Query 039381
Match_columns 138
No_of_seqs 124 out of 1375
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 09:07:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039381.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039381hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1053 Glutamate-gated NMDA-t 99.9 1.1E-24 2.3E-29 186.5 5.5 124 6-130 720-847 (1258)
2 smart00079 PBPe Eukaryotic hom 99.8 5.7E-19 1.2E-23 122.5 10.3 86 2-89 48-134 (134)
3 KOG4440 NMDA selective glutama 99.8 1.9E-19 4E-24 150.6 4.7 115 4-121 721-839 (993)
4 KOG1054 Glutamate-gated AMPA-t 99.6 1.8E-15 3.8E-20 126.4 8.2 120 6-125 707-831 (897)
5 KOG1052 Glutamate-gated kainat 99.5 4.2E-14 9E-19 121.3 10.3 124 3-128 484-613 (656)
6 PRK10797 glutamate and asparta 99.5 7.5E-13 1.6E-17 104.2 11.1 89 2-90 181-273 (302)
7 PRK09495 glnH glutamine ABC tr 99.4 2.5E-12 5.4E-17 97.6 11.2 89 2-90 155-245 (247)
8 PRK11260 cystine transporter s 99.4 3.7E-12 7.9E-17 97.8 11.6 90 2-91 173-264 (266)
9 PF00497 SBP_bac_3: Bacterial 99.4 4.1E-12 8.8E-17 93.0 9.3 88 2-89 135-225 (225)
10 TIGR01096 3A0103s03R lysine-ar 99.3 3.3E-11 7.2E-16 90.9 11.0 86 2-87 156-250 (250)
11 COG0834 HisJ ABC-type amino ac 99.3 3E-11 6.4E-16 91.8 9.7 89 2-90 172-266 (275)
12 PRK15007 putative ABC transpor 99.3 5.8E-11 1.3E-15 89.4 10.8 86 2-88 150-242 (243)
13 TIGR02285 conserved hypothetic 99.2 5.8E-11 1.3E-15 91.3 9.4 88 3-90 167-263 (268)
14 PRK15010 ABC transporter lysin 99.2 2.9E-10 6.2E-15 87.0 11.5 89 2-90 159-256 (260)
15 PRK11917 bifunctional adhesin/ 99.2 2E-10 4.3E-15 88.4 10.0 81 2-87 176-258 (259)
16 PRK15437 histidine ABC transpo 99.1 7.2E-10 1.6E-14 84.8 10.7 89 2-90 159-256 (259)
17 TIGR02995 ectoine_ehuB ectoine 99.1 5.4E-10 1.2E-14 86.3 9.8 87 2-89 169-262 (275)
18 PRK10859 membrane-bound lytic 99.1 6.4E-10 1.4E-14 92.8 9.7 85 4-89 180-267 (482)
19 PRK09959 hybrid sensory histid 99.0 1.6E-09 3.4E-14 98.2 9.0 88 1-89 430-521 (1197)
20 TIGR03870 ABC_MoxJ methanol ox 99.0 4.5E-09 9.7E-14 80.1 9.8 78 7-86 151-241 (246)
21 smart00062 PBPb Bacterial peri 99.0 9.7E-09 2.1E-13 73.3 10.1 86 2-87 130-219 (219)
22 cd00134 PBPb Bacterial peripla 98.9 1.4E-08 3.1E-13 72.6 10.7 86 2-87 129-218 (218)
23 TIGR03871 ABC_peri_MoxJ_2 quin 98.9 1.9E-08 4.2E-13 75.1 9.9 82 5-88 140-229 (232)
24 PRK09959 hybrid sensory histid 98.9 1.3E-08 2.8E-13 92.3 10.0 89 1-90 187-279 (1197)
25 TIGR01098 3A0109s03R phosphate 98.2 5.4E-06 1.2E-10 62.7 7.7 71 3-73 178-254 (254)
26 PRK00489 hisG ATP phosphoribos 97.9 2.9E-05 6.3E-10 60.9 5.3 80 2-89 137-220 (287)
27 TIGR03431 PhnD phosphonate ABC 97.7 0.00015 3.3E-09 56.2 7.6 79 4-82 172-258 (288)
28 COG4623 Predicted soluble lyti 97.5 0.00071 1.5E-08 55.3 8.3 82 7-89 164-248 (473)
29 PF03401 TctC: Tripartite tric 96.4 0.045 9.8E-07 42.6 9.6 86 2-87 135-243 (274)
30 PF12974 Phosphonate-bd: ABC t 95.2 0.095 2.1E-06 39.5 6.9 82 5-86 143-230 (243)
31 COG3181 Uncharacterized protei 95.1 0.097 2.1E-06 42.0 6.9 85 2-86 179-285 (319)
32 PRK11553 alkanesulfonate trans 94.1 0.22 4.7E-06 39.0 6.7 34 4-37 161-194 (314)
33 PF00060 Lig_chan: Ligand-gate 93.3 0.0098 2.1E-07 41.2 -1.9 32 89-120 116-148 (148)
34 COG3221 PhnD ABC-type phosphat 93.0 0.65 1.4E-05 37.0 7.7 82 4-85 181-270 (299)
35 PF09084 NMT1: NMT1/THI5 like; 92.7 0.29 6.4E-06 35.8 5.1 59 2-61 25-84 (216)
36 TIGR01729 taurine_ABC_bnd taur 87.8 2.5 5.3E-05 32.8 6.7 66 7-73 135-209 (300)
37 smart00094 TR_FER Transferrin. 87.7 1.8 3.8E-05 35.0 5.9 57 3-61 32-97 (332)
38 TIGR01728 SsuA_fam ABC transpo 85.8 1.4 3.1E-05 33.2 4.3 59 2-61 33-92 (288)
39 TIGR00363 lipoprotein, YaeC fa 85.8 5.2 0.00011 31.0 7.5 43 2-44 50-94 (258)
40 TIGR01729 taurine_ABC_bnd taur 85.3 2.7 5.8E-05 32.6 5.7 25 2-26 31-55 (300)
41 PF03180 Lipoprotein_9: NLPA l 85.2 1.7 3.7E-05 33.4 4.4 77 1-80 29-123 (237)
42 TIGR01256 modA molybdenum ABC 84.9 3.7 8E-05 30.0 6.1 80 4-86 134-215 (216)
43 PRK11553 alkanesulfonate trans 84.7 3.2 6.8E-05 32.4 5.9 60 2-62 60-121 (314)
44 TIGR02122 TRAP_TAXI TRAP trans 84.0 4.9 0.00011 31.0 6.7 24 3-26 174-197 (320)
45 PF12974 Phosphonate-bd: ABC t 83.6 3.6 7.7E-05 30.8 5.6 59 2-62 33-97 (243)
46 PRK11063 metQ DL-methionine tr 81.2 2.5 5.5E-05 33.0 4.0 41 2-42 63-104 (271)
47 PRK03537 molybdate ABC transpo 80.9 12 0.00026 27.2 7.4 77 8-87 101-181 (188)
48 PF13531 SBP_bac_11: Bacterial 80.9 15 0.00032 27.1 8.0 80 4-86 143-227 (230)
49 TIGR01728 SsuA_fam ABC transpo 80.6 6.7 0.00015 29.4 6.2 33 5-37 134-166 (288)
50 TIGR00787 dctP tripartite ATP- 78.6 6 0.00013 30.2 5.3 67 5-73 160-234 (257)
51 PF13379 NMT1_2: NMT1-like fam 76.6 7.7 0.00017 29.2 5.4 57 2-59 39-99 (252)
52 TIGR03427 ABC_peri_uca ABC tra 75.8 11 0.00023 30.3 6.3 29 2-30 39-68 (328)
53 PF00405 Transferrin: Transfer 75.3 6.7 0.00014 31.6 4.9 52 5-58 34-94 (330)
54 COG1910 Periplasmic molybdate- 75.2 4.7 0.0001 30.8 3.8 58 7-71 138-198 (223)
55 PF13379 NMT1_2: NMT1-like fam 74.5 4.2 9.2E-05 30.7 3.5 57 2-59 154-213 (252)
56 TIGR01098 3A0109s03R phosphate 73.6 17 0.00038 27.0 6.7 61 2-62 68-133 (254)
57 cd00134 PBPb Bacterial peripla 73.2 8 0.00017 26.8 4.5 24 3-27 43-66 (218)
58 PF03480 SBP_bac_7: Bacterial 70.4 9.8 0.00021 29.4 4.7 66 7-74 162-235 (286)
59 COG1464 NlpA ABC-type metal io 69.2 5.3 0.00011 31.4 2.9 75 1-79 60-153 (268)
60 COG0715 TauA ABC-type nitrate/ 66.8 14 0.0003 28.9 4.9 62 2-64 65-130 (335)
61 TIGR03414 ABC_choline_bnd chol 65.5 15 0.00032 28.8 4.9 53 7-59 44-100 (290)
62 smart00062 PBPb Bacterial peri 64.6 16 0.00035 25.1 4.6 24 3-27 44-67 (219)
63 PRK11480 tauA taurine transpor 64.5 25 0.00055 27.6 6.1 25 2-26 55-79 (320)
64 TIGR03261 phnS2 putative 2-ami 63.9 48 0.0011 26.0 7.6 124 6-134 201-330 (334)
65 TIGR03427 ABC_peri_uca ABC tra 63.4 47 0.001 26.6 7.5 30 7-36 141-170 (328)
66 TIGR00363 lipoprotein, YaeC fa 63.2 46 0.00099 25.8 7.2 79 8-86 171-250 (258)
67 PRK04168 molybdate ABC transpo 62.6 59 0.0013 26.1 7.9 81 4-89 207-315 (334)
68 cd08501 PBP2_Lpqw The substrat 62.1 32 0.0007 28.4 6.6 68 2-71 202-277 (486)
69 TIGR03431 PhnD phosphonate ABC 61.2 51 0.0011 25.1 7.2 25 3-27 64-88 (288)
70 cd08512 PBP2_NikA_DppA_OppA_li 60.6 37 0.0008 27.9 6.6 23 2-24 206-228 (476)
71 PRK09861 cytoplasmic membrane 60.3 13 0.00027 29.1 3.6 41 2-42 64-105 (272)
72 PF14503 YhfZ_C: YhfZ C-termin 60.0 23 0.00051 27.2 4.9 57 7-67 145-208 (232)
73 cd00995 PBP2_NikA_DppA_OppA_li 59.6 45 0.00097 27.0 6.9 68 2-71 192-266 (466)
74 COG0725 ModA ABC-type molybdat 59.5 66 0.0014 24.9 7.5 80 2-87 169-253 (258)
75 PRK11063 metQ DL-methionine tr 59.4 54 0.0012 25.5 7.0 80 7-86 183-263 (271)
76 COG4521 TauA ABC-type taurine 58.5 19 0.0004 28.5 4.1 59 2-61 61-121 (334)
77 PRK11119 proX glycine betaine 57.2 24 0.00051 28.4 4.8 54 7-60 66-123 (331)
78 cd08503 PBP2_NikA_DppA_OppA_li 56.7 52 0.0011 26.9 6.9 68 2-71 195-269 (460)
79 COG3221 PhnD ABC-type phosphat 56.6 51 0.0011 26.2 6.5 59 4-62 73-136 (299)
80 cd08519 PBP2_NikA_DppA_OppA_li 56.4 48 0.001 27.3 6.6 23 2-24 192-214 (469)
81 PRK15413 glutathione ABC trans 56.3 42 0.00092 28.1 6.3 67 2-71 220-294 (512)
82 TIGR02743 TraW type-F conjugat 56.2 14 0.0003 27.8 3.1 37 52-88 25-62 (202)
83 TIGR01276 thiB thiamine ABC tr 55.6 94 0.002 24.0 8.0 70 5-74 176-249 (309)
84 PRK15437 histidine ABC transpo 55.4 14 0.0003 27.8 3.1 19 7-25 73-91 (259)
85 cd08492 PBP2_NikA_DppA_OppA_li 54.8 70 0.0015 26.3 7.3 23 2-24 203-225 (484)
86 cd08518 PBP2_NikA_DppA_OppA_li 51.8 61 0.0013 26.6 6.5 23 2-25 184-206 (464)
87 COG0687 PotD Spermidine/putres 51.5 1.2E+02 0.0025 24.3 8.0 70 3-72 218-291 (363)
88 PF04069 OpuAC: Substrate bind 51.4 9.8 0.00021 28.9 1.6 59 2-60 33-96 (257)
89 PRK00489 hisG ATP phosphoribos 51.1 62 0.0013 25.2 6.1 75 6-89 51-130 (287)
90 PRK13738 conjugal transfer pil 50.9 19 0.00042 27.2 3.1 36 52-87 23-59 (209)
91 TIGR02122 TRAP_TAXI TRAP trans 50.0 30 0.00065 26.6 4.2 58 4-62 67-133 (320)
92 cd08499 PBP2_Ylib_like The sub 48.5 73 0.0016 26.2 6.5 23 2-24 191-213 (474)
93 cd08517 PBP2_NikA_DppA_OppA_li 47.6 66 0.0014 26.4 6.1 24 2-25 195-218 (480)
94 cd08515 PBP2_NikA_DppA_OppA_li 47.3 92 0.002 25.5 6.9 23 2-24 195-217 (460)
95 PRK09861 cytoplasmic membrane 47.2 94 0.002 24.2 6.6 78 8-86 185-264 (272)
96 cd08514 PBP2_AppA_like The sub 47.1 72 0.0016 26.2 6.2 24 2-25 196-219 (483)
97 PRK07377 hypothetical protein; 46.8 24 0.00053 26.2 3.0 24 2-25 112-135 (184)
98 TIGR03339 phn_lysR aminoethylp 46.7 30 0.00065 25.8 3.7 51 6-64 120-170 (279)
99 cd08513 PBP2_thermophilic_Hb8_ 46.4 93 0.002 25.6 6.8 23 2-24 195-217 (482)
100 PF12727 PBP_like: PBP superfa 46.2 72 0.0016 23.4 5.5 52 4-61 129-180 (193)
101 cd08438 PBP2_CidR The C-termin 44.8 33 0.00072 23.2 3.4 50 7-64 37-86 (197)
102 cd08490 PBP2_NikA_DppA_OppA_li 44.4 86 0.0019 25.6 6.3 23 2-24 183-205 (470)
103 cd08493 PBP2_DppA_like The sub 44.2 74 0.0016 26.2 5.9 23 2-24 208-230 (482)
104 cd08516 PBP2_NikA_DppA_OppA_li 43.7 94 0.002 25.2 6.4 23 2-24 188-210 (457)
105 PRK10859 membrane-bound lytic 43.5 36 0.00077 28.6 3.9 24 2-25 84-107 (482)
106 PRK10677 modA molybdate transp 43.0 75 0.0016 24.3 5.4 78 5-87 173-253 (257)
107 cd08502 PBP2_NikA_DppA_OppA_li 42.8 95 0.0021 25.6 6.3 66 2-71 203-275 (472)
108 cd08494 PBP2_NikA_DppA_OppA_li 42.4 1.1E+02 0.0024 24.7 6.7 23 2-24 188-210 (448)
109 PF12849 PBP_like_2: PBP super 42.1 37 0.00081 25.7 3.6 59 5-63 44-110 (281)
110 cd08498 PBP2_NikA_DppA_OppA_li 42.0 1E+02 0.0022 25.4 6.4 23 2-24 191-213 (481)
111 PF00800 PDT: Prephenate dehyd 42.0 32 0.00069 25.0 3.1 56 2-60 26-91 (181)
112 cd08496 PBP2_NikA_DppA_OppA_li 41.5 98 0.0021 25.3 6.2 66 2-71 189-261 (454)
113 TIGR02995 ectoine_ehuB ectoine 41.3 39 0.00084 25.7 3.6 23 4-26 77-99 (275)
114 PRK15010 ABC transporter lysin 40.8 38 0.00082 25.4 3.4 20 7-26 73-92 (260)
115 PF00496 SBP_bac_5: Bacterial 40.5 69 0.0015 25.1 5.0 82 2-88 154-239 (374)
116 PRK11205 tbpA thiamine transpo 39.0 1.9E+02 0.004 22.6 8.0 71 5-75 197-271 (330)
117 PRK11622 hypothetical protein; 38.9 2.1E+02 0.0046 23.2 7.7 70 7-76 254-329 (401)
118 PRK10677 modA molybdate transp 38.5 1.4E+02 0.0029 22.8 6.2 56 4-61 59-118 (257)
119 PRK09755 putative ABC transpor 37.0 1.1E+02 0.0024 25.9 5.9 68 2-71 244-317 (535)
120 TIGR02294 nickel_nikA nickel A 36.2 1.4E+02 0.0031 24.8 6.4 23 2-24 198-220 (500)
121 PRK11480 tauA taurine transpor 36.0 50 0.0011 25.9 3.5 26 8-33 158-183 (320)
122 cd08511 PBP2_NikA_DppA_OppA_li 35.6 1.4E+02 0.0031 24.4 6.3 23 2-24 192-214 (467)
123 PRK15109 antimicrobial peptide 35.6 1.2E+02 0.0026 25.8 6.0 22 2-23 249-270 (547)
124 PF12916 DUF3834: Protein of u 35.5 30 0.00065 26.1 2.0 70 2-77 97-171 (201)
125 cd08495 PBP2_NikA_DppA_OppA_li 35.5 1.2E+02 0.0026 25.0 5.9 23 2-24 204-226 (482)
126 PRK11242 DNA-binding transcrip 34.2 48 0.001 25.1 3.1 49 7-63 128-176 (296)
127 PRK15104 oligopeptide ABC tran 33.8 1.5E+02 0.0033 25.1 6.3 23 2-24 249-271 (543)
128 cd08415 PBP2_LysR_opines_like 33.4 68 0.0015 21.6 3.6 49 7-63 37-85 (196)
129 cd08489 PBP2_NikA The substrat 33.0 1.6E+02 0.0035 24.2 6.3 23 2-24 191-213 (488)
130 PRK11899 prephenate dehydratas 32.8 61 0.0013 25.5 3.5 24 2-25 30-53 (279)
131 PRK11898 prephenate dehydratas 32.6 61 0.0013 25.4 3.5 57 2-59 30-95 (283)
132 cd08425 PBP2_CynR The C-termin 32.5 79 0.0017 21.4 3.8 50 7-64 38-87 (197)
133 cd08504 PBP2_OppA The substrat 32.4 1.3E+02 0.0028 24.8 5.6 24 2-25 211-234 (498)
134 cd08508 PBP2_NikA_DppA_OppA_li 32.3 1.7E+02 0.0037 24.0 6.3 24 2-25 197-220 (470)
135 cd08447 PBP2_LTTR_aromatics_li 30.6 64 0.0014 21.9 3.0 49 7-63 37-85 (198)
136 TIGR00070 hisG ATP phosphoribo 30.3 1.1E+02 0.0024 22.6 4.3 77 8-89 49-126 (182)
137 COG0077 PheA Prephenate dehydr 29.5 63 0.0014 25.6 3.0 54 2-58 29-92 (279)
138 PRK09986 DNA-binding transcrip 29.4 47 0.001 25.1 2.3 52 7-64 134-185 (294)
139 cd08445 PBP2_BenM_CatM_CatR Th 29.0 87 0.0019 21.5 3.5 49 7-63 38-86 (203)
140 cd08509 PBP2_TmCBP_oligosaccha 28.1 2E+02 0.0042 24.0 6.0 24 2-25 201-224 (509)
141 cd08414 PBP2_LTTR_aromatics_li 27.7 65 0.0014 21.7 2.6 49 7-63 37-85 (197)
142 PF06345 Drf_DAD: DRF Autoregu 27.3 65 0.0014 13.8 1.6 12 8-19 3-14 (15)
143 TIGR02136 ptsS_2 phosphate bin 27.1 58 0.0013 25.2 2.5 57 6-63 71-131 (287)
144 PRK12683 transcriptional regul 27.1 58 0.0013 25.2 2.5 51 6-63 129-179 (309)
145 TIGR02637 RhaS rhamnose ABC tr 25.3 1.2E+02 0.0027 22.9 4.1 28 2-29 215-242 (302)
146 PRK00910 ribB 3,4-dihydroxy-2- 25.3 81 0.0018 24.1 2.9 23 4-26 13-35 (218)
147 COG0715 TauA ABC-type nitrate/ 24.8 57 0.0012 25.3 2.1 81 8-88 173-266 (335)
148 TIGR03061 pip_yhgE_Nterm YhgE/ 24.4 1E+02 0.0023 21.6 3.3 19 7-25 84-102 (164)
149 PF03466 LysR_substrate: LysR 24.1 2.4E+02 0.0051 19.1 7.7 67 3-73 134-204 (209)
150 PLN02317 arogenate dehydratase 24.1 1E+02 0.0022 25.5 3.5 56 2-59 120-184 (382)
151 COG4166 OppA ABC-type oligopep 24.0 2E+02 0.0043 24.7 5.4 68 2-71 254-331 (562)
152 PF14836 Ubiquitin_3: Ubiquiti 23.0 32 0.00069 22.5 0.3 9 130-138 79-87 (88)
153 PF10991 DUF2815: Protein of u 22.7 1.4E+02 0.0029 22.1 3.6 31 50-80 30-61 (181)
154 PRK10752 sulfate transporter s 22.6 3.6E+02 0.0079 21.6 6.3 32 4-35 60-93 (329)
155 TIGR03270 methan_mark_4 putati 22.5 93 0.002 23.5 2.7 23 3-25 2-24 (202)
156 KOG1348 Asparaginyl peptidases 22.5 65 0.0014 26.9 2.0 29 54-82 170-199 (477)
157 PRK09906 DNA-binding transcrip 22.5 74 0.0016 24.1 2.3 50 7-64 127-176 (296)
158 TIGR00506 ribB 3,4-dihydroxy-2 22.2 1E+02 0.0022 23.2 2.8 22 5-26 2-23 (199)
159 cd08505 PBP2_NikA_DppA_OppA_li 22.0 3.3E+02 0.0071 23.0 6.3 23 2-24 225-247 (528)
160 COG5436 Predicted integral mem 21.6 1.3E+02 0.0029 21.9 3.2 57 15-71 111-172 (182)
161 COG5566 Uncharacterized conser 21.5 2.2E+02 0.0049 20.0 4.2 40 50-89 75-115 (137)
162 PF00072 Response_reg: Respons 21.5 1.1E+02 0.0024 19.0 2.7 25 2-26 26-50 (112)
163 COG4890 Predicted outer membra 21.3 40 0.00086 18.1 0.4 6 125-130 2-7 (37)
164 PRK13895 conjugal transfer pro 20.9 1E+02 0.0022 22.0 2.5 38 52-89 16-65 (144)
165 PRK09501 potD spermidine/putre 20.9 4.2E+02 0.0091 20.8 9.4 79 3-84 207-289 (348)
166 COG0324 MiaA tRNA delta(2)-iso 20.6 2.1E+02 0.0046 22.9 4.6 39 49-87 189-228 (308)
167 PRK15408 autoinducer 2-binding 20.6 1.8E+02 0.0039 23.1 4.2 27 2-28 238-264 (336)
168 cd08510 PBP2_Lactococcal_OppA_ 20.5 3.6E+02 0.0079 22.5 6.2 23 3-26 219-241 (516)
169 PRK15421 DNA-binding transcrip 20.4 86 0.0019 24.4 2.3 50 7-64 126-175 (317)
170 PF14503 YhfZ_C: YhfZ C-termin 20.3 1E+02 0.0023 23.7 2.7 50 9-59 53-106 (232)
171 cd08457 PBP2_OccR The C-termin 20.2 77 0.0017 21.6 1.9 48 8-63 38-85 (196)
172 COG2113 ProX ABC-type proline/ 20.1 1.7E+02 0.0037 23.3 3.9 53 7-59 67-123 (302)
No 1
>KOG1053 consensus Glutamate-gated NMDA-type ion channel receptor subunit GRIN2A and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=99.90 E-value=1.1e-24 Score=186.53 Aligned_cols=124 Identities=21% Similarity=0.355 Sum_probs=114.9
Q ss_pred CCHHHHHHHHHcCCceEEEecHHHHHHHHHhc--CCCeeeC--CCCCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHH
Q 039381 6 FSENRHRQALTSGEIAAAFLEVPYVKLFLAKN--CKNFTTG--PTYSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLRE 81 (138)
Q Consensus 6 ~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~--~~~~~~~--~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~ 81 (138)
..++++++.|++|++||+|+|.+++.|.+.++ |+.+++| +.|..++||||+|||||++..||.+|+++..+|++++
T Consensus 720 ~~v~dal~sLK~gKLDAFIyDaAVLnY~agkDegCKLvTIGsgKvFAttGYGIal~k~Spwkr~IdlallQy~gdGeme~ 799 (1258)
T KOG1053|consen 720 PGVEDALESLKNGKLDAFIYDAAVLNYMAGKDEGCKLVTIGSGKVFATTGYGIALPKNSPWKRQIDLALLQYLGDGEMEM 799 (1258)
T ss_pred CchHHHHHHHhcccchhHHHHHHHHHHhhccCCCceEEEecCCceeeecceeeecCCCCcchhhHHHHHHHHhccchHHH
Confidence 46799999999999999999999999998764 8744466 8999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCCCCCCCCCccCCcccccccceeeeehhhhhhhHhhhhhh
Q 039381 82 LEEAMLSPYNCSTKENNEDLEGLGLRSFQDEQSSPSQSRTREHWLSAWE 130 (138)
Q Consensus 82 l~~kW~~~~~c~~~~~~~~~~~l~~~~~~G~F~~~g~~~~~~~~~~~~~ 130 (138)
|.++|+. +.|+++.+++++.+|+++||+|+||+|++++..+...+.||
T Consensus 800 Le~~Wlt-gic~n~k~evmSsqLdIdnmaGvFymL~~amgLSllvfi~E 847 (1258)
T KOG1053|consen 800 LETLWLT-GICHNSKNEVMSSQLDIDNMAGVFYMLAVAMGLSLLVFIWE 847 (1258)
T ss_pred HHHHHhh-cccccchhhhhhcccChhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 9999996 79998878899999999999999999999999999999887
No 2
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.80 E-value=5.7e-19 Score=122.55 Aligned_cols=86 Identities=33% Similarity=0.502 Sum_probs=79.9
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLR 80 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~ 80 (138)
++.|++.++++++|++|+ ||++.|.+++.+++++.|. +. ++..+..++||||+|||++|++.||.+|.+|+++|+++
T Consensus 48 ~~~~~~~~~~~~~l~~g~-da~v~d~~~~~~~~~~~~~-~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~G~~~ 125 (134)
T smart00079 48 SVFVKSYAEGVQRVRVSN-YAFLMESTYLDYELSQNCD-LMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELQ 125 (134)
T ss_pred CCCCCCHHHHHHHHHcCC-CEEEeehHhHHHHHhCCCC-eEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhcCcHH
Confidence 467899999999999999 9999999999998887775 88 88889899999999999999999999999999999999
Q ss_pred HHHHHhcCC
Q 039381 81 ELEEAMLSP 89 (138)
Q Consensus 81 ~l~~kW~~~ 89 (138)
+|++|||++
T Consensus 126 ~l~~kw~~~ 134 (134)
T smart00079 126 KLENKWWKK 134 (134)
T ss_pred HHHHhhccC
Confidence 999999973
No 3
>KOG4440 consensus NMDA selective glutamate-gated ion channel receptor subunit GRIN1 [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=99.77 E-value=1.9e-19 Score=150.57 Aligned_cols=115 Identities=20% Similarity=0.364 Sum_probs=103.6
Q ss_pred ecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHHH
Q 039381 4 PIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLREL 82 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~l 82 (138)
.|.+.+|++++|++|+.+|+|+|++.++|-.+++|+ +. .|+-|...+|||+++||||+.+.+..+|+++.|+|.+++|
T Consensus 721 Ny~~A~eAiq~v~~gkL~AFIWDS~rLEfEAs~~Ce-LvT~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~~hEsGfMEkL 799 (993)
T KOG4440|consen 721 NYESAAEAIQAVRDGKLHAFIWDSARLEFEASQKCE-LVTTGELFGRSGYGIGLQKDSPWTQNVTLAILKSHESGFMEKL 799 (993)
T ss_pred chhhHHHHHHHHHcCceeEEEeecceeeehhhcccc-eEeccccccccccccccccCCCCcchhhHHHHHhhhcchHHHH
Confidence 467889999999999999999999999999999998 66 9999999999999999999999999999999999999999
Q ss_pred HHHhcCC---CCCCCCCCCCccCCcccccccceeeeehhhhh
Q 039381 83 EEAMLSP---YNCSTKENNEDLEGLGLRSFQDEQSSPSQSRT 121 (138)
Q Consensus 83 ~~kW~~~---~~c~~~~~~~~~~~l~~~~~~G~F~~~g~~~~ 121 (138)
-++|... +.|... ...+..||+.||+|+|++++.+..
T Consensus 800 Dk~Wi~~Ggpq~c~~~--~k~PatLgl~NMagvFiLV~~Gia 839 (993)
T KOG4440|consen 800 DKTWIRYGGPQECDSR--SKAPATLGLENMAGVFILVAGGIA 839 (993)
T ss_pred HHHHHhcCCcchhhhh--ccCcccccccccccEEEEEecchh
Confidence 9999865 455543 347999999999999998866543
No 4
>KOG1054 consensus Glutamate-gated AMPA-type ion channel receptor subunit GluR2 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=99.61 E-value=1.8e-15 Score=126.43 Aligned_cols=120 Identities=18% Similarity=0.243 Sum_probs=99.4
Q ss_pred CCHHHHHHHHH-cCCceEEEecHHHHHHHHHhc-CCCeeeCCCCCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHHHH
Q 039381 6 FSENRHRQALT-SGEIAAAFLEVPYVKLFLAKN-CKNFTTGPTYSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLRELE 83 (138)
Q Consensus 6 ~~~~e~~~aL~-~G~vdA~i~d~~~l~~~~~~~-~~~~~~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~l~ 83 (138)
.+.+|++..++ ++.-.|++.+.+.-+|..+.. |+..++|..++..+||||.||||.|+..+|.+++.|.|.|.+++|.
T Consensus 707 ~t~aeGv~rVRksKGkyAfLLEsTmNey~eqRkPCDTMKVGgNLds~GYGiATp~Gsslr~~vNLAvLkL~E~G~LdKLk 786 (897)
T KOG1054|consen 707 RTTAEGVARVRKSKGKYAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLK 786 (897)
T ss_pred ehhhhHHHHHHhcCCceEeehHhhhhhhhhccCCccceecccccCCcceeecCCCCcccccchhhhhhhhcccchHHHhh
Confidence 46788999997 556889999988888876655 7733399999999999999999999999999999999999999999
Q ss_pred HHhcC-CCCCCCC--CCCCccCCcccccccceeeeehhhhhhhHh
Q 039381 84 EAMLS-PYNCSTK--ENNEDLEGLGLRSFQDEQSSPSQSRTREHW 125 (138)
Q Consensus 84 ~kW~~-~~~c~~~--~~~~~~~~l~~~~~~G~F~~~g~~~~~~~~ 125 (138)
+||+- +++|... +..+..+.|.|++++|+||||-.++.+.-+
T Consensus 787 NKWWYDkGeC~sg~~ds~~ktsaLsLSnVAGvFYIL~gGl~laMl 831 (897)
T KOG1054|consen 787 NKWWYDKGECGSGGGDSKDKTSALSLSNVAGVFYILVGGLGLAML 831 (897)
T ss_pred hhhcccccccCCCCCCCCcchhhcchhhccceeeeehhhHHHHHH
Confidence 99864 5899874 344566889999999999999655444333
No 5
>KOG1052 consensus Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=99.54 E-value=4.2e-14 Score=121.30 Aligned_cols=124 Identities=25% Similarity=0.328 Sum_probs=99.6
Q ss_pred eecCCHHHHHHHHHcCC--ceEEEecHHHHHHHHHhc--CCCee-eCCCCCcceeEEEEeCCChhHHHHHHHHHHHhhcC
Q 039381 3 EPIFSENRHRQALTSGE--IAAAFLEVPYVKLFLAKN--CKNFT-TGPTYSVGGFGFAFPKDSAYLADFSQAILQLSEEG 77 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~--vdA~i~d~~~l~~~~~~~--~~~~~-~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G 77 (138)
+.+.+.+++++++++|. -.+++.+.....+....+ |+ +. +++.+...+|| |+||||||+..++.+|+++.+.|
T Consensus 484 ~~~~~~~e~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~c~-~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e~g 561 (656)
T KOG1052|consen 484 VPLASPEEGVERVRKGPSGGYAFASDELYLAYLFLRDEICD-LTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQETG 561 (656)
T ss_pred ccCCCHHHHHHHHHcCCCCceEEEeccHHHHHHHhhcCCCc-eEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhcccc
Confidence 56789999999999996 566666666666665554 65 99 99999999999 99999999999999999999999
Q ss_pred cHHHHHHHhcCCCCCCCCCCCC-ccCCcccccccceeeeehhhhhhhHhhhh
Q 039381 78 KLRELEEAMLSPYNCSTKENNE-DLEGLGLRSFQDEQSSPSQSRTREHWLSA 128 (138)
Q Consensus 78 ~~~~l~~kW~~~~~c~~~~~~~-~~~~l~~~~~~G~F~~~g~~~~~~~~~~~ 128 (138)
.++++.+||+....|....... ....|+++++.|+|++++++++...-++.
T Consensus 562 ~l~~~~~kw~~~~~~~~~~~~~~~~~~l~~~~~~g~F~i~~~g~~lal~vfi 613 (656)
T KOG1052|consen 562 ILQKLKRKWFSKKPCLPKCSQTEKTKALDLESFWGLFLILLVGYLLALLVFI 613 (656)
T ss_pred HHHHHHHHhccCCCCCCCCCCcccccccchhhHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999975443221111 57889999999999999886444444333
No 6
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.46 E-value=7.5e-13 Score=104.22 Aligned_cols=89 Identities=18% Similarity=0.193 Sum_probs=77.9
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHh--cCCCee-eCCCCCcceeEEEEeCCCh-hHHHHHHHHHHHhhcC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAK--NCKNFT-TGPTYSVGGFGFAFPKDSA-YLADFSQAILQLSEEG 77 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~--~~~~~~-~~~~~~~~~~g~a~~Kgsp-l~~~in~~l~~l~~~G 77 (138)
++.+++.++++.+|.+||+||++.|.+++.+.+.+ ..+.+. ++..+...+|+++++|+++ |++.+|.+|.+|+++|
T Consensus 181 i~~~~~~~~~l~~L~~GrvDa~i~d~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~~a~~k~~~~L~~~in~~L~~l~~~G 260 (302)
T PRK10797 181 IISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQAQTSG 260 (302)
T ss_pred EEEeCCHHHHHHHHHcCCceEEEccHHHHHHHHHcCCCCcceEECCccCCcCceeEEEeCCCHHHHHHHHHHHHHHHhCc
Confidence 57789999999999999999999998887665443 234477 7877888899999999987 9999999999999999
Q ss_pred cHHHHHHHhcCCC
Q 039381 78 KLRELEEAMLSPY 90 (138)
Q Consensus 78 ~~~~l~~kW~~~~ 90 (138)
++++|++|||+.+
T Consensus 261 ~l~~i~~kw~~~~ 273 (302)
T PRK10797 261 EAEKWFDKWFKNP 273 (302)
T ss_pred hHHHHHHHHcCCC
Confidence 9999999999964
No 7
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.42 E-value=2.5e-12 Score=97.58 Aligned_cols=89 Identities=20% Similarity=0.353 Sum_probs=78.8
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhc-CCCee-eCCCCCcceeEEEEeCCChhHHHHHHHHHHHhhcCcH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKN-CKNFT-TGPTYSVGGFGFAFPKDSAYLADFSQAILQLSEEGKL 79 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~-~~~~~-~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~ 79 (138)
++.+++.++++++|.+|++|+++.|.+.+.+++++. ...+. ++.......++++++|++++++.+|++|.+|+++|++
T Consensus 155 i~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~n~al~~~~~~g~~ 234 (247)
T PRK09495 155 LRQFPNIDNAYLELGTGRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSELREKVNGALKTLKENGTY 234 (247)
T ss_pred eEEcCCHHHHHHHHHcCceeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEEEcCcHHHHHHHHHHHHHHHHCCcH
Confidence 567889999999999999999999999888887765 33466 7776777889999999999999999999999999999
Q ss_pred HHHHHHhcCCC
Q 039381 80 RELEEAMLSPY 90 (138)
Q Consensus 80 ~~l~~kW~~~~ 90 (138)
++|.+||++..
T Consensus 235 ~~i~~k~~~~~ 245 (247)
T PRK09495 235 AEIYKKWFGTE 245 (247)
T ss_pred HHHHHHHcCCC
Confidence 99999999864
No 8
>PRK11260 cystine transporter subunit; Provisional
Probab=99.41 E-value=3.7e-12 Score=97.83 Aligned_cols=90 Identities=21% Similarity=0.300 Sum_probs=79.7
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCCCh-hHHHHHHHHHHHhhcCcH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKDSA-YLADFSQAILQLSEEGKL 79 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kgsp-l~~~in~~l~~l~~~G~~ 79 (138)
+..+++..+++.+|.+|++|+++.|...+.+++++.+..+. ....+...+++++++|+++ |++.+|.+|.+++++|++
T Consensus 173 i~~~~~~~~~l~~L~~GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~~ln~~l~~~~~~g~~ 252 (266)
T PRK11260 173 VRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGVALRKGNPDLLKAVNQAIAEMQKDGTL 252 (266)
T ss_pred eEecCCHHHHHHHHHcCCCCEEEechHHHHHHHHhCCCcceecCCccccCceEEEEeCCCHHHHHHHHHHHHHHHhCCcH
Confidence 57799999999999999999999999888888877654456 5666778899999999987 999999999999999999
Q ss_pred HHHHHHhcCCCC
Q 039381 80 RELEEAMLSPYN 91 (138)
Q Consensus 80 ~~l~~kW~~~~~ 91 (138)
++|.+||++...
T Consensus 253 ~~i~~k~~~~~~ 264 (266)
T PRK11260 253 KALSEKWFGADV 264 (266)
T ss_pred HHHHHHhcCCcc
Confidence 999999998643
No 9
>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=99.37 E-value=4.1e-12 Score=93.04 Aligned_cols=88 Identities=24% Similarity=0.295 Sum_probs=76.4
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee--eCCCCCcceeEEEEeCCCh-hHHHHHHHHHHHhhcCc
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT--TGPTYSVGGFGFAFPKDSA-YLADFSQAILQLSEEGK 78 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~--~~~~~~~~~~g~a~~Kgsp-l~~~in~~l~~l~~~G~ 78 (138)
++.+++..+++.+|.+|++|+++.+...+.+++++...... ........+++++++++++ |++.||++|.+|+++|+
T Consensus 135 ~~~~~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~i~~l~~~G~ 214 (225)
T PF00497_consen 135 IVEVDSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRKKNPELLEIFNKAIRELKQSGE 214 (225)
T ss_dssp EEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEETTTHHHHHHHHHHHHHHHHTTH
T ss_pred hcccccHHHHHHHHhcCCeeeeeccchhhhhhhhhcccccccccccccccceeEEeecccccHHHHHHHHHHHHHHhCcH
Confidence 56789999999999999999999999999999888743233 4455667888999988776 99999999999999999
Q ss_pred HHHHHHHhcCC
Q 039381 79 LRELEEAMLSP 89 (138)
Q Consensus 79 ~~~l~~kW~~~ 89 (138)
+++|.+|||+.
T Consensus 215 ~~~i~~ky~g~ 225 (225)
T PF00497_consen 215 IQKILKKYLGD 225 (225)
T ss_dssp HHHHHHHHHSS
T ss_pred HHHHHHHHcCC
Confidence 99999999973
No 10
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.30 E-value=3.3e-11 Score=90.88 Aligned_cols=86 Identities=22% Similarity=0.385 Sum_probs=73.5
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcC--CCee-eCCCCCcc-----eeEEEEeCCCh-hHHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNC--KNFT-TGPTYSVG-----GFGFAFPKDSA-YLADFSQAILQ 72 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~--~~~~-~~~~~~~~-----~~g~a~~Kgsp-l~~~in~~l~~ 72 (138)
++.+++..+++++|.+|++|+++.+.+.+.+++++.+ +.+. ++..+..+ .++|+++++++ |+..||++|.+
T Consensus 156 ~~~~~s~~~~~~~L~~g~vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ln~~l~~ 235 (250)
T TIGR01096 156 IVEYDSYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKGDTELKAAFNKALAA 235 (250)
T ss_pred EEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccCCceEEEEeCCCHHHHHHHHHHHHH
Confidence 5678999999999999999999999999988877653 2366 65544432 48999999987 99999999999
Q ss_pred HhhcCcHHHHHHHhc
Q 039381 73 LSEEGKLRELEEAML 87 (138)
Q Consensus 73 l~~~G~~~~l~~kW~ 87 (138)
|+++|++++|.+||+
T Consensus 236 l~~~g~~~~i~~kw~ 250 (250)
T TIGR01096 236 IRADGTYQKISKKWF 250 (250)
T ss_pred HHHCCcHHHHHHhhC
Confidence 999999999999996
No 11
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.28 E-value=3e-11 Score=91.83 Aligned_cols=89 Identities=20% Similarity=0.216 Sum_probs=74.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHH--HHhcCCCee-eCCCCCc-ceeEEEEeCC--ChhHHHHHHHHHHHhh
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLF--LAKNCKNFT-TGPTYSV-GGFGFAFPKD--SAYLADFSQAILQLSE 75 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~--~~~~~~~~~-~~~~~~~-~~~g~a~~Kg--spl~~~in~~l~~l~~ 75 (138)
++.|++.++++++|++|++||++.|.+++.++ ..+...... ....... ++|+++++|+ +.+++.+|.+|.++++
T Consensus 172 ~~~~~~~~~~~~al~~Gr~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~in~~l~~l~~ 251 (275)
T COG0834 172 IVAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIALRKGDDPELLEAVNKALKELKA 251 (275)
T ss_pred EEeeCCHHHHHHHHHcCCccEEEcchHhhhhhhhhhcCCCCceeeeccCCCcceeEEEeccCCcHHHHHHHHHHHHHHHh
Confidence 67899999999999999999999999999884 433332222 3434444 8999999999 3699999999999999
Q ss_pred cCcHHHHHHHhcCCC
Q 039381 76 EGKLRELEEAMLSPY 90 (138)
Q Consensus 76 ~G~~~~l~~kW~~~~ 90 (138)
+|++++|.+||+...
T Consensus 252 ~G~~~~i~~kw~~~~ 266 (275)
T COG0834 252 DGTLQKISDKWFGPD 266 (275)
T ss_pred CccHHHHHHHhcCcc
Confidence 999999999999853
No 12
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.27 E-value=5.8e-11 Score=89.43 Aligned_cols=86 Identities=20% Similarity=0.315 Sum_probs=72.4
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCC-----cceeEEEEeCCCh-hHHHHHHHHHHHh
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYS-----VGGFGFAFPKDSA-YLADFSQAILQLS 74 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~-----~~~~g~a~~Kgsp-l~~~in~~l~~l~ 74 (138)
++.+++..+++++|.+|++||++.+..++.++.++.+. +. ++.... ..+++|+++++++ |++.+|++|.+|+
T Consensus 150 ~~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ln~~l~~l~ 228 (243)
T PRK15007 150 TVPYDSYQNAKLDLQNGRIDAVFGDTAVVTEWLKDNPK-LAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVK 228 (243)
T ss_pred EEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHhcCCC-ceeecCcccccccCCcceEEEEeCCCHHHHHHHHHHHHHHH
Confidence 45688999999999999999999999988888776654 44 443322 3457999999876 9999999999999
Q ss_pred hcCcHHHHHHHhcC
Q 039381 75 EEGKLRELEEAMLS 88 (138)
Q Consensus 75 ~~G~~~~l~~kW~~ 88 (138)
++|++++|.+||+.
T Consensus 229 ~~g~~~~i~~~w~~ 242 (243)
T PRK15007 229 KDGTYETIYNKWFQ 242 (243)
T ss_pred hCCcHHHHHHHhcC
Confidence 99999999999986
No 13
>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=99.24 E-value=5.8e-11 Score=91.35 Aligned_cols=88 Identities=18% Similarity=0.112 Sum_probs=70.6
Q ss_pred eecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhc---CCCee-eCCCC--CcceeEEEEeCCC---hhHHHHHHHHHHH
Q 039381 3 EPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKN---CKNFT-TGPTY--SVGGFGFAFPKDS---AYLADFSQAILQL 73 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~---~~~~~-~~~~~--~~~~~g~a~~Kgs---pl~~~in~~l~~l 73 (138)
..+++.++++++|.+||+|+++.|..++.+++++. ...+. ..... ....++|+++|++ .|++.||++|.+|
T Consensus 167 ~~~~~~~~~~~~L~~GrvD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~k~~~~~~l~~~in~~L~~l 246 (268)
T TIGR02285 167 IGNAAMGNLFKMLEKGRVNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMPAHISVWVACPKTEWGRKVIADIDQALSEL 246 (268)
T ss_pred eccchHHHHHHHHHcCCccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCccceEEEEEeCCCHHHHHHHHHHHHHHHHH
Confidence 45677888999999999999999999999888753 22344 43222 2346899999974 3999999999999
Q ss_pred hhcCcHHHHHHHhcCCC
Q 039381 74 SEEGKLRELEEAMLSPY 90 (138)
Q Consensus 74 ~~~G~~~~l~~kW~~~~ 90 (138)
+++|++++|.+|||+..
T Consensus 247 ~~dG~~~~i~~k~~~~~ 263 (268)
T TIGR02285 247 NVDPKYYKYFDRWLSPE 263 (268)
T ss_pred hhCHHHHHHHHHhCCHh
Confidence 99999999999999753
No 14
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.20 E-value=2.9e-10 Score=87.05 Aligned_cols=89 Identities=22% Similarity=0.371 Sum_probs=70.3
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHH-HHHhc-CCCee-eCCCCC-----cceeEEEEeCCCh-hHHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKL-FLAKN-CKNFT-TGPTYS-----VGGFGFAFPKDSA-YLADFSQAILQ 72 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~-~~~~~-~~~~~-~~~~~~-----~~~~g~a~~Kgsp-l~~~in~~l~~ 72 (138)
++.+++.++++++|.+|++||++.|..++.+ +.++. ...+. .+.... ...++|+++++++ |++.+|.+|.+
T Consensus 159 ~~~~~~~~~~~~~l~~griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~L~~~ln~~l~~ 238 (260)
T PRK15010 159 VVAYANQDLVYSDLAAGRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGE 238 (260)
T ss_pred EEecCCHHHHHHHHHcCCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEEEEeCCCHHHHHHHHHHHHH
Confidence 4567888999999999999999999887764 34432 33355 443332 2346899999976 99999999999
Q ss_pred HhhcCcHHHHHHHhcCCC
Q 039381 73 LSEEGKLRELEEAMLSPY 90 (138)
Q Consensus 73 l~~~G~~~~l~~kW~~~~ 90 (138)
|+++|++++|.+||++.+
T Consensus 239 l~~~G~~~~i~~ky~~~~ 256 (260)
T PRK15010 239 LRQDGTYDKMAKKYFDFN 256 (260)
T ss_pred HHhCCcHHHHHHHhcCCc
Confidence 999999999999999753
No 15
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.18 E-value=2e-10 Score=88.45 Aligned_cols=81 Identities=9% Similarity=0.121 Sum_probs=70.2
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCCCh-hHHHHHHHHHHHhhcCcH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKDSA-YLADFSQAILQLSEEGKL 79 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kgsp-l~~~in~~l~~l~~~G~~ 79 (138)
++.+++..+++++|.+|++||++.|.+++.++..+. .. ++..+..++|+++++|+++ |++.+|.+|.+|+. ++
T Consensus 176 ~~~~~~~~~~~~~l~~GrvDa~~~d~~~~~~~~~~~---~~~~~~~~~~~~~~~a~~k~~~~l~~~ln~~l~~~~~--~~ 250 (259)
T PRK11917 176 FSEFPDYPSIKAALDAKRVDAFSVDKSILLGYVDDK---SEILPDSFEPQSYGIVTKKDDPAFAKYVDDFVKEHKN--EI 250 (259)
T ss_pred EEecCCHHHHHHHHHcCCCcEEEecHHHHHHhhhcC---CeecCCcCCCCceEEEEeCCCHHHHHHHHHHHHHHHH--HH
Confidence 457899999999999999999999988877665432 35 6777888899999999987 99999999999975 99
Q ss_pred HHHHHHhc
Q 039381 80 RELEEAML 87 (138)
Q Consensus 80 ~~l~~kW~ 87 (138)
++|++||.
T Consensus 251 ~~i~~kw~ 258 (259)
T PRK11917 251 DALAKKWG 258 (259)
T ss_pred HHHHHHhC
Confidence 99999995
No 16
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.12 E-value=7.2e-10 Score=84.77 Aligned_cols=89 Identities=21% Similarity=0.336 Sum_probs=69.7
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHH-HHHhc-CCCee-eCCCCC-----cceeEEEEeCCCh-hHHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKL-FLAKN-CKNFT-TGPTYS-----VGGFGFAFPKDSA-YLADFSQAILQ 72 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~-~~~~~-~~~~~-~~~~~~-----~~~~g~a~~Kgsp-l~~~in~~l~~ 72 (138)
++.+++..+++++|.+||+|+++.|...+.+ +.++. ...+. .+..+. ...++|+++++++ |++.+|.+|.+
T Consensus 159 ~~~~~~~~~~i~~L~~grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ia~~~~~~~l~~~~n~~l~~ 238 (259)
T PRK15437 159 IVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAE 238 (259)
T ss_pred EEecCCHHHHHHHHHcCCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEEEEeCCCHHHHHHHHHHHHH
Confidence 5678899999999999999999999877654 33332 22244 333232 2347899998876 99999999999
Q ss_pred HhhcCcHHHHHHHhcCCC
Q 039381 73 LSEEGKLRELEEAMLSPY 90 (138)
Q Consensus 73 l~~~G~~~~l~~kW~~~~ 90 (138)
|+++|++++|.+||++.+
T Consensus 239 ~~~~G~~~~i~~k~~~~~ 256 (259)
T PRK15437 239 MRADGTYEKLAKKYFDFD 256 (259)
T ss_pred HHHCCcHHHHHHHhcCCc
Confidence 999999999999999864
No 17
>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=99.12 E-value=5.4e-10 Score=86.33 Aligned_cols=87 Identities=17% Similarity=0.156 Sum_probs=70.6
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcC-CCee-eCCCCCc----ceeEEEEeCCCh-hHHHHHHHHHHHh
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNC-KNFT-TGPTYSV----GGFGFAFPKDSA-YLADFSQAILQLS 74 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~-~~~~-~~~~~~~----~~~g~a~~Kgsp-l~~~in~~l~~l~ 74 (138)
++.+++.++++.+|.+|++|+++.|.+++.+++++.. ..+. +.. +.. ..++|+++++++ |++.+|++|.+|+
T Consensus 169 i~~~~~~~~~i~~L~~grvDa~i~d~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~ 247 (275)
T TIGR02995 169 IIVVPDGQSGLKMVQDGRADAYSLTVLTINDLASKAGDPNVEVLAP-FKDAPVRYYGGAAFRPEDKELRDAFNVELAKLK 247 (275)
T ss_pred EEEeCCHHHHHHHHHcCCCCEEecChHHHHHHHHhCCCCCceeecC-ccCCccccceeEEECCCCHHHHHHHHHHHHHHH
Confidence 5678999999999999999999999999988877642 2244 322 211 234899999876 9999999999999
Q ss_pred hcCcHHHHHHHhcCC
Q 039381 75 EEGKLRELEEAMLSP 89 (138)
Q Consensus 75 ~~G~~~~l~~kW~~~ 89 (138)
++|++++|.+||--.
T Consensus 248 ~sG~~~~i~~ky~~~ 262 (275)
T TIGR02995 248 ESGEFAKIIAPYGFS 262 (275)
T ss_pred hChHHHHHHHHhCCC
Confidence 999999999999543
No 18
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.09 E-value=6.4e-10 Score=92.81 Aligned_cols=85 Identities=15% Similarity=0.157 Sum_probs=70.9
Q ss_pred ecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCC-Ch-hHHHHHHHHHHHhhcCcHH
Q 039381 4 PIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKD-SA-YLADFSQAILQLSEEGKLR 80 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kg-sp-l~~~in~~l~~l~~~G~~~ 80 (138)
.+.+.++++++|.+|++|+++.|...+.......++ +. ........+++|+++|+ ++ |++.+|++|.+++++|+++
T Consensus 180 ~~~s~~e~l~aL~~G~iDa~v~d~~~~~~~~~~~p~-l~v~~~l~~~~~~~~av~k~~~~~L~~~ln~~L~~i~~~G~l~ 258 (482)
T PRK10859 180 DDKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPE-LAVAFDLTDEQPVAWALPPSGDDSLYAALLDFFNQIKEDGTLA 258 (482)
T ss_pred CCCCHHHHHHHHHCCCCCEEEECcHHHHHHHHhCCC-ceeeeecCCCceeEEEEeCCCCHHHHHHHHHHHHHhhcCCHHH
Confidence 467899999999999999999998877655444454 55 44444567899999994 56 9999999999999999999
Q ss_pred HHHHHhcCC
Q 039381 81 ELEEAMLSP 89 (138)
Q Consensus 81 ~l~~kW~~~ 89 (138)
+|.+|||+.
T Consensus 259 ~L~~kyfg~ 267 (482)
T PRK10859 259 RLEEKYFGH 267 (482)
T ss_pred HHHHHHhhh
Confidence 999999986
No 19
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.00 E-value=1.6e-09 Score=98.16 Aligned_cols=88 Identities=13% Similarity=0.186 Sum_probs=76.1
Q ss_pred CeeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhc-CCC-ee-eCCCCCcceeEEEEeCCCh-hHHHHHHHHHHHhhc
Q 039381 1 NIEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKN-CKN-FT-TGPTYSVGGFGFAFPKDSA-YLADFSQAILQLSEE 76 (138)
Q Consensus 1 ~i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~-~~~-~~-~~~~~~~~~~g~a~~Kgsp-l~~~in~~l~~l~~~ 76 (138)
+++.|++..+++++|.+|++||++.+.+++.|++++. ... +. ....+....++||++|++| |++.+|++|.++.++
T Consensus 430 ~~~~~~~~~~~l~av~~G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~av~k~~~~L~~~lnk~l~~i~~~ 509 (1197)
T PRK09959 430 EWIKVDNASAAFHKVKEGELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGEPELKDIINKALNAIPPS 509 (1197)
T ss_pred EEEEcCCHHHHHHHHHcCCCCEEehhhHHHHHHHHhcccccceeeecCCCCchheEEeeCCCCHHHHHHHHHHHHhCCHH
Confidence 3678999999999999999999999999999998874 222 33 4445566789999999987 999999999999999
Q ss_pred CcHHHHHHHhcCC
Q 039381 77 GKLRELEEAMLSP 89 (138)
Q Consensus 77 G~~~~l~~kW~~~ 89 (138)
++++|++||++.
T Consensus 510 -~~~~i~~kW~~~ 521 (1197)
T PRK09959 510 -EVLRLTEKWIKM 521 (1197)
T ss_pred -HHHHHHhhcccC
Confidence 999999999975
No 20
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=98.98 E-value=4.5e-09 Score=80.13 Aligned_cols=78 Identities=12% Similarity=0.137 Sum_probs=61.3
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee---eCCCC-------Ccc--eeEEEEeCCCh-hHHHHHHHHHHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT---TGPTY-------SVG--GFGFAFPKDSA-YLADFSQAILQL 73 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~---~~~~~-------~~~--~~g~a~~Kgsp-l~~~in~~l~~l 73 (138)
+.++++++|.+|++||++.|.+.+.+++++....+. ++... ... .+|||++|+++ |++.||++|.+|
T Consensus 151 ~~~~~~~aL~~GrvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~~l 230 (246)
T TIGR03870 151 DPRKLVSEVATGKADLAVAFAPEVARYVKASPEPLRMTVIPDDATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALAKA 230 (246)
T ss_pred CHHHHHHHHHcCCCCEEEeeHHhHHHHHHhCCCCceEEeccccccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHHHh
Confidence 357899999999999999998888787765432232 33221 112 36999999997 999999999999
Q ss_pred hhcCcHHHHHHHh
Q 039381 74 SEEGKLRELEEAM 86 (138)
Q Consensus 74 ~~~G~~~~l~~kW 86 (138)
+ +++++|.++|
T Consensus 231 ~--~~~~~i~~~y 241 (246)
T TIGR03870 231 K--PRIDAILKEE 241 (246)
T ss_pred H--HHHHHHHHHc
Confidence 9 4999999999
No 21
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=98.95 E-value=9.7e-09 Score=73.28 Aligned_cols=86 Identities=22% Similarity=0.385 Sum_probs=73.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcC-CCee-eCCCCCc-ceeEEEEeCCCh-hHHHHHHHHHHHhhcC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNC-KNFT-TGPTYSV-GGFGFAFPKDSA-YLADFSQAILQLSEEG 77 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~-~~~~-~~~~~~~-~~~g~a~~Kgsp-l~~~in~~l~~l~~~G 77 (138)
+..+++..+++.+|.+|++||++.+.+.+.+..++.. ..+. +...... ..++++++++++ +.+.++++|..+.++|
T Consensus 130 ~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 209 (219)
T smart00062 130 IVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFAVRKGDPELLDKINKALKELKADG 209 (219)
T ss_pred EEEcCCHHHHHHHhhcCcccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEEEECCCHHHHHHHHHHHHHHHhCc
Confidence 4567888999999999999999999998888776652 3366 5555544 789999999986 9999999999999999
Q ss_pred cHHHHHHHhc
Q 039381 78 KLRELEEAML 87 (138)
Q Consensus 78 ~~~~l~~kW~ 87 (138)
++++|.+||+
T Consensus 210 ~~~~i~~~~~ 219 (219)
T smart00062 210 TLKKIYEKWF 219 (219)
T ss_pred hHHHHHhccC
Confidence 9999999996
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=98.94 E-value=1.4e-08 Score=72.63 Aligned_cols=86 Identities=22% Similarity=0.366 Sum_probs=71.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCC--CCCcceeEEEEeCCCh-hHHHHHHHHHHHhhcC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGP--TYSVGGFGFAFPKDSA-YLADFSQAILQLSEEG 77 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~--~~~~~~~g~a~~Kgsp-l~~~in~~l~~l~~~G 77 (138)
+..+++.++++++|.+|++|+++.+.+.+.++.++....+. +.. ......++|+.+++++ +.+.+|++|.+|+++|
T Consensus 129 ~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~g 208 (218)
T cd00134 129 VVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPELKIVGPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADG 208 (218)
T ss_pred EEEeCCHHHHHHHHHcCCccEEEeccHHHHHHHHhcCCCcEEeccccCCCccceEEEEcCCCHHHHHHHHHHHHHHHhCc
Confidence 56788899999999999999999998988887766522366 544 3445567788888775 9999999999999999
Q ss_pred cHHHHHHHhc
Q 039381 78 KLRELEEAML 87 (138)
Q Consensus 78 ~~~~l~~kW~ 87 (138)
++++|.+|||
T Consensus 209 ~~~~i~~~~~ 218 (218)
T cd00134 209 ELKKISKKWF 218 (218)
T ss_pred cHHHHHHhhC
Confidence 9999999996
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=98.88 E-value=1.9e-08 Score=75.13 Aligned_cols=82 Identities=11% Similarity=0.074 Sum_probs=64.3
Q ss_pred cCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCC------CcceeEEEEeCCCh-hHHHHHHHHHHHhhc
Q 039381 5 IFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTY------SVGGFGFAFPKDSA-YLADFSQAILQLSEE 76 (138)
Q Consensus 5 ~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~------~~~~~g~a~~Kgsp-l~~~in~~l~~l~~~ 76 (138)
+.+.++++++|.+|++||++.|..++.+++++....+. ..... ...+++|+++++++ |++.+|.+|.++.
T Consensus 140 ~~~~~~~~~~l~~G~~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~-- 217 (232)
T TIGR03871 140 ESPPGRMVEDLAAGEIDVAIVWGPIAGYFAKQAGPPLVVVPLLPEDGGIPFDYRIAMGVRKGDKAWKDELNAVLDRRQ-- 217 (232)
T ss_pred cCCHHHHHHHHHcCCcCEEEeccHHHHHHHHhCCCCceeeccccCCCCCCccceEEEEEecCCHHHHHHHHHHHHHHH--
Confidence 34789999999999999999998888888776432344 33211 22357889999976 9999999999986
Q ss_pred CcHHHHHHHhcC
Q 039381 77 GKLRELEEAMLS 88 (138)
Q Consensus 77 G~~~~l~~kW~~ 88 (138)
+++++|.+||.-
T Consensus 218 ~~~~~i~~kyg~ 229 (232)
T TIGR03871 218 AEIDAILREYGV 229 (232)
T ss_pred HHHHHHHHHcCC
Confidence 489999999964
No 24
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=98.87 E-value=1.3e-08 Score=92.25 Aligned_cols=89 Identities=10% Similarity=0.014 Sum_probs=74.3
Q ss_pred CeeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcC-CCee-eCC-CCCcceeEEEEeCCCh-hHHHHHHHHHHHhhc
Q 039381 1 NIEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNC-KNFT-TGP-TYSVGGFGFAFPKDSA-YLADFSQAILQLSEE 76 (138)
Q Consensus 1 ~i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~-~~~~-~~~-~~~~~~~g~a~~Kgsp-l~~~in~~l~~l~~~ 76 (138)
+++.|++..++++||.+|++||++.+.+++.|++++.. ..+. ++. ......+.|+++|+++ |++.+|++|..+.++
T Consensus 187 ~i~~~~s~~~al~av~~G~~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~lnkal~~i~~~ 266 (1197)
T PRK09959 187 TIISFTNLYQALASVSAGQNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKESVILNEVLNRFVDALTNE 266 (1197)
T ss_pred EEEeCCCHHHHHHHHHcCCCCEEEccHHHHHHHHhcccccceEEEeeccCCCCceeEEEcCCcHHHHHHHHHHHHhCCHH
Confidence 46899999999999999999999999999999988742 2344 332 2334557789999988 899999999999999
Q ss_pred CcHHHHHHHhcCCC
Q 039381 77 GKLRELEEAMLSPY 90 (138)
Q Consensus 77 G~~~~l~~kW~~~~ 90 (138)
|.. +|++||++..
T Consensus 267 ~~~-~i~~kW~~~~ 279 (1197)
T PRK09959 267 VRY-EVSQNWLDTG 279 (1197)
T ss_pred HHH-HHHHhccCCC
Confidence 998 9999999764
No 25
>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=98.24 E-value=5.4e-06 Score=62.74 Aligned_cols=71 Identities=17% Similarity=0.077 Sum_probs=57.5
Q ss_pred eecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcC---CCee-eCCCCCcceeEEEEeCC-Ch-hHHHHHHHHHHH
Q 039381 3 EPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNC---KNFT-TGPTYSVGGFGFAFPKD-SA-YLADFSQAILQL 73 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~---~~~~-~~~~~~~~~~g~a~~Kg-sp-l~~~in~~l~~l 73 (138)
....+.++++++|.+|++||++.+.+.+..+..+.+ ..+. ++..+....++|+++|+ ++ +++.||++|..+
T Consensus 178 ~~~~~~~~~~~al~~G~~Da~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 178 VFSGSHDASALAVANGKVDAATNNSSAIGRLKKRGPSDMKKVRVIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred eecCchHHHHHHHHcCCCCeEEecHHHHHHHHHhCccchhheEEEEecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 344567889999999999999999998877766542 2477 77667677899999999 66 999999999864
No 26
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=97.85 E-value=2.9e-05 Score=60.90 Aligned_cols=80 Identities=16% Similarity=0.030 Sum_probs=64.5
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeC--CCh-hHHHHHHHHHHHhhcC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPK--DSA-YLADFSQAILQLSEEG 77 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~K--gsp-l~~~in~~l~~l~~~G 77 (138)
++.+++..++ ++..|++||++.+.++...+.++ .+. + ++......+++.+| ++| +++.+|..+.+| +|
T Consensus 137 iv~~~gs~ea--a~~~G~aDaivd~~~~~~~l~~~---~L~~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~g 208 (287)
T PRK00489 137 VVELSGAVEV--APRLGLADAIVDVVSTGTTLRAN---GLKIV-EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--QG 208 (287)
T ss_pred EEECCCchhh--hhcCCcccEEEeeHHHHHHHHHC---CCEEE-EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--HH
Confidence 4567766665 78889999999887777666553 377 7 56666679999999 676 889999999999 59
Q ss_pred cHHHHHHHhcCC
Q 039381 78 KLRELEEAMLSP 89 (138)
Q Consensus 78 ~~~~l~~kW~~~ 89 (138)
.+++++.|||+.
T Consensus 209 ~l~a~~~k~~~~ 220 (287)
T PRK00489 209 VLRARESKYLMM 220 (287)
T ss_pred HHHhhceEEEEE
Confidence 999999999985
No 27
>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=97.73 E-value=0.00015 Score=56.19 Aligned_cols=79 Identities=16% Similarity=0.111 Sum_probs=58.4
Q ss_pred ecC-CHHHHHHHHHcCCceEEEecHHHHHHHHHhc-C---CCee-eCCCCCcceeEEEEeCC-Ch-hHHHHHHHHHHHhh
Q 039381 4 PIF-SENRHRQALTSGEIAAAFLEVPYVKLFLAKN-C---KNFT-TGPTYSVGGFGFAFPKD-SA-YLADFSQAILQLSE 75 (138)
Q Consensus 4 ~~~-~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~-~---~~~~-~~~~~~~~~~g~a~~Kg-sp-l~~~in~~l~~l~~ 75 (138)
.|. +.++++++|.+|++||++.+.+.+..+.+.. . ..+. +...-.....+++++++ .+ +++.++++|.++.+
T Consensus 172 ~~~~~~~~~~~al~~G~vDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~ 251 (288)
T TIGR03431 172 TFSGSHEAAILAVANGTVDAATTNDENLDRMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHK 251 (288)
T ss_pred eecCchHHHHHHHHcCCCCeEeccHHHHHHHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCC
Confidence 355 6788999999999999999988777766532 2 1244 33222223468999999 45 99999999999999
Q ss_pred cCcHHHH
Q 039381 76 EGKLREL 82 (138)
Q Consensus 76 ~G~~~~l 82 (138)
+++.+.+
T Consensus 252 ~~~~~~~ 258 (288)
T TIGR03431 252 TDKACFE 258 (288)
T ss_pred CcHHHHH
Confidence 9776643
No 28
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=97.49 E-value=0.00071 Score=55.27 Aligned_cols=82 Identities=16% Similarity=0.232 Sum_probs=68.6
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCC-CcceeEEEEeCCC--hhHHHHHHHHHHHhhcCcHHHHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTY-SVGGFGFAFPKDS--AYLADFSQAILQLSEEGKLRELE 83 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~-~~~~~g~a~~Kgs--pl~~~in~~l~~l~~~G~~~~l~ 83 (138)
+.+|.+..+..|++|-.|.|++.+..+.+-.++ +.+...+ ...+.+..+|.++ .|...++..+.+++++|.++.|.
T Consensus 164 ~~~dLle~v~~Gkldytiads~~is~~q~i~P~-laVafd~tde~~v~Wy~~~~dd~tL~a~ll~F~~~~~e~g~larle 242 (473)
T COG4623 164 GVEDLLEMVAEGKLDYTIADSVEISLFQRVHPE-LAVAFDLTDEQPVAWYLPRDDDSTLSAALLDFLNEAKEDGLLARLE 242 (473)
T ss_pred cHHHHHHHHhcCCcceeeeccHHHHHHHHhCcc-ceeeeecccccCceeeccCCchHHHHHHHHHHHHHhhcchHHHHHH
Confidence 568899999999999999999988877776775 5533333 3477999999964 49999999999999999999999
Q ss_pred HHhcCC
Q 039381 84 EAMLSP 89 (138)
Q Consensus 84 ~kW~~~ 89 (138)
+||++-
T Consensus 243 eky~gH 248 (473)
T COG4623 243 EKYLGH 248 (473)
T ss_pred HHHhcc
Confidence 999973
No 29
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=96.37 E-value=0.045 Score=42.64 Aligned_cols=86 Identities=21% Similarity=0.200 Sum_probs=59.5
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcC-CCee-eC-C---------CCC---------cceeEEEEeCCC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNC-KNFT-TG-P---------TYS---------VGGFGFAFPKDS 60 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~-~~~~-~~-~---------~~~---------~~~~g~a~~Kgs 60 (138)
.+.|++..+++.+|..|++|+.+........+++... ..+. .+ + ++. ...+|+++|||-
T Consensus 135 ~Vpy~G~~~~~~allgG~vd~~~~~~~~~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gt 214 (274)
T PF03401_consen 135 HVPYDGGAEALTALLGGHVDAAFGSPGEALPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGT 214 (274)
T ss_dssp EEE-SSHHHHHHHHHTTSSSEEEEEHHHHHHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS
T ss_pred EEEeCCccHHHHHHhCCeeeEEeecHHHHHHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCC
Confidence 5789999999999999999999987555544444311 1111 11 0 011 123699999996
Q ss_pred h--hHHHHHHHHHHHhhcCcHHHHHHHhc
Q 039381 61 A--YLADFSQAILQLSEEGKLRELEEAML 87 (138)
Q Consensus 61 p--l~~~in~~l~~l~~~G~~~~l~~kW~ 87 (138)
| .++.+..++.+..++-++++..++-.
T Consensus 215 p~~~~~~l~~a~~~~~~~pe~~~~~~~~g 243 (274)
T PF03401_consen 215 PDEIVDKLADAIKKALEDPEFQEFLEKMG 243 (274)
T ss_dssp -HHHHHHHHHHHHHHHT-HHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHHHhCCHHHHHHHHHCC
Confidence 5 89999999999999999988777643
No 30
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=95.19 E-value=0.095 Score=39.47 Aligned_cols=82 Identities=16% Similarity=0.154 Sum_probs=59.9
Q ss_pred cCCHHHHHHHHHcCCceEEEecHHHHHHHHHhc---CCCee-eCCCCCcceeEEEEeCC-Ch-hHHHHHHHHHHHhhcCc
Q 039381 5 IFSENRHRQALTSGEIAAAFLEVPYVKLFLAKN---CKNFT-TGPTYSVGGFGFAFPKD-SA-YLADFSQAILQLSEEGK 78 (138)
Q Consensus 5 ~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~---~~~~~-~~~~~~~~~~g~a~~Kg-sp-l~~~in~~l~~l~~~G~ 78 (138)
..+....+.+|.+|++||.+.+......+.... ...+. +...-......++++++ ++ +++.|-.+|..|..+-.
T Consensus 143 ~~~~~~~~~~l~~G~~Da~~~~~~~~~~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~~~ 222 (243)
T PF12974_consen 143 VGSHDAVLEALLNGKADAAAIPSDAFERLEAEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKDPE 222 (243)
T ss_dssp EE-HHHHHHHHHTTSSSEEEEEHHHHHHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSSHH
T ss_pred eCCHHHHHHHHHcCCccEEEEechhHHHHHHccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCChh
Confidence 457788999999999999999888777766542 34477 65544445678888888 44 89999999999999766
Q ss_pred HHHHHHHh
Q 039381 79 LRELEEAM 86 (138)
Q Consensus 79 ~~~l~~kW 86 (138)
-.++.+.+
T Consensus 223 ~~~~l~~~ 230 (243)
T PF12974_consen 223 GKAILDAF 230 (243)
T ss_dssp HHHHHHHT
T ss_pred hHHHHHhc
Confidence 66666665
No 31
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.10 E-value=0.097 Score=42.01 Aligned_cols=85 Identities=12% Similarity=0.062 Sum_probs=62.4
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhc-CCCee-e-CCCC-----------------CcceeEEEEeCCCh
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKN-CKNFT-T-GPTY-----------------SVGGFGFAFPKDSA 61 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~-~~~~~-~-~~~~-----------------~~~~~g~a~~Kgsp 61 (138)
.++|+...+++++|..|++|+.+...+...-+++.. -..+. . .+.. ...-.||..|+|-|
T Consensus 179 ~Vpy~g~gea~taLlgg~v~a~~~~~se~~~~vksG~lr~Lav~s~eRl~~~pdvPT~~E~G~~~~~~~wrgvfap~g~~ 258 (319)
T COG3181 179 YVPYKGGGEALTALLGGHVDAGSTNLSELLSQVKSGTLRLLAVFSEERLPGLPDVPTLKEQGYDVVMSIWRGVFAPAGTP 258 (319)
T ss_pred EEeecCccHHHHHHhcCceeeeecChhhhhhhhccCceEEEEeechhhcCCCCCCCChHhcCCceeeeeeeEEEeCCCCC
Confidence 578999999999999999999999877666555542 11111 1 1110 12336788899943
Q ss_pred --hHHHHHHHHHHHhhcCcHHHHHHHh
Q 039381 62 --YLADFSQAILQLSEEGKLRELEEAM 86 (138)
Q Consensus 62 --l~~~in~~l~~l~~~G~~~~l~~kW 86 (138)
..+.++.+++++.++.++++..++-
T Consensus 259 ~e~~~~~~~a~kk~l~s~e~~~~~~~~ 285 (319)
T COG3181 259 DEIIAKLSAALKKALASPEWQKRLKEL 285 (319)
T ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHhc
Confidence 9999999999999999998777663
No 32
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=94.09 E-value=0.22 Score=38.98 Aligned_cols=34 Identities=21% Similarity=0.277 Sum_probs=26.9
Q ss_pred ecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhc
Q 039381 4 PIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKN 37 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~ 37 (138)
.+.+.++++++|.+|++||++...|.......+.
T Consensus 161 v~~~~~~~~~al~~G~vDa~~~~ep~~~~~~~~~ 194 (314)
T PRK11553 161 TYLTPADARAAFQQGNVDAWAIWDPYYSAALLQG 194 (314)
T ss_pred EecChHHHHHHHHcCCCCEEEEcCcHHHHHHhcC
Confidence 3557788999999999999998878776655543
No 33
>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=93.35 E-value=0.0098 Score=41.24 Aligned_cols=32 Identities=19% Similarity=0.170 Sum_probs=20.8
Q ss_pred CCCCCCCC-CCCccCCcccccccceeeeehhhh
Q 039381 89 PYNCSTKE-NNEDLEGLGLRSFQDEQSSPSQSR 120 (138)
Q Consensus 89 ~~~c~~~~-~~~~~~~l~~~~~~G~F~~~g~~~ 120 (138)
.+.|.... ....+.+|+++|++|+|+++++|+
T Consensus 116 ~~~c~~~~~~~~~~~~l~l~~~~g~F~il~~G~ 148 (148)
T PF00060_consen 116 KSECSSKEDDSNEPVPLTLDNLAGAFLILLIGL 148 (148)
T ss_dssp TSSSSHHHHSTT---S--SHHHHHHHHHHHHHH
T ss_pred CCCCCCCCccCCCCCcccHHHHHHHHHHHHHhC
Confidence 45787643 256899999999999999998864
No 34
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=92.97 E-value=0.65 Score=36.96 Aligned_cols=82 Identities=13% Similarity=0.099 Sum_probs=58.9
Q ss_pred ecCC-HHHHHHHHHcCCceEEEecHHHHHHHHHhcC----CCee-eCCCCCcceeEEEEeCC-Ch-hHHHHHHHHHHHhh
Q 039381 4 PIFS-ENRHRQALTSGEIAAAFLEVPYVKLFLAKNC----KNFT-TGPTYSVGGFGFAFPKD-SA-YLADFSQAILQLSE 75 (138)
Q Consensus 4 ~~~~-~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~----~~~~-~~~~~~~~~~g~a~~Kg-sp-l~~~in~~l~~l~~ 75 (138)
.|.. .+.++.+|.+|++|+...............+ +.+. +...-......|+++++ ++ ++++|-+++..|-+
T Consensus 181 ~~~G~H~~a~~aV~nG~vDva~~~~~~~~~~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 181 IFSGGHDAAVLAVANGQVDVAAVNSSARGLLKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred eccChHHHHHHHHHcCCceEEeccHHHHhhhhhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHHhcCc
Confidence 4555 7889999999999999887665555444332 2466 66666667789999998 44 99999999999987
Q ss_pred cCcHHHHHHH
Q 039381 76 EGKLRELEEA 85 (138)
Q Consensus 76 ~G~~~~l~~k 85 (138)
+-....+.+-
T Consensus 261 ~~~~~~l~~~ 270 (299)
T COG3221 261 TEDKKILLDL 270 (299)
T ss_pred cccchHHHHh
Confidence 3333334433
No 35
>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=92.68 E-value=0.29 Score=35.78 Aligned_cols=59 Identities=22% Similarity=0.158 Sum_probs=42.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCCCh
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKDSA 61 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kgsp 61 (138)
++.+.+..+.+++|.+|++|+.+...........+.- .++ +.........++++++++.
T Consensus 25 ~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~-~~~~i~~~~~~~~~~l~~~~~s~ 84 (216)
T PF09084_consen 25 IVFFGGGGDVLEALASGKADIAVAGPDAVLFARAKGA-DIKIIAASYQSSPNALVVRKDSG 84 (216)
T ss_dssp EEEESSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTS-TEEEEEEEEEECCEEEEEETTTS
T ss_pred EEEecChhHHHHHHhcCCceEEeccchHHHHHHhcCC-eeEEEEEecCCCceEEEEeccCC
Confidence 5678888999999999999998876554443334333 367 6655555667888887755
No 36
>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=87.83 E-value=2.5 Score=32.75 Aligned_cols=66 Identities=20% Similarity=0.312 Sum_probs=41.2
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCC--CC-cceeEEEEeCC----Ch-hHHHHHHHHHHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPT--YS-VGGFGFAFPKD----SA-YLADFSQAILQL 73 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~--~~-~~~~g~a~~Kg----sp-l~~~in~~l~~l 73 (138)
+.+++..+|.+|++||++...|......++. ..+. .... .. ....+++++++ +| +.+.+.+++.+.
T Consensus 135 ~~~~~~~al~~G~vDa~~~~~p~~~~~~~~g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~a~~~a 209 (300)
T TIGR01729 135 KPPQIVAAWQRGDIDAAYVWPPALSELLKSG-KVISDSEQVGAWGAPTFDGWVVRKDFAEKNPEFVAAFTKVLADA 209 (300)
T ss_pred CcHHHHHHHHcCCcCEEEEecHHHHHHHhcC-cEEecchhccccCCCceeEEEECHHHHHHCHHHHHHHHHHHHHH
Confidence 4578999999999999999888776554432 2122 1111 11 12346777655 56 777777666654
No 37
>smart00094 TR_FER Transferrin.
Probab=87.72 E-value=1.8 Score=35.01 Aligned_cols=57 Identities=25% Similarity=0.214 Sum_probs=35.7
Q ss_pred eecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee--eCCCCC------cceeEEEE-eCCCh
Q 039381 3 EPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT--TGPTYS------VGGFGFAF-PKDSA 61 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~--~~~~~~------~~~~g~a~-~Kgsp 61 (138)
+.-.+..++++++++|++|+++.|.... |... .+..+. +.+... ...|++|+ +|+++
T Consensus 32 v~~~s~~~Ci~~I~~g~AD~a~ldg~~~-y~A~-~~~~l~pi~~E~~~~~~~~~~~Y~aVaVVkk~S~ 97 (332)
T smart00094 32 VSASSTEECIKAIQKGEADAVTLDGGDV-YTAG-KPYNLVPVFAENYGSEEEPETGYYAVAVVKKGSA 97 (332)
T ss_pred EEcCCHHHHHHHHHCCCCCEEEECcHHH-Hhhc-ccCCceEEEEEeeccCCCCCceeEEEEEEECCCC
Confidence 4557889999999999999999985532 3222 222233 322221 25677766 46665
No 38
>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=85.82 E-value=1.4 Score=33.17 Aligned_cols=59 Identities=12% Similarity=0.062 Sum_probs=34.2
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCCCh
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKDSA 61 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kgsp 61 (138)
++.+++.++.+++|.+|++|..+...........+. ..+. +..........++++++++
T Consensus 33 ~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g-~~~~~i~~~~~~~~~~~v~~~~~~ 92 (288)
T TIGR01728 33 WVEFPAGPPALEALGAGSLDFGYIGPGPALFAYAAG-ADIKAVGLVSDNKATAIVVIKGSP 92 (288)
T ss_pred EEecCCCcHHHHHHhcCCccccccCCcHHHHHHhcC-CCEEEEEEecCCCceEEEECCCCC
Confidence 456778889999999999999765432222222222 2355 4322222456666666554
No 39
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=85.82 E-value=5.2 Score=31.04 Aligned_cols=43 Identities=14% Similarity=0.221 Sum_probs=32.3
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe-cHHHHHHHHHhcCCCee-eC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL-EVPYVKLFLAKNCKNFT-TG 44 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~-d~~~l~~~~~~~~~~~~-~~ 44 (138)
++.|++..+..+||.+|++|+-+. ..+.+..+.+.++..+. ++
T Consensus 50 ~~~f~d~~~~~~Al~~G~ID~~~~q~~~~l~~~~~~~g~~lv~v~ 94 (258)
T TIGR00363 50 LVEFNDYALPNEAVSKGDLDANAFQHKPYLDQDAKAKGYKLVAVG 94 (258)
T ss_pred EEEeCCcHHHHHHHHcCCCCeEecCCHHHHHHHHHhCCCcEEEEe
Confidence 678999999999999999999865 66766655555443355 54
No 40
>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=85.32 E-value=2.7 Score=32.57 Aligned_cols=25 Identities=20% Similarity=0.199 Sum_probs=21.7
Q ss_pred eeecCCHHHHHHHHHcCCceEEEec
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLE 26 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d 26 (138)
++.|++..+.+++|.+|++|..+..
T Consensus 31 ~~~~~~~~~~~~al~~G~iD~~~~~ 55 (300)
T TIGR01729 31 WRKFDSGADISTALASGNVPIGVIG 55 (300)
T ss_pred EEecCcHHHHHHHHHcCCCCEeccC
Confidence 5678888899999999999988754
No 41
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=85.16 E-value=1.7 Score=33.44 Aligned_cols=77 Identities=31% Similarity=0.516 Sum_probs=53.9
Q ss_pred CeeecCCHHHHHHHHHcCCceEEEe-cHHHHHHHHHhcCCCee-eCCCCC----------------cceeEEEEeCCChh
Q 039381 1 NIEPIFSENRHRQALTSGEIAAAFL-EVPYVKLFLAKNCKNFT-TGPTYS----------------VGGFGFAFPKDSAY 62 (138)
Q Consensus 1 ~i~~~~~~~e~~~aL~~G~vdA~i~-d~~~l~~~~~~~~~~~~-~~~~~~----------------~~~~g~a~~Kgspl 62 (138)
+++.|++..+.-.||.+|++||-+. ..+.+..+.+.+...+. ++..+. .++--||+|.+
T Consensus 29 evv~f~D~~~~N~AL~~G~iDaN~fQh~~yl~~~n~~~~~~L~~v~~~~~~p~glYS~k~~sl~~lp~Ga~VaIpnD--- 105 (237)
T PF03180_consen 29 EVVEFSDYVQPNEALADGEIDANFFQHIPYLEQFNKENGYNLVPVGPTYIEPMGLYSKKYKSLDDLPDGATVAIPND--- 105 (237)
T ss_dssp EEEEESSTTHHHHHHHTTSSSEEEEEEHHHHHHHHHHHT--EEEEEEEEE---EEEESSSSSGGGS-TTEEEEEESS---
T ss_pred EEEEecchhhcChHHHCCCcceeccCCHHHHHHHHHHCCCcEEEecceeEEeEEEeecccCchhhcCCCCEEEEeCC---
Confidence 3688999999999999999999777 68888888777655577 665431 13344555543
Q ss_pred HHHHHHHHHHHhhcCcHH
Q 039381 63 LADFSQAILQLSEEGKLR 80 (138)
Q Consensus 63 ~~~in~~l~~l~~~G~~~ 80 (138)
-....++|.-|.+-|.+.
T Consensus 106 ~sN~~RaL~lLq~aGLI~ 123 (237)
T PF03180_consen 106 PSNQARALKLLQEAGLIT 123 (237)
T ss_dssp HHHHHHHHHHHHHTTSEE
T ss_pred ccchhHHHHHHHhCCeEE
Confidence 234667788888888663
No 42
>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=84.86 E-value=3.7 Score=30.05 Aligned_cols=80 Identities=14% Similarity=-0.004 Sum_probs=43.7
Q ss_pred ecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCC-CCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHH
Q 039381 4 PIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPT-YSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLRE 81 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~-~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~ 81 (138)
...+..+.+..+.+|++|+.+.....+... ..... .. ++.. .....|++++.|+++-.+.-.+.|.-| -+-+-++
T Consensus 134 ~~~~~~~~~~~~~~Ge~~~~~~~~~~~~~~-~~~~~-~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl-~s~e~q~ 210 (216)
T TIGR01256 134 YGEDVRQALQFVETGNAPAGIVALSDVIPS-KKVGS-VATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYL-KSPEAKE 210 (216)
T ss_pred ecCcHHHHHHHHHcCCCCEEeeehhhhccc-CCccE-EEEeCccccCCccccEEEEECCCChHHHHHHHHHH-cCHHHHH
Confidence 345677889999999999988754322111 11121 22 4433 234568999999876443333333222 2223345
Q ss_pred HHHHh
Q 039381 82 LEEAM 86 (138)
Q Consensus 82 l~~kW 86 (138)
+..+|
T Consensus 211 ~~~~~ 215 (216)
T TIGR01256 211 ILRKY 215 (216)
T ss_pred HHHHc
Confidence 55444
No 43
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=84.68 E-value=3.2 Score=32.37 Aligned_cols=60 Identities=12% Similarity=-0.046 Sum_probs=34.2
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eC-CCCCcceeEEEEeCCChh
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TG-PTYSVGGFGFAFPKDSAY 62 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~-~~~~~~~~g~a~~Kgspl 62 (138)
++.+++..+...+|.+|++|..+...+........ ...+. ++ .........+++++++++
T Consensus 60 ~~~~~~~~~~~~aL~~G~iDia~~~~~~~~~~~~~-g~~~~~v~~~~~~~~~~~lvv~~~s~i 121 (314)
T PRK11553 60 WVEFPAGPQMLEALNVGSIDLGSTGDIPPIFAQAA-GADLVYVGVEPPKPKAEVILVAENSPI 121 (314)
T ss_pred EEECCCcHHHHHHHHcCCCCEEccCCHHHHHHHhC-CCCEEEEEEecCCCcceEEEEeCCCCC
Confidence 34566667899999999999988653222111111 21234 33 223344456677776654
No 44
>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=84.04 E-value=4.9 Score=31.03 Aligned_cols=24 Identities=29% Similarity=0.368 Sum_probs=21.6
Q ss_pred eecCCHHHHHHHHHcCCceEEEec
Q 039381 3 EPIFSENRHRQALTSGEIAAAFLE 26 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~d 26 (138)
..|.+..+++++|.+|++|+++.+
T Consensus 174 v~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 174 VEYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred hhcCCHHHHHHHHHCCCccEEEEe
Confidence 467788999999999999999987
No 45
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=83.56 E-value=3.6 Score=30.82 Aligned_cols=59 Identities=19% Similarity=0.063 Sum_probs=35.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCC-----CcceeEEEEeCCChh
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTY-----SVGGFGFAFPKDSAY 62 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~-----~~~~~g~a~~Kgspl 62 (138)
++.+++..+..+++++|++|.++..........++. . +. +.... ......|+++++++.
T Consensus 33 ~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~-~-~~~la~~~~~~g~~~~~~~ivv~~ds~i 97 (243)
T PF12974_consen 33 LVPADDYAEFIEALRSGEIDLAFMGPLPYVQARQRA-G-VEPLATPVGPDGSPSYRSVIVVRADSPI 97 (243)
T ss_dssp EE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-S-EEEEEEEEETTT-SCEEEEEEEETTSS-
T ss_pred EEEcCCHHHHHHHHHcCCccEEEECcHHHHHHhhcC-c-EEEEEEecccCCCcceeEEEEEECCCCC
Confidence 567889999999999999999998744333333332 2 33 22211 245677889999875
No 46
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=81.19 E-value=2.5 Score=32.96 Aligned_cols=41 Identities=17% Similarity=0.217 Sum_probs=30.2
Q ss_pred eeecCCHHHHHHHHHcCCceEEE-ecHHHHHHHHHhcCCCee
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF-LEVPYVKLFLAKNCKNFT 42 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i-~d~~~l~~~~~~~~~~~~ 42 (138)
++.|++..+.+++|.+|++|+.. ...+++..+....+..+.
T Consensus 63 l~~f~~~~~~~~ALa~GdID~~~~qh~~~l~~~~~~~g~~l~ 104 (271)
T PRK11063 63 LVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLV 104 (271)
T ss_pred EEEecCcHHHHHHHHcCCcceecccCHHHHHHHHHHcCCcEE
Confidence 57788999999999999999954 466776655554443355
No 47
>PRK03537 molybdate ABC transporter periplasmic molybdate-binding protein; Provisional
Probab=80.90 E-value=12 Score=27.23 Aligned_cols=77 Identities=8% Similarity=-0.015 Sum_probs=44.1
Q ss_pred HHHHHH-HHHcCCceEEEecHHHHHHHHHhc-CCCee-eCCC-CCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHHHH
Q 039381 8 ENRHRQ-ALTSGEIAAAFLEVPYVKLFLAKN-CKNFT-TGPT-YSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLRELE 83 (138)
Q Consensus 8 ~~e~~~-aL~~G~vdA~i~d~~~l~~~~~~~-~~~~~-~~~~-~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~l~ 83 (138)
..+.++ .+.+|++|+.+.-...+....... ...+. ++.. .....|.+++-|+++ ..-+...+...+.+-+++.
T Consensus 101 ~~~~~~~~v~~G~adag~vy~s~~~~~~~~~~~~~~i~iP~~~~~~i~y~iav~k~~~---~~A~~F~~fl~s~eaq~i~ 177 (188)
T PRK03537 101 GRNAAEWLIENKQADIFIGYASNAPLAQREVPSLQVVDLPEPLAVGAEYGLAILKDAS---PQAKRLADFLLSPKGQAIL 177 (188)
T ss_pred cchHHHHHHHCCCCCEEEEEecHHHHHhccCCCCeEEeCCCCcceeeeeeEEEecCCh---HHHHHHHHHHhCHHHHHHH
Confidence 345556 778999998765433322211111 12223 4433 345678999999876 3344445555666667777
Q ss_pred HHhc
Q 039381 84 EAML 87 (138)
Q Consensus 84 ~kW~ 87 (138)
.+|.
T Consensus 178 ~~~G 181 (188)
T PRK03537 178 AQYG 181 (188)
T ss_pred HHcC
Confidence 7763
No 48
>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=80.85 E-value=15 Score=27.07 Aligned_cols=80 Identities=13% Similarity=0.007 Sum_probs=50.6
Q ss_pred ecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee---eCCCCC--cceeEEEEeCCChhHHHHHHHHHHHhhcCc
Q 039381 4 PIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT---TGPTYS--VGGFGFAFPKDSAYLADFSQAILQLSEEGK 78 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~---~~~~~~--~~~~g~a~~Kgspl~~~in~~l~~l~~~G~ 78 (138)
..++..+.+.++.+|++|+.+.-...+.+. .+.. .+. +.+... ...|++++-++++-.+.....+.-|. +.+
T Consensus 143 ~~~~~~~~~~~v~~g~~d~~~~~~s~~~~~-~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~a~~f~~~L~-s~~ 219 (230)
T PF13531_consen 143 YVPSTSQVLSAVASGEADAGIVYESQAIFA-RQGD-PLSYVYPPDGVNSPPIDYPIAILKNAPHPEAARAFIDFLL-SPE 219 (230)
T ss_dssp EESSHHHHHHHHHTTSSSEEEEEHHHHHHC-TSHT-TEEEEE-STTTSSSEEEEEEEEBTTCTTHHHHHHHHHHHT-SHH
T ss_pred cccchHHHHHHHHcCCCcceeeHHHHHHHh-hcCC-CeEEEECCchhcCCCEEEEEEEecCCCCHHHHHHHHHHHC-CHH
Confidence 456788999999999999999865544222 2222 243 455554 35799999998765555555444444 344
Q ss_pred HHHHHHHh
Q 039381 79 LRELEEAM 86 (138)
Q Consensus 79 ~~~l~~kW 86 (138)
-+++..++
T Consensus 220 ~q~~l~~~ 227 (230)
T PF13531_consen 220 GQQILAKY 227 (230)
T ss_dssp HHHHHHHT
T ss_pred HHHHHHHc
Confidence 66666654
No 49
>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=80.57 E-value=6.7 Score=29.43 Aligned_cols=33 Identities=15% Similarity=0.289 Sum_probs=26.1
Q ss_pred cCCHHHHHHHHHcCCceEEEecHHHHHHHHHhc
Q 039381 5 IFSENRHRQALTSGEIAAAFLEVPYVKLFLAKN 37 (138)
Q Consensus 5 ~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~ 37 (138)
+.+.++++++|++|++|+++...|....+..+.
T Consensus 134 ~~~~~~~~~al~~g~vda~~~~~p~~~~~~~~~ 166 (288)
T TIGR01728 134 YLGPSDARAAFAAGQVDAWAIWEPWGSALVEEG 166 (288)
T ss_pred ecCcHHHHHHHHCCCCCEEEeccchHhHHhhcc
Confidence 345678999999999999999888776655543
No 50
>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=78.63 E-value=6 Score=30.16 Aligned_cols=67 Identities=15% Similarity=0.035 Sum_probs=40.3
Q ss_pred cCCHHHHHHHHHcCCceEEEecHHHHHHH-HHhcCCCee-eCCCCCcceeEEEEeCC-----Ch-hHHHHHHHHHHH
Q 039381 5 IFSENRHRQALTSGEIAAAFLEVPYVKLF-LAKNCKNFT-TGPTYSVGGFGFAFPKD-----SA-YLADFSQAILQL 73 (138)
Q Consensus 5 ~~~~~e~~~aL~~G~vdA~i~d~~~l~~~-~~~~~~~~~-~~~~~~~~~~g~a~~Kg-----sp-l~~~in~~l~~l 73 (138)
+.+.+|.+++|++|.+|+++.....+... ..+..+.+. .+ .....+.+.+.++ ++ +++.|..+..+.
T Consensus 160 ~~~~~e~~~aL~~G~vDg~~~~~~~~~~~~~~ev~~y~~~~~--~~~~~~~~~~n~~~~~~L~~e~q~~i~~a~~~~ 234 (257)
T TIGR00787 160 PMAFSEVYTALQTGVVDGQENPLSNVYSSKFYEVQKYLSMTN--HGYLGYLVVVNKAFWKSLPPDLQAVVKEAAKEA 234 (257)
T ss_pred ccCHHHHHHHHHcCCcccccCCHHHHhhcchhhhcchheecC--CcccceEEEEeHHHHhcCCHHHHHHHHHHHHHH
Confidence 56789999999999999999875443221 111122233 33 2335567888775 22 555565555543
No 51
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=76.61 E-value=7.7 Score=29.23 Aligned_cols=57 Identities=21% Similarity=0.194 Sum_probs=37.8
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhc---CCCee-eCCCCCcceeEEEEeCC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKN---CKNFT-TGPTYSVGGFGFAFPKD 59 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~---~~~~~-~~~~~~~~~~g~a~~Kg 59 (138)
++.|++..+..++|.+|++|+.....+.+....... ...+. +. .....+..+.++++
T Consensus 39 ~~~~~~g~~~~~al~~G~iD~a~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~~g~~lvv~~~ 99 (252)
T PF13379_consen 39 WVQFASGADILEALAAGEIDIAFVLAPALIAIAKGAGGPDVDIVVLA-GLSQNGNALVVRND 99 (252)
T ss_dssp EEEESSHHHHHHHHHCTSSSEEEECTHHHHHHHTTTTT----EEEEE-ECSBSSEEEEECGG
T ss_pred EEEcCCHHHHHHHHHcCCCCEEEechHHHHHHHcCCCCcccceEEee-ccCCCceEEEEcCc
Confidence 578999999999999999999888444444433222 12355 43 24566778888764
No 52
>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=75.84 E-value=11 Score=30.27 Aligned_cols=29 Identities=10% Similarity=0.125 Sum_probs=23.6
Q ss_pred eeecCCHHHHHHHHHcCCceE-EEecHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAA-AFLEVPYV 30 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA-~i~d~~~l 30 (138)
++.|++..++++++.+|++|+ .+.+.+.+
T Consensus 39 ~~~f~~~~~~l~Al~aG~iD~~~~g~~~~~ 68 (328)
T TIGR03427 39 VVQINDYVESINQYTAGKFDGCTMTNMDAL 68 (328)
T ss_pred EEECCChHHHHHHHHcCCCCEEeecCHHHH
Confidence 567999999999999999996 55565544
No 53
>PF00405 Transferrin: Transferrin; InterPro: IPR001156 Transferrins are eukaryotic iron-binding glycoproteins that control the level of free iron in biological fluids []. The proteins have arisen by duplication of a domain, each duplicated domain binding one iron atom. Members of the family include blood serotransferrin (siderophilin); milk lactotransferrin (lactoferrin); egg white ovotransferrin (conalbumin); and membrane-associated melanotransferrin. Additional members of this family include inhibitor of carbonic anhydrase (ICA; mammals), major yolk protein (sea urchins), saxiphilin (frog), pacifastin (crayfish), and TTF-1 (algae). Most family members contain two transferrin-like domains of around 340 amino acids, the result of an ancient duplication event []. Each of the duplicated domains can be further divided into two subdomains that form a cleft inside of which the iron atom is bound in iron-transporting transferrin []. The iron-coordinating residues consist of an aspartic acid, two tyrosines and a histidine, as well as an arginine that coordinates a requisite anion. In addition to iron and anion liganding residues, the transferrin-like domain contains conserved cysteine residues involved in disulphide bond formation. Human lactoferrin is a serine peptidase belonging to MEROPS peptidase family S60, clan SR. It is found at high concentrations in all human secretions, where it plays a major role in mucosal defence. Lactoferrin cleaves IgA1 protease at an arginine-rich region defined by amino acids RRSRRSVR and digests Hap at a similar arginine-rich sequence (VRSRRAAR). Ser259 and Lys73 form a catalytic dyad, reminiscent of a number of bacterial serine proteases. ; GO: 0008199 ferric iron binding, 0006826 iron ion transport, 0006879 cellular iron ion homeostasis, 0005576 extracellular region; PDB: 1JNF_A 1TFD_A 1JW1_A 1DTZ_A 2J4U_X 1I6Q_A 1BIY_A 1CE2_A 1H76_A 1F9B_A ....
Probab=75.28 E-value=6.7 Score=31.57 Aligned_cols=52 Identities=17% Similarity=0.220 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHcCCceEEEecHHHHHHHHH-hcCCCee--eCCCCC------cceeEEEEeC
Q 039381 5 IFSENRHRQALTSGEIAAAFLEVPYVKLFLA-KNCKNFT--TGPTYS------VGGFGFAFPK 58 (138)
Q Consensus 5 ~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~-~~~~~~~--~~~~~~------~~~~g~a~~K 58 (138)
-.+..++++++++|++|+++.|..-+ |... ...+ +. +.+.+. ...|++|+-|
T Consensus 34 ~~s~~dCm~~I~~g~AD~v~ld~~~~-y~A~~~~~~-L~pi~~E~y~~~~~~~~~y~aVAVVk 94 (330)
T PF00405_consen 34 ATSREDCMRRIKKGEADAVTLDGGDV-YIAGLRKYN-LKPIAAEVYGSEEEPEASYYAVAVVK 94 (330)
T ss_dssp ESSHHHHHHHHHTTSSSBEEEEHHHH-HHHHSTTTT-EEEEEEEEESSSSSEESEEEEEEEEE
T ss_pred CCCHHHHHHHHhhccCCEEEeCchhh-hhhhccccC-CEEeeeeeccccccccceeEEEEEEe
Confidence 46889999999999999999995543 3333 3444 44 433332 3458887744
No 54
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=75.23 E-value=4.7 Score=30.80 Aligned_cols=58 Identities=17% Similarity=0.209 Sum_probs=37.7
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCC---hhHHHHHHHHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDS---AYLADFSQAIL 71 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgs---pl~~~in~~l~ 71 (138)
+....-.++.+|++||-+.-.+.+. +..-.| + ++..|.|=|+++|+. |..+.+-++|.
T Consensus 138 th~avA~aVa~G~AD~GvGlr~~A~----~~gL~F-i--pl~~E~YD~virke~~~~~~vr~fi~~L~ 198 (223)
T COG1910 138 THDAVASAVASGRADAGVGLRHAAE----KYGLDF-I--PLGDEEYDFVIRKERLDKPVVRAFIKALK 198 (223)
T ss_pred ccHHHHHHHHcCCCCccccHHHHHH----HcCCce-E--EcccceEEEEEehhHccCHHHHHHHHHhc
Confidence 3445668899999999998544443 222112 2 356889999999984 55555555444
No 55
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=74.54 E-value=4.2 Score=30.68 Aligned_cols=57 Identities=23% Similarity=0.209 Sum_probs=34.2
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCC-Cee-eCCCCCcce-eEEEEeCC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCK-NFT-TGPTYSVGG-FGFAFPKD 59 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~-~~~-~~~~~~~~~-~g~a~~Kg 59 (138)
++.++. +++.++|++|++|+++.-.|......++... .+. .++.+...+ ..+++++.
T Consensus 154 ~~~~~~-~~~~~al~~g~iDa~~~~eP~~~~~~~~g~g~~v~~~~~~~~~~p~~~~~~~~~ 213 (252)
T PF13379_consen 154 LVNVPP-PEMVAALRAGEIDAAVLWEPFASQAEAKGIGKIVADSGDVWGNHPCCVIVARRD 213 (252)
T ss_dssp EEE--G-HHHHHHHHTTS-SEEEEETTHHHHHHHTTS-EEEEEHHHCSTT-B-EEEEEEHH
T ss_pred EEecCH-HHHHHHHhCCCcCEEEecCCHHHHHHhccCCeEEEEeccccCCCCeEEEEECHH
Confidence 344555 8999999999999999988888777655432 122 222233323 33577664
No 56
>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=73.62 E-value=17 Score=26.96 Aligned_cols=61 Identities=15% Similarity=0.005 Sum_probs=35.4
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHH-HHhcCCCee-eCC---CCCcceeEEEEeCCChh
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLF-LAKNCKNFT-TGP---TYSVGGFGFAFPKDSAY 62 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~-~~~~~~~~~-~~~---~~~~~~~g~a~~Kgspl 62 (138)
++.+.+..+.++++++|++|.++......... .+.....+. .-. ........++++++++.
T Consensus 68 ~~~~~~~~~~~~~l~~g~~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~~i 133 (254)
T TIGR01098 68 LFVATDYSAVIEAMRFGRVDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADSPI 133 (254)
T ss_pred EEeCCCHHHHHHHHHcCCccEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCCCC
Confidence 34567888999999999999998764332222 222111122 110 11123357888988764
No 57
>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=73.22 E-value=8 Score=26.81 Aligned_cols=24 Identities=17% Similarity=0.050 Sum_probs=19.4
Q ss_pred eecCCHHHHHHHHHcCCceEEEecH
Q 039381 3 EPIFSENRHRQALTSGEIAAAFLEV 27 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~d~ 27 (138)
+.++ ..+..++|++|++|+++...
T Consensus 43 ~~~~-~~~~~~~l~~g~~D~~~~~~ 66 (218)
T cd00134 43 VEVD-WDGLITALKSGKVDLIAAGM 66 (218)
T ss_pred EeCC-HHHHHHHHhcCCcCEEeecC
Confidence 4444 67899999999999998764
No 58
>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=70.38 E-value=9.8 Score=29.36 Aligned_cols=66 Identities=18% Similarity=0.094 Sum_probs=40.6
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHH-HhcCCCee-eCCCCCcceeEEEEeCC-----Ch-hHHHHHHHHHHHh
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFL-AKNCKNFT-TGPTYSVGGFGFAFPKD-----SA-YLADFSQAILQLS 74 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~-~~~~~~~~-~~~~~~~~~~g~a~~Kg-----sp-l~~~in~~l~~l~ 74 (138)
..+|.+++|++|.||++....+.....- ....+.+. .+ .....+.+++.+. ++ .++.|..+..+..
T Consensus 162 p~~evy~aLq~G~vDg~~~~~~~~~~~~~~ev~~y~~~~~--~~~~~~~~~~n~~~w~~L~~e~q~~l~~~~~~~~ 235 (286)
T PF03480_consen 162 PWSEVYQALQQGVVDGAENSASSIYSLGLYEVAKYFTDTN--HGWSPYAVIMNKDWWDSLPDEDQEALDDAADEAE 235 (286)
T ss_dssp TGGGHHHHHHTTSSSEEEEEHHHHHHTTGGGTSSEEEEEE--EEEEEEEEEEEHHHHHHS-HHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHhcCCcCeEecCHHHHHhcChhhhCCeeEeec--ccCcceEEEEcHHHHhcCCHHHHHHHHHHHHHHH
Confidence 3568999999999999999866653221 11233223 33 4456788888775 22 4555555555443
No 59
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=69.15 E-value=5.3 Score=31.41 Aligned_cols=75 Identities=27% Similarity=0.385 Sum_probs=50.6
Q ss_pred CeeecCCHHHHHHHHHcCCceEEE-ecHHHHHHHHHhc-CCCee-eCCCC----------------CcceeEEEEeCCCh
Q 039381 1 NIEPIFSENRHRQALTSGEIAAAF-LEVPYVKLFLAKN-CKNFT-TGPTY----------------SVGGFGFAFPKDSA 61 (138)
Q Consensus 1 ~i~~~~~~~e~~~aL~~G~vdA~i-~d~~~l~~~~~~~-~~~~~-~~~~~----------------~~~~~g~a~~Kgsp 61 (138)
+|+.|+++.+=-.||.+|++||=. --.|++..+.+.+ +. +. ++... -+++--||+|.+.
T Consensus 60 ~i~~FtDY~~PN~AL~~gdiDaN~FQH~pyL~~~~k~~~~~-Lv~vg~~~i~Pmg~YSkk~ksl~el~~GatIaiPNDp- 137 (268)
T COG1464 60 KIVEFTDYVQPNEALADGDIDANAFQHKPYLDQFNKEHGGK-LVAVGNTHIEPMGLYSKKYKSLAELKDGATIAIPNDP- 137 (268)
T ss_pred EEEEecCCcchhHHHhcCCccchhhhchHHHHHHHHHcCCC-EEEEeeEEeccceecchhcCcHhhCCCCCEEECCCCC-
Confidence 378899999999999999999944 5789999888874 54 76 76543 1345667777651
Q ss_pred hHHHHHHHHHHHhhcCcH
Q 039381 62 YLADFSQAILQLSEEGKL 79 (138)
Q Consensus 62 l~~~in~~l~~l~~~G~~ 79 (138)
..-.++|.=|++.|-+
T Consensus 138 --sN~gRAL~lL~~aGLI 153 (268)
T COG1464 138 --TNEGRALLLLQKAGLI 153 (268)
T ss_pred --CchhHHHHHHHHCCcE
Confidence 1233444445555543
No 60
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=66.84 E-value=14 Score=28.87 Aligned_cols=62 Identities=15% Similarity=0.083 Sum_probs=42.8
Q ss_pred eeecCCHHHHHHHHHcCCceEE--EecHHHHHHHHHhcCCCee-eCCCCCc-ceeEEEEeCCChhHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAA--FLEVPYVKLFLAKNCKNFT-TGPTYSV-GGFGFAFPKDSAYLA 64 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~--i~d~~~l~~~~~~~~~~~~-~~~~~~~-~~~g~a~~Kgspl~~ 64 (138)
++.+.+..+..++|.+|++|.. ....+......... ..+. ++..... ...++..+++++...
T Consensus 65 ~~~~~~~~~~~~~l~~G~~D~a~~~~~~~~~~~~~~~g-~pv~~va~~~~~~~~~~i~~~~~~~i~~ 130 (335)
T COG0715 65 LVEFTGGAPVLEALAAGALDFAVYYTGDTPLIAAGAAG-APVKVVAALVQNGNGIALLVLKDSGIKS 130 (335)
T ss_pred EEEcCCChHHHHHHhcCCcCccccccCchHHHHhhccC-CCeEEeeecccCCceeEEEeccCCCccc
Confidence 5678889999999999999998 44444433322222 2466 6655554 578888888887654
No 61
>TIGR03414 ABC_choline_bnd choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PubMed:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins.
Probab=65.46 E-value=15 Score=28.84 Aligned_cols=53 Identities=15% Similarity=0.187 Sum_probs=36.6
Q ss_pred CHHHHHHHHHcCCceEEEec-HHHH-HHHHHhc-CCCee-eCCCCCcceeEEEEeCC
Q 039381 7 SENRHRQALTSGEIAAAFLE-VPYV-KLFLAKN-CKNFT-TGPTYSVGGFGFAFPKD 59 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d-~~~l-~~~~~~~-~~~~~-~~~~~~~~~~g~a~~Kg 59 (138)
+..-++++|.+|++|+++.- .|.. ..+.+.. ...+. ++.......||+++|+-
T Consensus 44 ~~~~~~~al~~GdiD~~~e~W~p~~~~~~~~~~~~~~l~~lg~~~~~~~~g~~Vp~y 100 (290)
T TIGR03414 44 SVPVTYAGLKDGDLDVFLGNWMPAMEPDIKPYLESGSVEVLGPNLEGAKYTLAVPTY 100 (290)
T ss_pred cHHHHHHHHHcCCceEeccccCCcCHHHHHhhccCCeEEEecccCCCceEEEEEChh
Confidence 56778999999999998854 2222 2222221 22477 88777778899999985
No 62
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=64.64 E-value=16 Score=25.09 Aligned_cols=24 Identities=25% Similarity=0.212 Sum_probs=19.6
Q ss_pred eecCCHHHHHHHHHcCCceEEEecH
Q 039381 3 EPIFSENRHRQALTSGEIAAAFLEV 27 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~d~ 27 (138)
+.+ +..+++++|.+|++|+++...
T Consensus 44 ~~~-~~~~~~~~l~~g~~D~~~~~~ 67 (219)
T smart00062 44 VEV-SFDNLLTALKSGKIDVVAAGM 67 (219)
T ss_pred Eec-cHHHHHHHHHCCcccEEeccc
Confidence 444 678899999999999988753
No 63
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=64.52 E-value=25 Score=27.55 Aligned_cols=25 Identities=24% Similarity=0.187 Sum_probs=21.5
Q ss_pred eeecCCHHHHHHHHHcCCceEEEec
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLE 26 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d 26 (138)
++.+++.++.+++|.+|++|..+..
T Consensus 55 ~~~~~~~~~~~~al~~G~~D~a~~~ 79 (320)
T PRK11480 55 WRKFDSGASIVRALASGDVQIGNLG 79 (320)
T ss_pred EEEeCCHHHHHHHHHCCCCCEECcC
Confidence 5678899999999999999987653
No 64
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=63.89 E-value=48 Score=25.97 Aligned_cols=124 Identities=10% Similarity=-0.040 Sum_probs=62.4
Q ss_pred CCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee--eCCC-CCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHHH
Q 039381 6 FSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT--TGPT-YSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLREL 82 (138)
Q Consensus 6 ~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~--~~~~-~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~l 82 (138)
.+.++..+++.+|++++.+...........+. ..+. .++. ......++++.||+|-.+.-.+.|.-|. +.+.++.
T Consensus 201 ~s~~~~~~~v~~Ge~~i~~~~~~~~~~~~~~g-~~v~~~~P~eG~~~~~~~~ai~k~a~~~e~A~~fidfll-S~e~Q~~ 278 (334)
T TIGR03261 201 HSGSKPCKLAGMGEFPIGISMAYRALKEKKKG-APIDVVFPKEGLGWDIEATAIIKGSKNNDAAKKLVDWSI-SDEAMEL 278 (334)
T ss_pred CCChHHHHHHhCCCceEEEEecHHHHHHHhCC-CCeEEEecCCCCeeeeeeeEEEcCCCCHHHHHHHHHHHc-CHHHHHH
Confidence 45667888999999998875433322222322 2344 3322 1233468999999876555555454443 3333444
Q ss_pred HHHhcCCCCCCCCCCCCccCCccccccc-ceeeee--hhhhhhhHhhhhhhhccC
Q 039381 83 EEAMLSPYNCSTKENNEDLEGLGLRSFQ-DEQSSP--SQSRTREHWLSAWEMENR 134 (138)
Q Consensus 83 ~~kW~~~~~c~~~~~~~~~~~l~~~~~~-G~F~~~--g~~~~~~~~~~~~~~~~~ 134 (138)
..+++....+..... ....+. .++. -++.+- -+.--++.|+..|+.+=+
T Consensus 279 ~~~~~~~~~~~~v~~--~~~~~~-~~~~~~~~~~d~~~~~~~~~~~~~rw~~~~~ 330 (334)
T TIGR03261 279 YAKNYAVVATPGVAK--PDAGFP-KNVEDLLIKNDFVWAAANRDKILEEWSKRYG 330 (334)
T ss_pred HHhcCcccccCCccc--CcccCC-cchhhhcccCCHHHHHHhHHHHHHHHHHHhh
Confidence 455544322221100 000010 1221 122111 135678888988987643
No 65
>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=63.44 E-value=47 Score=26.60 Aligned_cols=30 Identities=17% Similarity=0.148 Sum_probs=23.6
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHh
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAK 36 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~ 36 (138)
+.+++..||.+|+|||++.-.|.+.....+
T Consensus 141 ~~~d~~aAl~~G~VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 141 SDADIVAAFITKDVTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred ChHHHHHHHhcCCCcEEEEcCchHHHHHhC
Confidence 457889999999999998877876655444
No 66
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=63.18 E-value=46 Score=25.77 Aligned_cols=79 Identities=10% Similarity=0.006 Sum_probs=40.1
Q ss_pred HHHHHHHHHcCCceEEEecHHHHHHHHHhc-CCCeeeCCCCCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHHHHHHh
Q 039381 8 ENRHRQALTSGEIAAAFLEVPYVKLFLAKN-CKNFTTGPTYSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLRELEEAM 86 (138)
Q Consensus 8 ~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~-~~~~~~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~l~~kW 86 (138)
.+++..+|.+|++||++.-.+.+.....+. .+.+.....-...--.+++++++.=.+.+..-+..++.+..-+-|.++|
T Consensus 171 ~~~~~~al~~g~vDaa~v~~~~~~~agl~~~~~~i~~e~~~~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 250 (258)
T TIGR00363 171 TSQLPRALDDPKVDLAVINTTYAGQVGLNPQDDGVFVEDKDSPYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAAQKHF 250 (258)
T ss_pred HHHHHHHhhcccccEEEEChHHHHHcCCCcCcCceeecCCCCCeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 356789999999999999877665432211 1112122111122244566665333344444444444444333344443
No 67
>PRK04168 molybdate ABC transporter periplasmic substrate-binding protein; Provisional
Probab=62.56 E-value=59 Score=26.09 Aligned_cols=81 Identities=16% Similarity=0.084 Sum_probs=47.1
Q ss_pred ecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCC---------------------------CcceeEEE
Q 039381 4 PIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTY---------------------------SVGGFGFA 55 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~---------------------------~~~~~g~a 55 (138)
..++..+.+..|.+|++|+.+.-...+.. ..- .+. ++..+ ....|+++
T Consensus 207 ~~~~~~~~~~~v~~G~aDagivy~S~a~~---~~~-~~i~lP~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~pi~y~~a 282 (334)
T PRK04168 207 VRPKEVELLSLLETGNMDYAFIYKSVAVQ---HNL-KYIELPDEINLGNYKYADFYKKVSVTVTGTGKTITAKPIVYGIT 282 (334)
T ss_pred ecccchhhHHHHhcCCccEEEEEeeehhh---CCC-CeeECchhhcCCChhhhhhhhEEEEEecCCCccccCceeeeeee
Confidence 34556789999999999998874333221 111 111 22211 23568999
Q ss_pred EeCCChhHHHHHHHHHHHhhcCcHHHHHHHhcCC
Q 039381 56 FPKDSAYLADFSQAILQLSEEGKLRELEEAMLSP 89 (138)
Q Consensus 56 ~~Kgspl~~~in~~l~~l~~~G~~~~l~~kW~~~ 89 (138)
+.++++-.+.-.+.+.-| .+.+-+++..++.-.
T Consensus 283 i~~~s~n~e~A~~Fi~fl-~S~e~q~il~~~Gf~ 315 (334)
T PRK04168 283 VPKNAPNREAAIEFLKYL-LSEPGGEVLENNGQP 315 (334)
T ss_pred eecCCCCHHHHHHHHHHH-cCHHHHHHHHHcCCC
Confidence 999876544444433333 445557777776543
No 68
>cd08501 PBP2_Lpqw The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic binding fold. LpqW is one of key players in synthesis and transport of the unique components of the mycobacterial cell wall which is a complex structure rich in two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly conserved lipoprotein that transport intermediates from a pathway for mature PIMs production into a pathway for LAMs biosynthesis, thus controlling the relative abundance of these two essential components of cell wall. LpqW is thought to have been adapted by the cell-wall biosynthesis machinery of mycobacteria and other closely related pathogens, evolving to play an important role in PIMs/LAMs biosynthesis. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the LpqW protein. The structural topology of these domains is most similar to
Probab=62.14 E-value=32 Score=28.35 Aligned_cols=68 Identities=16% Similarity=0.029 Sum_probs=37.9
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHH-HHHHHHHhcCCCee-eCCCCCcceeEEEEeCC-----Ch-hHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVP-YVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKD-----SA-YLADFSQAIL 71 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~-~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kg-----sp-l~~~in~~l~ 71 (138)
++.+.+.+..+.+|++|++|.+....+ ......+...+ +. ... .....+.+++..+ ++ +|++|+.+|.
T Consensus 202 ~~~~~~~~~~~~al~~G~iD~~~~~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~l~~N~~~~~~~d~~vR~Ai~~aiD 277 (486)
T cd08501 202 FRAMEDPDAQINALRNGEIDAADVGPTEDTLEALGLLPG-VEVRTG-DGPRYLHLTLNTKSPALADVAVRKAFLKAID 277 (486)
T ss_pred EEecCChHHHHHHHHcCCCceEecCCCHHHHHHhccCCC-eEEEEc-CCCcEEEEEecCCCcccCCHHHHHHHHHhCC
Confidence 456778889999999999998754222 22222222222 44 222 2233455666554 33 5666666654
No 69
>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=61.20 E-value=51 Score=25.15 Aligned_cols=25 Identities=8% Similarity=-0.043 Sum_probs=21.1
Q ss_pred eecCCHHHHHHHHHcCCceEEEecH
Q 039381 3 EPIFSENRHRQALTSGEIAAAFLEV 27 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~d~ 27 (138)
....+..+.+++|.+|++|.++...
T Consensus 64 ~~~~~~~~~~~al~~g~~D~~~~~~ 88 (288)
T TIGR03431 64 FFATDYAGVIEGMRFGKVDIAWYGP 88 (288)
T ss_pred EeCCCHHHHHHHHHcCCccEEEECh
Confidence 4567888999999999999999763
No 70
>cd08512 PBP2_NikA_DppA_OppA_like_7 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=60.59 E-value=37 Score=27.90 Aligned_cols=23 Identities=22% Similarity=0.221 Sum_probs=19.3
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+....+++|++|++|.+.
T Consensus 206 ~~~~~d~~~~~~al~~GevD~~~ 228 (476)
T cd08512 206 IRHVPEAATRRLLLERGDADIAR 228 (476)
T ss_pred EEeCCCHHHHHHHHHcCCcCEec
Confidence 45677888899999999999864
No 71
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=60.29 E-value=13 Score=29.12 Aligned_cols=41 Identities=12% Similarity=0.129 Sum_probs=31.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe-cHHHHHHHHHhcCCCee
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL-EVPYVKLFLAKNCKNFT 42 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~-d~~~l~~~~~~~~~~~~ 42 (138)
++.|++.....+||.+|++|+.+. +.+++..+.+..+..+.
T Consensus 64 lv~fsd~~~~n~AL~~G~ID~n~~qh~~yl~~~~~~~g~~lv 105 (272)
T PRK09861 64 LVGFSGSLLPNDATNHGELDANVFQHRPFLEQDNQAHGYKLV 105 (272)
T ss_pred EEecCchhhHHHHHHcCCcceehhhhHHHHHHHHHhcCCCeE
Confidence 457888888889999999999776 77787776665443355
No 72
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=59.96 E-value=23 Score=27.22 Aligned_cols=57 Identities=19% Similarity=0.113 Sum_probs=28.9
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee---eCC-CC--CcceeEEEEeCCCh-hHHHHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT---TGP-TY--SVGGFGFAFPKDSA-YLADFS 67 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~---~~~-~~--~~~~~g~a~~Kgsp-l~~~in 67 (138)
+..+.+..|.+|.|||+|+... ..-..+ .+ +. +.. +. ....-.++++|+++ +...++
T Consensus 145 ~Y~q~~~~l~~g~IDA~IWN~d--~i~~~~-~~-l~~~~l~~~~~~~~~seAVivi~~~~~~i~~ll~ 208 (232)
T PF14503_consen 145 PYNQLLELLRSGEIDAAIWNYD--EIEDKN-FG-LKYVPLKDDPMSKDASEAVIVIRKDNEPIKALLR 208 (232)
T ss_dssp -HHHHHHHHHHTS--EEEEE----HHCCHH-CT-EEEEE--SSCHHHHTT-EEEEEETT-HHHHHHHH
T ss_pred cHHHHHHHHHCCCccEEEECCc--cccccc-CC-eeEEeCCchHHHHhcCeeEEEEeCCCHHHHHHHH
Confidence 3578899999999999999744 111112 21 33 222 11 23446678899875 544444
No 73
>cd00995 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is inv
Probab=59.64 E-value=45 Score=26.99 Aligned_cols=68 Identities=26% Similarity=0.117 Sum_probs=38.0
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCC-----Ch-hHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKD-----SA-YLADFSQAIL 71 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kg-----sp-l~~~in~~l~ 71 (138)
++.+.+....+++|++|++|++....+......++..+ +. ... -....+.+.+... ++ +|+.|+.+|.
T Consensus 192 ~~~~~d~~~~~~~l~~GevD~~~~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~l~~N~~~~~~~d~~vR~Al~~aid 266 (466)
T cd00995 192 FKVIPDASTRVAALQSGEIDIADDVPPSALETLKKNPG-IRLVTV-PSLGTGYLGFNTNKPPFDDKRVRQAISYAID 266 (466)
T ss_pred EEEecCHHHHHHHHHcCCccEecCCCHHHHHHHhcCCC-ceEEec-cCCceEEEEeecCCCCCCCHHHHHHHHHhcC
Confidence 45667788899999999999875443322222233332 33 211 1123344555433 33 6777777764
No 74
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=59.55 E-value=66 Score=24.92 Aligned_cols=80 Identities=18% Similarity=0.127 Sum_probs=47.9
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCC-cceeEEEEeCCChh---HHHHHHHHHHHhhc
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYS-VGGFGFAFPKDSAY---LADFSQAILQLSEE 76 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~-~~~~g~a~~Kgspl---~~~in~~l~~l~~~ 76 (138)
++.-++..+.+.-|.+|.+|+.+.-.+.+.. ...-..+. +..... ...|.+++.+++.- ...+-..|. +
T Consensus 169 ~v~~~~v~~~l~~V~~G~ad~g~vy~sd~~~--~~~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~----s 242 (258)
T COG0725 169 LVLATNVRQALAYVETGEADAGFVYVSDALL--SKKVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLL----S 242 (258)
T ss_pred EEecCcHHHHHHHHHcCCCCeEEEEEEhhhc--cCCceEEEEcccccCCCeEEEEEEEcCCCCHHHHHHHHHHHh----C
Confidence 3455677788999999999997764332211 11112233 444443 57899999998654 444444443 3
Q ss_pred CcHHHHHHHhc
Q 039381 77 GKLRELEEAML 87 (138)
Q Consensus 77 G~~~~l~~kW~ 87 (138)
..=+++.++|.
T Consensus 243 ~~a~~il~~~G 253 (258)
T COG0725 243 PEAQEILEKYG 253 (258)
T ss_pred HHHHHHHHHcC
Confidence 44466666664
No 75
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=59.41 E-value=54 Score=25.48 Aligned_cols=80 Identities=9% Similarity=0.023 Sum_probs=41.2
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhc-CCCeeeCCCCCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHHHHHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKN-CKNFTTGPTYSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLRELEEA 85 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~-~~~~~~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~l~~k 85 (138)
..+++..+|..|++|+++...+.+...-.+. .+.+.....-...--.+++++++.--+.+..-+.-++.+..-+-|.++
T Consensus 183 ~~~~~~~al~~g~vDaa~i~~~~a~~a~~~~~~~~l~~e~~~~~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i~~~ 262 (271)
T PRK11063 183 EAPQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAANKV 262 (271)
T ss_pred cHHHHHHhcccccccEEEEChHHHHHcCCCCCCCeeEECCCCCCeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence 3467889999999999999888775432221 121222211111123456666543333444434444444433344444
Q ss_pred h
Q 039381 86 M 86 (138)
Q Consensus 86 W 86 (138)
|
T Consensus 263 ~ 263 (271)
T PRK11063 263 F 263 (271)
T ss_pred c
Confidence 3
No 76
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=58.49 E-value=19 Score=28.46 Aligned_cols=59 Identities=14% Similarity=0.042 Sum_probs=36.3
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe-cHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCCCh
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL-EVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKDSA 61 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~-d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kgsp 61 (138)
.+.|++..+.+.+|.+|.++.-.. .+|.+....++-+-.+. +-..+ ...-+.++++|+.
T Consensus 61 WRkFdSG~~vv~AlASGdvqiG~iGSsplaaAaSr~vpie~f~~~~~i-g~sEALVvr~gsg 121 (334)
T COG4521 61 WRKFDSGASIVRALASGDVQIGNIGSSPLAAAASRQVPIEVFLLASQI-GNSEALVVRKGSG 121 (334)
T ss_pred hhhcCchhHHHHHHhcCCccccccCCchhhHHhhcCCceEEeehhhhc-CccceeeeecCCC
Confidence 478999999999999999997655 55544433333332122 22222 3334677777653
No 77
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=57.22 E-value=24 Score=28.40 Aligned_cols=54 Identities=17% Similarity=0.271 Sum_probs=36.2
Q ss_pred CHHHHHHHHHcCCceEEEec-HHHH-HHHHHhc-CCCee-eCCCCCcceeEEEEeCCC
Q 039381 7 SENRHRQALTSGEIAAAFLE-VPYV-KLFLAKN-CKNFT-TGPTYSVGGFGFAFPKDS 60 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d-~~~l-~~~~~~~-~~~~~-~~~~~~~~~~g~a~~Kgs 60 (138)
+...++++|.+|.+|+++.. .|.. .++.+.. ...+. ++..+.....|+++|+-.
T Consensus 66 ~~~~~~~ala~GdiDv~~~~W~P~~~~~~~~~~~~~~v~~~g~~~~~a~~G~~VP~yv 123 (331)
T PRK11119 66 DYNVFYTSIANGDATFTAVNWFPLHDDMYEAAGGDKKFYREGVYVGGAAQGYLIDKKT 123 (331)
T ss_pred CcHHHHHHHHcCCCeEehhhcccccHHHHHHhhccCcEEeccccCCCcceeeeecHHH
Confidence 34778999999999998854 3322 2232222 22355 677777778999999853
No 78
>cd08503 PBP2_NikA_DppA_OppA_like_17 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=56.70 E-value=52 Score=26.94 Aligned_cols=68 Identities=15% Similarity=0.117 Sum_probs=37.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEE-ecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCC-----Ch-hHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF-LEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKD-----SA-YLADFSQAIL 71 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i-~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kg-----sp-l~~~in~~l~ 71 (138)
++.+++.+..+++|++|++|++. .....+..+ ....+ +.+........+.+.+... ++ +|++|+.+|.
T Consensus 195 ~~~~~~~~~~~~~l~~G~id~~~~~~~~~~~~~-~~~~~-~~~~~~~~~~~~~l~~N~~~~~~~d~~vRkAi~~aid 269 (460)
T cd08503 195 FIDIPDPAARVNALLSGQVDVINQVDPKTADLL-KRNPG-VRVLRSPTGTHYTFVMRTDTAPFDDPRVRRALKLAVD 269 (460)
T ss_pred EEecCCHHHHHHHHHcCCcceecCCCHHHHHHH-hcCCC-eEEEccCCcceEEEeecCCCCCCCCHHHHHHHHHhcC
Confidence 45678888999999999999853 222222222 22222 4421112223455666543 23 5666666664
No 79
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=56.65 E-value=51 Score=26.22 Aligned_cols=59 Identities=20% Similarity=0.191 Sum_probs=32.7
Q ss_pred ecCCHHHHHHHHHcCCceEEEe-cHHHHHHHHHhcC-CCee-e-CCCCCcceeE-EEEeCCChh
Q 039381 4 PIFSENRHRQALTSGEIAAAFL-EVPYVKLFLAKNC-KNFT-T-GPTYSVGGFG-FAFPKDSAY 62 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~-d~~~l~~~~~~~~-~~~~-~-~~~~~~~~~g-~a~~Kgspl 62 (138)
...+....++++.+|++|...+ ..+.+.......+ ..+. . ...-...+|. |.++++||+
T Consensus 73 ~a~dy~~vieal~~g~~D~A~~~~~a~~~a~~~~~~~e~~~~~~~~dg~~~Y~S~~i~~~ds~i 136 (299)
T COG3221 73 VATDYAAVIEALRAGQVDIAWLGPSAYVEAVDRALAGEPLAQTVQKDGSPGYYSVIIVRADSPI 136 (299)
T ss_pred ecccHHHHHHHHhCCCeeEEecCchhHHHHHhhcccccceeeeeccCCCcceeEEEEEeCCCCc
Confidence 4567889999999999995444 4433333222212 2222 2 2222334444 466777774
No 80
>cd08519 PBP2_NikA_DppA_OppA_like_20 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=56.41 E-value=48 Score=27.27 Aligned_cols=23 Identities=30% Similarity=0.316 Sum_probs=19.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+....+++|++|++|++.
T Consensus 192 ~~~~~d~~~~~~al~~G~vD~~~ 214 (469)
T cd08519 192 IRFYSDSSNLFLALQTGEIDVAY 214 (469)
T ss_pred EEEcCChHHHHHHHHCCCcceec
Confidence 45567778889999999999985
No 81
>PRK15413 glutathione ABC transporter substrate-binding protein GsiB; Provisional
Probab=56.29 E-value=42 Score=28.10 Aligned_cols=67 Identities=19% Similarity=0.213 Sum_probs=37.0
Q ss_pred eeecCCHHHHHHHHHcCCceEEE-ecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCC-----Ch-hHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF-LEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKD-----SA-YLADFSQAIL 71 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i-~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kg-----sp-l~~~in~~l~ 71 (138)
++.+++.+....+|++|++|.+. .+...+. .++..++ +. ...+ ......+.|... ++ +|+.|+.+|.
T Consensus 220 ~~~i~d~~~~~~al~~GeiD~~~~~~~~~~~-~l~~~~~-~~~~~~~-~~~~~~l~fN~~~~~~~d~~vRqAi~~AiD 294 (512)
T PRK15413 220 WRPVADNNTRAAMLQTGEAQFAFPIPYEQAA-LLEKNKN-LELVASP-SIMQRYISMNVTQKPFDNPKVREALNYAIN 294 (512)
T ss_pred EEEcCCHHHHHHHHHcCCCCEecCCCHHHHH-HHhcCCC-eEEEecC-CceEEEEEecCCCCCcCCHHHHHHHHHhcC
Confidence 45678888999999999999864 2222222 2233333 44 2222 122233455432 33 6777777764
No 82
>TIGR02743 TraW type-F conjugative transfer system protein TraW. This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm.
Probab=56.17 E-value=14 Score=27.81 Aligned_cols=37 Identities=24% Similarity=0.516 Sum_probs=30.7
Q ss_pred eEEEEeCCCh-hHHHHHHHHHHHhhcCcHHHHHHHhcC
Q 039381 52 FGFAFPKDSA-YLADFSQAILQLSEEGKLRELEEAMLS 88 (138)
Q Consensus 52 ~g~a~~Kgsp-l~~~in~~l~~l~~~G~~~~l~~kW~~ 88 (138)
+|=.+|-..+ +++.|...|..|..+|+++++.++|-.
T Consensus 25 ~G~t~pI~E~D~L~~I~~rl~~~e~sGel~~~~~~~~~ 62 (202)
T TIGR02743 25 YGQTFPIAEPDMLEVIEQRLKRLEQSGELKAMQQRFQS 62 (202)
T ss_pred ccccccccchHHHHHHHHHHHhhhhCchHHHHHHHHHH
Confidence 3444566666 999999999999999999999998764
No 83
>TIGR01276 thiB thiamine ABC transporter, periplasmic binding protein. This model finds the thiamine (and thiamine pyrophosphate) ABC transporter periplasmic binding protein ThiB in proteobacteria. Completed genomes having this protein (E. coli, Vibrio cholera, Haemophilus influenzae) also have the permease ThiP, described by TIGRFAMs equivalog model TIGR01253.
Probab=55.60 E-value=94 Score=23.95 Aligned_cols=70 Identities=10% Similarity=-0.128 Sum_probs=38.6
Q ss_pred cCCHHHHHHHHHcCCceEEEecHH-HHHHHHHhcCCCe--e-eCCCCCcceeEEEEeCCChhHHHHHHHHHHHh
Q 039381 5 IFSENRHRQALTSGEIAAAFLEVP-YVKLFLAKNCKNF--T-TGPTYSVGGFGFAFPKDSAYLADFSQAILQLS 74 (138)
Q Consensus 5 ~~~~~e~~~aL~~G~vdA~i~d~~-~l~~~~~~~~~~~--~-~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~ 74 (138)
+.+..+....+.+|++++.+.... ............+ . ..+.......++++.||++-.+.-.+.|.-|.
T Consensus 176 ~~~~~~~~~~~~~Ge~~i~i~~~~~~~~~~~~~~~~~~~~~~~~eG~~~~~~~~ai~k~a~n~e~A~~Fidfll 249 (309)
T TIGR01276 176 TKGWSEAYGLFLKGESDLVLSYTTSPAYHILEEKKDNYAAANFSEGHYLQVEVAARTAASKQPELAQKFLQFLV 249 (309)
T ss_pred CCChHHHHHHHHcCCcCEEEecCCcHHHHhhcccCcccceEecCCCCEeEEEEEEEeCCCCCHHHHHHHHHHHc
Confidence 445667788999999998875422 2211111211123 2 32222334568899999875555444444444
No 84
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=55.39 E-value=14 Score=27.81 Aligned_cols=19 Identities=16% Similarity=0.106 Sum_probs=16.5
Q ss_pred CHHHHHHHHHcCCceEEEe
Q 039381 7 SENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~ 25 (138)
..+.++.++++|++|+++.
T Consensus 73 pw~~~~~~l~~g~~D~~~~ 91 (259)
T PRK15437 73 PLDALIPSLKAKKIDAIMS 91 (259)
T ss_pred CHHHHHHHHHCCCCCEEEe
Confidence 4788999999999998775
No 85
>cd08492 PBP2_NikA_DppA_OppA_like_15 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=54.78 E-value=70 Score=26.28 Aligned_cols=23 Identities=22% Similarity=0.166 Sum_probs=19.0
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+....+++|++|++|++.
T Consensus 203 ~~~~~d~~~~~~~l~~G~iD~~~ 225 (484)
T cd08492 203 FRFIPEASVRVGALQSGQVDVIT 225 (484)
T ss_pred EEeCCcHHHHHHHHHcCCcceec
Confidence 45567888899999999999864
No 86
>cd08518 PBP2_NikA_DppA_OppA_like_19 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=51.80 E-value=61 Score=26.60 Aligned_cols=23 Identities=26% Similarity=0.314 Sum_probs=18.9
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~ 25 (138)
++.+++ +..+.+|++|++|.+..
T Consensus 184 ~~~~~d-~~~~~al~~GeiD~~~~ 206 (464)
T cd08518 184 FLFLPD-DAAAAALKSGEVDLALI 206 (464)
T ss_pred EEEcCC-HHHHHHHHcCCCceeec
Confidence 456778 88999999999998643
No 87
>COG0687 PotD Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]
Probab=51.48 E-value=1.2e+02 Score=24.34 Aligned_cols=70 Identities=20% Similarity=0.050 Sum_probs=41.9
Q ss_pred eecCCHHHHHHHHHcCCceEEEe-cHHHHHHHHHhcCCCee-eCCC--CCcceeEEEEeCCChhHHHHHHHHHH
Q 039381 3 EPIFSENRHRQALTSGEIAAAFL-EVPYVKLFLAKNCKNFT-TGPT--YSVGGFGFAFPKDSAYLADFSQAILQ 72 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~-d~~~l~~~~~~~~~~~~-~~~~--~~~~~~g~a~~Kgspl~~~in~~l~~ 72 (138)
+.+.+.++..+.|.+|.+++.+. ..........+.+..+. +-+. ...-.-.+++|||+|-.+.--+.|.-
T Consensus 218 ~~~~~~~~~~~~l~~Gev~~a~~w~g~~~~~~~~~~~~~i~~~~p~eG~~~w~D~~~ipk~a~n~~~A~~fInf 291 (363)
T COG0687 218 VYWFDGSQYVQLLANGEVVLAMGWSGDAAAAKAAKNGAPIEFVIPKEGSILWFDNLAIPKGAKNVDAAYKFINF 291 (363)
T ss_pred EEEecchHHHHHHhcCCEEEEEEeChHHHHHHHhhcCCceEEEcCCCCceeeeEeeeeeCCCCCHHHHHHHHHH
Confidence 34667788999999999998776 32222211123343366 4332 33445778999998754444444443
No 88
>PF04069 OpuAC: Substrate binding domain of ABC-type glycine betaine transport system; InterPro: IPR007210 This domain is a part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation. This domain is often fused to the permease component of the transporter complex. It is often found in integral membrane proteins or proteins predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis []. OpuBC is closely related and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine []. L-carnitine is important for osmoregulation in Listeria monocytogenes. This domain is found also in proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA).; GO: 0005215 transporter activity, 0005488 binding, 0006810 transport; PDB: 3R6U_A 3TMG_C 3MAM_A 1SW5_C 1SW4_B 1SW1_A 1SW2_A 3O66_A 1R9Q_A 1R9L_A ....
Probab=51.40 E-value=9.8 Score=28.93 Aligned_cols=59 Identities=24% Similarity=0.214 Sum_probs=38.2
Q ss_pred eeecCCHHHHHHHHHcCCceEEEec-HHHH-HHHHHhcC--CCee-eCCCCCcceeEEEEeCCC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLE-VPYV-KLFLAKNC--KNFT-TGPTYSVGGFGFAFPKDS 60 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d-~~~l-~~~~~~~~--~~~~-~~~~~~~~~~g~a~~Kgs 60 (138)
++..++.+.++++|.+|++|++... .+.. ..+.+... ..+. ++.......+|+++|+..
T Consensus 33 ~~~~~~~~~~~~al~~G~iD~~~~~w~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~g~~Vp~~~ 96 (257)
T PF04069_consen 33 VVNLGSTPVIFAALASGDIDIYPEEWTPTTYEAYKKALEEKLGVVWLGPLGAGNTYGWAVPKYV 96 (257)
T ss_dssp EEEESSHHHHHHHHHTTSSSEEEEEEETTTHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEEHHH
T ss_pred EecCCchHHHHHHHHCCCCeEEhhhcCchhHHHHHHhhhhcCccccCCccccCCEEEEEEeccc
Confidence 4566777889999999999999932 2322 22222111 1244 565566778999999764
No 89
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=51.05 E-value=62 Score=25.20 Aligned_cols=75 Identities=11% Similarity=0.154 Sum_probs=48.1
Q ss_pred CCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-e-CCCCCcceeEEEEeCCChhHHHHHHHHHHHhh---cCcHH
Q 039381 6 FSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-T-GPTYSVGGFGFAFPKDSAYLADFSQAILQLSE---EGKLR 80 (138)
Q Consensus 6 ~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~-~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~---~G~~~ 80 (138)
-+.++....|.+|++|..+........ ....+. + .-.|......+++|+++++.. +.+|.. .-.+.
T Consensus 51 ~~~~~i~~~L~sG~vDlgi~g~~~~~e----r~~~v~~~~~l~~~~~~lvvvvp~~~~i~s-----l~DL~Gk~ia~~~~ 121 (287)
T PRK00489 51 LRPDDIPGYVADGVVDLGITGEDLLEE----SGADVEELLDLGFGKCRLVLAVPEDSDWQG-----VEDLAGKRIATSYP 121 (287)
T ss_pred ECcHHHHHHHHcCCCCEEEcchHHHHH----CCCCceEeeeccCCceEEEEEEECCCCCCC-----hHHhCCCEEEEcCc
Confidence 345788999999999999986433211 111233 2 335677889999999988643 344422 23566
Q ss_pred HHHHHhcCC
Q 039381 81 ELEEAMLSP 89 (138)
Q Consensus 81 ~l~~kW~~~ 89 (138)
.+.++||..
T Consensus 122 ~~~~~~l~~ 130 (287)
T PRK00489 122 NLTRRYLAE 130 (287)
T ss_pred HHHHHHHHH
Confidence 677777764
No 90
>PRK13738 conjugal transfer pilus assembly protein TraW; Provisional
Probab=50.86 E-value=19 Score=27.24 Aligned_cols=36 Identities=19% Similarity=0.333 Sum_probs=29.9
Q ss_pred eEEEEeCCCh-hHHHHHHHHHHHhhcCcHHHHHHHhc
Q 039381 52 FGFAFPKDSA-YLADFSQAILQLSEEGKLRELEEAML 87 (138)
Q Consensus 52 ~g~a~~Kgsp-l~~~in~~l~~l~~~G~~~~l~~kW~ 87 (138)
+|=.+|-..+ +++.|...|..|.++|+++++.+++-
T Consensus 23 ~G~t~pI~E~D~L~~I~~rL~~~e~sGel~~~~~~~~ 59 (209)
T PRK13738 23 WGDLWPVKEPDMLTVIMQRLQALEQSGEMGRKMDAFK 59 (209)
T ss_pred cccccCccchhHHHHHHHHHHHhHhccHHHHHHHHHH
Confidence 4445566766 99999999999999999999888765
No 91
>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=50.01 E-value=30 Score=26.60 Aligned_cols=58 Identities=12% Similarity=0.066 Sum_probs=33.9
Q ss_pred ecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhc--------CCCee-eCCCCCcceeEEEEeCCChh
Q 039381 4 PIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKN--------CKNFT-TGPTYSVGGFGFAFPKDSAY 62 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~--------~~~~~-~~~~~~~~~~g~a~~Kgspl 62 (138)
...+..+.+++|.+|++|..+...+......... ...+. +.. +..+.+.+++++++++
T Consensus 67 ~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~-~~~~~~~lvv~~d~~i 133 (320)
T TIGR02122 67 STGGSVENVNLLEAGEADLAIVQSDVAYYAYEGDGEFEFEGPVEKLRALAS-LYPEYIQIVVRKDSGI 133 (320)
T ss_pred eCcchHHHHHHHhCCCCcEEEEcchhHHHHhcCcCccccCCCCccHHhHHH-hccccEEEEEECCCCC
Confidence 3455668899999999998887643322211111 11133 322 3345566888888765
No 92
>cd08499 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains 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
Probab=48.45 E-value=73 Score=26.15 Aligned_cols=23 Identities=17% Similarity=0.316 Sum_probs=18.9
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+++......+|.+|++|++.
T Consensus 191 ~~~~~d~~~~~~~l~~G~iD~~~ 213 (474)
T cd08499 191 FKVVPEDGTRVAMLETGEADIAY 213 (474)
T ss_pred EEEcCCHHHHHHHHHcCCCCeec
Confidence 45567888889999999999864
No 93
>cd08517 PBP2_NikA_DppA_OppA_like_13 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=47.58 E-value=66 Score=26.36 Aligned_cols=24 Identities=17% Similarity=0.200 Sum_probs=19.8
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~ 25 (138)
++.+++.+..+++|++|++|.+..
T Consensus 195 ~~~~~d~~~~~~al~~G~vD~~~~ 218 (480)
T cd08517 195 FRIIPDAAARAAAFETGEVDVLPF 218 (480)
T ss_pred EEEcCCHHHHHHHHHcCCcceecC
Confidence 456778888999999999998653
No 94
>cd08515 PBP2_NikA_DppA_OppA_like_10 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=47.27 E-value=92 Score=25.50 Aligned_cols=23 Identities=17% Similarity=0.107 Sum_probs=19.2
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+.+..+.++++|++|.+.
T Consensus 195 ~~~~~d~~~~~~~~~~G~~D~~~ 217 (460)
T cd08515 195 FRVIPDVSTRVAELLSGGVDIIT 217 (460)
T ss_pred EEEcCCHHHHHHHHHcCCCCEEc
Confidence 45667888899999999999864
No 95
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=47.24 E-value=94 Score=24.21 Aligned_cols=78 Identities=8% Similarity=0.032 Sum_probs=39.8
Q ss_pred HHHHHHHHHcCCceEEEecHHHHHHHHHhcC--CCeeeCCCCCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHHHHHH
Q 039381 8 ENRHRQALTSGEIAAAFLEVPYVKLFLAKNC--KNFTTGPTYSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLRELEEA 85 (138)
Q Consensus 8 ~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~--~~~~~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~l~~k 85 (138)
.+++..+|..|++|+++.-.+.+... .-.+ +.+..........-.++++.++.=...+.+-+..++.+..-+-|.++
T Consensus 185 ~~q~~~al~dg~vD~a~i~~~~~~~a-g~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~ 263 (272)
T PRK09861 185 GAQLPRVLDDPKVDVAIISTTYIQQT-GLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAETI 263 (272)
T ss_pred HHHhHhhccCcccCEEEEchhHHHHc-CCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence 46688999999999999887765431 1111 11112221111123455665533344455545555544444444444
Q ss_pred h
Q 039381 86 M 86 (138)
Q Consensus 86 W 86 (138)
|
T Consensus 264 ~ 264 (272)
T PRK09861 264 F 264 (272)
T ss_pred c
Confidence 4
No 96
>cd08514 PBP2_AppA_like The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold. This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains correspondin
Probab=47.05 E-value=72 Score=26.24 Aligned_cols=24 Identities=21% Similarity=0.169 Sum_probs=19.8
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~ 25 (138)
++.+.+.+..+.+|++|++|..-.
T Consensus 196 ~~~~~d~~~~~~al~~G~vD~~~~ 219 (483)
T cd08514 196 FRIIPDPTTALLELKAGELDIVEL 219 (483)
T ss_pred EEEecCHHHHHHHHhCCCcceecC
Confidence 456788889999999999998643
No 97
>PRK07377 hypothetical protein; Provisional
Probab=46.81 E-value=24 Score=26.17 Aligned_cols=24 Identities=25% Similarity=0.140 Sum_probs=22.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~ 25 (138)
+..|++.++..+||.+|+||+...
T Consensus 112 lv~y~~~~~l~~aL~~~eVh~~c~ 135 (184)
T PRK07377 112 LVVYPDLQALEQALRDKEVHAICL 135 (184)
T ss_pred EEecCCHHHHHHHHhcCCccEEec
Confidence 578999999999999999999876
No 98
>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=46.68 E-value=30 Score=25.81 Aligned_cols=51 Identities=10% Similarity=-0.051 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhHH
Q 039381 6 FSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYLA 64 (138)
Q Consensus 6 ~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~~ 64 (138)
.+..+....|.+|++|..+...+. ....+. ..++..+.++++++++.|+..
T Consensus 120 ~~~~~~~~~l~~g~~Dl~i~~~~~-------~~~~~~-~~~l~~~~~~lv~s~~~pl~~ 170 (279)
T TIGR03339 120 GNSQEVLQALQSYRVDVAVSSEVV-------DDPRLD-RVVLGNDPLVAVVHRQHPLAE 170 (279)
T ss_pred CCHHHHHHHHHcCCCcEEEEeccc-------CCCceE-EEEcCCceEEEEECCCCcccc
Confidence 467788999999999998863221 111122 223556789999999988754
No 99
>cd08513 PBP2_thermophilic_Hb8_like The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold. This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium, and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporter
Probab=46.44 E-value=93 Score=25.57 Aligned_cols=23 Identities=35% Similarity=0.501 Sum_probs=19.5
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+++......+|++|++|.+.
T Consensus 195 ~~~~~d~~~~~~~l~~G~vD~~~ 217 (482)
T cd08513 195 LKGVPDTDAARAALRSGEIDLAW 217 (482)
T ss_pred EEEeCCHHHHHHHHhCCCCCEec
Confidence 45677888999999999999864
No 100
>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=46.18 E-value=72 Score=23.43 Aligned_cols=52 Identities=12% Similarity=0.108 Sum_probs=34.9
Q ss_pred ecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCCh
Q 039381 4 PIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSA 61 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgsp 61 (138)
...+..+...+|.+|++|+.+.-.+.+..+ +.-.|. +...+.|=+++++..-
T Consensus 129 ~~~th~~vA~aVa~G~AD~G~g~~~~A~~~---~gL~Fv---pl~~E~~dlv~~~~~~ 180 (193)
T PF12727_consen 129 EANTHLAVAAAVASGKADAGIGIRAAAEEF---YGLDFV---PLAEERYDLVIRREDL 180 (193)
T ss_pred cccChHHHHHHHHcCCCCEEeehHHHHHhh---cCCCcE---EccccceEEEEEhhHc
Confidence 346678888999999999999765554311 121132 2345889999999843
No 101
>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=44.79 E-value=33 Score=23.18 Aligned_cols=50 Identities=14% Similarity=0.267 Sum_probs=32.4
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYLA 64 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~~ 64 (138)
+..+....|.+|++|..+...+. ....+. ...+..+.+.++++++.|+..
T Consensus 37 ~~~~~~~~L~~~~~Dl~i~~~~~-------~~~~~~-~~~l~~~~~~~v~~~~~~l~~ 86 (197)
T cd08438 37 GGKKVEQAVLNGELDVGITVLPV-------DEEEFD-SQPLCNEPLVAVLPRGHPLAG 86 (197)
T ss_pred CcHHHHHHHHcCCCCEEEEeccc-------ccCCce-eEEeccccEEEEecCCCChhh
Confidence 45677899999999998865332 111122 223456778888888887643
No 102
>cd08490 PBP2_NikA_DppA_OppA_like_3 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=44.45 E-value=86 Score=25.59 Aligned_cols=23 Identities=35% Similarity=0.458 Sum_probs=19.3
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+.+....+|.+|++|++.
T Consensus 183 ~~~~~d~~~~~~~l~~G~iD~~~ 205 (470)
T cd08490 183 VKFIPDANTRALALQSGEVDIAY 205 (470)
T ss_pred EEEcCCHHHHHHHHHcCCcceec
Confidence 45677888899999999999864
No 103
>cd08493 PBP2_DppA_like The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains 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 li
Probab=44.24 E-value=74 Score=26.17 Aligned_cols=23 Identities=17% Similarity=0.099 Sum_probs=19.3
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+....+++|++|++|+..
T Consensus 208 ~~~~~~~~~~~~al~~G~iD~~~ 230 (482)
T cd08493 208 FRIIPDNSVRLAKLLAGECDIVA 230 (482)
T ss_pred EEECCChHHHHHHHHCCCccEec
Confidence 45677888899999999999864
No 104
>cd08516 PBP2_NikA_DppA_OppA_like_11 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=43.75 E-value=94 Score=25.24 Aligned_cols=23 Identities=26% Similarity=0.237 Sum_probs=19.2
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+++....+.+|.+|++|.+.
T Consensus 188 ~~~~~d~~~~~~~l~~G~iD~~~ 210 (457)
T cd08516 188 FKIYPDENTRLAALQSGDVDIIE 210 (457)
T ss_pred EEECCCHHHHHHHHhcCCccEec
Confidence 45677888999999999999864
No 105
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=43.51 E-value=36 Score=28.61 Aligned_cols=24 Identities=21% Similarity=0.055 Sum_probs=19.8
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~ 25 (138)
++.+.+.++++.+|++|++|.++.
T Consensus 84 ~v~~~~~~~ll~aL~~G~iDi~~~ 107 (482)
T PRK10859 84 IKVRDNISQLFDALDKGKADLAAA 107 (482)
T ss_pred EEecCCHHHHHHHHhCCCCCEEec
Confidence 345678999999999999997654
No 106
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=42.95 E-value=75 Score=24.29 Aligned_cols=78 Identities=9% Similarity=-0.060 Sum_probs=44.7
Q ss_pred cCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee--eCCC-CCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHH
Q 039381 5 IFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT--TGPT-YSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLRE 81 (138)
Q Consensus 5 ~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~--~~~~-~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~ 81 (138)
-++..+.++.+.+|++|+.|.-...+. ..+... .. ++.. .....|++++.|+++- + .-+.+.+...+-+-++
T Consensus 173 ~~~v~~~~~~v~~G~ad~gi~~~s~a~--~~~~~~-~~~~~P~e~~~~i~~~~avlk~~~~-~-~Ak~Fi~fl~S~eaq~ 247 (257)
T PRK10677 173 AEDVRGALALVERNEAPLGIVYGSDAV--ASKKVK-VVGTFPEDSHKPVEYPMAIVKGHNN-A-TVKAFYDYLKGPQAAA 247 (257)
T ss_pred cccHHHHHHHHHcCCCCEEEEEeeeee--ccCCCe-EEEECCcccCCcceeeEEEEcCCCC-H-HHHHHHHHHcCHHHHH
Confidence 456778889999999998875322211 111211 22 2332 3456789999888642 2 2333444445555566
Q ss_pred HHHHhc
Q 039381 82 LEEAML 87 (138)
Q Consensus 82 l~~kW~ 87 (138)
+.++|.
T Consensus 248 i~~~~G 253 (257)
T PRK10677 248 IFKRYG 253 (257)
T ss_pred HHHHcC
Confidence 766663
No 107
>cd08502 PBP2_NikA_DppA_OppA_like_16 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=42.82 E-value=95 Score=25.59 Aligned_cols=66 Identities=18% Similarity=-0.012 Sum_probs=36.4
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCCC-----h-hHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKDS-----A-YLADFSQAIL 71 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kgs-----p-l~~~in~~l~ 71 (138)
++.+.+.+....+|++|++|.+....+.....+++... +. .... ....+.+...+ + +|+.|+.+|.
T Consensus 203 ~~~~~d~~~~~~al~~G~vD~~~~~~~~~~~~l~~~~~-~~~~~~~---~~~~l~~N~~~~~~~d~~vR~Ai~~aid 275 (472)
T cd08502 203 FIVVPDANTAVAALQSGEIDFAEQPPADLLPTLKADPV-VVLKPLG---GQGVLRFNHLQPPFDNPKIRRAVLAALD 275 (472)
T ss_pred EEEeCCHHHHHHHHHcCCcceecCCCHHHHHHHhhCCC-eEEecCC---ceEEEEEcCCCCCCcCHHHHHHHHHhcC
Confidence 45677888899999999999875322222222233332 44 3221 33445554432 2 5666666654
No 108
>cd08494 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=42.40 E-value=1.1e+02 Score=24.71 Aligned_cols=23 Identities=26% Similarity=0.222 Sum_probs=19.5
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+++.+..+.+|.+|++|.+-
T Consensus 188 ~~~~~~~~~~~~~l~~g~iD~~~ 210 (448)
T cd08494 188 FRYFSDPTALTNALLAGDIDAAP 210 (448)
T ss_pred EEEcCCHHHHHHHHHCCCCceec
Confidence 45677888899999999999874
No 109
>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=42.06 E-value=37 Score=25.74 Aligned_cols=59 Identities=15% Similarity=0.077 Sum_probs=42.2
Q ss_pred cCCHHHHHHHHHcCCceEEEecHHHHHHHHH-hcCC--C----ee-eCCCCCcceeEEEEeCCChhH
Q 039381 5 IFSENRHRQALTSGEIAAAFLEVPYVKLFLA-KNCK--N----FT-TGPTYSVGGFGFAFPKDSAYL 63 (138)
Q Consensus 5 ~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~-~~~~--~----~~-~~~~~~~~~~g~a~~Kgspl~ 63 (138)
.....+++.+|.+|++|..+.++++-..... +.+. . .. ...++.....+|++.+.+|+.
T Consensus 44 ~~gS~~g~~~l~~g~~di~~~sr~l~~~e~~~~~~~~~~~~~~~~~~~~~va~d~i~iv~n~~np~~ 110 (281)
T PF12849_consen 44 SSGSGAGIQALINGKVDIAISSRPLTAAEIASEGYNAKGQKWGGGLVQIPVARDAIVIVVNKDNPLN 110 (281)
T ss_dssp EE-HHHHHHHHHTTSSSEEEESSHHHHHHHHHHTCCCCCHHHHCTEEEEEEEEEEEEEEEETTTTTE
T ss_pred eCCCHHHHHHHHhCCCEEEEeCCCCcHHHHhHhhhhhcccccccccEEEEEEEeeEEEEEcCCCccc
Confidence 3456789999999999999999887665442 2221 1 12 344567788999999998876
No 110
>cd08498 PBP2_NikA_DppA_OppA_like_2 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=41.97 E-value=1e+02 Score=25.39 Aligned_cols=23 Identities=30% Similarity=0.384 Sum_probs=19.3
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+++....+.+|++|++|++-
T Consensus 191 ~~~~~d~~~~~~al~~G~iD~~~ 213 (481)
T cd08498 191 FRPIPNDATRVAALLSGEVDVIE 213 (481)
T ss_pred EEECCCHHHHHHHHHcCCCCEec
Confidence 45677888899999999999863
No 111
>PF00800 PDT: Prephenate dehydratase Caution this is only a partial structure.; InterPro: IPR001086 Prephenate dehydratase (4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate to phenylpyruvate. In microorganisms it is part of the terminal pathway of phenylalanine biosynthesis. In some bacteria such as Escherichia coli PDT is part of a bifunctional enzyme (P-protein) that also catalyses the transformation of chorismate into prephenate (chorismate mutase, IPR002701 from INTERPRO, 5.4.99.5 from EC) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional PDT aligns well with the C-terminal part of P-proteins [].; GO: 0004664 prephenate dehydratase activity, 0009094 L-phenylalanine biosynthetic process; PDB: 3MWB_B 2QMX_A 2QMW_A 3LUY_A.
Probab=41.97 E-value=32 Score=24.95 Aligned_cols=56 Identities=14% Similarity=0.077 Sum_probs=36.5
Q ss_pred eeecCCHHHHHHHHHcCCceEEEec--H-------HHHHHHHHhcCCCee-eCCCCCcceeEEEEeCCC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLE--V-------PYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKDS 60 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d--~-------~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kgs 60 (138)
++.+++.++++.++..|++|..|.. . .++..+.. . .+. +++..-...+.++.+++.
T Consensus 26 ~~~~~s~~~v~~av~~~~~d~~vvPiENs~~G~V~~t~d~L~~--~-~l~i~~e~~l~i~~~L~~~~~~ 91 (181)
T PF00800_consen 26 IVPCDSFEEVFDAVEEGEADYGVVPIENSLEGSVSETLDLLID--S-DLYIVGEIVLPIHHCLLAKPGT 91 (181)
T ss_dssp EEEESSHHHHHHHHHCTSSSEEEEEEECTTTCECHHHHHHHHT--S-SCEEEEEEEEE--EEEEECTT-
T ss_pred eEecCCHHHHHHHHHcCCCceEEEeEeeecCCEeHHHHHHHhc--C-CceEEEEEEeccccEEeccCCC
Confidence 6789999999999999999987752 1 22333322 2 366 777666666667666664
No 112
>cd08496 PBP2_NikA_DppA_OppA_like_9 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=41.54 E-value=98 Score=25.29 Aligned_cols=66 Identities=18% Similarity=0.137 Sum_probs=36.7
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCC-----Ch-hHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKD-----SA-YLADFSQAIL 71 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kg-----sp-l~~~in~~l~ 71 (138)
++.+.+.+....++.+|++|++....+... ..+..+ +. ...+ ....+.+.|... ++ +|+.|..+|.
T Consensus 189 ~~~~~~~~~~~~~~~~G~iD~~~~~~~~~~--~~~~~~-~~~~~~~-~~~~~~l~fN~~~~~~~d~~vRkAl~~aid 261 (454)
T cd08496 189 LSVIPDPTARVNALQSGQVDFAQLLAAQVK--IARAAG-LDVVVEP-TLAATLLLLNITGAPFDDPKVRQAINYAID 261 (454)
T ss_pred EEEcCCHHHHHHHHhcCCCcEeccCchhHH--HhhcCC-ceEEecC-CCceEEEEecCCCCCCCCHHHHHHHHhhcC
Confidence 456778889999999999999754333222 122222 33 2111 123455666543 22 5666666654
No 113
>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=41.32 E-value=39 Score=25.68 Aligned_cols=23 Identities=17% Similarity=0.083 Sum_probs=18.5
Q ss_pred ecCCHHHHHHHHHcCCceEEEec
Q 039381 4 PIFSENRHRQALTSGEIAAAFLE 26 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~d 26 (138)
.+.+.++++.+|++|++|+++..
T Consensus 77 ~~~~w~~~~~~l~~G~~Di~~~~ 99 (275)
T TIGR02995 77 SITEYGALIPGLQAGRFDAIAAG 99 (275)
T ss_pred ccCCHHHHHHHHHCCCcCEEeec
Confidence 34567889999999999997653
No 114
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=40.81 E-value=38 Score=25.41 Aligned_cols=20 Identities=15% Similarity=0.077 Sum_probs=17.0
Q ss_pred CHHHHHHHHHcCCceEEEec
Q 039381 7 SENRHRQALTSGEIAAAFLE 26 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d 26 (138)
+.++++.++++|++|+++..
T Consensus 73 ~~~~~~~~l~~g~~Di~~~~ 92 (260)
T PRK15010 73 DFDALIPSLKAKKIDAIISS 92 (260)
T ss_pred CHHHHHHHHHCCCCCEEEec
Confidence 57889999999999987753
No 115
>PF00496 SBP_bac_5: Bacterial extracellular solute-binding proteins, family 5 Middle; InterPro: IPR000914 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 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 Gram-positive bacteria which are surrounded by a single membrane and therefore have 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 of clusters, which generally correlate with the nature of the solute bound. Family 5 currently includes periplasmic oligopeptide-binding proteins (oppA) of Gram-negative bacteria and homologous lipoproteins in Gram-positive bacteria (oppA, amiA or appA); periplasmic dipeptide-binding proteins of Escherichia coli (dppA) and Bacillus subtilis (dppE); periplasmic murein peptide-binding protein of E. coli (mppA); periplasmic peptide-binding proteins sapA of E. coli, Salmonella typhimurium and Haemophilus influenzae; periplasmic nickel-binding protein (nikA) of E. coli; haem-binding lipoprotein (hbpA or dppA) from H. influenzae; lipoprotein xP55 from Streptomyces lividans; and hypothetical proteins from H. influenzae (HI0213) and Rhizobium sp. (strain NGR234) symbiotic plasmid (y4tO and y4wM).; GO: 0005215 transporter activity, 0006810 transport; PDB: 1B51_A 1B0H_A 1QKA_A 1B9J_A 1B6H_A 1OLA_A 1B3L_C 1JEV_A 1B5H_A 1JET_A ....
Probab=40.46 E-value=69 Score=25.08 Aligned_cols=82 Identities=16% Similarity=0.152 Sum_probs=42.0
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe-cHHHHHHHHHhcCCCeee-CCCCCcceeEEEEeCCCh-h-HHHHHHHHHHHhhcC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL-EVPYVKLFLAKNCKNFTT-GPTYSVGGFGFAFPKDSA-Y-LADFSQAILQLSEEG 77 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~-d~~~l~~~~~~~~~~~~~-~~~~~~~~~g~a~~Kgsp-l-~~~in~~l~~l~~~G 77 (138)
++.+.+....+.+|++|++|.+.. ....+...... .. ..+ -.......+.+.+.-.++ + -..+-+||.....
T Consensus 154 ~~~~~~~~~~~~al~~G~iD~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~l~fN~~~~~~~d~~vR~Al~~aid-- 229 (374)
T PF00496_consen 154 LRVIPDADSAVAALQSGEIDDIAEVPPSDIDQLKSD-PN-LSVYYSYPSPGYYYLAFNTNNPPFSDKAVRQALAYAID-- 229 (374)
T ss_dssp EEEESSHHHHHHHHHTTSSSEEESSSGGTHHHHHHH-TT-EEEEEEEEEEEEEEEEE-TTSTTTTSHHHHHHHHHHS---
T ss_pred ccccccchhhhhcccceeeeeeeccccccccccccc-Cc-cccccccccccceeeeccccccccchhhhHHHHHhhhh--
Confidence 466788999999999999977743 33333333222 22 222 112233445666655532 2 2234444444333
Q ss_pred cHHHHHHHhcC
Q 039381 78 KLRELEEAMLS 88 (138)
Q Consensus 78 ~~~~l~~kW~~ 88 (138)
.+.|.+..+.
T Consensus 230 -r~~i~~~~~~ 239 (374)
T PF00496_consen 230 -REAIVKNIFG 239 (374)
T ss_dssp -HHHHHHHTTT
T ss_pred -HHHHHHHHHh
Confidence 3445555543
No 116
>PRK11205 tbpA thiamine transporter substrate binding subunit; Provisional
Probab=38.96 E-value=1.9e+02 Score=22.58 Aligned_cols=71 Identities=8% Similarity=-0.107 Sum_probs=39.5
Q ss_pred cCCHHHHHHHHHcCCceEEEecHHHHHH-HHHhcCCCee---eCCCCCcceeEEEEeCCChhHHHHHHHHHHHhh
Q 039381 5 IFSENRHRQALTSGEIAAAFLEVPYVKL-FLAKNCKNFT---TGPTYSVGGFGFAFPKDSAYLADFSQAILQLSE 75 (138)
Q Consensus 5 ~~~~~e~~~aL~~G~vdA~i~d~~~l~~-~~~~~~~~~~---~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~ 75 (138)
.++..+..+.+.+|++++.+.......+ ..++....+. ..+.......++++.||+|-.+.-.+.|.-|..
T Consensus 197 ~~~~~~~~~~~~~Ge~~~~i~~~~~~~~~~~~~~~~~~~~~~~~eG~~~~~~~~ai~k~a~n~e~A~~Fi~fllS 271 (330)
T PRK11205 197 TKGWSEAYGLFLKGEADLVLSYTTSPAYHIIAEKKDNYAAANFSEGHYLQVEVAARTAASKQPELAQKFLQFMVS 271 (330)
T ss_pred CCChHHHHHHHHcCCccEEEeCCCcHHHHHhhccCCceeEEEcCCCCeEEEEEEEEeCCCCCHHHHHHHHHHHcC
Confidence 4566788899999999998765322212 2222221232 222112234578999998755555554444433
No 117
>PRK11622 hypothetical protein; Provisional
Probab=38.88 E-value=2.1e+02 Score=23.21 Aligned_cols=70 Identities=16% Similarity=-0.008 Sum_probs=40.7
Q ss_pred CHHHHHHHHHcCCceEEEe-cHHHHHHHHHhc--CCCee-e--CCCCCcceeEEEEeCCChhHHHHHHHHHHHhhc
Q 039381 7 SENRHRQALTSGEIAAAFL-EVPYVKLFLAKN--CKNFT-T--GPTYSVGGFGFAFPKDSAYLADFSQAILQLSEE 76 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~-d~~~l~~~~~~~--~~~~~-~--~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~ 76 (138)
+..+..+.|.+|+++..+. +...+...+.+. +..+. + .+.......+++++|++|-.+.--+.|.-|...
T Consensus 254 ~~~~~~~~~~~GEv~~~~~~~~~~~~~~~~~g~~p~~~~~~~~~~G~~~~~~~~~Ipk~a~n~~~A~~finfllS~ 329 (401)
T PRK11622 254 SPAELDQLLADGELDLAMTFNPNHAQSKIANGELPASTRSFVFDDGTIGNTHFVAIPFNANAKAGAKVVANFLLSP 329 (401)
T ss_pred ChHHHHHHHHCCCeEEEEecChHHHHHHHhcCCCCCceeEEcCCCCeeccceeEEeeCCCCCHHHHHHHHHHHcCH
Confidence 6677889999999999875 322232223322 22233 2 122223457899999988655555544444443
No 118
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=38.54 E-value=1.4e+02 Score=22.85 Aligned_cols=56 Identities=14% Similarity=0.108 Sum_probs=32.4
Q ss_pred ecCCHHHHHHHHHcCC-ceEEEecH-HHHHHHHHhcCCCee--eCCCCCcceeEEEEeCCCh
Q 039381 4 PIFSENRHRQALTSGE-IAAAFLEV-PYVKLFLAKNCKNFT--TGPTYSVGGFGFAFPKDSA 61 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~-vdA~i~d~-~~l~~~~~~~~~~~~--~~~~~~~~~~g~a~~Kgsp 61 (138)
.|.........+.+|. .|.++.+. ....+..++.. +. ....+.....++++++++|
T Consensus 59 ~~~~Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl--~~~~~~~~~a~n~lvl~~~~~~~ 118 (257)
T PRK10677 59 SFASSSTLARQIEQGAPADLFISADQKWMDYAVDKKA--IDTATRYTLLGNSLVVVAPKASE 118 (257)
T ss_pred EecccHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCC--CCCcchheeecCEEEEEEECCCc
Confidence 4556667778888877 99999865 44444444321 11 1123445556666666643
No 119
>PRK09755 putative ABC transporter periplasmic-binding protein; Provisional
Probab=37.04 E-value=1.1e+02 Score=25.90 Aligned_cols=68 Identities=6% Similarity=0.024 Sum_probs=36.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeC-----CCh-hHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPK-----DSA-YLADFSQAIL 71 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~K-----gsp-l~~~in~~l~ 71 (138)
++.+++......+|++|++|++-.....+..+.+.....+..... ...+.+++.. +++ +|+.|..+|.
T Consensus 244 ~~~~~d~~~~~~al~sGeiD~~~i~~~~~~~l~~~~~~~~~~~~~--~~~~~l~~N~~~~~~~d~~vRqAl~~AID 317 (535)
T PRK09755 244 YLALDNSVTGYNRYRAGEVDLTWVPAQQIPAIEKSLPGELRIIPR--LNSEYYNFNLEKPPFNDVRVRRALYLTVD 317 (535)
T ss_pred EEEecCchHHHHHHhcCCcccccCCHHHHHHHHhccccceEEccc--ceEEEEEEcCCCCccCCHHHHHHHHHHhC
Confidence 456677888899999999998533322222222221112331111 2234455543 233 6777777665
No 120
>TIGR02294 nickel_nikA nickel ABC transporter, periplasmic nickel-binding protein. Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Nickel is bound specifically, albeit weakly, through water molecules positioned in the binding site. The amino acids whose side chains line the binding site include Tyr-44, Met-49, Trp-122, Arg-159, Trp-420, and Tyr-424 (numbering based on the precursor sequence of E. coli NikA) with the Arg contributing a hydrogen bond indirectly through a water molecule. Sequences that exactly (or mostly) have the same binding site residues score above the trusted (or noise) cutoffs to this model. Most appear to be lipoproteins.
Probab=36.22 E-value=1.4e+02 Score=24.75 Aligned_cols=23 Identities=26% Similarity=0.390 Sum_probs=19.4
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+.+....+|++|++|.+.
T Consensus 198 ~~~~~~~~~~~~al~~G~iD~~~ 220 (500)
T TIGR02294 198 VKVIPDAETRALAFESGEVDLIF 220 (500)
T ss_pred EEEcCCHHHHHHHHHcCCccEec
Confidence 45677888899999999999974
No 121
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=35.98 E-value=50 Score=25.86 Aligned_cols=26 Identities=23% Similarity=0.305 Sum_probs=20.8
Q ss_pred HHHHHHHHHcCCceEEEecHHHHHHH
Q 039381 8 ENRHRQALTSGEIAAAFLEVPYVKLF 33 (138)
Q Consensus 8 ~~e~~~aL~~G~vdA~i~d~~~l~~~ 33 (138)
.+++.++|.+|++||++.-.|.....
T Consensus 158 ~~~~~~Al~~G~VDAa~~~~p~~~~~ 183 (320)
T PRK11480 158 PPAIIAAWQRGDIDGAYVWAPAVNAL 183 (320)
T ss_pred cHHHHHHHHcCCcCEEEEcchHHHHH
Confidence 57889999999999988766765433
No 122
>cd08511 PBP2_NikA_DppA_OppA_like_5 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is mos
Probab=35.63 E-value=1.4e+02 Score=24.37 Aligned_cols=23 Identities=22% Similarity=0.244 Sum_probs=19.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+.+..+.++++|++|..-
T Consensus 192 ~~~~~~~~~~~~al~~G~id~~~ 214 (467)
T cd08511 192 YRPIPDATVRLANLRSGDLDIIE 214 (467)
T ss_pred EEECCCHHHHHHHHHcCCccEec
Confidence 45677888899999999999864
No 123
>PRK15109 antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
Probab=35.59 E-value=1.2e+02 Score=25.80 Aligned_cols=22 Identities=14% Similarity=0.084 Sum_probs=18.2
Q ss_pred eeecCCHHHHHHHHHcCCceEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAA 23 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~ 23 (138)
++.+.+.+..+.+|++|++|++
T Consensus 249 ~~~~~d~~~~~~al~~GeiD~~ 270 (547)
T PRK15109 249 VDLGSGGTGRLSKLLTGECDVL 270 (547)
T ss_pred EEecCCHHHHHHHHHCCCCCee
Confidence 4556778888999999999975
No 124
>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=35.54 E-value=30 Score=26.05 Aligned_cols=70 Identities=19% Similarity=0.308 Sum_probs=37.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee--eC--CCCCcceeEEEEeCCCh-hHHHHHHHHHHHhhc
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT--TG--PTYSVGGFGFAFPKDSA-YLADFSQAILQLSEE 76 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~--~~--~~~~~~~~g~a~~Kgsp-l~~~in~~l~~l~~~ 76 (138)
++-.++.+++++.+.+|++|..+...++-.. ..|. ++ .-+.....|..+.-+.. +.+.-+..|.-+++|
T Consensus 97 vVytdD~~~i~~Ml~~g~vdsAVv~~~~~~G------~~fEdl~~~~g~~~PgsCga~v~~~~~~fi~aY~~GI~~~r~d 170 (201)
T PF12916_consen 97 VVYTDDMSEIVKMLNEGEVDSAVVGSEFSKG------ETFEDLLGSLGLYAPGSCGAYVNGDPDYFISAYEEGIDLIRED 170 (201)
T ss_dssp EEE---HHHHHHHHHTT-E--EEEETTT---------EEHHHHHHHTT------EEEEESS--HHHHHHHHHHHHHHHH-
T ss_pred eEEecCHHHHHHHHhcCceeeeeecchhccc------hhHHHHHhhcCCCCChhhhhhhcCChHHHHHHHHHHHHHHHhC
Confidence 4556799999999999999987776443211 1111 11 11334467777766644 888899999988887
Q ss_pred C
Q 039381 77 G 77 (138)
Q Consensus 77 G 77 (138)
-
T Consensus 171 p 171 (201)
T PF12916_consen 171 P 171 (201)
T ss_dssp H
T ss_pred h
Confidence 4
No 125
>cd08495 PBP2_NikA_DppA_OppA_like_8 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=35.48 E-value=1.2e+02 Score=24.99 Aligned_cols=23 Identities=30% Similarity=0.355 Sum_probs=19.6
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+.+..+.+|++|++|++.
T Consensus 204 ~~~~~d~~~~~~~l~~G~iD~~~ 226 (482)
T cd08495 204 LIPMPDANARLAALLSGQVDAIE 226 (482)
T ss_pred EEEcCCHHHHHHHHHcCCCceec
Confidence 56677888999999999999864
No 126
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=34.24 E-value=48 Score=25.07 Aligned_cols=49 Identities=10% Similarity=0.165 Sum_probs=31.9
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYL 63 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~ 63 (138)
+..++.++|.+|++|.++...+. ....+ ....+..+.+.+++++++|+.
T Consensus 128 ~~~~~~~~l~~g~~Dl~i~~~~~-------~~~~l-~~~~l~~~~~~~~~~~~~pl~ 176 (296)
T PRK11242 128 SQERIEALLADDELDVGIAFAPV-------HSPEI-EAQPLFTETLALVVGRHHPLA 176 (296)
T ss_pred CHHHHHHHHHCCCCcEEEEecCC-------CCcce-eEEEeeeccEEEEEcCCCccc
Confidence 45778889999999999864321 11112 223345677788888888764
No 127
>PRK15104 oligopeptide ABC transporter substrate-binding protein OppA; Provisional
Probab=33.82 E-value=1.5e+02 Score=25.08 Aligned_cols=23 Identities=35% Similarity=0.408 Sum_probs=18.4
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+.+....+|++|++|++.
T Consensus 249 ~~~~~d~~~~~~al~~GeiD~~~ 271 (543)
T PRK15104 249 YLPISSEVTDVNRYRSGEIDMTY 271 (543)
T ss_pred EEEecCchHHHHHHHCCCcceec
Confidence 35567778888999999999764
No 128
>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=33.44 E-value=68 Score=21.61 Aligned_cols=49 Identities=14% Similarity=0.190 Sum_probs=30.5
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYL 63 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~ 63 (138)
+..+..+.|.+|++|.++...+.. .. .+ ....+..+.+.++++++.|+.
T Consensus 37 ~~~~~~~~l~~~~~Dl~i~~~~~~------~~-~~-~~~~l~~~~~~~v~~~~~~l~ 85 (196)
T cd08415 37 SSSTVVEAVLSGQADLGLASLPLD------HP-GL-ESEPLASGRAVCVLPPGHPLA 85 (196)
T ss_pred chHHHHHHHHcCCccEEEEeCCCC------CC-cc-eeeeecccceEEEEcCCCChH
Confidence 446778889999999988643311 11 12 222344667778888887754
No 129
>cd08489 PBP2_NikA The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides,
Probab=32.99 E-value=1.6e+02 Score=24.22 Aligned_cols=23 Identities=30% Similarity=0.380 Sum_probs=19.3
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+++.+..+++|.+|++|++.
T Consensus 191 ~~~~~~~~~~~~al~~G~iD~~~ 213 (488)
T cd08489 191 VKVIPDAQTRLLALQSGEIDLIY 213 (488)
T ss_pred EEEcCCHHHHHHHHHcCCccEec
Confidence 45667888899999999999875
No 130
>PRK11899 prephenate dehydratase; Provisional
Probab=32.75 E-value=61 Score=25.52 Aligned_cols=24 Identities=25% Similarity=0.220 Sum_probs=21.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~ 25 (138)
++.+++.++++.+|.+|++|..|.
T Consensus 30 ~v~~~s~~~vf~av~~g~~d~gVv 53 (279)
T PRK11899 30 PLPCATFEDAFEAVESGEADLAMI 53 (279)
T ss_pred eeecCCHHHHHHHHHCCCCCEEEE
Confidence 567999999999999999987665
No 131
>PRK11898 prephenate dehydratase; Provisional
Probab=32.61 E-value=61 Score=25.44 Aligned_cols=57 Identities=14% Similarity=0.046 Sum_probs=36.7
Q ss_pred eeecCCHHHHHHHHHcCCceEEEec--HH----HHHHH--HHhcCCCee-eCCCCCcceeEEEEeCC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLE--VP----YVKLF--LAKNCKNFT-TGPTYSVGGFGFAFPKD 59 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d--~~----~l~~~--~~~~~~~~~-~~~~~~~~~~g~a~~Kg 59 (138)
++.+++.++.+.+|.+|++|..|.. .. +...+ +.+.. .+. +++..-...+.++.+++
T Consensus 30 ~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~v~~~~d~L~~~~-~~~iv~E~~l~I~~~L~~~~~ 95 (283)
T PRK11898 30 LVPYDSIPDVLDAVEAGEVDYAVVPIENSIEGSVNPTLDYLAHGS-PLQIVAEIVLPIAQHLLVHPG 95 (283)
T ss_pred eEecCCHHHHHHHHHcCCCCEEEEEecccCceecHHHHHHhccCC-CcEEEEEEEeeeeEEEeCCCC
Confidence 5789999999999999999877763 11 11111 11222 366 77666666677766555
No 132
>cd08425 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold. CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding
Probab=32.47 E-value=79 Score=21.42 Aligned_cols=50 Identities=8% Similarity=0.104 Sum_probs=31.9
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYLA 64 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~~ 64 (138)
+..+..+.|.+|++|..+...+. ....+. ...+..+.+.++.+++.|+..
T Consensus 38 ~~~~~~~~l~~g~~Dl~i~~~~~-------~~~~~~-~~~l~~~~~~~v~~~~~pl~~ 87 (197)
T cd08425 38 PQERIEAALADDRLDLGIAFAPV-------RSPDID-AQPLFDERLALVVGATHPLAQ 87 (197)
T ss_pred cHHHHHHHHHcCCccEEEEecCC-------CCCCcE-EEEeccccEEEEecCCCchhH
Confidence 45677889999999998864331 111122 223456677888888887543
No 133
>cd08504 PBP2_OppA The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which
Probab=32.44 E-value=1.3e+02 Score=24.82 Aligned_cols=24 Identities=25% Similarity=0.187 Sum_probs=19.4
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~ 25 (138)
++.+.+.+....+|++|++|++-.
T Consensus 211 ~~~~~d~~~~~~al~~GeiD~~~~ 234 (498)
T cd08504 211 FLVIKDPNTALNLFEAGELDIAGL 234 (498)
T ss_pred EEEEECcHHHHHHHHcCCCccccC
Confidence 456777888999999999997643
No 134
>cd08508 PBP2_NikA_DppA_OppA_like_1 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=32.25 E-value=1.7e+02 Score=24.03 Aligned_cols=24 Identities=25% Similarity=0.167 Sum_probs=19.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~ 25 (138)
++.+.+......+|++|++|++-.
T Consensus 197 ~~~~~d~~~~~~al~~GeiD~~~~ 220 (470)
T cd08508 197 YRFIPNDASRELAFESGEIDMTQG 220 (470)
T ss_pred EEECCCHHHHHHHHhcCCcceecC
Confidence 355677788889999999998743
No 135
>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=30.60 E-value=64 Score=21.87 Aligned_cols=49 Identities=18% Similarity=0.222 Sum_probs=31.4
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYL 63 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~ 63 (138)
+..+..+.|.+|++|..+...+. ....+. ...+..+.+.++++++.|+.
T Consensus 37 ~~~~~~~~l~~g~~D~~i~~~~~-------~~~~~~-~~~l~~~~~~~v~~~~~pl~ 85 (198)
T cd08447 37 VTTDQIEALESGRIDLGLLRPPF-------ARPGLE-TRPLVREPLVAAVPAGHPLA 85 (198)
T ss_pred CHHHHHHHHHcCCceEEEecCCC-------CCCCee-EEEeecCceEEEecCCCchh
Confidence 46678899999999998863221 111122 22344667788888888764
No 136
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=30.31 E-value=1.1e+02 Score=22.56 Aligned_cols=77 Identities=8% Similarity=0.046 Sum_probs=51.4
Q ss_pred HHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCcceeEEEEeCCChhHHHHHHHHHHHhhcCcHHHHHHHh
Q 039381 8 ENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSVGGFGFAFPKDSAYLADFSQAILQLSEEGKLRELEEAM 86 (138)
Q Consensus 8 ~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~~~~l~~kW 86 (138)
..|...-+..|.+|..|.-..++.. +..+-+. ..-.|..-.+.+|.|++++.... ..+..++=-=+|..+.++|
T Consensus 49 ~~Dip~yV~~G~aDlGI~G~D~l~E---~~~~v~~~~dL~fg~crl~vA~p~~~~~~~~--~~l~~~rIATkyp~i~~~~ 123 (182)
T TIGR00070 49 PQDIPTYVEHGAADLGITGYDVLLE---SGADVYELLDLGFGKCRLVLAVPQESDISSV--EDLKGKRIATKYPNLARRY 123 (182)
T ss_pred cchhHHHHhCCCccEEEecchhhhh---CCCCEEEEeecCcCceEEEEEEECCCCCCCh--HHhCCCEEEECCHHHHHHH
Confidence 4567788999999999976555422 2333233 55678888999999999764321 2222344445688899999
Q ss_pred cCC
Q 039381 87 LSP 89 (138)
Q Consensus 87 ~~~ 89 (138)
|..
T Consensus 124 f~~ 126 (182)
T TIGR00070 124 FEK 126 (182)
T ss_pred HHH
Confidence 975
No 137
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=29.51 E-value=63 Score=25.60 Aligned_cols=54 Identities=11% Similarity=0.055 Sum_probs=36.4
Q ss_pred eeecCCHHHHHHHHHcCCceEEEec------HHHH---HHHHHhcCCCee-eCCCCCcceeEEEEeC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLE------VPYV---KLFLAKNCKNFT-TGPTYSVGGFGFAFPK 58 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d------~~~l---~~~~~~~~~~~~-~~~~~~~~~~g~a~~K 58 (138)
...+.+.+|++.++.+|.+|..|.. .++. ..+. .. .+. +|+..-.....++..+
T Consensus 29 ~~p~~ti~evf~ave~g~aD~gVVPIENS~eG~V~~tlDlL~--~~-~l~IvgE~~lpI~h~L~~~~ 92 (279)
T COG0077 29 LLPCSTIEDVFKAVENGEADYGVVPIENSIEGSVNETLDLLA--ET-DLQIVGEIVLPIHHCLLVKG 92 (279)
T ss_pred eccCCCHHHHHHHHHcCCCceEEEEeeecCCcchHHHHHhhc--cC-CcEEEEEEEEEEEEEEEecC
Confidence 3568899999999999999987752 2222 2222 22 367 8877767777777753
No 138
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=29.39 E-value=47 Score=25.09 Aligned_cols=52 Identities=19% Similarity=0.280 Sum_probs=32.5
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYLA 64 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~~ 64 (138)
+..+.+++|.+|++|..+...+.. .....+. -.++..+.+.++++++.|+..
T Consensus 134 ~~~~~~~~l~~g~~D~~i~~~~~~-----~~~~~l~-~~~l~~~~~~~v~~~~~~l~~ 185 (294)
T PRK09986 134 SPSMQMAALERRELDAGIWRMADL-----EPNPGFT-SRRLHESAFAVAVPEEHPLAS 185 (294)
T ss_pred CHHHHHHHHHcCCCCEEEecCCcc-----CCCCCeE-EEEeecccEEEEEcCCCCccc
Confidence 456788999999999988632100 0011122 123445788999999988643
No 139
>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=28.98 E-value=87 Score=21.49 Aligned_cols=49 Identities=14% Similarity=0.147 Sum_probs=31.6
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYL 63 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~ 63 (138)
+.++..+.|.+|++|..+...+. ....+. ...+..+.+.++++++.|+.
T Consensus 38 ~~~~~~~~l~~~~~Dl~i~~~~~-------~~~~~~-~~~l~~~~~~~v~~~~hpl~ 86 (203)
T cd08445 38 TTVQQIEALKEGRIDVGFGRLRI-------EDPAIR-RIVLREEPLVVALPAGHPLA 86 (203)
T ss_pred ChHHHHHHHHcCCCcEEEecCCC-------CCCCce-eEEEEeccEEEEeeCCCCCc
Confidence 46788899999999998854221 111122 22344667888888888753
No 140
>cd08509 PBP2_TmCBP_oligosaccharides_like The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of a cellulose-binding protein from the hyperthermophilic bacterium Thermotoga maritima (TmCBP) and its closest related proteins. TmCBP binds a variety of lengths of beta-1,4-linked glucose oligomers, ranging from two sugar rings (cellobiose) to five (cellopentose). TmCBP is structurally homologous to domains I and III of the ATP-binding cassette (ABC)-type oligopeptide-binding proteins and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. L
Probab=28.08 E-value=2e+02 Score=24.03 Aligned_cols=24 Identities=29% Similarity=0.228 Sum_probs=19.7
Q ss_pred eeecCCHHHHHHHHHcCCceEEEe
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~ 25 (138)
++.+.+......+|++|++|.+..
T Consensus 201 ~~~~~d~~~~~~al~~Ge~D~~~~ 224 (509)
T cd08509 201 YPAYSSNDQALLALANGEVDWAGL 224 (509)
T ss_pred EeecCCHHHHHHHHHcCCcceecc
Confidence 456778888999999999998653
No 141
>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=27.68 E-value=65 Score=21.69 Aligned_cols=49 Identities=16% Similarity=0.238 Sum_probs=31.0
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYL 63 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~ 63 (138)
+..+....|.+|++|..+...+.. .. .+. ..++..+.+.++++++.|+.
T Consensus 37 ~~~~~~~~l~~~~~Dl~i~~~~~~------~~-~~~-~~~l~~~~~~~v~~~~~~l~ 85 (197)
T cd08414 37 TTAEQLEALRAGRLDVGFVRPPPD------PP-GLA-SRPLLREPLVVALPADHPLA 85 (197)
T ss_pred ChHHHHHHHHcCCccEEEEcCCCC------CC-Cee-EEEEeeccEEEEecCCCccc
Confidence 356788899999999988653321 11 122 12344567788888887753
No 142
>PF06345 Drf_DAD: DRF Autoregulatory Domain; InterPro: IPR010465 This domain is found in Diaphanous-related formins (Drfs). It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of diaphanous activating domains (DAD) to mammalian cells induces actin filament formation, stabilises microtubules, and activates serum-response mediated transcription [].; PDB: 3O4X_H 3OBV_E 2BAP_C 2F31_B.
Probab=27.28 E-value=65 Score=13.77 Aligned_cols=12 Identities=25% Similarity=0.343 Sum_probs=8.3
Q ss_pred HHHHHHHHHcCC
Q 039381 8 ENRHRQALTSGE 19 (138)
Q Consensus 8 ~~e~~~aL~~G~ 19 (138)
++..++||+.|.
T Consensus 3 mdsllealqtg~ 14 (15)
T PF06345_consen 3 MDSLLEALQTGS 14 (15)
T ss_dssp HHHHHHHHHHST
T ss_pred HHHHHHHHHccC
Confidence 355678888775
No 143
>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=27.09 E-value=58 Score=25.18 Aligned_cols=57 Identities=12% Similarity=0.099 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHcCCceEEEecHHHH-HHH--HHhcCCCeeeCCCCCcceeEEEEeCCC-hhH
Q 039381 6 FSENRHRQALTSGEIAAAFLEVPYV-KLF--LAKNCKNFTTGPTYSVGGFGFAFPKDS-AYL 63 (138)
Q Consensus 6 ~~~~e~~~aL~~G~vdA~i~d~~~l-~~~--~~~~~~~~~~~~~~~~~~~g~a~~Kgs-pl~ 63 (138)
.+..+.+++|.+|++|+.+...+.. ... ..+....+ .-.++..+.+.+++++++ |+.
T Consensus 71 ~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l-~~~~l~~~~l~lvv~~~h~pl~ 131 (287)
T TIGR02136 71 AGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKL-IEHKVAVDGLAVVVNKKNVPVD 131 (287)
T ss_pred CCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCc-eEEEEEEeeEEEEECCCCCccc
Confidence 3567899999999999977754322 111 11111112 233456678888999997 864
No 144
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=27.06 E-value=58 Score=25.22 Aligned_cols=51 Identities=14% Similarity=0.081 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhH
Q 039381 6 FSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYL 63 (138)
Q Consensus 6 ~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~ 63 (138)
.+.++..+.|.+|++|..+...+.. ... .+.. .++..+.+.+++++++|+.
T Consensus 129 ~~~~~~~~~L~~~~~D~~i~~~~~~-----~~~-~l~~-~~l~~~~~~~v~~~~hpl~ 179 (309)
T PRK12683 129 GSPQEIAEMLLNGEADIGIATEALD-----REP-DLVS-FPYYSWHHVVVVPKGHPLT 179 (309)
T ss_pred CCHHHHHHHHHcCCccEEEecCCCC-----CCC-CceE-EEcccCeEEEEecCCCCcc
Confidence 3567889999999999988632110 011 1221 1244566677788888764
No 145
>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein. This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of this gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source.
Probab=25.32 E-value=1.2e+02 Score=22.91 Aligned_cols=28 Identities=14% Similarity=0.109 Sum_probs=22.8
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPY 29 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~ 29 (138)
+..|+..++.+++|++|.+++.+.-.|.
T Consensus 215 vvg~d~~~~~~~~l~~g~i~~~~~q~p~ 242 (302)
T TIGR02637 215 LTGLGLPSEMAKYVKNGTVKAFALWNPI 242 (302)
T ss_pred EEEcCCcHHHHHHHhcCccceEEEeCHH
Confidence 5678888889999999999998875553
No 146
>PRK00910 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=25.28 E-value=81 Score=24.07 Aligned_cols=23 Identities=26% Similarity=0.226 Sum_probs=19.3
Q ss_pred ecCCHHHHHHHHHcCCceEEEec
Q 039381 4 PIFSENRHRQALTSGEIAAAFLE 26 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G~vdA~i~d 26 (138)
.++++++++++|++|+.-.++.|
T Consensus 13 ~~~~ie~ai~al~~G~~Viv~Dd 35 (218)
T PRK00910 13 PITRVENALQALREGRGVLLLDD 35 (218)
T ss_pred ccccHHHHHHHHHCCCeEEEEeC
Confidence 46789999999999998777764
No 147
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=24.81 E-value=57 Score=25.33 Aligned_cols=81 Identities=12% Similarity=0.106 Sum_probs=47.2
Q ss_pred HHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee-eCCCCCc-c-eeEEEEeC----CCh-----hHHHHHHHHHHHhh
Q 039381 8 ENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT-TGPTYSV-G-GFGFAFPK----DSA-----YLADFSQAILQLSE 75 (138)
Q Consensus 8 ~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~-~~~~~~~-~-~~g~a~~K----gsp-----l~~~in~~l~~l~~ 75 (138)
.+++..+|.+|++||++.-.|.......+....+. .+..... . ...+.+++ .+| +++.+-++...+.+
T Consensus 173 ~~~~~~al~~g~vda~~~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~l~a~~~a~~~~~~ 252 (335)
T COG0715 173 PADAVAALAAGQVDAFVVWEPWNAAAEGEGGGRVLLDGADLWGNHPELVLVVRKEFIEANPEAVKAFLKALAKATAWANA 252 (335)
T ss_pred cHHHHHHHhcCCcceEEecCCchhhhhccCCeEEEEcchhhhccCchhhhhhHHHHHHHCHHHHHHHHHHHHHHHHHHHH
Confidence 45889999999999988877877666555432133 3333322 2 23333332 133 45555555556666
Q ss_pred -cCcHHHHHHHhcC
Q 039381 76 -EGKLRELEEAMLS 88 (138)
Q Consensus 76 -~G~~~~l~~kW~~ 88 (138)
.-+..++..+..+
T Consensus 253 ~p~~a~~~~~~~~~ 266 (335)
T COG0715 253 HPDEAAEILAKAAG 266 (335)
T ss_pred CHHHHHHHHHHHhc
Confidence 3446667777766
No 148
>TIGR03061 pip_yhgE_Nterm YhgE/Pip N-terminal domain. This family contains the N-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03062, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057.
Probab=24.43 E-value=1e+02 Score=21.63 Aligned_cols=19 Identities=16% Similarity=0.249 Sum_probs=16.5
Q ss_pred CHHHHHHHHHcCCceEEEe
Q 039381 7 SENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~ 25 (138)
+.+++-++|++|++++++.
T Consensus 84 ~~~ea~~~l~~g~~~~~iv 102 (164)
T TIGR03061 84 SAKEAEKGLADGKYYMVIT 102 (164)
T ss_pred CHHHHHHHhHcCcEEEEEE
Confidence 7788889999999998886
No 149
>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=24.12 E-value=2.4e+02 Score=19.15 Aligned_cols=67 Identities=12% Similarity=-0.016 Sum_probs=42.3
Q ss_pred eecCCHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee---eCC-CCCcceeEEEEeCCChhHHHHHHHHHHH
Q 039381 3 EPIFSENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT---TGP-TYSVGGFGFAFPKDSAYLADFSQAILQL 73 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~---~~~-~~~~~~~g~a~~Kgspl~~~in~~l~~l 73 (138)
...++...+...+.+|..-+++-+.....+. .. .. +. +.. .+. ..+.++.+++.+....+...+..+
T Consensus 134 ~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~-~~-~~-l~~~~~~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~l 204 (209)
T PF03466_consen 134 IEVDSFESILSLVASGDGIAILPDSLAQDEL-ES-GE-LVFLPLPDPPLP-RPIYLVWRKDRPLSPAIQWFIDLL 204 (209)
T ss_dssp EEESSHHHHHHHHHTTSEBEEEEHHHHHHHH-HC-TT-EEEEEESSSTEE-EEEEEEEETTGTTHHHHHHHHHHH
T ss_pred ccccchhhhccccccccceeecCcccccccc-cC-CC-EEEEECCCCCCc-eEEEEEEECCCCCCHHHHHHHHHH
Confidence 4578889999999999887877764443333 22 22 33 444 444 778889999865444444444333
No 150
>PLN02317 arogenate dehydratase
Probab=24.06 E-value=1e+02 Score=25.53 Aligned_cols=56 Identities=13% Similarity=-0.050 Sum_probs=34.6
Q ss_pred eeecCCHHHHHHHHHcCCceEEEec--HHH----HH-H-HHHhcCCCee-eCCCCCcceeEEEEeCC
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLE--VPY----VK-L-FLAKNCKNFT-TGPTYSVGGFGFAFPKD 59 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d--~~~----l~-~-~~~~~~~~~~-~~~~~~~~~~g~a~~Kg 59 (138)
++.+++.++++++|..|++|..|.. ..+ .. | .+.+ . .+. +++..-....-+...+|
T Consensus 120 ~vp~~sf~~vf~AVe~g~ad~gVvPIENS~~GsV~~t~DlL~~-~-~l~IvgEv~l~I~h~Ll~~~g 184 (382)
T PLN02317 120 AVPCEQFEAAFQAVELWLADRAVLPIENSLGGSIHRNYDLLLR-H-RLHIVGEVQLPVHHCLLALPG 184 (382)
T ss_pred eeecCCHHHHHHHHHCCCCCEEEEEEeccCccchHHHHHHHhc-C-CCEEEEEEEEEeeeEEecCCC
Confidence 5689999999999999999977652 211 11 1 1111 2 256 77665555555554455
No 151
>COG4166 OppA ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]
Probab=24.04 E-value=2e+02 Score=24.70 Aligned_cols=68 Identities=24% Similarity=0.184 Sum_probs=40.1
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHHH---HHHHHHhc-CCCeeeCCCCCcceeEEEEeCC-----Ch-hHHHHHHHHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVPY---VKLFLAKN-CKNFTTGPTYSVGGFGFAFPKD-----SA-YLADFSQAIL 71 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~~---l~~~~~~~-~~~~~~~~~~~~~~~g~a~~Kg-----sp-l~~~in~~l~ 71 (138)
+..+++...+++++++|++|......+. ..+..... ...+..... ...+.+++... ++ +|+.|+.++.
T Consensus 254 ~~~~~d~~~~~~~f~~G~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~fN~~~~~f~d~~vR~ALslaiD 331 (562)
T COG4166 254 YDYIDDANTALEAFKAGEIDIASEPPASPWALDYVLKLKDNGDVYKEPT--LGTQYLAFNTRRPPFNDPRVRKALSLAID 331 (562)
T ss_pred EEEEcCChHHHHHHhcCCcceeccccccchhhhhhhhhccCCcEEEccc--CceEEEEecCCCccccCHHHHHHHHHhhh
Confidence 4457788889999999999999875322 23333332 333442222 33455555443 23 6777777665
No 152
>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A.
Probab=22.96 E-value=32 Score=22.47 Aligned_cols=9 Identities=44% Similarity=1.129 Sum_probs=3.8
Q ss_pred hhccCCCCC
Q 039381 130 EMENRGLWP 138 (138)
Q Consensus 130 ~~~~~~~~~ 138 (138)
++..||+||
T Consensus 79 ~rn~DGtWP 87 (88)
T PF14836_consen 79 ERNEDGTWP 87 (88)
T ss_dssp E--TTS--T
T ss_pred eeccCCCCC
Confidence 456689998
No 153
>PF10991 DUF2815: Protein of unknown function (DUF2815); InterPro: IPR022595 This entry is represented by Bacteriophage APSE-1, protein 50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.72 E-value=1.4e+02 Score=22.11 Aligned_cols=31 Identities=26% Similarity=0.182 Sum_probs=25.8
Q ss_pred ceeEEEEeCCCh-hHHHHHHHHHHHhhcCcHH
Q 039381 50 GGFGFAFPKDSA-YLADFSQAILQLSEEGKLR 80 (138)
Q Consensus 50 ~~~g~a~~Kgsp-l~~~in~~l~~l~~~G~~~ 80 (138)
-...+.+||.++ ..+.|..+|.+..+.|.-.
T Consensus 30 Ys~t~lipK~d~~t~~~I~~Ai~~a~~~~~~~ 61 (181)
T PF10991_consen 30 YSATLLIPKSDKETIAAIKAAIEAAIEEGWGN 61 (181)
T ss_pred eeEEEEEcCCCHHHHHHHHHHHHHHHHhcccc
Confidence 346678899987 7999999999999998744
No 154
>PRK10752 sulfate transporter subunit; Provisional
Probab=22.62 E-value=3.6e+02 Score=21.58 Aligned_cols=32 Identities=13% Similarity=0.106 Sum_probs=22.3
Q ss_pred ecCCHHHHHHHHHcC-CceEEEecH-HHHHHHHH
Q 039381 4 PIFSENRHRQALTSG-EIAAAFLEV-PYVKLFLA 35 (138)
Q Consensus 4 ~~~~~~e~~~aL~~G-~vdA~i~d~-~~l~~~~~ 35 (138)
+|.+..+...++.+| .+|.++... .....+.+
T Consensus 60 s~ggSg~l~~qI~~g~~aDV~~~a~~~~~~~l~~ 93 (329)
T PRK10752 60 SHGGSGKQATSVINGIEADVVTLALAYDVDAIAE 93 (329)
T ss_pred CCCChHHHHHHHHcCCCCCEEEeCCHHHHHHHHH
Confidence 567788889999876 589988754 44444443
No 155
>TIGR03270 methan_mark_4 putative methanogen marker protein 4. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely linked to it. Some members have been suggested to be a methyltransferase, based on the proximity of its gene to genes of the multi-subunit complex, N5-methyl-tetrahydromethanopterin--coenzyme M methyltransferase. That context is not conserved, however. The family shows similarity to various phosphate acyltranferases.
Probab=22.54 E-value=93 Score=23.46 Aligned_cols=23 Identities=26% Similarity=0.187 Sum_probs=18.8
Q ss_pred eecCCHHHHHHHHHcCCceEEEe
Q 039381 3 EPIFSENRHRQALTSGEIAAAFL 25 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~ 25 (138)
+.-+...+.++.+++|++|+++=
T Consensus 2 ~~~~~~~~lv~lv~~G~ad~lmK 24 (202)
T TIGR03270 2 ELEDPEEELIDDLVNGRLDAAVR 24 (202)
T ss_pred cccCCHHHHHHHHHCCCCCEEEe
Confidence 44567788889999999999884
No 156
>KOG1348 consensus Asparaginyl peptidases [Posttranslational modification, protein turnover, chaperones]
Probab=22.52 E-value=65 Score=26.86 Aligned_cols=29 Identities=10% Similarity=0.460 Sum_probs=22.6
Q ss_pred EEEeCCCh-hHHHHHHHHHHHhhcCcHHHH
Q 039381 54 FAFPKDSA-YLADFSQAILQLSEEGKLREL 82 (138)
Q Consensus 54 ~a~~Kgsp-l~~~in~~l~~l~~~G~~~~l 82 (138)
++||-+.. ..+.+|..|..|.++|+|+++
T Consensus 170 l~mP~~~~l~akdlnevL~kmhk~k~Y~~m 199 (477)
T KOG1348|consen 170 LGMPTSPDLYAKDLNEVLKKMHKSKTYKKM 199 (477)
T ss_pred EecCCCcchhHHHHHHHHHHHHhccchheE
Confidence 45555433 789999999999999999754
No 157
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=22.46 E-value=74 Score=24.12 Aligned_cols=50 Identities=14% Similarity=0.212 Sum_probs=33.3
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYLA 64 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~~ 64 (138)
+.++.+..|.+|++|.++...+. ....+. ..++..+.+.++++++.|+..
T Consensus 127 ~~~~~~~~l~~~~~D~~i~~~~~-------~~~~l~-~~~l~~~~~~~v~~~~~pl~~ 176 (296)
T PRK09906 127 ITTQQEEKLRRGELDVGFMRHPV-------YSDEID-YLELLDEPLVVVLPVDHPLAH 176 (296)
T ss_pred CcHHHHHHHHcCCeeEEEecCCC-------CCCCce-EEEEecccEEEEecCCCcccc
Confidence 35677899999999999975432 111122 234566778888998888643
No 158
>TIGR00506 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase. Several members of the family are bifunctional, involving both ribA and ribB function. In these cases, ribA tends to be on the C-terminal end of the protein and ribB tends to be on the N-terminal.
Probab=22.19 E-value=1e+02 Score=23.19 Aligned_cols=22 Identities=23% Similarity=0.283 Sum_probs=18.4
Q ss_pred cCCHHHHHHHHHcCCceEEEec
Q 039381 5 IFSENRHRQALTSGEIAAAFLE 26 (138)
Q Consensus 5 ~~~~~e~~~aL~~G~vdA~i~d 26 (138)
|+++++++++|++|+.-.++.|
T Consensus 2 ~~~ie~ai~al~~G~~Viv~Dd 23 (199)
T TIGR00506 2 FERVEEALEALKKGEIVLVYDD 23 (199)
T ss_pred cchHHHHHHHHHCCCeEEEEeC
Confidence 5778999999999998777664
No 159
>cd08505 PBP2_NikA_DppA_OppA_like_18 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=21.99 E-value=3.3e+02 Score=23.02 Aligned_cols=23 Identities=4% Similarity=-0.146 Sum_probs=18.9
Q ss_pred eeecCCHHHHHHHHHcCCceEEE
Q 039381 2 IEPIFSENRHRQALTSGEIAAAF 24 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i 24 (138)
++.+.+.+..+.+|++|++|+.-
T Consensus 225 ~~~~~d~~~~~~al~~GeiD~~~ 247 (528)
T cd08505 225 FSLEKEAQPRWLKFLQGYYDVSG 247 (528)
T ss_pred EEEeCCHHHHHHHHHCCCCcEec
Confidence 45567788889999999999863
No 160
>COG5436 Predicted integral membrane protein [Function unknown]
Probab=21.56 E-value=1.3e+02 Score=21.92 Aligned_cols=57 Identities=12% Similarity=0.166 Sum_probs=28.0
Q ss_pred HHcCCceEEEecHHHHHHHHHhcCCCee---eCCCCCcceeEE--EEeCCChhHHHHHHHHH
Q 039381 15 LTSGEIAAAFLEVPYVKLFLAKNCKNFT---TGPTYSVGGFGF--AFPKDSAYLADFSQAIL 71 (138)
Q Consensus 15 L~~G~vdA~i~d~~~l~~~~~~~~~~~~---~~~~~~~~~~g~--a~~Kgspl~~~in~~l~ 71 (138)
...|+.|++|.+..-+....+..+..++ +-+.-..++|++ ++-+++.+...++..+.
T Consensus 111 a~~gkLDlVvatPiqmi~lrkd~pe~~t~aI~veakd~eG~avlR~fvPdds~~~qv~rfld 172 (182)
T COG5436 111 AKGGKLDLVVATPIQMILLRKDGPEVLTDAIFVEAKDEEGFAVLRTFVPDDSWIPQVDRFLD 172 (182)
T ss_pred ccCCccceEEecchhheeeccccchhccccEEEEecCCCceEEEEEecCccccHHHHHHHHH
Confidence 4678999999984444333333333222 112223444444 23344445555554443
No 161
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=21.53 E-value=2.2e+02 Score=19.98 Aligned_cols=40 Identities=20% Similarity=0.228 Sum_probs=30.8
Q ss_pred ceeEEEEeCCCh-hHHHHHHHHHHHhhcCcHHHHHHHhcCC
Q 039381 50 GGFGFAFPKDSA-YLADFSQAILQLSEEGKLRELEEAMLSP 89 (138)
Q Consensus 50 ~~~g~a~~Kgsp-l~~~in~~l~~l~~~G~~~~l~~kW~~~ 89 (138)
.+-+|-+|+|+. -....|..|-.=-+.-.+.+|.+||--+
T Consensus 75 GGrsfYlP~G~s~r~t~Rn~~ifsd~dG~n~~eLaKkYrlS 115 (137)
T COG5566 75 GGRSFYLPKGDSIRATLRNKQIFSDFDGSNYVELAKKYRLS 115 (137)
T ss_pred CCeeEEeeCchHHHHHHHHHHHHHhcCCccHHHHHHHhccc
Confidence 467899999977 5666788777766666899999998543
No 162
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=21.47 E-value=1.1e+02 Score=19.04 Aligned_cols=25 Identities=8% Similarity=0.050 Sum_probs=21.6
Q ss_pred eeecCCHHHHHHHHHcCCceEEEec
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLE 26 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d 26 (138)
+..+.+.+++++.+.+...|.++.|
T Consensus 26 v~~~~~~~~~~~~~~~~~~d~iiid 50 (112)
T PF00072_consen 26 VTTASSGEEALELLKKHPPDLIIID 50 (112)
T ss_dssp EEEESSHHHHHHHHHHSTESEEEEE
T ss_pred EEEECCHHHHHHHhcccCceEEEEE
Confidence 4567889999999999999999877
No 163
>COG4890 Predicted outer membrane lipoprotein [Function unknown]
Probab=21.29 E-value=40 Score=18.12 Aligned_cols=6 Identities=50% Similarity=1.403 Sum_probs=4.6
Q ss_pred hhhhhh
Q 039381 125 WLSAWE 130 (138)
Q Consensus 125 ~~~~~~ 130 (138)
|+|+|-
T Consensus 2 WYFaWi 7 (37)
T COG4890 2 WYFAWI 7 (37)
T ss_pred hhHHHH
Confidence 788884
No 164
>PRK13895 conjugal transfer protein TraM; Provisional
Probab=20.94 E-value=1e+02 Score=21.98 Aligned_cols=38 Identities=18% Similarity=0.277 Sum_probs=27.9
Q ss_pred eEEEEeCCCh--hHHHHHHHHHHHhhc----------CcHHHHHHHhcCC
Q 039381 52 FGFAFPKDSA--YLADFSQAILQLSEE----------GKLRELEEAMLSP 89 (138)
Q Consensus 52 ~g~a~~Kgsp--l~~~in~~l~~l~~~----------G~~~~l~~kW~~~ 89 (138)
-||++.+++| .+..+|..|.+=.+. .+++.+..+|-..
T Consensus 16 HGIal~rDDPILilqTiNerLlees~kAQq~mL~~FkeelE~iasrW~~d 65 (144)
T PRK13895 16 HGIAVGRDDPILILQTINDRLMQDSAKAQQEMLDQFKEELESIASRWGDD 65 (144)
T ss_pred cCcccCCCCCchhHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 4799999999 488899887642221 4778888888764
No 165
>PRK09501 potD spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed
Probab=20.85 E-value=4.2e+02 Score=20.79 Aligned_cols=79 Identities=10% Similarity=0.042 Sum_probs=39.8
Q ss_pred eecCCHHHHHHHHHcCCceEEEe-cHHHHHHHHHhcCCCee-e-CCC-CCcceeEEEEeCCChhHHHHHHHHHHHhhcCc
Q 039381 3 EPIFSENRHRQALTSGEIAAAFL-EVPYVKLFLAKNCKNFT-T-GPT-YSVGGFGFAFPKDSAYLADFSQAILQLSEEGK 78 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~-d~~~l~~~~~~~~~~~~-~-~~~-~~~~~~g~a~~Kgspl~~~in~~l~~l~~~G~ 78 (138)
..|.+ .+..+++.+|++++.+. +.... . ..+....+. + ++. -..-.-+++++|+++-.+.--+.|.-|.....
T Consensus 207 ~~~~~-~~~~~~l~~Gev~i~~~w~~~~~-~-~~~~g~~i~~~~P~eG~~~~~~~~~i~k~a~n~e~A~~Fi~~llspe~ 283 (348)
T PRK09501 207 AAFNS-DNPANPYMEGEVNLGMIWNGSAF-V-ARQAGTPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDV 283 (348)
T ss_pred EEEcC-cHHHHHHHcCCEEEEEeehHHHH-H-HHhcCCCceEEecCCCcceEEEeeeEECCCCCHHHHHHHHHHHhCHHH
Confidence 34433 34567899999997665 43322 2 222222344 2 221 11222478999998755555555554444333
Q ss_pred HHHHHH
Q 039381 79 LRELEE 84 (138)
Q Consensus 79 ~~~l~~ 84 (138)
-..+.+
T Consensus 284 q~~~~~ 289 (348)
T PRK09501 284 AKQVAE 289 (348)
T ss_pred HHHHHH
Confidence 333333
No 166
>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=20.58 E-value=2.1e+02 Score=22.95 Aligned_cols=39 Identities=13% Similarity=0.181 Sum_probs=31.7
Q ss_pred cceeEEEEeCCC-hhHHHHHHHHHHHhhcCcHHHHHHHhc
Q 039381 49 VGGFGFAFPKDS-AYLADFSQAILQLSEEGKLRELEEAML 87 (138)
Q Consensus 49 ~~~~g~a~~Kgs-pl~~~in~~l~~l~~~G~~~~l~~kW~ 87 (138)
-..+-|++..+. .|.+.|+..+..|.++|-++++..-+-
T Consensus 189 ~~~~~~~l~~~r~~L~~rI~~R~d~Ml~~Gli~EV~~L~~ 228 (308)
T COG0324 189 YDILIIALAADREVLYERINRRVDAMLEQGLIEEVKALYA 228 (308)
T ss_pred cceEEEEEeCCHHHHHHHHHHHHHHHHHccHHHHHHHHHh
Confidence 345667777664 499999999999999999999887773
No 167
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=20.57 E-value=1.8e+02 Score=23.08 Aligned_cols=27 Identities=19% Similarity=0.014 Sum_probs=22.0
Q ss_pred eeecCCHHHHHHHHHcCCceEEEecHH
Q 039381 2 IEPIFSENRHRQALTSGEIAAAFLEVP 28 (138)
Q Consensus 2 i~~~~~~~e~~~aL~~G~vdA~i~d~~ 28 (138)
+..|++.+++.+++++|.+++.+.-.|
T Consensus 238 VvG~D~~~~~~~~i~~G~i~~~~~~~p 264 (336)
T PRK15408 238 IVGFSTPNVMRPYVKRGTVKEFGLWDV 264 (336)
T ss_pred EEEeCCcHHHHHHHhcCCcceEEecCH
Confidence 567899999999999999998875444
No 168
>cd08510 PBP2_Lactococcal_OppA_like The substrate binding component of an ABC-type lactococcal OppA-like transport system contains. This family represents the substrate binding domain of an ATP-binding cassette (ABC)-type oligopeptide import system from Lactococcus lactis and other gram-positive bacteria, as well as its closet homologs from gram-negative bacteria. Oligopeptide-binding protein (OppA) from Lactococcus lactis can bind peptides of length from 4 to at least 35 residues without sequence preference. The oligopeptide import system OppABCDEF is consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in sev
Probab=20.49 E-value=3.6e+02 Score=22.46 Aligned_cols=23 Identities=22% Similarity=0.091 Sum_probs=17.5
Q ss_pred eecCCHHHHHHHHHcCCceEEEec
Q 039381 3 EPIFSENRHRQALTSGEIAAAFLE 26 (138)
Q Consensus 3 ~~~~~~~e~~~aL~~G~vdA~i~d 26 (138)
+.++ ......+|++|++|++...
T Consensus 219 ~~~~-~~~~~~al~~GeiD~~~~~ 241 (516)
T cd08510 219 KVVS-PSTIVAALKSGKYDIAESP 241 (516)
T ss_pred EEcC-hHHHHHHHHCCCcceecCC
Confidence 4454 4667899999999998654
No 169
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=20.40 E-value=86 Score=24.42 Aligned_cols=50 Identities=12% Similarity=0.020 Sum_probs=32.7
Q ss_pred CHHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhHH
Q 039381 7 SENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYLA 64 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~~ 64 (138)
...+....|.+|++|++|...+. ....+. -..+..+.+.++++++.|+.+
T Consensus 126 ~~~~~~~~L~~g~~Dl~i~~~~~-------~~~~~~-~~~l~~~~~~lv~~~~hpl~~ 175 (317)
T PRK15421 126 VTFDPQPALQQGELDLVMTSDIL-------PRSGLH-YSPMFDYEVRLVLAPDHPLAA 175 (317)
T ss_pred ccHHHHHHHHCCCcCEEEecCcc-------cCCCce-EEEeccceEEEEEcCCCCccc
Confidence 45678899999999999874321 111122 233556778888888888644
No 170
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=20.31 E-value=1e+02 Score=23.69 Aligned_cols=50 Identities=16% Similarity=0.224 Sum_probs=29.6
Q ss_pred HHHHHHHHcCCceEEEecHHHHHHHHHhcCCCee----eCCCCCcceeEEEEeCC
Q 039381 9 NRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFT----TGPTYSVGGFGFAFPKD 59 (138)
Q Consensus 9 ~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~----~~~~~~~~~~g~a~~Kg 59 (138)
..-+++|.+|+.|-+|.....+..++++..+ +. +|..--...-.+.++++
T Consensus 53 ~~Rie~l~~g~yDfaVvS~lAA~~~i~~~~~-l~i~~~fG~~sYvs~Hvli~~~~ 106 (232)
T PF14503_consen 53 ENRIEALKNGRYDFAVVSKLAAEHYIEEGED-LEIVLEFGPGSYVSEHVLIFRDG 106 (232)
T ss_dssp HHHHHHHHTTS-SEEEEEHHHHCCCCCC-SS-EEEEEE--TTSSS--EEEEEETT
T ss_pred hHHHHHHHhCCcceEeehHHHHHHHHhhccC-eEEEEeeCCCCcccceEEEEecC
Confidence 4457899999999999998888777766432 33 44433334445555554
No 171
>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=20.24 E-value=77 Score=21.55 Aligned_cols=48 Identities=13% Similarity=-0.004 Sum_probs=29.4
Q ss_pred HHHHHHHHHcCCceEEEecHHHHHHHHHhcCCCeeeCCCCCcceeEEEEeCCChhH
Q 039381 8 ENRHRQALTSGEIAAAFLEVPYVKLFLAKNCKNFTTGPTYSVGGFGFAFPKDSAYL 63 (138)
Q Consensus 8 ~~e~~~aL~~G~vdA~i~d~~~l~~~~~~~~~~~~~~~~~~~~~~g~a~~Kgspl~ 63 (138)
..+..++|.+|++|..+...+. ....+. ...+..+.+.++++++.|+.
T Consensus 38 ~~~~~~~l~~~~~Dl~i~~~~~-------~~~~~~-~~~l~~~~~~~~~~~~~~l~ 85 (196)
T cd08457 38 SSQVLEAVASGRADLGIADGPL-------EERQGF-LIETRSLPAVVAVPMGHPLA 85 (196)
T ss_pred cHHHHHHHHcCCccEEEeccCC-------CCCCcE-EEEeccCCeEEEeeCCCccc
Confidence 4567788999999998864321 111122 12244566778888877653
No 172
>COG2113 ProX ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]
Probab=20.08 E-value=1.7e+02 Score=23.30 Aligned_cols=53 Identities=19% Similarity=0.202 Sum_probs=33.7
Q ss_pred CHHHHHHHHHcCCceEEEec-HHHH-HHHHHhc-CCCee-eCCCCCcceeEEEEeCC
Q 039381 7 SENRHRQALTSGEIAAAFLE-VPYV-KLFLAKN-CKNFT-TGPTYSVGGFGFAFPKD 59 (138)
Q Consensus 7 ~~~e~~~aL~~G~vdA~i~d-~~~l-~~~~~~~-~~~~~-~~~~~~~~~~g~a~~Kg 59 (138)
+..-+++.|.+|++|++... .|.. ..+.+.. ...+. .+.......+|+++|+=
T Consensus 67 ~~~~~~~sla~gd~D~~~~~W~p~~~~~~~~~~~~~~v~~~~~~~~Ga~~g~~vp~y 123 (302)
T COG2113 67 DTAVMYQSLAKGDLDVFPEAWLPTTPDDYKKAVKDKKVELGGTNLEGAKQGWAVPKY 123 (302)
T ss_pred cHHHHHHHHHcCCCccccceecCCChHHHHHHhccCceeecccccCCceEEEEecee
Confidence 45668999999999998765 3333 2222322 33344 55344567799999874
Done!