|..|++|++++....
T Consensus 15 ~f~~~gl~ve~~~~~-----------~~~~~~~~l~~G~~D~~~~~~~~ 52 (216)
T PF09084_consen 15 YFKEEGLDVEIVFFG-----------GGGDVLEALASGKADIAVAGPDA 52 (216)
T ss_dssp HHHHTTEEEEEEEES-----------SHHHHHHHHHTTSHSEEEEECHH
T ss_pred CCccCeEEEEEEEec-----------ChhHHHHHHhcCCceEEeccchH
Confidence 345668889998663 45678999999999999887753
No 101
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=75.24 E-value=30 Score=33.43 Aligned_cols=68 Identities=7% Similarity=0.129 Sum_probs=45.9
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
++-.+++..+.++. +.++++.. ++...+++.|.+|++|+++...... ...+. ..++.. ..++
T Consensus 125 ~~l~~~l~~f~~~~P~i~l~i~~------------~~~~~~~~~l~~g~~Di~i~~~~~~---~~~l~-~~~l~~-~~~~ 187 (314)
T PRK09508 125 RLTSQIYNRIEQIAPNIHVVFKS------------SLNQNIEHQLRYQETEFVISYEEFD---RPEFT-SVPLFK-DELV 187 (314)
T ss_pred HHHHHHHHHHHHhCCCcEEEEEe------------CcchhHHHHHhcCCccEEEecCCCC---ccccc-eeeeec-CceE
Confidence 34566677777776 67888873 2446789999999999999754322 22343 345666 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 188 lv~~~~ 193 (314)
T PRK09508 188 LVASKN 193 (314)
T ss_pred EEEcCC
Confidence 888765
No 102
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=75.19 E-value=6.1 Score=39.00 Aligned_cols=57 Identities=28% Similarity=0.350 Sum_probs=43.9
Q ss_pred eeecHH-HHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeeccccccc
Q psy12229 31 YKGYCI-DLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAE 93 (444)
Q Consensus 31 ~~G~~~-dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~ 93 (444)
..|-.. .+.+++.++.|-++++...|++..|.. ..++++|++|.+|+...+......
T Consensus 41 p~~~~~~~fa~~v~ekt~G~l~i~vfP~~qLG~~------~~~ie~l~~G~id~~~~s~~~l~~ 98 (332)
T COG1638 41 PKGKAAKKFAELVEEKTGGRLKIEVFPNSQLGGE------AEMIEQLRSGTLDIGVVSLGFLAG 98 (332)
T ss_pred cHHHHHHHHHHHHHHHhCCeEEEEECCCcccCcH------HHHHHHHhcCCeeEEeccchhhcc
Confidence 444444 457789999999999999887766633 678999999999999888765544
No 103
>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=74.58 E-value=57 Score=28.29 Aligned_cols=70 Identities=13% Similarity=0.189 Sum_probs=46.5
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
.++-.+++..+.++. +.++++... +...+++.+.+|++|+++..-... ....+ .+.+... ..+
T Consensus 12 ~~~l~~~l~~~~~~~P~v~l~i~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~-~~~ 75 (198)
T cd08444 12 RYALPWVVQAFKEQFPNVHLVLHQG------------SPEEIASMLANGQADIGIATEALE--NHPEL-VSFPYYD-WHH 75 (198)
T ss_pred hhhhhHHHHHHHHHCCCeEEEEEeC------------CHHHHHHHHHCCCccEEEeccccC--CCcCc-EEeeccc-cce
Confidence 356677888888876 567777632 446788999999999998632211 11223 2456666 778
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 76 ~~~~~~~ 82 (198)
T cd08444 76 HIIVPVG 82 (198)
T ss_pred eEEecCC
Confidence 8888665
No 104
>cd00915 MD-1_MD-2 MD-1 and MD-2 are cofactors required for LPS signaling through cell surface receptors. MD-2 and its binding partner, Toll-like receptor 4 (TLR4), are essential for the innate immune responses of mammalian cells to bacterial lipopolysaccharide (LPS); MD-2 directly binds the lipid A moiety of LPS. The TLR4-like receptor, RP105, which mediates LPS-induced lymphocyte proliferation, interacts with MD-1; MD-1 enhances RP105-mediated LPS-induced growth of B cells. These proteins belong to the ML domain family.
Probab=74.48 E-value=3.1 Score=34.94 Aligned_cols=40 Identities=18% Similarity=0.236 Sum_probs=32.0
Q ss_pred CCCcccccccccCCCCcccCCCCCCceeEee--eeeeccccCCCcccC
Q psy12229 397 DGTSVCSSIFDTDGKTKVSCPLKKDHVYRYI--NTFKILDRYPKCSKD 442 (444)
Q Consensus 397 ~~~~~~~~kw~~~~~~~~~c~~~~~~~~~~~--~~~~~l~~~~~~~~~ 442 (444)
+|. +|.. ++ +....||...++.+.|. .+.++++ ||+.+++
T Consensus 69 ~e~-~C~~---g~-~~~s~CP~~kGet~~Y~~p~slpi~~-yP~~~y~ 110 (130)
T cd00915 69 SEI-ICHG---YL-DKYSFCGALKGETVYYVGPFSFKGIL-IPQGQYR 110 (130)
T ss_pred Ccc-cccC---CC-cccccCCccCCceEEEeeeecccccc-cCCccEE
Confidence 344 7854 22 24579999999999999 9999999 9998875
No 105
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=71.48 E-value=88 Score=29.15 Aligned_cols=67 Identities=19% Similarity=0.293 Sum_probs=43.9
Q ss_pred cHHHHHHHHHHHcC-CeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLVG-FEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~ln-ft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-.+++..+.+... .+++++.. +...++..+.+|++|+++....... ..+. ..|+.. ..+++
T Consensus 98 ~~~~~l~~~~~~~p~v~l~i~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~~-~~~l~~-~~~~l 160 (279)
T TIGR03339 98 YVLDLVARFRQRYPGIEVSVRIG------------NSQEVLQALQSYRVDVAVSSEVVDD---PRLD-RVVLGN-DPLVA 160 (279)
T ss_pred HHHHHHHHHHHHCCCcEEEEEEC------------CHHHHHHHHHcCCCcEEEEecccCC---CceE-EEEcCC-ceEEE
Confidence 44566777776663 67777632 4467889999999999996433221 2232 355666 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 161 v~s~~ 165 (279)
T TIGR03339 161 VVHRQ 165 (279)
T ss_pred EECCC
Confidence 88655
No 106
>KOG0498|consensus
Probab=70.64 E-value=6 Score=42.95 Aligned_cols=68 Identities=15% Similarity=0.277 Sum_probs=54.9
Q ss_pred chhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcc-----cCCCCCCChHHhhh
Q psy12229 167 IRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVS-----RLDTPIESLDDLSK 241 (444)
Q Consensus 167 ~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~-----~~~~~I~sl~dL~~ 241 (444)
.++||++++|...| +....+.+.+..++.++.+++++++.+..-|++++++-.- .+...++.+++-++
T Consensus 297 ~aLyw~l~tLstvG-------~g~~~s~~~~E~iFsi~~mi~GllL~A~lIGNmt~~iqs~tsR~~~~r~k~rd~e~~m~ 369 (727)
T KOG0498|consen 297 YALYWGLSTLSTVG-------YGLVHANNMGEKIFSIFIMLFGLLLFAYLIGNMTALLQSLTSRTEEMRDKMRDAEQWMS 369 (727)
T ss_pred HHHHHHhhHhhhcc-------CCccCCCCcHHHHHHHHHHHHhHHHHHHHHhhHHHhHHHHhHHHHHHHHHHHHHHHHHH
Confidence 47789999999999 5788899999999999999999999999999999998542 23344455555444
No 107
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=70.21 E-value=5.8 Score=44.34 Aligned_cols=68 Identities=15% Similarity=0.216 Sum_probs=54.5
Q ss_pred hhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhccc-----CCCCCCChHHhhhC
Q psy12229 168 RAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSR-----LDTPIESLDDLSKQ 242 (444)
Q Consensus 168 ~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~-----~~~~I~sl~dL~~~ 242 (444)
+++|++.++++.| +++..|.+...|++.++++++++.+.++..+++++++.... +...++.+.+..++
T Consensus 254 slYwai~TmtTVG-------YGDi~p~t~~E~i~~i~~ml~g~~~~a~~ig~i~~li~~~~~~~~~f~~~~~~~~~ym~~ 326 (823)
T PLN03192 254 AIYWSITTMTTVG-------YGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVEGTRRTMEFRNSIEAASNFVGR 326 (823)
T ss_pred HHHHHHHHHhhcc-------CCCcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6889999999998 78889999999999999999999999999999999876432 23344444454443
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=70.03 E-value=69 Score=27.32 Aligned_cols=70 Identities=7% Similarity=0.074 Sum_probs=45.0
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+...++..+.++. +.++++.. +.....++.+.+|++|++++...... +...+. ..+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~------------~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~-~~~l~~-~~~~ 77 (197)
T cd08449 13 GGLGPALRRFKRQYPNVTVRFHE------------LSPEAQKAALLSKRIDLGFVRFADTL-NDPPLA-SELLWR-EPMV 77 (197)
T ss_pred hhHHHHHHHHHHHCCCeEEEEEE------------CCHHHHHHHHhCCCccEEEecccccC-CCCCce-EEEEEE-eeEE
Confidence 45567778887776 46677663 24567889999999999986443210 122232 355666 7777
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 78 ~v~~~~ 83 (197)
T cd08449 78 VALPEE 83 (197)
T ss_pred EEecCC
Confidence 777654
No 109
>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=70.02 E-value=70 Score=27.39 Aligned_cols=67 Identities=13% Similarity=0.201 Sum_probs=43.5
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+...++..+.++. +.++++... ...++...+.+|++|+++...... ...+ ...++.. ..+++
T Consensus 15 ~l~~~l~~~~~~~P~v~i~i~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~-~~~~~ 77 (197)
T cd08425 15 LIGPLIDRFHARYPGIALSLREM------------PQERIEAALADDRLDLGIAFAPVR---SPDI-DAQPLFD-ERLAL 77 (197)
T ss_pred hhHHHHHHHHHHCCCcEEEEEEC------------cHHHHHHHHHcCCccEEEEecCCC---CCCc-EEEEecc-ccEEE
Confidence 3456677777665 467777632 345788999999999998643322 2233 2455666 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 78 v~~~~ 82 (197)
T cd08425 78 VVGAT 82 (197)
T ss_pred EecCC
Confidence 87665
No 110
>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=69.67 E-value=78 Score=30.09 Aligned_cols=68 Identities=10% Similarity=0.168 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEEE
Q psy12229 35 CIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITIL 113 (444)
Q Consensus 35 ~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~il 113 (444)
-.+++..+.++. +.++.+... +...++.++.+|++|++++..... .....+. ..|... ...+++
T Consensus 108 ~~~~l~~~~~~~P~~~i~~~~~------------~~~~~~~~l~~g~~D~~i~~~~~~-~~~~~~~-~~~l~~-~~~~~~ 172 (300)
T TIGR02424 108 MPEVVKRFLARAPRLRVRIMTG------------PNAYLLDQLRVGALDLVVGRLGAP-ETMQGLS-FEHLYN-EPVVFV 172 (300)
T ss_pred hHHHHHHHHHhCCCcEEEEEeC------------chHHHHHHHHCCCCCEEEEecCCc-cccccee-eeeecC-CceEEE
Confidence 345555555554 356666532 446788999999999999754321 1122332 446666 788888
Q ss_pred EeCC
Q psy12229 114 MKKP 117 (444)
Q Consensus 114 vp~~ 117 (444)
+++.
T Consensus 173 ~~~~ 176 (300)
T TIGR02424 173 VRAG 176 (300)
T ss_pred EcCC
Confidence 8754
No 111
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=68.49 E-value=1.2e+02 Score=29.42 Aligned_cols=44 Identities=7% Similarity=0.184 Sum_probs=30.9
Q ss_pred cchhHHHHhcccccEEeecccccccccccccccccceecccEEEEEeCC
Q psy12229 69 WNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKP 117 (444)
Q Consensus 69 ~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilvp~~ 117 (444)
.+++++.|.+|++|+++...... ...+. +.+... ..+++++++.
T Consensus 153 ~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~-~~~~lv~~~~ 196 (317)
T PRK11482 153 ISDAENQLSQFQTDLIIDTHSCS---NRTIQ-HHVLFT-DNVVLVCRQG 196 (317)
T ss_pred chhHHHHHHCCCcCEEEeccCCC---CCceE-EEEEec-CcEEEEEeCC
Confidence 35688999999999999755432 23343 456777 7888888765
No 112
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=64.93 E-value=1.4e+02 Score=28.93 Aligned_cols=66 Identities=12% Similarity=0.112 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEEE
Q psy12229 35 CIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITIL 113 (444)
Q Consensus 35 ~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~il 113 (444)
--+++..+.++. +.++++... ....+...|.+|++|+++..-.. ....+. ..++.. ..++++
T Consensus 104 l~~~l~~~~~~~P~i~l~~~~~------------~~~~~~~~L~~g~~Dl~i~~~~~---~~~~~~-~~~l~~-~~~~lv 166 (317)
T PRK15421 104 LTPALENFHKNWPQVEMDFKSG------------VTFDPQPALQQGELDLVMTSDIL---PRSGLH-YSPMFD-YEVRLV 166 (317)
T ss_pred HHHHHHHHHHHCCCceEEEEeC------------ccHHHHHHHHCCCcCEEEecCcc---cCCCce-EEEecc-ceEEEE
Confidence 344556666554 467776632 33577899999999999864322 123343 356667 788888
Q ss_pred EeCC
Q psy12229 114 MKKP 117 (444)
Q Consensus 114 vp~~ 117 (444)
+++.
T Consensus 167 ~~~~ 170 (317)
T PRK15421 167 LAPD 170 (317)
T ss_pred EcCC
Confidence 8765
No 113
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=64.09 E-value=1.2e+02 Score=27.97 Aligned_cols=68 Identities=12% Similarity=0.157 Sum_probs=42.4
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+..+++..+.+.. +.+++++. +...++...+.+|++|+++...... ....+. ..+... ..+++
T Consensus 81 ~~~~~l~~~~~~~p~i~l~i~~------------~~~~~~~~~l~~~~~D~~i~~~~~~--~~~~~~-~~~l~~-~~~~~ 144 (269)
T PRK11716 81 HLPPILDRFRAEHPLVEIKLTT------------GDAADAVEKVQSGEADLAIAAKPET--LPASVA-FSPIDE-IPLVL 144 (269)
T ss_pred HHHHHHHHHHHHCCCeEEEEEE------------CCHHHHHHHHHCCCccEEEEecCCC--CCcceE-EEEccc-ceEEE
Confidence 3456667777765 46777763 2446789999999999999653321 111232 344555 67777
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 145 v~~~~ 149 (269)
T PRK11716 145 IAPAL 149 (269)
T ss_pred EEcCC
Confidence 77554
No 114
>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=63.66 E-value=98 Score=26.75 Aligned_cols=69 Identities=19% Similarity=0.298 Sum_probs=46.1
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
.++-.+++..+.++. +.++++... ....++..+.+|++|++++..... ...+. +.+... ..+
T Consensus 13 ~~~l~~~l~~~~~~~P~i~l~i~~~------------~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~-~~~ 75 (203)
T cd08445 13 YGLLPELIRRFRQAAPDVEIELIEM------------TTVQQIEALKEGRIDVGFGRLRIE---DPAIR-RIVLRE-EPL 75 (203)
T ss_pred HhHHHHHHHHHHHHCCCeEEEEEeC------------ChHHHHHHHHcCCCcEEEecCCCC---CCCce-eEEEEe-ccE
Confidence 345667778887776 567777632 446889999999999999643221 12332 445666 788
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 76 ~~v~~~~ 82 (203)
T cd08445 76 VVALPAG 82 (203)
T ss_pred EEEeeCC
Confidence 8888765
No 115
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=63.19 E-value=1.5e+02 Score=28.83 Aligned_cols=68 Identities=16% Similarity=0.098 Sum_probs=44.9
Q ss_pred cHHHHHHHHHHHcC-CeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLVG-FEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~ln-ft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-.++++.+.++.. .++++... ....++.+|.+|++|+++....... ..... ..|... ..+++
T Consensus 107 ~l~~~l~~f~~~~P~v~i~l~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~~--~~~~~-~~~l~~-~~~~l 170 (327)
T PRK12680 107 VLPPAVAQIKQAYPQVSVHLQQA------------AESAALDLLGQGDADIAIVSTAGGE--PSAGI-AVPLYR-WRRLV 170 (327)
T ss_pred hhHHHHHHHHHHCCCcEEEEEeC------------ChHHHHHHHHCCCCcEEEEecCCCC--CCcce-EEEeec-cceEE
Confidence 44567777777764 57777632 4578899999999999986432111 11222 467777 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 171 ~~~~~ 175 (327)
T PRK12680 171 VVPRG 175 (327)
T ss_pred EEeCC
Confidence 88765
No 116
>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=62.52 E-value=1e+02 Score=26.46 Aligned_cols=69 Identities=9% Similarity=0.140 Sum_probs=44.0
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
..+-.+++..+.++. +.++++... ...++...+.+|++|+++...... ...+. ..+... ..+
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~~~~~------------~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~-~~~ 74 (196)
T cd08457 12 NGFLPRFLAAFLRLRPNLHLSLMGL------------SSSQVLEAVASGRADLGIADGPLE---ERQGF-LIETRS-LPA 74 (196)
T ss_pred ccccHHHHHHHHHHCCCeEEEEEec------------CcHHHHHHHHcCCccEEEeccCCC---CCCcE-EEEecc-CCe
Confidence 345567788888776 466777632 235778899999999998644321 22232 345566 677
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
++++++.
T Consensus 75 ~~~~~~~ 81 (196)
T cd08457 75 VVAVPMG 81 (196)
T ss_pred EEEeeCC
Confidence 7777654
No 117
>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=62.50 E-value=1e+02 Score=26.46 Aligned_cols=69 Identities=14% Similarity=0.173 Sum_probs=44.3
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-.+++..+.++. +.++++... +...+.+.+.+|++|+++.... .......+. ..+... ..+++
T Consensus 14 ~l~~~l~~~~~~~P~v~i~~~~~------------~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~l~-~~~l~~-~~~~~ 78 (198)
T cd08437 14 YFPKLAKDLIKTGLMIQIDTYEG------------GSAELLEQLLQGDLDIALLGSL-TPLENSALH-SKIIKT-QHFMI 78 (198)
T ss_pred HhHHHHHHHHHhCCceEEEEEEc------------CHHHHHHHHHcCCCCEEEecCC-CCCCcccce-EEEeec-ceEEE
Confidence 4456777777775 467777632 4567889999999999986431 111123343 455666 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 79 ~~~~~ 83 (198)
T cd08437 79 IVSKD 83 (198)
T ss_pred EecCC
Confidence 87654
No 118
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=62.12 E-value=1e+02 Score=26.48 Aligned_cols=68 Identities=9% Similarity=-0.014 Sum_probs=43.5
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.++++.+.++. +.++++.. ++..++...+.+|++|+++...... ...+ -+.+... ..++
T Consensus 13 ~~l~~~l~~f~~~~P~v~i~~~~------------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~-~~~~ 75 (196)
T cd08458 13 SFMSGVIQTFIADRPDVSVYLDT------------VPSQTVLELVSLQHYDLGISILAGD---YPGL-TTEPVPS-FRAV 75 (196)
T ss_pred hhhHHHHHHHHHHCCCcEEEEec------------cChHHHHHHHHcCCCCEEEEeccCC---CCCc-eEEEecc-CceE
Confidence 34457778887776 45666652 2345678899999999998743321 1223 2355666 6777
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~v~~~~ 81 (196)
T cd08458 76 CLLPPG 81 (196)
T ss_pred EEecCC
Confidence 777654
No 119
>PRK07377 hypothetical protein; Provisional
Probab=58.94 E-value=24 Score=31.30 Aligned_cols=47 Identities=17% Similarity=0.145 Sum_probs=39.4
Q ss_pred eeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecc
Q psy12229 31 YKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSL 88 (444)
Q Consensus 31 ~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~ 88 (444)
.-+-.++.++.+.++++.++|++..+ +.+.+.+++..|++|++.+.-
T Consensus 91 ~~~~l~~~l~~~~~~y~~rlElv~y~-----------~~~~l~~aL~~~eVh~~c~~~ 137 (184)
T PRK07377 91 VFDQLIDQLRTILDKYHLRLELVVYP-----------DLQALEQALRDKEVHAICLES 137 (184)
T ss_pred cHHHHHHHHHHHHHHhCceeeEEecC-----------CHHHHHHHHhcCCccEEecCC
Confidence 44557788899999999999999876 568899999999999877644
No 120
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=57.58 E-value=1.7e+02 Score=27.61 Aligned_cols=66 Identities=11% Similarity=0.050 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEEE
Q psy12229 35 CIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITIL 113 (444)
Q Consensus 35 ~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~il 113 (444)
..+++..+.++. +.++.+.. ++..+++..+.+|++|+++..... ....+. +.|... ..++++
T Consensus 105 l~~~~~~~~~~~p~v~i~~~~------------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~l~-~~~l~~-~~~~~v 167 (296)
T PRK09906 105 LPKVLPMFRLRHPDTLIELVS------------LITTQQEEKLRRGELDVGFMRHPV---YSDEID-YLELLD-EPLVVV 167 (296)
T ss_pred HHHHHHHHHHHCCCeEEEEEe------------CCcHHHHHHHHcCCeeEEEecCCC---CCCCce-EEEEec-ccEEEE
Confidence 335555555554 45555552 245688999999999999975543 233444 467777 788888
Q ss_pred EeCC
Q psy12229 114 MKKP 117 (444)
Q Consensus 114 vp~~ 117 (444)
+++.
T Consensus 168 ~~~~ 171 (296)
T PRK09906 168 LPVD 171 (296)
T ss_pred ecCC
Confidence 8765
No 121
>KOG1419|consensus
Probab=54.72 E-value=17 Score=37.79 Aligned_cols=55 Identities=24% Similarity=0.281 Sum_probs=48.1
Q ss_pred cchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhcc
Q psy12229 166 VIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVS 227 (444)
Q Consensus 166 ~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~ 227 (444)
..+.||..-+++..| |+++.|.++.+|+++..+.++++-+-+.=.+.|.|-|+-.
T Consensus 271 ADALWWG~ITltTIG-------YGDk~P~TWlGr~laa~fsligiSFFALPAGILGSGfALK 325 (654)
T KOG1419|consen 271 ADALWWGVITLTTIG-------YGDKTPQTWLGRLLAACFSLIGISFFALPAGILGSGFALK 325 (654)
T ss_pred HHHHHhhheeEEeec-------cCCcCcccchhHHHHHHHHHHHHHHHhcccccccchhhhh
Confidence 468889999999998 8999999999999999999999888888888888877743
No 122
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=54.57 E-value=1.9e+02 Score=27.19 Aligned_cols=72 Identities=11% Similarity=0.120 Sum_probs=43.3
Q ss_pred ecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhccc-ccEEeecccccccccc---cc-ccc-cccee
Q psy12229 33 GYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKR-ADIALGSLSVMAEREN---VV-DFT-VPYYD 106 (444)
Q Consensus 33 G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~-~Di~~~~~~~t~~r~~---~~-dfS-~p~~~ 106 (444)
...-++.+.+.++.|.++++... ....+..++.+|. +|+.+.+-....++.. .+ ..+ .++..
T Consensus 39 ~~~~~l~~~Fe~~~g~~v~~~~~------------~Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~~~a~ 106 (257)
T PRK10677 39 NALQDIAAQYKKEKGVDVVSSFA------------SSSTLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATRYTLLG 106 (257)
T ss_pred HHHHHHHHHHHhhhCCeEEEEec------------ccHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcchheeec
Confidence 45566777777777888887643 2235666777666 9998876532222221 12 111 24566
Q ss_pred cccEEEEEeCC
Q psy12229 107 LVGITILMKKP 117 (444)
Q Consensus 107 ~~~~~ilvp~~ 117 (444)
..+++++++.
T Consensus 107 -n~lvl~~~~~ 116 (257)
T PRK10677 107 -NSLVVVAPKA 116 (257)
T ss_pred -CEEEEEEECC
Confidence 7788888875
No 123
>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=52.13 E-value=45 Score=28.61 Aligned_cols=70 Identities=13% Similarity=0.178 Sum_probs=47.1
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
..+-.+++..+.++. +.++++... +...+.+.+.+|++|+++....... ...+. +.+... ..+
T Consensus 12 ~~~l~~~l~~~~~~~P~v~l~~~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~~--~~~l~-~~~l~~-~~~ 75 (199)
T cd08430 12 YSFLPPILERFRAQHPQVEIKLHTG------------DPADAIDKVLNGEADIAIAARPDKL--PARLA-FLPLAT-SPL 75 (199)
T ss_pred eeeccHHHHHHHHHCCCceEEEEeC------------CHHHHHHHHHCCCCCEEEEecCCCC--CcccE-EEeecc-ceE
Confidence 345567888888887 678888732 4567889999999999986432111 12232 455666 678
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
.+++++.
T Consensus 76 ~~~~~~~ 82 (199)
T cd08430 76 VFIAPNI 82 (199)
T ss_pred EEEEeCC
Confidence 8888765
No 124
>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=50.57 E-value=1.6e+02 Score=25.05 Aligned_cols=68 Identities=13% Similarity=0.068 Sum_probs=43.4
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.++. +.++++.. +....+...+.+|++|+++..... ....+ .+.+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~v~~~~------------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~-~~~~l~~-~~~~ 75 (198)
T cd08447 13 SFLPRLLAAARAALPDVDLVLRE------------MVTTDQIEALESGRIDLGLLRPPF---ARPGL-ETRPLVR-EPLV 75 (198)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEe------------CCHHHHHHHHHcCCceEEEecCCC---CCCCe-eEEEeec-CceE
Confidence 44556777777665 56777763 245678999999999999864321 12223 2345666 6777
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~v~~~~ 81 (198)
T cd08447 76 AAVPAG 81 (198)
T ss_pred EEecCC
Confidence 777654
No 125
>KOG1418|consensus
Probab=50.32 E-value=13 Score=37.28 Aligned_cols=55 Identities=25% Similarity=0.354 Sum_probs=46.9
Q ss_pred ccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchhhhhc
Q psy12229 165 EVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTV 226 (444)
Q Consensus 165 ~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~ 226 (444)
...+.+|++.+++..| |+...|++..+|+++++|.++|+-+.-..-+.+..+|+.
T Consensus 116 f~~al~fs~tv~TTIG-------YG~i~P~T~~Gr~~~i~YaliGIPl~li~l~~~g~~l~~ 170 (433)
T KOG1418|consen 116 FSSALLFSITVITTIG-------YGNIAPRTDAGRLFTILYALVGIPLMLLILADIGKFLAD 170 (433)
T ss_pred cchhHhhhhheeeecc-------CCcccCCcCcchhHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 3457778888888887 899999999999999999999998888888888877764
No 126
>PF13531 SBP_bac_11: Bacterial extracellular solute-binding protein; PDB: 2HXW_B 3FJG_C 3FJM_B 3FJ7_B 3FIR_B 3AXF_C 1WOD_A 1AMF_A 3R26_A 1SBP_A ....
Probab=49.26 E-value=2e+02 Score=25.99 Aligned_cols=74 Identities=19% Similarity=0.224 Sum_probs=50.7
Q ss_pred eeecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcc-cccEEeeccccccccc---cccc--ccccc
Q psy12229 31 YKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEK-RADIALGSLSVMAERE---NVVD--FTVPY 104 (444)
Q Consensus 31 ~~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g-~~Di~~~~~~~t~~r~---~~~d--fS~p~ 104 (444)
..+..-++++.+++.-++++++... ....+...+..| ++|+.+..-....++. ..+. -..|+
T Consensus 9 ~~~~~~~l~~~f~~~~g~~v~v~~~------------~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~ 76 (230)
T PF13531_consen 9 LAPALEELAEAFEKQPGIKVEVSFG------------GSGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPL 76 (230)
T ss_dssp GHHHHHHHHHHHHHHHCEEEEEEEE------------CHHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEE
T ss_pred HHHHHHHHHHHHHhccCCeEEEEEC------------ChHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCccccc
Confidence 4556678899998899999988854 335677777765 8999887653222222 2233 56778
Q ss_pred eecccEEEEEeCC
Q psy12229 105 YDLVGITILMKKP 117 (444)
Q Consensus 105 ~~~~~~~ilvp~~ 117 (444)
.. +.+++++++.
T Consensus 77 ~~-~~~vl~~~~~ 88 (230)
T PF13531_consen 77 AR-SPLVLAVPKG 88 (230)
T ss_dssp EE-EEEEEEEETT
T ss_pred cc-CceEEEeccC
Confidence 88 8899999877
No 127
>PRK10918 phosphate ABC transporter periplasmic substrate-binding protein PstS; Provisional
Probab=47.47 E-value=50 Score=32.85 Aligned_cols=68 Identities=18% Similarity=0.245 Sum_probs=45.9
Q ss_pred HHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccc-cccccceecccEEEEEeC
Q psy12229 38 LIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVV-DFTVPYYDLVGITILMKK 116 (444)
Q Consensus 38 il~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~-dfS~p~~~~~~~~ilvp~ 116 (444)
..+.+.+.-+.++++. ..|+-.| +.++.+|++||+.....++++..+.. -...|... +.+++++..
T Consensus 44 ~a~~y~~~~~v~v~~~-----------~~GSG~G-i~~~~~g~vd~a~ssr~l~~~E~~~~~~~~~pva~-daIaivvN~ 110 (346)
T PRK10918 44 WADTYQKETGNKVNYQ-----------GIGSSGG-VKQIIANTVDFGASDAPLSDEKLAQEGLFQFPTVI-GGVVLAVNI 110 (346)
T ss_pred HHHHHHhhcCCEEEEe-----------cCccHHH-HHHHHhCCCcEEecCccCCHHHHhhcCCeeeeEEE-EEEEEEEeC
Confidence 3444444445555554 2455445 78899999999999999987543321 24577888 899999986
Q ss_pred CC
Q psy12229 117 PK 118 (444)
Q Consensus 117 ~~ 118 (444)
+.
T Consensus 111 ~~ 112 (346)
T PRK10918 111 PG 112 (346)
T ss_pred CC
Confidence 53
No 128
>cd00912 ML The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2 and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids.
Probab=46.05 E-value=22 Score=29.48 Aligned_cols=41 Identities=22% Similarity=0.490 Sum_probs=31.8
Q ss_pred CCcccccccccCCCCcccCCCCCCceeEeeeeeeccc-cCCCcccC
Q psy12229 398 GTSVCSSIFDTDGKTKVSCPLKKDHVYRYINTFKILD-RYPKCSKD 442 (444)
Q Consensus 398 ~~~~~~~kw~~~~~~~~~c~~~~~~~~~~~~~~~~l~-~~~~~~~~ 442 (444)
+.|+|..-+-. ...||...+..+.|..+.++-+ .+|.++++
T Consensus 66 ~~d~C~~~~~~----~~~CPl~~G~~~~~~~~~~v~~~~~P~~~~~ 107 (127)
T cd00912 66 SYDFCEAGLPK----PSFCPLRKGQQYSYAKTVNVPEFTIPTIEYQ 107 (127)
T ss_pred CCCcccccCcc----cccCCcCCCCEEEEEEEEecCcccCCCeeEE
Confidence 47889653211 2489999999999999999877 89987764
No 129
>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=46.01 E-value=63 Score=28.10 Aligned_cols=68 Identities=6% Similarity=0.041 Sum_probs=45.6
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
++-.+++..+.++. +.++++... ....+++.|.+|++|+++..... ....++ +.+... ..+.
T Consensus 14 ~~l~~~l~~f~~~~P~v~i~i~~~------------~~~~l~~~l~~g~~D~~~~~~~~---~~~~~~-~~~l~~-~~~~ 76 (198)
T cd08486 14 RSLPLLLRAFLTSTPTATVSLTHM------------TKDEQVEGLLAGTIHVGFSRFFP---RHPGIE-IVNIAQ-EDLY 76 (198)
T ss_pred HHHHHHHHHHHHhCCCeEEEEEEC------------CHHHHHHHHHcCCceEEEecCCC---CCCceE-EEEEee-ccEE
Confidence 34556777777765 677777632 55789999999999999864321 112232 455666 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 77 lv~~~~ 82 (198)
T cd08486 77 LAVHRS 82 (198)
T ss_pred EEecCC
Confidence 888765
No 130
>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=45.42 E-value=75 Score=27.20 Aligned_cols=67 Identities=12% Similarity=0.052 Sum_probs=44.4
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+--+++..+.++. +.++++.. +....+...+.+|++|+++..... ....+ -+.+... ..+.+
T Consensus 15 ~l~~~i~~~~~~~P~v~l~i~~------------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~-~~~~l~~-~~~~~ 77 (198)
T cd08446 15 TVPRLLRAFLTARPDVTVSLHN------------MTKDEQIEALRAGRIHIGFGRFYP---VEPDI-AVENVAQ-ERLYL 77 (198)
T ss_pred HHHHHHHHHHHHCCCeEEEEee------------CCHHHHHHHHHCCCccEEEEecCC---CCCCc-eeEEeee-ccEEE
Confidence 4456677777665 56777763 345678899999999999864322 12223 2456667 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 78 v~~~~ 82 (198)
T cd08446 78 AVPKS 82 (198)
T ss_pred EEeCC
Confidence 88765
No 131
>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=43.91 E-value=40 Score=32.35 Aligned_cols=72 Identities=19% Similarity=0.174 Sum_probs=46.0
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeeccccccccc-----cccc-ccccce
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERE-----NVVD-FTVPYY 105 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~-----~~~d-fS~p~~ 105 (444)
++--+++..+.++. +.++++.. +....++..|.+|++|+++.......+.. +..+ -..++.
T Consensus 48 ~~lp~~l~~f~~~~P~i~v~i~~------------~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~~~~l~ 115 (287)
T TIGR02136 48 PLAEAAAEEFQKIHPGVSVTVQG------------AGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKLIEHKVA 115 (287)
T ss_pred HHHHHHHHHHHhhCCCceEEEcc------------CCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCceEEEEE
Confidence 34455566666666 45666652 35678999999999999886543332220 1111 245677
Q ss_pred ecccEEEEEeCC
Q psy12229 106 DLVGITILMKKP 117 (444)
Q Consensus 106 ~~~~~~ilvp~~ 117 (444)
. +.+++++++.
T Consensus 116 ~-~~l~lvv~~~ 126 (287)
T TIGR02136 116 V-DGLAVVVNKK 126 (287)
T ss_pred E-eeEEEEECCC
Confidence 7 7889898765
No 132
>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=43.27 E-value=92 Score=26.82 Aligned_cols=68 Identities=15% Similarity=0.182 Sum_probs=45.1
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.++++.+.++. +.++++.. +....+...+.+|++|+++..... ....+. +.+... ..+.
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~i~~------------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~-~~~~ 75 (197)
T cd08452 13 EFLPPIVREYRKKFPSVKVELRE------------LSSPDQVEELLKGRIDIGFLHPPI---QHTALH-IETVQS-SPCV 75 (197)
T ss_pred hHHHHHHHHHHHHCCCcEEEEEe------------cChHHHHHHHHCCCccEEEeeCCC---CCCCee-EEEeee-ccEE
Confidence 34467778887776 56777763 245678999999999999864321 122333 456666 7788
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 lv~~~~ 81 (197)
T cd08452 76 LALPKQ 81 (197)
T ss_pred EEEeCC
Confidence 888765
No 133
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=42.97 E-value=3e+02 Score=26.10 Aligned_cols=65 Identities=3% Similarity=-0.072 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcCCCccEEeCC-cccccceEEEecCCCchhhhhHHHHH
Q psy12229 314 PNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGD-EFSRKPYAIAVQQDRDARELFCNVHA 384 (444)
Q Consensus 314 ~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c~l~~~~~-~~~~~~~~~~~~k~sp~~~~in~~il 384 (444)
+++..-..+.+..|. +.+++-.. .+.-.. +..++..++. ......+.++.+++.+....+...+.
T Consensus 222 ~~~~~~~~~~v~~g~----Gi~~lp~~-~~~~~~-~~~~l~~l~~~~~~~~~~~lv~~~~~~~~~~~~~f~~ 287 (296)
T PRK11062 222 FDDAALMKAFGAYHD----AIFVAPSL-YAQDFY-ADHSVVEIGRVDNVKEEYHVIFAERMIQHPAVQRICN 287 (296)
T ss_pred eCcHHHHHHHHHcCC----ceEECCHH-HHHHHH-HcCCeEEcCCccccceEEEEEEecCCCCcHHHHHHHh
Confidence 468888888899985 55555442 222221 2234555532 22245677888888766655554443
No 134
>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=42.03 E-value=84 Score=26.79 Aligned_cols=68 Identities=7% Similarity=0.103 Sum_probs=45.9
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.++++.+.++. +.++++... ....+...+.+|++|+++...... ...+ .+.+... ..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~------------~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~-~~~~ 75 (196)
T cd08450 13 QWLPEVLPILREEHPDLDVELSSL------------FSPQLAEALMRGKLDVAFMRPEIQ---SDGI-DYQLLLK-EPLI 75 (196)
T ss_pred hhHHHHHHHHHhhCCCcEEEEEec------------ChHHHHHHHhcCCccEEEEeCCCC---CCCc-EEEEEEc-cceE
Confidence 45567777777775 467777732 346788999999999998643221 2233 2456667 7888
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 76 ~~~~~~ 81 (196)
T cd08450 76 VVLPAD 81 (196)
T ss_pred EEecCC
Confidence 888765
No 135
>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=40.81 E-value=91 Score=26.50 Aligned_cols=65 Identities=9% Similarity=-0.008 Sum_probs=43.3
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+..+++..+.++. +.++++... ....+.+++.+|++|+++.... ...+ .+.+... ..+++
T Consensus 14 ~l~~~l~~~~~~~P~v~i~~~~~------------~~~~~~~~l~~~~~Dl~i~~~~-----~~~~-~~~~l~~-~~~~~ 74 (185)
T cd08439 14 ILPFLLNRFASVYPRLAIEVVCK------------RTPRLMEMLERGEVDLALITHP-----PPGA-SATILRR-SPTVW 74 (185)
T ss_pred HHHHHHHHHHHHCCCeEEEEEEC------------ChHHHHHHHHCCCCcEEEEecc-----CCCC-CceEEEE-ecCEE
Confidence 3456666776665 677777632 3457889999999999986431 1122 2466677 78888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 75 v~~~~ 79 (185)
T cd08439 75 YCAAG 79 (185)
T ss_pred EECCC
Confidence 88765
No 136
>TIGR01256 modA molybdenum ABC transporter, periplasmic molybdate-binding protein. The model describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represent hydrophylioc periplasmic-binding protein in gram-negative organisms and its counterpart in gram-positive organisms is a lipoprotein. The other components of the system include the ModB, an integral membrane protein and ModC the ATP-binding subunit. Invariably almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.
Probab=39.92 E-value=77 Score=28.58 Aligned_cols=72 Identities=10% Similarity=0.094 Sum_probs=43.6
Q ss_pred ecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcc-cccEEeeccccccccc---cccccccc--cee
Q psy12229 33 GYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEK-RADIALGSLSVMAERE---NVVDFTVP--YYD 106 (444)
Q Consensus 33 G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g-~~Di~~~~~~~t~~r~---~~~dfS~p--~~~ 106 (444)
-..-++++.+.++.+.++++..- ....++..+..| ++|+.+++-.....+. ..++-..+ +..
T Consensus 6 ~~~~~~~~~f~~~~gi~V~~~~~------------gs~~l~~~l~~~~~aDv~~~~~~~~~~~l~~~g~~~~~~~~~~~~ 73 (216)
T TIGR01256 6 DALKEIAKQFEKRTGNKVVFSFG------------SSGTLYTQIENGAPADLFISADNKWPKKLVDKGLVVAGSRFTYAG 73 (216)
T ss_pred HHHHHHHHHHHHhhCCeEEEEeC------------ChHHHHHHHHcCCCCcEEEECCHHHHHHHHHCCCCCCCchheEEc
Confidence 34457888899999988887632 234567777765 4999988643222221 12222223 455
Q ss_pred cccEEEEEeCC
Q psy12229 107 LVGITILMKKP 117 (444)
Q Consensus 107 ~~~~~ilvp~~ 117 (444)
..+++++++.
T Consensus 74 -~~~~l~~~~~ 83 (216)
T TIGR01256 74 -NKLVLISPKN 83 (216)
T ss_pred -cEEEEEEECC
Confidence 6778888765
No 137
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=39.32 E-value=77 Score=29.89 Aligned_cols=68 Identities=12% Similarity=0.182 Sum_probs=44.9
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
++-.+++..+.+.. +..++++.. ....+++.|.+|++|+++...... ...+ ...|... ..++
T Consensus 102 ~~l~~~l~~f~~~~P~v~v~~~~~------------~~~~~~~~l~~g~~Dl~i~~~~~~---~~~l-~~~~l~~-~~~~ 164 (275)
T PRK03601 102 CMLTPWLGRLYQNQEALQFEARIA------------QRQSLVKQLHERQLDLLITTEAPK---MDEF-SSQLLGH-FTLA 164 (275)
T ss_pred HHHHHHHHHHHHhCCCcEEEEEEC------------ChHHHHHHHHcCCCCEEEEcCCCc---cCCc-cEEEecc-eeEE
Confidence 34445555665543 566776633 456789999999999999754332 1234 3556777 7889
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 165 ~v~~~~ 170 (275)
T PRK03601 165 LYTSAP 170 (275)
T ss_pred EEecCc
Confidence 999765
No 138
>PF14034 Spore_YtrH: Sporulation protein YtrH
Probab=36.60 E-value=29 Score=27.73 Aligned_cols=41 Identities=29% Similarity=0.540 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHHHHhhhcchhhhhcccCCCCCCChHHhhhC
Q psy12229 199 RLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQ 242 (444)
Q Consensus 199 Rl~~~~w~l~~lvl~~~Y~a~L~s~Lt~~~~~~~I~sl~dL~~~ 242 (444)
+++..++.-+++++..+.-+.+.++|+. ++|.+++.+|+++
T Consensus 2 ~~i~~ffiA~GVvlGGsliGglga~l~~---~pPl~~m~~lA~~ 42 (102)
T PF14034_consen 2 KLILDFFIAFGVVLGGSLIGGLGAFLTG---QPPLKTMLDLAND 42 (102)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHcC---CChHHHHHHHHHH
Confidence 3566677888999999999999999997 6788888888885
No 139
>PF12849 PBP_like_2: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.; PDB: 1QUL_A 1OIB_A 1A54_A 1IXH_A 1A40_A 1QUJ_A 1A55_A 1IXI_A 2ABH_A 1QUK_A ....
Probab=36.21 E-value=55 Score=30.94 Aligned_cols=75 Identities=21% Similarity=0.268 Sum_probs=50.2
Q ss_pred eecHHHHHHHHHHH-cCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeeccccccccc-------------cc
Q psy12229 32 KGYCIDLIEEIRKL-VGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERE-------------NV 97 (444)
Q Consensus 32 ~G~~~dil~~la~~-lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~-------------~~ 97 (444)
..+.-++.+.+.+. -+.++.+.. .|+ ...+.+|.+|++|+++.+..++++.. ..
T Consensus 21 ~~~~~~~~~~~~~~~~~~~v~v~~-----------~gS-~~g~~~l~~g~~di~~~sr~l~~~e~~~~~~~~~~~~~~~~ 88 (281)
T PF12849_consen 21 APIMEALAEAFERQYPGVKVTVES-----------SGS-GAGIQALINGKVDIAISSRPLTAAEIASEGYNAKGQKWGGG 88 (281)
T ss_dssp HHHHHHHHHHHHHHSTTBEEEEEE-----------E-H-HHHHHHHHTTSSSEEEESSHHHHHHHHHHTCCCCCHHHHCT
T ss_pred HHHHHHHHHHHHHHCCCcEEEEEe-----------CCC-HHHHHHHHhCCCEEEEeCCCCcHHHHhHhhhhhcccccccc
Confidence 33444455555555 477777753 334 56689999999999999987776533 11
Q ss_pred ccccccceecccEEEEEeCCCCC
Q psy12229 98 VDFTVPYYDLVGITILMKKPKTP 120 (444)
Q Consensus 98 ~dfS~p~~~~~~~~ilvp~~~~~ 120 (444)
+ ...|+.. +.++++++++.+.
T Consensus 89 ~-~~~~va~-d~i~iv~n~~np~ 109 (281)
T PF12849_consen 89 L-VQIPVAR-DAIVIVVNKDNPL 109 (281)
T ss_dssp E-EEEEEEE-EEEEEEEETTTTT
T ss_pred c-EEEEEEE-eeEEEEEcCCCcc
Confidence 1 2477777 8999999987543
No 140
>PF12916 DUF3834: Protein of unknown function (DUF3834); InterPro: IPR024533 This family is likely to be related to solute-binding lipo-proteins.; PDB: 3MST_A.
Probab=35.98 E-value=44 Score=30.08 Aligned_cols=45 Identities=24% Similarity=0.333 Sum_probs=31.8
Q ss_pred eecHHHH-HHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeec
Q psy12229 32 KGYCIDL-IEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGS 87 (444)
Q Consensus 32 ~G~~~di-l~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~ 87 (444)
+|-..|+ ++++++..|.+.|++..+ +|..++.++.+|++|-++-+
T Consensus 76 kGsaADvl~Ral~d~~~~~~EvVytd-----------D~~~i~~Ml~~g~vdsAVv~ 121 (201)
T PF12916_consen 76 KGSAADVLTRALLDLKGIKAEVVYTD-----------DMSEIVKMLNEGEVDSAVVG 121 (201)
T ss_dssp TTSHHHHHHHHHHHHH--T-EEEE--------------HHHHHHHHHTT-E--EEEE
T ss_pred cccHHHHHHHHHHhhccccceeEEec-----------CHHHHHHHHhcCceeeeeec
Confidence 5888888 789999999999999775 78999999999999988766
No 141
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=34.05 E-value=4.3e+02 Score=25.28 Aligned_cols=69 Identities=14% Similarity=0.147 Sum_probs=42.8
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-.+++..+.++. +.++++... ...++.+++.+|++|++++... .......+. ..+... ..+++
T Consensus 107 ~l~~~l~~~~~~~P~i~l~l~~~------------~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l~-~~~l~~-~~~~~ 171 (308)
T PRK10094 107 AVAQLLAWLNERYPFTQFHISRQ------------IYMGVWDSLLYEGFSLAIGVTG-TEALANTFS-LDPLGS-VQWRF 171 (308)
T ss_pred HHHHHHHHHHHhCCCcEEEEEee------------hhhhHHHHHhCCCccEEEeccc-CccccCCee-EEEecc-eeEEE
Confidence 3456777777665 456666532 3467889999999999886321 111123333 445666 68888
Q ss_pred EEeCC
Q psy12229 113 LMKKP 117 (444)
Q Consensus 113 lvp~~ 117 (444)
++++.
T Consensus 172 v~~~~ 176 (308)
T PRK10094 172 VMAAD 176 (308)
T ss_pred EECCC
Confidence 88654
No 142
>TIGR00975 3a0107s03 phosphate ABC transporter, phosphate-binding protein. This family represents one type of (periplasmic, in Gram-negative bacteria) phosphate-binding protein found in phosphate ABC (ATP-binding cassette) transporters. This protein is accompanied, generally in the same operon, by an ATP binding protein and (usually) two permease proteins.
Probab=33.80 E-value=94 Score=30.34 Aligned_cols=50 Identities=12% Similarity=0.060 Sum_probs=35.9
Q ss_pred CCccchhHHHHhcccccEEeecccccccccccc---cccccceecccEEEEEeCC
Q psy12229 66 NGQWNGMIKELIEKRADIALGSLSVMAERENVV---DFTVPYYDLVGITILMKKP 117 (444)
Q Consensus 66 ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~---dfS~p~~~~~~~~ilvp~~ 117 (444)
.|+-. -+.++.+|++||+.....++++..+.. -...|+.. +.+++++.++
T Consensus 34 ~GSg~-Gi~~l~~g~~dia~ssr~l~~~E~~~~~~~~~~~pva~-dai~vivn~~ 86 (314)
T TIGR00975 34 IGSGA-GIAQFAAGTVDFGASDAPLSEADLASRGSGLLQFPTVI-GAIVVTYNLP 86 (314)
T ss_pred CCCHH-HHHHHHcCCCCEEecCCCCCHHHHHhhcCCcEEeeEEe-eeEEEEEeCC
Confidence 34544 478899999999999999887543321 12356777 8999999864
No 143
>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=32.88 E-value=1.3e+02 Score=25.99 Aligned_cols=68 Identities=13% Similarity=0.050 Sum_probs=43.4
Q ss_pred ecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEE
Q psy12229 33 GYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGIT 111 (444)
Q Consensus 33 G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ 111 (444)
.+-.+++..+.++. +.++++... +.+.+..++.+|++|+++...... ...+. +.++.. ..+.
T Consensus 14 ~~l~~~l~~~~~~~P~i~l~~~~~------------~~~~~~~~l~~~~~D~~i~~~~~~---~~~l~-~~~l~~-~~~~ 76 (198)
T cd08485 14 HTLPLLLRQLLSVAPSATVSLTQM------------SKNRQIEALDAGTIDIGFGRFYPY---QEGVV-VRNVTN-ERLF 76 (198)
T ss_pred HHHHHHHHHHHHhCCCcEEEEEEC------------CHHHHHHHHHcCCccEEEecCCCC---CCCeE-EEEeec-cceE
Confidence 34566677776654 677777632 346789999999999998643221 12332 456666 6777
Q ss_pred EEEeCC
Q psy12229 112 ILMKKP 117 (444)
Q Consensus 112 ilvp~~ 117 (444)
+++++.
T Consensus 77 ~~~~~~ 82 (198)
T cd08485 77 LGAQKS 82 (198)
T ss_pred EEeCCC
Confidence 777554
No 144
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=29.21 E-value=1.2e+02 Score=28.90 Aligned_cols=53 Identities=23% Similarity=0.261 Sum_probs=39.8
Q ss_pred HHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccc
Q psy12229 36 IDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAER 94 (444)
Q Consensus 36 ~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r 94 (444)
-.+.+.++++-|-++++...+.+..| +...+++.++.|.+||+.........+
T Consensus 16 ~~fa~~v~e~t~G~v~i~v~~~g~lg------~~~e~~~~v~~G~vdm~~~~~~~~~~~ 68 (286)
T PF03480_consen 16 EKFAEEVEERTGGRVKIEVFPAGQLG------KEAEVLEAVQDGAVDMAVVSPSYLAGF 68 (286)
T ss_dssp HHHHHHHHHHTTTSEEEEEEETTSSS------SHHHHHHHHHTTSSSEEEEEGGGGTTT
T ss_pred HHHHHHHHHHcCCeEEEEEecCcccC------CHHHHHHHHhCCCccEEeecchhhhhh
Confidence 67788999999988888766544333 346899999999999998776544433
No 145
>PRK10537 voltage-gated potassium channel; Provisional
Probab=28.44 E-value=65 Score=32.65 Aligned_cols=52 Identities=15% Similarity=0.240 Sum_probs=41.2
Q ss_pred cccchhhhhhhHhHhcccccccCCCCCCCCCChhhHHHHHHHHHHHHHHHHHhhhcchh
Q psy12229 164 PEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAA 222 (444)
Q Consensus 164 ~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~s~Rl~~~~w~l~~lvl~~~Y~a~L~s 222 (444)
....++||++.++...| +++..|.+..+|++.+++.++++.+..+..+.++.
T Consensus 168 s~~dA~y~svvt~tTvG-------yGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~~ 219 (393)
T PRK10537 168 SLSTAFYFSIVTMSTVG-------YGDIVPVSESARLFTISVIILGITVFATSISAIFG 219 (393)
T ss_pred CHHHHHHhhheeeeccc-------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35567888888888888 68888999999999999999998776555555444
No 146
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=28.12 E-value=98 Score=26.43 Aligned_cols=70 Identities=20% Similarity=0.181 Sum_probs=45.8
Q ss_pred eecHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccE
Q psy12229 32 KGYCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGI 110 (444)
Q Consensus 32 ~G~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~ 110 (444)
.++-.+++..+.++. +.++++... ..+.++.++.+|++|+++...... ....+ .+.+... ..+
T Consensus 12 ~~~l~~~l~~~~~~~P~v~i~i~~~------------~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~-~~~~l~~-~~~ 75 (195)
T cd08431 12 LQPLYPLIAEFYQLNKATRIRLSEE------------VLGGTWDALASGRADLVIGATGEL--PPGGV-KTRPLGE-VEF 75 (195)
T ss_pred hHHHHHHHHHHHHHCCCCceEEEEe------------ccchHHHHHhCCCCCEEEEecCCC--CCCce-EEEeccc-ceE
Confidence 356678888888887 578887632 345788999999999998642211 11223 2455556 677
Q ss_pred EEEEeCC
Q psy12229 111 TILMKKP 117 (444)
Q Consensus 111 ~ilvp~~ 117 (444)
.+++++.
T Consensus 76 ~~v~~~~ 82 (195)
T cd08431 76 VFAVAPN 82 (195)
T ss_pred EEEEcCC
Confidence 7777654
No 147
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=26.25 E-value=1.6e+02 Score=24.79 Aligned_cols=50 Identities=24% Similarity=0.282 Sum_probs=33.8
Q ss_pred HHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEee
Q psy12229 37 DLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALG 86 (444)
Q Consensus 37 dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~ 86 (444)
+.++..|+..|+.+.-+....+.-|.....-.+..++.++..|++|.++-
T Consensus 25 ~~l~~~a~~~g~~i~~~~~D~~~SG~~~~Rp~l~~ll~~~~~g~vd~vvv 74 (140)
T cd03770 25 AILEEYAKENGLENIRHYIDDGFSGTTFDRPGFNRMIEDIEAGKIDIVIV 74 (140)
T ss_pred HHHHHHHHHCCCEEEEEEEcCCCcCCcCCCHHHHHHHHHHHcCCCCEEEE
Confidence 34778888889886444333333444333446788999999999998665
No 148
>COG4588 AcfC Accessory colonization factor AcfC, contains ABC-type periplasmic domain [General function prediction only]
Probab=25.73 E-value=3.3e+02 Score=24.92 Aligned_cols=44 Identities=25% Similarity=0.460 Sum_probs=30.1
Q ss_pred eecHHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecc
Q psy12229 32 KGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSL 88 (444)
Q Consensus 32 ~G~~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~ 88 (444)
.-.-.++.+...++-+.++++..-|+ .+|. +=..+.+|+..|+-
T Consensus 32 htaL~~vA~~~~ektg~kVnvt~GPq---------~tW~----~kAkknADilfgas 75 (252)
T COG4588 32 HTALKDVAKKYEEKTGIKVNVTAGPQ---------ATWN----EKAKKNADILFGAS 75 (252)
T ss_pred cHHHHHHHHHHHHHhCeEEEEecCCc---------chhh----hhhhccCceeeccc
Confidence 34556778888888888888876543 2453 23567889887754
No 149
>cd08428 PBP2_IciA_ArgP The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold. The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-
Probab=24.71 E-value=2.2e+02 Score=24.22 Aligned_cols=66 Identities=5% Similarity=-0.062 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEEEE
Q psy12229 35 CIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILM 114 (444)
Q Consensus 35 ~~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~ilv 114 (444)
-..++..+.++.+.++++... +...+...+.+|++|+++..-.. ....+ .+.+... ....+++
T Consensus 15 l~~~l~~f~~~~~v~l~l~~~------------~~~~~~~~l~~~~~D~~i~~~~~---~~~~~-~~~~l~~-~~~~~~~ 77 (195)
T cd08428 15 FLPALAPVLKRERILLDLIVD------------DEDRTHDLLRDGEVVGCISTQAQ---PMQGC-RSDYLGS-MDYLLVA 77 (195)
T ss_pred hHHHHHHHHhCcCeEEEEEeC------------CchhHHHHHHcCcceEEEEecCC---CCCCc-eeEEeee-eeEEEEE
Confidence 345677777776656666532 34578899999999987753221 12223 3455666 6777777
Q ss_pred eCC
Q psy12229 115 KKP 117 (444)
Q Consensus 115 p~~ 117 (444)
++.
T Consensus 78 ~~~ 80 (195)
T cd08428 78 SPD 80 (195)
T ss_pred CCc
Confidence 654
No 150
>PF02879 PGM_PMM_II: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II; InterPro: IPR005845 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 2F7L_A 3PDK_B 1KFQ_B 1KFI_A 1C47_A 1VKL_B 1LXT_A 1JDY_B 3PMG_A 1C4G_B ....
Probab=23.41 E-value=2.4e+02 Score=22.10 Aligned_cols=66 Identities=24% Similarity=0.333 Sum_probs=44.5
Q ss_pred eeecHHHHHHHHHHHcCCeEEEEE-cCCCCCcc-ccCC---CccchhHHHHhcccccEEeeccccccccccc
Q psy12229 31 YKGYCIDLIEEIRKLVGFEYEIFV-APDNSFGN-MDEN---GQWNGMIKELIEKRADIALGSLSVMAERENV 97 (444)
Q Consensus 31 ~~G~~~dil~~la~~lnft~~~~~-~~~~~~g~-~~~n---g~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~ 97 (444)
..|....++..+.+++|+...... .++..|+. ..++ .++..+...+....+|+++. +.-..+|.-.
T Consensus 29 ~~G~~~~~~~~ll~~lg~~~~~~n~~~d~~f~~~~~p~p~~~~l~~~~~~v~~~~ad~g~~-~DgDaDRl~~ 99 (104)
T PF02879_consen 29 MNGAGSDILPRLLERLGCDVIELNCDPDPDFPNQHAPNPEEESLQRLIKIVRESGADLGIA-FDGDADRLGV 99 (104)
T ss_dssp TTSTTHHHHHHHHHHTTCEEEEESSS-STTGTTTSTSSTSTTTTHHHHHHHHHSTTSEEEE-E-TTSSBEEE
T ss_pred CCCHHHHHHHHHHHHcCCcEEEEecccccccccccccccccchhHHHHHHhhccCceEEEE-ECCcCceeEE
Confidence 468999999999999999765543 35557766 3333 35667777788889999775 4434455443
No 151
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=22.72 E-value=2.2e+02 Score=27.11 Aligned_cols=69 Identities=17% Similarity=0.185 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEEE
Q psy12229 35 CIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITIL 113 (444)
Q Consensus 35 ~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~il 113 (444)
-.+++..+.++. +.++.+.. ++...++..+.+|++|++++..... .....+. ..+... ..++++
T Consensus 107 l~~~l~~~~~~~p~i~i~i~~------------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~l~-~~~l~~-~~~~~v 171 (300)
T PRK11074 107 TRQLIVDFYRHFDDVELIIRQ------------EVFNGVWDALADGRVDIAIGATRAI-PVGGRFA-FRDMGM-LSWACV 171 (300)
T ss_pred HHHHHHHHHHhCCCceEEEEe------------hhhhHHHHHHHCCCCCEEEecCccC-Ccccccc-eeeccc-ceEEEE
Confidence 344555555444 34565552 2446788999999999999743211 1112232 344566 688888
Q ss_pred EeCCC
Q psy12229 114 MKKPK 118 (444)
Q Consensus 114 vp~~~ 118 (444)
+++..
T Consensus 172 ~~~~h 176 (300)
T PRK11074 172 VSSDH 176 (300)
T ss_pred EcCCC
Confidence 87653
No 152
>smart00737 ML Domain involved in innate immunity and lipid metabolism. ML (MD-2-related lipid-recognition) is a novel domain identified in MD-1, MD-2, GM2A, Npc2 and multiple proteins of unknown function in plants, animals and fungi. These single-domain proteins were predicted to form a beta-rich fold containing multiple strands, and to mediate diverse biological functions through interacting with specific lipids.
Probab=22.33 E-value=84 Score=25.47 Aligned_cols=37 Identities=19% Similarity=0.522 Sum_probs=30.1
Q ss_pred CcccccccccCCCCcccCCCCCCceeEeeeeeeccccCCCcccC
Q psy12229 399 TSVCSSIFDTDGKTKVSCPLKKDHVYRYINTFKILDRYPKCSKD 442 (444)
Q Consensus 399 ~~~~~~kw~~~~~~~~~c~~~~~~~~~~~~~~~~l~~~~~~~~~ 442 (444)
.|+|..- ...||.+.+....|..+.++...+|+..++
T Consensus 62 ~d~C~~~-------~~~CPl~~G~~~~~~~~~~v~~~~P~~~~~ 98 (118)
T smart00737 62 YDLCKLL-------GSKCPIEKGETVNYTNSLTVPGIFPPGKYT 98 (118)
T ss_pred CCccccC-------CCCCCCCCCeeEEEEEeeEccccCCCeEEE
Confidence 6788532 138999999999999999999999987664
No 153
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=21.79 E-value=2.9e+02 Score=25.90 Aligned_cols=70 Identities=7% Similarity=-0.005 Sum_probs=43.8
Q ss_pred cHHHHHHHHHHHc-CCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEeecccccccccccccccccceecccEEE
Q psy12229 34 YCIDLIEEIRKLV-GFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITI 112 (444)
Q Consensus 34 ~~~dil~~la~~l-nft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~~~~~t~~r~~~~dfS~p~~~~~~~~i 112 (444)
+-.++++.+.++. +.++.+... +-...+.++.+|++|+++.... .......+. +.|... ..+.+
T Consensus 111 ~l~~~l~~f~~~~p~i~l~i~~~------------~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l~-~~~l~~-~~~~~ 175 (294)
T PRK09986 111 RLRPAMRHFLKENPNVEWLLREL------------SPSMQMAALERRELDAGIWRMA-DLEPNPGFT-SRRLHE-SAFAV 175 (294)
T ss_pred HHHHHHHHHHHhCCCeEEEEEeC------------CHHHHHHHHHcCCCCEEEecCC-ccCCCCCeE-EEEeec-ccEEE
Confidence 3455566666665 356666522 3357889999999999986321 011223443 466677 78888
Q ss_pred EEeCCC
Q psy12229 113 LMKKPK 118 (444)
Q Consensus 113 lvp~~~ 118 (444)
++++..
T Consensus 176 v~~~~~ 181 (294)
T PRK09986 176 AVPEEH 181 (294)
T ss_pred EEcCCC
Confidence 888764
No 154
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=20.62 E-value=2.2e+02 Score=23.72 Aligned_cols=51 Identities=12% Similarity=0.201 Sum_probs=34.3
Q ss_pred HHHHHHHHHHcCCeEEEEEcCCCCCccccCCCccchhHHHHhcccccEEee
Q psy12229 36 IDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALG 86 (444)
Q Consensus 36 ~dil~~la~~lnft~~~~~~~~~~~g~~~~ng~~~g~i~~l~~g~~Di~~~ 86 (444)
.+.++..|+..|+++.-+....+.-|.......+..++.++..|++|.++.
T Consensus 21 ~~~~~~~a~~~g~~i~~~~~d~~~Sg~~~~Rp~l~~ll~~~~~g~~~~ivv 71 (148)
T smart00857 21 LEALRAYAKANGWEVVRIYEDEGVSGKKADRPGLQRLLADLRAGDIDVLVV 71 (148)
T ss_pred HHHHHHHHHHCCCEEEEEEEeCCCcCCCCCCHHHHHHHHHHHcCCCCEEEE
Confidence 344788889999987544333333344333456889999999999887654
No 155
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=20.31 E-value=1.9e+02 Score=27.01 Aligned_cols=106 Identities=11% Similarity=0.090 Sum_probs=0.0
Q ss_pred CCCCCChHHhhhCCceeeEecCCChhhHHhhhhhhhhhHHHHHHhhhccCCCCcHHHHhhhhcccCCcchhHHHHHHHHH
Q psy12229 230 DTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMK 309 (444)
Q Consensus 230 ~~~I~sl~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~y~~~~~~~~ 309 (444)
..+|+|++||.+ +++.+..++...++++...
T Consensus 125 ~~~i~s~~Dl~G---~kir~~~~~~~~~~~~~~G---------------------------------------------- 155 (257)
T TIGR00787 125 KKPITKPEDLKG---LKIRIPNSPMNEAQFKALG---------------------------------------------- 155 (257)
T ss_pred CCccCChHHhCC---CEEecCCCHHHHHHHHHcC----------------------------------------------
Q ss_pred hcCCCCCHHHHHHHHHhcCCCCCceEEEecccchhhhhcCCCccEEeCCcccccceEEEecCCC--chhhhhHHHHHHHh
Q psy12229 310 EAKLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQQDR--DARELFCNVHANIL 387 (444)
Q Consensus 310 ~~~~~~~~~e~~~~v~~~~~~~~~~a~i~d~~~~~y~~~~~c~l~~~~~~~~~~~~~~~~~k~s--p~~~~in~~il~l~ 387 (444)
-.+...+..|.+..+.+|. .++.+.....+....-..--=++...........+.+.++. .+-+....+|.+..
T Consensus 156 a~~v~~~~~e~~~aL~~G~----vDg~~~~~~~~~~~~~~ev~~y~~~~~~~~~~~~~~~n~~~~~~L~~e~q~~i~~a~ 231 (257)
T TIGR00787 156 ANPEPMAFSEVYTALQTGV----VDGQENPLSNVYSSKFYEVQKYLSMTNHGYLGYLVVVNKAFWKSLPPDLQAVVKEAA 231 (257)
T ss_pred CcccccCHHHHHHHHHcCC----cccccCCHHHHhhcchhhhcchheecCCcccceEEEEeHHHHhcCCHHHHHHHHHHH
Q ss_pred c
Q psy12229 388 S 388 (444)
Q Consensus 388 e 388 (444)
+
T Consensus 232 ~ 232 (257)
T TIGR00787 232 K 232 (257)
T ss_pred H
Done!