Query psy17442
Match_columns 90
No_of_seqs 150 out of 1030
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 22:34:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17442.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17442hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00079 PBPe Eukaryotic hom 99.9 6.8E-22 1.5E-26 118.8 9.4 84 4-88 50-133 (134)
2 KOG1053|consensus 99.8 7.6E-20 1.7E-24 135.0 5.7 87 2-88 716-806 (1258)
3 KOG4440|consensus 99.8 9E-19 1.9E-23 126.2 5.4 87 2-88 719-805 (993)
4 PRK10797 glutamate and asparta 99.6 7.6E-15 1.6E-19 99.2 9.3 87 4-90 183-273 (302)
5 PRK09495 glnH glutamine ABC tr 99.5 1.1E-13 2.4E-18 90.5 8.7 85 5-89 158-244 (247)
6 PRK11260 cystine transporter s 99.5 1.2E-13 2.7E-18 91.2 9.0 87 4-90 175-263 (266)
7 PF00497 SBP_bac_3: Bacterial 99.5 1.3E-13 2.7E-18 87.4 8.3 86 4-89 137-225 (225)
8 TIGR01096 3A0103s03R lysine-ar 99.5 4E-13 8.7E-18 87.4 9.1 84 4-87 158-250 (250)
9 PRK15007 putative ABC transpor 99.4 1.2E-12 2.7E-17 85.0 8.6 84 5-88 153-242 (243)
10 PRK11917 bifunctional adhesin/ 99.4 1.8E-12 3.9E-17 85.8 8.7 81 4-88 178-259 (259)
11 TIGR02285 conserved hypothetic 99.4 1.5E-12 3.2E-17 86.2 7.9 84 5-88 169-261 (268)
12 COG0834 HisJ ABC-type amino ac 99.4 1.9E-12 4.1E-17 84.8 7.6 87 3-89 173-265 (275)
13 KOG1054|consensus 99.4 5.3E-13 1.2E-17 96.4 5.2 85 5-89 706-792 (897)
14 PRK15010 ABC transporter lysin 99.4 9E-12 1.9E-16 82.1 9.1 85 5-89 162-255 (260)
15 PRK10859 membrane-bound lytic 99.4 5.5E-12 1.2E-16 90.0 8.6 85 5-89 181-267 (482)
16 PRK15437 histidine ABC transpo 99.3 3.7E-11 8E-16 79.2 9.3 86 4-89 161-255 (259)
17 TIGR02995 ectoine_ehuB ectoine 99.3 2.7E-11 5.9E-16 80.5 8.6 86 4-89 171-262 (275)
18 KOG1052|consensus 99.3 3.2E-11 6.9E-16 88.6 9.0 85 4-89 485-573 (656)
19 TIGR03870 ABC_MoxJ methanol ox 99.2 1.2E-10 2.5E-15 76.5 8.6 79 8-88 152-243 (246)
20 smart00062 PBPb Bacterial peri 99.2 1.6E-10 3.5E-15 71.6 8.4 84 4-87 132-219 (219)
21 PRK09959 hybrid sensory histid 99.2 1.1E-10 2.5E-15 89.8 7.8 85 4-89 433-521 (1197)
22 cd00134 PBPb Bacterial peripla 99.2 3.4E-10 7.4E-15 70.3 8.6 84 4-87 131-218 (218)
23 TIGR03871 ABC_peri_MoxJ_2 quin 99.2 4E-10 8.7E-15 72.7 8.8 82 6-89 141-230 (232)
24 PRK09959 hybrid sensory histid 99.0 1.7E-09 3.7E-14 83.5 8.0 84 4-88 190-277 (1197)
25 TIGR01098 3A0109s03R phosphate 98.5 3.5E-07 7.6E-12 59.8 6.2 69 5-73 180-254 (254)
26 PRK00489 hisG ATP phosphoribos 98.4 1.1E-06 2.4E-11 59.3 5.6 78 5-89 140-220 (287)
27 COG4623 Predicted soluble lyti 98.2 1.2E-05 2.7E-10 56.4 7.3 82 7-88 164-247 (473)
28 TIGR03431 PhnD phosphonate ABC 98.2 7.3E-06 1.6E-10 54.8 6.1 81 7-87 176-265 (288)
29 PF12974 Phosphonate-bd: ABC t 96.9 0.0053 1.1E-07 40.1 6.7 81 6-86 144-230 (243)
30 PF03401 TctC: Tripartite tric 96.8 0.023 4.9E-07 38.3 8.7 83 4-86 137-242 (274)
31 COG3221 PhnD ABC-type phosphat 95.9 0.034 7.3E-07 38.2 5.9 71 5-75 182-260 (299)
32 PF09084 NMT1: NMT1/THI5 like; 95.7 0.042 9.1E-07 34.9 5.5 59 4-62 27-85 (216)
33 PRK11553 alkanesulfonate trans 95.7 0.067 1.5E-06 36.1 6.6 75 5-79 162-239 (314)
34 COG3181 Uncharacterized protei 95.1 0.11 2.5E-06 36.0 6.4 83 4-86 181-285 (319)
35 smart00094 TR_FER Transferrin. 93.6 0.32 6.8E-06 33.9 5.9 57 5-62 34-98 (332)
36 PF00405 Transferrin: Transfer 93.2 0.58 1.3E-05 32.5 6.7 57 5-61 34-98 (330)
37 TIGR01256 modA molybdenum ABC 93.0 0.74 1.6E-05 29.3 6.6 79 6-86 136-215 (216)
38 PRK03537 molybdate ABC transpo 92.8 1.6 3.4E-05 27.7 8.5 78 8-88 101-182 (188)
39 TIGR01728 SsuA_fam ABC transpo 92.5 0.32 6.8E-06 31.9 4.5 57 6-62 37-93 (288)
40 PRK11553 alkanesulfonate trans 92.2 0.66 1.4E-05 31.3 5.9 59 5-63 63-122 (314)
41 TIGR01729 taurine_ABC_bnd taur 90.7 1.2 2.6E-05 29.8 5.9 66 7-73 135-209 (300)
42 PF12974 Phosphonate-bd: ABC t 89.6 1.7 3.6E-05 28.2 5.7 58 5-63 36-98 (243)
43 TIGR03261 phnS2 putative 2-ami 89.3 5.2 0.00011 27.3 9.3 80 6-86 201-282 (334)
44 TIGR01728 SsuA_fam ABC transpo 89.0 2.2 4.7E-05 27.9 6.0 31 6-36 135-165 (288)
45 TIGR01729 taurine_ABC_bnd taur 88.8 1.6 3.5E-05 29.2 5.3 25 4-28 33-57 (300)
46 PF03466 LysR_substrate: LysR 88.1 1.2 2.6E-05 27.1 4.1 51 5-63 41-91 (209)
47 PF14503 YhfZ_C: YhfZ C-termin 87.2 1 2.2E-05 30.0 3.5 59 7-68 145-209 (232)
48 TIGR00363 lipoprotein, YaeC fa 87.1 4.3 9.3E-05 27.3 6.5 41 4-44 52-94 (258)
49 COG1910 Periplasmic molybdate- 87.1 1.5 3.3E-05 29.0 4.2 64 4-74 135-198 (223)
50 PF13531 SBP_bac_11: Bacterial 86.6 6.4 0.00014 25.2 7.4 81 5-87 144-228 (230)
51 TIGR01098 3A0109s03R phosphate 86.2 4.7 0.0001 26.1 6.2 25 6-30 72-96 (254)
52 PF13379 NMT1_2: NMT1-like fam 85.9 2.1 4.5E-05 28.0 4.5 52 8-59 159-213 (252)
53 TIGR03427 ABC_peri_uca ABC tra 84.8 4.2 9E-05 28.3 5.7 28 4-31 41-69 (328)
54 PF14503 YhfZ_C: YhfZ C-termin 84.7 1.8 3.8E-05 28.9 3.6 54 8-61 52-108 (232)
55 TIGR03339 phn_lysR aminoethylp 82.8 1.9 4.2E-05 28.1 3.3 51 5-63 119-169 (279)
56 cd00134 PBPb Bacterial peripla 82.1 4 8.6E-05 24.7 4.4 21 7-27 46-66 (218)
57 COG0715 TauA ABC-type nitrate/ 81.8 4.4 9.4E-05 27.4 4.8 60 4-63 67-129 (335)
58 COG0725 ModA ABC-type molybdat 81.6 13 0.00029 25.0 7.9 83 5-89 172-255 (258)
59 PRK10677 modA molybdate transp 81.6 7.4 0.00016 25.9 5.8 80 5-88 173-254 (257)
60 PF03180 Lipoprotein_9: NLPA l 81.2 5.3 0.00012 26.6 4.9 72 4-79 32-122 (237)
61 TIGR00787 dctP tripartite ATP- 80.3 8.5 0.00018 25.4 5.7 53 5-59 160-214 (257)
62 PRK04168 molybdate ABC transpo 80.3 17 0.00037 25.3 7.7 77 7-87 210-313 (334)
63 PRK00489 hisG ATP phosphoribos 80.0 7.1 0.00015 26.4 5.3 58 4-64 49-107 (287)
64 PF13379 NMT1_2: NMT1-like fam 80.0 7.4 0.00016 25.4 5.3 55 4-59 41-99 (252)
65 PF12849 PBP_like_2: PBP super 79.9 2.3 5E-05 28.1 2.9 61 3-63 42-110 (281)
66 PRK11063 metQ DL-methionine tr 79.8 16 0.00035 24.7 7.7 76 7-85 183-262 (271)
67 TIGR03414 ABC_choline_bnd chol 79.6 4.6 0.0001 27.4 4.4 53 7-59 44-100 (290)
68 TIGR00363 lipoprotein, YaeC fa 79.3 16 0.00036 24.5 7.7 79 7-85 170-249 (258)
69 PF12727 PBP_like: PBP superfa 78.9 12 0.00026 23.9 5.9 62 4-71 129-190 (193)
70 cd08438 PBP2_CidR The C-termin 78.6 8.2 0.00018 22.9 4.9 23 6-28 36-58 (197)
71 TIGR03431 PhnD phosphonate ABC 78.4 17 0.00037 24.2 6.9 25 5-29 66-90 (288)
72 TIGR02743 TraW type-F conjugat 78.3 2.4 5.2E-05 27.7 2.5 34 53-86 26-60 (202)
73 COG3221 PhnD ABC-type phosphat 77.5 11 0.00024 26.0 5.7 61 3-63 72-137 (299)
74 TIGR02122 TRAP_TAXI TRAP trans 76.8 7.7 0.00017 25.9 4.8 23 4-26 175-197 (320)
75 cd08486 PBP2_CbnR The C-termin 75.6 3.9 8.6E-05 24.9 2.9 49 6-62 37-85 (198)
76 TIGR03427 ABC_peri_uca ABC tra 74.7 19 0.00042 25.0 6.4 30 7-36 141-170 (328)
77 cd08411 PBP2_OxyR The C-termin 74.2 4.6 9.9E-05 24.3 2.9 22 6-27 37-58 (200)
78 COG0687 PotD Spermidine/putres 73.7 28 0.0006 24.3 8.7 71 5-75 220-294 (363)
79 PRK11622 hypothetical protein; 73.5 29 0.00064 24.5 8.0 71 6-76 253-329 (401)
80 PF04069 OpuAC: Substrate bind 73.4 3.1 6.8E-05 27.4 2.2 56 4-59 35-95 (257)
81 PRK13738 conjugal transfer pil 73.3 4 8.6E-05 26.8 2.6 35 52-86 23-58 (209)
82 PRK11063 metQ DL-methionine tr 73.2 6.4 0.00014 26.6 3.7 40 4-43 65-106 (271)
83 PF03480 SBP_bac_7: Bacterial 72.5 13 0.00028 24.9 5.0 51 8-59 163-214 (286)
84 cd08445 PBP2_BenM_CatM_CatR Th 72.4 7.5 0.00016 23.5 3.6 48 7-62 38-85 (203)
85 cd08415 PBP2_LysR_opines_like 72.0 11 0.00023 22.4 4.2 23 6-28 36-58 (196)
86 PRK11242 DNA-binding transcrip 71.9 7.9 0.00017 25.5 3.9 50 6-63 127-176 (296)
87 cd08425 PBP2_CynR The C-termin 71.7 8.9 0.00019 22.9 3.8 48 7-62 38-85 (197)
88 cd08414 PBP2_LTTR_aromatics_li 71.0 15 0.00031 21.8 4.7 23 6-28 36-58 (197)
89 PRK15437 histidine ABC transpo 71.0 11 0.00023 24.7 4.3 22 5-26 71-92 (259)
90 PRK11119 proX glycine betaine 70.7 13 0.00028 25.9 4.8 54 7-60 66-123 (331)
91 cd08436 PBP2_LTTR_like_3 The C 69.9 17 0.00036 21.4 4.7 23 6-28 36-58 (194)
92 PRK11480 tauA taurine transpor 69.7 20 0.00044 24.4 5.5 25 4-28 57-81 (320)
93 cd08467 PBP2_SyrM The C-termin 69.4 8.5 0.00018 23.3 3.4 20 7-26 37-56 (200)
94 TIGR01276 thiB thiamine ABC tr 69.2 32 0.00069 23.1 8.3 68 7-74 178-249 (309)
95 COG4521 TauA ABC-type taurine 68.0 14 0.00031 25.4 4.3 58 3-61 62-121 (334)
96 cd08448 PBP2_LTTR_aromatics_li 67.5 12 0.00026 22.2 3.7 22 6-27 36-57 (197)
97 cd08447 PBP2_LTTR_aromatics_li 67.3 8.2 0.00018 23.0 3.0 21 6-26 36-56 (198)
98 TIGR02995 ectoine_ehuB ectoine 66.1 8.8 0.00019 25.4 3.1 24 3-26 76-99 (275)
99 PF03466 LysR_substrate: LysR 65.9 26 0.00057 21.0 7.4 69 3-74 134-205 (209)
100 cd08456 PBP2_LysR The C-termin 65.7 15 0.00032 21.8 3.9 21 7-27 37-57 (196)
101 cd08450 PBP2_HcaR The C-termin 65.4 12 0.00027 22.2 3.5 48 7-62 37-84 (196)
102 PRK09906 DNA-binding transcrip 64.5 7.3 0.00016 25.8 2.5 50 6-63 126-175 (296)
103 PRK09861 cytoplasmic membrane 64.1 42 0.00092 22.7 7.4 78 7-86 184-264 (272)
104 cd08452 PBP2_AlsR The C-termin 63.1 18 0.00039 21.7 3.9 49 6-62 36-84 (197)
105 COG0077 PheA Prephenate dehydr 62.3 25 0.00054 24.2 4.8 54 4-59 31-93 (279)
106 PRK15421 DNA-binding transcrip 61.1 9.8 0.00021 25.8 2.7 50 6-63 125-174 (317)
107 PRK03601 transcriptional regul 60.9 13 0.00028 24.5 3.2 24 5-28 124-147 (275)
108 PRK09501 potD spermidine/putre 60.8 52 0.0011 22.6 9.3 75 10-84 213-289 (348)
109 TIGR02136 ptsS_2 phosphate bin 59.9 8.7 0.00019 25.8 2.3 57 5-63 70-131 (287)
110 PRK10677 modA molybdate transp 59.9 42 0.0009 22.3 5.5 58 3-61 58-118 (257)
111 cd08451 PBP2_BudR The C-termin 59.3 26 0.00056 20.7 4.2 22 6-27 37-58 (199)
112 cd08416 PBP2_MdcR The C-termin 59.1 24 0.00052 20.9 4.0 52 6-63 36-87 (199)
113 COG1732 OpuBC Periplasmic glyc 58.7 36 0.00078 23.7 5.0 56 4-59 68-145 (300)
114 PRK09986 DNA-binding transcrip 58.7 22 0.00047 23.4 4.0 52 6-63 133-184 (294)
115 COG1464 NlpA ABC-type metal io 58.6 12 0.00025 25.6 2.6 43 4-46 63-107 (268)
116 cd08446 PBP2_Chlorocatechol Th 57.7 16 0.00036 21.7 3.1 20 7-26 38-57 (198)
117 cd08512 PBP2_NikA_DppA_OppA_li 57.3 68 0.0015 22.9 6.8 65 5-70 209-279 (476)
118 cd08457 PBP2_OccR The C-termin 56.3 13 0.00028 22.3 2.4 21 7-27 37-57 (196)
119 cd08485 PBP2_ClcR The C-termin 56.1 14 0.00031 22.3 2.7 21 7-27 38-58 (198)
120 PF10941 DUF2620: Protein of u 55.2 14 0.0003 22.1 2.3 24 3-26 28-51 (117)
121 cd08465 PBP2_ToxR The C-termin 53.9 33 0.00072 20.7 4.1 22 6-27 36-57 (200)
122 PRK14498 putative molybdopteri 53.5 21 0.00045 27.0 3.5 59 3-63 445-512 (633)
123 PRK11898 prephenate dehydratas 53.2 57 0.0012 22.2 5.3 56 5-60 33-96 (283)
124 cd00995 PBP2_NikA_DppA_OppA_li 53.1 52 0.0011 23.1 5.4 65 5-70 195-265 (466)
125 cd08453 PBP2_IlvR The C-termin 51.7 42 0.00091 20.0 4.2 21 7-27 37-57 (200)
126 TIGR03730 tungstate_WtpA tungs 51.4 75 0.0016 21.6 5.7 23 6-28 182-204 (273)
127 cd08449 PBP2_XapR The C-termin 50.7 27 0.00057 20.6 3.2 20 7-26 37-56 (197)
128 TIGR00030 S21p ribosomal prote 50.5 36 0.00078 17.6 3.7 36 54-89 3-38 (58)
129 PRK09508 leuO leucine transcri 50.1 29 0.00062 23.3 3.5 48 7-62 149-196 (314)
130 COG0416 PlsX Fatty acid/phosph 49.9 22 0.00047 25.2 2.9 28 7-34 84-111 (338)
131 cd08418 PBP2_TdcA The C-termin 49.8 53 0.0011 19.4 6.8 66 3-70 128-195 (201)
132 COG2358 Imp TRAP-type uncharac 49.6 15 0.00033 25.7 2.1 35 9-43 176-213 (321)
133 PRK13846 putative glycerol-3-p 49.1 26 0.00056 24.5 3.2 29 6-34 84-112 (316)
134 PRK11482 putative DNA-binding 49.0 31 0.00067 23.4 3.6 48 7-62 152-199 (317)
135 PRK11205 tbpA thiamine transpo 48.5 84 0.0018 21.3 8.2 69 6-74 198-270 (330)
136 TIGR00070 hisG ATP phosphoribo 48.3 57 0.0012 20.9 4.5 75 9-88 50-125 (182)
137 PF11195 DUF2829: Protein of u 48.3 15 0.00032 20.0 1.6 13 7-19 2-14 (75)
138 cd08503 PBP2_NikA_DppA_OppA_li 47.9 81 0.0017 22.4 5.7 20 5-24 198-217 (460)
139 PRK11013 DNA-binding transcrip 47.9 38 0.00082 22.7 3.9 23 5-27 129-151 (309)
140 PRK12680 transcriptional regul 47.7 41 0.0009 22.9 4.1 23 5-27 128-150 (327)
141 PRK11480 tauA taurine transpor 47.6 32 0.00069 23.4 3.5 27 8-34 158-184 (320)
142 PF00325 Crp: Bacterial regula 47.3 23 0.0005 16.1 1.9 16 63-78 16-31 (32)
143 cd08501 PBP2_Lpqw The substrat 45.8 63 0.0014 23.1 4.9 65 5-70 205-276 (486)
144 PRK00270 rpsU 30S ribosomal pr 45.5 47 0.001 17.6 3.8 36 54-89 4-39 (64)
145 PRK00910 ribB 3,4-dihydroxy-2- 44.7 7.7 0.00017 25.7 0.1 22 5-26 14-35 (218)
146 smart00851 MGS MGS-like domain 44.3 30 0.00065 19.0 2.5 19 8-26 44-62 (90)
147 cd08462 PBP2_NodD The C-termin 44.3 69 0.0015 19.1 5.1 58 3-62 127-186 (200)
148 cd05466 PBP2_LTTR_substrate Th 43.2 64 0.0014 18.5 6.4 63 3-68 128-192 (197)
149 cd08518 PBP2_NikA_DppA_OppA_li 43.0 88 0.0019 22.3 5.2 19 5-24 187-205 (464)
150 PF01715 IPPT: IPP transferase 42.9 42 0.00091 22.5 3.4 34 51-84 154-188 (253)
151 cd08498 PBP2_NikA_DppA_OppA_li 42.7 86 0.0019 22.4 5.2 20 5-24 194-213 (481)
152 TIGR00506 ribB 3,4-dihydroxy-2 42.5 33 0.00072 22.4 2.8 22 5-26 2-23 (199)
153 TIGR03061 pip_yhgE_Nterm YhgE/ 42.4 30 0.00066 21.2 2.5 23 6-28 83-105 (164)
154 PRK15413 glutathione ABC trans 42.2 1.3E+02 0.0029 21.8 6.8 65 5-70 223-293 (512)
155 COG2113 ProX ABC-type proline/ 41.8 52 0.0011 22.8 3.8 54 6-59 66-123 (302)
156 PRK11899 prephenate dehydratas 41.6 94 0.002 21.3 5.0 57 4-60 32-95 (279)
157 cd08470 PBP2_CrgA_like_1 The C 41.2 75 0.0016 18.7 6.9 69 3-73 123-193 (197)
158 cd08490 PBP2_NikA_DppA_OppA_li 40.4 1.3E+02 0.0029 21.3 6.2 20 5-24 186-205 (470)
159 COG0324 MiaA tRNA delta(2)-iso 40.2 53 0.0011 22.9 3.6 37 50-86 190-227 (308)
160 cd01422 MGS Methylglyoxal synt 40.2 37 0.00081 19.8 2.6 21 6-26 57-77 (115)
161 COG0108 RibB 3,4-dihydroxy-2-b 39.7 35 0.00077 22.4 2.6 22 4-26 2-23 (203)
162 cd08492 PBP2_NikA_DppA_OppA_li 39.5 1.4E+02 0.003 21.3 7.0 20 5-24 206-225 (484)
163 cd08417 PBP2_Nitroaromatics_li 38.7 84 0.0018 18.5 5.6 62 3-66 127-190 (200)
164 TIGR00174 miaA tRNA isopenteny 38.3 39 0.00085 23.2 2.8 32 53-84 188-220 (287)
165 TIGR00971 3a0106s03 sulfate/th 38.1 1.2E+02 0.0026 20.9 5.1 33 3-35 48-82 (315)
166 PTZ00148 40S ribosomal protein 38.0 32 0.0007 22.6 2.2 19 17-35 180-198 (205)
167 cd08493 PBP2_DppA_like The sub 37.9 1.5E+02 0.0032 21.2 6.5 53 5-59 211-263 (482)
168 cd08502 PBP2_NikA_DppA_OppA_li 37.5 1.4E+02 0.003 21.4 5.5 63 5-70 206-274 (472)
169 PRK01792 ribB 3,4-dihydroxy-2- 37.4 11 0.00024 24.9 0.0 22 5-26 13-34 (214)
170 PRK11233 nitrogen assimilation 37.4 1.3E+02 0.0027 20.1 5.8 74 4-78 218-295 (305)
171 cd08496 PBP2_NikA_DppA_OppA_li 37.3 1.5E+02 0.0033 21.0 6.0 22 5-26 192-213 (454)
172 CHL00180 rbcR LysR transcripti 37.2 1.3E+02 0.0027 20.1 7.6 69 4-74 230-300 (305)
173 PRK10682 putrescine transporte 37.1 1.4E+02 0.003 20.6 9.1 75 9-83 227-309 (370)
174 cd08421 PBP2_LTTR_like_1 The C 36.8 90 0.002 18.3 6.3 65 3-69 128-194 (198)
175 cd08516 PBP2_NikA_DppA_OppA_li 36.7 1.2E+02 0.0026 21.4 5.1 20 5-24 191-210 (457)
176 KOG1284|consensus 36.5 22 0.00048 25.2 1.3 54 4-62 62-115 (357)
177 PRK11151 DNA-binding transcrip 36.5 1.3E+02 0.0028 20.0 6.9 69 3-73 219-289 (305)
178 cd08422 PBP2_CrgA_like The C-t 36.1 91 0.002 18.1 5.4 64 3-68 127-192 (197)
179 cd08494 PBP2_NikA_DppA_OppA_li 35.7 1.4E+02 0.0031 21.0 5.4 21 4-24 190-210 (448)
180 cd08433 PBP2_Nac The C-teminal 35.6 96 0.0021 18.3 6.5 65 3-69 128-194 (198)
181 PRK09801 transcriptional activ 35.6 1.4E+02 0.003 20.1 7.9 71 3-75 223-294 (310)
182 PF12916 DUF3834: Protein of u 35.4 1.3E+02 0.0028 19.8 4.7 67 5-78 100-172 (201)
183 PF00800 PDT: Prephenate dehyd 35.3 1.2E+02 0.0025 19.1 5.4 55 4-60 28-91 (181)
184 PRK00091 miaA tRNA delta(2)-is 35.2 47 0.001 23.0 2.8 32 53-84 192-224 (307)
185 PF00496 SBP_bac_5: Bacterial 35.0 1.5E+02 0.0032 20.2 5.9 71 5-75 157-229 (374)
186 cd08427 PBP2_LTTR_like_2 The C 34.9 96 0.0021 18.1 6.1 61 3-66 126-188 (195)
187 PF13416 SBP_bac_8: Bacterial 34.9 1.3E+02 0.0027 19.4 9.7 72 6-77 174-249 (281)
188 cd08439 PBP2_LrhA_like The C-t 34.4 50 0.0011 19.5 2.6 22 6-27 36-57 (185)
189 PF02504 FA_synthesis: Fatty a 34.0 49 0.0011 23.2 2.7 30 6-35 81-110 (323)
190 PLN02165 adenylate isopentenyl 33.7 56 0.0012 23.1 3.0 34 53-86 178-212 (334)
191 PRK14729 miaA tRNA delta(2)-is 33.7 51 0.0011 22.8 2.8 32 53-84 190-222 (300)
192 cd08499 PBP2_Ylib_like The sub 33.3 1.8E+02 0.0039 20.7 7.2 20 5-24 194-213 (474)
193 COG1654 BirA Biotin operon rep 32.9 41 0.0009 18.6 1.8 17 62-78 32-48 (79)
194 PF02142 MGS: MGS-like domain 32.8 53 0.0012 18.2 2.4 21 10-30 51-71 (95)
195 PRK05234 mgsA methylglyoxal sy 32.4 50 0.0011 20.2 2.3 20 7-26 63-82 (142)
196 PRK05773 3,4-dihydroxy-2-butan 32.3 59 0.0013 21.6 2.8 19 7-26 2-20 (219)
197 cd08437 PBP2_MleR The substrat 31.9 57 0.0012 19.3 2.6 51 6-62 36-86 (198)
198 TIGR02294 nickel_nikA nickel A 31.8 1.6E+02 0.0034 21.3 5.1 20 5-24 201-220 (500)
199 PRK13895 conjugal transfer pro 31.6 72 0.0016 19.8 2.9 37 51-87 15-63 (144)
200 TIGR03418 chol_sulf_TF putativ 31.5 1.5E+02 0.0033 19.4 6.1 70 3-73 218-288 (291)
201 COG0828 RpsU Ribosomal protein 31.5 91 0.002 16.8 3.6 36 54-89 4-39 (67)
202 cd08519 PBP2_NikA_DppA_OppA_li 31.4 1.5E+02 0.0032 21.2 4.9 21 5-25 195-215 (469)
203 PRK12684 transcriptional regul 31.0 1.7E+02 0.0036 19.7 6.6 68 3-73 222-291 (313)
204 COG1663 LpxK Tetraacyldisaccha 31.0 78 0.0017 22.4 3.3 59 6-66 126-186 (336)
205 COG0583 LysR Transcriptional r 31.0 1.1E+02 0.0023 19.8 3.9 25 5-29 125-149 (297)
206 cd08513 PBP2_thermophilic_Hb8_ 30.8 1.8E+02 0.004 20.7 5.3 20 5-24 198-217 (482)
207 TIGR00975 3a0107s03 phosphate 30.6 75 0.0016 21.8 3.2 52 5-58 33-85 (314)
208 cd08520 PBP2_NikA_DppA_OppA_li 30.5 93 0.002 22.2 3.8 62 7-70 197-264 (468)
209 TIGR02863 spore_sspJ small, ac 30.4 26 0.00056 17.2 0.6 11 58-68 32-42 (47)
210 cd08514 PBP2_AppA_like The sub 30.4 1.7E+02 0.0037 20.9 5.1 20 5-24 199-218 (483)
211 PRK12485 bifunctional 3,4-dihy 30.3 69 0.0015 23.0 3.0 22 4-25 2-23 (369)
212 PF02256 Fe_hyd_SSU: Iron hydr 30.2 51 0.0011 17.0 1.8 18 72-89 25-42 (60)
213 PF13730 HTH_36: Helix-turn-he 30.0 37 0.00081 16.6 1.3 16 63-78 39-54 (55)
214 PRK13845 putative glycerol-3-p 29.8 73 0.0016 23.4 3.1 29 6-34 181-209 (437)
215 PRK15109 antimicrobial peptide 29.7 1.5E+02 0.0032 22.0 4.8 19 5-23 252-270 (547)
216 TIGR00182 plsX fatty acid/phos 29.6 77 0.0017 22.2 3.1 27 7-33 71-97 (322)
217 cd08517 PBP2_NikA_DppA_OppA_li 29.4 2.1E+02 0.0046 20.3 7.0 21 5-25 198-218 (480)
218 PLN02317 arogenate dehydratase 29.3 1.9E+02 0.004 21.0 5.0 55 4-60 122-185 (382)
219 cd08510 PBP2_Lactococcal_OppA_ 29.2 1.8E+02 0.0039 21.1 5.1 20 8-27 223-242 (516)
220 cd08420 PBP2_CysL_like C-termi 28.6 1.3E+02 0.0027 17.5 6.7 63 3-67 131-195 (201)
221 cd08495 PBP2_NikA_DppA_OppA_li 28.5 1.7E+02 0.0036 21.0 4.8 20 5-24 207-226 (482)
222 PF04198 Sugar-bind: Putative 28.2 1.1E+02 0.0024 20.4 3.6 28 7-34 227-254 (255)
223 PRK10622 pheA bifunctional cho 28.1 2E+02 0.0043 20.7 5.0 56 5-60 136-198 (386)
224 cd08511 PBP2_NikA_DppA_OppA_li 28.1 1.9E+02 0.0042 20.5 5.0 20 5-24 195-214 (467)
225 cd08477 PBP2_CrgA_like_8 The C 27.8 1.3E+02 0.0029 17.5 6.2 63 3-67 127-191 (197)
226 KOG1348|consensus 27.6 47 0.001 24.1 1.8 29 54-82 170-199 (477)
227 KOG0024|consensus 27.4 47 0.001 23.6 1.7 21 2-22 298-318 (354)
228 TIGR02637 RhaS rhamnose ABC tr 27.0 1.2E+02 0.0026 20.0 3.6 27 4-30 217-243 (302)
229 cd08489 PBP2_NikA The substrat 26.8 2.1E+02 0.0045 20.5 5.0 20 5-24 194-213 (488)
230 cd08473 PBP2_CrgA_like_4 The C 25.9 1.5E+02 0.0032 17.4 5.9 65 3-69 132-198 (202)
231 cd08459 PBP2_DntR_NahR_LinR_li 25.9 1.5E+02 0.0033 17.5 6.5 64 3-68 127-192 (201)
232 PF12363 DUF3647: Phage protei 25.8 1.2E+02 0.0025 17.7 3.0 26 62-87 87-112 (113)
233 PRK09319 bifunctional 3,4-dihy 25.7 88 0.0019 23.8 3.0 25 2-26 2-26 (555)
234 PF14044 NETI: NETI protein 25.5 37 0.00081 17.7 0.8 16 64-79 8-23 (57)
235 cd00532 MGS-like MGS-like doma 25.4 74 0.0016 18.2 2.1 20 7-26 55-75 (112)
236 cd08476 PBP2_CrgA_like_7 The C 25.4 1.5E+02 0.0032 17.2 5.7 64 3-68 127-192 (197)
237 PLN02748 tRNA dimethylallyltra 25.3 83 0.0018 23.3 2.8 32 53-84 230-262 (468)
238 TIGR00496 frr ribosome recycli 24.8 12 0.00026 23.8 -1.4 29 5-33 8-36 (176)
239 cd03770 SR_TndX_transposase Se 24.6 65 0.0014 19.2 1.9 21 6-26 55-75 (140)
240 PRK14498 putative molybdopteri 24.6 2.7E+02 0.0058 21.2 5.4 67 3-76 558-624 (633)
241 PRK13699 putative methylase; P 24.5 61 0.0013 21.3 1.8 25 6-30 7-31 (227)
242 PF13545 HTH_Crp_2: Crp-like h 24.5 75 0.0016 16.4 1.9 18 63-80 42-59 (76)
243 PRK05331 putative phosphate ac 24.5 1E+02 0.0023 21.6 3.0 27 7-33 83-109 (334)
244 PRK09314 bifunctional 3,4-dihy 24.3 93 0.002 22.1 2.8 23 4-26 2-24 (339)
245 smart00550 Zalpha Z-DNA-bindin 24.3 17 0.00036 19.2 -0.7 25 64-88 37-64 (68)
246 cd08484 PBP2_LTTR_beta_lactama 24.0 1.6E+02 0.0035 17.2 7.0 65 3-68 120-184 (189)
247 cd03769 SR_IS607_transposase_l 24.0 74 0.0016 18.9 2.0 21 6-26 49-69 (134)
248 COG5566 Uncharacterized conser 23.8 1.3E+02 0.0028 18.5 2.9 39 49-87 74-113 (137)
249 PRK10752 sulfate transporter s 23.7 2.6E+02 0.0057 19.5 5.4 30 4-33 60-90 (329)
250 cd08565 GDPD_pAtGDE_like Glyce 23.5 88 0.0019 20.4 2.5 8 21-28 224-231 (235)
251 cd08575 GDPD_GDE4_like Glycero 23.5 80 0.0017 21.0 2.3 9 20-28 253-261 (264)
252 cd08466 PBP2_LeuO The C-termin 23.3 1.7E+02 0.0037 17.2 5.5 57 3-61 127-185 (200)
253 cd01424 MGS_CPS_II Methylglyox 23.2 1.1E+02 0.0023 17.3 2.5 20 7-26 55-74 (110)
254 cd08469 PBP2_PnbR The C-termin 22.9 1.9E+02 0.004 17.5 5.0 56 4-61 149-206 (221)
255 TIGR01254 sfuA ABC transporter 22.7 2.4E+02 0.0053 18.8 8.6 68 7-74 179-250 (304)
256 cd08509 PBP2_TmCBP_oligosaccha 22.6 2.2E+02 0.0049 20.6 4.6 21 5-25 204-224 (509)
257 cd00092 HTH_CRP helix_turn_hel 22.5 19 0.00042 18.1 -0.7 21 63-83 39-59 (67)
258 PRK10632 transcriptional regul 22.5 2.5E+02 0.0054 18.8 6.9 57 3-61 218-276 (309)
259 COG2107 Predicted periplasmic 22.4 58 0.0013 22.4 1.4 67 4-72 121-198 (272)
260 PF10991 DUF2815: Protein of u 22.0 1.1E+02 0.0024 19.6 2.6 29 52-80 32-61 (181)
261 cd08435 PBP2_GbpR The C-termin 21.9 1.8E+02 0.0039 16.9 6.1 62 4-67 132-195 (201)
262 COG1197 Mfd Transcription-repa 21.8 91 0.002 25.8 2.5 35 9-43 687-722 (1139)
263 PF06576 DUF1133: Protein of u 21.8 77 0.0017 20.3 1.8 16 63-78 57-72 (176)
264 PRK05703 flhF flagellar biosyn 21.8 1E+02 0.0022 22.4 2.6 27 2-29 5-33 (424)
265 COG0278 Glutaredoxin-related p 21.8 1.2E+02 0.0025 17.8 2.4 17 68-84 86-102 (105)
266 cd06311 PBP1_ABC_sugar_binding 21.7 1.6E+02 0.0036 18.9 3.5 25 5-29 218-244 (274)
267 TIGR03499 FlhF flagellar biosy 21.6 91 0.002 21.1 2.3 26 2-28 5-32 (282)
268 cd00520 RRF Ribosome recycling 21.5 9.8 0.00021 24.2 -2.3 29 5-33 13-41 (179)
269 PF04422 FrhB_FdhB_N: Coenzyme 21.5 1E+02 0.0022 16.8 2.1 17 11-27 27-43 (82)
270 PRK00014 ribB 3,4-dihydroxy-2- 21.4 1.1E+02 0.0025 20.4 2.6 20 6-25 19-38 (230)
271 PRK10082 cell density-dependen 21.3 1.1E+02 0.0025 20.2 2.7 22 6-27 134-155 (303)
272 smart00685 DM14 Repeats in fly 21.3 61 0.0013 17.0 1.1 15 5-19 34-48 (59)
273 TIGR00557 pdxA 4-hydroxythreon 21.1 52 0.0011 23.1 1.0 23 4-26 92-114 (320)
274 PF05225 HTH_psq: helix-turn-h 21.1 44 0.00095 16.2 0.5 13 7-19 4-16 (45)
275 PRK01906 tetraacyldisaccharide 21.1 1.1E+02 0.0024 21.6 2.6 50 8-59 136-187 (338)
276 PF10657 RC-P840_PscD: Photosy 21.1 1.4E+02 0.0031 18.1 2.8 25 2-26 57-81 (144)
277 COG1026 Predicted Zn-dependent 21.0 1.2E+02 0.0025 24.8 3.0 26 65-90 422-447 (978)
278 PRK09755 putative ABC transpor 21.0 2.4E+02 0.0052 20.8 4.5 19 5-23 247-265 (535)
279 PF02295 z-alpha: Adenosine de 20.9 1E+02 0.0022 16.3 1.9 17 63-79 34-50 (66)
280 PRK07377 hypothetical protein; 20.9 1.1E+02 0.0025 19.8 2.4 24 3-26 113-136 (184)
281 PF02606 LpxK: Tetraacyldisacc 20.8 1E+02 0.0022 21.6 2.4 50 9-59 117-167 (326)
282 PF13407 Peripla_BP_4: Peripla 20.7 1.9E+02 0.0041 18.3 3.6 27 5-31 215-241 (257)
283 PRK15104 oligopeptide ABC tran 20.7 3.2E+02 0.0069 20.2 5.0 20 5-24 252-271 (543)
284 PF09575 Spore_SspJ: Small spo 20.7 51 0.0011 16.0 0.7 11 58-68 31-41 (46)
285 PRK10837 putative DNA-binding 20.6 2.5E+02 0.0055 18.2 7.5 70 4-75 217-288 (290)
286 PF13343 SBP_bac_6: Bacterial 20.6 2.4E+02 0.0052 18.0 9.6 70 8-77 129-201 (242)
287 cd08471 PBP2_CrgA_like_2 The C 20.5 2E+02 0.0042 16.8 7.0 65 3-69 127-193 (201)
288 PRK12723 flagellar biosynthesi 20.5 79 0.0017 22.7 1.9 28 1-29 2-34 (388)
289 cd08481 PBP2_GcdR_like The C-t 20.5 1.9E+02 0.0042 16.7 5.9 63 4-68 125-189 (194)
290 PF00072 Response_reg: Respons 20.4 1.2E+02 0.0026 16.3 2.3 24 4-27 28-51 (112)
291 TIGR02298 HpaD_Fe 3,4-dihydrox 20.3 97 0.0021 21.1 2.2 23 62-84 205-227 (282)
292 cd08461 PBP2_DntR_like_3 The C 20.3 2E+02 0.0043 16.8 5.8 58 4-66 129-188 (198)
293 COG0011 Uncharacterized conser 20.2 1.5E+02 0.0032 17.2 2.6 24 55-78 9-35 (100)
294 PRK10094 DNA-binding transcrip 20.2 2.8E+02 0.0061 18.5 6.8 56 3-60 220-277 (308)
295 PF12698 ABC2_membrane_3: ABC- 20.1 76 0.0016 20.8 1.6 22 4-25 62-83 (344)
296 TIGR02424 TF_pcaQ pca operon t 20.1 2.7E+02 0.0058 18.3 5.9 65 4-70 225-291 (300)
297 PF05952 ComX: Bacillus compet 20.1 1.1E+02 0.0023 16.0 1.8 24 7-30 11-34 (57)
298 PF04166 PdxA: Pyridoxal phosp 20.0 51 0.0011 22.9 0.8 24 4-27 73-96 (298)
No 1
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.88 E-value=6.8e-22 Score=118.84 Aligned_cols=84 Identities=39% Similarity=0.555 Sum_probs=79.3
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCChHHHHHHHHHhhhccHHHHHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLFM 83 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~ 83 (90)
.+++.++++.+|++|+ ||++.|.+++.++++++|++.+++..+..++|||++|||++|++.||.+|.+|+++|+++++.
T Consensus 50 ~~~~~~~~~~~l~~g~-da~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~G~~~~l~ 128 (134)
T smart00079 50 FVKSYAEGVQRVRVSN-YAFLMESTYLDYELSQNCDLMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELQKLE 128 (134)
T ss_pred CCCCHHHHHHHHHcCC-CEEEeehHhHHHHHhCCCCeEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhcCcHHHHH
Confidence 4689999999999999 999999999999988788899998888889999999999999999999999999999999999
Q ss_pred HHhcc
Q psy17442 84 AKVHL 88 (90)
Q Consensus 84 ~kW~~ 88 (90)
+|||.
T Consensus 129 ~kw~~ 133 (134)
T smart00079 129 NKWWK 133 (134)
T ss_pred Hhhcc
Confidence 99985
No 2
>KOG1053|consensus
Probab=99.80 E-value=7.6e-20 Score=135.00 Aligned_cols=87 Identities=29% Similarity=0.529 Sum_probs=83.2
Q ss_pred ccccCChHHHHHHhhcCCceEEEeehhHHhHHHhc--CCCeEEeC--CcccccceEEEEeCCCCChHHHHHHHHHhhhcc
Q psy17442 2 RFDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ--DCELVTAG--ELFGRSGYAIGLQKGSPWADAVTLAILDFHEST 77 (90)
Q Consensus 2 ~~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~--~~~l~~~~--~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G 77 (90)
+|+..+.++|+..||+|++||||+|..+++|.+.+ +|.+..+| ..|..++||||++|||||+..||.+|++++.+|
T Consensus 716 kyNq~~v~dal~sLK~gKLDAFIyDaAVLnY~agkDegCKLvTIGsgKvFAttGYGIal~k~Spwkr~IdlallQy~gdG 795 (1258)
T KOG1053|consen 716 KYNQPGVEDALESLKNGKLDAFIYDAAVLNYMAGKDEGCKLVTIGSGKVFATTGYGIALPKNSPWKRQIDLALLQYLGDG 795 (1258)
T ss_pred HhccCchHHHHHHHhcccchhHHHHHHHHHHhhccCCCceEEEecCCceeeecceeeecCCCCcchhhHHHHHHHHhccc
Confidence 58889999999999999999999999999999987 59999997 899999999999999999999999999999999
Q ss_pred HHHHHHHHhcc
Q psy17442 78 VCYLFMAKVHL 88 (90)
Q Consensus 78 ~~~~l~~kW~~ 88 (90)
+|++|+.+|+.
T Consensus 796 eme~Le~~Wlt 806 (1258)
T KOG1053|consen 796 EMEMLETLWLT 806 (1258)
T ss_pred hHHHHHHHHhh
Confidence 99999999985
No 3
>KOG4440|consensus
Probab=99.76 E-value=9e-19 Score=126.17 Aligned_cols=87 Identities=52% Similarity=0.794 Sum_probs=84.1
Q ss_pred ccccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCChHHHHHHHHHhhhccHHHH
Q psy17442 2 RFDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYL 81 (90)
Q Consensus 2 ~~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~ 81 (90)
.|++.+..||+++|++|+++|||+|+..+++.++++|++...|+.|...+|||+++|||||++.|..+|+++.|+|.|++
T Consensus 719 ~hNy~~A~eAiq~v~~gkL~AFIWDS~rLEfEAs~~CeLvT~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~~hEsGfMEk 798 (993)
T KOG4440|consen 719 KHNYESAAEAIQAVRDGKLHAFIWDSARLEFEASQKCELVTTGELFGRSGYGIGLQKDSPWTQNVTLAILKSHESGFMEK 798 (993)
T ss_pred hcchhhHHHHHHHHHcCceeEEEeecceeeehhhcccceEeccccccccccccccccCCCCcchhhHHHHHhhhcchHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcc
Q psy17442 82 FMAKVHL 88 (90)
Q Consensus 82 l~~kW~~ 88 (90)
|-++|.-
T Consensus 799 LDk~Wi~ 805 (993)
T KOG4440|consen 799 LDKTWIR 805 (993)
T ss_pred HHHHHHh
Confidence 9999963
No 4
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.60 E-value=7.6e-15 Score=99.23 Aligned_cols=87 Identities=18% Similarity=0.171 Sum_probs=74.9
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhc--C-CCeEEeCCcccccceEEEEeCCCC-ChHHHHHHHHHhhhccHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ--D-CELVTAGELFGRSGYAIGLQKGSP-WADAVTLAILDFHESTVC 79 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~--~-~~l~~~~~~~~~~~~~ia~~kgs~-l~~~vn~~l~~l~~~G~~ 79 (90)
.+++.++++.+|.+|++||++.|..++.+.+.+ . ..+.++++.+...+|+++++|+++ |++.+|.+|.+++++|+|
T Consensus 183 ~~~~~~~~l~~L~~GrvDa~i~d~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~~a~~k~~~~L~~~in~~L~~l~~~G~l 262 (302)
T PRK10797 183 SAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQAQTSGEA 262 (302)
T ss_pred EeCCHHHHHHHHHcCCceEEEccHHHHHHHHHcCCCCcceEECCccCCcCceeEEEeCCCHHHHHHHHHHHHHHHhCchH
Confidence 457889999999999999999999887665432 2 347788877778899999999976 999999999999999999
Q ss_pred HHHHHHhccCC
Q psy17442 80 YLFMAKVHLNN 90 (90)
Q Consensus 80 ~~l~~kW~~~~ 90 (90)
++|.+|||..+
T Consensus 263 ~~i~~kw~~~~ 273 (302)
T PRK10797 263 EKWFDKWFKNP 273 (302)
T ss_pred HHHHHHHcCCC
Confidence 99999999753
No 5
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.52 E-value=1.1e-13 Score=90.46 Aligned_cols=85 Identities=16% Similarity=0.182 Sum_probs=75.2
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcC--CCeEEeCCcccccceEEEEeCCCCChHHHHHHHHHhhhccHHHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD--CELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLF 82 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~--~~l~~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l 82 (90)
+++..+++.+|.+|++|+++.+...+.+++++. ..+.+++......++++++++++++++.+|++|.+++++|+++++
T Consensus 158 ~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~n~al~~~~~~g~~~~i 237 (247)
T PRK09495 158 FPNIDNAYLELGTGRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSELREKVNGALKTLKENGTYAEI 237 (247)
T ss_pred cCCHHHHHHHHHcCceeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEEEcCcHHHHHHHHHHHHHHHHCCcHHHH
Confidence 578889999999999999999999998888763 356677666677789999999989999999999999999999999
Q ss_pred HHHhccC
Q psy17442 83 MAKVHLN 89 (90)
Q Consensus 83 ~~kW~~~ 89 (90)
.+||+..
T Consensus 238 ~~k~~~~ 244 (247)
T PRK09495 238 YKKWFGT 244 (247)
T ss_pred HHHHcCC
Confidence 9999864
No 6
>PRK11260 cystine transporter subunit; Provisional
Probab=99.52 E-value=1.2e-13 Score=91.22 Aligned_cols=87 Identities=21% Similarity=0.219 Sum_probs=75.3
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCC-eEEeCCcccccceEEEEeCCCC-ChHHHHHHHHHhhhccHHHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCE-LVTAGELFGRSGYAIGLQKGSP-WADAVTLAILDFHESTVCYL 81 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~-l~~~~~~~~~~~~~ia~~kgs~-l~~~vn~~l~~l~~~G~~~~ 81 (90)
.+++..+++.+|.+|++|+++.+...+.+++++.+. +.+....+...+++++++++++ |++.+|.+|.+++++|++++
T Consensus 175 ~~~~~~~~l~~L~~GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~~ln~~l~~~~~~g~~~~ 254 (266)
T PRK11260 175 TYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGVALRKGNPDLLKAVNQAIAEMQKDGTLKA 254 (266)
T ss_pred ecCCHHHHHHHHHcCCCCEEEechHHHHHHHHhCCCcceecCCccccCceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHH
Confidence 367888999999999999999999988888876433 5555556677889999999986 99999999999999999999
Q ss_pred HHHHhccCC
Q psy17442 82 FMAKVHLNN 90 (90)
Q Consensus 82 l~~kW~~~~ 90 (90)
+.+||+.+.
T Consensus 255 i~~k~~~~~ 263 (266)
T PRK11260 255 LSEKWFGAD 263 (266)
T ss_pred HHHHhcCCc
Confidence 999999763
No 7
>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=99.51 E-value=1.3e-13 Score=87.39 Aligned_cols=86 Identities=15% Similarity=0.130 Sum_probs=72.8
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcC-C-CeEEeCCcccccceEEEEeCCC-CChHHHHHHHHHhhhccHHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD-C-ELVTAGELFGRSGYAIGLQKGS-PWADAVTLAILDFHESTVCY 80 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~-~-~l~~~~~~~~~~~~~ia~~kgs-~l~~~vn~~l~~l~~~G~~~ 80 (90)
.+++..+++.+|.+|++|+++.+...+.+++++. . ............++++++++.+ +|++.+|++|.+|+++|+++
T Consensus 137 ~~~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~i~~l~~~G~~~ 216 (225)
T PF00497_consen 137 EVDSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRKKNPELLEIFNKAIRELKQSGEIQ 216 (225)
T ss_dssp EESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEETTTHHHHHHHHHHHHHHHHTTHHH
T ss_pred ccccHHHHHHHHhcCCeeeeeccchhhhhhhhhcccccccccccccccceeEEeecccccHHHHHHHHHHHHHHhCcHHH
Confidence 4689999999999999999999999999998874 2 2333244556777888888875 49999999999999999999
Q ss_pred HHHHHhccC
Q psy17442 81 LFMAKVHLN 89 (90)
Q Consensus 81 ~l~~kW~~~ 89 (90)
+|.+|||.+
T Consensus 217 ~i~~ky~g~ 225 (225)
T PF00497_consen 217 KILKKYLGD 225 (225)
T ss_dssp HHHHHHHSS
T ss_pred HHHHHHcCC
Confidence 999999974
No 8
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.48 E-value=4e-13 Score=87.40 Aligned_cols=84 Identities=18% Similarity=0.162 Sum_probs=71.6
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCC---CeEEeCCccccc-----ceEEEEeCCCC-ChHHHHHHHHHhh
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDC---ELVTAGELFGRS-----GYAIGLQKGSP-WADAVTLAILDFH 74 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~---~l~~~~~~~~~~-----~~~ia~~kgs~-l~~~vn~~l~~l~ 74 (90)
.+++..+++.+|.+|++|+++.+.+.+.+++++.. ++.+++..+... +++++++++++ |+..+|++|.+|+
T Consensus 158 ~~~s~~~~~~~L~~g~vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ln~~l~~l~ 237 (250)
T TIGR01096 158 EYDSYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKGDTELKAAFNKALAAIR 237 (250)
T ss_pred EcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccCCceEEEEeCCCHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999998887632 366665544332 47899999986 9999999999999
Q ss_pred hccHHHHHHHHhc
Q psy17442 75 ESTVCYLFMAKVH 87 (90)
Q Consensus 75 ~~G~~~~l~~kW~ 87 (90)
++|+++++.+||+
T Consensus 238 ~~g~~~~i~~kw~ 250 (250)
T TIGR01096 238 ADGTYQKISKKWF 250 (250)
T ss_pred HCCcHHHHHHhhC
Confidence 9999999999996
No 9
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.43 E-value=1.2e-12 Score=84.98 Aligned_cols=84 Identities=11% Similarity=0.113 Sum_probs=70.3
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCccc-----ccceEEEEeCCCC-ChHHHHHHHHHhhhccH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFG-----RSGYAIGLQKGSP-WADAVTLAILDFHESTV 78 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~-----~~~~~ia~~kgs~-l~~~vn~~l~~l~~~G~ 78 (90)
+++..+++.+|.+|++||++.+..++.++..+.+.+..++..+. ..+.+|+++++++ |++.+|++|..++++|+
T Consensus 153 ~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ln~~l~~l~~~g~ 232 (243)
T PRK15007 153 YDSYQNAKLDLQNGRIDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGT 232 (243)
T ss_pred cCCHHHHHHHHHcCCCCEEEeCHHHHHHHHhcCCCceeecCcccccccCCcceEEEEeCCCHHHHHHHHHHHHHHHhCCc
Confidence 57889999999999999999999998888877655555443221 3357899999875 99999999999999999
Q ss_pred HHHHHHHhcc
Q psy17442 79 CYLFMAKVHL 88 (90)
Q Consensus 79 ~~~l~~kW~~ 88 (90)
++++.+|||.
T Consensus 233 ~~~i~~~w~~ 242 (243)
T PRK15007 233 YETIYNKWFQ 242 (243)
T ss_pred HHHHHHHhcC
Confidence 9999999985
No 10
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.41 E-value=1.8e-12 Score=85.82 Aligned_cols=81 Identities=21% Similarity=0.136 Sum_probs=69.5
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCC-ChHHHHHHHHHhhhccHHHHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSP-WADAVTLAILDFHESTVCYLF 82 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~-l~~~vn~~l~~l~~~G~~~~l 82 (90)
.+++.++++++|.+|++||++.|.+++.++..+. ..+++..+...+|+++++|+++ |++.+|.+|.+++. ++++|
T Consensus 178 ~~~~~~~~~~~l~~GrvDa~~~d~~~~~~~~~~~--~~~~~~~~~~~~~~~a~~k~~~~l~~~ln~~l~~~~~--~~~~i 253 (259)
T PRK11917 178 EFPDYPSIKAALDAKRVDAFSVDKSILLGYVDDK--SEILPDSFEPQSYGIVTKKDDPAFAKYVDDFVKEHKN--EIDAL 253 (259)
T ss_pred ecCCHHHHHHHHHcCCCcEEEecHHHHHHhhhcC--CeecCCcCCCCceEEEEeCCCHHHHHHHHHHHHHHHH--HHHHH
Confidence 3678899999999999999999999887766543 3566667788899999999986 99999999999965 99999
Q ss_pred HHHhcc
Q psy17442 83 MAKVHL 88 (90)
Q Consensus 83 ~~kW~~ 88 (90)
.+||.+
T Consensus 254 ~~kw~~ 259 (259)
T PRK11917 254 AKKWGL 259 (259)
T ss_pred HHHhCc
Confidence 999974
No 11
>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=99.40 E-value=1.5e-12 Score=86.21 Aligned_cols=84 Identities=5% Similarity=-0.091 Sum_probs=67.8
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhc-C---CCeEEeCCcc--cccceEEEEeCCC---CChHHHHHHHHHhhh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ-D---CELVTAGELF--GRSGYAIGLQKGS---PWADAVTLAILDFHE 75 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~-~---~~l~~~~~~~--~~~~~~ia~~kgs---~l~~~vn~~l~~l~~ 75 (90)
+++..+++++|.+||+|+++.+..++.+++++ + ..+....... ...+++|+++|++ .|++.||++|.+|++
T Consensus 169 ~~~~~~~~~~L~~GrvD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~k~~~~~~l~~~in~~L~~l~~ 248 (268)
T TIGR02285 169 NAAMGNLFKMLEKGRVNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMPAHISVWVACPKTEWGRKVIADIDQALSELNV 248 (268)
T ss_pred cchHHHHHHHHHcCCccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCccceEEEEEeCCCHHHHHHHHHHHHHHHHHhh
Confidence 45677899999999999999999999988874 2 2344443221 2235899999974 499999999999999
Q ss_pred ccHHHHHHHHhcc
Q psy17442 76 STVCYLFMAKVHL 88 (90)
Q Consensus 76 ~G~~~~l~~kW~~ 88 (90)
+|++++|.+|||.
T Consensus 249 dG~~~~i~~k~~~ 261 (268)
T TIGR02285 249 DPKYYKYFDRWLS 261 (268)
T ss_pred CHHHHHHHHHhCC
Confidence 9999999999995
No 12
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.39 E-value=1.9e-12 Score=84.83 Aligned_cols=87 Identities=16% Similarity=0.012 Sum_probs=70.9
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHH--HhcCCCe-EEeCCcccc-cceEEEEeCC--CCChHHHHHHHHHhhhc
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFE--AAQDCEL-VTAGELFGR-SGYAIGLQKG--SPWADAVTLAILDFHES 76 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~--~~~~~~l-~~~~~~~~~-~~~~ia~~kg--s~l~~~vn~~l~~l~~~ 76 (90)
..+++.++++++|++|++||++.|.+++.++ ..+.... ......... ++++++++|+ +++++.+|.+|.+++++
T Consensus 173 ~~~~~~~~~~~al~~Gr~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~in~~l~~l~~~ 252 (275)
T COG0834 173 VAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIALRKGDDPELLEAVNKALKELKAD 252 (275)
T ss_pred EeeCCHHHHHHHHHcCCccEEEcchHhhhhhhhhhcCCCCceeeeccCCCcceeEEEeccCCcHHHHHHHHHHHHHHHhC
Confidence 4578889999999999999999999999984 3333222 233333333 7899999999 36999999999999999
Q ss_pred cHHHHHHHHhccC
Q psy17442 77 TVCYLFMAKVHLN 89 (90)
Q Consensus 77 G~~~~l~~kW~~~ 89 (90)
|+++++.+||+..
T Consensus 253 G~~~~i~~kw~~~ 265 (275)
T COG0834 253 GTLQKISDKWFGP 265 (275)
T ss_pred ccHHHHHHHhcCc
Confidence 9999999999974
No 13
>KOG1054|consensus
Probab=99.39 E-value=5.3e-13 Score=96.35 Aligned_cols=85 Identities=26% Similarity=0.411 Sum_probs=74.0
Q ss_pred cCChHHHHHHhhcCC-ceEEEeehhHHhHHHhc-CCCeEEeCCcccccceEEEEeCCCCChHHHHHHHHHhhhccHHHHH
Q psy17442 5 VKFSPSTVVRHGTKK-LMAFIWDSSRLDFEAAQ-DCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLF 82 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~-ida~i~d~~~~~~~~~~-~~~l~~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l 82 (90)
+.+..|++.+++.-+ -.|++.+.+.-+|.... .|+...+|..+...+||||.||||.|+..+|.+++.|.|.|.+++|
T Consensus 706 v~t~aeGv~rVRksKGkyAfLLEsTmNey~eqRkPCDTMKVGgNLds~GYGiATp~Gsslr~~vNLAvLkL~E~G~LdKL 785 (897)
T KOG1054|consen 706 VRTTAEGVARVRKSKGKYAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKL 785 (897)
T ss_pred eehhhhHHHHHHhcCCceEeehHhhhhhhhhccCCccceecccccCCcceeecCCCCcccccchhhhhhhhcccchHHHh
Confidence 567899999998433 38999887766655443 7999999999999999999999999999999999999999999999
Q ss_pred HHHhccC
Q psy17442 83 MAKVHLN 89 (90)
Q Consensus 83 ~~kW~~~ 89 (90)
..||+.+
T Consensus 786 kNKWWYD 792 (897)
T KOG1054|consen 786 KNKWWYD 792 (897)
T ss_pred hhhhccc
Confidence 9999864
No 14
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.35 E-value=9e-12 Score=82.12 Aligned_cols=85 Identities=15% Similarity=0.062 Sum_probs=67.1
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhH-HHhc--CCCeEEeCCccc-----ccceEEEEeCCCC-ChHHHHHHHHHhhh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDF-EAAQ--DCELVTAGELFG-----RSGYAIGLQKGSP-WADAVTLAILDFHE 75 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~-~~~~--~~~l~~~~~~~~-----~~~~~ia~~kgs~-l~~~vn~~l~~l~~ 75 (90)
+++..+++.+|.+|++|+++.|...+.+ +.++ ...+.+++.... ..+++++++++++ |.+.+|++|.++++
T Consensus 162 ~~~~~~~~~~l~~griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~L~~~ln~~l~~l~~ 241 (260)
T PRK15010 162 YANQDLVYSDLAAGRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELRQ 241 (260)
T ss_pred cCCHHHHHHHHHcCCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEEEEeCCCHHHHHHHHHHHHHHHh
Confidence 5677889999999999999999887764 4444 234555543322 2346799999875 99999999999999
Q ss_pred ccHHHHHHHHhccC
Q psy17442 76 STVCYLFMAKVHLN 89 (90)
Q Consensus 76 ~G~~~~l~~kW~~~ 89 (90)
+|++++|.+||+..
T Consensus 242 ~G~~~~i~~ky~~~ 255 (260)
T PRK15010 242 DGTYDKMAKKYFDF 255 (260)
T ss_pred CCcHHHHHHHhcCC
Confidence 99999999999975
No 15
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.35 E-value=5.5e-12 Score=90.03 Aligned_cols=85 Identities=18% Similarity=0.015 Sum_probs=71.2
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCC-CC-ChHHHHHHHHHhhhccHHHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKG-SP-WADAVTLAILDFHESTVCYLF 82 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kg-s~-l~~~vn~~l~~l~~~G~~~~l 82 (90)
+.+..+++.+|.+|++|+++.|...+.......+++.+........+++++++|+ ++ |++.+|++|.+++++|++++|
T Consensus 181 ~~s~~e~l~aL~~G~iDa~v~d~~~~~~~~~~~p~l~v~~~l~~~~~~~~av~k~~~~~L~~~ln~~L~~i~~~G~l~~L 260 (482)
T PRK10859 181 DKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPELAVAFDLTDEQPVAWALPPSGDDSLYAALLDFFNQIKEDGTLARL 260 (482)
T ss_pred CCCHHHHHHHHHCCCCCEEEECcHHHHHHHHhCCCceeeeecCCCceeEEEEeCCCCHHHHHHHHHHHHHhhcCCHHHHH
Confidence 4678999999999999999999988765544456666654444567899999994 55 999999999999999999999
Q ss_pred HHHhccC
Q psy17442 83 MAKVHLN 89 (90)
Q Consensus 83 ~~kW~~~ 89 (90)
.+|||..
T Consensus 261 ~~kyfg~ 267 (482)
T PRK10859 261 EEKYFGH 267 (482)
T ss_pred HHHHhhh
Confidence 9999964
No 16
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.29 E-value=3.7e-11 Score=79.16 Aligned_cols=86 Identities=13% Similarity=0.013 Sum_probs=66.4
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhH-HHhc--CCCeEEeCCcc-----cccceEEEEeCCCC-ChHHHHHHHHHhh
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDF-EAAQ--DCELVTAGELF-----GRSGYAIGLQKGSP-WADAVTLAILDFH 74 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~-~~~~--~~~l~~~~~~~-----~~~~~~ia~~kgs~-l~~~vn~~l~~l~ 74 (90)
.+++..+++.+|.+||+|+++.+...+.+ +.++ ...+.+.+..+ ...+++++++++++ |++.+|.+|.+|+
T Consensus 161 ~~~~~~~~i~~L~~grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ia~~~~~~~l~~~~n~~l~~~~ 240 (259)
T PRK15437 161 SYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMR 240 (259)
T ss_pred ecCCHHHHHHHHHcCCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEEEEeCCCHHHHHHHHHHHHHHH
Confidence 35677899999999999999999887764 3333 22344433222 22356899988865 9999999999999
Q ss_pred hccHHHHHHHHhccC
Q psy17442 75 ESTVCYLFMAKVHLN 89 (90)
Q Consensus 75 ~~G~~~~l~~kW~~~ 89 (90)
++|++++|.+|||..
T Consensus 241 ~~G~~~~i~~k~~~~ 255 (259)
T PRK15437 241 ADGTYEKLAKKYFDF 255 (259)
T ss_pred HCCcHHHHHHHhcCC
Confidence 999999999999974
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=99.29 E-value=2.7e-11 Score=80.54 Aligned_cols=86 Identities=10% Similarity=-0.014 Sum_probs=68.7
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcC--CCeEEeCCc-ccc--cceEEEEeCCCC-ChHHHHHHHHHhhhcc
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD--CELVTAGEL-FGR--SGYAIGLQKGSP-WADAVTLAILDFHEST 77 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~--~~l~~~~~~-~~~--~~~~ia~~kgs~-l~~~vn~~l~~l~~~G 77 (90)
.+++..+++.+|.+|++|+++.+..++.+++++. ..+..+... ..+ ..++++++++++ |++.+|.+|.+|+++|
T Consensus 171 ~~~~~~~~i~~L~~grvDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~~sG 250 (275)
T TIGR02995 171 VVPDGQSGLKMVQDGRADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPVRYYGGAAFRPEDKELRDAFNVELAKLKESG 250 (275)
T ss_pred EeCCHHHHHHHHHcCCCCEEecChHHHHHHHHhCCCCCceeecCccCCccccceeEEECCCCHHHHHHHHHHHHHHHhCh
Confidence 4678899999999999999999999999888752 344443221 111 223899998875 9999999999999999
Q ss_pred HHHHHHHHhccC
Q psy17442 78 VCYLFMAKVHLN 89 (90)
Q Consensus 78 ~~~~l~~kW~~~ 89 (90)
++++|.+||-..
T Consensus 251 ~~~~i~~ky~~~ 262 (275)
T TIGR02995 251 EFAKIIAPYGFS 262 (275)
T ss_pred HHHHHHHHhCCC
Confidence 999999999653
No 18
>KOG1052|consensus
Probab=99.27 E-value=3.2e-11 Score=88.56 Aligned_cols=85 Identities=27% Similarity=0.347 Sum_probs=76.6
Q ss_pred ccCChHHHHHHhhcCC--ceEEEeehhHHhHHHhcC--CCeEEeCCcccccceEEEEeCCCCChHHHHHHHHHhhhccHH
Q psy17442 4 DVKFSPSTVVRHGTKK--LMAFIWDSSRLDFEAAQD--CELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHESTVC 79 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~--ida~i~d~~~~~~~~~~~--~~l~~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~ 79 (90)
.+.+..+++.++++|. -.+++.+...+.+....+ |++..+++.+...+|| ++||||||+..++.+|+++.+.|.+
T Consensus 485 ~~~~~~e~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e~g~l 563 (656)
T KOG1052|consen 485 PLASPEEGVERVRKGPSGGYAFASDELYLAYLFLRDEICDLTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQETGIL 563 (656)
T ss_pred cCCCHHHHHHHHHcCCCCceEEEeccHHHHHHHhhcCCCceEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhccccHH
Confidence 4678899999999996 477888877777776654 9999999999999999 9999999999999999999999999
Q ss_pred HHHHHHhccC
Q psy17442 80 YLFMAKVHLN 89 (90)
Q Consensus 80 ~~l~~kW~~~ 89 (90)
+++.+||+..
T Consensus 564 ~~~~~kw~~~ 573 (656)
T KOG1052|consen 564 QKLKRKWFSK 573 (656)
T ss_pred HHHHHHhccC
Confidence 9999999974
No 19
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=99.21 E-value=1.2e-10 Score=76.52 Aligned_cols=79 Identities=9% Similarity=-0.039 Sum_probs=62.0
Q ss_pred hHHHHHHhhcCCceEEEeehhHHhHHHhcC-CCeE--EeCCcc-------ccc--ceEEEEeCCCC-ChHHHHHHHHHhh
Q psy17442 8 SPSTVVRHGTKKLMAFIWDSSRLDFEAAQD-CELV--TAGELF-------GRS--GYAIGLQKGSP-WADAVTLAILDFH 74 (90)
Q Consensus 8 ~~~~~~~l~~G~ida~i~d~~~~~~~~~~~-~~l~--~~~~~~-------~~~--~~~ia~~kgs~-l~~~vn~~l~~l~ 74 (90)
..+++++|.+|++||++.+.+.+.+++++. ..+. .++... ... ++||+++|+++ |++.||++|.+|+
T Consensus 152 ~~~~~~aL~~GrvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~~l~ 231 (246)
T TIGR03870 152 PRKLVSEVATGKADLAVAFAPEVARYVKASPEPLRMTVIPDDATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALAKAK 231 (246)
T ss_pred HHHHHHHHHcCCCCEEEeeHHhHHHHHHhCCCCceEEeccccccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHHHhH
Confidence 578999999999999999988888887753 2343 233221 112 36999999986 9999999999999
Q ss_pred hccHHHHHHHHhcc
Q psy17442 75 ESTVCYLFMAKVHL 88 (90)
Q Consensus 75 ~~G~~~~l~~kW~~ 88 (90)
|++++|.++|.+
T Consensus 232 --~~~~~i~~~y~~ 243 (246)
T TIGR03870 232 --PRIDAILKEEGI 243 (246)
T ss_pred --HHHHHHHHHcCC
Confidence 599999999964
No 20
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.20 E-value=1.6e-10 Score=71.61 Aligned_cols=84 Identities=19% Similarity=0.238 Sum_probs=72.4
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcC--CCeEEeCCcccc-cceEEEEeCCCC-ChHHHHHHHHHhhhccHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD--CELVTAGELFGR-SGYAIGLQKGSP-WADAVTLAILDFHESTVC 79 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~--~~l~~~~~~~~~-~~~~ia~~kgs~-l~~~vn~~l~~l~~~G~~ 79 (90)
.+++..+++.+|.+|++||++...+.+.++..+. +.+.++...... .+++++++++++ +.+.++++|..+.++|++
T Consensus 132 ~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 211 (219)
T smart00062 132 SYDSQAEALAALKAGRADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFAVRKGDPELLDKINKALKELKADGTL 211 (219)
T ss_pred EcCCHHHHHHHhhcCcccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEEEECCCHHHHHHHHHHHHHHHhCchH
Confidence 3567889999999999999999999888887663 567776655555 788999999985 999999999999999999
Q ss_pred HHHHHHhc
Q psy17442 80 YLFMAKVH 87 (90)
Q Consensus 80 ~~l~~kW~ 87 (90)
+++.+||+
T Consensus 212 ~~i~~~~~ 219 (219)
T smart00062 212 KKIYEKWF 219 (219)
T ss_pred HHHHhccC
Confidence 99999996
No 21
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.17 E-value=1.1e-10 Score=89.84 Aligned_cols=85 Identities=13% Similarity=0.063 Sum_probs=72.1
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcC--CCe-EEeCCcccccceEEEEeCCCC-ChHHHHHHHHHhhhccHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD--CEL-VTAGELFGRSGYAIGLQKGSP-WADAVTLAILDFHESTVC 79 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~--~~l-~~~~~~~~~~~~~ia~~kgs~-l~~~vn~~l~~l~~~G~~ 79 (90)
.+++..+++.+|.+|++||++.+.+++.|++++. ..+ .+....+...+++||++|++| |++.+|++|..+.++ ++
T Consensus 433 ~~~~~~~~l~av~~G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~av~k~~~~L~~~lnk~l~~i~~~-~~ 511 (1197)
T PRK09959 433 KVDNASAAFHKVKEGELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGEPELKDIINKALNAIPPS-EV 511 (1197)
T ss_pred EcCCHHHHHHHHHcCCCCEEehhhHHHHHHHHhcccccceeeecCCCCchheEEeeCCCCHHHHHHHHHHHHhCCHH-HH
Confidence 4789999999999999999999999999998862 223 333344556789999999986 999999999999999 99
Q ss_pred HHHHHHhccC
Q psy17442 80 YLFMAKVHLN 89 (90)
Q Consensus 80 ~~l~~kW~~~ 89 (90)
.+|.+|||..
T Consensus 512 ~~i~~kW~~~ 521 (1197)
T PRK09959 512 LRLTEKWIKM 521 (1197)
T ss_pred HHHHhhcccC
Confidence 9999999863
No 22
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=99.16 E-value=3.4e-10 Score=70.35 Aligned_cols=84 Identities=17% Similarity=0.125 Sum_probs=69.6
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcC-CCeEEeCCc--ccccceEEEEeCCC-CChHHHHHHHHHhhhccHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD-CELVTAGEL--FGRSGYAIGLQKGS-PWADAVTLAILDFHESTVC 79 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~-~~l~~~~~~--~~~~~~~ia~~kgs-~l~~~vn~~l~~l~~~G~~ 79 (90)
.+++..+++..|.+|++|+++.+.+.+.++..+. +.+.++... .....++++.++++ ++.+.++++|..|+++|++
T Consensus 131 ~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~g~~ 210 (218)
T cd00134 131 SYDDNAEALAALENGRADAVIVDEIALAALLKKHPPELKIVGPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADGEL 210 (218)
T ss_pred EeCCHHHHHHHHHcCCccEEEeccHHHHHHHHhcCCCcEEeccccCCCccceEEEEcCCCHHHHHHHHHHHHHHHhCccH
Confidence 4677899999999999999999999998887764 667777553 23344567677766 4999999999999999999
Q ss_pred HHHHHHhc
Q psy17442 80 YLFMAKVH 87 (90)
Q Consensus 80 ~~l~~kW~ 87 (90)
+++.+|||
T Consensus 211 ~~i~~~~~ 218 (218)
T cd00134 211 KKISKKWF 218 (218)
T ss_pred HHHHHhhC
Confidence 99999997
No 23
>TIGR03871 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein. This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme.
Probab=99.15 E-value=4e-10 Score=72.71 Aligned_cols=82 Identities=16% Similarity=0.082 Sum_probs=64.5
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhc-CCCeEEeCCcc------cccceEEEEeCCCC-ChHHHHHHHHHhhhcc
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ-DCELVTAGELF------GRSGYAIGLQKGSP-WADAVTLAILDFHEST 77 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~-~~~l~~~~~~~------~~~~~~ia~~kgs~-l~~~vn~~l~~l~~~G 77 (90)
.+..+++++|.+|++||++.+..++.+++++ ...+.+..... ...+.+++++++++ |++.+|.+|.+++ |
T Consensus 141 ~~~~~~~~~l~~G~~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~--~ 218 (232)
T TIGR03871 141 SPPGRMVEDLAAGEIDVAIVWGPIAGYFAKQAGPPLVVVPLLPEDGGIPFDYRIAMGVRKGDKAWKDELNAVLDRRQ--A 218 (232)
T ss_pred CCHHHHHHHHHcCCcCEEEeccHHHHHHHHhCCCCceeeccccCCCCCCccceEEEEEecCCHHHHHHHHHHHHHHH--H
Confidence 3679999999999999999999988888775 33444443221 12356888999875 9999999999985 5
Q ss_pred HHHHHHHHhccC
Q psy17442 78 VCYLFMAKVHLN 89 (90)
Q Consensus 78 ~~~~l~~kW~~~ 89 (90)
++++|.+||...
T Consensus 219 ~~~~i~~kyg~~ 230 (232)
T TIGR03871 219 EIDAILREYGVP 230 (232)
T ss_pred HHHHHHHHcCCC
Confidence 899999999864
No 24
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.00 E-value=1.7e-09 Score=83.46 Aligned_cols=84 Identities=7% Similarity=-0.156 Sum_probs=70.6
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcC--CCeEEeCCc-ccccceEEEEeCCCC-ChHHHHHHHHHhhhccHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD--CELVTAGEL-FGRSGYAIGLQKGSP-WADAVTLAILDFHESTVC 79 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~--~~l~~~~~~-~~~~~~~ia~~kgs~-l~~~vn~~l~~l~~~G~~ 79 (90)
.+++..+++.+|.+|++||++.+.+++.+++++. ..+.+++.. .....++++++|+++ |.+.+|++|..+.++|..
T Consensus 190 ~~~s~~~al~av~~G~~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~lnkal~~i~~~~~~ 269 (1197)
T PRK09959 190 SFTNLYQALASVSAGQNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKESVILNEVLNRFVDALTNEVRY 269 (1197)
T ss_pred eCCCHHHHHHHHHcCCCCEEEccHHHHHHHHhcccccceEEEeeccCCCCceeEEEcCCcHHHHHHHHHHHHhCCHHHHH
Confidence 5789999999999999999999999999999863 345555332 233456788999987 999999999999999999
Q ss_pred HHHHHHhcc
Q psy17442 80 YLFMAKVHL 88 (90)
Q Consensus 80 ~~l~~kW~~ 88 (90)
+|.+||+.
T Consensus 270 -~i~~kW~~ 277 (1197)
T PRK09959 270 -EVSQNWLD 277 (1197)
T ss_pred -HHHHhccC
Confidence 99999985
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=98.52 E-value=3.5e-07 Score=59.76 Aligned_cols=69 Identities=13% Similarity=0.033 Sum_probs=56.9
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcC----CCeEEeCCcccccceEEEEeCC-CC-ChHHHHHHHHHh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD----CELVTAGELFGRSGYAIGLQKG-SP-WADAVTLAILDF 73 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~----~~l~~~~~~~~~~~~~ia~~kg-s~-l~~~vn~~l~~l 73 (90)
+.+.++++.+|.+|++||++.+.+.+..+.+++ ..+.+++......+++++++|+ ++ +++.||++|..|
T Consensus 180 ~~~~~~~~~al~~G~~Da~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 180 SGSHDASALAVANGKVDAATNNSSAIGRLKKRGPSDMKKVRVIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred cCchHHHHHHHHcCCCCeEEecHHHHHHHHHhCccchhheEEEEecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 345688999999999999999999988776653 2577887766667789999999 65 999999999764
No 26
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.36 E-value=1.1e-06 Score=59.35 Aligned_cols=78 Identities=14% Similarity=-0.054 Sum_probs=61.8
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeC--CCC-ChHHHHHHHHHhhhccHHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQK--GSP-WADAVTLAILDFHESTVCYL 81 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~k--gs~-l~~~vn~~l~~l~~~G~~~~ 81 (90)
+++..++ ++..|++||++.+.++...+.++ .+.++ +.+.....+++.+| +++ +++.+|..+.++ +|.+.+
T Consensus 140 ~~gs~ea--a~~~G~aDaivd~~~~~~~l~~~--~L~~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~g~l~a 212 (287)
T PRK00489 140 LSGAVEV--APRLGLADAIVDVVSTGTTLRAN--GLKIV-EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--QGVLRA 212 (287)
T ss_pred CCCchhh--hhcCCcccEEEeeHHHHHHHHHC--CCEEE-EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--HHHHHh
Confidence 4556665 67779999999888877766653 46666 45556678899999 666 889999999999 599999
Q ss_pred HHHHhccC
Q psy17442 82 FMAKVHLN 89 (90)
Q Consensus 82 l~~kW~~~ 89 (90)
+..|||..
T Consensus 213 ~~~k~~~~ 220 (287)
T PRK00489 213 RESKYLMM 220 (287)
T ss_pred hceEEEEE
Confidence 99999964
No 27
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=98.16 E-value=1.2e-05 Score=56.41 Aligned_cols=82 Identities=17% Similarity=-0.021 Sum_probs=70.9
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCC--CChHHHHHHHHHhhhccHHHHHHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGS--PWADAVTLAILDFHESTVCYLFMA 84 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs--~l~~~vn~~l~~l~~~G~~~~l~~ 84 (90)
+..+.+..|..|++|..|.|++.+.-...-.+++.+.-+.-...+.++.+|.++ .|...++.++.+++++|.++++.+
T Consensus 164 ~~~dLle~v~~Gkldytiads~~is~~q~i~P~laVafd~tde~~v~Wy~~~~dd~tL~a~ll~F~~~~~e~g~larlee 243 (473)
T COG4623 164 GVEDLLEMVAEGKLDYTIADSVEISLFQRVHPELAVAFDLTDEQPVAWYLPRDDDSTLSAALLDFLNEAKEDGLLARLEE 243 (473)
T ss_pred cHHHHHHHHhcCCcceeeeccHHHHHHHHhCccceeeeecccccCceeeccCCchHHHHHHHHHHHHHhhcchHHHHHHH
Confidence 457888999999999999999988776665788888766556688999999964 499999999999999999999999
Q ss_pred Hhcc
Q psy17442 85 KVHL 88 (90)
Q Consensus 85 kW~~ 88 (90)
|++.
T Consensus 244 ky~g 247 (473)
T COG4623 244 KYLG 247 (473)
T ss_pred HHhc
Confidence 9984
No 28
>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=98.16 E-value=7.3e-06 Score=54.78 Aligned_cols=81 Identities=11% Similarity=0.038 Sum_probs=60.0
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhc-C----CCeEEeCCcccccceEEEEeCC-CC-ChHHHHHHHHHhhhccHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ-D----CELVTAGELFGRSGYAIGLQKG-SP-WADAVTLAILDFHESTVC 79 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~-~----~~l~~~~~~~~~~~~~ia~~kg-s~-l~~~vn~~l~~l~~~G~~ 79 (90)
+..+++++|.+|++||++.+.+.+..+.++ . .++.++.......+.+++++++ .+ +++.++++|.++.+++..
T Consensus 176 ~~~~~~~al~~G~vDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~ 255 (288)
T TIGR03431 176 SHEAAILAVANGTVDAATTNDENLDRMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKTDKA 255 (288)
T ss_pred chHHHHHHHHcCCCCeEeccHHHHHHHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCCcHH
Confidence 578899999999999999998888777753 2 2355543322233467899998 44 999999999999999776
Q ss_pred HH--HHHHhc
Q psy17442 80 YL--FMAKVH 87 (90)
Q Consensus 80 ~~--l~~kW~ 87 (90)
++ ...+|+
T Consensus 256 ~~~~~~~~~~ 265 (288)
T TIGR03431 256 CFEKIAGGDL 265 (288)
T ss_pred HHHhhhcccc
Confidence 64 344563
No 29
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=96.94 E-value=0.0053 Score=40.06 Aligned_cols=81 Identities=10% Similarity=-0.018 Sum_probs=61.4
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhc----CCCeEEeCCcccccceEEEEeCC-CC-ChHHHHHHHHHhhhccHH
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ----DCELVTAGELFGRSGYAIGLQKG-SP-WADAVTLAILDFHESTVC 79 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~----~~~l~~~~~~~~~~~~~ia~~kg-s~-l~~~vn~~l~~l~~~G~~ 79 (90)
.+...++.+|.+|++||.+........+... ..++.++...-....+.++++++ ++ +++.|-.+|..+..+-.-
T Consensus 144 ~~~~~~~~~l~~G~~Da~~~~~~~~~~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~~~~ 223 (243)
T PF12974_consen 144 GSHDAVLEALLNGKADAAAIPSDAFERLEAEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKDPEG 223 (243)
T ss_dssp E-HHHHHHHHHTTSSSEEEEEHHHHHHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSSHHH
T ss_pred CCHHHHHHHHHcCCccEEEEechhHHHHHHccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCChhh
Confidence 4678899999999999999999888877654 24688886654455667888887 44 899999999999987666
Q ss_pred HHHHHHh
Q psy17442 80 YLFMAKV 86 (90)
Q Consensus 80 ~~l~~kW 86 (90)
.++.+.+
T Consensus 224 ~~~l~~~ 230 (243)
T PF12974_consen 224 KAILDAF 230 (243)
T ss_dssp HHHHHHT
T ss_pred HHHHHhc
Confidence 6666554
No 30
>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=96.75 E-value=0.023 Score=38.26 Aligned_cols=83 Identities=17% Similarity=0.045 Sum_probs=57.9
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhc-C-CCeEEeC--------C--cccc---------cceEEEEeCCCC-
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ-D-CELVTAG--------E--LFGR---------SGYAIGLQKGSP- 61 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~-~-~~l~~~~--------~--~~~~---------~~~~ia~~kgs~- 61 (90)
.+++..+++.+|..|++|+.+........+++. + ..+.+.+ + ++.. ..+|+.+|||-|
T Consensus 137 py~G~~~~~~allgG~vd~~~~~~~~~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~ 216 (274)
T PF03401_consen 137 PYDGGAEALTALLGGHVDAAFGSPGEALPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPD 216 (274)
T ss_dssp E-SSHHHHHHHHHTTSSSEEEEEHHHHHHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-H
T ss_pred EeCCccHHHHHHhCCeeeEEeecHHHHHHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCH
Confidence 467889999999999999999887666655543 1 1121211 1 1111 224899999954
Q ss_pred -ChHHHHHHHHHhhhccHHHHHHHHh
Q psy17442 62 -WADAVTLAILDFHESTVCYLFMAKV 86 (90)
Q Consensus 62 -l~~~vn~~l~~l~~~G~~~~l~~kW 86 (90)
.++.+..++.+..++-++.+..++-
T Consensus 217 ~~~~~l~~a~~~~~~~pe~~~~~~~~ 242 (274)
T PF03401_consen 217 EIVDKLADAIKKALEDPEFQEFLEKM 242 (274)
T ss_dssp HHHHHHHHHHHHHHT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHC
Confidence 8999999999999999999877664
No 31
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=95.92 E-value=0.034 Score=38.17 Aligned_cols=71 Identities=11% Similarity=0.012 Sum_probs=56.9
Q ss_pred cCC-hHHHHHHhhcCCceEEEeehhHHhHHHhc--C---CCeEEeCCcccccceEEEEeCC-CC-ChHHHHHHHHHhhh
Q psy17442 5 VKF-SPSTVVRHGTKKLMAFIWDSSRLDFEAAQ--D---CELVTAGELFGRSGYAIGLQKG-SP-WADAVTLAILDFHE 75 (90)
Q Consensus 5 ~~~-~~~~~~~l~~G~ida~i~d~~~~~~~~~~--~---~~l~~~~~~~~~~~~~ia~~kg-s~-l~~~vn~~l~~l~~ 75 (90)
+.+ ...++.+|.+|++|+.............. . .+++++...-...+..|++++. ++ +++.+-.++..|.+
T Consensus 182 ~~G~H~~a~~aV~nG~vDva~~~~~~~~~~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 182 FSGGHDAAVLAVANGQVDVAAVNSSARGLLKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred ccChHHHHHHHHHcCCceEEeccHHHHhhhhhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHHhcCc
Confidence 444 88999999999999988887777665543 2 3688887766667778999998 44 99999999999976
No 32
>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=95.71 E-value=0.042 Score=34.90 Aligned_cols=59 Identities=12% Similarity=0.017 Sum_probs=43.7
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
.+.+..+.+.+|.+|++|+.+...........+..+++++.......+.++.++++++.
T Consensus 27 ~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i 85 (216)
T PF09084_consen 27 FFGGGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSSPNALVVRKDSGI 85 (216)
T ss_dssp EESSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEECCEEEEEETTTS-
T ss_pred EecChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCCceEEEEeccCCC
Confidence 34677899999999999998888776665555556677776555556677888888663
No 33
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=95.66 E-value=0.067 Score=36.15 Aligned_cols=75 Identities=7% Similarity=0.045 Sum_probs=47.4
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcC-CCeEEeCCcccccc-eEEEEeCC-CCChHHHHHHHHHhhhccHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD-CELVTAGELFGRSG-YAIGLQKG-SPWADAVTLAILDFHESTVC 79 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~-~~l~~~~~~~~~~~-~~ia~~kg-s~l~~~vn~~l~~l~~~G~~ 79 (90)
..+.++++.+|.+|++||++...|....+..+. ..+...+..+...+ +.++.++. ....+.+++.+..+.+...+
T Consensus 162 ~~~~~~~~~al~~G~vDa~~~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~~l~a~~~A~~~ 239 (314)
T PRK11553 162 YLTPADARAAFQQGNVDAWAIWDPYYSAALLQGGVRVLKDGTDLNQTGSFYLAARPYAEKNGAFIQQVLATLTEADAL 239 (314)
T ss_pred ecChHHHHHHHHcCCCCEEEEcCcHHHHHHhcCCcEEeecCcccCcCceEEEEcHHHHHHCHHHHHHHHHHHHHHHHH
Confidence 346678999999999999998888776665543 22222233333333 33344443 34667788877777776544
No 34
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.15 E-value=0.11 Score=35.96 Aligned_cols=83 Identities=10% Similarity=-0.106 Sum_probs=60.1
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhc-CC-CeEEeC--------C--ccc--------ccceEEEEeCC-C-C
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ-DC-ELVTAG--------E--LFG--------RSGYAIGLQKG-S-P 61 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~-~~-~l~~~~--------~--~~~--------~~~~~ia~~kg-s-~ 61 (90)
-+++..+++.+|..|++|+.+...+...-+++. .- .+-+.. + ++. ....||..|+| + +
T Consensus 181 py~g~gea~taLlgg~v~a~~~~~se~~~~vksG~lr~Lav~s~eRl~~~pdvPT~~E~G~~~~~~~wrgvfap~g~~~e 260 (319)
T COG3181 181 PYKGGGEALTALLGGHVDAGSTNLSELLSQVKSGTLRLLAVFSEERLPGLPDVPTLKEQGYDVVMSIWRGVFAPAGTPDE 260 (319)
T ss_pred eecCccHHHHHHhcCceeeeecChhhhhhhhccCceEEEEeechhhcCCCCCCCChHhcCCceeeeeeeEEEeCCCCCHH
Confidence 478889999999999999999998777766664 11 111111 0 111 12237788999 4 4
Q ss_pred ChHHHHHHHHHhhhccHHHHHHHHh
Q psy17442 62 WADAVTLAILDFHESTVCYLFMAKV 86 (90)
Q Consensus 62 l~~~vn~~l~~l~~~G~~~~l~~kW 86 (90)
..++++.+++++.++.++.+..++=
T Consensus 261 ~~~~~~~a~kk~l~s~e~~~~~~~~ 285 (319)
T COG3181 261 IIAKLSAALKKALASPEWQKRLKEL 285 (319)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHhc
Confidence 9999999999999999999877653
No 35
>smart00094 TR_FER Transferrin.
Probab=93.62 E-value=0.32 Score=33.95 Aligned_cols=57 Identities=19% Similarity=0.226 Sum_probs=35.3
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEE-eCCccc------ccceEEEE-eCCCCC
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVT-AGELFG------RSGYAIGL-QKGSPW 62 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~-~~~~~~------~~~~~ia~-~kgs~l 62 (90)
..+..+++.++++|++|++..|......+ .+...+.. +.+... ...|++++ +|+|+.
T Consensus 34 ~~s~~~Ci~~I~~g~AD~a~ldg~~~y~A-~~~~~l~pi~~E~~~~~~~~~~~Y~aVaVVkk~S~i 98 (332)
T smart00094 34 ASSTEECIKAIQKGEADAVTLDGGDVYTA-GKPYNLVPVFAENYGSEEEPETGYYAVAVVKKGSAI 98 (332)
T ss_pred cCCHHHHHHHHHCCCCCEEEECcHHHHhh-cccCCceEEEEEeeccCCCCCceeEEEEEEECCCCC
Confidence 46789999999999999999987743322 23222332 222211 24566554 678773
No 36
>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=93.19 E-value=0.58 Score=32.53 Aligned_cols=57 Identities=21% Similarity=0.254 Sum_probs=38.2
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeE-EeCCccc------ccceEEEE-eCCCC
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELV-TAGELFG------RSGYAIGL-QKGSP 61 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~-~~~~~~~------~~~~~ia~-~kgs~ 61 (90)
-.+..+++.++++|++|+++.|..-+..+..+..++. ++.+... ...|++|+ +|++.
T Consensus 34 ~~s~~dCm~~I~~g~AD~v~ld~~~~y~A~~~~~~L~pi~~E~y~~~~~~~~~y~aVAVVkk~s~ 98 (330)
T PF00405_consen 34 ATSREDCMRRIKKGEADAVTLDGGDVYIAGLRKYNLKPIAAEVYGSEEEPEASYYAVAVVKKSSN 98 (330)
T ss_dssp ESSHHHHHHHHHTTSSSBEEEEHHHHHHHHSTTTTEEEEEEEEESSSSSEESEEEEEEEEETTSS
T ss_pred CCCHHHHHHHHhhccCCEEEeCchhhhhhhccccCCEEeeeeeccccccccceeEEEEEEecCCC
Confidence 4578899999999999999999766544332455664 3333332 23467776 55664
No 37
>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=92.99 E-value=0.74 Score=29.28 Aligned_cols=79 Identities=18% Similarity=0.011 Sum_probs=46.1
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCc-ccccceEEEEeCCCCChHHHHHHHHHhhhccHHHHHHH
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGEL-FGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLFMA 84 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~-~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~~ 84 (90)
.+..+.+..+.+|++|+.+.....+... .......+++.. .....+++++.|+++-.+...+.| +..-+.+-+++..
T Consensus 136 ~~~~~~~~~~~~Ge~~~~~~~~~~~~~~-~~~~~~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi-~fl~s~e~q~~~~ 213 (216)
T TIGR01256 136 EDVRQALQFVETGNAPAGIVALSDVIPS-KKVGSVATFPEDLYKPIRYPAVIVKGGKNNAAAKAFI-DYLKSPEAKEILR 213 (216)
T ss_pred CcHHHHHHHHHcCCCCEEeeehhhhccc-CCccEEEEeCccccCCccccEEEEECCCChHHHHHHH-HHHcCHHHHHHHH
Confidence 3557888999999999988755433211 112223333332 234467899999976555444444 3344445556655
Q ss_pred Hh
Q psy17442 85 KV 86 (90)
Q Consensus 85 kW 86 (90)
+|
T Consensus 214 ~~ 215 (216)
T TIGR01256 214 KY 215 (216)
T ss_pred Hc
Confidence 55
No 38
>PRK03537 molybdate ABC transporter periplasmic molybdate-binding protein; Provisional
Probab=92.83 E-value=1.6 Score=27.67 Aligned_cols=78 Identities=15% Similarity=0.117 Sum_probs=46.3
Q ss_pred hHHHHH-HhhcCCceEEEeehhHHhHHHhc--CCCeEEeCCc-ccccceEEEEeCCCCChHHHHHHHHHhhhccHHHHHH
Q psy17442 8 SPSTVV-RHGTKKLMAFIWDSSRLDFEAAQ--DCELVTAGEL-FGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLFM 83 (90)
Q Consensus 8 ~~~~~~-~l~~G~ida~i~d~~~~~~~~~~--~~~l~~~~~~-~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~ 83 (90)
..+++. .+.+|++|+.|.-...+...... .-.+..+++. .....|.+++.++++ ..-+.+.+...+.+-+++.
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 345666 78999999976544433322111 1222333432 335568888888875 3345555556777778888
Q ss_pred HHhcc
Q psy17442 84 AKVHL 88 (90)
Q Consensus 84 ~kW~~ 88 (90)
.+|..
T Consensus 178 ~~~Gf 182 (188)
T PRK03537 178 AQYGF 182 (188)
T ss_pred HHcCC
Confidence 77754
No 39
>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=92.49 E-value=0.32 Score=31.85 Aligned_cols=57 Identities=21% Similarity=0.179 Sum_probs=33.0
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
.+.++.+.+|.+|++|..+...........+..++.++.......+..+++++++++
T Consensus 37 ~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~~v~~~~~~i 93 (288)
T TIGR01728 37 PAGPPALEALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSDNKATAIVVIKGSPI 93 (288)
T ss_pred CCCcHHHHHHhcCCccccccCCcHHHHHHhcCCCEEEEEEecCCCceEEEECCCCCC
Confidence 466789999999999997654432222222333555543222223556666666543
No 40
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=92.24 E-value=0.66 Score=31.33 Aligned_cols=59 Identities=15% Similarity=0.027 Sum_probs=34.1
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCC-cccccceEEEEeCCCCCh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGE-LFGRSGYAIGLQKGSPWA 63 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~-~~~~~~~~ia~~kgs~l~ 63 (90)
+.+.++.+.+|.+|++|..+.............-++..++. .....+.++++++++++.
T Consensus 63 ~~~~~~~~~aL~~G~iDia~~~~~~~~~~~~~g~~~~~v~~~~~~~~~~~lvv~~~s~i~ 122 (314)
T PRK11553 63 FPAGPQMLEALNVGSIDLGSTGDIPPIFAQAAGADLVYVGVEPPKPKAEVILVAENSPIK 122 (314)
T ss_pred CCCcHHHHHHHHcCCCCEEccCCHHHHHHHhCCCCEEEEEEecCCCcceEEEEeCCCCCC
Confidence 34567899999999999988653322222222333444322 223344567777776653
No 41
>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=90.75 E-value=1.2 Score=29.84 Aligned_cols=66 Identities=17% Similarity=0.096 Sum_probs=39.6
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcc---c-ccceEEEEeCC----CC-ChHHHHHHHHHh
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELF---G-RSGYAIGLQKG----SP-WADAVTLAILDF 73 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~---~-~~~~~ia~~kg----s~-l~~~vn~~l~~l 73 (90)
+.++++.+|.+|++||++...|....+.++.. ........ . ....+++++++ +| +.+.+.+++.+.
T Consensus 135 ~~~~~~~al~~G~vDa~~~~~p~~~~~~~~g~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~a~~~a 209 (300)
T TIGR01729 135 KPPQIVAAWQRGDIDAAYVWPPALSELLKSGK-VISDSEQVGAWGAPTFDGWVVRKDFAEKNPEFVAAFTKVLADA 209 (300)
T ss_pred CcHHHHHHHHcCCcCEEEEecHHHHHHHhcCc-EEecchhccccCCCceeEEEECHHHHHHCHHHHHHHHHHHHHH
Confidence 45789999999999999999887765554432 11111111 1 11235666654 44 666666555543
No 42
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=89.56 E-value=1.7 Score=28.24 Aligned_cols=58 Identities=5% Similarity=-0.098 Sum_probs=33.8
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcc-----cccceEEEEeCCCCCh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELF-----GRSGYAIGLQKGSPWA 63 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~-----~~~~~~ia~~kgs~l~ 63 (90)
..++.+...++.+|++|.++........+.++. .+..+.... ......|.++++|+..
T Consensus 36 ~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~-~~~~la~~~~~~g~~~~~~~ivv~~ds~i~ 98 (243)
T PF12974_consen 36 ADDYAEFIEALRSGEIDLAFMGPLPYVQARQRA-GVEPLATPVGPDGSPSYRSVIVVRADSPIT 98 (243)
T ss_dssp -SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-SEEEEEEEEETTT-SCEEEEEEEETTSS--
T ss_pred cCCHHHHHHHHHcCCccEEEECcHHHHHHhhcC-cEEEEEEecccCCCcceeEEEEEECCCCCC
Confidence 467899999999999999998765544444333 333332111 1334568889999853
No 43
>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=89.31 E-value=5.2 Score=27.28 Aligned_cols=80 Identities=18% Similarity=-0.018 Sum_probs=45.5
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe-CCc-ccccceEEEEeCCCCChHHHHHHHHHhhhccHHHHHH
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA-GEL-FGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLFM 83 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~-~~~-~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~ 83 (90)
.+..+..+.+.+|++++.+.....+.....+..++.++ .+. ......++++.||+|-.+..-..|.-|. +.+.++..
T Consensus 201 ~s~~~~~~~v~~Ge~~i~~~~~~~~~~~~~~g~~v~~~~P~eG~~~~~~~~ai~k~a~~~e~A~~fidfll-S~e~Q~~~ 279 (334)
T TIGR03261 201 HSGSKPCKLAGMGEFPIGISMAYRALKEKKKGAPIDVVFPKEGLGWDIEATAIIKGSKNNDAAKKLVDWSI-SDEAMELY 279 (334)
T ss_pred CCChHHHHHHhCCCceEEEEecHHHHHHHhCCCCeEEEecCCCCeeeeeeeEEEcCCCCHHHHHHHHHHHc-CHHHHHHH
Confidence 35567888999999998776544333333333445443 221 1223458999999876666555555443 34444333
Q ss_pred HHh
Q psy17442 84 AKV 86 (90)
Q Consensus 84 ~kW 86 (90)
.++
T Consensus 280 ~~~ 282 (334)
T TIGR03261 280 AKN 282 (334)
T ss_pred Hhc
Confidence 333
No 44
>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=89.02 E-value=2.2 Score=27.85 Aligned_cols=31 Identities=3% Similarity=-0.187 Sum_probs=25.8
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhc
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ 36 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~ 36 (90)
.+..+++.+|++|++|+++...+....+..+
T Consensus 135 ~~~~~~~~al~~g~vda~~~~~p~~~~~~~~ 165 (288)
T TIGR01728 135 LGPSDARAAFAAGQVDAWAIWEPWGSALVEE 165 (288)
T ss_pred cCcHHHHHHHHCCCCCEEEeccchHhHHhhc
Confidence 4567899999999999999988887766554
No 45
>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=88.81 E-value=1.6 Score=29.24 Aligned_cols=25 Identities=8% Similarity=-0.047 Sum_probs=19.5
Q ss_pred ccCChHHHHHHhhcCCceEEEeehh
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSS 28 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~ 28 (90)
.+.+.++.+.+|.+|++|..+....
T Consensus 33 ~~~~~~~~~~al~~G~iD~~~~~~~ 57 (300)
T TIGR01729 33 KFDSGADISTALASGNVPIGVIGSS 57 (300)
T ss_pred ecCcHHHHHHHHHcCCCCEeccCCC
Confidence 3566778999999999998875433
No 46
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=88.13 E-value=1.2 Score=27.11 Aligned_cols=51 Identities=16% Similarity=0.025 Sum_probs=32.1
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCCh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWA 63 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~ 63 (90)
..+..+.+..|.+|++|..|...+. ....+.. ..+..+.+.++++++.|+.
T Consensus 41 ~~~~~~~~~~l~~g~~Dl~i~~~~~------~~~~~~~--~~l~~~~~~~~~~~~~pl~ 91 (209)
T PF03466_consen 41 EGDSDELIEALRSGELDLAITFGPP------PPPGLES--EPLGEEPLVLVVSPDHPLA 91 (209)
T ss_dssp EESHHHHHHHHHTTSSSEEEESSSS------SSTTEEE--EEEEEEEEEEEEETTSGGG
T ss_pred eccchhhhHHHhcccccEEEEEeec------ccccccc--ccccceeeeeeeecccccc
Confidence 3456789999999999999987665 2222222 1234555666666665543
No 47
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=87.24 E-value=1 Score=30.01 Aligned_cols=59 Identities=12% Similarity=0.108 Sum_probs=30.4
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe--CC-cc-c-ccceEEEEeCCCC-ChHHHHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA--GE-LF-G-RSGYAIGLQKGSP-WADAVTL 68 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~--~~-~~-~-~~~~~ia~~kgs~-l~~~vn~ 68 (90)
++.+.+..|.+|.|||+||...... .++..+..+ .. .. . ...-.++++|+++ +...+.+
T Consensus 145 ~Y~q~~~~l~~g~IDA~IWN~d~i~---~~~~~l~~~~l~~~~~~~~~seAVivi~~~~~~i~~ll~~ 209 (232)
T PF14503_consen 145 PYNQLLELLRSGEIDAAIWNYDEIE---DKNFGLKYVPLKDDPMSKDASEAVIVIRKDNEPIKALLRK 209 (232)
T ss_dssp -HHHHHHHHHHTS--EEEEE--HHC---CHHCTEEEEE--SSCHHHHTT-EEEEEETT-HHHHHHHHH
T ss_pred cHHHHHHHHHCCCccEEEECCcccc---cccCCeeEEeCCchHHHHhcCeeEEEEeCCCHHHHHHHHH
Confidence 5678999999999999999866211 112333332 21 11 1 2234578899875 5554443
No 48
>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=87.14 E-value=4.3 Score=27.28 Aligned_cols=41 Identities=20% Similarity=0.140 Sum_probs=28.8
Q ss_pred ccCChHHHHHHhhcCCceEEEe-ehhHHhHHHhc-CCCeEEeC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIW-DSSRLDFEAAQ-DCELVTAG 44 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~-d~~~~~~~~~~-~~~l~~~~ 44 (90)
.|++.++...+|.+|++|+.+. ..+.+..+.+. +-++..++
T Consensus 52 ~f~d~~~~~~Al~~G~ID~~~~q~~~~l~~~~~~~g~~lv~v~ 94 (258)
T TIGR00363 52 EFNDYALPNEAVSKGDLDANAFQHKPYLDQDAKAKGYKLVAVG 94 (258)
T ss_pred EeCCcHHHHHHHHcCCCCeEecCCHHHHHHHHHhCCCcEEEEe
Confidence 4788999999999999999754 55555544443 44555554
No 49
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=87.09 E-value=1.5 Score=29.00 Aligned_cols=64 Identities=9% Similarity=0.021 Sum_probs=40.0
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCChHHHHHHHHHhh
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFH 74 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~ 74 (90)
...+....-.++.+|++||-+.-...+.. -+-+|. ++..+.|=|+++|+.--...+-..+..|+
T Consensus 135 e~~th~avA~aVa~G~AD~GvGlr~~A~~---~gL~Fi----pl~~E~YD~virke~~~~~~vr~fi~~L~ 198 (223)
T COG1910 135 EATTHDAVASAVASGRADAGVGLRHAAEK---YGLDFI----PLGDEEYDFVIRKERLDKPVVRAFIKALK 198 (223)
T ss_pred cccccHHHHHHHHcCCCCccccHHHHHHH---cCCceE----EcccceEEEEEehhHccCHHHHHHHHHhc
Confidence 34566677889999999999984444322 133333 35788999999997433333334444444
No 50
>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=86.59 E-value=6.4 Score=25.16 Aligned_cols=81 Identities=21% Similarity=0.108 Sum_probs=52.6
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeE--EeCCccc--ccceEEEEeCCCCChHHHHHHHHHhhhccHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELV--TAGELFG--RSGYAIGLQKGSPWADAVTLAILDFHESTVCY 80 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~--~~~~~~~--~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~ 80 (90)
.++..+.+..+.+|++|+.+.-...+.+. .+...+. .+.+... ...|++++-++++-.+.....+. ...+.+-+
T Consensus 144 ~~~~~~~~~~v~~g~~d~~~~~~s~~~~~-~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~a~~f~~-~L~s~~~q 221 (230)
T PF13531_consen 144 VPSTSQVLSAVASGEADAGIVYESQAIFA-RQGDPLSYVYPPDGVNSPPIDYPIAILKNAPHPEAARAFID-FLLSPEGQ 221 (230)
T ss_dssp ESSHHHHHHHHHTTSSSEEEEEHHHHHHC-TSHTTEEEEE-STTTSSSEEEEEEEEBTTCTTHHHHHHHHH-HHTSHHHH
T ss_pred ccchHHHHHHHHcCCCcceeeHHHHHHHh-hcCCCeEEEECCchhcCCCEEEEEEEecCCCCHHHHHHHHH-HHCCHHHH
Confidence 56778899999999999999876665322 2223343 3344444 35688999888766665555544 44456677
Q ss_pred HHHHHhc
Q psy17442 81 LFMAKVH 87 (90)
Q Consensus 81 ~l~~kW~ 87 (90)
++..++.
T Consensus 222 ~~l~~~G 228 (230)
T PF13531_consen 222 QILAKYG 228 (230)
T ss_dssp HHHHHTT
T ss_pred HHHHHcC
Confidence 7766653
No 51
>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=86.16 E-value=4.7 Score=26.08 Aligned_cols=25 Identities=4% Similarity=-0.092 Sum_probs=20.6
Q ss_pred CChHHHHHHhhcCCceEEEeehhHH
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRL 30 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~ 30 (90)
.+.++.+.++++|++|.++......
T Consensus 72 ~~~~~~~~~l~~g~~Di~~~~~~~~ 96 (254)
T TIGR01098 72 TDYSAVIEAMRFGRVDIAWFGPSSY 96 (254)
T ss_pred CCHHHHHHHHHcCCccEEEECcHHH
Confidence 5678899999999999998765443
No 52
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=85.87 E-value=2.1 Score=28.02 Aligned_cols=52 Identities=15% Similarity=0.183 Sum_probs=33.4
Q ss_pred hHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe--CCcccccce-EEEEeCC
Q psy17442 8 SPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA--GELFGRSGY-AIGLQKG 59 (90)
Q Consensus 8 ~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~--~~~~~~~~~-~ia~~kg 59 (90)
.+++..+|++|++|+++...|.......+.....++ ++.+...++ .+++++.
T Consensus 159 ~~~~~~al~~g~iDa~~~~eP~~~~~~~~g~g~~v~~~~~~~~~~p~~~~~~~~~ 213 (252)
T PF13379_consen 159 PPEMVAALRAGEIDAAVLWEPFASQAEAKGIGKIVADSGDVWGNHPCCVIVARRD 213 (252)
T ss_dssp GHHHHHHHHTTS-SEEEEETTHHHHHHHTTS-EEEEEHHHCSTT-B-EEEEEEHH
T ss_pred HHHHHHHHhCCCcCEEEecCCHHHHHHhccCCeEEEEeccccCCCCeEEEEECHH
Confidence 389999999999999999999988777664323333 222233233 3677664
No 53
>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=84.82 E-value=4.2 Score=28.25 Aligned_cols=28 Identities=7% Similarity=0.016 Sum_probs=22.5
Q ss_pred ccCChHHHHHHhhcCCceE-EEeehhHHh
Q psy17442 4 DVKFSPSTVVRHGTKKLMA-FIWDSSRLD 31 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida-~i~d~~~~~ 31 (90)
.+++..+++.++.+|++|+ .+.+.+.+.
T Consensus 41 ~f~~~~~~l~Al~aG~iD~~~~g~~~~~~ 69 (328)
T TIGR03427 41 QINDYVESINQYTAGKFDGCTMTNMDALT 69 (328)
T ss_pred ECCChHHHHHHHHcCCCCEEeecCHHHHH
Confidence 5778999999999999996 666656553
No 54
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=84.67 E-value=1.8 Score=28.91 Aligned_cols=54 Identities=7% Similarity=-0.037 Sum_probs=35.8
Q ss_pred hHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe---CCcccccceEEEEeCCCC
Q psy17442 8 SPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA---GELFGRSGYAIGLQKGSP 61 (90)
Q Consensus 8 ~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~---~~~~~~~~~~ia~~kgs~ 61 (90)
...=+..|++|+.|.+|.++-.+..++++..++.++ |+.-......+.+++++.
T Consensus 52 a~~Rie~l~~g~yDfaVvS~lAA~~~i~~~~~l~i~~~fG~~sYvs~Hvli~~~~~~ 108 (232)
T PF14503_consen 52 AENRIEALKNGRYDFAVVSKLAAEHYIEEGEDLEIVLEFGPGSYVSEHVLIFRDGEK 108 (232)
T ss_dssp HHHHHHHHHTTS-SEEEEEHHHHCCCCCC-SSEEEEEE--TTSSS--EEEEEETT-G
T ss_pred chHHHHHHHhCCcceEeehHHHHHHHHhhccCeEEEEeeCCCCcccceEEEEecCCc
Confidence 344578899999999999999999888875566655 433344556777777643
No 55
>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=82.78 E-value=1.9 Score=28.07 Aligned_cols=51 Identities=12% Similarity=0.103 Sum_probs=33.5
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCCh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWA 63 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~ 63 (90)
..+..+.+..|.+|++|..+...+. ..+++.. ..+..++++++++++.|+.
T Consensus 119 ~~~~~~~~~~l~~g~~Dl~i~~~~~------~~~~~~~--~~l~~~~~~lv~s~~~pl~ 169 (279)
T TIGR03339 119 IGNSQEVLQALQSYRVDVAVSSEVV------DDPRLDR--VVLGNDPLVAVVHRQHPLA 169 (279)
T ss_pred ECCHHHHHHHHHcCCCcEEEEeccc------CCCceEE--EEcCCceEEEEECCCCccc
Confidence 4567889999999999999864321 1222222 2345667777777777654
No 56
>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=82.13 E-value=4 Score=24.67 Aligned_cols=21 Identities=5% Similarity=-0.209 Sum_probs=18.0
Q ss_pred ChHHHHHHhhcCCceEEEeeh
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~ 27 (90)
...+++..|.+|++|+++...
T Consensus 46 ~~~~~~~~l~~g~~D~~~~~~ 66 (218)
T cd00134 46 DWDGLITALKSGKVDLIAAGM 66 (218)
T ss_pred CHHHHHHHHhcCCcCEEeecC
Confidence 367899999999999998765
No 57
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=81.77 E-value=4.4 Score=27.44 Aligned_cols=60 Identities=13% Similarity=0.022 Sum_probs=40.2
Q ss_pred ccCChHHHHHHhhcCCceEE--EeehhHHhHHHhcCCCeEEeCCcccc-cceEEEEeCCCCCh
Q psy17442 4 DVKFSPSTVVRHGTKKLMAF--IWDSSRLDFEAAQDCELVTAGELFGR-SGYAIGLQKGSPWA 63 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~--i~d~~~~~~~~~~~~~l~~~~~~~~~-~~~~ia~~kgs~l~ 63 (90)
.+.+-++...+|.+|++|.. +...+...........+.++...... .+.++..+++++.+
T Consensus 67 ~~~~~~~~~~~l~~G~~D~a~~~~~~~~~~~~~~~g~pv~~va~~~~~~~~~~i~~~~~~~i~ 129 (335)
T COG0715 67 EFTGGAPVLEALAAGALDFAVYYTGDTPLIAAGAAGAPVKVVAALVQNGNGIALLVLKDSGIK 129 (335)
T ss_pred EcCCChHHHHHHhcCCcCccccccCchHHHHhhccCCCeEEeeecccCCceeEEEeccCCCcc
Confidence 34577889999999999998 44444443333333366766655444 47778888887754
No 58
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=81.65 E-value=13 Score=24.96 Aligned_cols=83 Identities=13% Similarity=-0.014 Sum_probs=49.7
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcc-cccceEEEEeCCCCChHHHHHHHHHhhhccHHHHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELF-GRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLFM 83 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~-~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~ 83 (90)
..+..+++.-|.+|.+|+.+.-.+.+...- .......+.... .+..|.+++.++++-.+ .-..+.++..+..=+++.
T Consensus 172 ~~~v~~~l~~V~~G~ad~g~vy~sd~~~~~-~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~-~A~~f~~fl~s~~a~~il 249 (258)
T COG0725 172 ATNVRQALAYVETGEADAGFVYVSDALLSK-KVKIVGVFPEDLHSPIVYPIAVLKNAKNPE-LAKEFVDFLLSPEAQEIL 249 (258)
T ss_pred cCcHHHHHHHHHcCCCCeEEEEEEhhhccC-CceEEEEcccccCCCeEEEEEEEcCCCCHH-HHHHHHHHHhCHHHHHHH
Confidence 456678999999999999766544222111 112234444333 35789999999876533 233344444556666777
Q ss_pred HHhccC
Q psy17442 84 AKVHLN 89 (90)
Q Consensus 84 ~kW~~~ 89 (90)
++|..+
T Consensus 250 ~~~Gf~ 255 (258)
T COG0725 250 EKYGFE 255 (258)
T ss_pred HHcCCC
Confidence 777543
No 59
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=81.56 E-value=7.4 Score=25.89 Aligned_cols=80 Identities=14% Similarity=0.076 Sum_probs=47.3
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeE-EeCC-cccccceEEEEeCCCCChHHHHHHHHHhhhccHHHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELV-TAGE-LFGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLF 82 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~-~~~~-~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l 82 (90)
..+..+++..+.+|++|+.|.-...+. ..+..... +++. ......|++++.++++- + .-+.+.+...+.+-+++
T Consensus 173 ~~~v~~~~~~v~~G~ad~gi~~~s~a~--~~~~~~~~~~~P~e~~~~i~~~~avlk~~~~-~-~Ak~Fi~fl~S~eaq~i 248 (257)
T PRK10677 173 AEDVRGALALVERNEAPLGIVYGSDAV--ASKKVKVVGTFPEDSHKPVEYPMAIVKGHNN-A-TVKAFYDYLKGPQAAAI 248 (257)
T ss_pred cccHHHHHHHHHcCCCCEEEEEeeeee--ccCCCeEEEECCcccCCcceeeEEEEcCCCC-H-HHHHHHHHHcCHHHHHH
Confidence 356788899999999999775433221 11222332 2232 23356788888888652 2 24444555566666777
Q ss_pred HHHhcc
Q psy17442 83 MAKVHL 88 (90)
Q Consensus 83 ~~kW~~ 88 (90)
.++|..
T Consensus 249 ~~~~Gf 254 (257)
T PRK10677 249 FKRYGF 254 (257)
T ss_pred HHHcCC
Confidence 777653
No 60
>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=81.15 E-value=5.3 Score=26.58 Aligned_cols=72 Identities=11% Similarity=0.084 Sum_probs=44.0
Q ss_pred ccCChHHHHHHhhcCCceEEE-eehhHHhHHHhc-CCCeEEeCCcccccceE-----------------EEEeCCCCChH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFI-WDSSRLDFEAAQ-DCELVTAGELFGRSGYA-----------------IGLQKGSPWAD 64 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i-~d~~~~~~~~~~-~~~l~~~~~~~~~~~~~-----------------ia~~kgs~l~~ 64 (90)
.|+++.+.=.+|.+|.+||-+ -..+.+..+.+. +.++..++..+ ..++| ||+|-+ | .
T Consensus 32 ~f~D~~~~N~AL~~G~iDaN~fQh~~yl~~~n~~~~~~L~~v~~~~-~~p~glYS~k~~sl~~lp~Ga~VaIpnD-~--s 107 (237)
T PF03180_consen 32 EFSDYVQPNEALADGEIDANFFQHIPYLEQFNKENGYNLVPVGPTY-IEPMGLYSKKYKSLDDLPDGATVAIPND-P--S 107 (237)
T ss_dssp EESSTTHHHHHHHTTSSSEEEEEEHHHHHHHHHHHT--EEEEEEEE-E---EEEESSSSSGGGS-TTEEEEEESS-H--H
T ss_pred EecchhhcChHHHCCCcceeccCCHHHHHHHHHHCCCcEEEeccee-EEeEEEeecccCchhhcCCCCEEEEeCC-c--c
Confidence 577889999999999999955 456667666554 45677665432 23344 444432 1 3
Q ss_pred HHHHHHHHhhhccHH
Q psy17442 65 AVTLAILDFHESTVC 79 (90)
Q Consensus 65 ~vn~~l~~l~~~G~~ 79 (90)
...++|.-|++-|.+
T Consensus 108 N~~RaL~lLq~aGLI 122 (237)
T PF03180_consen 108 NQARALKLLQEAGLI 122 (237)
T ss_dssp HHHHHHHHHHHTTSE
T ss_pred chhHHHHHHHhCCeE
Confidence 356677777777653
No 61
>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=80.34 E-value=8.5 Score=25.38 Aligned_cols=53 Identities=13% Similarity=-0.046 Sum_probs=32.2
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHH-HhcCCC-eEEeCCcccccceEEEEeCC
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFE-AAQDCE-LVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~-~~~~~~-l~~~~~~~~~~~~~ia~~kg 59 (90)
..+.+|.+.+|++|.+|+++.....+... .....+ +...+ ....++.+.+.++
T Consensus 160 ~~~~~e~~~aL~~G~vDg~~~~~~~~~~~~~~ev~~y~~~~~--~~~~~~~~~~n~~ 214 (257)
T TIGR00787 160 PMAFSEVYTALQTGVVDGQENPLSNVYSSKFYEVQKYLSMTN--HGYLGYLVVVNKA 214 (257)
T ss_pred ccCHHHHHHHHHcCCcccccCCHHHHhhcchhhhcchheecC--CcccceEEEEeHH
Confidence 45678999999999999999875543221 111122 22222 2335566778775
No 62
>PRK04168 molybdate ABC transporter periplasmic substrate-binding protein; Provisional
Probab=80.31 E-value=17 Score=25.31 Aligned_cols=77 Identities=10% Similarity=-0.082 Sum_probs=44.6
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCc---------------------------ccccceEEEEeCC
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGEL---------------------------FGRSGYAIGLQKG 59 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~---------------------------~~~~~~~ia~~kg 59 (90)
+..+.+..|.+|++|+.|.-.+.+.. .+-.+..+++. -.+..|++++.++
T Consensus 210 ~~~~~~~~v~~G~aDagivy~S~a~~---~~~~~i~lP~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~pi~y~~ai~~~ 286 (334)
T PRK04168 210 KEVELLSLLETGNMDYAFIYKSVAVQ---HNLKYIELPDEINLGNYKYADFYKKVSVTVTGTGKTITAKPIVYGITVPKN 286 (334)
T ss_pred cchhhHHHHhcCCccEEEEEeeehhh---CCCCeeECchhhcCCChhhhhhhhEEEEEecCCCccccCceeeeeeeeecC
Confidence 45689999999999997765443321 11111111111 1235678999998
Q ss_pred CCChHHHHHHHHHhhhccHHHHHHHHhc
Q psy17442 60 SPWADAVTLAILDFHESTVCYLFMAKVH 87 (90)
Q Consensus 60 s~l~~~vn~~l~~l~~~G~~~~l~~kW~ 87 (90)
++-.+...+.+.-| .+.+-+++..++.
T Consensus 287 s~n~e~A~~Fi~fl-~S~e~q~il~~~G 313 (334)
T PRK04168 287 APNREAAIEFLKYL-LSEPGGEVLENNG 313 (334)
T ss_pred CCCHHHHHHHHHHH-cCHHHHHHHHHcC
Confidence 87555555544444 4555566666653
No 63
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=80.03 E-value=7.1 Score=26.42 Aligned_cols=58 Identities=10% Similarity=0.010 Sum_probs=37.9
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeC-CcccccceEEEEeCCCCChH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAG-ELFGRSGYAIGLQKGSPWAD 64 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~-~~~~~~~~~ia~~kgs~l~~ 64 (90)
..-+.++....|.+|++|..+........ ....+..+. -.+......+++|+++++..
T Consensus 49 ~~~~~~~i~~~L~sG~vDlgi~g~~~~~e---r~~~v~~~~~l~~~~~~lvvvvp~~~~i~s 107 (287)
T PRK00489 49 LFLRPDDIPGYVADGVVDLGITGEDLLEE---SGADVEELLDLGFGKCRLVLAVPEDSDWQG 107 (287)
T ss_pred EEECcHHHHHHHHcCCCCEEEcchHHHHH---CCCCceEeeeccCCceEEEEEEECCCCCCC
Confidence 34456788999999999999987554322 122222222 23556678889999988654
No 64
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=79.98 E-value=7.4 Score=25.41 Aligned_cols=55 Identities=9% Similarity=0.053 Sum_probs=35.1
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcC----CCeEEeCCcccccceEEEEeCC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD----CELVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~----~~l~~~~~~~~~~~~~ia~~kg 59 (90)
.+.+..+.+.+|.+|++|+.....+.+..+.+.. ..+.++.. ....+.++.++++
T Consensus 41 ~~~~g~~~~~al~~G~iD~a~~~~~~~~~~~~g~~~~~~~~~~~~~-~~~~g~~lvv~~~ 99 (252)
T PF13379_consen 41 QFASGADILEALAAGEIDIAFVLAPALIAIAKGAGGPDVDIVVLAG-LSQNGNALVVRND 99 (252)
T ss_dssp EESSHHHHHHHHHCTSSSEEEECTHHHHHHHTTTTT----EEEEEE-CSBSSEEEEECGG
T ss_pred EcCCHHHHHHHHHcCCCCEEEechHHHHHHHcCCCCcccceEEeec-cCCCceEEEEcCc
Confidence 4678899999999999999888444444333322 25555432 3456677777754
No 65
>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=79.92 E-value=2.3 Score=28.14 Aligned_cols=61 Identities=15% Similarity=-0.010 Sum_probs=42.8
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHh-cCCC-------eEEeCCcccccceEEEEeCCCCCh
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAA-QDCE-------LVTAGELFGRSGYAIGLQKGSPWA 63 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~-~~~~-------l~~~~~~~~~~~~~ia~~kgs~l~ 63 (90)
+...+..+++.+|.+|.+|..+.+++.-..... +.|. ..+....+.....+|++.+.+|+.
T Consensus 42 v~~~gS~~g~~~l~~g~~di~~~sr~l~~~e~~~~~~~~~~~~~~~~~~~~~va~d~i~iv~n~~np~~ 110 (281)
T PF12849_consen 42 VESSGSGAGIQALINGKVDIAISSRPLTAAEIASEGYNAKGQKWGGGLVQIPVARDAIVIVVNKDNPLN 110 (281)
T ss_dssp EEEE-HHHHHHHHHTTSSSEEEESSHHHHHHHHHHTCCCCCHHHHCTEEEEEEEEEEEEEEEETTTTTE
T ss_pred EEeCCCHHHHHHHHhCCCEEEEeCCCCcHHHHhHhhhhhcccccccccEEEEEEEeeEEEEEcCCCccc
Confidence 344567899999999999999999888766442 1111 122223466778899999998876
No 66
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=79.79 E-value=16 Score=24.67 Aligned_cols=76 Identities=11% Similarity=0.034 Sum_probs=43.0
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcC-CCeEEeCCcccccce--EEEEeCCCCChHHHHHHHHHhhhccHHH-HH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD-CELVTAGELFGRSGY--AIGLQKGSPWADAVTLAILDFHESTVCY-LF 82 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~-~~l~~~~~~~~~~~~--~ia~~kgs~l~~~vn~~l~~l~~~G~~~-~l 82 (90)
..++...++..|++|+++...+.+...-.+. .+-...... ..+| .+++++++.=.+.+...+.-++ +.+.. .+
T Consensus 183 ~~~~~~~al~~g~vDaa~i~~~~a~~a~~~~~~~~l~~e~~--~~~~~~~~~v~~~~~~~~~~~~l~~a~~-s~~v~~~i 259 (271)
T PRK11063 183 EAPQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDK--DSPYVNLIVAREDNKDAENVKKFVQAYQ-SDEVYEAA 259 (271)
T ss_pred cHHHHHHhcccccccEEEEChHHHHHcCCCCCCCeeEECCC--CCCeEEEEEECCcccCCHHHHHHHHHHc-CHHHHHHH
Confidence 4567888999999999999988876543222 122222221 2244 3667776433355555444444 44444 44
Q ss_pred HHH
Q psy17442 83 MAK 85 (90)
Q Consensus 83 ~~k 85 (90)
.++
T Consensus 260 ~~~ 262 (271)
T PRK11063 260 NKV 262 (271)
T ss_pred HHH
Confidence 444
No 67
>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=79.65 E-value=4.6 Score=27.44 Aligned_cols=53 Identities=11% Similarity=0.044 Sum_probs=36.8
Q ss_pred ChHHHHHHhhcCCceEEEeehh-HH-hHHHhc--CCCeEEeCCcccccceEEEEeCC
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSS-RL-DFEAAQ--DCELVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~-~~-~~~~~~--~~~l~~~~~~~~~~~~~ia~~kg 59 (90)
+..-++.+|.+|.+|++..--. .. ..+.+. ...+..++.......||+++|+-
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 5677899999999999885422 21 222222 23678888777777899999974
No 68
>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=79.31 E-value=16 Score=24.51 Aligned_cols=79 Identities=9% Similarity=-0.100 Sum_probs=42.8
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcC-CCeEEeCCcccccceEEEEeCCCCChHHHHHHHHHhhhccHHHHHHHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD-CELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLFMAK 85 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~-~~l~~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~~k 85 (90)
..++...+|..|++||.+...+.+...-.+. ..-......-.+.-..++++.++.=.+.+...+..++.+..-+-|.++
T Consensus 170 ~~~~~~~al~~g~vDaa~v~~~~~~~agl~~~~~~i~~e~~~~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~ 249 (258)
T TIGR00363 170 ETSQLPRALDDPKVDLAVINTTYAGQVGLNPQDDGVFVEDKDSPYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAAQKH 249 (258)
T ss_pred CHHHHHHHhhcccccEEEEChHHHHHcCCCcCcCceeecCCCCCeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence 3466789999999999999888765442221 111122111111113467777643445666655555544433344444
No 69
>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=78.86 E-value=12 Score=23.94 Aligned_cols=62 Identities=11% Similarity=0.005 Sum_probs=42.1
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCChHHHHHHHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTLAIL 71 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~ 71 (90)
...+..++..+|.+|+.|+.+.-.+.+..+ ..-++.. +..+.|=+++++..-....+...|.
T Consensus 129 ~~~th~~vA~aVa~G~AD~G~g~~~~A~~~--~gL~Fvp----l~~E~~dlv~~~~~~~~~~vq~ll~ 190 (193)
T PF12727_consen 129 EANTHLAVAAAVASGKADAGIGIRAAAEEF--YGLDFVP----LAEERYDLVIRREDLEDPAVQALLD 190 (193)
T ss_pred cccChHHHHHHHHcCCCCEEeehHHHHHhh--cCCCcEE----ccccceEEEEEhhHcCCHHHHHHHH
Confidence 467788999999999999999866655421 1222333 4568899999997655555555443
No 70
>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=78.63 E-value=8.2 Score=22.87 Aligned_cols=23 Identities=9% Similarity=-0.364 Sum_probs=18.5
Q ss_pred CChHHHHHHhhcCCceEEEeehh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSS 28 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~ 28 (90)
.+..+....|.+|++|..+...+
T Consensus 36 ~~~~~~~~~L~~~~~Dl~i~~~~ 58 (197)
T cd08438 36 YGGKKVEQAVLNGELDVGITVLP 58 (197)
T ss_pred cCcHHHHHHHHcCCCCEEEEecc
Confidence 46677889999999999887543
No 71
>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=78.43 E-value=17 Score=24.16 Aligned_cols=25 Identities=8% Similarity=-0.093 Sum_probs=20.1
Q ss_pred cCChHHHHHHhhcCCceEEEeehhH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSR 29 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~ 29 (90)
..+..+.+.+|.+|++|+++.....
T Consensus 66 ~~~~~~~~~al~~g~~D~~~~~~~~ 90 (288)
T TIGR03431 66 ATDYAGVIEGMRFGKVDIAWYGPSS 90 (288)
T ss_pred CCCHHHHHHHHHcCCccEEEEChHH
Confidence 4567788999999999999876443
No 72
>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=78.29 E-value=2.4 Score=27.67 Aligned_cols=34 Identities=6% Similarity=0.090 Sum_probs=28.1
Q ss_pred EEEEeCCCC-ChHHHHHHHHHhhhccHHHHHHHHh
Q psy17442 53 AIGLQKGSP-WADAVTLAILDFHESTVCYLFMAKV 86 (90)
Q Consensus 53 ~ia~~kgs~-l~~~vn~~l~~l~~~G~~~~l~~kW 86 (90)
|=.+|-..+ +.+.|...|..+..+|+++++.++|
T Consensus 26 G~t~pI~E~D~L~~I~~rl~~~e~sGel~~~~~~~ 60 (202)
T TIGR02743 26 GQTFPIAEPDMLEVIEQRLKRLEQSGELKAMQQRF 60 (202)
T ss_pred cccccccchHHHHHHHHHHHhhhhCchHHHHHHHH
Confidence 334455555 8999999999999999999999887
No 73
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=77.49 E-value=11 Score=25.97 Aligned_cols=61 Identities=15% Similarity=0.054 Sum_probs=32.5
Q ss_pred cccCChHHHHHHhhcCCceE-EEeehhHHhHHHhcCC-C-e-EEeCCcccccceE-EEEeCCCCCh
Q psy17442 3 FDVKFSPSTVVRHGTKKLMA-FIWDSSRLDFEAAQDC-E-L-VTAGELFGRSGYA-IGLQKGSPWA 63 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida-~i~d~~~~~~~~~~~~-~-l-~~~~~~~~~~~~~-ia~~kgs~l~ 63 (90)
+...++...++++.+|++|. .+...+.+.....+.+ . + ..+...-....+. |.++++|+..
T Consensus 72 ~~a~dy~~vieal~~g~~D~A~~~~~a~~~a~~~~~~~e~~~~~~~~dg~~~Y~S~~i~~~ds~i~ 137 (299)
T COG3221 72 FVATDYAAVIEALRAGQVDIAWLGPSAYVEAVDRALAGEPLAQTVQKDGSPGYYSVIIVRADSPIK 137 (299)
T ss_pred EecccHHHHHHHHhCCCeeEEecCchhHHHHHhhcccccceeeeeccCCCcceeEEEEEeCCCCcc
Confidence 34568899999999999994 4444422222222212 1 1 1111111122233 7778899854
No 74
>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=76.85 E-value=7.7 Score=25.93 Aligned_cols=23 Identities=9% Similarity=-0.081 Sum_probs=20.5
Q ss_pred ccCChHHHHHHhhcCCceEEEee
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d 26 (90)
.+.+..+++.+|.+|++|+++.+
T Consensus 175 ~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 175 EYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred hcCCHHHHHHHHHCCCccEEEEe
Confidence 45678899999999999999988
No 75
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=75.64 E-value=3.9 Score=24.88 Aligned_cols=49 Identities=2% Similarity=-0.175 Sum_probs=29.7
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
.+..+....|.+|++|+.+...+.. +..+.. ..+..+++.++++++.|+
T Consensus 37 ~~~~~l~~~l~~g~~D~~~~~~~~~------~~~~~~--~~l~~~~~~lv~~~~h~l 85 (198)
T cd08486 37 MTKDEQVEGLLAGTIHVGFSRFFPR------HPGIEI--VNIAQEDLYLAVHRSQSG 85 (198)
T ss_pred CCHHHHHHHHHcCCceEEEecCCCC------CCceEE--EEEeeccEEEEecCCCcc
Confidence 4677899999999999988643321 112211 123445666666666553
No 76
>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=74.73 E-value=19 Score=24.98 Aligned_cols=30 Identities=23% Similarity=0.068 Sum_probs=24.1
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhc
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ 36 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~ 36 (90)
+.+++..++.+|+|||.+.-.|.+.....+
T Consensus 141 ~~~d~~aAl~~G~VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 141 SDADIVAAFITKDVTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred ChHHHHHHHhcCCCcEEEEcCchHHHHHhC
Confidence 347889999999999998888886655554
No 77
>cd08411 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repre
Probab=74.17 E-value=4.6 Score=24.25 Aligned_cols=22 Identities=9% Similarity=-0.005 Sum_probs=17.9
Q ss_pred CChHHHHHHhhcCCceEEEeeh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~ 27 (90)
.+..+.+..|.+|++|..+...
T Consensus 37 ~~~~~~~~~l~~~~~Dl~i~~~ 58 (200)
T cd08411 37 DQTERLLEKLRSGELDAALLAL 58 (200)
T ss_pred CcHHHHHHHHHcCCccEEEEec
Confidence 3567889999999999988643
No 78
>COG0687 PotD Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]
Probab=73.68 E-value=28 Score=24.27 Aligned_cols=71 Identities=10% Similarity=-0.172 Sum_probs=45.3
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHH--hcCCCeEEeCCc--ccccceEEEEeCCCCChHHHHHHHHHhhh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEA--AQDCELVTAGEL--FGRSGYAIGLQKGSPWADAVTLAILDFHE 75 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~--~~~~~l~~~~~~--~~~~~~~ia~~kgs~l~~~vn~~l~~l~~ 75 (90)
..+..+..+.|.+|.+++.+.-...+.... ....++..+-+. ...-.-.+++|||++-.+.--+.|.-|..
T Consensus 220 ~~~~~~~~~~l~~Gev~~a~~w~g~~~~~~~~~~~~~i~~~~p~eG~~~w~D~~~ipk~a~n~~~A~~fInf~~~ 294 (363)
T COG0687 220 WFDGSQYVQLLANGEVVLAMGWSGDAAAAKAAKNGAPIEFVIPKEGSILWFDNLAIPKGAKNVDAAYKFINFLLD 294 (363)
T ss_pred EecchHHHHHHhcCCEEEEEEeChHHHHHHHhhcCCceEEEcCCCCceeeeEeeeeeCCCCCHHHHHHHHHHhhC
Confidence 446778999999999998776544444442 333457666433 22233468999999866666666655444
No 79
>PRK11622 hypothetical protein; Provisional
Probab=73.48 E-value=29 Score=24.49 Aligned_cols=71 Identities=3% Similarity=-0.186 Sum_probs=41.9
Q ss_pred CChHHHHHHhhcCCceEEEeehh-HHhHHHhcC---CCeEEe--CCcccccceEEEEeCCCCChHHHHHHHHHhhhc
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSS-RLDFEAAQD---CELVTA--GELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~-~~~~~~~~~---~~l~~~--~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~ 76 (90)
.+..+..+.+.+|++++.+.-.. .+...+.+. ..+..+ .+.......+++++||+|-.+..-+.|.-+...
T Consensus 253 ~~~~~~~~~~~~GEv~~~~~~~~~~~~~~~~~g~~p~~~~~~~~~~G~~~~~~~~~Ipk~a~n~~~A~~finfllS~ 329 (401)
T PRK11622 253 ASPAELDQLLADGELDLAMTFNPNHAQSKIANGELPASTRSFVFDDGTIGNTHFVAIPFNANAKAGAKVVANFLLSP 329 (401)
T ss_pred CChHHHHHHHHCCCeEEEEecChHHHHHHHhcCCCCCceeEEcCCCCeeccceeEEeeCCCCCHHHHHHHHHHHcCH
Confidence 35667889999999998874332 333333332 133332 222223356799999988666665555555443
No 80
>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=73.40 E-value=3.1 Score=27.42 Aligned_cols=56 Identities=11% Similarity=0.015 Sum_probs=36.2
Q ss_pred ccCChHHHHHHhhcCCceEEE-eehhHHhHHHhc----CCCeEEeCCcccccceEEEEeCC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFI-WDSSRLDFEAAQ----DCELVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i-~d~~~~~~~~~~----~~~l~~~~~~~~~~~~~ia~~kg 59 (90)
..++.+..+.+|.+|++|++. .-.+.......+ ...+..++.......+|+++|+.
T Consensus 35 ~~~~~~~~~~al~~G~iD~~~~~w~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~g~~Vp~~ 95 (257)
T PF04069_consen 35 NLGSTPVIFAALASGDIDIYPEEWTPTTYEAYKKALEEKLGVVWLGPLGAGNTYGWAVPKY 95 (257)
T ss_dssp EESSHHHHHHHHHTTSSSEEEEEEETTTHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEEHH
T ss_pred cCCchHHHHHHHHCCCCeEEhhhcCchhHHHHHHhhhhcCccccCCccccCCEEEEEEecc
Confidence 345558899999999999999 444443222222 22344446556677788999864
No 81
>PRK13738 conjugal transfer pilus assembly protein TraW; Provisional
Probab=73.31 E-value=4 Score=26.81 Aligned_cols=35 Identities=9% Similarity=-0.034 Sum_probs=28.2
Q ss_pred eEEEEeCCCC-ChHHHHHHHHHhhhccHHHHHHHHh
Q psy17442 52 YAIGLQKGSP-WADAVTLAILDFHESTVCYLFMAKV 86 (90)
Q Consensus 52 ~~ia~~kgs~-l~~~vn~~l~~l~~~G~~~~l~~kW 86 (90)
+|=.+|-..+ +.+.|...|..+.++|+++++.++|
T Consensus 23 ~G~t~pI~E~D~L~~I~~rL~~~e~sGel~~~~~~~ 58 (209)
T PRK13738 23 WGDLWPVKEPDMLTVIMQRLQALEQSGEMGRKMDAF 58 (209)
T ss_pred cccccCccchhHHHHHHHHHHHhHhccHHHHHHHHH
Confidence 3344555555 9999999999999999999988875
No 82
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=73.20 E-value=6.4 Score=26.57 Aligned_cols=40 Identities=13% Similarity=-0.023 Sum_probs=27.2
Q ss_pred ccCChHHHHHHhhcCCceEE-EeehhHHhHHHhc-CCCeEEe
Q psy17442 4 DVKFSPSTVVRHGTKKLMAF-IWDSSRLDFEAAQ-DCELVTA 43 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~-i~d~~~~~~~~~~-~~~l~~~ 43 (90)
.+++.++...+|.+|++|+. +...+.+..+... ..++..+
T Consensus 65 ~f~~~~~~~~ALa~GdID~~~~qh~~~l~~~~~~~g~~l~~~ 106 (271)
T PRK11063 65 TFNDYVLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLVAV 106 (271)
T ss_pred EecCcHHHHHHHHcCCcceecccCHHHHHHHHHHcCCcEEEE
Confidence 36778999999999999994 4445565544443 3445544
No 83
>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=72.48 E-value=13 Score=24.85 Aligned_cols=51 Identities=14% Similarity=-0.003 Sum_probs=33.7
Q ss_pred hHHHHHHhhcCCceEEEeehhHHhHHH-hcCCCeEEeCCcccccceEEEEeCC
Q psy17442 8 SPSTVVRHGTKKLMAFIWDSSRLDFEA-AQDCELVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 8 ~~~~~~~l~~G~ida~i~d~~~~~~~~-~~~~~l~~~~~~~~~~~~~ia~~kg 59 (90)
.+|.+.+|++|.+|++....+....+- ..-+++.+... ....++.+++.+.
T Consensus 163 ~~evy~aLq~G~vDg~~~~~~~~~~~~~~ev~~y~~~~~-~~~~~~~~~~n~~ 214 (286)
T PF03480_consen 163 WSEVYQALQQGVVDGAENSASSIYSLGLYEVAKYFTDTN-HGWSPYAVIMNKD 214 (286)
T ss_dssp GGGHHHHHHTTSSSEEEEEHHHHHHTTGGGTSSEEEEEE-EEEEEEEEEEEHH
T ss_pred HHHHHHHHhcCCcCeEecCHHHHHhcChhhhCCeeEeec-ccCcceEEEEcHH
Confidence 468899999999999999877763221 12344443322 4556677778764
No 84
>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=72.43 E-value=7.5 Score=23.50 Aligned_cols=48 Identities=8% Similarity=0.023 Sum_probs=29.5
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
+..+.+..|.+|++|..+...+.. ...+ ....+..+++.++.+++.|+
T Consensus 38 ~~~~~~~~l~~~~~Dl~i~~~~~~------~~~~--~~~~l~~~~~~~v~~~~hpl 85 (203)
T cd08445 38 TTVQQIEALKEGRIDVGFGRLRIE------DPAI--RRIVLREEPLVVALPAGHPL 85 (203)
T ss_pred ChHHHHHHHHcCCCcEEEecCCCC------CCCc--eeEEEEeccEEEEeeCCCCC
Confidence 567889999999999988643211 1121 11234455666777776654
No 85
>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=71.99 E-value=11 Score=22.42 Aligned_cols=23 Identities=9% Similarity=-0.243 Sum_probs=17.9
Q ss_pred CChHHHHHHhhcCCceEEEeehh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSS 28 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~ 28 (90)
.+..+....|.+|++|..|...+
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~~ 58 (196)
T cd08415 36 LSSSTVVEAVLSGQADLGLASLP 58 (196)
T ss_pred cchHHHHHHHHcCCccEEEEeCC
Confidence 35567888999999999887543
No 86
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=71.89 E-value=7.9 Score=25.53 Aligned_cols=50 Identities=12% Similarity=-0.057 Sum_probs=30.8
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCCh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWA 63 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~ 63 (90)
.+..+++..|.+|++|.++...+.. ..++. ...+..+.+.++.+++.|+.
T Consensus 127 ~~~~~~~~~l~~g~~Dl~i~~~~~~------~~~l~--~~~l~~~~~~~~~~~~~pl~ 176 (296)
T PRK11242 127 MSQERIEALLADDELDVGIAFAPVH------SPEIE--AQPLFTETLALVVGRHHPLA 176 (296)
T ss_pred CCHHHHHHHHHCCCCcEEEEecCCC------Cccee--EEEeeeccEEEEEcCCCccc
Confidence 3567788999999999998743321 11221 12345566667777776653
No 87
>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=71.67 E-value=8.9 Score=22.89 Aligned_cols=48 Identities=8% Similarity=-0.096 Sum_probs=29.0
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
+..+....|.+|++|..|...+.. ...+. ...+..+.+.++.+++.|+
T Consensus 38 ~~~~~~~~l~~g~~Dl~i~~~~~~------~~~~~--~~~l~~~~~~~v~~~~~pl 85 (197)
T cd08425 38 PQERIEAALADDRLDLGIAFAPVR------SPDID--AQPLFDERLALVVGATHPL 85 (197)
T ss_pred cHHHHHHHHHcCCccEEEEecCCC------CCCcE--EEEeccccEEEEecCCCch
Confidence 456788899999999988654321 11111 1234455666666666654
No 88
>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=71.03 E-value=15 Score=21.77 Aligned_cols=23 Identities=4% Similarity=-0.116 Sum_probs=18.4
Q ss_pred CChHHHHHHhhcCCceEEEeehh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSS 28 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~ 28 (90)
.+..+....|.+|++|..|...+
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~~ 58 (197)
T cd08414 36 MTTAEQLEALRAGRLDVGFVRPP 58 (197)
T ss_pred CChHHHHHHHHcCCccEEEEcCC
Confidence 35678899999999999887543
No 89
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=70.97 E-value=11 Score=24.68 Aligned_cols=22 Identities=14% Similarity=0.004 Sum_probs=17.6
Q ss_pred cCChHHHHHHhhcCCceEEEee
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d 26 (90)
......++.++.+|++|+++..
T Consensus 71 ~~pw~~~~~~l~~g~~D~~~~~ 92 (259)
T PRK15437 71 ENPLDALIPSLKAKKIDAIMSS 92 (259)
T ss_pred eCCHHHHHHHHHCCCCCEEEec
Confidence 3456789999999999987753
No 90
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=70.68 E-value=13 Score=25.93 Aligned_cols=54 Identities=11% Similarity=-0.031 Sum_probs=36.4
Q ss_pred ChHHHHHHhhcCCceEEEeeh-hHH-hHHHhc--CCCeEEeCCcccccceEEEEeCCC
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDS-SRL-DFEAAQ--DCELVTAGELFGRSGYAIGLQKGS 60 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~-~~~-~~~~~~--~~~l~~~~~~~~~~~~~ia~~kgs 60 (90)
+.+..+.+|.+|.+|++...- |.- .++.+. ...+..++..+.....|+++|+..
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 557899999999999988543 322 222221 234556666667778999999853
No 91
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=69.90 E-value=17 Score=21.43 Aligned_cols=23 Identities=9% Similarity=-0.153 Sum_probs=18.5
Q ss_pred CChHHHHHHhhcCCceEEEeehh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSS 28 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~ 28 (90)
.+..+....|.+|++|..+...+
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~~ 58 (194)
T cd08436 36 AGSDDLLAAVREGRLDLAFVGLP 58 (194)
T ss_pred CCHHHHHHHHHcCCccEEEEecC
Confidence 35677889999999999987544
No 92
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=69.66 E-value=20 Score=24.38 Aligned_cols=25 Identities=16% Similarity=-0.041 Sum_probs=19.8
Q ss_pred ccCChHHHHHHhhcCCceEEEeehh
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSS 28 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~ 28 (90)
.+.+.++.+.+|.+|++|..+....
T Consensus 57 ~~~~~~~~~~al~~G~~D~a~~~~~ 81 (320)
T PRK11480 57 KFDSGASIVRALASGDVQIGNLGSS 81 (320)
T ss_pred EeCCHHHHHHHHHCCCCCEECcCch
Confidence 4567888999999999998755443
No 93
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=69.44 E-value=8.5 Score=23.30 Aligned_cols=20 Identities=0% Similarity=-0.336 Sum_probs=16.7
Q ss_pred ChHHHHHHhhcCCceEEEee
Q psy17442 7 FSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d 26 (90)
+..+....|.+|++|..+..
T Consensus 37 ~~~~~~~~l~~g~~D~~i~~ 56 (200)
T cd08467 37 GDDLAERGLEQGTIDLAVGR 56 (200)
T ss_pred CcccHHHHhhCCCcCEEEec
Confidence 45678999999999998864
No 94
>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=69.16 E-value=32 Score=23.09 Aligned_cols=68 Identities=3% Similarity=-0.278 Sum_probs=38.0
Q ss_pred ChHHHHHHhhcCCceEEEeehh-HHhHHHh-cCCCe--EEeCCcccccceEEEEeCCCCChHHHHHHHHHhh
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSS-RLDFEAA-QDCEL--VTAGELFGRSGYAIGLQKGSPWADAVTLAILDFH 74 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~-~~~~~~~-~~~~l--~~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~ 74 (90)
+..+....+.+|++++.+.... ....... ....+ ....+.......+++++||++-.+..-+.|.-|.
T Consensus 178 ~~~~~~~~~~~Ge~~i~i~~~~~~~~~~~~~~~~~~~~~~~~eG~~~~~~~~ai~k~a~n~e~A~~Fidfll 249 (309)
T TIGR01276 178 GWSEAYGLFLKGESDLVLSYTTSPAYHILEEKKDNYAAANFSEGHYLQVEVAARTAASKQPELAQKFLQFLV 249 (309)
T ss_pred ChHHHHHHHHcCCcCEEEecCCcHHHHhhcccCcccceEecCCCCEeEEEEEEEeCCCCCHHHHHHHHHHHc
Confidence 4567788999999998875432 2211222 22223 2222222233457889999876665555554444
No 95
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=68.03 E-value=14 Score=25.35 Aligned_cols=58 Identities=17% Similarity=0.067 Sum_probs=37.2
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEE--eCCcccccceEEEEeCCCC
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVT--AGELFGRSGYAIGLQKGSP 61 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~--~~~~~~~~~~~ia~~kgs~ 61 (90)
..|++-.+.+.+|.+|.++.....++.+....++.-.+.+ +-..+ ...-++++++||.
T Consensus 62 RkFdSG~~vv~AlASGdvqiG~iGSsplaaAaSr~vpie~f~~~~~i-g~sEALVvr~gsg 121 (334)
T COG4521 62 RKFDSGASIVRALASGDVQIGNIGSSPLAAAASRQVPIEVFLLASQI-GNSEALVVRKGSG 121 (334)
T ss_pred hhcCchhHHHHHHhcCCccccccCCchhhHHhhcCCceEEeehhhhc-CccceeeeecCCC
Confidence 3689999999999999999855555555555555433332 22222 2334678888765
No 96
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=67.54 E-value=12 Score=22.16 Aligned_cols=22 Identities=14% Similarity=-0.174 Sum_probs=17.8
Q ss_pred CChHHHHHHhhcCCceEEEeeh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~ 27 (90)
.+..+....|.+|++|..|...
T Consensus 36 ~~~~~~~~~l~~~~~Di~i~~~ 57 (197)
T cd08448 36 MSSAEQIEALLRGELDLGFVHS 57 (197)
T ss_pred CCHHHHHHHHHcCCcceEEEeC
Confidence 3567888999999999988654
No 97
>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=67.27 E-value=8.2 Score=23.02 Aligned_cols=21 Identities=0% Similarity=-0.045 Sum_probs=17.5
Q ss_pred CChHHHHHHhhcCCceEEEee
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d 26 (90)
.+..+....|.+|++|..+..
T Consensus 36 ~~~~~~~~~l~~g~~D~~i~~ 56 (198)
T cd08447 36 MVTTDQIEALESGRIDLGLLR 56 (198)
T ss_pred CCHHHHHHHHHcCCceEEEec
Confidence 356788999999999998864
No 98
>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=66.12 E-value=8.8 Score=25.38 Aligned_cols=24 Identities=4% Similarity=-0.115 Sum_probs=19.3
Q ss_pred cccCChHHHHHHhhcCCceEEEee
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d 26 (90)
+.+.+..+++..|++|++|+++..
T Consensus 76 ~~~~~w~~~~~~l~~G~~Di~~~~ 99 (275)
T TIGR02995 76 ASITEYGALIPGLQAGRFDAIAAG 99 (275)
T ss_pred eccCCHHHHHHHHHCCCcCEEeec
Confidence 445577899999999999997653
No 99
>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=65.90 E-value=26 Score=20.98 Aligned_cols=69 Identities=19% Similarity=0.078 Sum_probs=42.7
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeE--EeCC-cccccceEEEEeCCCCChHHHHHHHHHhh
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELV--TAGE-LFGRSGYAIGLQKGSPWADAVTLAILDFH 74 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~--~~~~-~~~~~~~~ia~~kgs~l~~~vn~~l~~l~ 74 (90)
+.+++...++..+.+|..-+++-+....... . ...+. .+.. .+. .++.++.+++.+....+...+..++
T Consensus 134 ~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~-~-~~~l~~~~~~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~l~ 205 (209)
T PF03466_consen 134 IEVDSFESILSLVASGDGIAILPDSLAQDEL-E-SGELVFLPLPDPPLP-RPIYLVWRKDRPLSPAIQWFIDLLR 205 (209)
T ss_dssp EEESSHHHHHHHHHTTSEBEEEEHHHHHHHH-H-CTTEEEEEESSSTEE-EEEEEEEETTGTTHHHHHHHHHHHH
T ss_pred ccccchhhhccccccccceeecCcccccccc-c-CCCEEEEECCCCCCc-eEEEEEEECCCCCCHHHHHHHHHHH
Confidence 4578889999999999855565544433333 3 23344 2333 344 7788888998766555555555444
No 100
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=65.65 E-value=15 Score=21.82 Aligned_cols=21 Identities=10% Similarity=-0.073 Sum_probs=16.9
Q ss_pred ChHHHHHHhhcCCceEEEeeh
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~ 27 (90)
+..+.+..|.+|++|..|...
T Consensus 37 ~~~~~~~~l~~g~~Dl~i~~~ 57 (196)
T cd08456 37 DSPTVEQWLSAQQCDLGLVST 57 (196)
T ss_pred CHHHHHHHHHcCCccEEEEec
Confidence 456778889999999988653
No 101
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=65.35 E-value=12 Score=22.15 Aligned_cols=48 Identities=15% Similarity=0.035 Sum_probs=28.5
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
+..+.+..|.+|++|..|...+.. ..++.. ..+..+.+.++.+++.|+
T Consensus 37 ~~~~~~~~l~~~~~Dl~i~~~~~~------~~~~~~--~~l~~~~~~~~~~~~~pl 84 (196)
T cd08450 37 FSPQLAEALMRGKLDVAFMRPEIQ------SDGIDY--QLLLKEPLIVVLPADHRL 84 (196)
T ss_pred ChHHHHHHHhcCCccEEEEeCCCC------CCCcEE--EEEEccceEEEecCCCCc
Confidence 457788999999999988643321 112211 123445566666666554
No 102
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=64.48 E-value=7.3 Score=25.78 Aligned_cols=50 Identities=10% Similarity=-0.059 Sum_probs=32.3
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCCh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWA 63 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~ 63 (90)
.+..+.+..|.+|++|..+...+.. ...+.. ..+..+.+.++++++.|+.
T Consensus 126 ~~~~~~~~~l~~~~~D~~i~~~~~~------~~~l~~--~~l~~~~~~~v~~~~~pl~ 175 (296)
T PRK09906 126 LITTQQEEKLRRGELDVGFMRHPVY------SDEIDY--LELLDEPLVVVLPVDHPLA 175 (296)
T ss_pred CCcHHHHHHHHcCCeeEEEecCCCC------CCCceE--EEEecccEEEEecCCCccc
Confidence 3567788999999999999865431 112222 2455666777777777643
No 103
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=64.10 E-value=42 Score=22.70 Aligned_cols=78 Identities=10% Similarity=0.014 Sum_probs=42.8
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcC-CCeEEeCCcccccce--EEEEeCCCCChHHHHHHHHHhhhccHHHHHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD-CELVTAGELFGRSGY--AIGLQKGSPWADAVTLAILDFHESTVCYLFM 83 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~-~~l~~~~~~~~~~~~--~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~ 83 (90)
..++...+|..|++|+.+...+.+...-... .+-...... ..+| .++++.++.=.+++-..+..++.+..-+-|.
T Consensus 184 ~~~q~~~al~dg~vD~a~i~~~~~~~ag~~~~~~~l~~e~~--~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~ 261 (272)
T PRK09861 184 EGAQLPRVLDDPKVDVAIISTTYIQQTGLSPVHDSVFIEDK--NSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAE 261 (272)
T ss_pred CHHHhHhhccCcccCEEEEchhHHHHcCCCcccceeEEcCC--CCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHH
Confidence 4567888999999999988877764311111 111122211 1234 3667776444566666666566444444444
Q ss_pred HHh
Q psy17442 84 AKV 86 (90)
Q Consensus 84 ~kW 86 (90)
++|
T Consensus 262 ~~~ 264 (272)
T PRK09861 262 TIF 264 (272)
T ss_pred HHc
Confidence 443
No 104
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=63.07 E-value=18 Score=21.74 Aligned_cols=49 Identities=18% Similarity=0.089 Sum_probs=29.3
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
.+..+....|.+|++|..+...+.. ...+.. ..+..+++.++++++.|+
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~~~~------~~~~~~--~~l~~~~~~lv~~~~hpl 84 (197)
T cd08452 36 LSSPDQVEELLKGRIDIGFLHPPIQ------HTALHI--ETVQSSPCVLALPKQHPL 84 (197)
T ss_pred cChHHHHHHHHCCCccEEEeeCCCC------CCCeeE--EEeeeccEEEEEeCCCcc
Confidence 3567889999999999988643221 112221 223445566666666554
No 105
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=62.31 E-value=25 Score=24.17 Aligned_cols=54 Identities=15% Similarity=0.057 Sum_probs=38.2
Q ss_pred ccCChHHHHHHhhcCCceEEEee------hh---HHhHHHhcCCCeEEeCCcccccceEEEEeCC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWD------SS---RLDFEAAQDCELVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d------~~---~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kg 59 (90)
-..+.+|++.++.+|.+|..+.. .+ ++..+. ..++.++++..-+-.+.++..++
T Consensus 31 p~~ti~evf~ave~g~aD~gVVPIENS~eG~V~~tlDlL~--~~~l~IvgE~~lpI~h~L~~~~~ 93 (279)
T COG0077 31 PCSTIEDVFKAVENGEADYGVVPIENSIEGSVNETLDLLA--ETDLQIVGEIVLPIHHCLLVKGG 93 (279)
T ss_pred cCCCHHHHHHHHHcCCCceEEEEeeecCCcchHHHHHhhc--cCCcEEEEEEEEEEEEEEEecCC
Confidence 35789999999999999987743 12 222222 45789999887777777777643
No 106
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=61.05 E-value=9.8 Score=25.80 Aligned_cols=50 Identities=10% Similarity=-0.098 Sum_probs=31.2
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCCh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWA 63 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~ 63 (90)
.+..+....|.+|++|+.|...+.- ..++.. ..+....+.++++++.|+.
T Consensus 125 ~~~~~~~~~L~~g~~Dl~i~~~~~~------~~~~~~--~~l~~~~~~lv~~~~hpl~ 174 (317)
T PRK15421 125 GVTFDPQPALQQGELDLVMTSDILP------RSGLHY--SPMFDYEVRLVLAPDHPLA 174 (317)
T ss_pred CccHHHHHHHHCCCcCEEEecCccc------CCCceE--EEeccceEEEEEcCCCCcc
Confidence 4567889999999999999754321 112221 2345566666677776653
No 107
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=60.91 E-value=13 Score=24.52 Aligned_cols=24 Identities=17% Similarity=0.116 Sum_probs=19.9
Q ss_pred cCChHHHHHHhhcCCceEEEeehh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSS 28 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~ 28 (90)
.....+.+..|.+|++|.+|...+
T Consensus 124 ~~~~~~~~~~l~~g~~Dl~i~~~~ 147 (275)
T PRK03601 124 IAQRQSLVKQLHERQLDLLITTEA 147 (275)
T ss_pred ECChHHHHHHHHcCCCCEEEEcCC
Confidence 456788999999999999997543
No 108
>PRK09501 potD spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed
Probab=60.76 E-value=52 Score=22.58 Aligned_cols=75 Identities=3% Similarity=-0.227 Sum_probs=40.8
Q ss_pred HHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe-CCc-ccccceEEEEeCCCCChHHHHHHHHHhhhccHHHHHHH
Q psy17442 10 STVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA-GEL-FGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLFMA 84 (90)
Q Consensus 10 ~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~-~~~-~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~~ 84 (90)
+....+.+|++++.+............+.++.++ ++. -..-.-+++++|+++-.+.--+.|.-+.......++.+
T Consensus 213 ~~~~~l~~Gev~i~~~w~~~~~~~~~~g~~i~~~~P~eG~~~~~~~~~i~k~a~n~e~A~~Fi~~llspe~q~~~~~ 289 (348)
T PRK09501 213 NPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAE 289 (348)
T ss_pred HHHHHHHcCCEEEEEeehHHHHHHHhcCCCceEEecCCCcceEEEeeeEECCCCCHHHHHHHHHHHhCHHHHHHHHH
Confidence 3467889999887665433222222334445444 211 11112368999998766666666666665443344433
No 109
>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=59.90 E-value=8.7 Score=25.85 Aligned_cols=57 Identities=14% Similarity=-0.041 Sum_probs=36.3
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHh-HH--Hhc-CCCeEEeCCcccccceEEEEeCCC-CCh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLD-FE--AAQ-DCELVTAGELFGRSGYAIGLQKGS-PWA 63 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~-~~--~~~-~~~l~~~~~~~~~~~~~ia~~kgs-~l~ 63 (90)
..+..+.+.+|.+|++|+.+...+... .. ..+ ..++.. ..+..+++.+++++++ |+.
T Consensus 70 ~~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~~--~~l~~~~l~lvv~~~h~pl~ 131 (287)
T TIGR02136 70 GAGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKLIE--HKVAVDGLAVVVNKKNVPVD 131 (287)
T ss_pred cCCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCceE--EEEEEeeEEEEECCCCCccc
Confidence 346789999999999999776654321 11 111 122222 2456778888888887 864
No 110
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=59.85 E-value=42 Score=22.31 Aligned_cols=58 Identities=14% Similarity=0.085 Sum_probs=32.2
Q ss_pred cccCChHHHHHHhhcCC-ceEEEeehhH-HhHHHhcCCCeEEe-CCcccccceEEEEeCCCC
Q psy17442 3 FDVKFSPSTVVRHGTKK-LMAFIWDSSR-LDFEAAQDCELVTA-GELFGRSGYAIGLQKGSP 61 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~-ida~i~d~~~-~~~~~~~~~~l~~~-~~~~~~~~~~ia~~kgs~ 61 (90)
+.+.+......++..|. .|.++..... ..++.+... +.-. ...+.....++++++|++
T Consensus 58 ~~~~~Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl-~~~~~~~~~a~n~lvl~~~~~~~ 118 (257)
T PRK10677 58 SSFASSSTLARQIEQGAPADLFISADQKWMDYAVDKKA-IDTATRYTLLGNSLVVVAPKASE 118 (257)
T ss_pred EEecccHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCC-CCCcchheeecCEEEEEEECCCc
Confidence 34566778888888887 9999988744 333433321 1000 012333445566666643
No 111
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=59.27 E-value=26 Score=20.73 Aligned_cols=22 Identities=9% Similarity=-0.077 Sum_probs=17.6
Q ss_pred CChHHHHHHhhcCCceEEEeeh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~ 27 (90)
.+..+....|.+|++|..|...
T Consensus 37 ~~~~~~~~~l~~g~~Dl~i~~~ 58 (199)
T cd08451 37 ANTAELLEALREGRLDAAFVRP 58 (199)
T ss_pred CChHHHHHHHHCCCccEEEEec
Confidence 3566788999999999988643
No 112
>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom
Probab=59.12 E-value=24 Score=20.92 Aligned_cols=52 Identities=12% Similarity=0.027 Sum_probs=29.8
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCCh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWA 63 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~ 63 (90)
.+..+....|.+|++|..|...+.- ....++. ...+..+.+.++++++.|+.
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~~~~----~~~~~l~--~~~l~~~~~~~v~~~~hp~~ 87 (199)
T cd08416 36 GSNKDLLKKLKDGELDAILVATPEG----LNDPDFE--VVPLFEDDIFLAVPATSPLA 87 (199)
T ss_pred cCcHHHHHHHhCCCCCEEEEecCCc----CCCCCeE--EEEeecceEEEEECCCCccc
Confidence 3456678899999999999754320 0111221 12344555666667766643
No 113
>COG1732 OpuBC Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]
Probab=58.75 E-value=36 Score=23.71 Aligned_cols=56 Identities=9% Similarity=-0.092 Sum_probs=35.2
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHH-hHHHh-----------------c----CCCeEEeCCcccccceEEEEeCC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRL-DFEAA-----------------Q----DCELVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~-~~~~~-----------------~----~~~l~~~~~~~~~~~~~ia~~kg 59 (90)
++-+.+-...+|++|.||.+..-..++ ....+ + ..++..+.+.-....||+|++++
T Consensus 68 ~lG~t~v~~~Al~~G~IDiYpEYTGt~~~~~lk~~~~~~~dp~~~y~~vK~~~~k~~~l~wl~p~~~nNTyA~av~~~ 145 (300)
T COG1732 68 GLGGTAVVRNALKSGDIDIYPEYTGTALFSFLKKDPPASKDPKKVYETVKKLDAKQFKLVWLKPAGFNNTYALAVRKD 145 (300)
T ss_pred CCCchHHHHHHHHcCCCCeEeeecchhhhhhcccCccccCCHHHHHHHHHHHHHhcCCEEEecccCCCcceEEEecHH
Confidence 455666778999999999985322221 11111 1 12356666555577899999986
No 114
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=58.69 E-value=22 Score=23.39 Aligned_cols=52 Identities=17% Similarity=0.270 Sum_probs=31.1
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCCh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWA 63 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~ 63 (90)
.+..+.+..|.+|++|..|...+.. ....++.. ..+..+++.++++++.|+.
T Consensus 133 ~~~~~~~~~l~~g~~D~~i~~~~~~----~~~~~l~~--~~l~~~~~~~v~~~~~~l~ 184 (294)
T PRK09986 133 LSPSMQMAALERRELDAGIWRMADL----EPNPGFTS--RRLHESAFAVAVPEEHPLA 184 (294)
T ss_pred CCHHHHHHHHHcCCCCEEEecCCcc----CCCCCeEE--EEeecccEEEEEcCCCCcc
Confidence 3567889999999999988632100 00122222 2344567777777776643
No 115
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=58.56 E-value=12 Score=25.63 Aligned_cols=43 Identities=14% Similarity=0.021 Sum_probs=32.6
Q ss_pred ccCChHHHHHHhhcCCceE-EEeehhHHhHHHhc-CCCeEEeCCc
Q psy17442 4 DVKFSPSTVVRHGTKKLMA-FIWDSSRLDFEAAQ-DCELVTAGEL 46 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida-~i~d~~~~~~~~~~-~~~l~~~~~~ 46 (90)
.|.++.+-=.+|.+|.+|| ++--.|.+..+.+. .+.+..++.+
T Consensus 63 ~FtDY~~PN~AL~~gdiDaN~FQH~pyL~~~~k~~~~~Lv~vg~~ 107 (268)
T COG1464 63 EFTDYVQPNEALADGDIDANAFQHKPYLDQFNKEHGGKLVAVGNT 107 (268)
T ss_pred EecCCcchhHHHhcCCccchhhhchHHHHHHHHHcCCCEEEEeeE
Confidence 3566666667899999999 77778899888776 5667766653
No 116
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=57.66 E-value=16 Score=21.71 Aligned_cols=20 Identities=0% Similarity=-0.172 Sum_probs=16.1
Q ss_pred ChHHHHHHhhcCCceEEEee
Q psy17442 7 FSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d 26 (90)
+..+....|.+|++|..+..
T Consensus 38 ~~~~~~~~l~~~~~Dl~i~~ 57 (198)
T cd08446 38 TKDEQIEALRAGRIHIGFGR 57 (198)
T ss_pred CHHHHHHHHHCCCccEEEEe
Confidence 45667889999999998864
No 117
>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=57.35 E-value=68 Score=22.86 Aligned_cols=65 Identities=9% Similarity=-0.084 Sum_probs=33.7
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCC-C-----ChHHHHHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGS-P-----WADAVTLAI 70 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs-~-----l~~~vn~~l 70 (90)
+.+....+.+|++|++|.+..-.+.....+.....+.+... .......+.+.... | +|+.|+.+|
T Consensus 209 ~~d~~~~~~al~~GevD~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~N~~~~~~~d~~vR~Al~~ai 279 (476)
T cd08512 209 VPEAATRRLLLERGDADIARNLPPDDVAALEGNPGVKVISL-PSLTVFYLALNTKKAPFDNPKVRQAIAYAI 279 (476)
T ss_pred CCCHHHHHHHHHcCCcCEecCCCHHHHHHHhcCCCeEEEec-CCceEEEEEeeCCCCCCCCHHHHHHHHHhc
Confidence 45677889999999999864222211111233344544321 12223446665432 2 455555555
No 118
>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=56.28 E-value=13 Score=22.26 Aligned_cols=21 Identities=14% Similarity=-0.064 Sum_probs=16.7
Q ss_pred ChHHHHHHhhcCCceEEEeeh
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~ 27 (90)
+..+....|..|++|..|...
T Consensus 37 ~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08457 37 SSSQVLEAVASGRADLGIADG 57 (196)
T ss_pred CcHHHHHHHHcCCccEEEecc
Confidence 446778889999999988654
No 119
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=56.14 E-value=14 Score=22.27 Aligned_cols=21 Identities=0% Similarity=-0.278 Sum_probs=17.5
Q ss_pred ChHHHHHHhhcCCceEEEeeh
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~ 27 (90)
+..+.+..|.+|++|..+...
T Consensus 38 ~~~~~~~~l~~~~~D~~i~~~ 58 (198)
T cd08485 38 SKNRQIEALDAGTIDIGFGRF 58 (198)
T ss_pred CHHHHHHHHHcCCccEEEecC
Confidence 567888999999999988653
No 120
>PF10941 DUF2620: Protein of unknown function DUF2620; InterPro: IPR021238 This is a bacterial family of proteins with unknown function.
Probab=55.22 E-value=14 Score=22.11 Aligned_cols=24 Identities=4% Similarity=-0.003 Sum_probs=19.7
Q ss_pred cccCChHHHHHHhhcCCceEEEee
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d 26 (90)
..+.|.-||..+|++|++|.++..
T Consensus 28 v~i~sDmeAAm~vK~G~aDYY~GA 51 (117)
T PF10941_consen 28 VTIKSDMEAAMAVKSGQADYYLGA 51 (117)
T ss_pred EEEechHHHHHHhhcCCcCEeEee
Confidence 345677789999999999999864
No 121
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=53.88 E-value=33 Score=20.66 Aligned_cols=22 Identities=0% Similarity=-0.179 Sum_probs=18.3
Q ss_pred CChHHHHHHhhcCCceEEEeeh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~ 27 (90)
.+..+.+..|.+|++|..+...
T Consensus 36 ~~~~~~~~~L~~g~~Dl~i~~~ 57 (200)
T cd08465 36 ASREAMLAQVADGEIDLALGVF 57 (200)
T ss_pred CChHhHHHHHHCCCccEEEecc
Confidence 4668889999999999988643
No 122
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=53.49 E-value=21 Score=26.97 Aligned_cols=59 Identities=10% Similarity=-0.179 Sum_probs=35.5
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHh------HHHhc---CCCeEEeCCcccccceEEEEeCCCCCh
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLD------FEAAQ---DCELVTAGELFGRSGYAIGLQKGSPWA 63 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~------~~~~~---~~~l~~~~~~~~~~~~~ia~~kgs~l~ 63 (90)
....+..+.+.+|++|++|..+...+... .+.++ +..+.. ..+..+.+.+++++++|+.
T Consensus 445 v~~~~s~~vl~~L~~GeiDlai~~~~~~~~~~~~~~~~~~~~~~~~l~~--~~l~~d~lvlvvp~~hPl~ 512 (633)
T PRK14498 445 SLHVGSMGGLMALKRGEADIAGIHLLDPETGEYNIPYIKKYLLGEDAVL--VKGYRREQGLVVRKGNPKG 512 (633)
T ss_pred EEecCCHHHHHHHHcCCceEEEEcccCcccccccHHHHHhhcCCCCEEE--EEEEEEeEEEEECCCCCCC
Confidence 34467889999999999999875432210 01111 112322 2355667777888887753
No 123
>PRK11898 prephenate dehydratase; Provisional
Probab=53.22 E-value=57 Score=22.25 Aligned_cols=56 Identities=11% Similarity=-0.044 Sum_probs=37.1
Q ss_pred cCChHHHHHHhhcCCceEEEeeh------hHHhHH--HhcCCCeEEeCCcccccceEEEEeCCC
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDS------SRLDFE--AAQDCELVTAGELFGRSGYAIGLQKGS 60 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~------~~~~~~--~~~~~~l~~~~~~~~~~~~~ia~~kgs 60 (90)
+++..+++.+|.+|++|..+..- .+...+ +....++.++++..-+..+.+..++|+
T Consensus 33 ~~s~~~v~~av~~~~~d~gvvPiENS~~G~v~~~~d~L~~~~~~~iv~E~~l~I~~~L~~~~~~ 96 (283)
T PRK11898 33 YDSIPDVLDAVEAGEVDYAVVPIENSIEGSVNPTLDYLAHGSPLQIVAEIVLPIAQHLLVHPGH 96 (283)
T ss_pred cCCHHHHHHHHHcCCCCEEEEEecccCceecHHHHHHhccCCCcEEEEEEEeeeeEEEeCCCCC
Confidence 67899999999999988776541 111111 112236788888766777777766653
No 124
>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=53.10 E-value=52 Score=23.09 Aligned_cols=65 Identities=8% Similarity=-0.069 Sum_probs=35.5
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCC-----CC-ChHHHHHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKG-----SP-WADAVTLAI 70 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kg-----s~-l~~~vn~~l 70 (90)
+.+....+.++++|++|++....+.......+...+.+.... ....+.+.+... ++ +|+.|+.+|
T Consensus 195 ~~d~~~~~~~l~~GevD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~N~~~~~~~d~~vR~Al~~ai 265 (466)
T cd00995 195 IPDASTRVAALQSGEIDIADDVPPSALETLKKNPGIRLVTVP-SLGTGYLGFNTNKPPFDDKRVRQAISYAI 265 (466)
T ss_pred ecCHHHHHHHHHcCCccEecCCCHHHHHHHhcCCCceEEecc-CCceEEEEeecCCCCCCCHHHHHHHHHhc
Confidence 456678899999999998754433332223333444433211 223344666543 22 566666665
No 125
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport
Probab=51.69 E-value=42 Score=19.95 Aligned_cols=21 Identities=14% Similarity=-0.203 Sum_probs=17.3
Q ss_pred ChHHHHHHhhcCCceEEEeeh
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~ 27 (90)
+..+....|.+|++|..+...
T Consensus 37 ~~~~~~~~l~~g~~D~~i~~~ 57 (200)
T cd08453 37 TSDVQLEALLAGEIDAGIVIP 57 (200)
T ss_pred CHHHHHHHHHcCCCCEEEEec
Confidence 456789999999999988654
No 126
>TIGR03730 tungstate_WtpA tungstate ABC transporter binding protein WtpA. Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterized in Pyrococcus furiosus. Model seed members and cutoffs, pending experimental evidence for more distant homologs, were chosen such that this model identifies select archaeal proteins, excluding weaker archaeal and all bacterial homologs. Note that this family is homologous to molybdate transporters, and that at least one other family of tungstate transporter binding protein, TupA, also exists.
Probab=51.37 E-value=75 Score=21.57 Aligned_cols=23 Identities=4% Similarity=-0.216 Sum_probs=18.6
Q ss_pred CChHHHHHHhhcCCceEEEeehh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSS 28 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~ 28 (90)
.+..+++..|.+|++|+.|.-.+
T Consensus 182 ~~v~~~~~~v~sG~aD~g~vY~S 204 (273)
T TIGR03730 182 PKEVELLSLLESGEIDYAFIYKS 204 (273)
T ss_pred CchHhHHHHHHCCCCcEEEEEee
Confidence 45788999999999999776444
No 127
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=50.72 E-value=27 Score=20.64 Aligned_cols=20 Identities=5% Similarity=-0.187 Sum_probs=16.9
Q ss_pred ChHHHHHHhhcCCceEEEee
Q psy17442 7 FSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d 26 (90)
+..+.+..|.+|++|..+..
T Consensus 37 ~~~~~~~~l~~~~~Dl~i~~ 56 (197)
T cd08449 37 SPEAQKAALLSKRIDLGFVR 56 (197)
T ss_pred CHHHHHHHHhCCCccEEEec
Confidence 46788899999999998864
No 128
>TIGR00030 S21p ribosomal protein S21. This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents.
Probab=50.50 E-value=36 Score=17.63 Aligned_cols=36 Identities=6% Similarity=0.068 Sum_probs=26.1
Q ss_pred EEEeCCCCChHHHHHHHHHhhhccHHHHHHHHhccC
Q psy17442 54 IGLQKGSPWADAVTLAILDFHESTVCYLFMAKVHLN 89 (90)
Q Consensus 54 ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~~kW~~~ 89 (90)
|.+..|.++-..+-..=..+..+|.+.++..+.+.+
T Consensus 3 V~V~~~e~ie~alrrfkr~~~~~gil~e~r~r~~ye 38 (58)
T TIGR00030 3 VKVKEGESIDSALRRFKRKLEKEGILRELKKRRYYE 38 (58)
T ss_pred eEeCCCCcHHHHHHHHHHHHHHcchHHHHHHHHhhc
Confidence 445666666666666666778999999999876643
No 129
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=50.10 E-value=29 Score=23.33 Aligned_cols=48 Identities=8% Similarity=-0.061 Sum_probs=30.9
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
+..+.+..|.+|++|..|...+.. ..++.. ..+..+++.++++++.|+
T Consensus 149 ~~~~~~~~l~~g~~Di~i~~~~~~------~~~l~~--~~l~~~~~~lv~~~~hpl 196 (314)
T PRK09508 149 LNQNIEHQLRYQETEFVISYEEFD------RPEFTS--VPLFKDELVLVASKNHPR 196 (314)
T ss_pred cchhHHHHHhcCCccEEEecCCCC------ccccce--eeeecCceEEEEcCCCCc
Confidence 467788999999999998754321 122221 234556777777777664
No 130
>COG0416 PlsX Fatty acid/phospholipid biosynthesis enzyme [Lipid metabolism]
Probab=49.89 E-value=22 Score=25.17 Aligned_cols=28 Identities=11% Similarity=-0.166 Sum_probs=23.3
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEA 34 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~ 34 (90)
|..-|++.|+.|++||++....+.....
T Consensus 84 SM~~Ai~lVkeg~ADa~VSAGnTGAlma 111 (338)
T COG0416 84 SMRVALDLVKEGKADACVSAGNTGALMA 111 (338)
T ss_pred HHHHHHHHHhcCcCCEEEecCchHHHHH
Confidence 6788999999999999999877665543
No 131
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=49.84 E-value=53 Score=19.38 Aligned_cols=66 Identities=11% Similarity=0.009 Sum_probs=36.1
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeC--CcccccceEEEEeCCCCChHHHHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAG--ELFGRSGYAIGLQKGSPWADAVTLAI 70 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~--~~~~~~~~~ia~~kgs~l~~~vn~~l 70 (90)
+.+++...++..+.+|..-+++-. ..+..... ...+..+. .......+.++.+++.+....+...+
T Consensus 128 ~~~~~~~~~~~~v~~g~gi~~~p~-~~~~~~~~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 195 (201)
T cd08418 128 VRTDSIVSIINLVEKADFLTILSR-DMGRGPLD-SFRLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLV 195 (201)
T ss_pred EEecCHHHHHHHHHhCCEEEEeEH-HHhhhhhh-cCCEEEecCCCCCCCCceEEEEecCCCCCHHHHHHH
Confidence 356778888889999985455443 33333332 22344432 22233467778887755444444433
No 132
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=49.58 E-value=15 Score=25.72 Aligned_cols=35 Identities=9% Similarity=0.119 Sum_probs=22.9
Q ss_pred HHHHHHhhcCCceEEEeehhHHhHHHh---cCCCeEEe
Q psy17442 9 PSTVVRHGTKKLMAFIWDSSRLDFEAA---QDCELVTA 43 (90)
Q Consensus 9 ~~~~~~l~~G~ida~i~d~~~~~~~~~---~~~~l~~~ 43 (90)
.++..++++|++||+++-...-.-.+. ..|++.++
T Consensus 176 a~~~~~l~~g~iDA~~~~~G~p~~ai~el~~~~~i~lv 213 (321)
T COG2358 176 AESADALKNGTIDAAFYVAGVPNPAISELATTCDIVLV 213 (321)
T ss_pred hhhHHHhhCCcccEEEEecCCCCccHHHHHhhCCeEEE
Confidence 345889999999998876554333322 24666655
No 133
>PRK13846 putative glycerol-3-phosphate acyltransferase PlsX; Provisional
Probab=49.12 E-value=26 Score=24.54 Aligned_cols=29 Identities=17% Similarity=0.028 Sum_probs=23.9
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHH
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEA 34 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~ 34 (90)
.|..-|++.|++|++||++....+-....
T Consensus 84 SSm~~a~~lvk~g~ada~VSaGnTGAl~a 112 (316)
T PRK13846 84 SSMALGLDYLQEDKLDAFISTGNTAALVT 112 (316)
T ss_pred CHHHHHHHHHHcCCCCEEEecChHHHHHH
Confidence 46678999999999999999887665544
No 134
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=49.04 E-value=31 Score=23.37 Aligned_cols=48 Identities=8% Similarity=-0.026 Sum_probs=31.7
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
...+.+..|.+|++|..|...+.. ..++.. ..+..+++.++++++.|+
T Consensus 152 ~~~~~~~~l~~g~~Dl~i~~~~~~------~~~~~~--~~l~~~~~~lv~~~~hpl 199 (317)
T PRK11482 152 PISDAENQLSQFQTDLIIDTHSCS------NRTIQH--HVLFTDNVVLVCRQGHPL 199 (317)
T ss_pred cchhHHHHHHCCCcCEEEeccCCC------CCceEE--EEEecCcEEEEEeCCCCc
Confidence 446789999999999998654321 122222 235567777788888775
No 135
>PRK11205 tbpA thiamine transporter substrate binding subunit; Provisional
Probab=48.48 E-value=84 Score=21.33 Aligned_cols=69 Identities=6% Similarity=-0.237 Sum_probs=38.4
Q ss_pred CChHHHHHHhhcCCceEEEeehhH-HhHHHhc-CCCeEE--eCCcccccceEEEEeCCCCChHHHHHHHHHhh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSR-LDFEAAQ-DCELVT--AGELFGRSGYAIGLQKGSPWADAVTLAILDFH 74 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~-~~~~~~~-~~~l~~--~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~ 74 (90)
.+..+....+.+|++++.+..... ......+ ..++.+ ..+.......++++.||++-.+...+.+.-|.
T Consensus 198 ~~~~~~~~~~~~Ge~~~~i~~~~~~~~~~~~~~~~~~~~~~~~eG~~~~~~~~ai~k~a~n~e~A~~Fi~fll 270 (330)
T PRK11205 198 KGWSEAYGLFLKGEADLVLSYTTSPAYHIIAEKKDNYAAANFSEGHYLQVEVAARTAASKQPELAQKFLQFMV 270 (330)
T ss_pred CChHHHHHHHHcCCccEEEeCCCcHHHHHhhccCCceeEEEcCCCCeEEEEEEEEeCCCCCHHHHHHHHHHHc
Confidence 455677889999999998765432 1122222 223322 22211123347899999875555555554443
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=48.33 E-value=57 Score=20.94 Aligned_cols=75 Identities=8% Similarity=-0.094 Sum_probs=45.9
Q ss_pred HHHHHHhhcCCceEEEeehhHHhHHHhcCCCeE-EeCCcccccceEEEEeCCCCChHHHHHHHHHhhhccHHHHHHHHhc
Q psy17442 9 PSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELV-TAGELFGRSGYAIGLQKGSPWADAVTLAILDFHESTVCYLFMAKVH 87 (90)
Q Consensus 9 ~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~-~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~~kW~ 87 (90)
.+.-.-|..|.+|..|....++.. +..++. +..-.|..-.+.+|.|++++.... ..+..++=-=+|..+.++||
T Consensus 50 ~Dip~yV~~G~aDlGI~G~D~l~E---~~~~v~~~~dL~fg~crl~vA~p~~~~~~~~--~~l~~~rIATkyp~i~~~~f 124 (182)
T TIGR00070 50 QDIPTYVEHGAADLGITGYDVLLE---SGADVYELLDLGFGKCRLVLAVPQESDISSV--EDLKGKRIATKYPNLARRYF 124 (182)
T ss_pred chhHHHHhCCCccEEEecchhhhh---CCCCEEEEeecCcCceEEEEEEECCCCCCCh--HHhCCCEEEECCHHHHHHHH
Confidence 445567889999999988777642 333443 334456777889999998764322 11222333334666666666
Q ss_pred c
Q psy17442 88 L 88 (90)
Q Consensus 88 ~ 88 (90)
-
T Consensus 125 ~ 125 (182)
T TIGR00070 125 E 125 (182)
T ss_pred H
Confidence 3
No 137
>PF11195 DUF2829: Protein of unknown function (DUF2829) ; InterPro: IPR021361 This entry is represented by Bacteriophage 16-3, p046. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=48.31 E-value=15 Score=20.01 Aligned_cols=13 Identities=8% Similarity=-0.209 Sum_probs=11.6
Q ss_pred ChHHHHHHhhcCC
Q psy17442 7 FSPSTVVRHGTKK 19 (90)
Q Consensus 7 ~~~~~~~~l~~G~ 19 (90)
++.+|+.+|++|+
T Consensus 2 ~F~eAl~alK~Gk 14 (75)
T PF11195_consen 2 NFGEALEALKQGK 14 (75)
T ss_pred CHHHHHHHHHcCC
Confidence 5789999999998
No 138
>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=47.95 E-value=81 Score=22.44 Aligned_cols=20 Identities=5% Similarity=-0.116 Sum_probs=16.8
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+.+.++.++++|++|++.
T Consensus 198 ~~~~~~~~~~l~~G~id~~~ 217 (460)
T cd08503 198 IPDPAARVNALLSGQVDVIN 217 (460)
T ss_pred cCCHHHHHHHHHcCCcceec
Confidence 56778899999999999853
No 139
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=47.89 E-value=38 Score=22.69 Aligned_cols=23 Identities=9% Similarity=-0.109 Sum_probs=18.1
Q ss_pred cCChHHHHHHhhcCCceEEEeeh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~ 27 (90)
..+..+....|.+|++|..|...
T Consensus 129 ~~~~~~~~~~l~~~~~Dl~i~~~ 151 (309)
T PRK11013 129 PQESPLLEEWLSAQRHDLGLTET 151 (309)
T ss_pred eCCHHHHHHHHHcCCCCEEEEcC
Confidence 44567788899999999988753
No 140
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=47.71 E-value=41 Score=22.94 Aligned_cols=23 Identities=9% Similarity=-0.070 Sum_probs=18.9
Q ss_pred cCChHHHHHHhhcCCceEEEeeh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~ 27 (90)
..+..+.+..|.+|++|..|...
T Consensus 128 ~~~~~~~~~~l~~g~~Dl~i~~~ 150 (327)
T PRK12680 128 QAAESAALDLLGQGDADIAIVST 150 (327)
T ss_pred eCChHHHHHHHHCCCCcEEEEec
Confidence 34568899999999999998754
No 141
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=47.56 E-value=32 Score=23.43 Aligned_cols=27 Identities=4% Similarity=-0.024 Sum_probs=21.3
Q ss_pred hHHHHHHhhcCCceEEEeehhHHhHHH
Q psy17442 8 SPSTVVRHGTKKLMAFIWDSSRLDFEA 34 (90)
Q Consensus 8 ~~~~~~~l~~G~ida~i~d~~~~~~~~ 34 (90)
.++++.+|.+|++||++.-.|....+.
T Consensus 158 ~~~~~~Al~~G~VDAa~~~~p~~~~~~ 184 (320)
T PRK11480 158 PPAIIAAWQRGDIDGAYVWAPAVNALE 184 (320)
T ss_pred cHHHHHHHHcCCcCEEEEcchHHHHHH
Confidence 578899999999999887777654443
No 142
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=47.35 E-value=23 Score=16.11 Aligned_cols=16 Identities=6% Similarity=0.200 Sum_probs=13.5
Q ss_pred hHHHHHHHHHhhhccH
Q psy17442 63 ADAVTLAILDFHESTV 78 (90)
Q Consensus 63 ~~~vn~~l~~l~~~G~ 78 (90)
++.|++.+.+++++|.
T Consensus 16 ~ETVSR~l~~l~~~gl 31 (32)
T PF00325_consen 16 RETVSRILKKLERQGL 31 (32)
T ss_dssp HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHHHcCC
Confidence 5789999999998884
No 143
>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=45.84 E-value=63 Score=23.11 Aligned_cols=65 Identities=11% Similarity=-0.110 Sum_probs=35.1
Q ss_pred cCChHHHHHHhhcCCceEEEeehhH-HhHHHhcCCCeEEeCCcccccceEEEEeCCC-C-----ChHHHHHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSR-LDFEAAQDCELVTAGELFGRSGYAIGLQKGS-P-----WADAVTLAI 70 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~-~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs-~-----l~~~vn~~l 70 (90)
+.+....+.+|++|++|......+. .....+....+.+... .....+.+++...+ + +|+.|+.+|
T Consensus 205 ~~~~~~~~~al~~G~iD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~N~~~~~~~d~~vR~Ai~~ai 276 (486)
T cd08501 205 MEDPDAQINALRNGEIDAADVGPTEDTLEALGLLPGVEVRTG-DGPRYLHLTLNTKSPALADVAVRKAFLKAI 276 (486)
T ss_pred cCChHHHHHHHHcCCCceEecCCCHHHHHHhccCCCeEEEEc-CCCcEEEEEecCCCcccCCHHHHHHHHHhC
Confidence 4567789999999999986543222 2222223334444422 12333456765542 2 455555554
No 144
>PRK00270 rpsU 30S ribosomal protein S21; Reviewed
Probab=45.48 E-value=47 Score=17.55 Aligned_cols=36 Identities=3% Similarity=0.017 Sum_probs=26.3
Q ss_pred EEEeCCCCChHHHHHHHHHhhhccHHHHHHHHhccC
Q psy17442 54 IGLQKGSPWADAVTLAILDFHESTVCYLFMAKVHLN 89 (90)
Q Consensus 54 ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~~kW~~~ 89 (90)
|.+..|.++-..+-..=..+..+|.+.++..+.+.+
T Consensus 4 V~V~~~e~ie~Alrrfkr~~~k~gil~e~r~r~~ye 39 (64)
T PRK00270 4 VKVRENESIDKALRRFKRKVEKAGILRELRRREFYE 39 (64)
T ss_pred eEeCCCChHHHHHHHHHHHHHHcchHHHHHHHHhhc
Confidence 455666666666666666778999999999876643
No 145
>PRK00910 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=44.74 E-value=7.7 Score=25.67 Aligned_cols=22 Identities=5% Similarity=-0.019 Sum_probs=16.7
Q ss_pred cCChHHHHHHhhcCCceEEEee
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d 26 (90)
+.+.++++.+|++|+.-.++.|
T Consensus 14 ~~~ie~ai~al~~G~~Viv~Dd 35 (218)
T PRK00910 14 ITRVENALQALREGRGVLLLDD 35 (218)
T ss_pred cccHHHHHHHHHCCCeEEEEeC
Confidence 5678999999999994444443
No 146
>smart00851 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site PUBMED:10526357.
Probab=44.34 E-value=30 Score=18.96 Aligned_cols=19 Identities=5% Similarity=-0.181 Sum_probs=14.5
Q ss_pred hHHHHHHhhcCCceEEEee
Q psy17442 8 SPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 8 ~~~~~~~l~~G~ida~i~d 26 (90)
.+..+..+++|++|.+|.-
T Consensus 44 ~~~i~~~i~~g~id~VIn~ 62 (90)
T smart00851 44 ILAILDLIKNGEIDLVINT 62 (90)
T ss_pred CHHHHHHhcCCCeEEEEEC
Confidence 3557788888888888874
No 147
>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T
Probab=44.26 E-value=69 Score=19.12 Aligned_cols=58 Identities=9% Similarity=-0.217 Sum_probs=30.4
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeC--CcccccceEEEEeCCCCC
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAG--ELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~--~~~~~~~~~ia~~kgs~l 62 (90)
+..++....+..+..|..-+++-... ...... ...+..+. .......++++.+|+...
T Consensus 127 ~~~~~~~~~~~~v~~g~giailp~~~-~~~~~~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~ 186 (200)
T cd08462 127 VVTPSFSSIPPLLVGTNRIATLHRRL-AEQFAR-RLPLRILPLPFPLPPMREALQWHRYRNN 186 (200)
T ss_pred EEeChHHHHHHHHHcCchhhhhHHHH-HHhhhh-cCCceEeCCCcCCCCeeEEEEEcccccC
Confidence 34667777778888887444443322 222222 22233332 223345678888887543
No 148
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=43.21 E-value=64 Score=18.48 Aligned_cols=63 Identities=16% Similarity=0.062 Sum_probs=34.9
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe--CCcccccceEEEEeCCCCChHHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA--GELFGRSGYAIGLQKGSPWADAVTL 68 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~--~~~~~~~~~~ia~~kgs~l~~~vn~ 68 (90)
+.+++...++..+.+|..-+++.. ..+. .... ..+..+ .......++.++.+++++....+..
T Consensus 128 ~~~~~~~~~~~~~~~~~g~~~~p~-~~~~-~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 (197)
T cd05466 128 LEVDSLEAIKALVAAGLGIALLPE-SAVE-ELAD-GGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARA 192 (197)
T ss_pred EEeccHHHHHHHHHhCCCEEEehH-HHHh-hhhc-CCeEEEEecCCcceEEEEEEEcCCCccCHHHHH
Confidence 456778888888999985444443 3333 2222 234433 2223345677788877654443333
No 149
>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=42.96 E-value=88 Score=22.32 Aligned_cols=19 Identities=0% Similarity=-0.102 Sum_probs=15.9
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+ ...+.+|++|++|...
T Consensus 187 ~~d-~~~~~al~~GeiD~~~ 205 (464)
T cd08518 187 LPD-DAAAAALKSGEVDLAL 205 (464)
T ss_pred cCC-HHHHHHHHcCCCceee
Confidence 456 8899999999999863
No 150
>PF01715 IPPT: IPP transferase; InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) [].; GO: 0005524 ATP binding, 0008033 tRNA processing; PDB: 2ZXU_A 3FOZ_A 2ZM5_B 3D3Q_A 3EXA_B 2QGN_A 3A8T_A 3EPK_B 3EPH_A 3EPJ_A ....
Probab=42.89 E-value=42 Score=22.46 Aligned_cols=34 Identities=15% Similarity=0.124 Sum_probs=27.3
Q ss_pred ceEEEEeCCC-CChHHHHHHHHHhhhccHHHHHHH
Q psy17442 51 GYAIGLQKGS-PWADAVTLAILDFHESTVCYLFMA 84 (90)
Q Consensus 51 ~~~ia~~kgs-~l~~~vn~~l~~l~~~G~~~~l~~ 84 (90)
...|.+...- .|.+.||..+.+|.+.|.++|...
T Consensus 154 ~~~i~L~~~r~~L~~RI~~Rvd~Ml~~GlleEv~~ 188 (253)
T PF01715_consen 154 FLVIGLDRDREELYERINKRVDEMLEQGLLEEVRA 188 (253)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHHHTTHHHHHHH
T ss_pred eEEEEeCCCHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 3456676654 499999999999999999998654
No 151
>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=42.66 E-value=86 Score=22.44 Aligned_cols=20 Identities=5% Similarity=-0.049 Sum_probs=16.6
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+....+.++++|++|++-
T Consensus 194 ~~d~~~~~~al~~G~iD~~~ 213 (481)
T cd08498 194 IPNDATRVAALLSGEVDVIE 213 (481)
T ss_pred CCCHHHHHHHHHcCCCCEec
Confidence 46777889999999999863
No 152
>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=42.53 E-value=33 Score=22.38 Aligned_cols=22 Identities=5% Similarity=-0.058 Sum_probs=16.9
Q ss_pred cCChHHHHHHhhcCCceEEEee
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d 26 (90)
+++.++++.+|++|+.-.++.|
T Consensus 2 ~~~ie~ai~al~~G~~Viv~Dd 23 (199)
T TIGR00506 2 FERVEEALEALKKGEIVLVYDD 23 (199)
T ss_pred cchHHHHHHHHHCCCeEEEEeC
Confidence 5678999999999995444443
No 153
>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=42.41 E-value=30 Score=21.20 Aligned_cols=23 Identities=9% Similarity=-0.150 Sum_probs=17.9
Q ss_pred CChHHHHHHhhcCCceEEEeehh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSS 28 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~ 28 (90)
.+..++-.+|++|++++++.=..
T Consensus 83 ~~~~ea~~~l~~g~~~~~ivIP~ 105 (164)
T TIGR03061 83 VSAKEAEKGLADGKYYMVITIPE 105 (164)
T ss_pred cCHHHHHHHhHcCcEEEEEEECc
Confidence 36788889999999888776544
No 154
>PRK15413 glutathione ABC transporter substrate-binding protein GsiB; Provisional
Probab=42.23 E-value=1.3e+02 Score=21.84 Aligned_cols=65 Identities=12% Similarity=-0.043 Sum_probs=34.0
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCC-----CC-ChHHHHHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKG-----SP-WADAVTLAI 70 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kg-----s~-l~~~vn~~l 70 (90)
+.+....+.+|++|++|....-.+.....++...++.+.... ......+.|... ++ +|+.|+.+|
T Consensus 223 i~d~~~~~~al~~GeiD~~~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~l~fN~~~~~~~d~~vRqAi~~Ai 293 (512)
T PRK15413 223 VADNNTRAAMLQTGEAQFAFPIPYEQAALLEKNKNLELVASP-SIMQRYISMNVTQKPFDNPKVREALNYAI 293 (512)
T ss_pred cCCHHHHHHHHHcCCCCEecCCCHHHHHHHhcCCCeEEEecC-CceEEEEEecCCCCCcCCHHHHHHHHHhc
Confidence 466778899999999997642222222223334455544221 222334556433 22 556666555
No 155
>COG2113 ProX ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]
Probab=41.82 E-value=52 Score=22.79 Aligned_cols=54 Identities=9% Similarity=-0.084 Sum_probs=34.6
Q ss_pred CChHHHHHHhhcCCceEEEeeh-hHHhHHHhc---CCCeEEeCCcccccceEEEEeCC
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDS-SRLDFEAAQ---DCELVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~-~~~~~~~~~---~~~l~~~~~~~~~~~~~ia~~kg 59 (90)
-+..-+++.|.+|.+|++...- |.......+ ...+...+......-+|+++|+-
T Consensus 66 ~~~~~~~~sla~gd~D~~~~~W~p~~~~~~~~~~~~~~v~~~~~~~~Ga~~g~~vp~y 123 (302)
T COG2113 66 LDTAVMYQSLAKGDLDVFPEAWLPTTPDDYKKAVKDKKVELGGTNLEGAKQGWAVPKY 123 (302)
T ss_pred ccHHHHHHHHHcCCCccccceecCCChHHHHHHhccCceeecccccCCceEEEEecee
Confidence 3567789999999999987653 333233332 23444555345567788888884
No 156
>PRK11899 prephenate dehydratase; Provisional
Probab=41.65 E-value=94 Score=21.28 Aligned_cols=57 Identities=11% Similarity=-0.023 Sum_probs=36.9
Q ss_pred ccCChHHHHHHhhcCCceEEEeehh------HHhHH-HhcCCCeEEeCCcccccceEEEEeCCC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSS------RLDFE-AAQDCELVTAGELFGRSGYAIGLQKGS 60 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~------~~~~~-~~~~~~l~~~~~~~~~~~~~ia~~kgs 60 (90)
-+++.++++.+|.+|++|..+..-. +..-+ +-...++.++++..-+..+.+...+|.
T Consensus 32 ~~~s~~~vf~av~~g~~d~gVvPiENS~~G~V~~~~Dll~~~~l~Iv~E~~l~I~h~Ll~~~~~ 95 (279)
T PRK11899 32 PCATFEDAFEAVESGEADLAMIPIENSLAGRVADIHHLLPESGLHIVGEYFLPIRHQLMALPGA 95 (279)
T ss_pred ecCCHHHHHHHHHCCCCCEEEEEeeccCCccHHHHHHHHhcCCCEEEEEEEEEeeEEEecCCCC
Confidence 3678999999999999887664321 11111 111345788888776777776666664
No 157
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=41.22 E-value=75 Score=18.70 Aligned_cols=69 Identities=13% Similarity=-0.054 Sum_probs=38.5
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeC-C-cccccceEEEEeCCCCChHHHHHHHHHh
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAG-E-LFGRSGYAIGLQKGSPWADAVTLAILDF 73 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~-~-~~~~~~~~ia~~kgs~l~~~vn~~l~~l 73 (90)
+.+++...++..+..|.--+++-. ..+...... ..+..+. . ......++++.+++......+...+..+
T Consensus 123 ~~~~~~~~~~~~v~~g~Gi~~lp~-~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 193 (197)
T cd08470 123 WRCNSGVALLDAALKGMGLAQLPD-YYVDEHLAA-GRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYL 193 (197)
T ss_pred EEECCHHHHHHHHHcCCcEEEech-HHhHHHHHc-CCcEEccccccCCCCcEEEEeCCchhccHHHHHHHHHH
Confidence 456778888888999985555554 333333332 2233331 1 2233567788888765555555544433
No 158
>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=40.39 E-value=1.3e+02 Score=21.28 Aligned_cols=20 Identities=0% Similarity=-0.089 Sum_probs=16.6
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+...++.++.+|++|++.
T Consensus 186 ~~d~~~~~~~l~~G~iD~~~ 205 (470)
T cd08490 186 IPDANTRALALQSGEVDIAY 205 (470)
T ss_pred cCCHHHHHHHHHcCCcceec
Confidence 45677889999999999864
No 159
>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=40.21 E-value=53 Score=22.94 Aligned_cols=37 Identities=11% Similarity=-0.038 Sum_probs=29.6
Q ss_pred cceEEEEeCCC-CChHHHHHHHHHhhhccHHHHHHHHh
Q psy17442 50 SGYAIGLQKGS-PWADAVTLAILDFHESTVCYLFMAKV 86 (90)
Q Consensus 50 ~~~~ia~~kgs-~l~~~vn~~l~~l~~~G~~~~l~~kW 86 (90)
..+.|++.... .|.+.|+..+..|.++|.++|...-+
T Consensus 190 ~~~~~~l~~~r~~L~~rI~~R~d~Ml~~Gli~EV~~L~ 227 (308)
T COG0324 190 DILIIALAADREVLYERINRRVDAMLEQGLIEEVKALY 227 (308)
T ss_pred ceEEEEEeCCHHHHHHHHHHHHHHHHHccHHHHHHHHH
Confidence 34567777664 49999999999999999999886543
No 160
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=40.20 E-value=37 Score=19.81 Aligned_cols=21 Identities=10% Similarity=-0.126 Sum_probs=16.1
Q ss_pred CChHHHHHHhhcCCceEEEee
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d 26 (90)
++.++.+..+++|++|.+|.-
T Consensus 57 ~g~~~i~~~i~~g~i~~VInt 77 (115)
T cd01422 57 GGDQQIGALIAEGEIDAVIFF 77 (115)
T ss_pred CchhHHHHHHHcCceeEEEEc
Confidence 344778888889998888765
No 161
>COG0108 RibB 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]
Probab=39.70 E-value=35 Score=22.39 Aligned_cols=22 Identities=9% Similarity=-0.017 Sum_probs=17.0
Q ss_pred ccCChHHHHHHhhcCCceEEEee
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d 26 (90)
.+.+..+++.++++|+ -.++.|
T Consensus 2 ~~~~ie~ai~al~~G~-~Viv~D 23 (203)
T COG0108 2 MFERVEEAIEALRAGK-PVIVVD 23 (203)
T ss_pred chhhHHHHHHHHHCCC-eEEEEc
Confidence 5678899999999999 444444
No 162
>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=39.52 E-value=1.4e+02 Score=21.30 Aligned_cols=20 Identities=5% Similarity=-0.052 Sum_probs=16.3
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+....+.++++|++|++.
T Consensus 206 ~~d~~~~~~~l~~G~iD~~~ 225 (484)
T cd08492 206 IPEASVRVGALQSGQVDVIT 225 (484)
T ss_pred CCcHHHHHHHHHcCCcceec
Confidence 45667789999999999864
No 163
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate
Probab=38.74 E-value=84 Score=18.50 Aligned_cols=62 Identities=10% Similarity=-0.123 Sum_probs=32.1
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeC--CcccccceEEEEeCCCCChHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAG--ELFGRSGYAIGLQKGSPWADAV 66 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~--~~~~~~~~~ia~~kgs~l~~~v 66 (90)
+.+++...++..+.+|.--+++- ...+..... ...+..+. .......+.++.+++.+....+
T Consensus 127 ~~~~~~~~~~~~v~~g~gi~~lp-~~~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 (200)
T cd08417 127 LTVPHFLAAPALVAGTDLIATVP-RRLAEALAE-RLGLRVLPLPFELPPFTVSLYWHPRRDRDPAH 190 (200)
T ss_pred EeeCcHHHHHHHHhcCCeeeecc-HHHHHhhcc-cCCcEEecCCCCCCcceeEEEeccccccChHH
Confidence 45667777888888887444433 333332221 23344432 2222345777777765433333
No 164
>TIGR00174 miaA tRNA isopentenyltransferase (miaA). Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.
Probab=38.29 E-value=39 Score=23.20 Aligned_cols=32 Identities=25% Similarity=0.297 Sum_probs=25.8
Q ss_pred EEEEeCCC-CChHHHHHHHHHhhhccHHHHHHH
Q psy17442 53 AIGLQKGS-PWADAVTLAILDFHESTVCYLFMA 84 (90)
Q Consensus 53 ~ia~~kgs-~l~~~vn~~l~~l~~~G~~~~l~~ 84 (90)
.|.+..+- .|.+.||..+..|.+.|.++|...
T Consensus 188 ~i~l~~dr~~L~~rI~~Rv~~Mi~~Gl~eEv~~ 220 (287)
T TIGR00174 188 QIGLASSREPLHQRIEQRVHDMLESGLLAEVKA 220 (287)
T ss_pred EEEECCCHHHHHHHHHHHHHHHHHCCHHHHHHH
Confidence 35565553 499999999999999999998764
No 165
>TIGR00971 3a0106s03 sulfate/thiosulfate-binding protein. This model describes binding proteins functionally associated with the sulfate ABC transporter. In the model bacterium E. coli, two different members work with the same transporter; mutation analysis says each enables the uptake of both sulfate and thiosulfate. In many species, a single binding protein is found, and may be referred to in general terms as a sulfate ABC transporter sulfate-binding protein.
Probab=38.08 E-value=1.2e+02 Score=20.87 Aligned_cols=33 Identities=9% Similarity=-0.234 Sum_probs=24.0
Q ss_pred cccCChHHHHHHhhcCC-ceEEEeehhH-HhHHHh
Q psy17442 3 FDVKFSPSTVVRHGTKK-LMAFIWDSSR-LDFEAA 35 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~-ida~i~d~~~-~~~~~~ 35 (90)
+.+.++......+.+|. .|.|+..... +..+.+
T Consensus 48 ~~~g~Sg~l~~Qi~~Ga~~Dvf~sa~~~~~~~l~~ 82 (315)
T TIGR00971 48 QSHGGSGKQATSVINGIEADVVTLALAYDVDAIAE 82 (315)
T ss_pred EecCCcHHHHHHHHcCCCcCEEecCCHHHHHHHHH
Confidence 46788889999999876 8998887653 333433
No 166
>PTZ00148 40S ribosomal protein S8; Provisional
Probab=37.99 E-value=32 Score=22.60 Aligned_cols=19 Identities=16% Similarity=0.366 Sum_probs=11.8
Q ss_pred cCCceEEEeehhHHhHHHh
Q psy17442 17 TKKLMAFIWDSSRLDFEAA 35 (90)
Q Consensus 17 ~G~ida~i~d~~~~~~~~~ 35 (90)
.|++|++|.+..-|.+|.+
T Consensus 180 ~Gr~dGyILEGkEL~FY~k 198 (205)
T PTZ00148 180 SGRADGYILEGKELEFYLK 198 (205)
T ss_pred ccceeEEEEecHHHHHHHH
Confidence 4566666666666666654
No 167
>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=37.94 E-value=1.5e+02 Score=21.19 Aligned_cols=53 Identities=6% Similarity=-0.087 Sum_probs=28.6
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCC
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kg 59 (90)
+.+...++.++++|++|+...-.+.... .....++.+.... ......+++...
T Consensus 211 ~~~~~~~~~al~~G~iD~~~~~~~~~~~-~~~~~~~~~~~~~-~~~~~~l~~N~~ 263 (482)
T cd08493 211 IPDNSVRLAKLLAGECDIVAYPNPSDLA-ILADAGLQLLERP-GLNVGYLAFNTQ 263 (482)
T ss_pred CCChHHHHHHHHCCCccEeccCChhhcc-hhcCCCcEEEecC-CccEEEEEEecC
Confidence 4567788999999999986422222111 2333344444211 122345777654
No 168
>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=37.52 E-value=1.4e+02 Score=21.42 Aligned_cols=63 Identities=14% Similarity=-0.027 Sum_probs=33.5
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCC------ChHHHHHHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSP------WADAVTLAI 70 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~------l~~~vn~~l 70 (90)
+.+....+.+|++|++|.+....+.....+++...+.+... .....+.+...++ +|+.|+.+|
T Consensus 206 ~~d~~~~~~al~~G~vD~~~~~~~~~~~~l~~~~~~~~~~~---~~~~~l~~N~~~~~~~d~~vR~Ai~~ai 274 (472)
T cd08502 206 VPDANTAVAALQSGEIDFAEQPPADLLPTLKADPVVVLKPL---GGQGVLRFNHLQPPFDNPKIRRAVLAAL 274 (472)
T ss_pred eCCHHHHHHHHHcCCcceecCCCHHHHHHHhhCCCeEEecC---CceEEEEEcCCCCCCcCHHHHHHHHHhc
Confidence 45778889999999999874322222222233334444321 1334466654432 445555544
No 169
>PRK01792 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=37.42 E-value=11 Score=24.87 Aligned_cols=22 Identities=5% Similarity=-0.130 Sum_probs=16.6
Q ss_pred cCChHHHHHHhhcCCceEEEee
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d 26 (90)
+.+..+++.+|++|+.-.++.|
T Consensus 13 ~~~i~~ai~al~~G~~Viv~Dd 34 (214)
T PRK01792 13 EERVINAINAFKQGNGVLVLDD 34 (214)
T ss_pred cccHHHHHHHHHCCCeEEEEeC
Confidence 4678999999999995444443
No 170
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=37.38 E-value=1.3e+02 Score=20.12 Aligned_cols=74 Identities=9% Similarity=0.001 Sum_probs=33.9
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcC-CCeEEeCCcccccceEEEEeCCCCChHH---HHHHHHHhhhccH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQD-CELVTAGELFGRSGYAIGLQKGSPWADA---VTLAILDFHESTV 78 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~-~~l~~~~~~~~~~~~~ia~~kgs~l~~~---vn~~l~~l~~~G~ 78 (90)
.+++...+...+.+|.-=+++-. ..+......+ ..+..+...-...+++++.+++++.... +-..|.+....--
T Consensus 218 ~~~~~~~~~~~v~~g~gi~~lp~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~ 295 (305)
T PRK11233 218 EIESIATLTAAIASGMGVTVLPE-SAARSLCGAVNGWMARITTPSMSLSLSLNLSARLPLSPQAQAVKEILLSLVSSPV 295 (305)
T ss_pred EEcCHHHHHHHHHcCCeeEecch-hHhhcccccCceeEEeecCCccceEEEEEecCCCCCCHHHHHHHHHHHHHHHHHh
Confidence 35666667777777764333333 2222221111 1112222121235578888887544444 4444444433333
No 171
>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=37.33 E-value=1.5e+02 Score=21.03 Aligned_cols=22 Identities=5% Similarity=-0.200 Sum_probs=17.4
Q ss_pred cCChHHHHHHhhcCCceEEEee
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d 26 (90)
+.+....+.++++|++|+.-..
T Consensus 192 ~~~~~~~~~~~~~G~iD~~~~~ 213 (454)
T cd08496 192 IPDPTARVNALQSGQVDFAQLL 213 (454)
T ss_pred cCCHHHHHHHHhcCCCcEeccC
Confidence 4567788999999999996543
No 172
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=37.20 E-value=1.3e+02 Score=20.08 Aligned_cols=69 Identities=10% Similarity=-0.142 Sum_probs=39.9
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe--CCcccccceEEEEeCCCCChHHHHHHHHHhh
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA--GELFGRSGYAIGLQKGSPWADAVTLAILDFH 74 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~--~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~ 74 (90)
.+++...++..+..|.--+++-.... ..... ...+..+ ........+.++.+++.+....+...+..++
T Consensus 230 ~~~~~~~~~~~v~~g~g~~~lp~~~~-~~~~~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~ 300 (305)
T CHL00180 230 ELNSIEAIKNAVQSGLGAAFVSVSAI-EKELE-LGLLHWIKIENITIKRMLSIITNPNRYKSKASETFYNEIL 300 (305)
T ss_pred EeCCHHHHHHHHHcCCcEEEeEhHHH-HHHhh-cCcEEEEEcCCCCceEEEEEEEeCCCccCHHHHHHHHHHH
Confidence 46677888888888886666654322 22222 2234433 2222234677888888766666666655544
No 173
>PRK10682 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional
Probab=37.14 E-value=1.4e+02 Score=20.64 Aligned_cols=75 Identities=4% Similarity=-0.174 Sum_probs=44.6
Q ss_pred HHHHHHhhcCCceEEEeehhHHhHHH------hcCCCeEE-eCC-cccccceEEEEeCCCCChHHHHHHHHHhhhccHHH
Q psy17442 9 PSTVVRHGTKKLMAFIWDSSRLDFEA------AQDCELVT-AGE-LFGRSGYAIGLQKGSPWADAVTLAILDFHESTVCY 80 (90)
Q Consensus 9 ~~~~~~l~~G~ida~i~d~~~~~~~~------~~~~~l~~-~~~-~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G~~~ 80 (90)
.+..+.+.+|++.+.+.......... ..+.++.. .++ .......+++++|+++-.+..-+.|.-|.......
T Consensus 227 ~~~~~~l~~Gev~~~~~w~~~~~~~~~~~~~~~~~~~i~~v~P~eG~~~~~d~~~I~k~a~~~e~A~~Fi~f~lspe~qa 306 (370)
T PRK10682 227 SQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSYSIPKEGALAFFDVFAMPADAKNKDEAYQFLNYLLRPDVIA 306 (370)
T ss_pred cHHHHHHhcCCEEEEEeecHHHHHHHHHHHhcccCCceEEEECCCcchhheeeeEEECCCCCHHHHHHHHHHHhCHHHHH
Confidence 46778999999888776544332221 12345654 332 12223467899999887777777776666544444
Q ss_pred HHH
Q psy17442 81 LFM 83 (90)
Q Consensus 81 ~l~ 83 (90)
++.
T Consensus 307 ~~a 309 (370)
T PRK10682 307 HIS 309 (370)
T ss_pred HHH
Confidence 443
No 174
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=36.82 E-value=90 Score=18.32 Aligned_cols=65 Identities=9% Similarity=-0.028 Sum_probs=35.1
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe--CCcccccceEEEEeCCCCChHHHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA--GELFGRSGYAIGLQKGSPWADAVTLA 69 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~--~~~~~~~~~~ia~~kgs~l~~~vn~~ 69 (90)
+.+++...+...+.+|..-+++-.. .+..... ...+..+ .+......+.++.+++......+...
T Consensus 128 ~~~~~~~~~~~~v~~g~gia~~p~~-~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (198)
T cd08421 128 VQVSSFDAVCRMVAAGLGIGIVPES-AARRYAR-ALGLRVVPLDDAWARRRLLLCVRSFDALPPAARAL 194 (198)
T ss_pred EEECCHHHHHHHHHcCCCeEEccch-hhhhhcc-cCCeEEEeccCCcccceEEEEEeCCCcCCHHHHHH
Confidence 3467778888888888855555443 2222222 2234333 22222346778888876555544443
No 175
>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=36.67 E-value=1.2e+02 Score=21.39 Aligned_cols=20 Identities=0% Similarity=-0.164 Sum_probs=16.5
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+++...++.++.+|++|...
T Consensus 191 ~~d~~~~~~~l~~G~iD~~~ 210 (457)
T cd08516 191 YPDENTRLAALQSGDVDIIE 210 (457)
T ss_pred CCCHHHHHHHHhcCCccEec
Confidence 45678889999999999864
No 176
>KOG1284|consensus
Probab=36.54 E-value=22 Score=25.20 Aligned_cols=54 Identities=19% Similarity=0.157 Sum_probs=39.7
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
.+.+.++++..++.|++..+++|.... +..++.++...+..+..+|.+|.++-+
T Consensus 62 ~~~si~~ri~~~r~gk~~ivldd~~rd-----neg~L~~a~~~~~~~~~aF~vr~~~g~ 115 (357)
T KOG1284|consen 62 VFCSIPARIPTFRHGKFVIVLDDEDRD-----NEGDLIIAAGNVIREDMAFLVRHGSGI 115 (357)
T ss_pred ceechhhhhhcccCCcEEEEEeccccc-----CCCCcceecccccchhhhhhhhcCCce
Confidence 356788999999999987777764432 224567777777788888888888754
No 177
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=36.53 E-value=1.3e+02 Score=19.97 Aligned_cols=69 Identities=9% Similarity=-0.076 Sum_probs=39.4
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCC--cccccceEEEEeCCCCChHHHHHHHHHh
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGE--LFGRSGYAIGLQKGSPWADAVTLAILDF 73 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~--~~~~~~~~ia~~kgs~l~~~vn~~l~~l 73 (90)
+.+++...+...+..|..-+++-.. .+..... ...+..++. .....++.++.+++.++...+...+..+
T Consensus 219 ~~~~~~~~~~~~v~~g~gi~ilp~~-~~~~~~~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 289 (305)
T PRK11151 219 FRATSLETLRNMVAAGSGITLLPAL-AVPNERK-RDGVCYLPCIKPEPRRTIGLVYRPGSPLRSRYEQLAEAI 289 (305)
T ss_pred EEeccHHHHHHHHHcCCCEEEeeHH-hhhhhcc-cCCEEEEECcCCccceEEEEEEcCCCcchHHHHHHHHHH
Confidence 4567788888888888854454443 3322211 133444432 2223567888888876666666555544
No 178
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=36.09 E-value=91 Score=18.14 Aligned_cols=64 Identities=11% Similarity=-0.153 Sum_probs=34.9
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCC--cccccceEEEEeCCCCChHHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGE--LFGRSGYAIGLQKGSPWADAVTL 68 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~--~~~~~~~~ia~~kgs~l~~~vn~ 68 (90)
+.+++...++..+..|.--+++.. ..+...... ..+..+.. ......++++.+|+......+..
T Consensus 127 ~~~~~~~~~~~~v~~g~gi~~~p~-~~~~~~~~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 192 (197)
T cd08422 127 LVVNDGEALRAAALAGLGIALLPD-FLVAEDLAS-GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRA 192 (197)
T ss_pred EEEccHHHHHHHHHcCCcEEEecH-HHHhhhccC-CeEEEecCcccCCCceEEEEEcccccCCHHHHH
Confidence 356778888888999985444444 333322222 22333321 22345677888887654444443
No 179
>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=35.67 E-value=1.4e+02 Score=20.95 Aligned_cols=21 Identities=5% Similarity=-0.292 Sum_probs=17.1
Q ss_pred ccCChHHHHHHhhcCCceEEE
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i 24 (90)
.+.+....+.++++|++|.+.
T Consensus 190 ~~~~~~~~~~~l~~g~iD~~~ 210 (448)
T cd08494 190 YFSDPTALTNALLAGDIDAAP 210 (448)
T ss_pred EcCCHHHHHHHHHCCCCceec
Confidence 346677889999999999974
No 180
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=35.60 E-value=96 Score=18.26 Aligned_cols=65 Identities=12% Similarity=0.038 Sum_probs=35.2
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe--CCcccccceEEEEeCCCCChHHHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA--GELFGRSGYAIGLQKGSPWADAVTLA 69 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~--~~~~~~~~~~ia~~kgs~l~~~vn~~ 69 (90)
+.+++...++..++.|.--|++-.. .+...... ..+..+ .......++.++.+|+......+...
T Consensus 128 ~~~~~~~~~~~~v~~g~gia~~p~~-~~~~~~~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 194 (198)
T cd08433 128 VEIDSVATLKALVAAGLGYTILPAS-AVAAEVAA-GRLVAAPIVDPALTRTLSLATPRDRPLSPAALAV 194 (198)
T ss_pred EEeCcHHHHHHHHHcCCcEEEcchh-hhhhhhhc-CceEEEECCCCCcceEEEEEEcCCCCCCHHHHHH
Confidence 4567777888888888855555433 22222222 234333 22223456777788876555444443
No 181
>PRK09801 transcriptional activator TtdR; Provisional
Probab=35.58 E-value=1.4e+02 Score=20.10 Aligned_cols=71 Identities=6% Similarity=-0.158 Sum_probs=43.1
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEE-eCCcccccceEEEEeCCCCChHHHHHHHHHhhh
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVT-AGELFGRSGYAIGLQKGSPWADAVTLAILDFHE 75 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~-~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~ 75 (90)
+..++.......+.+|.--+++-... +.....+ ..+.. +.+......++++.+++..+...+...+..+.+
T Consensus 223 ~~~~~~~~i~~~v~~g~Gia~lp~~~-~~~~~~~-~~l~~~~~~~~~~~~~~lv~~~~~~~~~~~~~~i~~l~~ 294 (310)
T PRK09801 223 LSSNSGEIVLQWALEGKGIMLRSEWD-VLPFLES-GKLVQVLPEYAQSANIWAVYREPLYRSMKLRVCVEFLAA 294 (310)
T ss_pred EEECCHHHHHHHHHcCCCEEecchhh-HHHHHhC-CCeEEeCCCCCCCCcEEEEEcCCCcCCHHHHHHHHHHHH
Confidence 44677888889999998555554433 3323232 23432 222223456888999987777777776666543
No 182
>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=35.42 E-value=1.3e+02 Score=19.77 Aligned_cols=67 Identities=9% Similarity=-0.075 Sum_probs=32.7
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHh-----HHHhcCCCeEEeCCcccccceEEEEeCCCC-ChHHHHHHHHHhhhccH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLD-----FEAAQDCELVTAGELFGRSGYAIGLQKGSP-WADAVTLAILDFHESTV 78 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~-----~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~-l~~~vn~~l~~l~~~G~ 78 (90)
.++.+++++.+.+|++|..+...++-. .++... ..+-+..+|+.+.-+.. +.+.-+.+|.-++++-+
T Consensus 100 tdD~~~i~~Ml~~g~vdsAVv~~~~~~G~~fEdl~~~~-------g~~~PgsCga~v~~~~~~fi~aY~~GI~~~r~dpe 172 (201)
T PF12916_consen 100 TDDMSEIVKMLNEGEVDSAVVGSEFSKGETFEDLLGSL-------GLYAPGSCGAYVNGDPDYFISAYEEGIDLIREDPE 172 (201)
T ss_dssp ---HHHHHHHHHTT-E--EEEETTT---EEHHHHHHHT-------T------EEEEESS--HHHHHHHHHHHHHHHH-HH
T ss_pred ecCHHHHHHHHhcCceeeeeecchhccchhHHHHHhhc-------CCCCChhhhhhhcCChHHHHHHHHHHHHHHHhChh
Confidence 357788888888888887666543321 111100 01223356666665543 88888888888888754
No 183
>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=35.26 E-value=1.2e+02 Score=19.10 Aligned_cols=55 Identities=11% Similarity=-0.026 Sum_probs=36.3
Q ss_pred ccCChHHHHHHhhcCCceEEEeeh---------hHHhHHHhcCCCeEEeCCcccccceEEEEeCCC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDS---------SRLDFEAAQDCELVTAGELFGRSGYAIGLQKGS 60 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~---------~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs 60 (90)
-+++..+++.+|..|++|..+..- .++..+.. .++.++++..-+..+.+..+++.
T Consensus 28 ~~~s~~~v~~av~~~~~d~~vvPiENs~~G~V~~t~d~L~~--~~l~i~~e~~l~i~~~L~~~~~~ 91 (181)
T PF00800_consen 28 PCDSFEEVFDAVEEGEADYGVVPIENSLEGSVSETLDLLID--SDLYIVGEIVLPIHHCLLAKPGT 91 (181)
T ss_dssp EESSHHHHHHHHHCTSSSEEEEEEECTTTCECHHHHHHHHT--SSCEEEEEEEEE--EEEEECTT-
T ss_pred ecCCHHHHHHHHHcCCCceEEEeEeeecCCEeHHHHHHHhc--CCceEEEEEEeccccEEeccCCC
Confidence 367899999999999988866432 23333333 46888888766777777776664
No 184
>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
Probab=35.16 E-value=47 Score=22.99 Aligned_cols=32 Identities=16% Similarity=0.128 Sum_probs=25.9
Q ss_pred EEEEeCCC-CChHHHHHHHHHhhhccHHHHHHH
Q psy17442 53 AIGLQKGS-PWADAVTLAILDFHESTVCYLFMA 84 (90)
Q Consensus 53 ~ia~~kgs-~l~~~vn~~l~~l~~~G~~~~l~~ 84 (90)
.|.+..+. .|.+.|+..+..|.+.|.++|...
T Consensus 192 ~~~l~~dr~~L~~rI~~Rv~~Ml~~Gl~eEv~~ 224 (307)
T PRK00091 192 IIGLDPDREELYERINQRVDQMLEQGLLEEVRA 224 (307)
T ss_pred EEEEcCCHHHHHHHHHHHHHHHHHCcHHHHHHH
Confidence 45565553 499999999999999999998764
No 185
>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=34.95 E-value=1.5e+02 Score=20.18 Aligned_cols=71 Identities=13% Similarity=0.018 Sum_probs=36.8
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCC-CC-hHHHHHHHHHhhh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGS-PW-ADAVTLAILDFHE 75 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs-~l-~~~vn~~l~~l~~ 75 (90)
+.+....+.+|.+|++|.+..-.+.....+.......+.........+.+.+.-.+ ++ -..+-++|.....
T Consensus 157 ~~~~~~~~~al~~G~iD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~fN~~~~~~~d~~vR~Al~~aid 229 (374)
T PF00496_consen 157 IPDADSAVAALQSGEIDDIAEVPPSDIDQLKSDPNLSVYYSYPSPGYYYLAFNTNNPPFSDKAVRQALAYAID 229 (374)
T ss_dssp ESSHHHHHHHHHTTSSSEEESSSGGTHHHHHHHTTEEEEEEEEEEEEEEEEE-TTSTTTTSHHHHHHHHHHS-
T ss_pred cccchhhhhcccceeeeeeecccccccccccccCccccccccccccceeeeccccccccchhhhHHHHHhhhh
Confidence 45788999999999997774333333333333333333111223445567776653 33 2444455544433
No 186
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=34.88 E-value=96 Score=18.09 Aligned_cols=61 Identities=8% Similarity=0.011 Sum_probs=33.7
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe--CCcccccceEEEEeCCCCChHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA--GELFGRSGYAIGLQKGSPWADAV 66 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~--~~~~~~~~~~ia~~kgs~l~~~v 66 (90)
+.+++...++..+.+|.--+++-+. .+. .. ....+..+ ........++++.+++......+
T Consensus 126 ~~~~~~~~~~~~v~~g~gia~~p~~-~~~-~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 188 (195)
T cd08427 126 MELDSLEAIAAMVAQGLGVAIVPDI-AVP-LP-AGPRVRVLPLGDPAFSRRVGLLWRRSSPRSRLI 188 (195)
T ss_pred EEeccHHHHHHHHHhCCcEEEccHH-HHh-hh-ccCceEEEECCCCCceEEEEEEEeCCccCCHHH
Confidence 3567788888899999855555443 333 22 22234333 22223356777777775544333
No 187
>PF13416 SBP_bac_8: Bacterial extracellular solute-binding protein; PDB: 2FNC_A 1ELJ_A 3TTM_B 3TTK_C 2W7Y_A 3RPW_A 2GHB_C 2GHA_A 1POY_3 1POT_A ....
Probab=34.85 E-value=1.3e+02 Score=19.44 Aligned_cols=72 Identities=11% Similarity=-0.056 Sum_probs=46.8
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe-C-CcccccceEEEEeCCCCChHH--HHHHHHHhhhcc
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA-G-ELFGRSGYAIGLQKGSPWADA--VTLAILDFHEST 77 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~-~-~~~~~~~~~ia~~kgs~l~~~--vn~~l~~l~~~G 77 (90)
.+..+....+.+|++...+.....+..+.+...++.++ . ......+.+++++++++-.+. .-..|.-|...-
T Consensus 174 ~~~~~~~~~f~~G~~~~~~~~~~~~~~~~~~~~~~~~~~P~~g~~~~~~~~~i~~~~~~~~~~aA~~fl~~l~s~e 249 (281)
T PF13416_consen 174 GSGDDARQLFASGKVAMIIGGSWSISNLQKAGPDFGVAPPKDGTFVGGNGFAIPKNSKNPEAEAAWEFLKFLTSPE 249 (281)
T ss_dssp TSHHHHHHHHHTTSESEEEEEGHHHHHHHHTTTTEEEEECTTTEEEEEEEEEEBTTSSTHHHHHHHHHHHHHTSHH
T ss_pred cchhHHHHHhcCCCeeeecccHhHHHHHHHhCCCeeEecCccccccCcceEEEeCCCChHHHHHHHHHHHHHcCHH
Confidence 45578899999999888887766666555555556555 1 111223346889999876665 666666665433
No 188
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari
Probab=34.45 E-value=50 Score=19.45 Aligned_cols=22 Identities=9% Similarity=-0.014 Sum_probs=17.6
Q ss_pred CChHHHHHHhhcCCceEEEeeh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~ 27 (90)
.+..+....|.+|++|..+...
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~ 57 (185)
T cd08439 36 KRTPRLMEMLERGEVDLALITH 57 (185)
T ss_pred CChHHHHHHHHCCCCcEEEEec
Confidence 3456788999999999988753
No 189
>PF02504 FA_synthesis: Fatty acid synthesis protein; InterPro: IPR003664 The plsX gene is part of the bacterial fab gene cluster which encodes several key fatty acid biosynthetic enzymes []. The plsX gene encodes a poorly understood enzyme of phospholipid metabolism [].; GO: 0003824 catalytic activity, 0006633 fatty acid biosynthetic process; PDB: 1VI1_B 1U7N_B.
Probab=33.96 E-value=49 Score=23.20 Aligned_cols=30 Identities=13% Similarity=-0.062 Sum_probs=23.5
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAA 35 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~ 35 (90)
.|...++..++.|++||++.-..+......
T Consensus 81 SSm~~a~~lvk~g~ada~vSaGnTGA~~a~ 110 (323)
T PF02504_consen 81 SSMVVALELVKEGEADAFVSAGNTGALMAA 110 (323)
T ss_dssp CHHHHHHHHHHTTS-SEEEESS-HHHHHHH
T ss_pred CcHHHHHHHhhcCCceEEEecCchHHHHHH
Confidence 567889999999999999999887766654
No 190
>PLN02165 adenylate isopentenyltransferase
Probab=33.72 E-value=56 Score=23.06 Aligned_cols=34 Identities=6% Similarity=-0.059 Sum_probs=27.2
Q ss_pred EEEEeCCC-CChHHHHHHHHHhhhccHHHHHHHHh
Q psy17442 53 AIGLQKGS-PWADAVTLAILDFHESTVCYLFMAKV 86 (90)
Q Consensus 53 ~ia~~kgs-~l~~~vn~~l~~l~~~G~~~~l~~kW 86 (90)
-+.+.... .|.+.|+..+..|.+.|.++|...-+
T Consensus 178 ~i~l~~dr~~L~~RI~~Rvd~Ml~~GlldEv~~L~ 212 (334)
T PLN02165 178 FIWVDVSEPVLFEYLSKRVDEMMDSGMFEELAEFY 212 (334)
T ss_pred EEEECCCHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Confidence 45565553 49999999999999999999987543
No 191
>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional
Probab=33.66 E-value=51 Score=22.81 Aligned_cols=32 Identities=13% Similarity=0.182 Sum_probs=26.0
Q ss_pred EEEEeCC-CCChHHHHHHHHHhhhccHHHHHHH
Q psy17442 53 AIGLQKG-SPWADAVTLAILDFHESTVCYLFMA 84 (90)
Q Consensus 53 ~ia~~kg-s~l~~~vn~~l~~l~~~G~~~~l~~ 84 (90)
-|++..+ ..|.+.||..+..|.+.|.++|...
T Consensus 190 ~i~l~~~r~~L~~rI~~Rv~~Ml~~GlieEv~~ 222 (300)
T PRK14729 190 AIGLKRPMEEMKSRIISRVNNMIDCGLLSEIKS 222 (300)
T ss_pred EEEeCCCHHHHHHHHHHHHHHHHHCCHHHHHHH
Confidence 4556544 3499999999999999999998764
No 192
>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=33.34 E-value=1.8e+02 Score=20.74 Aligned_cols=20 Identities=15% Similarity=-0.117 Sum_probs=16.2
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+....+.++.+|++|++.
T Consensus 194 ~~d~~~~~~~l~~G~iD~~~ 213 (474)
T cd08499 194 VPEDGTRVAMLETGEADIAY 213 (474)
T ss_pred cCCHHHHHHHHHcCCCCeec
Confidence 45667788999999999863
No 193
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=32.92 E-value=41 Score=18.58 Aligned_cols=17 Identities=29% Similarity=0.149 Sum_probs=14.4
Q ss_pred ChHHHHHHHHHhhhccH
Q psy17442 62 WADAVTLAILDFHESTV 78 (90)
Q Consensus 62 l~~~vn~~l~~l~~~G~ 78 (90)
-+..|++.|+.|++.|.
T Consensus 32 SRtaVwK~Iq~Lr~~G~ 48 (79)
T COG1654 32 SRTAVWKHIQQLREEGV 48 (79)
T ss_pred cHHHHHHHHHHHHHhCC
Confidence 36889999999999884
No 194
>PF02142 MGS: MGS-like domain This is a subfamily of this family; InterPro: IPR011607 This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. The known structures in this domain show a common phosphate binding site []. ; PDB: 4A1O_A 3ZZM_A 1ZCZ_A 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A ....
Probab=32.85 E-value=53 Score=18.20 Aligned_cols=21 Identities=10% Similarity=-0.091 Sum_probs=15.7
Q ss_pred HHHHHhhcCCceEEEeehhHH
Q psy17442 10 STVVRHGTKKLMAFIWDSSRL 30 (90)
Q Consensus 10 ~~~~~l~~G~ida~i~d~~~~ 30 (90)
+.+..+++|++|.+|.-....
T Consensus 51 ~i~~~i~~~~IdlVIn~~~~~ 71 (95)
T PF02142_consen 51 QIMDLIKNGKIDLVINTPYPF 71 (95)
T ss_dssp HHHHHHHTTSEEEEEEE--TH
T ss_pred HHHHHHHcCCeEEEEEeCCCC
Confidence 488999999999998765433
No 195
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=32.38 E-value=50 Score=20.17 Aligned_cols=20 Identities=10% Similarity=-0.100 Sum_probs=16.4
Q ss_pred ChHHHHHHhhcCCceEEEee
Q psy17442 7 FSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d 26 (90)
+.++.+..+++|+++++|.-
T Consensus 63 g~~~i~~~I~~g~i~lVInt 82 (142)
T PRK05234 63 GDQQIGALIAEGKIDMLIFF 82 (142)
T ss_pred CchhHHHHHHcCceeEEEEe
Confidence 34778899999999998874
No 196
>PRK05773 3,4-dihydroxy-2-butanone 4-phosphate synthase; Validated
Probab=32.31 E-value=59 Score=21.57 Aligned_cols=19 Identities=11% Similarity=-0.054 Sum_probs=14.8
Q ss_pred ChHHHHHHhhcCCceEEEee
Q psy17442 7 FSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d 26 (90)
+..+++.+|++|+ -.+++|
T Consensus 2 ~ie~ai~al~~G~-~Viv~D 20 (219)
T PRK05773 2 DFEEARKALESGI-PVLIYD 20 (219)
T ss_pred CHHHHHHHHHCCC-eEEEEE
Confidence 5789999999999 455554
No 197
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=31.87 E-value=57 Score=19.33 Aligned_cols=51 Identities=14% Similarity=0.081 Sum_probs=29.2
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCC
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPW 62 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l 62 (90)
.+..+....|.+|++|..+...+.. ....++.. ..+..+.+.++.+++.|+
T Consensus 36 ~~~~~~~~~l~~g~~Dl~i~~~~~~----~~~~~l~~--~~l~~~~~~~~~~~~hpl 86 (198)
T cd08437 36 GGSAELLEQLLQGDLDIALLGSLTP----LENSALHS--KIIKTQHFMIIVSKDHPL 86 (198)
T ss_pred cCHHHHHHHHHcCCCCEEEecCCCC----CCcccceE--EEeecceEEEEecCCCcc
Confidence 3567889999999999988643210 00111211 233455566666666554
No 198
>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=31.80 E-value=1.6e+02 Score=21.33 Aligned_cols=20 Identities=0% Similarity=0.027 Sum_probs=16.6
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+...+..+|.+|++|...
T Consensus 201 ~~~~~~~~~al~~G~iD~~~ 220 (500)
T TIGR02294 201 IPDAETRALAFESGEVDLIF 220 (500)
T ss_pred cCCHHHHHHHHHcCCccEec
Confidence 45667889999999999974
No 199
>PRK13895 conjugal transfer protein TraM; Provisional
Probab=31.64 E-value=72 Score=19.81 Aligned_cols=37 Identities=5% Similarity=0.044 Sum_probs=24.9
Q ss_pred ceEEEEeCCCC--ChHHHHHHHHHhhhc----------cHHHHHHHHhc
Q psy17442 51 GYAIGLQKGSP--WADAVTLAILDFHES----------TVCYLFMAKVH 87 (90)
Q Consensus 51 ~~~ia~~kgs~--l~~~vn~~l~~l~~~----------G~~~~l~~kW~ 87 (90)
..||++.+++| ....+|..|.+=.+. .+++.+..+|-
T Consensus 15 KHGIal~rDDPILilqTiNerLlees~kAQq~mL~~FkeelE~iasrW~ 63 (144)
T PRK13895 15 KHGIAVGRDDPILILQTINDRLMQDSAKAQQEMLDQFKEELESIASRWG 63 (144)
T ss_pred HcCcccCCCCCchhHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47899999999 468888877542221 25666666664
No 200
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=31.50 E-value=1.5e+02 Score=19.36 Aligned_cols=70 Identities=11% Similarity=-0.053 Sum_probs=37.2
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcc-cccceEEEEeCCCCChHHHHHHHHHh
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELF-GRSGYAIGLQKGSPWADAVTLAILDF 73 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~-~~~~~~ia~~kgs~l~~~vn~~l~~l 73 (90)
+.+++...+...+..|.--+++.. ...........-...+.+.. ....+.++.+|++.....+...+..+
T Consensus 218 ~~~~~~~~~~~~v~~g~gi~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~ 288 (291)
T TIGR03418 218 LTFNNYTLVIQAAIGGQGVALGWA-PLVDELLEAGQLVRLIDEPVVTERGYYLVRPPRKRRGPAVRRFRDWL 288 (291)
T ss_pred eeeccHHHHHHHHHhCCceEEech-HhhHHHHhCCcccccCCcccCCCCcEEEEeCchhhcChHHHHHHHHH
Confidence 346778888888888875555543 33333333222112222222 23567888888765544455444433
No 201
>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]
Probab=31.46 E-value=91 Score=16.77 Aligned_cols=36 Identities=6% Similarity=0.090 Sum_probs=26.8
Q ss_pred EEEeCCCCChHHHHHHHHHhhhccHHHHHHHHhccC
Q psy17442 54 IGLQKGSPWADAVTLAILDFHESTVCYLFMAKVHLN 89 (90)
Q Consensus 54 ia~~kgs~l~~~vn~~l~~l~~~G~~~~l~~kW~~~ 89 (90)
|.+..|+|+-..+-..=..+.+.|.+.+....-|.+
T Consensus 4 v~V~ene~~d~ALrrFKr~~~k~gil~e~k~r~~yE 39 (67)
T COG0828 4 VKVRENEPLDKALRRFKRKVEKEGILREMKEREFYE 39 (67)
T ss_pred eeecCCChHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 567777777666666667778889999988776654
No 202
>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=31.44 E-value=1.5e+02 Score=21.19 Aligned_cols=21 Identities=10% Similarity=-0.108 Sum_probs=16.6
Q ss_pred cCChHHHHHHhhcCCceEEEe
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIW 25 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~ 25 (90)
+.+....+.+|++|++|++..
T Consensus 195 ~~d~~~~~~al~~G~vD~~~~ 215 (469)
T cd08519 195 YSDSSNLFLALQTGEIDVAYR 215 (469)
T ss_pred cCChHHHHHHHHCCCcceecC
Confidence 345667889999999999853
No 203
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=31.01 E-value=1.7e+02 Score=19.66 Aligned_cols=68 Identities=22% Similarity=0.176 Sum_probs=38.0
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeC--CcccccceEEEEeCCCCChHHHHHHHHHh
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAG--ELFGRSGYAIGLQKGSPWADAVTLAILDF 73 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~--~~~~~~~~~ia~~kgs~l~~~vn~~l~~l 73 (90)
+..++.......+..|.--+++.. .....+. ...+..+. .......+.++.+++.++...+...+..+
T Consensus 222 ~~~~~~~~~~~~v~~g~Gv~~lp~-~~~~~~~--~~~l~~~~i~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l 291 (313)
T PRK12684 222 LEAIDADVIKTYVELGLGVGIVAD-MAFDPER--DRNLRAIDAGHLFGSSTTRLGLRRGAYLRGYVYTFIELF 291 (313)
T ss_pred EEeCCHHHHHHHHHhCCceEEeeh-hhccccc--cCCeEEEECCCCCcceeEEEEEECCCcCCHHHHHHHHHH
Confidence 345677778888888875455543 3332221 22454442 22233467899999876655555544433
No 204
>COG1663 LpxK Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]
Probab=31.01 E-value=78 Score=22.45 Aligned_cols=59 Identities=14% Similarity=0.092 Sum_probs=40.4
Q ss_pred CChHHHHHHhhc--CCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCChHHH
Q psy17442 6 KFSPSTVVRHGT--KKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAV 66 (90)
Q Consensus 6 ~~~~~~~~~l~~--G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~~~v 66 (90)
.+..++...|.. ..+|.+|.|...-.+.+..+-++.++... ...+-|+.+|.| ||++.+
T Consensus 126 ~~R~~~~~~l~~~~~~~diIi~DDG~Qh~rL~rD~eIvvvd~~-r~fGng~~lPaG-pLRep~ 186 (336)
T COG1663 126 PDRKDAAKALLAAHLGCDIIVLDDGLQHYRLHRDFEIVVVDGQ-RGFGNGFLLPAG-PLREPP 186 (336)
T ss_pred hhHHHHHHHHHhhCCCCCEEEEcCcchhhHhhcceeEEEEecc-ccCCCcccccCC-cccCCh
Confidence 355677777777 56899999998888877777666666432 234556788887 444444
No 205
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=30.98 E-value=1.1e+02 Score=19.76 Aligned_cols=25 Identities=12% Similarity=-0.098 Sum_probs=18.5
Q ss_pred cCChHHHHHHhhcCCceEEEeehhH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSR 29 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~ 29 (90)
.........++.+|++|..|...+.
T Consensus 125 ~~~~~~~~~~l~~~~~D~~i~~~~~ 149 (297)
T COG0583 125 LGTSDRLLEDLVEGELDLAIRAGPP 149 (297)
T ss_pred eCchHHHHHHHHcCCCCEEEecCCC
Confidence 3344556888889999999887654
No 206
>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=30.78 E-value=1.8e+02 Score=20.71 Aligned_cols=20 Identities=5% Similarity=-0.139 Sum_probs=16.8
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+....+.+|++|++|...
T Consensus 198 ~~d~~~~~~~l~~G~vD~~~ 217 (482)
T cd08513 198 VPDTDAARAALRSGEIDLAW 217 (482)
T ss_pred eCCHHHHHHHHhCCCCCEec
Confidence 45678899999999999864
No 207
>TIGR00975 3a0107s03 phosphate ABC transporter, phosphate-binding protein. This family represents one type of (periplasmic, in Gram-negative bacteria) phosphate-binding protein found in phosphate ABC (ATP-binding cassette) transporters. This protein is accompanied, generally in the same operon, by an ATP binding protein and (usually) two permease proteins.
Probab=30.55 E-value=75 Score=21.81 Aligned_cols=52 Identities=8% Similarity=-0.129 Sum_probs=34.5
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHHHhcCC-CeEEeCCcccccceEEEEeC
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDC-ELVTAGELFGRSGYAIGLQK 58 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~-~l~~~~~~~~~~~~~ia~~k 58 (90)
-.+...++.+|.+|.+|....+++.-....++.+ .+.-+ ++...+.++++.+
T Consensus 33 ~~GSg~Gi~~l~~g~~dia~ssr~l~~~E~~~~~~~~~~~--pva~dai~vivn~ 85 (314)
T TIGR00975 33 GIGSGAGIAQFAAGTVDFGASDAPLSEADLASRGSGLLQF--PTVIGAIVVTYNL 85 (314)
T ss_pred cCCCHHHHHHHHcCCCCEEecCCCCCHHHHHhhcCCcEEe--eEEeeeEEEEEeC
Confidence 3467889999999999999999887655443321 22222 2445566777764
No 208
>cd08520 PBP2_NikA_DppA_OppA_like_21 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=30.51 E-value=93 Score=22.18 Aligned_cols=62 Identities=13% Similarity=0.095 Sum_probs=31.9
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCC-C-----ChHHHHHHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGS-P-----WADAVTLAI 70 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs-~-----l~~~vn~~l 70 (90)
..++.+.+|++|++|..-.....+.. .+....+.+... .....+.+++...+ | +|+.|+.+|
T Consensus 197 ~~~d~~~~l~~G~iD~~~~~~~~~~~-~~~~~~~~~~~~-~~~~~~~l~~N~~~~~~~d~~vR~Al~~ai 264 (468)
T cd08520 197 PVSDALLALENGEVDAISILPDTLAA-LENNKGFKVIEG-PGFWVYRLMFNHDKNPFSDKEFRQAIAYAI 264 (468)
T ss_pred EChhHHHHHHCCCcccccCCHHHHHH-hhcCCCeEEEec-CCcceEEEEecCCCCcccCHHHHHHHHHhc
Confidence 34458899999999986322222221 223345555421 12233456665432 2 455665555
No 209
>TIGR02863 spore_sspJ small, acid-soluble spore protein, SspJ family. RL J Bacteriol. 1998 Dec;180(24):6704-12.
Probab=30.41 E-value=26 Score=17.16 Aligned_cols=11 Identities=36% Similarity=0.528 Sum_probs=8.4
Q ss_pred CCCCChHHHHH
Q psy17442 58 KGSPWADAVTL 68 (90)
Q Consensus 58 kgs~l~~~vn~ 68 (90)
||+||.+.|++
T Consensus 32 k~DPLQEAV~K 42 (47)
T TIGR02863 32 KDDPLQEAVNK 42 (47)
T ss_pred cCChHHHHHHH
Confidence 57888888775
No 210
>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=30.35 E-value=1.7e+02 Score=20.90 Aligned_cols=20 Identities=5% Similarity=0.001 Sum_probs=16.6
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+....+.+|++|++|..-
T Consensus 199 ~~d~~~~~~al~~G~vD~~~ 218 (483)
T cd08514 199 IPDPTTALLELKAGELDIVE 218 (483)
T ss_pred ecCHHHHHHHHhCCCcceec
Confidence 45677899999999999863
No 211
>PRK12485 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional
Probab=30.31 E-value=69 Score=22.96 Aligned_cols=22 Identities=5% Similarity=-0.019 Sum_probs=17.0
Q ss_pred ccCChHHHHHHhhcCCceEEEe
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIW 25 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~ 25 (90)
.+++.++++.+|++|+.-.++.
T Consensus 2 ~~~~i~~ai~~l~~G~~viv~D 23 (369)
T PRK12485 2 AFNTIEEIIEDYRQGKMVLLVD 23 (369)
T ss_pred CcccHHHHHHHHHCCCeEEEEe
Confidence 4678999999999999444443
No 212
>PF02256 Fe_hyd_SSU: Iron hydrogenase small subunit; InterPro: IPR003149 Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production. Fe only hydrogenases (1.12.7.2 from EC) show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters []. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein. The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold [].; PDB: 3LX4_A 1C4C_A 1FEH_A 3C8Y_A 1C4A_A 1HFE_S 1GX7_D 1E08_D.
Probab=30.18 E-value=51 Score=17.02 Aligned_cols=18 Identities=11% Similarity=-0.022 Sum_probs=13.0
Q ss_pred HhhhccHHHHHHHHhccC
Q psy17442 72 DFHESTVCYLFMAKVHLN 89 (90)
Q Consensus 72 ~l~~~G~~~~l~~kW~~~ 89 (90)
.-.++-.+.+|++.|+..
T Consensus 25 ~s~eNp~v~~lY~~~lg~ 42 (60)
T PF02256_consen 25 KSHENPEVQELYKEFLGG 42 (60)
T ss_dssp SGGG-HHHHHHHHHTTSS
T ss_pred CCCcCHHHHHHHHHHhCC
Confidence 345677888999999875
No 213
>PF13730 HTH_36: Helix-turn-helix domain
Probab=30.04 E-value=37 Score=16.56 Aligned_cols=16 Identities=25% Similarity=0.308 Sum_probs=13.7
Q ss_pred hHHHHHHHHHhhhccH
Q psy17442 63 ADAVTLAILDFHESTV 78 (90)
Q Consensus 63 ~~~vn~~l~~l~~~G~ 78 (90)
++.|.++|.+|.+.|.
T Consensus 39 ~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 39 RRTVQRAIKELEEKGL 54 (55)
T ss_pred HHHHHHHHHHHHHCcC
Confidence 6889999999998885
No 214
>PRK13845 putative glycerol-3-phosphate acyltransferase PlsX; Provisional
Probab=29.81 E-value=73 Score=23.45 Aligned_cols=29 Identities=10% Similarity=-0.141 Sum_probs=23.4
Q ss_pred CChHHHHHHhhcCCceEEEeehhHHhHHH
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRLDFEA 34 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~~~~~ 34 (90)
.|..-|+..|++|++||++....+.....
T Consensus 181 SSm~vA~~LVk~G~ADA~VSAGNTGAlmA 209 (437)
T PRK13845 181 ASINVAMDLVKKGKALAVYSAGNSGAMMA 209 (437)
T ss_pred CHHHHHHHHHHcCCCCEEEeCchHHHHHH
Confidence 45678999999999999999877665544
No 215
>PRK15109 antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
Probab=29.73 E-value=1.5e+02 Score=21.96 Aligned_cols=19 Identities=5% Similarity=-0.178 Sum_probs=15.5
Q ss_pred cCChHHHHHHhhcCCceEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAF 23 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~ 23 (90)
+.+....+.++++|++|++
T Consensus 252 ~~d~~~~~~al~~GeiD~~ 270 (547)
T PRK15109 252 GSGGTGRLSKLLTGECDVL 270 (547)
T ss_pred cCCHHHHHHHHHCCCCCee
Confidence 4566778899999999975
No 216
>TIGR00182 plsX fatty acid/phospholipid synthesis protein PlsX. This protein of fatty acid/phospholipid biosynthesis, called PlsX after the member in Streptococcus pneumoniae, is proposed to be a phosphate acyltransferase that partners with PlsY (TIGR00023) in a two-step 1-acylglycerol-3-phosphate biosynthesis pathway alternative to the one-step PlsB (EC 2.3.1.15) pathway.
Probab=29.61 E-value=77 Score=22.17 Aligned_cols=27 Identities=7% Similarity=-0.185 Sum_probs=20.7
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFE 33 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~ 33 (90)
+..-|+..|++|++|+++....+..+.
T Consensus 71 s~~~A~~lVk~G~ADa~VSgg~Tga~m 97 (322)
T TIGR00182 71 SMQLAMNLVKEGRADAVISAGNSGALM 97 (322)
T ss_pred HHHHHHHHHHCCCCCEEEeCCcHHHHH
Confidence 456788999999999999765555443
No 217
>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=29.36 E-value=2.1e+02 Score=20.32 Aligned_cols=21 Identities=5% Similarity=0.058 Sum_probs=17.0
Q ss_pred cCChHHHHHHhhcCCceEEEe
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIW 25 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~ 25 (90)
+.+....+.+|++|++|.+..
T Consensus 198 ~~d~~~~~~al~~G~vD~~~~ 218 (480)
T cd08517 198 IPDAAARAAAFETGEVDVLPF 218 (480)
T ss_pred cCCHHHHHHHHHcCCcceecC
Confidence 456778899999999998643
No 218
>PLN02317 arogenate dehydratase
Probab=29.32 E-value=1.9e+02 Score=20.97 Aligned_cols=55 Identities=9% Similarity=-0.128 Sum_probs=37.3
Q ss_pred ccCChHHHHHHhhcCCceEEEeehh---------HHhHHHhcCCCeEEeCCcccccceEEEEeCCC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSS---------RLDFEAAQDCELVTAGELFGRSGYAIGLQKGS 60 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~---------~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs 60 (90)
-.+++.+++.+|..|.+|..+..-. +++ ++. ..++.++++..-+-.+.+...+|.
T Consensus 122 p~~sf~~vf~AVe~g~ad~gVvPIENS~~GsV~~t~D-lL~-~~~l~IvgEv~l~I~h~Ll~~~g~ 185 (382)
T PLN02317 122 PCEQFEAAFQAVELWLADRAVLPIENSLGGSIHRNYD-LLL-RHRLHIVGEVQLPVHHCLLALPGV 185 (382)
T ss_pred ecCCHHHHHHHHHCCCCCEEEEEEeccCccchHHHHH-HHh-cCCCEEEEEEEEEeeeEEecCCCC
Confidence 3678999999999999887664321 112 111 245788888776777776666664
No 219
>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=29.21 E-value=1.8e+02 Score=21.14 Aligned_cols=20 Identities=10% Similarity=-0.117 Sum_probs=15.9
Q ss_pred hHHHHHHhhcCCceEEEeeh
Q psy17442 8 SPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 8 ~~~~~~~l~~G~ida~i~d~ 27 (90)
....+.++++|++|++....
T Consensus 223 ~~~~~~al~~GeiD~~~~~~ 242 (516)
T cd08510 223 PSTIVAALKSGKYDIAESPP 242 (516)
T ss_pred hHHHHHHHHCCCcceecCCC
Confidence 46678999999999986543
No 220
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=28.61 E-value=1.3e+02 Score=17.51 Aligned_cols=63 Identities=8% Similarity=-0.078 Sum_probs=34.3
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCc--ccccceEEEEeCCCCChHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGEL--FGRSGYAIGLQKGSPWADAVT 67 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~--~~~~~~~ia~~kgs~l~~~vn 67 (90)
+.+++...+...+.+|..-+++-+. .+..... ...+..+... .....++++.+++......+.
T Consensus 131 ~~~~~~~~~~~~v~~g~gi~~~p~~-~~~~~~~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 195 (201)
T cd08420 131 MELGSTEAIKEAVEAGLGISILSRL-AVRKELE-LGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAE 195 (201)
T ss_pred EEECCHHHHHHHHHcCCCEEEeeHH-HHHhhhc-CCceEEEECCCCcceEEEEEEEecCCcCCHHHH
Confidence 3467888888888898855555543 3332222 2345444222 223456777777654333333
No 221
>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=28.47 E-value=1.7e+02 Score=20.99 Aligned_cols=20 Identities=5% Similarity=-0.097 Sum_probs=16.3
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+....+.++++|++|++.
T Consensus 207 ~~d~~~~~~~l~~G~iD~~~ 226 (482)
T cd08495 207 MPDANARLAALLSGQVDAIE 226 (482)
T ss_pred cCCHHHHHHHHHcCCCceec
Confidence 45667889999999999864
No 222
>PF04198 Sugar-bind: Putative sugar-binding domain; InterPro: IPR007324 This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. One of these proteins, Q8U7I7 from SWISSPROT, has an N-terminal helix-turn-helix IPR000792 from INTERPRO that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates.; GO: 0030246 carbohydrate binding; PDB: 3KV1_A 3EFB_C 2W48_A 3BXH_A 3BXE_A 2OKG_A 3BXF_A 3BXG_A 2R5F_A 2O0M_A ....
Probab=28.23 E-value=1.1e+02 Score=20.39 Aligned_cols=28 Identities=11% Similarity=-0.066 Sum_probs=22.8
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFEA 34 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~~ 34 (90)
..+....+|+.|-++..|.|..++...+
T Consensus 227 K~~aI~aALr~g~i~~LItDe~tA~~lL 254 (255)
T PF04198_consen 227 KAEAILAALRGGYINVLITDESTARALL 254 (255)
T ss_dssp GHHHHHHHHHTTSTSEEEEEHHHHHHHH
T ss_pred hHHHHHHHHhcCCCCEEEECHHHHHHHh
Confidence 3455677888999999999999988765
No 223
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=28.08 E-value=2e+02 Score=20.66 Aligned_cols=56 Identities=11% Similarity=-0.073 Sum_probs=34.0
Q ss_pred cCChHHHHHHhhcCCceEEEeeh------hHHhHH-HhcCCCeEEeCCcccccceEEEEeCCC
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDS------SRLDFE-AAQDCELVTAGELFGRSGYAIGLQKGS 60 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~------~~~~~~-~~~~~~l~~~~~~~~~~~~~ia~~kgs 60 (90)
+++..+++.+|.+|++|..+..- ++...+ +-...++.++++..-+..+.+...+|.
T Consensus 136 ~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~DlL~~~~l~I~~E~~l~I~h~Ll~~~~~ 198 (386)
T PRK10622 136 CAKFADIFNQVETGQADYAVLPIENTSSGAINDVYDLLQHTSLSIVGEMTLPIDHCVLVSGTT 198 (386)
T ss_pred CCCHHHHHHHHHCCCCCEEEEEEecCCceehHHHHHHHhcCCCEEEEEEEEEEEEEEecCCCC
Confidence 67899999999999998876543 111111 111235777777655555555444443
No 224
>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=28.06 E-value=1.9e+02 Score=20.52 Aligned_cols=20 Identities=5% Similarity=-0.052 Sum_probs=16.4
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+....+.++.+|++|..-
T Consensus 195 ~~~~~~~~~al~~G~id~~~ 214 (467)
T cd08511 195 IPDATVRLANLRSGDLDIIE 214 (467)
T ss_pred CCCHHHHHHHHHcCCccEec
Confidence 45667789999999999864
No 225
>cd08477 PBP2_CrgA_like_8 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=27.75 E-value=1.3e+02 Score=17.52 Aligned_cols=63 Identities=10% Similarity=-0.127 Sum_probs=35.7
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe-C-CcccccceEEEEeCCCCChHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA-G-ELFGRSGYAIGLQKGSPWADAVT 67 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~-~-~~~~~~~~~ia~~kgs~l~~~vn 67 (90)
+.+++...++..+..|.--+++-+...... ... ..+..+ . .......+.++.+++......+.
T Consensus 127 ~~~~~~~~~~~~v~~g~Gia~~p~~~~~~~-~~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 191 (197)
T cd08477 127 LTVNSGQALRVAALAGLGIVLQPEALLAED-LAS-GRLVELLPDYLPPPRPMHLLYPPDRRPTPKLR 191 (197)
T ss_pred EEEcCHHHHHHHHHcCCceEechHHHHHHH-HHc-CCcEEeCCcccCCCCcEEEEecCCccccHHHH
Confidence 456788888899999986666655443322 222 233322 1 11224567788888765444333
No 226
>KOG1348|consensus
Probab=27.60 E-value=47 Score=24.13 Aligned_cols=29 Identities=14% Similarity=0.320 Sum_probs=23.8
Q ss_pred EEEeCCCC-ChHHHHHHHHHhhhccHHHHH
Q psy17442 54 IGLQKGSP-WADAVTLAILDFHESTVCYLF 82 (90)
Q Consensus 54 ia~~kgs~-l~~~vn~~l~~l~~~G~~~~l 82 (90)
+++|-+.. ..+.+|..|.++.++|+|.++
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 56666443 789999999999999999865
No 227
>KOG0024|consensus
Probab=27.38 E-value=47 Score=23.63 Aligned_cols=21 Identities=14% Similarity=0.121 Sum_probs=17.8
Q ss_pred ccccCChHHHHHHhhcCCceE
Q psy17442 2 RFDVKFSPSTVVRHGTKKLMA 22 (90)
Q Consensus 2 ~~~~~~~~~~~~~l~~G~ida 22 (90)
||-...++++++.+.+|++|.
T Consensus 298 ry~~~~y~~ai~li~sGki~~ 318 (354)
T KOG0024|consen 298 RYCNGDYPTAIELVSSGKIDV 318 (354)
T ss_pred eeccccHHHHHHHHHcCCcCc
Confidence 556668999999999999886
No 228
>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=27.01 E-value=1.2e+02 Score=19.99 Aligned_cols=27 Identities=7% Similarity=-0.069 Sum_probs=21.8
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRL 30 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~ 30 (90)
.++..++.+..|++|.+++.+.-.|..
T Consensus 217 g~d~~~~~~~~l~~g~i~~~~~q~p~~ 243 (302)
T TIGR02637 217 GLGLPSEMAKYVKNGTVKAFALWNPID 243 (302)
T ss_pred EcCCcHHHHHHHhcCccceEEEeCHHH
Confidence 456678899999999999988777743
No 229
>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=26.81 E-value=2.1e+02 Score=20.50 Aligned_cols=20 Identities=0% Similarity=0.016 Sum_probs=16.5
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+....+.++.+|++|++.
T Consensus 194 ~~~~~~~~~al~~G~iD~~~ 213 (488)
T cd08489 194 IPDAQTRLLALQSGEIDLIY 213 (488)
T ss_pred cCCHHHHHHHHHcCCccEec
Confidence 45667889999999999865
No 230
>cd08473 PBP2_CrgA_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=25.88 E-value=1.5e+02 Score=17.38 Aligned_cols=65 Identities=11% Similarity=-0.188 Sum_probs=35.3
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCC--cccccceEEEEeCCCCChHHHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGE--LFGRSGYAIGLQKGSPWADAVTLA 69 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~--~~~~~~~~ia~~kgs~l~~~vn~~ 69 (90)
+.+++...++..+.+|.--+++-... +...... ..+..+.. ......+.++.+++..+...+...
T Consensus 132 ~~~~~~~~~~~~v~~g~gi~~~p~~~-~~~~~~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f 198 (202)
T cd08473 132 LVTDDLLTLRQAALAGVGIALLPDHL-CREALRA-GRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRAL 198 (202)
T ss_pred EEECCHHHHHHHHHhCCCeeeccHHH-HHHHHHc-CcEEEeccCCcCCCccEEEEecCCCCCCHHHhhH
Confidence 34577888888899998655555433 3322222 22332211 112345778888876555444443
No 231
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=25.86 E-value=1.5e+02 Score=17.46 Aligned_cols=64 Identities=8% Similarity=-0.125 Sum_probs=33.3
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe--CCcccccceEEEEeCCCCChHHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA--GELFGRSGYAIGLQKGSPWADAVTL 68 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~--~~~~~~~~~~ia~~kgs~l~~~vn~ 68 (90)
+.+++....+..+.+|.--+++-+ ..+...... ..+..+ ........++++.+++......+..
T Consensus 127 ~~~~~~~~~~~~v~~g~gi~~lp~-~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 (201)
T cd08459 127 LRVPHFLALPLIVAQTDLVATVPE-RLARLFARA-GGLRIVPLPFPLPPFEVKLYWHRRFHRDPGNRW 192 (201)
T ss_pred EEcCcHHHHHHHHhcCCEEEecHH-HHHHHHhhc-CCeeEecCCCCCCCceEEEEEccccCCChHHHH
Confidence 346677778888888874334333 333322222 234433 2223345677888776544333333
No 232
>PF12363 DUF3647: Phage protein ; InterPro: IPR024410 Proteins in this entry are frequently annotated as phage proteins, however there is little accompanying literature to back this up or to describe the nature of these phage proteins.
Probab=25.79 E-value=1.2e+02 Score=17.73 Aligned_cols=26 Identities=8% Similarity=0.032 Sum_probs=20.5
Q ss_pred ChHHHHHHHHHhhhccHHHHHHHHhc
Q psy17442 62 WADAVTLAILDFHESTVCYLFMAKVH 87 (90)
Q Consensus 62 l~~~vn~~l~~l~~~G~~~~l~~kW~ 87 (90)
+-+.++..+.+|.++|......++|+
T Consensus 87 ~~~l~~~vl~el~~s~~~k~~~k~~~ 112 (113)
T PF12363_consen 87 IEELFDEVLKELKKSNFFKRAVKKFL 112 (113)
T ss_pred HHHHHHHHHHHHHhChhHHHHHHHHh
Confidence 66778888888888888887777765
No 233
>PRK09319 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II/unknown domain fusion protein; Provisional
Probab=25.70 E-value=88 Score=23.78 Aligned_cols=25 Identities=4% Similarity=0.061 Sum_probs=19.8
Q ss_pred ccccCChHHHHHHhhcCCceEEEee
Q psy17442 2 RFDVKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 2 ~~~~~~~~~~~~~l~~G~ida~i~d 26 (90)
.+.+++..+++.+|++|+.-.++.|
T Consensus 2 ~~~~~~Ie~Ai~aLr~G~~VvV~Dd 26 (555)
T PRK09319 2 KIEFDSIDDALAAIRNGECVVVVDD 26 (555)
T ss_pred CCCcccHHHHHHHHHCCCeEEEEeC
Confidence 4678899999999999995555444
No 234
>PF14044 NETI: NETI protein
Probab=25.51 E-value=37 Score=17.66 Aligned_cols=16 Identities=0% Similarity=0.131 Sum_probs=13.3
Q ss_pred HHHHHHHHHhhhccHH
Q psy17442 64 DAVTLAILDFHESTVC 79 (90)
Q Consensus 64 ~~vn~~l~~l~~~G~~ 79 (90)
+.|+..|.+|++.|.+
T Consensus 8 ETI~~CL~RM~~eGY~ 23 (57)
T PF14044_consen 8 ETISDCLARMKKEGYM 23 (57)
T ss_pred CcHHHHHHHHHHcCCC
Confidence 4588899999999975
No 235
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=25.43 E-value=74 Score=18.24 Aligned_cols=20 Identities=15% Similarity=-0.054 Sum_probs=15.9
Q ss_pred ChHHHHHHhhc-CCceEEEee
Q psy17442 7 FSPSTVVRHGT-KKLMAFIWD 26 (90)
Q Consensus 7 ~~~~~~~~l~~-G~ida~i~d 26 (90)
..++....+++ |++|.+|.-
T Consensus 55 g~~~i~~~i~~~g~idlVIn~ 75 (112)
T cd00532 55 GEPTVDAAIAEKGKFDVVINL 75 (112)
T ss_pred CCcHHHHHHhCCCCEEEEEEc
Confidence 34778888899 999988874
No 236
>cd08476 PBP2_CrgA_like_7 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=25.37 E-value=1.5e+02 Score=17.23 Aligned_cols=64 Identities=13% Similarity=-0.018 Sum_probs=34.7
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe-C-CcccccceEEEEeCCCCChHHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA-G-ELFGRSGYAIGLQKGSPWADAVTL 68 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~-~-~~~~~~~~~ia~~kgs~l~~~vn~ 68 (90)
+.+++...++..+.+|.--+++-... +...... ..+..+ . +......+.++.+++......+..
T Consensus 127 ~~~~~~~~~~~~v~~g~Gi~ilp~~~-~~~~~~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 192 (197)
T cd08476 127 LVCNNIEALIEFALQGLGIACLPDFS-VREALAD-GRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRV 192 (197)
T ss_pred eEECCHHHHHHHHHhCCeEEEcCHHH-HHHHhhc-CCeEEccccccCCCCCEEEEecccccCCHHHHH
Confidence 45677888888888988555555433 3222222 223322 1 122334677888887654444433
No 237
>PLN02748 tRNA dimethylallyltransferase
Probab=25.26 E-value=83 Score=23.28 Aligned_cols=32 Identities=6% Similarity=-0.077 Sum_probs=25.8
Q ss_pred EEEEeCCC-CChHHHHHHHHHhhhccHHHHHHH
Q psy17442 53 AIGLQKGS-PWADAVTLAILDFHESTVCYLFMA 84 (90)
Q Consensus 53 ~ia~~kgs-~l~~~vn~~l~~l~~~G~~~~l~~ 84 (90)
-|.+.... .|.+.|+..+..|.+.|.++|...
T Consensus 230 ~i~l~~~r~~L~~RI~~Rvd~Mle~GlleEv~~ 262 (468)
T PLN02748 230 FICVDADTAVLDRYVNQRVDCMIDAGLLDEVYD 262 (468)
T ss_pred EEEeCCCHHHHHHHHHHHHHHHHHCCHHHHHHH
Confidence 45555443 499999999999999999999864
No 238
>TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
Probab=24.80 E-value=12 Score=23.79 Aligned_cols=29 Identities=7% Similarity=0.086 Sum_probs=19.2
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFE 33 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~ 33 (90)
++.+..-+..++.||+.+-+.|.....+|
T Consensus 8 i~~~~~~l~~irtGra~p~ild~I~V~~y 36 (176)
T TIGR00496 8 IQALKRELSKIRTGRANPSLLDRILVEYY 36 (176)
T ss_pred HHHHHHHHHHHhcCCCCHHHhCCeEEEeC
Confidence 44556667788888887666666555544
No 239
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=24.60 E-value=65 Score=19.23 Aligned_cols=21 Identities=10% Similarity=-0.135 Sum_probs=16.9
Q ss_pred CChHHHHHHhhcCCceEEEee
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d 26 (90)
+.+...+..++.|++|+++..
T Consensus 55 p~l~~ll~~~~~g~vd~vvv~ 75 (140)
T cd03770 55 PGFNRMIEDIEAGKIDIVIVK 75 (140)
T ss_pred HHHHHHHHHHHcCCCCEEEEe
Confidence 456778888999999997765
No 240
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=24.56 E-value=2.7e+02 Score=21.18 Aligned_cols=67 Identities=10% Similarity=-0.057 Sum_probs=41.8
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCChHHHHHHHHHhhhc
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~ 76 (90)
+.+.+.......+.+|.+|+.+.-.+... . ..+..+ .+....++++.+++......+...+..+.++
T Consensus 558 ~e~~s~~~i~~~V~~G~~d~Gi~i~~~~~----~-~~l~~i--~l~~~~~~l~~~~~~~~s~a~~aFl~~l~~~ 624 (633)
T PRK14498 558 REEKTHMAVAAAVAQGRADAGLGIRAAAK----A-LGLDFI--PLAEEEYDLLIPKERLEKPAVRAFLEALKSP 624 (633)
T ss_pred cccCCHHHHHHHHHcCCCcchHhHHHHHH----H-cCCCCe--eeeeEEEEEEEEhhHccCHHHHHHHHHHcCH
Confidence 45678889999999999999886555321 1 122211 1112357888888866666666655555443
No 241
>PRK13699 putative methylase; Provisional
Probab=24.52 E-value=61 Score=21.25 Aligned_cols=25 Identities=12% Similarity=0.048 Sum_probs=20.5
Q ss_pred CChHHHHHHhhcCCceEEEeehhHH
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDSSRL 30 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~~~~ 30 (90)
.+.-+.+..|..+.+|++|.|.|..
T Consensus 7 gD~le~l~~lpd~SVDLIiTDPPY~ 31 (227)
T PRK13699 7 GNCIDVMARFPDNAVDFILTDPPYL 31 (227)
T ss_pred chHHHHHHhCCccccceEEeCCCcc
Confidence 3455677888899999999999985
No 242
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=24.50 E-value=75 Score=16.41 Aligned_cols=18 Identities=6% Similarity=0.163 Sum_probs=15.5
Q ss_pred hHHHHHHHHHhhhccHHH
Q psy17442 63 ADAVTLAILDFHESTVCY 80 (90)
Q Consensus 63 ~~~vn~~l~~l~~~G~~~ 80 (90)
+..+++.|.+|++.|.++
T Consensus 42 r~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 42 RETVSRILKRLKDEGIIE 59 (76)
T ss_dssp HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHHCCCEE
Confidence 578999999999999764
No 243
>PRK05331 putative phosphate acyltransferase; Provisional
Probab=24.50 E-value=1e+02 Score=21.60 Aligned_cols=27 Identities=4% Similarity=-0.214 Sum_probs=19.8
Q ss_pred ChHHHHHHhhcCCceEEEeehhHHhHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRLDFE 33 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~~~~ 33 (90)
+.--|+..|+.|++|+++....+..+.
T Consensus 83 sm~~A~~lV~~G~AD~~vSgg~Tga~l 109 (334)
T PRK05331 83 SMRVALELVKEGEADACVSAGNTGALM 109 (334)
T ss_pred hHHHHHHHHhCCCCCEEEeCCcHHHHH
Confidence 344688899999999999755554433
No 244
>PRK09314 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional
Probab=24.33 E-value=93 Score=22.09 Aligned_cols=23 Identities=13% Similarity=0.160 Sum_probs=17.7
Q ss_pred ccCChHHHHHHhhcCCceEEEee
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d 26 (90)
.+++.++++.+|++|+.-.++.|
T Consensus 2 ~~~~i~~ai~~l~~G~~Viv~Dd 24 (339)
T PRK09314 2 PIKRVEEAIEDIKNGKMLIMVDD 24 (339)
T ss_pred CcccHHHHHHHHHCCCeEEEEeC
Confidence 46789999999999995444443
No 245
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=24.26 E-value=17 Score=19.21 Aligned_cols=25 Identities=8% Similarity=-0.024 Sum_probs=18.9
Q ss_pred HHHHHHHHHhhhccHHHHHH---HHhcc
Q psy17442 64 DAVTLAILDFHESTVCYLFM---AKVHL 88 (90)
Q Consensus 64 ~~vn~~l~~l~~~G~~~~l~---~kW~~ 88 (90)
..+++.|..|++.|.+..-. .+|.+
T Consensus 37 ~~v~r~L~~L~~~G~V~~~~~~~~~W~i 64 (68)
T smart00550 37 KEVNRVLYSLEKKGKVCKQGGTPPLWKL 64 (68)
T ss_pred HHHHHHHHHHHHCCCEEecCCCCCceEe
Confidence 57999999999999887632 45654
No 246
>cd08484 PBP2_LTTR_beta_lactamase The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topol
Probab=24.04 E-value=1.6e+02 Score=17.17 Aligned_cols=65 Identities=15% Similarity=-0.061 Sum_probs=33.6
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCCCCChHHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTL 68 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kgs~l~~~vn~ 68 (90)
+.+++...++..+.+|.--+++-.. .+.....+..-...+........++++.+|+......+..
T Consensus 120 ~~~~~~~~~~~~v~~g~Gi~~lp~~-~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 184 (189)
T cd08484 120 PVFDSSLLMVEAALQGAGVALAPPS-MFSRELASGALVQPFKITVSTGSYWLTRLKSKPETPAMSA 184 (189)
T ss_pred cccccHHHHHHHHHhCCCeEEecHH-hHHHHHHCCCEEeecccccCCCCEEEEeccccccchhhHH
Confidence 3457777888888888855554433 3332223221112222222234577788887654443333
No 247
>cd03769 SR_IS607_transposase_like Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subfamily is composed of proteins that catalyze the transposition of insertion sequence (IS) elements such as IS607 from Helicobacter and IS1535 from Mycobacterium, and similar proteins from other bacteria and several archaeal species. IS elements are DNA segments that move to new sites in prokaryotic and eukaryotic genomes causing insertion mutations and gene rearrangements.
Probab=23.98 E-value=74 Score=18.94 Aligned_cols=21 Identities=10% Similarity=-0.173 Sum_probs=16.9
Q ss_pred CChHHHHHHhhcCCceEEEee
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d 26 (90)
+.+.+.+..++.|++|.++..
T Consensus 49 p~l~~ll~~i~~g~~d~lvV~ 69 (134)
T cd03769 49 KGLLKLLEDVLAGKVERVVIT 69 (134)
T ss_pred HHHHHHHHHHHcCCCCEEEEE
Confidence 556788899999999987754
No 248
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=23.83 E-value=1.3e+02 Score=18.46 Aligned_cols=39 Identities=18% Similarity=0.140 Sum_probs=28.4
Q ss_pred ccceEEEEeCCCC-ChHHHHHHHHHhhhccHHHHHHHHhc
Q psy17442 49 RSGYAIGLQKGSP-WADAVTLAILDFHESTVCYLFMAKVH 87 (90)
Q Consensus 49 ~~~~~ia~~kgs~-l~~~vn~~l~~l~~~G~~~~l~~kW~ 87 (90)
..+-+|-+|+|.. .....|..|-.=.+--.+.+|.+||=
T Consensus 74 ~GGrsfYlP~G~s~r~t~Rn~~ifsd~dG~n~~eLaKkYr 113 (137)
T COG5566 74 GGGRSFYLPKGDSIRATLRNKQIFSDFDGSNYVELAKKYR 113 (137)
T ss_pred cCCeeEEeeCchHHHHHHHHHHHHHhcCCccHHHHHHHhc
Confidence 3456789999965 66777777776666557888888773
No 249
>PRK10752 sulfate transporter subunit; Provisional
Probab=23.71 E-value=2.6e+02 Score=19.50 Aligned_cols=30 Identities=3% Similarity=-0.398 Sum_probs=21.8
Q ss_pred ccCChHHHHHHhhcCC-ceEEEeehhHHhHH
Q psy17442 4 DVKFSPSTVVRHGTKK-LMAFIWDSSRLDFE 33 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~-ida~i~d~~~~~~~ 33 (90)
.+.++.+...++.+|. .|.++.....-...
T Consensus 60 s~ggSg~l~~qI~~g~~aDV~~~a~~~~~~~ 90 (329)
T PRK10752 60 SHGGSGKQATSVINGIEADVVTLALAYDVDA 90 (329)
T ss_pred CCCChHHHHHHHHcCCCCCEEEeCCHHHHHH
Confidence 4577888999999874 89988776544333
No 250
>cd08565 GDPD_pAtGDE_like Glycerophosphodiester phosphodiesterase domain of putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (pAtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=23.54 E-value=88 Score=20.45 Aligned_cols=8 Identities=13% Similarity=0.040 Sum_probs=3.4
Q ss_pred eEEEeehh
Q psy17442 21 MAFIWDSS 28 (90)
Q Consensus 21 da~i~d~~ 28 (90)
|+++.|.|
T Consensus 224 dgIiTD~P 231 (235)
T cd08565 224 RQLTTDRP 231 (235)
T ss_pred CEEEeCCc
Confidence 44444433
No 251
>cd08575 GDPD_GDE4_like Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE4 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1)) and similar proteins. Mammalian GDE4 is a transmembrane protein whose cellular function is not elucidated. It is expressed widely, including in placenta, liver, kidney, pancreas, spleen, thymus, ovary, small intestine and peripheral blood leukocytes. It is also expressed in the growth cones in neuroblastoma Neuro2a cells, which suggests mammalian GDE4 may play some distinct role from other members of mammalian GDEs family. Also included in this subfamily are uncharacterized mammalian glycerophosphodiester phosphodiesterase domain-containing protein 3 (GDPD3) and similar proteins which display very high sequence homology to mammalian GDE4.
Probab=23.47 E-value=80 Score=21.01 Aligned_cols=9 Identities=22% Similarity=0.102 Sum_probs=4.4
Q ss_pred ceEEEeehh
Q psy17442 20 LMAFIWDSS 28 (90)
Q Consensus 20 ida~i~d~~ 28 (90)
+|+++.|.|
T Consensus 253 VdgIiTD~P 261 (264)
T cd08575 253 ADGVMTDSP 261 (264)
T ss_pred CCEEEeCCc
Confidence 355555544
No 252
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=23.34 E-value=1.7e+02 Score=17.17 Aligned_cols=57 Identities=14% Similarity=-0.057 Sum_probs=28.1
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeC--CcccccceEEEEeCCCC
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAG--ELFGRSGYAIGLQKGSP 61 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~--~~~~~~~~~ia~~kgs~ 61 (90)
+.+++....+..+..|.--+++- ...+..... ...+..+. .......+.++.+++..
T Consensus 127 ~~~~~~~~~~~~v~~g~gi~~lp-~~~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~ 185 (200)
T cd08466 127 YEVSSLLSMLAVVSQTDLIAIAP-RWLADQYAE-QLNLQILPLPFKTKPIPLYMVWHKSRE 185 (200)
T ss_pred EEcCchhhHHHHHcCCCeehhhH-HHHHHHhhh-cCCeeEecCCCCCCCccEEEEEcCCCC
Confidence 34566677777777776333333 223222222 22344332 22223457777777643
No 253
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=23.22 E-value=1.1e+02 Score=17.35 Aligned_cols=20 Identities=15% Similarity=-0.011 Sum_probs=15.3
Q ss_pred ChHHHHHHhhcCCceEEEee
Q psy17442 7 FSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d 26 (90)
..++....+++|++|.+|.-
T Consensus 55 ~~~~i~~~i~~~~id~vIn~ 74 (110)
T cd01424 55 GRPNIVDLIKNGEIQLVINT 74 (110)
T ss_pred CchhHHHHHHcCCeEEEEEC
Confidence 44677788888888888874
No 254
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=22.91 E-value=1.9e+02 Score=17.50 Aligned_cols=56 Identities=11% Similarity=-0.087 Sum_probs=29.3
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCC--cccccceEEEEeCCCC
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGE--LFGRSGYAIGLQKGSP 61 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~--~~~~~~~~ia~~kgs~ 61 (90)
.+++...++..+..|..-++ .....+..... ...+..+.. ......+.++.+++..
T Consensus 149 ~~~~~~~~~~~v~~g~gi~~-~p~~~~~~~~~-~~~l~~~~~~~~~~~~~~~lv~~~~~~ 206 (221)
T cd08469 149 TVPHALAVPPLLADSDMLAL-LPRSLARAFAE-RGGLVMKEPPYPPPPVQIRAVWHERHD 206 (221)
T ss_pred EcCcHHHHHHHHhCCchhhh-HHHHHHHHHhh-cCCcEEeCCCCCCCCceEEEEeccccc
Confidence 46777778888888873333 33333333222 223444422 2223456677777643
No 255
>TIGR01254 sfuA ABC transporter periplasmic binding protein, thiB subfamily. The model describes thiamine ABC transporter, periplasmic protein in bacteria and archae. The protein belongs to the larger ABC transport system. It consists of at least three components: the thiamine binding periplasmic protein; an inner membrane permease; an ATP-binding subunit. It has been experimentally demonstrated that the mutants in the various steps in the de novo synthesis of the thiamine and the biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP).
Probab=22.66 E-value=2.4e+02 Score=18.77 Aligned_cols=68 Identities=4% Similarity=-0.226 Sum_probs=38.1
Q ss_pred ChHHHHHHhhcCCceEEEeehh-HHh-HHHhcCCCeEEe--CCcccccceEEEEeCCCCChHHHHHHHHHhh
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSS-RLD-FEAAQDCELVTA--GELFGRSGYAIGLQKGSPWADAVTLAILDFH 74 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~-~~~-~~~~~~~~l~~~--~~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~ 74 (90)
+..+....+.+|++++.+.... .+. ....+...+.++ ++.......+++++++++-.+..-+.|.-|.
T Consensus 179 ~~~~~~~~~~~Ge~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~ai~k~a~n~e~A~~fi~fll 250 (304)
T TIGR01254 179 GWSEAYGTFLGGEYDLVLSYATSPAYHVLFEKKDNYAALNFSEGHYLQVEGAARLKGAKQPELADKFVQFLL 250 (304)
T ss_pred CCHHHHHHHhcCCccEEEEeccchhhhhhhccCCceeEEecCCCCEEEEEEEEEECCCCCHHHHHHHHHHHc
Confidence 4466778899999888776432 122 222223334332 2111123458999999876566656555444
No 256
>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=22.58 E-value=2.2e+02 Score=20.61 Aligned_cols=21 Identities=0% Similarity=-0.202 Sum_probs=16.7
Q ss_pred cCChHHHHHHhhcCCceEEEe
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIW 25 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~ 25 (90)
+.+....+.++++|++|.+..
T Consensus 204 ~~d~~~~~~al~~Ge~D~~~~ 224 (509)
T cd08509 204 YSSNDQALLALANGEVDWAGL 224 (509)
T ss_pred cCCHHHHHHHHHcCCcceecc
Confidence 456677899999999998653
No 257
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=22.50 E-value=19 Score=18.14 Aligned_cols=21 Identities=10% Similarity=0.072 Sum_probs=16.3
Q ss_pred hHHHHHHHHHhhhccHHHHHH
Q psy17442 63 ADAVTLAILDFHESTVCYLFM 83 (90)
Q Consensus 63 ~~~vn~~l~~l~~~G~~~~l~ 83 (90)
...+++.|..|.+.|.+....
T Consensus 39 ~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 39 RETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHHHHHHHHHHHHCCCEEecC
Confidence 467888999999988876544
No 258
>PRK10632 transcriptional regulator; Provisional
Probab=22.48 E-value=2.5e+02 Score=18.76 Aligned_cols=57 Identities=11% Similarity=-0.161 Sum_probs=31.4
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCc--ccccceEEEEeCCCC
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGEL--FGRSGYAIGLQKGSP 61 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~--~~~~~~~ia~~kgs~ 61 (90)
+.+++...++..+.+|.--+++-....... .. +..+.++... .....+.++.+++.+
T Consensus 218 ~~~~~~~~~~~~V~~g~Gv~~lp~~~~~~~-~~-~~~l~~~~~~~~~~~~~~~l~~~~~~~ 276 (309)
T PRK10632 218 FVTNDPQTLVRWLTAGAGIAYVPLMWVIDE-IN-RGELEILFPRYQSDPRPVYALYTEKDK 276 (309)
T ss_pred EEECCHHHHHHHHHcCCcEEEcCHHHHHHH-Hh-cCCeEEeCCCccCCCCcEEEEecCCCC
Confidence 456778888888999985555543333222 22 2234433222 234456677777644
No 259
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=22.35 E-value=58 Score=22.36 Aligned_cols=67 Identities=16% Similarity=-0.088 Sum_probs=35.4
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCCc--------ccccceE-EEEeCCCC--ChHHHHHHHHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGEL--------FGRSGYA-IGLQKGSP--WADAVTLAILD 72 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~~--------~~~~~~~-ia~~kgs~--l~~~vn~~l~~ 72 (90)
..-.+.+...++.+|++||.+.-+..-.-|... .+.++.+. --+-|.| ++++|+=| ....+..++.+
T Consensus 121 V~m~fdeI~~Avl~G~VDaGvlIHE~~~ty~~~--gL~~v~Dl~d~W~~~~~LPlPLG~~~irk~l~~~~a~~~~~al~~ 198 (272)
T COG2107 121 VYMPFDEIIPAVLEGKVDAGVLIHEEQLTYALY--GLKKVLDLGDWWKEKTGLPLPLGCIAIRKDLPKDTAEAIKDALRK 198 (272)
T ss_pred EEeeHHHHHHHHHcCCCccceEEeehhcchhhh--CceEeeeHHHHHHHhcCCCcCcchhhhhccCCHHHHHHHHHHHHH
Confidence 344577889999999999955433322222221 13333211 1234454 67777632 44555555543
No 260
>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=22.04 E-value=1.1e+02 Score=19.61 Aligned_cols=29 Identities=17% Similarity=-0.018 Sum_probs=23.6
Q ss_pred eEEEEeCCCC-ChHHHHHHHHHhhhccHHH
Q psy17442 52 YAIGLQKGSP-WADAVTLAILDFHESTVCY 80 (90)
Q Consensus 52 ~~ia~~kgs~-l~~~vn~~l~~l~~~G~~~ 80 (90)
..+.+||.+. ..+.|..+|.+..+.|.-.
T Consensus 32 ~t~lipK~d~~t~~~I~~Ai~~a~~~~~~~ 61 (181)
T PF10991_consen 32 ATLLIPKSDKETIAAIKAAIEAAIEEGWGN 61 (181)
T ss_pred EEEEEcCCCHHHHHHHHHHHHHHHHhcccc
Confidence 3477899886 6899999999999988743
No 261
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=21.93 E-value=1.8e+02 Score=16.93 Aligned_cols=62 Identities=15% Similarity=0.080 Sum_probs=31.9
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCC--cccccceEEEEeCCCCChHHHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGE--LFGRSGYAIGLQKGSPWADAVT 67 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~--~~~~~~~~ia~~kgs~l~~~vn 67 (90)
.+++...+...+.+|.--+++-+ ..+...... ..+..+.. ......+.++.+++......+.
T Consensus 132 ~~~~~~~~~~~v~~g~gi~~~p~-~~~~~~~~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 195 (201)
T cd08435 132 ETASISALLALLARSDMLAVLPR-SVAEDELRA-GVLRELPLPLPTSRRPIGITTRRGGPLSPAAR 195 (201)
T ss_pred EEccHHHHHHHHhcCCeEEEeEH-HHhhhhhcc-CceEEecccCCCCcccEEEEEcCCCCCCHHHH
Confidence 45667777788888874444443 333332222 23443322 2223456777777654433333
No 262
>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]
Probab=21.83 E-value=91 Score=25.84 Aligned_cols=35 Identities=14% Similarity=0.060 Sum_probs=24.3
Q ss_pred HHHHHHhhcCCceEEEeehhHHhHHHh-cCCCeEEe
Q psy17442 9 PSTVVRHGTKKLMAFIWDSSRLDFEAA-QDCELVTA 43 (90)
Q Consensus 9 ~~~~~~l~~G~ida~i~d~~~~~~~~~-~~~~l~~~ 43 (90)
.+.+..|++|++|.+|.-+-.+..-++ ++-.|.++
T Consensus 687 ~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlII 722 (1139)
T COG1197 687 KEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLII 722 (1139)
T ss_pred HHHHHHHhcCCccEEEechHhhCCCcEEecCCeEEE
Confidence 567889999999999998877653222 23344554
No 263
>PF06576 DUF1133: Protein of unknown function (DUF1133); InterPro: IPR010557 This family consists of a number of hypothetical proteins from Escherichia coli O157:H7 and Salmonella typhi. The function of this family is unknown.
Probab=21.83 E-value=77 Score=20.34 Aligned_cols=16 Identities=19% Similarity=0.275 Sum_probs=14.6
Q ss_pred hHHHHHHHHHhhhccH
Q psy17442 63 ADAVTLAILDFHESTV 78 (90)
Q Consensus 63 ~~~vn~~l~~l~~~G~ 78 (90)
+..||.+|..|+++|.
T Consensus 57 KtaI~~aLr~mkKsGi 72 (176)
T PF06576_consen 57 KTAINEALRRMKKSGI 72 (176)
T ss_pred HHHHHHHHHHHHHhcC
Confidence 6899999999999994
No 264
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=21.78 E-value=1e+02 Score=22.39 Aligned_cols=27 Identities=15% Similarity=0.119 Sum_probs=22.0
Q ss_pred ccccCChHHHHHHhh--cCCceEEEeehhH
Q psy17442 2 RFDVKFSPSTVVRHG--TKKLMAFIWDSSR 29 (90)
Q Consensus 2 ~~~~~~~~~~~~~l~--~G~ida~i~d~~~ 29 (90)
+|..+|..||+..++ -|. ||+|...-.
T Consensus 5 kf~a~~~~eAm~~vk~eLG~-dAVILs~r~ 33 (424)
T PRK05703 5 KFTAKDMREALKQIKEELGA-DAVILSNKK 33 (424)
T ss_pred EEecCCHHHHHHHHHHHhCC-CeEEEecce
Confidence 678899999999998 577 998877443
No 265
>COG0278 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=21.77 E-value=1.2e+02 Score=17.84 Aligned_cols=17 Identities=6% Similarity=-0.017 Sum_probs=13.8
Q ss_pred HHHHHhhhccHHHHHHH
Q psy17442 68 LAILDFHESTVCYLFMA 84 (90)
Q Consensus 68 ~~l~~l~~~G~~~~l~~ 84 (90)
..+.+|-++|+++++.+
T Consensus 86 DIv~Em~q~GELq~~l~ 102 (105)
T COG0278 86 DIVREMYQSGELQTLLK 102 (105)
T ss_pred HHHHHHHHcchHHHHHH
Confidence 35788999999998765
No 266
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=21.71 E-value=1.6e+02 Score=18.86 Aligned_cols=25 Identities=8% Similarity=-0.203 Sum_probs=17.3
Q ss_pred cCChHHHHHHhhcCC--ceEEEeehhH
Q psy17442 5 VKFSPSTVVRHGTKK--LMAFIWDSSR 29 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~--ida~i~d~~~ 29 (90)
++..++++..+++|+ +++.+...+.
T Consensus 218 ~d~~~~~~~~i~~g~~~~~~~v~~~~~ 244 (274)
T cd06311 218 GAGSKDMIKMIMDGDPLIPADVLYPPS 244 (274)
T ss_pred eCCCHHHHHHHHCCCCceeEEEecCHH
Confidence 466777888888885 7777765553
No 267
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=21.62 E-value=91 Score=21.08 Aligned_cols=26 Identities=15% Similarity=0.153 Sum_probs=21.3
Q ss_pred ccccCChHHHHHHhhc--CCceEEEeehh
Q psy17442 2 RFDVKFSPSTVVRHGT--KKLMAFIWDSS 28 (90)
Q Consensus 2 ~~~~~~~~~~~~~l~~--G~ida~i~d~~ 28 (90)
+|..+|..||+..++. |. ||+|...-
T Consensus 5 ~f~a~~~~eal~~ik~elG~-dAvIls~r 32 (282)
T TIGR03499 5 RFTAPTMREALAKVKEELGP-DAVILSTR 32 (282)
T ss_pred EEecCCHHHHHHHHHHHHCC-CcEEEEee
Confidence 5788999999999984 67 99887644
No 268
>cd00520 RRF Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species.
Probab=21.52 E-value=9.8 Score=24.22 Aligned_cols=29 Identities=10% Similarity=0.115 Sum_probs=17.8
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHhHH
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLDFE 33 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~~~ 33 (90)
++.+.+-+..+++|++..-+.|.....+|
T Consensus 13 i~~~~~~l~~irtGrasp~lld~I~V~~y 41 (179)
T cd00520 13 LEALKEELNKIRTGRANPALLDSITVEYY 41 (179)
T ss_pred HHHHHHHHHHHhcCCCCHHHhCCeEEEeC
Confidence 34455667778888876655555544444
No 269
>PF04422 FrhB_FdhB_N: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term; InterPro: IPR007516 Coenzyme F420 hydrogenase (1.12.99.1 from EC) reduces the low-potential two-electron acceptor coenzyme F420. This entry contains the N termini of F420 hydrogenase and dehydrogenase beta subunits [, ]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (1.2.1.2 from EC, P06130 from SWISSPROT) is also represented in this entry []. This region is often found in association with the 4Fe-4S binding domain, fer4 (IPR001450 from INTERPRO), and the C terminus IPR007525 from INTERPRO.
Probab=21.47 E-value=1e+02 Score=16.77 Aligned_cols=17 Identities=0% Similarity=-0.222 Sum_probs=13.0
Q ss_pred HHHHhhcCCceEEEeeh
Q psy17442 11 TVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 11 ~~~~l~~G~ida~i~d~ 27 (90)
+...|.+|.||+++.-.
T Consensus 27 l~~lLe~g~Vd~vv~~~ 43 (82)
T PF04422_consen 27 LAYLLESGLVDGVVVVG 43 (82)
T ss_pred HHHHHHcCCceEEEEEe
Confidence 44567899999988754
No 270
>PRK00014 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=21.45 E-value=1.1e+02 Score=20.44 Aligned_cols=20 Identities=0% Similarity=-0.139 Sum_probs=15.1
Q ss_pred CChHHHHHHhhcCCceEEEe
Q psy17442 6 KFSPSTVVRHGTKKLMAFIW 25 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~ 25 (90)
++..+++.+|++|+.-.++.
T Consensus 19 ~~i~~ai~al~~Gk~Viv~D 38 (230)
T PRK00014 19 TRLERALQHLRIGRPVILMD 38 (230)
T ss_pred hhHHHHHHHHHCCCeEEEEE
Confidence 45889999999999444443
No 271
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=21.32 E-value=1.1e+02 Score=20.24 Aligned_cols=22 Identities=5% Similarity=-0.262 Sum_probs=18.5
Q ss_pred CChHHHHHHhhcCCceEEEeeh
Q psy17442 6 KFSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 6 ~~~~~~~~~l~~G~ida~i~d~ 27 (90)
.+..+.+..|++|++|..|...
T Consensus 134 ~~~~~~~~~l~~g~~Dlai~~~ 155 (303)
T PRK10082 134 IDVDEAVDKLREGQSDCIFSFH 155 (303)
T ss_pred CCHHHHHHHHHCCCCCEEEEec
Confidence 4667899999999999999753
No 272
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=21.32 E-value=61 Score=16.95 Aligned_cols=15 Identities=7% Similarity=-0.008 Sum_probs=12.2
Q ss_pred cCChHHHHHHhhcCC
Q psy17442 5 VKFSPSTVVRHGTKK 19 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ 19 (90)
+..+++++.+.++|+
T Consensus 34 ~K~~~~~I~~~~aG~ 48 (59)
T smart00685 34 AKQFDDAIKAARAGR 48 (59)
T ss_pred HhhHHHHHHHHHCCC
Confidence 456788899999998
No 273
>TIGR00557 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase. This model represents PdxA, an NAD+-dependent 4-hydroxythreonine 4-phosphate dehydrogenase (EC 1.1.1.262) active in pyridoxal phosphate biosynthesis.
Probab=21.11 E-value=52 Score=23.07 Aligned_cols=23 Identities=9% Similarity=-0.174 Sum_probs=19.4
Q ss_pred ccCChHHHHHHhhcCCceEEEee
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d 26 (90)
.++....|+...++|++||++.-
T Consensus 92 a~~~l~~A~~~~~~g~~~aiVTa 114 (320)
T TIGR00557 92 VFETLERAVELCLAGEADALVTA 114 (320)
T ss_pred HHHHHHHHHHHHHcCCCCEEEEC
Confidence 45567889999999999999975
No 274
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=21.11 E-value=44 Score=16.16 Aligned_cols=13 Identities=8% Similarity=-0.151 Sum_probs=10.3
Q ss_pred ChHHHHHHhhcCC
Q psy17442 7 FSPSTVVRHGTKK 19 (90)
Q Consensus 7 ~~~~~~~~l~~G~ 19 (90)
+..+|+.++++|+
T Consensus 4 ~l~~Ai~~v~~g~ 16 (45)
T PF05225_consen 4 DLQKAIEAVKNGK 16 (45)
T ss_dssp HHHHHHHHHHTTS
T ss_pred HHHHHHHHHHhCC
Confidence 4578889999886
No 275
>PRK01906 tetraacyldisaccharide 4'-kinase; Provisional
Probab=21.10 E-value=1.1e+02 Score=21.56 Aligned_cols=50 Identities=16% Similarity=0.161 Sum_probs=34.4
Q ss_pred hHHHHHHhhc-C-CceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCC
Q psy17442 8 SPSTVVRHGT-K-KLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 8 ~~~~~~~l~~-G-~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kg 59 (90)
-.++...+.+ . ..|.+|.|...-.+.+..+.++.+++. ...+.+..+|.|
T Consensus 136 R~~aa~~l~~~~~~~dviIlDDGfQH~~L~RDleIvl~D~--~~~Gng~lLPaG 187 (338)
T PRK01906 136 RVAAAQALLAAHPGVDVIVSDDGLQHYRLARDVEIVVFDH--RLGGNGFLLPAG 187 (338)
T ss_pred HHHHHHHHHHhCCCCCEEEECCCCccchhcCCcEEEEEcC--CCCCCCcccCCc
Confidence 3455555543 2 478999998887777787878877754 334667788877
No 276
>PF10657 RC-P840_PscD: Photosystem P840 reaction centre protein PscD; InterPro: IPR019608 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin [].
Probab=21.06 E-value=1.4e+02 Score=18.12 Aligned_cols=25 Identities=12% Similarity=0.214 Sum_probs=20.3
Q ss_pred ccccCChHHHHHHhhcCCceEEEee
Q psy17442 2 RFDVKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 2 ~~~~~~~~~~~~~l~~G~ida~i~d 26 (90)
|......+|.+..|.+|+|..++..
T Consensus 57 rrkLspt~emi~~l~~geIel~VLt 81 (144)
T PF10657_consen 57 RRKLSPTPEMIDKLISGEIELFVLT 81 (144)
T ss_pred ccccCCcHHHHHHHhcCceEEEEEc
Confidence 3456678999999999999987754
No 277
>COG1026 Predicted Zn-dependent peptidases, insulinase-like [General function prediction only]
Probab=21.05 E-value=1.2e+02 Score=24.80 Aligned_cols=26 Identities=12% Similarity=0.054 Sum_probs=17.1
Q ss_pred HHHHHHHHhhhccHHHHHHHHhccCC
Q psy17442 65 AVTLAILDFHESTVCYLFMAKVHLNN 90 (90)
Q Consensus 65 ~vn~~l~~l~~~G~~~~l~~kW~~~~ 90 (90)
.++.--.++..++.+++|.+|||+++
T Consensus 422 ~~~~Lr~~le~~~~fe~LI~ky~l~N 447 (978)
T COG1026 422 YLQNLREKLEKGPYFEKLIRKYFLDN 447 (978)
T ss_pred HHHHHHHhhhcChHHHHHHHHHhhcC
Confidence 33333334444456999999999875
No 278
>PRK09755 putative ABC transporter periplasmic-binding protein; Provisional
Probab=21.02 E-value=2.4e+02 Score=20.76 Aligned_cols=19 Identities=11% Similarity=-0.097 Sum_probs=15.5
Q ss_pred cCChHHHHHHhhcCCceEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAF 23 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~ 23 (90)
+++......+|++|++|+.
T Consensus 247 ~~d~~~~~~al~sGeiD~~ 265 (535)
T PRK09755 247 LDNSVTGYNRYRAGEVDLT 265 (535)
T ss_pred ecCchHHHHHHhcCCcccc
Confidence 3566778889999999985
No 279
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=20.91 E-value=1e+02 Score=16.26 Aligned_cols=17 Identities=6% Similarity=0.108 Sum_probs=15.3
Q ss_pred hHHHHHHHHHhhhccHH
Q psy17442 63 ADAVTLAILDFHESTVC 79 (90)
Q Consensus 63 ~~~vn~~l~~l~~~G~~ 79 (90)
+..||..|-+|..+|.+
T Consensus 34 kk~VN~~LY~L~k~g~v 50 (66)
T PF02295_consen 34 KKEVNRVLYRLEKQGKV 50 (66)
T ss_dssp HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHHCCCE
Confidence 68999999999999875
No 280
>PRK07377 hypothetical protein; Provisional
Probab=20.91 E-value=1.1e+02 Score=19.76 Aligned_cols=24 Identities=8% Similarity=-0.125 Sum_probs=20.7
Q ss_pred cccCChHHHHHHhhcCCceEEEee
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWD 26 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d 26 (90)
..+++.++..++|.+|++|+....
T Consensus 113 v~y~~~~~l~~aL~~~eVh~~c~~ 136 (184)
T PRK07377 113 VVYPDLQALEQALRDKEVHAICLE 136 (184)
T ss_pred EecCCHHHHHHHHhcCCccEEecC
Confidence 468899999999999999998763
No 281
>PF02606 LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPro: IPR003758 Tetraacyldisaccharide 4'-kinase phosphorylates the 4'-position of a tetraacyldisaccharide 1-phosphate precursor (DS-1-P) of lipid A, but the enzyme has not yet been purified because of instability []. This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS).; GO: 0005524 ATP binding, 0009029 tetraacyldisaccharide 4'-kinase activity, 0009245 lipid A biosynthetic process
Probab=20.76 E-value=1e+02 Score=21.58 Aligned_cols=50 Identities=14% Similarity=0.009 Sum_probs=32.4
Q ss_pred HHHHHHhhc-CCceEEEeehhHHhHHHhcCCCeEEeCCcccccceEEEEeCC
Q psy17442 9 PSTVVRHGT-KKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKG 59 (90)
Q Consensus 9 ~~~~~~l~~-G~ida~i~d~~~~~~~~~~~~~l~~~~~~~~~~~~~ia~~kg 59 (90)
.++.+.+.+ +..|.+|.|...-.+.+..+.++.++.. ..+.+.+..+|-|
T Consensus 117 ~~~~~~~~~~~~~dviilDDGfQh~~L~rDl~Ivl~D~-~~~~gng~lLPaG 167 (326)
T PF02606_consen 117 VAAARAALKEFPADVIILDDGFQHRRLKRDLDIVLVDA-DRPFGNGFLLPAG 167 (326)
T ss_pred HHHHHHHHHHCCCCEEEEcCCcccccccCCcEEEEEeC-CCCCcCCccCCCC
Confidence 344444443 4589999998888887887877777753 2233445566655
No 282
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=20.70 E-value=1.9e+02 Score=18.35 Aligned_cols=27 Identities=11% Similarity=0.033 Sum_probs=17.4
Q ss_pred cCChHHHHHHhhcCCceEEEeehhHHh
Q psy17442 5 VKFSPSTVVRHGTKKLMAFIWDSSRLD 31 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i~d~~~~~ 31 (90)
++..++.+..+++|.+.+.+...+...
T Consensus 215 ~d~~~~~~~~i~~g~~~a~v~~~~~~~ 241 (257)
T PF13407_consen 215 FDGSPEALEAIKDGNITATVGQDPYQQ 241 (257)
T ss_dssp EECHHHHHHHHHTTSSSEEEEE-HHHH
T ss_pred CCCCHHHHHHHHCCCCeEEEeCCHHHH
Confidence 456677777777777777666655443
No 283
>PRK15104 oligopeptide ABC transporter substrate-binding protein OppA; Provisional
Probab=20.67 E-value=3.2e+02 Score=20.15 Aligned_cols=20 Identities=10% Similarity=0.016 Sum_probs=15.8
Q ss_pred cCChHHHHHHhhcCCceEEE
Q psy17442 5 VKFSPSTVVRHGTKKLMAFI 24 (90)
Q Consensus 5 ~~~~~~~~~~l~~G~ida~i 24 (90)
+.+......++++|++|++.
T Consensus 252 ~~d~~~~~~al~~GeiD~~~ 271 (543)
T PRK15104 252 ISSEVTDVNRYRSGEIDMTY 271 (543)
T ss_pred ecCchHHHHHHHCCCcceec
Confidence 35667778999999999764
No 284
>PF09575 Spore_SspJ: Small spore protein J (Spore_SspJ); InterPro: IPR014220 This entry represents a group of small acid-soluble proteins (SASP) from Bacillus species, which are present in spores but not in growing cells. The sspJ gene is transcribed in the forespore compartment by RNA polymerase with the forespore-specific sigmaG. Loss of SspJ causes a slight decrease in the rate of spore outgrowth in an otherwise wild-type background [].
Probab=20.67 E-value=51 Score=16.04 Aligned_cols=11 Identities=45% Similarity=0.709 Sum_probs=7.7
Q ss_pred CCCCChHHHHH
Q psy17442 58 KGSPWADAVTL 68 (90)
Q Consensus 58 kgs~l~~~vn~ 68 (90)
+|+||.+.|++
T Consensus 31 k~DPLQEAVqK 41 (46)
T PF09575_consen 31 KGDPLQEAVQK 41 (46)
T ss_pred cCChHHHHHHH
Confidence 57777777765
No 285
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=20.65 E-value=2.5e+02 Score=18.21 Aligned_cols=70 Identities=7% Similarity=-0.158 Sum_probs=38.5
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeC--CcccccceEEEEeCCCCChHHHHHHHHHhhh
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAG--ELFGRSGYAIGLQKGSPWADAVTLAILDFHE 75 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~--~~~~~~~~~ia~~kgs~l~~~vn~~l~~l~~ 75 (90)
.+++...+...+..|.--+++-+..+ ..... +..+..+. .......+.++.+++.+....+...+..+.+
T Consensus 217 ~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ 288 (290)
T PRK10837 217 ELGNSEAIKHAVRHGLGISCLSRRVI-ADQLQ-AGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLSYCQE 288 (290)
T ss_pred EeCCHHHHHHHHHhCCcEEEeeHHHH-HHHHh-CCcEEEEEcCCccceEEEEEEEeCCCCCCHHHHHHHHHHHh
Confidence 45677778888888885555554333 22222 22344332 2222345667778876666666665554443
No 286
>PF13343 SBP_bac_6: Bacterial extracellular solute-binding protein; PDB: 2QRY_D 1XVX_A 1SI1_A 1SI0_A 1Q35_A 1Y9U_A 2OWS_A 2OWT_A 2VP1_A 2VOZ_A ....
Probab=20.64 E-value=2.4e+02 Score=17.95 Aligned_cols=70 Identities=14% Similarity=-0.083 Sum_probs=42.1
Q ss_pred hHHHHHHhhcCCceEEEeehhHHhHHHhcCC-CeEEeCCc--ccccceEEEEeCCCCChHHHHHHHHHhhhcc
Q psy17442 8 SPSTVVRHGTKKLMAFIWDSSRLDFEAAQDC-ELVTAGEL--FGRSGYAIGLQKGSPWADAVTLAILDFHEST 77 (90)
Q Consensus 8 ~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~-~l~~~~~~--~~~~~~~ia~~kgs~l~~~vn~~l~~l~~~G 77 (90)
..+.+..+.+|+..+.+.-......+..+.. ++.++-.. ......++++.|+++-.+..-..|.-|...-
T Consensus 129 ~~~~~~~~~~Ge~~~~i~~~~~~~~~~~~~~~~i~~v~P~eG~~~~~~~~~i~k~a~~~~~A~~fi~~lls~e 201 (242)
T PF13343_consen 129 SSQAAQAVASGEGAVAIGISWYSRAAQAKEKGPIKFVYPEEGTVVWPDGIAIVKGAPNPEAAKKFINFLLSPE 201 (242)
T ss_dssp HHHHHHHHHTTSCSEEEEEHHHHHHHHHCTTTTEEEE-TTTGBEEEEEEEEEBTT-STHHHHHHHHHHHTSHH
T ss_pred chhhhhHhhCCCceEEEEEehHHHHHHhhhcCCeEEEecCCCcEEEEEEEEEeCCCCCHHHHHHHHHHHCCHH
Confidence 5788999999995555554444444433321 66665322 2234568999999877776666665555444
No 287
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=20.52 E-value=2e+02 Score=16.85 Aligned_cols=65 Identities=9% Similarity=-0.125 Sum_probs=34.9
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe--CCcccccceEEEEeCCCCChHHHHHH
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA--GELFGRSGYAIGLQKGSPWADAVTLA 69 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~--~~~~~~~~~~ia~~kgs~l~~~vn~~ 69 (90)
+.+++....+..+..|.--+++-.... ...... ..+..+ ........+.++.+++......+...
T Consensus 127 ~~~~~~~~~~~~v~~g~Gi~~~p~~~~-~~~~~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f 193 (201)
T cd08471 127 LTVNTVEAAIAAALAGLGLTRVLSYQV-AEELAA-GRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAF 193 (201)
T ss_pred EEECCHHHHHHHHHcCCcEEEechhHH-HHHhhc-CceEEecccccCCCCcEEEEecCcccCCHHHHHH
Confidence 456778888889999986555544333 222222 233322 21222356777787765443334433
No 288
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=20.48 E-value=79 Score=22.71 Aligned_cols=28 Identities=7% Similarity=-0.056 Sum_probs=21.4
Q ss_pred CccccC---ChHHHHHHhh--cCCceEEEeehhH
Q psy17442 1 MRFDVK---FSPSTVVRHG--TKKLMAFIWDSSR 29 (90)
Q Consensus 1 ~~~~~~---~~~~~~~~l~--~G~ida~i~d~~~ 29 (90)
|+|-++ |.+||+..++ -|. ||+|..+-.
T Consensus 2 ~~~~~~~a~~~~EAm~~ik~elG~-dAvILs~r~ 34 (388)
T PRK12723 2 VQYFTERGPTYNEVIETIKKKYGK-NARVMTYKT 34 (388)
T ss_pred chHHhHhcCCHHHHHHHHHHHHCC-CeEEEEeeE
Confidence 345555 9999999998 577 999987544
No 289
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=20.45 E-value=1.9e+02 Score=16.72 Aligned_cols=63 Identities=11% Similarity=-0.050 Sum_probs=34.4
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe-CCc-ccccceEEEEeCCCCChHHHHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA-GEL-FGRSGYAIGLQKGSPWADAVTL 68 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~-~~~-~~~~~~~ia~~kgs~l~~~vn~ 68 (90)
.+++...+...+.+|.--+++-... +..... ...+... ... .....++++.+++.+....+..
T Consensus 125 ~~~~~~~~~~~v~~g~Gi~~~p~~~-~~~~~~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 189 (194)
T cd08481 125 RFEQFSMLAQAAVAGLGVALLPRFL-IEEELA-RGRLVVPFNLPLTSDKAYYLVYPEDKAESPPVQA 189 (194)
T ss_pred EeccHHHHHHHHHhCCCeEEecHHH-HHHHHH-CCCEEeecCccccCCCeEEEEeCcccccCHHHHH
Confidence 4567778888888988655555433 332322 2233322 111 1234678888887554443333
No 290
>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=20.41 E-value=1.2e+02 Score=16.33 Aligned_cols=24 Identities=8% Similarity=-0.105 Sum_probs=19.9
Q ss_pred ccCChHHHHHHhhcCCceEEEeeh
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~ 27 (90)
.+.+..+++..+.+...|.++.|.
T Consensus 28 ~~~~~~~~~~~~~~~~~d~iiid~ 51 (112)
T PF00072_consen 28 TASSGEEALELLKKHPPDLIIIDL 51 (112)
T ss_dssp EESSHHHHHHHHHHSTESEEEEES
T ss_pred EECCHHHHHHHhcccCceEEEEEe
Confidence 457788999999999999998773
No 291
>TIGR02298 HpaD_Fe 3,4-dihydroxyphenylacetate 2,3-dioxygenase. This enzyme catalyzes the ring-opening step in the degradation of 4-hydroxyphenylacetate.
Probab=20.34 E-value=97 Score=21.09 Aligned_cols=23 Identities=22% Similarity=0.313 Sum_probs=19.8
Q ss_pred ChHHHHHHHHHhhhccHHHHHHH
Q psy17442 62 WADAVTLAILDFHESTVCYLFMA 84 (90)
Q Consensus 62 l~~~vn~~l~~l~~~G~~~~l~~ 84 (90)
+-+++++.+.++.++|.++++.+
T Consensus 205 f~~~~D~~v~~~l~~gd~~~l~~ 227 (282)
T TIGR02298 205 FNRQVDLRVLELWRERDYREFCA 227 (282)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHH
Confidence 46678999999999999998865
No 292
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=20.32 E-value=2e+02 Score=16.82 Aligned_cols=58 Identities=9% Similarity=-0.127 Sum_probs=30.7
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeC--CcccccceEEEEeCCCCChHHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAG--ELFGRSGYAIGLQKGSPWADAV 66 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~--~~~~~~~~~ia~~kgs~l~~~v 66 (90)
.+++...++..+..|.--+++-. ..+... ..+..+. .......+.++.+++.+....+
T Consensus 129 ~~~~~~~~~~~v~~g~Gi~~lp~-~~~~~~----~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 (198)
T cd08461 129 SVPSFLVVPEILAATDMVAFVPS-RLVPNL----EGLQEVELPLEPPGFDVVMAWHERTHRDPAH 188 (198)
T ss_pred EcCchhhHHHHHhcCCeEEEchH-HHHHhh----cCceeecCCCCCCCccEEEecChhhcCCHHH
Confidence 46677778888888874444433 333222 2344332 2223345777777775543333
No 293
>COG0011 Uncharacterized conserved protein [Function unknown]
Probab=20.21 E-value=1.5e+02 Score=17.24 Aligned_cols=24 Identities=29% Similarity=0.261 Sum_probs=19.2
Q ss_pred EEeCC--CC-ChHHHHHHHHHhhhccH
Q psy17442 55 GLQKG--SP-WADAVTLAILDFHESTV 78 (90)
Q Consensus 55 a~~kg--s~-l~~~vn~~l~~l~~~G~ 78 (90)
++|.| ++ +-+.|+.++..++++|.
T Consensus 9 viP~gt~~~svs~yVa~~i~~lk~~gl 35 (100)
T COG0011 9 VIPLGTGGPSVSKYVAEAIEILKESGL 35 (100)
T ss_pred EEecCCCCCCHHHHHHHHHHHHHHcCC
Confidence 34666 56 88999999999999873
No 294
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=20.18 E-value=2.8e+02 Score=18.54 Aligned_cols=56 Identities=14% Similarity=0.023 Sum_probs=32.0
Q ss_pred cccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEe--CCcccccceEEEEeCCC
Q psy17442 3 FDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTA--GELFGRSGYAIGLQKGS 60 (90)
Q Consensus 3 ~~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~--~~~~~~~~~~ia~~kgs 60 (90)
+.+++....+..+.+|..-+++-.... ..... ...+..+ +......++.++.+++.
T Consensus 220 ~~~~~~~~~~~~v~~g~gi~~lp~~~~-~~~~~-~~~l~~~~l~~~~~~~~~~l~~~~~~ 277 (308)
T PRK10094 220 IIVPDMETKIAAHLAGVGIGFLPKSLC-QSMID-NQQLVSRVIPTMRPPSPLSLAWRKFG 277 (308)
T ss_pred EEECCHHHHHHHHHcCCcEEeCChHhh-hHHhh-cCceEEEeCCCCCCCcceEEEEecCC
Confidence 346788888888889985555544333 22222 2234332 33333456778888874
No 295
>PF12698 ABC2_membrane_3: ABC-2 family transporter protein; PDB: 2P0S_B 3CNI_A.
Probab=20.13 E-value=76 Score=20.78 Aligned_cols=22 Identities=14% Similarity=-0.016 Sum_probs=14.6
Q ss_pred ccCChHHHHHHhhcCCceEEEe
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIW 25 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~ 25 (90)
.+++.+++.+++++|++++.+.
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~i~ 83 (344)
T PF12698_consen 62 EYDSEEEAKDALKNGKIDAIIV 83 (344)
T ss_dssp ECS-HHHHHHHHHHHT-SEEEE
T ss_pred eeCCHHHHHHHHHhCCCcEEEE
Confidence 4667777788888887777654
No 296
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=20.13 E-value=2.7e+02 Score=18.28 Aligned_cols=65 Identities=9% Similarity=-0.041 Sum_probs=32.3
Q ss_pred ccCChHHHHHHhhcCCceEEEeehhHHhHHHhcCCCeEEeCC--cccccceEEEEeCCCCChHHHHHHH
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGE--LFGRSGYAIGLQKGSPWADAVTLAI 70 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~~~~~~~~~~~~~l~~~~~--~~~~~~~~ia~~kgs~l~~~vn~~l 70 (90)
...+...++..+..|.--+++-+ ..+.... +...+..+.. ......++++.+|+...-..+...+
T Consensus 225 ~~~~~~~~~~~v~~g~gi~~lp~-~~~~~~~-~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 (300)
T TIGR02424 225 ETVSGSFGRRYVQESDAIWIISR-GVVALDL-ADGTLVELPFDTRETGGPVGLCTRPDTQLSRAAQLFV 291 (300)
T ss_pred EeccHHHHHHHHHhCCceEeCcH-HHHhhhh-cCCcEEEccCCCCCCCCceEEEEeCCCCCCHHHHHHH
Confidence 34455566777777764443322 2222222 1234555432 2223467888899754444444433
No 297
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=20.05 E-value=1.1e+02 Score=15.95 Aligned_cols=24 Identities=8% Similarity=0.001 Sum_probs=17.2
Q ss_pred ChHHHHHHhhcCCceEEEeehhHH
Q psy17442 7 FSPSTVVRHGTKKLMAFIWDSSRL 30 (90)
Q Consensus 7 ~~~~~~~~l~~G~ida~i~d~~~~ 30 (90)
..|+.+..|++|++..+=.+....
T Consensus 11 ~nPevl~kl~~g~asLIGv~~~e~ 34 (57)
T PF05952_consen 11 QNPEVLEKLKEGEASLIGVDKDEQ 34 (57)
T ss_pred HChHHHHHHHcCCeeEecCCHHHH
Confidence 468999999999977664444433
No 298
>PF04166 PdxA: Pyridoxal phosphate biosynthetic protein PdxA; InterPro: IPR005255 Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). Pyridoxal 5'-phosphate (PLP) is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination [, , ]. PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors []. Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy []. PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalysed reactions, enzymatic and non-enzymatic []. In Escherichia coli, the pdx genes involved in vitamin B6 have been characterised [, , ]. This entry represents 4-hydroxythreonine-4-phosphate dehydrogenase (PdxA, 1.1.1.262 from EC). PdxA takes part in vitamin B6 biosynthesis, forming pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate.; GO: 0050570 4-hydroxythreonine-4-phosphate dehydrogenase activity, 0051287 NAD binding, 0008615 pyridoxine biosynthetic process, 0055114 oxidation-reduction process; PDB: 1YXO_A 1PS6_A 1PS7_C 1PTM_B 1R8K_B 2HI1_A 3LXY_A 3TSN_B.
Probab=20.02 E-value=51 Score=22.86 Aligned_cols=24 Identities=8% Similarity=-0.021 Sum_probs=18.7
Q ss_pred ccCChHHHHHHhhcCCceEEEeeh
Q psy17442 4 DVKFSPSTVVRHGTKKLMAFIWDS 27 (90)
Q Consensus 4 ~~~~~~~~~~~l~~G~ida~i~d~ 27 (90)
.++....|+...++|++||++.-.
T Consensus 73 a~~~l~~A~~~~~~g~~dalVTaP 96 (298)
T PF04166_consen 73 AFESLEKAVELAKAGEIDALVTAP 96 (298)
T ss_dssp HHHHHHHHHHHHHTTSSSEEEE--
T ss_pred HHHHHHHHHHHHHcCCCcEEEECC
Confidence 355678899999999999999763
Done!