Query psy2313
Match_columns 62
No_of_seqs 152 out of 1013
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 21:28:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2313.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2313hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1053|consensus 99.7 8.7E-18 1.9E-22 118.3 4.3 58 1-62 470-527 (1258)
2 PF10613 Lig_chan-Glu_bd: Liga 99.7 2E-17 4.3E-22 85.7 3.4 43 1-46 23-65 (65)
3 KOG1054|consensus 99.7 6.9E-17 1.5E-21 110.7 4.4 60 1-62 450-509 (897)
4 KOG4440|consensus 99.5 5.5E-14 1.2E-18 97.2 4.6 62 1-62 467-533 (993)
5 KOG1052|consensus 99.3 3.7E-12 7.9E-17 87.3 4.6 57 1-62 249-305 (656)
6 TIGR03870 ABC_MoxJ methanol ox 98.6 3.4E-08 7.3E-13 60.9 3.8 46 1-62 23-71 (246)
7 PF00497 SBP_bac_3: Bacterial 98.6 2.8E-08 6E-13 58.5 3.1 47 1-62 26-72 (225)
8 PRK15437 histidine ABC transpo 98.6 7.1E-08 1.5E-12 59.5 4.4 47 1-62 53-99 (259)
9 PRK10859 membrane-bound lytic 98.6 9.7E-08 2.1E-12 64.2 4.5 48 1-62 68-115 (482)
10 PRK09495 glnH glutamine ABC tr 98.6 1E-07 2.2E-12 58.3 4.1 47 1-62 51-97 (247)
11 PRK15010 ABC transporter lysin 98.5 1.2E-07 2.6E-12 58.5 4.3 47 1-62 53-99 (260)
12 PRK15007 putative ABC transpor 98.5 1.7E-07 3.7E-12 56.9 4.3 47 1-62 48-94 (243)
13 PRK10797 glutamate and asparta 98.4 4.2E-07 9E-12 57.9 4.6 47 1-62 67-120 (302)
14 TIGR01096 3A0103s03R lysine-ar 98.4 7E-07 1.5E-11 54.2 4.4 47 1-62 51-97 (250)
15 PRK11260 cystine transporter s 98.3 8.6E-07 1.9E-11 54.9 4.4 47 1-62 68-114 (266)
16 PRK11917 bifunctional adhesin/ 98.3 1.4E-06 3.1E-11 54.2 4.2 47 1-62 66-115 (259)
17 PRK09959 hybrid sensory histid 98.2 2.1E-06 4.5E-11 62.1 4.7 48 1-62 84-131 (1197)
18 TIGR02995 ectoine_ehuB ectoine 98.2 1.4E-06 3.1E-11 54.3 3.4 47 1-62 59-106 (275)
19 COG0834 HisJ ABC-type amino ac 98.2 2.9E-06 6.2E-11 51.8 3.9 47 1-62 63-111 (275)
20 TIGR02285 conserved hypothetic 98.0 9.4E-06 2E-10 50.4 4.6 45 2-62 45-90 (268)
21 smart00062 PBPb Bacterial peri 97.7 8.3E-05 1.8E-09 42.5 4.2 45 1-60 27-71 (219)
22 cd00134 PBPb Bacterial peripla 97.7 0.0001 2.2E-09 42.3 4.5 45 2-61 27-71 (218)
23 TIGR03871 ABC_peri_MoxJ_2 quin 97.5 0.00022 4.7E-09 43.0 4.7 41 1-54 23-63 (232)
24 PRK09959 hybrid sensory histid 97.2 0.00073 1.6E-08 49.2 4.6 47 1-62 329-375 (1197)
25 TIGR01098 3A0109s03R phosphate 97.1 0.0018 3.8E-08 39.5 5.0 42 2-57 53-94 (254)
26 COG4623 Predicted soluble lyti 96.8 0.0027 5.9E-08 43.0 4.5 47 2-62 49-95 (473)
27 TIGR03431 PhnD phosphonate ABC 96.2 0.017 3.7E-07 36.2 5.0 40 3-56 49-88 (288)
28 PRK00489 hisG ATP phosphoribos 95.8 0.0085 1.8E-07 38.2 2.5 28 35-62 51-78 (287)
29 PF12974 Phosphonate-bd: ABC t 94.9 0.084 1.8E-06 32.2 4.7 39 3-55 19-57 (243)
30 TIGR01729 taurine_ABC_bnd taur 94.6 0.076 1.6E-06 33.4 4.0 37 7-57 21-57 (300)
31 COG3221 PhnD ABC-type phosphat 94.0 0.15 3.3E-06 33.1 4.5 39 3-55 57-95 (299)
32 cd05466 PBP2_LTTR_substrate Th 92.0 1.2 2.5E-05 24.4 5.8 23 35-57 36-58 (197)
33 cd08430 PBP2_IlvY The C-termin 92.0 0.75 1.6E-05 25.8 5.1 39 2-55 17-56 (199)
34 PF02879 PGM_PMM_II: Phosphogl 91.6 1.3 2.7E-05 23.9 5.6 53 2-54 35-89 (104)
35 cd08468 PBP2_Pa0477 The C-term 91.5 0.86 1.9E-05 26.0 5.0 39 3-56 18-57 (202)
36 TIGR02122 TRAP_TAXI TRAP trans 91.3 0.62 1.3E-05 29.2 4.6 40 3-56 50-90 (320)
37 cd08427 PBP2_LTTR_like_2 The C 91.0 1.2 2.5E-05 24.9 5.2 39 3-56 18-57 (195)
38 PF03466 LysR_substrate: LysR 90.7 1.7 3.7E-05 24.6 5.8 24 35-58 42-65 (209)
39 cd08446 PBP2_Chlorocatechol Th 89.5 2.3 4.9E-05 23.9 5.6 22 35-56 37-58 (198)
40 cd08448 PBP2_LTTR_aromatics_li 89.4 2.4 5.2E-05 23.5 5.7 38 3-55 18-56 (197)
41 cd08456 PBP2_LysR The C-termin 88.9 2.7 5.9E-05 23.4 5.8 39 3-56 18-57 (196)
42 PF09084 NMT1: NMT1/THI5 like; 88.9 1.2 2.5E-05 26.4 4.2 34 9-56 17-50 (216)
43 cd08486 PBP2_CbnR The C-termin 88.8 1.8 3.9E-05 24.7 4.9 21 35-55 37-57 (198)
44 cd08429 PBP2_NhaR The C-termin 88.8 2 4.3E-05 24.9 5.1 22 35-56 36-57 (204)
45 cd08451 PBP2_BudR The C-termin 88.5 2 4.3E-05 24.0 4.9 22 35-56 37-58 (199)
46 cd08466 PBP2_LeuO The C-termin 88.2 2 4.4E-05 24.1 4.8 38 3-55 18-56 (200)
47 cd08442 PBP2_YofA_SoxR_like Th 88.1 2.3 5.1E-05 23.6 5.0 38 3-55 18-56 (193)
48 PF12916 DUF3834: Protein of u 87.9 0.98 2.1E-05 28.1 3.5 39 3-55 83-121 (201)
49 PF13379 NMT1_2: NMT1-like fam 87.9 2.1 4.5E-05 26.3 5.0 34 7-54 29-62 (252)
50 cd08419 PBP2_CbbR_RubisCO_like 87.8 3.2 7E-05 23.0 5.7 39 3-56 17-56 (197)
51 cd08415 PBP2_LysR_opines_like 87.7 3.3 7.1E-05 23.0 5.7 22 35-56 36-57 (196)
52 cd08413 PBP2_CysB_like The C-t 87.7 2.5 5.5E-05 24.0 5.0 22 35-56 36-57 (198)
53 cd08459 PBP2_DntR_NahR_LinR_li 87.6 2.9 6.3E-05 23.5 5.2 22 35-56 36-57 (201)
54 cd08420 PBP2_CysL_like C-termi 87.6 3.3 7.1E-05 22.9 5.8 40 3-57 18-58 (201)
55 cd08434 PBP2_GltC_like The sub 87.4 3.3 7.2E-05 22.8 5.3 22 35-56 36-57 (195)
56 cd08437 PBP2_MleR The substrat 87.2 2.9 6.2E-05 23.5 5.0 21 35-55 36-56 (198)
57 cd08465 PBP2_ToxR The C-termin 87.1 2.6 5.7E-05 24.0 4.9 21 35-55 36-56 (200)
58 PRK11480 tauA taurine transpor 87.0 1.4 3E-05 28.2 4.0 35 8-56 46-80 (320)
59 cd08439 PBP2_LrhA_like The C-t 87.0 3.2 7E-05 23.2 5.2 21 35-55 36-56 (185)
60 cd08418 PBP2_TdcA The C-termin 87.0 3.1 6.7E-05 23.2 5.1 22 35-56 36-57 (201)
61 cd08421 PBP2_LTTR_like_1 The C 86.9 3.8 8.2E-05 22.9 5.6 39 3-56 18-57 (198)
62 cd08440 PBP2_LTTR_like_4 TThe 86.8 3.7 8E-05 22.6 5.8 22 35-56 36-57 (197)
63 cd08450 PBP2_HcaR The C-termin 86.8 3.8 8.3E-05 22.8 5.7 22 35-56 36-57 (196)
64 cd08411 PBP2_OxyR The C-termin 86.7 3.3 7.1E-05 23.2 5.1 21 35-55 37-57 (200)
65 cd08453 PBP2_IlvR The C-termin 86.6 3.4 7.3E-05 23.2 5.1 21 35-55 36-56 (200)
66 cd03770 SR_TndX_transposase Se 86.5 4.2 9.1E-05 23.2 5.4 49 3-54 26-74 (140)
67 cd08431 PBP2_HupR The C-termin 86.5 2.7 5.9E-05 23.5 4.7 38 3-55 18-56 (195)
68 cd08425 PBP2_CynR The C-termin 86.4 4.1 8.8E-05 22.8 5.8 22 35-56 37-58 (197)
69 cd08416 PBP2_MdcR The C-termin 86.3 3.4 7.3E-05 23.1 5.0 39 3-56 18-57 (199)
70 cd08467 PBP2_SyrM The C-termin 86.3 2.5 5.5E-05 24.0 4.5 21 35-55 36-56 (200)
71 cd08438 PBP2_CidR The C-termin 86.3 4.1 8.8E-05 22.6 5.6 22 35-56 36-57 (197)
72 cd08449 PBP2_XapR The C-termin 86.0 3.6 7.8E-05 22.9 5.0 22 35-56 36-57 (197)
73 cd08452 PBP2_AlsR The C-termin 85.9 3.7 7.9E-05 23.2 5.1 38 3-55 18-56 (197)
74 cd08444 PBP2_Cbl The C-termina 85.8 3.7 8E-05 23.2 5.0 21 35-55 36-56 (198)
75 cd08447 PBP2_LTTR_aromatics_li 84.8 4.4 9.6E-05 22.6 5.0 21 35-55 36-56 (198)
76 cd08436 PBP2_LTTR_like_3 The C 84.7 4.3 9.4E-05 22.4 4.9 23 35-57 36-58 (194)
77 cd08412 PBP2_PAO1_like The C-t 84.3 5.3 0.00011 22.2 5.2 38 3-55 18-56 (198)
78 cd08417 PBP2_Nitroaromatics_li 84.3 4.9 0.00011 22.4 5.0 22 35-56 36-57 (200)
79 cd08441 PBP2_MetR The C-termin 84.2 5.5 0.00012 22.3 5.5 21 35-55 36-56 (198)
80 cd08463 PBP2_DntR_like_4 The C 84.1 4.5 9.7E-05 23.2 4.9 40 2-55 17-57 (203)
81 TIGR01728 SsuA_fam ABC transpo 84.0 1.7 3.7E-05 26.5 3.2 22 36-57 38-59 (288)
82 PF03401 TctC: Tripartite tric 83.5 2.6 5.6E-05 26.7 3.9 39 4-56 122-160 (274)
83 cd08423 PBP2_LTTR_like_6 The C 83.4 5.8 0.00013 22.0 5.2 38 3-55 18-56 (200)
84 cd08461 PBP2_DntR_like_3 The C 83.2 6.1 0.00013 22.1 5.1 38 3-55 18-56 (198)
85 cd08445 PBP2_BenM_CatM_CatR Th 83.0 6.5 0.00014 22.2 5.7 22 35-56 37-58 (203)
86 cd08460 PBP2_DntR_like_1 The C 82.8 4.9 0.00011 22.7 4.7 20 35-55 36-55 (200)
87 PRK03601 transcriptional regul 82.7 7.4 0.00016 24.1 5.7 22 35-56 125-146 (275)
88 cd08464 PBP2_DntR_like_2 The C 82.4 4.5 9.8E-05 22.6 4.4 38 3-55 18-56 (200)
89 cd08414 PBP2_LTTR_aromatics_li 82.4 6.2 0.00013 21.8 4.9 22 35-56 36-57 (197)
90 cd08469 PBP2_PnbR The C-termin 82.3 5.9 0.00013 22.7 5.0 22 35-56 36-57 (221)
91 PRK00072 hemC porphobilinogen 82.0 7.9 0.00017 25.4 5.8 51 4-56 23-81 (295)
92 cd08485 PBP2_ClcR The C-termin 81.9 7.1 0.00015 22.1 5.1 21 35-55 37-57 (198)
93 cd08443 PBP2_CysB The C-termin 81.8 6.6 0.00014 22.2 5.0 21 35-55 36-56 (198)
94 smart00857 Resolvase Resolvase 81.8 7.1 0.00015 21.9 5.3 50 2-54 22-71 (148)
95 cd03087 PGM_like1 This archaea 81.6 5.3 0.00011 26.8 5.0 52 3-54 179-231 (439)
96 cd08462 PBP2_NodD The C-termin 80.8 6.5 0.00014 22.2 4.7 17 39-55 39-55 (200)
97 cd08426 PBP2_LTTR_like_5 The C 80.1 8.2 0.00018 21.5 5.6 22 35-56 36-57 (199)
98 cd08435 PBP2_GbpR The C-termin 79.4 8.5 0.00018 21.3 5.0 22 35-56 36-57 (201)
99 cd08428 PBP2_IciA_ArgP The C-t 79.4 6.5 0.00014 22.0 4.4 21 35-55 35-55 (195)
100 PRK11242 DNA-binding transcrip 79.2 12 0.00026 23.0 5.8 23 35-57 127-149 (296)
101 PRK12683 transcriptional regul 79.0 8.6 0.00019 24.3 5.2 21 35-55 129-149 (309)
102 PRK01066 porphobilinogen deami 78.6 12 0.00025 23.9 5.5 51 4-56 36-94 (231)
103 PRK11553 alkanesulfonate trans 78.6 4.7 0.0001 25.5 3.9 20 36-55 65-84 (314)
104 PRK09508 leuO leucine transcri 78.6 8.1 0.00018 24.4 5.0 22 35-56 148-169 (314)
105 TIGR02136 ptsS_2 phosphate bin 78.3 3.2 7E-05 26.2 3.1 22 35-56 71-92 (287)
106 cd08433 PBP2_Nac The C-teminal 78.2 9.6 0.00021 21.2 5.1 21 36-56 37-57 (198)
107 cd00494 HMBS Hydroxymethylbila 77.8 12 0.00026 24.5 5.6 51 4-56 19-77 (292)
108 TIGR00212 hemC porphobilinogen 77.7 12 0.00026 24.5 5.6 51 4-56 19-77 (292)
109 PRK10341 DNA-binding transcrip 77.0 12 0.00026 23.5 5.4 22 35-56 133-154 (312)
110 PF03480 SBP_bac_7: Bacterial 76.5 16 0.00035 22.9 6.1 46 3-57 18-63 (286)
111 TIGR03339 phn_lysR aminoethylp 76.1 15 0.00032 22.3 5.6 21 35-55 120-140 (279)
112 PRK11716 DNA-binding transcrip 75.9 12 0.00026 22.5 5.0 22 35-56 103-124 (269)
113 PRK12684 transcriptional regul 75.8 12 0.00025 23.7 5.1 21 35-55 129-149 (313)
114 cd08516 PBP2_NikA_DppA_OppA_li 75.8 9.5 0.0002 25.2 4.8 39 3-56 337-375 (457)
115 PRK11233 nitrogen assimilation 75.6 17 0.00037 22.8 5.8 21 35-55 128-148 (305)
116 PRK12680 transcriptional regul 74.4 13 0.00028 23.8 5.1 21 35-55 129-149 (327)
117 PRK07377 hypothetical protein; 74.3 10 0.00022 23.4 4.3 41 2-56 97-137 (184)
118 cd00338 Ser_Recombinase Serine 74.1 12 0.00027 20.5 5.3 50 3-54 22-71 (137)
119 PRK12681 cysB transcriptional 74.1 14 0.00029 23.7 5.1 21 35-55 129-149 (324)
120 PRK11151 DNA-binding transcrip 73.6 19 0.00042 22.4 5.8 22 35-56 127-148 (305)
121 PRK10837 putative DNA-binding 72.6 19 0.00042 22.0 5.7 21 35-55 125-145 (290)
122 PF04069 OpuAC: Substrate bind 72.2 16 0.00034 22.6 5.0 40 3-56 19-58 (257)
123 PRK11917 bifunctional adhesin/ 72.0 14 0.0003 22.9 4.7 21 36-56 181-201 (259)
124 cd08490 PBP2_NikA_DppA_OppA_li 72.0 13 0.00028 24.6 4.8 39 4-57 341-379 (470)
125 cd08457 PBP2_OccR The C-termin 71.8 15 0.00033 20.5 5.6 21 36-56 37-57 (196)
126 cd05800 PGM_like2 This PGM-lik 70.5 14 0.0003 25.0 4.7 53 2-54 187-240 (461)
127 PRK12682 transcriptional regul 70.1 17 0.00037 22.8 4.9 22 35-56 129-150 (309)
128 CHL00180 rbcR LysR transcripti 69.8 21 0.00045 22.3 5.2 21 35-55 131-151 (305)
129 cd08507 PBP2_SgrR_like The C-t 69.2 12 0.00026 25.0 4.2 40 3-57 316-355 (448)
130 COG1638 DctP TRAP-type C4-dica 68.9 22 0.00048 23.4 5.3 47 3-58 49-95 (332)
131 PRK11063 metQ DL-methionine tr 68.9 17 0.00036 23.2 4.6 36 4-53 49-85 (271)
132 TIGR00363 lipoprotein, YaeC fa 68.8 21 0.00045 22.7 5.0 31 10-54 43-73 (258)
133 TIGR01256 modA molybdenum ABC 68.5 22 0.00048 21.0 5.1 39 2-55 10-49 (216)
134 cd08512 PBP2_NikA_DppA_OppA_li 68.2 19 0.00042 23.9 5.0 38 4-56 354-391 (476)
135 cd08504 PBP2_OppA The substrat 68.2 16 0.00035 24.4 4.7 40 3-57 362-402 (498)
136 TIGR02424 TF_pcaQ pca operon t 68.2 25 0.00055 21.7 5.3 22 35-56 129-150 (300)
137 TIGR03414 ABC_choline_bnd chol 68.1 14 0.00029 23.7 4.1 38 3-55 26-63 (290)
138 cd06353 PBP1_BmpA_Med_like Per 68.0 18 0.00039 22.6 4.6 41 4-54 23-63 (258)
139 PRK09791 putative DNA-binding 67.7 22 0.00048 22.1 5.0 21 35-55 131-151 (302)
140 cd03089 PMM_PGM The phosphoman 67.2 19 0.00041 24.3 4.8 52 3-54 178-231 (443)
141 PRK09906 DNA-binding transcrip 66.6 28 0.0006 21.5 5.5 23 35-57 126-148 (296)
142 cd08498 PBP2_NikA_DppA_OppA_li 64.9 25 0.00054 23.6 5.0 38 4-56 351-388 (481)
143 COG2113 ProX ABC-type proline/ 64.6 15 0.00032 24.1 3.8 39 3-56 49-87 (302)
144 PRK10918 phosphate ABC transpo 64.0 21 0.00044 23.7 4.5 25 35-60 62-86 (346)
145 COG0715 TauA ABC-type nitrate/ 63.8 10 0.00022 24.0 2.9 31 9-53 56-87 (335)
146 cd08520 PBP2_NikA_DppA_OppA_li 63.6 26 0.00056 23.4 4.9 38 4-56 349-386 (468)
147 PRK10082 cell density-dependen 63.6 20 0.00043 22.4 4.2 22 35-56 134-155 (303)
148 PRK11482 putative DNA-binding 63.3 26 0.00057 22.3 4.8 22 36-57 152-173 (317)
149 PRK13348 chromosome replicatio 62.9 30 0.00065 21.4 4.9 22 35-56 125-146 (294)
150 cd08497 PBP2_NikA_DppA_OppA_li 62.8 28 0.0006 23.6 5.0 39 4-57 366-404 (491)
151 PRK12679 cbl transcriptional r 62.6 29 0.00062 22.0 4.8 22 35-56 129-150 (316)
152 cd08458 PBP2_NocR The C-termin 62.1 26 0.00056 19.6 5.6 22 35-56 36-57 (196)
153 cd08493 PBP2_DppA_like The sub 61.8 30 0.00066 23.1 5.0 39 4-57 359-397 (482)
154 cd08492 PBP2_NikA_DppA_OppA_li 61.4 25 0.00055 23.4 4.6 39 4-57 364-402 (484)
155 cd05799 PGM2 This CD includes 60.9 21 0.00045 24.4 4.2 52 2-54 200-258 (487)
156 cd08511 PBP2_NikA_DppA_OppA_li 60.6 41 0.00088 22.4 5.4 38 5-57 339-376 (467)
157 cd08489 PBP2_NikA The substrat 60.5 28 0.0006 23.3 4.7 34 5-53 355-388 (488)
158 PRK10094 DNA-binding transcrip 60.3 32 0.00069 21.7 4.8 19 36-54 130-148 (308)
159 PRK15092 DNA-binding transcrip 59.8 37 0.0008 21.6 5.0 20 36-55 136-155 (310)
160 PF00496 SBP_bac_5: Bacterial 59.6 30 0.00066 22.0 4.6 39 4-57 314-353 (374)
161 PLN02371 phosphoglucosamine mu 59.1 22 0.00047 25.2 4.1 52 3-54 278-332 (583)
162 cd08499 PBP2_Ylib_like The sub 58.4 36 0.00079 22.7 4.9 38 4-56 338-376 (474)
163 TIGR03427 ABC_peri_uca ABC tra 58.0 32 0.0007 22.5 4.6 32 9-54 31-62 (328)
164 cd08494 PBP2_NikA_DppA_OppA_li 57.8 37 0.0008 22.4 4.8 37 5-56 336-373 (448)
165 cd08501 PBP2_Lpqw The substrat 57.4 27 0.00058 23.4 4.2 39 4-57 366-405 (486)
166 TIGR00975 3a0107s03 phosphate 56.5 31 0.00067 22.3 4.3 25 35-60 35-59 (314)
167 cd05803 PGM_like4 This PGM-lik 56.4 41 0.0009 22.7 5.0 51 3-54 188-239 (445)
168 PRK11119 proX glycine betaine 56.0 23 0.00049 23.3 3.6 38 3-55 47-85 (331)
169 PRK03635 chromosome replicatio 55.9 40 0.00086 21.0 4.6 19 37-55 127-145 (294)
170 PRK11074 putative DNA-binding 54.9 38 0.00082 21.1 4.4 21 35-55 128-148 (300)
171 TIGR03298 argP transcriptional 54.8 42 0.00092 20.7 4.6 18 38-55 128-145 (292)
172 COG0583 LysR Transcriptional r 54.4 46 0.001 20.1 5.0 21 37-57 128-148 (297)
173 PRK09542 manB phosphomannomuta 54.2 46 0.001 22.5 4.9 52 3-54 179-232 (445)
174 PRK15421 DNA-binding transcrip 53.4 56 0.0012 20.7 5.1 20 37-56 127-146 (317)
175 cd03084 phosphohexomutase The 53.0 55 0.0012 21.3 5.0 52 3-54 127-180 (355)
176 PRK06034 hypothetical protein; 52.9 20 0.00042 23.4 2.9 22 35-56 126-147 (279)
177 PLN02691 porphobilinogen deami 52.8 65 0.0014 21.8 5.3 22 35-56 102-124 (351)
178 TIGR02294 nickel_nikA nickel A 52.7 38 0.00083 22.9 4.4 35 4-53 362-396 (500)
179 COG1910 Periplasmic molybdate- 52.6 21 0.00045 22.7 2.9 20 35-55 26-45 (223)
180 PRK15414 phosphomannomutase Cp 52.4 46 0.00099 22.7 4.7 47 8-54 193-243 (456)
181 cd03085 PGM1 Phosphoglucomutas 51.9 39 0.00085 23.8 4.4 52 3-54 222-276 (548)
182 cd08502 PBP2_NikA_DppA_OppA_li 51.9 59 0.0013 21.8 5.1 39 5-58 353-393 (472)
183 cd08514 PBP2_AppA_like The sub 51.8 18 0.00038 24.2 2.7 36 3-53 358-393 (483)
184 cd00995 PBP2_NikA_DppA_OppA_li 51.6 58 0.0013 21.3 5.0 38 4-56 343-381 (466)
185 PRK11013 DNA-binding transcrip 51.6 58 0.0013 20.4 5.8 20 37-56 132-151 (309)
186 PRK14321 glmM phosphoglucosami 51.1 65 0.0014 21.9 5.3 50 3-54 180-231 (449)
187 PRK11062 nhaR transcriptional 50.6 58 0.0013 20.3 4.7 21 35-55 129-149 (296)
188 PTZ00150 phosphoglucomutase-2- 50.5 23 0.0005 25.0 3.1 52 3-54 243-301 (584)
189 COG3181 Uncharacterized protei 50.3 42 0.0009 22.4 4.1 40 4-57 166-205 (319)
190 PF06345 Drf_DAD: DRF Autoregu 48.1 14 0.00031 13.5 1.0 13 37-49 3-15 (15)
191 cd08517 PBP2_NikA_DppA_OppA_li 48.0 78 0.0017 21.0 5.2 36 4-54 354-390 (480)
192 PF12849 PBP_like_2: PBP super 47.9 42 0.00091 20.7 3.8 23 37-59 47-69 (281)
193 PRK09861 cytoplasmic membrane 47.6 52 0.0011 21.0 4.2 37 3-53 49-86 (272)
194 smart00094 TR_FER Transferrin. 47.4 64 0.0014 21.4 4.7 20 35-54 35-54 (332)
195 PF03480 SBP_bac_7: Bacterial 47.0 56 0.0012 20.5 4.3 22 35-56 161-182 (286)
196 PRK11890 phosphate acetyltrans 46.6 40 0.00088 22.3 3.6 47 3-59 58-107 (312)
197 PF03180 Lipoprotein_9: NLPA l 46.2 69 0.0015 20.2 4.5 37 3-53 16-52 (237)
198 COG3888 Predicted transcriptio 46.1 16 0.00035 24.1 1.7 20 37-56 111-130 (321)
199 cd08500 PBP2_NikA_DppA_OppA_li 45.8 68 0.0015 21.8 4.8 39 4-57 364-403 (499)
200 cd05805 MPG1_transferase GTP-m 45.7 77 0.0017 21.4 5.0 51 3-54 183-234 (441)
201 PF13531 SBP_bac_11: Bacterial 44.9 66 0.0014 19.1 4.7 39 2-55 15-54 (230)
202 TIGR00787 dctP tripartite ATP- 44.6 75 0.0016 19.6 5.7 45 3-56 18-62 (257)
203 PRK14315 glmM phosphoglucosami 44.5 99 0.0021 21.0 5.6 50 3-54 191-241 (448)
204 PF11834 DUF3354: Domain of un 44.2 38 0.00082 17.5 2.7 21 2-22 30-50 (69)
205 cd08505 PBP2_NikA_DppA_OppA_li 44.2 93 0.002 21.5 5.3 38 4-56 400-437 (528)
206 KOG0024|consensus 43.8 29 0.00062 23.5 2.6 19 34-52 301-319 (354)
207 PRK09986 DNA-binding transcrip 43.4 77 0.0017 19.4 4.5 18 37-54 135-152 (294)
208 PRK14317 glmM phosphoglucosami 43.3 89 0.0019 21.3 5.0 50 3-54 203-253 (465)
209 TIGR00067 glut_race glutamate 43.2 30 0.00065 21.8 2.6 53 3-56 13-69 (251)
210 PRK11899 prephenate dehydratas 42.6 24 0.00051 22.8 2.1 22 35-56 34-55 (279)
211 PRK15109 antimicrobial peptide 41.5 1E+02 0.0023 21.3 5.2 40 3-57 399-438 (547)
212 COG0077 PheA Prephenate dehydr 41.4 25 0.00055 22.9 2.1 22 35-56 33-54 (279)
213 COG1428 Deoxynucleoside kinase 41.2 28 0.0006 22.0 2.2 22 3-24 20-41 (216)
214 PRK09755 putative ABC transpor 41.1 1E+02 0.0022 21.3 5.0 32 11-57 404-435 (535)
215 cd08496 PBP2_NikA_DppA_OppA_li 41.0 1.1E+02 0.0023 20.4 5.1 40 4-58 334-374 (454)
216 KOG1879|consensus 40.6 32 0.00069 27.3 2.7 19 2-20 1227-1245(1470)
217 cd08432 PBP2_GcdR_TrpI_HvrB_Am 40.6 53 0.0012 17.9 3.2 16 40-55 38-53 (194)
218 cd08312 Death_MyD88 Death doma 40.5 14 0.00031 19.2 0.7 12 4-15 19-30 (79)
219 cd08311 Death_p75NR Death doma 39.8 15 0.00033 19.3 0.7 15 4-18 18-32 (77)
220 PF14503 YhfZ_C: YhfZ C-termin 39.6 77 0.0017 20.2 4.0 29 12-55 136-164 (232)
221 PRK14316 glmM phosphoglucosami 39.4 1.2E+02 0.0026 20.5 5.5 50 3-54 188-238 (448)
222 PRK14320 glmM phosphoglucosami 37.8 1.1E+02 0.0024 20.7 4.8 50 3-54 187-237 (443)
223 PRK10116 universal stress prot 37.5 72 0.0016 17.4 5.0 21 35-55 89-109 (142)
224 PF00800 PDT: Prephenate dehyd 36.9 34 0.00073 20.3 2.0 23 35-57 30-52 (181)
225 PRK14324 glmM phosphoglucosami 36.8 1.4E+02 0.0029 20.4 5.5 50 3-54 190-240 (446)
226 PRK09590 celB cellobiose phosp 36.8 76 0.0016 17.5 4.6 17 3-19 20-36 (104)
227 PF01784 NIF3: NIF3 (NGG1p int 36.6 1.1E+02 0.0023 19.1 5.4 52 2-55 146-198 (241)
228 PRK14314 glmM phosphoglucosami 36.3 1.4E+02 0.003 20.3 5.4 50 3-54 192-242 (450)
229 PF13189 Cytidylate_kin2: Cyti 36.3 31 0.00067 20.3 1.8 13 3-15 15-27 (179)
230 PF11761 CbiG_mid: Cobalamin b 36.1 22 0.00048 18.3 1.0 14 35-48 19-32 (93)
231 cd08802 Death_UNC5B Death doma 35.9 19 0.00042 19.3 0.8 11 4-14 23-33 (84)
232 PF09568 RE_MjaI: MjaI restric 35.7 22 0.00048 21.7 1.1 24 3-26 97-120 (170)
233 PRK15046 2-aminoethylphosphona 35.5 1.2E+02 0.0027 19.5 4.8 38 3-55 52-93 (349)
234 cd08513 PBP2_thermophilic_Hb8_ 35.5 1.1E+02 0.0025 20.4 4.5 38 4-56 357-395 (482)
235 PRK14318 glmM phosphoglucosami 35.3 1.4E+02 0.0031 20.2 5.5 50 3-54 190-240 (448)
236 PRK10677 modA molybdate transp 35.2 1.1E+02 0.0025 19.0 5.0 38 3-55 44-82 (257)
237 PRK10216 DNA-binding transcrip 34.6 1.2E+02 0.0026 19.1 4.7 17 39-55 136-152 (319)
238 cd08506 PBP2_clavulanate_OppA2 34.4 1.4E+02 0.0031 19.9 4.9 38 4-56 338-378 (466)
239 cd08804 Death_ank2 Death domai 34.2 21 0.00045 18.9 0.8 15 4-18 18-32 (84)
240 COG1109 {ManB} Phosphomannomut 33.7 1.6E+02 0.0034 20.2 5.1 52 3-54 193-245 (464)
241 cd08803 Death_ank3 Death domai 33.5 21 0.00047 18.9 0.7 12 4-15 18-29 (84)
242 PF04509 CheC: CheC-like famil 33.3 54 0.0012 14.7 2.5 17 4-20 18-34 (38)
243 PF01379 Porphobil_deam: Porph 32.6 42 0.00092 21.1 2.0 22 35-56 56-78 (215)
244 cd08310 Death_NFkB-like Death 32.5 23 0.0005 18.2 0.7 13 4-16 15-27 (72)
245 PRK10622 pheA bifunctional cho 32.2 41 0.00089 22.7 2.0 22 35-56 137-158 (386)
246 COG1961 PinR Site-specific rec 32.0 1.2E+02 0.0026 18.3 5.1 47 2-53 22-68 (222)
247 PRK11898 prephenate dehydratas 31.8 44 0.00095 21.5 2.1 22 35-56 34-55 (283)
248 PRK15104 oligopeptide ABC tran 31.4 1.6E+02 0.0034 20.4 4.8 33 9-56 410-442 (543)
249 PF04914 DltD_C: DltD C-termin 31.0 66 0.0014 18.5 2.5 20 2-21 39-58 (130)
250 PRK14498 putative molybdopteri 30.9 1.1E+02 0.0024 21.7 4.1 22 35-56 448-469 (633)
251 COG0283 Cmk Cytidylate kinase 30.5 40 0.00087 21.4 1.7 13 3-15 20-32 (222)
252 PF07833 Cu_amine_oxidN1: Copp 30.4 53 0.0011 16.6 1.9 15 4-18 9-23 (93)
253 cd08777 Death_RIP1 Death Domai 29.5 39 0.00086 17.9 1.4 13 4-16 16-28 (86)
254 PF14399 Transpep_BrtH: NlpC/p 29.4 1.4E+02 0.0031 18.7 4.1 44 2-55 53-96 (317)
255 PF11057 Cortexin: Cortexin of 29.1 31 0.00068 18.4 0.9 20 35-54 62-81 (81)
256 PF05687 DUF822: Plant protein 28.9 48 0.001 19.8 1.7 15 2-16 49-63 (150)
257 PF09862 DUF2089: Protein of u 28.8 38 0.00082 19.2 1.2 47 4-50 52-104 (113)
258 PRK13626 transcriptional regul 28.1 1.8E+02 0.004 20.2 4.7 38 3-57 422-459 (552)
259 cd08318 Death_NMPP84 Death dom 27.9 44 0.00095 17.6 1.3 12 4-15 21-32 (86)
260 COG4143 TbpA ABC-type thiamine 27.6 1.2E+02 0.0026 20.5 3.6 42 3-54 46-87 (336)
261 PF13847 Methyltransf_31: Meth 26.8 97 0.0021 17.3 2.8 39 2-56 42-81 (152)
262 PF01976 DUF116: Protein of un 26.6 1.5E+02 0.0032 17.6 4.7 35 3-53 77-111 (158)
263 COG2358 Imp TRAP-type uncharac 26.5 94 0.002 20.7 2.9 38 3-54 46-84 (321)
264 PLN02307 phosphoglucomutase 26.4 1.7E+02 0.0036 21.0 4.3 29 3-31 239-270 (579)
265 PRK09501 potD spermidine/putre 25.7 1.9E+02 0.0041 18.6 5.1 39 2-54 41-82 (348)
266 COG1110 Reverse gyrase [DNA re 25.7 1.5E+02 0.0033 23.3 4.1 41 2-57 349-392 (1187)
267 cd08519 PBP2_NikA_DppA_OppA_li 25.6 2.1E+02 0.0046 19.1 4.9 22 35-56 364-385 (469)
268 TIGR01276 thiB thiamine ABC tr 25.5 1.8E+02 0.0039 18.2 5.0 38 3-54 22-63 (309)
269 cd08509 PBP2_TmCBP_oligosaccha 25.4 2.2E+02 0.0047 19.4 4.6 33 3-50 371-403 (509)
270 TIGR01254 sfuA ABC transporter 25.4 1.8E+02 0.0039 18.2 4.9 38 3-54 22-63 (304)
271 cd05802 GlmM GlmM is a bacteri 25.2 2.2E+02 0.0048 19.2 5.4 50 3-54 184-234 (434)
272 cd03088 ManB ManB is a bacteri 25.2 2.3E+02 0.005 19.3 5.1 51 3-54 180-231 (459)
273 TIGR00412 redox_disulf_2 small 25.2 1E+02 0.0022 15.4 2.9 19 3-21 19-37 (76)
274 PRK15118 universal stress glob 25.1 1.3E+02 0.0028 16.4 4.5 21 36-56 91-111 (144)
275 PRK15329 chaperone protein Sic 25.1 78 0.0017 18.7 2.1 16 2-17 6-21 (138)
276 PF00766 ETF_alpha: Electron t 24.9 72 0.0016 17.2 1.8 19 1-19 23-41 (86)
277 COG0181 HemC Porphobilinogen d 24.9 53 0.0012 21.8 1.6 22 35-56 58-80 (307)
278 PF00035 dsrm: Double-stranded 24.8 92 0.002 14.6 2.4 19 2-20 3-21 (67)
279 PF04111 APG6: Autophagy prote 24.6 95 0.0021 20.4 2.7 17 3-19 181-200 (314)
280 PLN02317 arogenate dehydratase 24.6 68 0.0015 21.9 2.1 22 35-56 124-145 (382)
281 cd08317 Death_ank Death domain 24.6 55 0.0012 17.0 1.4 12 4-15 18-29 (84)
282 TIGR01455 glmM phosphoglucosam 24.4 2.3E+02 0.005 19.1 5.5 50 3-54 187-237 (443)
283 PRK10887 glmM phosphoglucosami 24.2 2.4E+02 0.0051 19.1 5.4 50 3-54 186-236 (443)
284 TIGR02706 P_butyryltrans phosp 24.1 2.1E+02 0.0045 18.5 4.5 17 40-56 79-95 (294)
285 PF09140 MipZ: ATPase MipZ; I 23.9 62 0.0013 21.1 1.7 17 2-18 195-211 (261)
286 PF06506 PrpR_N: Propionate ca 23.7 1.7E+02 0.0036 17.2 4.1 43 4-57 92-134 (176)
287 TIGR00083 ribF riboflavin kina 23.5 64 0.0014 21.0 1.7 43 2-52 119-161 (288)
288 PF09379 FERM_N: FERM N-termin 23.4 61 0.0013 16.1 1.4 13 2-14 21-33 (80)
289 TIGR00246 tRNA_RlmH_YbeA rRNA 22.8 1.3E+02 0.0028 17.7 2.8 13 48-60 114-128 (153)
290 PF04459 DUF512: Protein of un 22.6 2E+02 0.0044 17.8 5.5 51 3-53 111-166 (204)
291 COG4002 Predicted phosphotrans 22.4 62 0.0013 20.7 1.4 33 9-54 37-69 (256)
292 cd08508 PBP2_NikA_DppA_OppA_li 22.3 2.5E+02 0.0055 18.8 5.5 17 4-20 345-361 (470)
293 PRK08190 bifunctional enoyl-Co 22.2 1.9E+02 0.0041 19.9 3.9 19 39-57 241-259 (466)
294 PRK04021 hypothetical protein; 22.1 1.2E+02 0.0026 16.4 2.4 17 2-18 50-66 (92)
295 PF02621 VitK2_biosynth: Menaq 22.1 1.7E+02 0.0037 18.3 3.4 22 35-56 31-52 (251)
296 PRK10222 PTS system L-ascorbat 22.0 1.4E+02 0.003 15.7 3.5 16 4-19 7-22 (85)
297 cd08799 Death_UNC5C Death doma 21.9 60 0.0013 17.4 1.2 11 4-14 23-33 (84)
298 cd00560 PanC Pantoate-beta-ala 21.7 97 0.0021 20.1 2.3 18 2-19 156-173 (277)
299 PF13207 AAA_17: AAA domain; P 21.7 84 0.0018 16.6 1.8 13 3-15 15-27 (121)
300 PF13369 Transglut_core2: Tran 21.5 1.4E+02 0.0031 17.1 2.8 21 3-23 73-93 (152)
301 TIGR00251 conserved hypothetic 20.9 1.4E+02 0.0031 16.0 2.5 17 2-18 49-65 (87)
302 cd08478 PBP2_CrgA The C-termin 20.8 62 0.0013 17.9 1.2 14 43-56 44-57 (199)
303 PRK11205 tbpA thiamine transpo 20.7 2.4E+02 0.0052 17.9 5.1 39 2-54 42-84 (330)
304 PF12727 PBP_like: PBP superfa 20.7 2.1E+02 0.0045 17.2 5.1 24 35-59 19-42 (193)
305 PF12953 DUF3842: Domain of un 20.5 39 0.00085 19.8 0.3 53 3-58 16-74 (131)
306 PF11823 DUF3343: Protein of u 20.2 1.3E+02 0.0028 15.0 2.2 20 4-23 17-36 (73)
307 cd08306 Death_FADD Fas-associa 20.2 76 0.0016 16.7 1.4 11 4-14 16-26 (86)
308 PF02310 B12-binding: B12 bind 20.2 1.6E+02 0.0034 15.6 5.0 41 3-56 19-59 (121)
309 cd02065 B12-binding_like B12 b 20.2 1.6E+02 0.0034 15.6 4.3 42 3-57 18-59 (125)
No 1
>KOG1053|consensus
Probab=99.71 E-value=8.7e-18 Score=118.30 Aligned_cols=58 Identities=33% Similarity=0.808 Sum_probs=56.1
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
||||++||+.++|+|+++.+.|++||.+.. |.|+||||+|..++|||||++++|++||
T Consensus 470 IDiLkKlA~~v~FtYDLYlVtnGKhGkk~n----g~WnGmIGev~~~rA~MAVgSltINeeR 527 (1258)
T KOG1053|consen 470 IDILKKLARDVKFTYDLYLVTNGKHGKKIN----GVWNGMIGEVVYQRADMAVGSLTINEER 527 (1258)
T ss_pred HHHHHHHHhhcCcceEEEEecCCcccceec----CcchhhHHHHHhhhhheeeeeeEechhh
Confidence 799999999999999999999999999874 8999999999999999999999999998
No 2
>PF10613 Lig_chan-Glu_bd: Ligated ion channel L-glutamate- and glycine-binding site; InterPro: IPR019594 This entry, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine [, ]. It is found in association with IPR001320 from INTERPRO. ; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 4E0W_A 3S9E_A 3QXM_B 2F34_A 3C34_B 3S2V_A 3GBB_B 2F36_D 4E0X_A 1TXF_A ....
Probab=99.69 E-value=2e-17 Score=85.74 Aligned_cols=43 Identities=47% Similarity=1.056 Sum_probs=36.6
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhc
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVT 46 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~ 46 (62)
||||++||+.+||+|+++.++|++||.+++ +|+|+||||+|++
T Consensus 23 iDll~~la~~l~F~y~i~~~~Dg~yG~~~~---~g~W~GmiGeli~ 65 (65)
T PF10613_consen 23 IDLLEELAEELNFTYEIYLVPDGKYGSKNP---NGSWNGMIGELIR 65 (65)
T ss_dssp HHHHHHHHHHHT-EEEEEE-TTS--EEBET---TSEBEHHHHHHHT
T ss_pred HHHHHHHHHHcCCeEEEEECCCCCCcCcCC---CCcCcCHHHHhcC
Confidence 699999999999999999999999999998 4999999999974
No 3
>KOG1054|consensus
Probab=99.66 E-value=6.9e-17 Score=110.71 Aligned_cols=60 Identities=38% Similarity=0.788 Sum_probs=56.3
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
|||+.+|||+.+++|++.+++|++||.++++ +..|+||+|+|.+|+||+|++|+|||.+|
T Consensus 450 vdLa~~iAkhi~~~Y~l~iv~dgkyGardaD--~k~WnGMvGeLv~grAdiavApLTIt~~R 509 (897)
T KOG1054|consen 450 VDLAAEIAKHIGIKYKLFIVGDGKYGARDAD--TKIWNGMVGELVYGRADIAVAPLTITLVR 509 (897)
T ss_pred HHHHHHHHHhcCceEEEEEecCCcccccCCC--cccccchhHHHhcCccceEEeeeeeehhh
Confidence 6999999999999999999999999999985 33499999999999999999999999987
No 4
>KOG4440|consensus
Probab=99.47 E-value=5.5e-14 Score=97.17 Aligned_cols=62 Identities=39% Similarity=0.839 Sum_probs=55.0
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceec-cC----CCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVR-EN----QKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~-~~----~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
||||-.|++.+||+|+....+|+++|.+.. ++ ...+|+||||+|.+++|||+++++||++||
T Consensus 467 IDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMivaplTINpER 533 (993)
T KOG4440|consen 467 IDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMIVAPLTINPER 533 (993)
T ss_pred HHHHHHHHHhhcceEEEEEeecccccceeeeecccccccceehhhhhhhhCCccceEeeceeeChhh
Confidence 699999999999999999999999997653 21 124699999999999999999999999998
No 5
>KOG1052|consensus
Probab=99.29 E-value=3.7e-12 Score=87.33 Aligned_cols=57 Identities=35% Similarity=0.800 Sum_probs=53.6
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+||++++++.+||+|+++.++++. |.++++ |.|+||+++|.+|++|++ ++++||++|
T Consensus 249 idll~~l~~~l~f~~~~~~~~~~~-g~~~~~---g~~~g~v~~l~~~~advg-~~~tit~~R 305 (656)
T KOG1052|consen 249 IDLLQALAKRLNFSYEIIFVPDGS-GSRDPN---GNWDGLVGQLVDGEADVG-ADITITPER 305 (656)
T ss_pred ehHHHHHHHhCCCceEEEEcCCCC-CCCCCC---CChhHHHHHHhcCccccc-cceEEeecc
Confidence 689999999999999999999988 888873 899999999999999999 999999987
No 6
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=98.65 E-value=3.4e-08 Score=60.88 Aligned_cols=46 Identities=9% Similarity=0.060 Sum_probs=40.6
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHH---HhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVV---GDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~i---g~l~~g~~D~av~~ltit~eR 62 (62)
|||+++||+++|++++++. ..|++++ ..|.+|++|+++ ++++|++|
T Consensus 23 vdl~~~ia~~lg~~~~~~~---------------~~~~~~~~~~~~L~~g~~Dii~-~~~~t~~r 71 (246)
T TIGR03870 23 NKIAAALAAAMGRKVVFVW---------------LAKPAIYLVRDGLDKKLCDVVL-GLDTGDPR 71 (246)
T ss_pred HHHHHHHHHHhCCCeEEEE---------------eccchhhHHHHHHhcCCccEEE-eCCCChHH
Confidence 5899999999999999985 4698877 699999999988 58998876
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=98.64 E-value=2.8e-08 Score=58.52 Aligned_cols=47 Identities=28% Similarity=0.483 Sum_probs=42.0
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+|+++++++++|++++++. ..|+.++..|.+|++|+++++++.|++|
T Consensus 26 ~dl~~~i~~~~g~~~~~~~---------------~~~~~~~~~l~~g~~D~~~~~~~~~~~r 72 (225)
T PF00497_consen 26 VDLLRAIAKRLGIKIEFVP---------------MPWSRLLEMLENGKADIIIGGLSITPER 72 (225)
T ss_dssp HHHHHHHHHHHTCEEEEEE---------------EEGGGHHHHHHTTSSSEEESSEB-BHHH
T ss_pred HHHHHHHHhhcccccceee---------------cccccccccccccccccccccccccccc
Confidence 4899999999999999986 2699999999999999999999988775
No 8
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=98.61 E-value=7.1e-08 Score=59.53 Aligned_cols=47 Identities=13% Similarity=0.305 Sum_probs=43.4
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+|+++++++++|.+++++. ..|+.++.++.+|++|+++++++.|++|
T Consensus 53 vdi~~~ia~~lg~~i~~~~---------------~pw~~~~~~l~~g~~D~~~~~~~~t~eR 99 (259)
T PRK15437 53 IDLAKELCKRINTQCTFVE---------------NPLDALIPSLKAKKIDAIMSSLSITEKR 99 (259)
T ss_pred HHHHHHHHHHcCCceEEEe---------------CCHHHHHHHHHCCCCCEEEecCCCCHHH
Confidence 5899999999999999985 4699999999999999999999999887
No 9
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=98.57 E-value=9.7e-08 Score=64.18 Aligned_cols=48 Identities=21% Similarity=0.333 Sum_probs=43.9
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+||++++++++|++++++.. ..|+.++..|.+|++|++++++++|++|
T Consensus 68 ~DLl~~ia~~LGv~~e~v~~--------------~~~~~ll~aL~~G~iDi~~~~lt~T~eR 115 (482)
T PRK10859 68 YELAKRFADYLGVKLEIKVR--------------DNISQLFDALDKGKADLAAAGLTYTPER 115 (482)
T ss_pred HHHHHHHHHHhCCcEEEEec--------------CCHHHHHHHHhCCCCCEEeccCcCChhh
Confidence 58999999999999999853 4799999999999999999999999987
No 10
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=98.56 E-value=1e-07 Score=58.32 Aligned_cols=47 Identities=28% Similarity=0.556 Sum_probs=42.7
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+||++++++++|.+++++. ..|.+++..|.+|++|+++++++.|++|
T Consensus 51 vdl~~~ia~~lg~~~~~~~---------------~~~~~~~~~l~~G~vDi~~~~~~~t~~R 97 (247)
T PRK09495 51 IDLWAAIAKELKLDYTLKP---------------MDFSGIIPALQTKNVDLALAGITITDER 97 (247)
T ss_pred HHHHHHHHHHhCCceEEEe---------------CCHHHHHHHHhCCCcCEEEecCccCHHH
Confidence 5899999999999999975 3699999999999999999899988876
No 11
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=98.55 E-value=1.2e-07 Score=58.53 Aligned_cols=47 Identities=13% Similarity=0.316 Sum_probs=43.1
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+||++++++++|.+++++. ..|+.++.++..|++|+++++++.|++|
T Consensus 53 vdl~~~ia~~lg~~~~~~~---------------~~~~~~~~~l~~g~~Di~~~~~~~t~eR 99 (260)
T PRK15010 53 IDLGNEMCKRMQVKCTWVA---------------SDFDALIPSLKAKKIDAIISSLSITDKR 99 (260)
T ss_pred HHHHHHHHHHhCCceEEEe---------------CCHHHHHHHHHCCCCCEEEecCcCCHHH
Confidence 5899999999999999985 3699999999999999999999999887
No 12
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=98.52 E-value=1.7e-07 Score=56.87 Aligned_cols=47 Identities=13% Similarity=0.313 Sum_probs=42.6
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+|++++|++++|++++++. ..|+.++..+..|++|+++++++.+++|
T Consensus 48 ~dl~~~i~~~lg~~~~~~~---------------~~~~~~~~~l~~g~~D~~~~~~~~~~~r 94 (243)
T PRK15007 48 VDLAQALCKEIDATCTFSN---------------QAFDSLIPSLKFRRVEAVMAGMDITPER 94 (243)
T ss_pred HHHHHHHHHHhCCcEEEEe---------------CCHHHHhHHHhCCCcCEEEEcCccCHHH
Confidence 5899999999999999975 4699999999999999998888888876
No 13
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=98.43 E-value=4.2e-07 Score=57.91 Aligned_cols=47 Identities=17% Similarity=0.159 Sum_probs=38.3
Q ss_pred ChHHHHHHH----HcC---CeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQ----ELE---FDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~----~l~---f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
||++++|++ ++| ++++++. ..|..++..|..|++|++++++++|++|
T Consensus 67 idl~~~ia~~l~~~lg~~~~~~~~v~---------------~~~~~~i~~L~~G~~Di~~~~~~~t~eR 120 (302)
T PRK10797 67 QDYSNAIVEAVKKKLNKPDLQVKLIP---------------ITSQNRIPLLQNGTFDFECGSTTNNLER 120 (302)
T ss_pred HHHHHHHHHHHHHhhCCCCceEEEEE---------------cChHhHHHHHHCCCccEEecCCccCcch
Confidence 476666665 554 6777775 4688899999999999999999999998
No 14
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=98.37 E-value=7e-07 Score=54.21 Aligned_cols=47 Identities=15% Similarity=0.374 Sum_probs=41.8
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+|+++.+++.+|++++++. ..|..++..|.+|++|+++++++.+++|
T Consensus 51 ~dl~~~i~~~lg~~~~~~~---------------~~~~~~~~~l~~G~~D~~~~~~~~~~~r 97 (250)
T TIGR01096 51 VDLAKALCKRMKAKCKFVE---------------QNFDGLIPSLKAKKVDAIMATMSITPKR 97 (250)
T ss_pred HHHHHHHHHHhCCeEEEEe---------------CCHHHHHHHHhCCCcCEEEecCccCHHH
Confidence 5899999999999999975 4699999999999999998888877765
No 15
>PRK11260 cystine transporter subunit; Provisional
Probab=98.34 E-value=8.6e-07 Score=54.88 Aligned_cols=47 Identities=21% Similarity=0.444 Sum_probs=42.2
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+|+++.|++++|.+++++. ..|..++..|.+|++|+++++++.+++|
T Consensus 68 ~dl~~~i~~~lg~~~e~~~---------------~~~~~~~~~l~~G~~D~~~~~~~~~~~r 114 (266)
T PRK11260 68 VEFAEALAKHLGVKASLKP---------------TKWDGMLASLDSKRIDVVINQVTISDER 114 (266)
T ss_pred HHHHHHHHHHHCCeEEEEe---------------CCHHHHHHHHhcCCCCEEEeccccCHHH
Confidence 5899999999999999986 3699999999999999999888888775
No 16
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=98.27 E-value=1.4e-06 Score=54.18 Aligned_cols=47 Identities=17% Similarity=0.197 Sum_probs=38.8
Q ss_pred ChHHHHHHHHc-CCe--EEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQEL-EFD--FHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l-~f~--~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+||++++++++ |.. ++++. ..|...+..|.+|++|++++++++|++|
T Consensus 66 vdl~~~ia~~llg~~~~~~~~~---------------~~~~~~~~~l~~g~~D~~~~~~~~t~eR 115 (259)
T PRK11917 66 IDVAKLLAKSILGDDKKIKLVA---------------VNAKTRGPLLDNGSVDAVIATFTITPER 115 (259)
T ss_pred HHHHHHHHHHhcCCCccEEEEE---------------cChhhHHHHHHCCCccEEEecccCChhh
Confidence 58999999995 754 55543 3577788999999999999999999988
No 17
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=98.22 E-value=2.1e-06 Score=62.05 Aligned_cols=48 Identities=17% Similarity=0.232 Sum_probs=43.7
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+|+++.|++.+|.+++++.. .+|+.++..|.+|++|++.+.++.|++|
T Consensus 84 ~D~l~~ia~~lG~~~e~v~~--------------~~~~~~l~~l~~g~iDl~~~~~~~~~~r 131 (1197)
T PRK09959 84 ADYLNLLKRALNIKLTLREY--------------ADHQKAMDALEEGEVDIVLSHLVASPPL 131 (1197)
T ss_pred HHHHHHHHHhcCCceEEEeC--------------CCHHHHHHHHHcCCCcEecCcccccccc
Confidence 58999999999999999863 3799999999999999999989888876
No 18
>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=98.22 E-value=1.4e-06 Score=54.25 Aligned_cols=47 Identities=19% Similarity=0.267 Sum_probs=41.1
Q ss_pred ChHHHHHHHHcCCe-EEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFD-FHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~-~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+||++++++++|.+ +++.. ..|+.++..|..|++|++++++++|++|
T Consensus 59 ~dl~~~i~~~lg~~~~~~~~---------------~~w~~~~~~l~~G~~Di~~~~~~~t~eR 106 (275)
T TIGR02995 59 PDVARAIFKRLGIADVNASI---------------TEYGALIPGLQAGRFDAIAAGLFIKPER 106 (275)
T ss_pred HHHHHHHHHHhCCCceeecc---------------CCHHHHHHHHHCCCcCEEeecccCCHHH
Confidence 58999999999997 56654 4799999999999999998889988876
No 19
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=98.17 E-value=2.9e-06 Score=51.79 Aligned_cols=47 Identities=26% Similarity=0.505 Sum_probs=40.9
Q ss_pred ChHHHHHHHHcCCe--EEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFD--FHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~--~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+|+++++++.++.. ++++. ..|++++..|.+|++|++++.+++|++|
T Consensus 63 vdl~~~ia~~l~~~~~~~~~~---------------~~~~~~~~~l~~g~~D~~~~~~~~t~er 111 (275)
T COG0834 63 VDLAKAIAKRLGGDKKVEFVP---------------VAWDGLIPALKAGKVDIIIAGMTITPER 111 (275)
T ss_pred HHHHHHHHHHhCCcceeEEec---------------cchhhhhHHHhcCCcCEEEeccccCHHH
Confidence 68999999998886 45543 5799999999999999999999999865
No 20
>TIGR02285 conserved hypothetical protein. Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown.
Probab=98.05 E-value=9.4e-06 Score=50.37 Aligned_cols=45 Identities=16% Similarity=0.307 Sum_probs=39.6
Q ss_pred hHHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 2 DLLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 2 dll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
++++++++.+ ++++++.. ..|+.++..| .++.|.++.++++|+||
T Consensus 45 ~i~~~i~~~~~~~~~~~~~---------------~pw~r~l~~l-~~~~d~~~~~~~~t~eR 90 (268)
T TIGR02285 45 VILQEIRRALPQYEHRFVR---------------VSFARSLKEL-QGKGGVCTVNLLRTPER 90 (268)
T ss_pred HHHHHHHHHcCCCceeEEE---------------CCHHHHHHHH-hcCCCeEEeeccCCcch
Confidence 6788999998 88888885 4799999999 78889888899999998
No 21
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=97.69 E-value=8.3e-05 Score=42.51 Aligned_cols=45 Identities=20% Similarity=0.387 Sum_probs=38.4
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCcccc
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSS 60 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~ 60 (62)
+|+++.+.+++|+++++.. ..|..++..+.+|++|+++++...+.
T Consensus 27 ~~~~~~~~~~~g~~~~~~~---------------~~~~~~~~~l~~g~~D~~~~~~~~~~ 71 (219)
T smart00062 27 VDLAKAIAKELGLKVEFVE---------------VSFDNLLTALKSGKIDVVAAGMTITP 71 (219)
T ss_pred HHHHHHHHHHhCCeEEEEe---------------ccHHHHHHHHHCCcccEEeccccCCH
Confidence 3689999999999999975 37999999999999999998765443
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=97.68 E-value=0.0001 Score=42.28 Aligned_cols=45 Identities=24% Similarity=0.508 Sum_probs=38.7
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccC
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSST 61 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~e 61 (62)
|+++.++++++.+++++. ..|..++..|.+|++|+++++.+.+.+
T Consensus 27 ~~~~~~~~~~g~~~~~~~---------------~~~~~~~~~l~~g~~D~~~~~~~~~~~ 71 (218)
T cd00134 27 DLAKAIAKELGVKVKFVE---------------VDWDGLITALKSGKVDLIAAGMTITPE 71 (218)
T ss_pred HHHHHHHHHhCCeEEEEe---------------CCHHHHHHHHhcCCcCEEeecCcCCHH
Confidence 789999999999988886 359999999999999999987755544
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=97.55 E-value=0.00022 Score=42.95 Aligned_cols=41 Identities=12% Similarity=0.179 Sum_probs=32.5
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
+||++++++++|.+++++..+ ..|.-++..|.+|++|++++
T Consensus 23 ~el~~~i~~~~g~~i~~~~~~-------------~~~~~~~~~l~~g~~Di~~~ 63 (232)
T TIGR03871 23 NKIAQLLADDLGLPLEYTWFP-------------QRRGFVRNTLNAGRCDVVIG 63 (232)
T ss_pred HHHHHHHHHHcCCceEEEecC-------------cchhhHHHHHhcCCccEEEe
Confidence 589999999999999998532 12443567899999999876
No 24
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.18 E-value=0.00073 Score=49.23 Aligned_cols=47 Identities=19% Similarity=0.102 Sum_probs=38.6
Q ss_pred ChHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 1 MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+|++++|++++|++++++.. ..|..+...|.+|++|++. +++.|++|
T Consensus 329 ~Dll~~i~~~~g~~~~~v~~--------------~~~~~~~~~l~~g~~D~i~-~~~~t~~r 375 (1197)
T PRK09959 329 GDILNIITLQTGLNFSPITV--------------SHNIHAGTQLNPGGWDIIP-GAIYSEDR 375 (1197)
T ss_pred HHHHHHHHHHHCCeEEEEec--------------CCHHHHHHHHHCCCceEee-cccCCccc
Confidence 58999999999999998863 3577788889999999864 55678776
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=97.07 E-value=0.0018 Score=39.54 Aligned_cols=42 Identities=14% Similarity=0.393 Sum_probs=36.2
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
++.+.+++++|++++++.. .+|+.++..+.+|++|+++++..
T Consensus 53 ~l~~~l~~~~g~~v~~~~~--------------~~~~~~~~~l~~g~~Di~~~~~~ 94 (254)
T TIGR01098 53 PLADYLEKKLGIKVQLFVA--------------TDYSAVIEAMRFGRVDIAWFGPS 94 (254)
T ss_pred HHHHHHHHHhCCcEEEEeC--------------CCHHHHHHHHHcCCccEEEECcH
Confidence 5788999999999999753 47999999999999999997653
No 26
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=96.81 E-value=0.0027 Score=42.96 Aligned_cols=47 Identities=23% Similarity=0.321 Sum_probs=41.0
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
+|+++.|+.||.+.++... ..-+.++.+|.+|++|++.+++...++|
T Consensus 49 elak~Fa~yLgV~Lki~~~--------------~n~dqLf~aL~ng~~DL~Aagl~~~~~~ 95 (473)
T COG4623 49 ELAKAFADYLGVKLKIIPA--------------DNIDQLFDALDNGNADLAAAGLLYNSER 95 (473)
T ss_pred HHHHHHHHHhCCeEEEEec--------------CCHHHHHHHHhCCCcceecccccCChhH
Confidence 6899999999999999863 3578999999999999999999877664
No 27
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=96.16 E-value=0.017 Score=36.16 Aligned_cols=40 Identities=15% Similarity=0.427 Sum_probs=33.9
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.+.+++++|.+++++.. ..|..++..|.+|++|+++.+.
T Consensus 49 l~~~l~~~~g~~v~~~~~--------------~~~~~~~~al~~g~~D~~~~~~ 88 (288)
T TIGR03431 49 LADYLSKKLGVKVKLFFA--------------TDYAGVIEGMRFGKVDIAWYGP 88 (288)
T ss_pred HHHHHHHHhCCcEEEEeC--------------CCHHHHHHHHHcCCccEEEECh
Confidence 567899999999997653 5799999999999999998653
No 28
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=95.81 E-value=0.0085 Score=38.16 Aligned_cols=28 Identities=7% Similarity=0.153 Sum_probs=25.2
Q ss_pred cchhhHHHhhhcCCccEEEeCCccccCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAALSVSSTR 62 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ltit~eR 62 (62)
..|..++..|.+|++|+++++++++.||
T Consensus 51 ~~~~~i~~~L~sG~vDlgi~g~~~~~er 78 (287)
T PRK00489 51 LRPDDIPGYVADGVVDLGITGEDLLEES 78 (287)
T ss_pred ECcHHHHHHHHcCCCCEEEcchHHHHHC
Confidence 5799999999999999999998887765
No 29
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=94.88 E-value=0.084 Score=32.24 Aligned_cols=39 Identities=18% Similarity=0.388 Sum_probs=30.8
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
+.+.|++.+|.+++++.. ..+..++..+.+|++|++..+
T Consensus 19 l~~~L~~~~g~~v~~~~~--------------~~~~~~~~~l~~g~~D~~~~~ 57 (243)
T PF12974_consen 19 LADYLSKQLGVPVELVPA--------------DDYAEFIEALRSGEIDLAFMG 57 (243)
T ss_dssp HHHHHHHHHTSEEEEE----------------SSHHHHHHHHHTTS-SEEE--
T ss_pred HHHHHHHHhCCCEEEEEc--------------CCHHHHHHHHHcCCccEEEEC
Confidence 678899999999999864 468999999999999999864
No 30
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=94.57 E-value=0.076 Score=33.41 Aligned_cols=37 Identities=16% Similarity=0.138 Sum_probs=29.5
Q ss_pred HHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 7 IAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 7 la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
+++++|++++++.. ..+..++..|.+|++|+++.+.+
T Consensus 21 ~~k~~Gl~Ve~~~~--------------~~~~~~~~al~~G~iD~~~~~~~ 57 (300)
T TIGR01729 21 AAKEAGATIDWRKF--------------DSGADISTALASGNVPIGVIGSS 57 (300)
T ss_pred hHHhcCCeeEEEec--------------CcHHHHHHHHHcCCCCEeccCCC
Confidence 45678999998864 35788999999999999976543
No 31
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=93.98 E-value=0.15 Score=33.14 Aligned_cols=39 Identities=15% Similarity=0.451 Sum_probs=33.7
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
|.+.|.+.+|+.+++... ....+++..+.+|++|+|..+
T Consensus 57 l~~~L~~~lG~~V~~~~a--------------~dy~~vieal~~g~~D~A~~~ 95 (299)
T COG3221 57 LADYLEKELGIPVEFFVA--------------TDYAAVIEALRAGQVDIAWLG 95 (299)
T ss_pred HHHHHHHHhCCceEEEec--------------ccHHHHHHHHhCCCeeEEecC
Confidence 578899999999999875 468999999999999987643
No 32
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=92.04 E-value=1.2 Score=24.38 Aligned_cols=23 Identities=17% Similarity=0.313 Sum_probs=18.9
Q ss_pred cchhhHHHhhhcCCccEEEeCCc
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~lt 57 (62)
..+..++..|.+|++|+++....
T Consensus 36 ~~~~~~~~~l~~g~~D~~i~~~~ 58 (197)
T cd05466 36 GGSSELLEALLEGELDLAIVALP 58 (197)
T ss_pred CChHHHHHHHHcCCceEEEEcCC
Confidence 35668999999999999997654
No 33
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=92.01 E-value=0.75 Score=25.75 Aligned_cols=39 Identities=18% Similarity=0.337 Sum_probs=28.9
Q ss_pred hHHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 2 DLLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 2 dll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
.++..+.++. +.+++++. +.+..+...|.+|++|+++..
T Consensus 17 ~~l~~~~~~~P~v~l~~~~---------------~~~~~~~~~l~~g~~Dl~i~~ 56 (199)
T cd08430 17 PILERFRAQHPQVEIKLHT---------------GDPADAIDKVLNGEADIAIAA 56 (199)
T ss_pred HHHHHHHHHCCCceEEEEe---------------CCHHHHHHHHHCCCCCEEEEe
Confidence 3456666665 66777764 467788999999999999975
No 34
>PF02879 PGM_PMM_II: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II; InterPro: IPR005845 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 2F7L_A 3PDK_B 1KFQ_B 1KFI_A 1C47_A 1VKL_B 1LXT_A 1JDY_B 3PMG_A 1C4G_B ....
Probab=91.61 E-value=1.3 Score=23.88 Aligned_cols=53 Identities=13% Similarity=0.188 Sum_probs=37.3
Q ss_pred hHHHHHHHHcCCeEEEE-EecCCcccc-eeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 2 DLLENIAQELEFDFHLY-IVADGLYGT-KVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 2 dll~~la~~l~f~~~~~-~~~~~~~G~-~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
.++..|.+++|+.+... ..++..|+. ..|+.....+..+...+....+|++++
T Consensus 35 ~~~~~ll~~lg~~~~~~n~~~d~~f~~~~~p~p~~~~l~~~~~~v~~~~ad~g~~ 89 (104)
T PF02879_consen 35 DILPRLLERLGCDVIELNCDPDPDFPNQHAPNPEEESLQRLIKIVRESGADLGIA 89 (104)
T ss_dssp HHHHHHHHHTTCEEEEESSS-STTGTTTSTSSTSTTTTHHHHHHHHHSTTSEEEE
T ss_pred HHHHHHHHHcCCcEEEEecccccccccccccccccchhHHHHHHhhccCceEEEE
Confidence 46788999999966443 456777865 444322256888888889999999874
No 35
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=91.49 E-value=0.86 Score=25.97 Aligned_cols=39 Identities=10% Similarity=0.167 Sum_probs=28.3
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
++..+.++. +.+++++. +..+.++..|.+|++|+++...
T Consensus 18 ~l~~~~~~~P~v~i~~~~---------------~~~~~~~~~l~~g~~Dl~i~~~ 57 (202)
T cd08468 18 LMARLEELAPSVRLNLVH---------------AEQKLPLDALLAGEIDFALGYS 57 (202)
T ss_pred HHHHHHhhCCCCEEEEEE---------------CChHhHHHHHHCCCccEEEecc
Confidence 455665554 55666653 4678899999999999998643
No 36
>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=91.26 E-value=0.62 Score=29.18 Aligned_cols=40 Identities=13% Similarity=0.081 Sum_probs=29.0
Q ss_pred HHHHHHHHcC-CeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQELE-FDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l~-f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.+.+++.++ ++++++.. +.....+..|.+|++|+++...
T Consensus 50 la~~~~~~~~~i~v~~~~~--------------~~~~~~~~~l~~G~~D~~~~~~ 90 (320)
T TIGR02122 50 IAQLINKKSGKLRVRVQST--------------GGSVENVNLLEAGEADLAIVQS 90 (320)
T ss_pred HHHHHhccCCCeeEEEEeC--------------cchHHHHHHHhCCCCcEEEEcc
Confidence 4566666666 77777641 3455788999999999998764
No 37
>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=90.96 E-value=1.2 Score=24.88 Aligned_cols=39 Identities=8% Similarity=0.167 Sum_probs=27.5
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
++..+.+.. +.++++.. +..+.+...|.+|++|+++..-
T Consensus 18 ~l~~~~~~~P~i~l~~~~---------------~~~~~~~~~l~~g~~Dl~i~~~ 57 (195)
T cd08427 18 ALARLRRRHPDLEVHIVP---------------GLSAELLARVDAGELDAAIVVE 57 (195)
T ss_pred HHHHHHHHCCCceEEEEe---------------CCcHHHHHHHHCCCCCEEEEcC
Confidence 444554444 56666653 4578899999999999999753
No 38
>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=90.68 E-value=1.7 Score=24.58 Aligned_cols=24 Identities=8% Similarity=0.128 Sum_probs=20.3
Q ss_pred cchhhHHHhhhcCCccEEEeCCcc
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAALSV 58 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~lti 58 (62)
+....++..|.+|++|+++.....
T Consensus 42 ~~~~~~~~~l~~g~~Dl~i~~~~~ 65 (209)
T PF03466_consen 42 GDSDELIEALRSGELDLAITFGPP 65 (209)
T ss_dssp ESHHHHHHHHHTTSSSEEEESSSS
T ss_pred ccchhhhHHHhcccccEEEEEeec
Confidence 456899999999999999987654
No 39
>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=89.48 E-value=2.3 Score=23.85 Aligned_cols=22 Identities=18% Similarity=0.327 Sum_probs=18.6
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.+..+...|.+|++|+++...
T Consensus 37 ~~~~~~~~~l~~~~~Dl~i~~~ 58 (198)
T cd08446 37 MTKDEQIEALRAGRIHIGFGRF 58 (198)
T ss_pred CCHHHHHHHHHCCCccEEEEec
Confidence 5678899999999999999643
No 40
>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=89.42 E-value=2.4 Score=23.54 Aligned_cols=38 Identities=16% Similarity=0.230 Sum_probs=27.7
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++..+.+.. +.+++++. +....+...|.+|++|+++..
T Consensus 18 ~l~~~~~~~P~i~i~i~~---------------~~~~~~~~~l~~~~~Di~i~~ 56 (197)
T cd08448 18 ILRAFRAEYPGIEVALHE---------------MSSAEQIEALLRGELDLGFVH 56 (197)
T ss_pred HHHHHHHHCCCCeEEEEe---------------CCHHHHHHHHHcCCcceEEEe
Confidence 455555544 66666653 467889999999999999864
No 41
>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=88.89 E-value=2.7 Score=23.43 Aligned_cols=39 Identities=8% Similarity=0.053 Sum_probs=26.9
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
++..+.+.. +.++++.. +....+...|.+|++|+++...
T Consensus 18 ~l~~~~~~~P~i~~~i~~---------------~~~~~~~~~l~~g~~Dl~i~~~ 57 (196)
T cd08456 18 AIKAFLQRHPDVTISIHT---------------RDSPTVEQWLSAQQCDLGLVST 57 (196)
T ss_pred HHHHHHHHCCCcEEEEEe---------------CCHHHHHHHHHcCCccEEEEec
Confidence 344555544 56666653 4566788999999999999643
No 42
>PF09084 NMT1: NMT1/THI5 like; InterPro: IPR015168 This entry is found in the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [, , ]. They are regulated by thiamine []. ; PDB: 2X26_A 3E4R_A 3KSJ_A 3KSX_A 3UIF_A 4DDD_A 1US4_A 1US5_A 3IX1_B 2X7P_A ....
Probab=88.89 E-value=1.2 Score=26.43 Aligned_cols=34 Identities=21% Similarity=0.301 Sum_probs=27.7
Q ss_pred HHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 9 QELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 9 ~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
++.|++++++.. ......+..|.+|++|++++..
T Consensus 17 ~~~gl~ve~~~~--------------~~~~~~~~~l~~G~~D~~~~~~ 50 (216)
T PF09084_consen 17 KEEGLDVEIVFF--------------GGGGDVLEALASGKADIAVAGP 50 (216)
T ss_dssp HHTTEEEEEEEE--------------SSHHHHHHHHHTTSHSEEEEEC
T ss_pred ccCeEEEEEEEe--------------cChhHHHHHHhcCCceEEeccc
Confidence 456788888864 4578899999999999998765
No 43
>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=88.85 E-value=1.8 Score=24.69 Aligned_cols=21 Identities=29% Similarity=0.420 Sum_probs=18.5
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+..+.+...|.+|++|+++..
T Consensus 37 ~~~~~l~~~l~~g~~D~~~~~ 57 (198)
T cd08486 37 MTKDEQVEGLLAGTIHVGFSR 57 (198)
T ss_pred CCHHHHHHHHHcCCceEEEec
Confidence 568899999999999999964
No 44
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=88.78 E-value=2 Score=24.93 Aligned_cols=22 Identities=23% Similarity=0.258 Sum_probs=19.1
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.+..++..|.+|++|+++...
T Consensus 36 ~~~~~~~~~L~~~~~D~~i~~~ 57 (204)
T cd08429 36 GKLEQLLADLALHRLDMVLADR 57 (204)
T ss_pred CCHHHHHHHHHcCCccEEEecC
Confidence 6788999999999999999644
No 45
>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=88.51 E-value=2 Score=24.00 Aligned_cols=22 Identities=14% Similarity=0.161 Sum_probs=18.4
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+..+.+...|.+|++|+++...
T Consensus 37 ~~~~~~~~~l~~g~~Dl~i~~~ 58 (199)
T cd08451 37 ANTAELLEALREGRLDAAFVRP 58 (199)
T ss_pred CChHHHHHHHHCCCccEEEEec
Confidence 4567889999999999999754
No 46
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=88.20 E-value=2 Score=24.08 Aligned_cols=38 Identities=13% Similarity=0.095 Sum_probs=26.7
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++..+.++. +.+++++. +....+...|.+|++|+++..
T Consensus 18 ~l~~f~~~~P~v~l~~~~---------------~~~~~~~~~l~~g~~Dl~i~~ 56 (200)
T cd08466 18 LLARLKQLAPNISLRESP---------------SSEEDLFEDLRLQEVDLVIDY 56 (200)
T ss_pred HHHHHHHHCCCCEEEEec---------------CchHhHHHHHHcCCccEEEec
Confidence 344454443 56666653 456788999999999999864
No 47
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=88.15 E-value=2.3 Score=23.56 Aligned_cols=38 Identities=18% Similarity=0.292 Sum_probs=27.1
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++..+.+.. +.+++++. +....+...|.+|++|+++..
T Consensus 18 ~l~~~~~~~P~i~l~i~~---------------~~~~~~~~~l~~g~~Dl~i~~ 56 (193)
T cd08442 18 LLAAYHARYPKVDLSLST---------------GTTGALIQAVLEGRLDGAFVA 56 (193)
T ss_pred HHHHHHHHCCCceEEEEe---------------CCcHHHHHHHHCCCccEEEEe
Confidence 445555443 56667663 456789999999999999864
No 48
>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=87.93 E-value=0.98 Score=28.09 Aligned_cols=39 Identities=13% Similarity=0.130 Sum_probs=26.0
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
+++.+.+.-|.+.++++. ..|..++.++..|++|-|+-+
T Consensus 83 l~Ral~d~~~~~~EvVyt--------------dD~~~i~~Ml~~g~vdsAVv~ 121 (201)
T PF12916_consen 83 LTRALLDLKGIKAEVVYT--------------DDMSEIVKMLNEGEVDSAVVG 121 (201)
T ss_dssp HHHHHHHHH--T-EEEE-----------------HHHHHHHHHTT-E--EEEE
T ss_pred HHHHHHhhccccceeEEe--------------cCHHHHHHHHhcCceeeeeec
Confidence 467778888999999984 479999999999999988865
No 49
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=87.88 E-value=2.1 Score=26.31 Aligned_cols=34 Identities=12% Similarity=0.240 Sum_probs=28.8
Q ss_pred HHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 7 IAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 7 la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
+.++.|++++++.. .++..++..|.+|++|++..
T Consensus 29 ~f~~~G~~ve~~~~--------------~~g~~~~~al~~G~iD~a~~ 62 (252)
T PF13379_consen 29 LFEKEGLDVEWVQF--------------ASGADILEALAAGEIDIAFV 62 (252)
T ss_dssp HHHHTTSCEEEEEE--------------SSHHHHHHHHHCTSSSEEEE
T ss_pred hHHHcCCEEEEEEc--------------CCHHHHHHHHHcCCCCEEEe
Confidence 55677999988864 46899999999999999987
No 50
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=87.82 E-value=3.2 Score=23.01 Aligned_cols=39 Identities=13% Similarity=0.223 Sum_probs=27.1
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
++..+.+.. +.++++.. +....+...|.+|++|+++...
T Consensus 17 ~l~~~~~~~P~i~l~i~~---------------~~~~~~~~~l~~g~~Dl~i~~~ 56 (197)
T cd08419 17 LLGAFCRRHPGVEVSLRV---------------GNREQVLERLADNEDDLAIMGR 56 (197)
T ss_pred HHHHHHHHCCCceEEEEE---------------CCHHHHHHHHhcCCccEEEecC
Confidence 445555543 56666653 4567788999999999998654
No 51
>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=87.74 E-value=3.3 Score=23.02 Aligned_cols=22 Identities=27% Similarity=0.388 Sum_probs=18.4
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08415 36 LSSSTVVEAVLSGQADLGLASL 57 (196)
T ss_pred cchHHHHHHHHcCCccEEEEeC
Confidence 4567899999999999999754
No 52
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=87.73 E-value=2.5 Score=23.96 Aligned_cols=22 Identities=14% Similarity=0.188 Sum_probs=18.5
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.+..+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~g~~D~~i~~~ 57 (198)
T cd08413 36 GTPSQIAEMVLKGEADIAIATE 57 (198)
T ss_pred CCHHHHHHHHHcCCCCEEEEcc
Confidence 4677899999999999999743
No 53
>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=87.65 E-value=2.9 Score=23.52 Aligned_cols=22 Identities=14% Similarity=0.152 Sum_probs=18.1
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+..+.+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~g~~D~~i~~~ 57 (201)
T cd08459 36 LPVDELEEALESGEIDLAIGYL 57 (201)
T ss_pred cCccCHHHHhhCCCceEEEEcC
Confidence 4566788999999999999754
No 54
>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=87.61 E-value=3.3 Score=22.92 Aligned_cols=40 Identities=15% Similarity=0.257 Sum_probs=27.0
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
++..+.+.. ++++++.. +.-..+...|.+|++|+++....
T Consensus 18 ~l~~~~~~~P~~~l~~~~---------------~~~~~~~~~l~~g~~D~~i~~~~ 58 (201)
T cd08420 18 LLARFRKRYPEVRVSLTI---------------GNTEEIAERVLDGEIDLGLVEGP 58 (201)
T ss_pred HHHHHHHHCCCceEEEEe---------------CCcHHHHHHHHCCCccEEEecCC
Confidence 455555544 56666653 34567888899999999997543
No 55
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=87.41 E-value=3.3 Score=22.84 Aligned_cols=22 Identities=14% Similarity=0.308 Sum_probs=17.9
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....++..|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~ 57 (195)
T cd08434 36 GSTDELLDDLKNGELDLALCSP 57 (195)
T ss_pred CcHHHHHHHHHcCCccEEEEcc
Confidence 4466788999999999998754
No 56
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=87.20 E-value=2.9 Score=23.49 Aligned_cols=21 Identities=10% Similarity=0.237 Sum_probs=17.8
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
...+.++..|.+|++|+++..
T Consensus 36 ~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08437 36 GGSAELLEQLLQGDLDIALLG 56 (198)
T ss_pred cCHHHHHHHHHcCCCCEEEec
Confidence 456789999999999999864
No 57
>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=87.14 E-value=2.6 Score=23.98 Aligned_cols=21 Identities=5% Similarity=0.302 Sum_probs=18.5
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+.+..++..|.+|++|+++..
T Consensus 36 ~~~~~~~~~L~~g~~Dl~i~~ 56 (200)
T cd08465 36 ASREAMLAQVADGEIDLALGV 56 (200)
T ss_pred CChHhHHHHHHCCCccEEEec
Confidence 568899999999999999964
No 58
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=87.04 E-value=1.4 Score=28.18 Aligned_cols=35 Identities=17% Similarity=0.144 Sum_probs=27.2
Q ss_pred HHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 8 AQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 8 a~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
.++.|++++++.. ..+..++..|.+|++|++..+.
T Consensus 46 ~~~~Gl~Ve~~~~--------------~~~~~~~~al~~G~~D~a~~~~ 80 (320)
T PRK11480 46 AKESGATVDWRKF--------------DSGASIVRALASGDVQIGNLGS 80 (320)
T ss_pred HHHcCCeeEEEEe--------------CCHHHHHHHHHCCCCCEECcCc
Confidence 4567888888764 3578899999999999986543
No 59
>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=87.02 E-value=3.2 Score=23.19 Aligned_cols=21 Identities=10% Similarity=0.192 Sum_probs=17.3
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....+..+|.+|++|+++..
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~ 56 (185)
T cd08439 36 KRTPRLMEMLERGEVDLALIT 56 (185)
T ss_pred CChHHHHHHHHCCCCcEEEEe
Confidence 345688999999999999863
No 60
>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=87.01 E-value=3.1 Score=23.23 Aligned_cols=22 Identities=14% Similarity=0.354 Sum_probs=18.5
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.....+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~g~~Dl~i~~~ 57 (201)
T cd08418 36 GQLSSLLPELRDGRLDFAIGTL 57 (201)
T ss_pred CcHHHHHHHHHcCCCcEEEEec
Confidence 4567899999999999999753
No 61
>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=86.88 E-value=3.8 Score=22.85 Aligned_cols=39 Identities=15% Similarity=0.119 Sum_probs=26.9
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
++..+.+.. +.++++.. +....++..|.+|++|+++...
T Consensus 18 ~l~~~~~~~P~i~i~~~~---------------~~~~~~~~~l~~~~~D~~i~~~ 57 (198)
T cd08421 18 DLASFLAAHPDVRIDLEE---------------RLSADIVRAVAEGRADLGIVAG 57 (198)
T ss_pred HHHHHHHHCCCceEEEEe---------------cCcHHHHHHHhcCCceEEEEec
Confidence 455555543 55566653 4567889999999999998643
No 62
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=86.82 E-value=3.7 Score=22.64 Aligned_cols=22 Identities=9% Similarity=0.139 Sum_probs=18.3
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~g~~D~~i~~~ 57 (197)
T cd08440 36 VSAEQVIEAVRSGEVDFGIGSE 57 (197)
T ss_pred CChHHHHHHHHcCCccEEEEeC
Confidence 4567889999999999999754
No 63
>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=86.76 E-value=3.8 Score=22.79 Aligned_cols=22 Identities=14% Similarity=0.088 Sum_probs=18.0
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08450 36 LFSPQLAEALMRGKLDVAFMRP 57 (196)
T ss_pred cChHHHHHHHhcCCccEEEEeC
Confidence 4567888999999999998643
No 64
>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=86.66 E-value=3.3 Score=23.21 Aligned_cols=21 Identities=19% Similarity=0.298 Sum_probs=17.7
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....++..|.+|++|+++..
T Consensus 37 ~~~~~~~~~l~~~~~Dl~i~~ 57 (200)
T cd08411 37 DQTERLLEKLRSGELDAALLA 57 (200)
T ss_pred CcHHHHHHHHHcCCccEEEEe
Confidence 456788999999999999864
No 65
>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=86.56 E-value=3.4 Score=23.23 Aligned_cols=21 Identities=10% Similarity=0.115 Sum_probs=17.5
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....+...|.+|++|+++..
T Consensus 36 ~~~~~~~~~l~~g~~D~~i~~ 56 (200)
T cd08453 36 ATSDVQLEALLAGEIDAGIVI 56 (200)
T ss_pred CCHHHHHHHHHcCCCCEEEEe
Confidence 456678999999999999864
No 66
>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=86.50 E-value=4.2 Score=23.16 Aligned_cols=49 Identities=22% Similarity=0.396 Sum_probs=32.7
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
.++..|+..|+...-++.+++.-|.... --.|..|+..+..|++|..+.
T Consensus 26 ~l~~~a~~~g~~i~~~~~D~~~SG~~~~---Rp~l~~ll~~~~~g~vd~vvv 74 (140)
T cd03770 26 ILEEYAKENGLENIRHYIDDGFSGTTFD---RPGFNRMIEDIEAGKIDIVIV 74 (140)
T ss_pred HHHHHHHHCCCEEEEEEEcCCCcCCcCC---CHHHHHHHHHHHcCCCCEEEE
Confidence 4667788889876444444444443221 135999999999999997664
No 67
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=86.45 E-value=2.7 Score=23.52 Aligned_cols=38 Identities=21% Similarity=0.238 Sum_probs=26.7
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++..+.+.. +.++++.. +..+.++.+|.+|++|+++..
T Consensus 18 ~l~~~~~~~P~v~i~i~~---------------~~~~~~~~~l~~g~~D~~i~~ 56 (195)
T cd08431 18 LIAEFYQLNKATRIRLSE---------------EVLGGTWDALASGRADLVIGA 56 (195)
T ss_pred HHHHHHHHCCCCceEEEE---------------eccchHHHHHhCCCCCEEEEe
Confidence 445555554 56666653 345678899999999999964
No 68
>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=86.41 E-value=4.1 Score=22.76 Aligned_cols=22 Identities=9% Similarity=0.022 Sum_probs=17.8
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.....+...|.+|++|+++...
T Consensus 37 ~~~~~~~~~l~~g~~Dl~i~~~ 58 (197)
T cd08425 37 MPQERIEAALADDRLDLGIAFA 58 (197)
T ss_pred CcHHHHHHHHHcCCccEEEEec
Confidence 3456788999999999999643
No 69
>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=86.27 E-value=3.4 Score=23.09 Aligned_cols=39 Identities=15% Similarity=0.248 Sum_probs=26.7
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
++..+.++. +.++++.. +....+...|.+|++|+++...
T Consensus 18 ~l~~~~~~~P~i~l~i~~---------------~~~~~~~~~l~~~~~Dl~i~~~ 57 (199)
T cd08416 18 IIMGLKLRRPELDIELTL---------------GSNKDLLKKLKDGELDAILVAT 57 (199)
T ss_pred HHHHHHHhCCCeEEEEEE---------------cCcHHHHHHHhCCCCCEEEEec
Confidence 344455444 56666653 4566788899999999999753
No 70
>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=86.26 E-value=2.5 Score=24.00 Aligned_cols=21 Identities=14% Similarity=-0.002 Sum_probs=17.6
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....++..|.+|++|+++..
T Consensus 36 ~~~~~~~~~l~~g~~D~~i~~ 56 (200)
T cd08467 36 IGDDLAERGLEQGTIDLAVGR 56 (200)
T ss_pred CCcccHHHHhhCCCcCEEEec
Confidence 456678999999999999964
No 71
>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=86.25 E-value=4.1 Score=22.59 Aligned_cols=22 Identities=14% Similarity=0.146 Sum_probs=18.1
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~L~~~~~Dl~i~~~ 57 (197)
T cd08438 36 YGGKKVEQAVLNGELDVGITVL 57 (197)
T ss_pred cCcHHHHHHHHcCCCCEEEEec
Confidence 4567888999999999999754
No 72
>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=86.05 E-value=3.6 Score=22.88 Aligned_cols=22 Identities=9% Similarity=0.105 Sum_probs=18.3
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....++..|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~ 57 (197)
T cd08449 36 LSPEAQKAALLSKRIDLGFVRF 57 (197)
T ss_pred CCHHHHHHHHhCCCccEEEecc
Confidence 4567889999999999999644
No 73
>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=85.94 E-value=3.7 Score=23.20 Aligned_cols=38 Identities=13% Similarity=0.227 Sum_probs=26.6
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++..+.++. +.++++.. +....+...|.+|++|+++..
T Consensus 18 ~l~~~~~~~P~v~i~i~~---------------~~~~~~~~~l~~~~~Dl~i~~ 56 (197)
T cd08452 18 IVREYRKKFPSVKVELRE---------------LSSPDQVEELLKGRIDIGFLH 56 (197)
T ss_pred HHHHHHHHCCCcEEEEEe---------------cChHHHHHHHHCCCccEEEee
Confidence 445555443 55666653 456788999999999999864
No 74
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=85.78 E-value=3.7 Score=23.25 Aligned_cols=21 Identities=19% Similarity=0.268 Sum_probs=17.7
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+..+.++..|.+|++|+++..
T Consensus 36 ~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08444 36 GSPEEIASMLANGQADIGIAT 56 (198)
T ss_pred CCHHHHHHHHHCCCccEEEec
Confidence 456778999999999999964
No 75
>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=84.80 E-value=4.4 Score=22.58 Aligned_cols=21 Identities=10% Similarity=0.096 Sum_probs=18.0
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+..+.+...|.+|++|+++..
T Consensus 36 ~~~~~~~~~l~~g~~D~~i~~ 56 (198)
T cd08447 36 MVTTDQIEALESGRIDLGLLR 56 (198)
T ss_pred CCHHHHHHHHHcCCceEEEec
Confidence 467789999999999999964
No 76
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=84.72 E-value=4.3 Score=22.41 Aligned_cols=23 Identities=13% Similarity=0.329 Sum_probs=18.3
Q ss_pred cchhhHHHhhhcCCccEEEeCCc
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~lt 57 (62)
+....+...|.+|++|+++....
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~~ 58 (194)
T cd08436 36 AGSDDLLAAVREGRLDLAFVGLP 58 (194)
T ss_pred CCHHHHHHHHHcCCccEEEEecC
Confidence 34567889999999999997543
No 77
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=84.31 E-value=5.3 Score=22.20 Aligned_cols=38 Identities=11% Similarity=0.199 Sum_probs=26.4
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++..+.+.. +.++++.. +....++..|.+|++|+++..
T Consensus 18 ~l~~~~~~~P~i~l~i~~---------------~~~~~~~~~l~~~~~D~~i~~ 56 (198)
T cd08412 18 LLRRFREAYPGVEVRVVE---------------GNQEELEEGLRSGELDLALTY 56 (198)
T ss_pred HHHHHHHHCCCcEEEEEE---------------CCHHHHHHHHHcCCCcEEEEc
Confidence 444454443 56666653 456778899999999999874
No 78
>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=84.28 E-value=4.9 Score=22.42 Aligned_cols=22 Identities=9% Similarity=0.202 Sum_probs=18.5
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.....+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~g~~D~~i~~~ 57 (200)
T cd08417 36 LDRDDLEEALESGEIDLAIGVF 57 (200)
T ss_pred CCHHHHHHHHHcCCCCEEEeec
Confidence 4567899999999999999754
No 79
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=84.22 E-value=5.5 Score=22.31 Aligned_cols=21 Identities=10% Similarity=0.112 Sum_probs=17.7
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....+...|.+|++|+++..
T Consensus 36 ~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08441 36 GFHFDPLPALLRGELDLVITS 56 (198)
T ss_pred CCchhHHHHHHcCCceEEEec
Confidence 456788999999999999864
No 80
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=84.14 E-value=4.5 Score=23.23 Aligned_cols=40 Identities=10% Similarity=0.112 Sum_probs=27.2
Q ss_pred hHHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 2 DLLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 2 dll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
+++..+.+.. +.++++... +.++.+...|.+|++|+++..
T Consensus 17 ~~l~~~~~~~P~~~v~~~~~--------------~~~~~l~~~L~~g~lDl~i~~ 57 (203)
T cd08463 17 ELVARFRREAPGARLEIHPL--------------GPDFDYERALASGELDLVIGN 57 (203)
T ss_pred HHHHHHHHHCCCCEEEEEeC--------------CcchhHHHHHhcCCeeEEEec
Confidence 3455555543 456666531 246789999999999999964
No 81
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=84.04 E-value=1.7 Score=26.47 Aligned_cols=22 Identities=9% Similarity=0.114 Sum_probs=18.1
Q ss_pred chhhHHHhhhcCCccEEEeCCc
Q psy2313 36 KWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 36 ~w~g~ig~l~~g~~D~av~~lt 57 (62)
.+..++..|.+|++|+++.+..
T Consensus 38 ~~~~~~~~l~~G~~D~~~~~~~ 59 (288)
T TIGR01728 38 AGPPALEALGAGSLDFGYIGPG 59 (288)
T ss_pred CCcHHHHHHhcCCccccccCCc
Confidence 5678899999999999876553
No 82
>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=83.47 E-value=2.6 Score=26.71 Aligned_cols=39 Identities=15% Similarity=0.166 Sum_probs=27.4
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
...+++.+|++++++.. ..-...+.+|..|++|+++..+
T Consensus 122 ~~~l~~~~G~~~~~Vpy--------------~G~~~~~~allgG~vd~~~~~~ 160 (274)
T PF03401_consen 122 AALLAKAAGIKFTHVPY--------------DGGAEALTALLGGHVDAAFGSP 160 (274)
T ss_dssp HHHHHHHHT---EEEE---------------SSHHHHHHHHHTTSSSEEEEEH
T ss_pred HHHHHHHhCCceEEEEe--------------CCccHHHHHHhCCeeeEEeecH
Confidence 35678889999888753 2456789999999999988764
No 83
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=83.41 E-value=5.8 Score=21.99 Aligned_cols=38 Identities=11% Similarity=0.107 Sum_probs=26.0
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++..+.+.. +.++++.. +.-..+...|.+|++|+++..
T Consensus 18 ~l~~~~~~~P~i~i~~~~---------------~~~~~~~~~l~~~~~Dl~i~~ 56 (200)
T cd08423 18 ALAALRARHPGLEVRLRE---------------AEPPESLDALRAGELDLAVVF 56 (200)
T ss_pred HHHHHHHhCCCCeEEEEe---------------CCHHHHHHHHhcCCccEEEEe
Confidence 445555543 56666653 345678899999999999964
No 84
>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=83.18 E-value=6.1 Score=22.05 Aligned_cols=38 Identities=16% Similarity=0.215 Sum_probs=25.7
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++..+.+.. +.++++.. +..+.+...|.+|++|+++..
T Consensus 18 ~l~~f~~~~P~v~i~i~~---------------~~~~~~~~~l~~~~~Di~i~~ 56 (198)
T cd08461 18 LLAALRQEAPGVRVAIRD---------------LESDNLEAQLERGEVDLALTT 56 (198)
T ss_pred HHHHHHHHCCCcEEEEee---------------CCcccHHHHHhcCCCcEEEec
Confidence 344444443 56666653 345678889999999999864
No 85
>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=82.97 E-value=6.5 Score=22.21 Aligned_cols=22 Identities=18% Similarity=0.184 Sum_probs=18.2
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....++..|.+|++|+++...
T Consensus 37 ~~~~~~~~~l~~~~~Dl~i~~~ 58 (203)
T cd08445 37 MTTVQQIEALKEGRIDVGFGRL 58 (203)
T ss_pred CChHHHHHHHHcCCCcEEEecC
Confidence 4567899999999999999643
No 86
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=82.80 E-value=4.9 Score=22.66 Aligned_cols=20 Identities=15% Similarity=0.157 Sum_probs=16.2
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+.. .++..|.+|++|+++..
T Consensus 36 ~~~-~~~~~l~~g~~D~~i~~ 55 (200)
T cd08460 36 ESD-KDVDALREGRIDLEIGV 55 (200)
T ss_pred Cch-hHHHHHHCCCccEEEec
Confidence 344 67889999999999964
No 87
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=82.74 E-value=7.4 Score=24.08 Aligned_cols=22 Identities=9% Similarity=0.092 Sum_probs=18.7
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....++..|.+|++|++++..
T Consensus 125 ~~~~~~~~~l~~g~~Dl~i~~~ 146 (275)
T PRK03601 125 AQRQSLVKQLHERQLDLLITTE 146 (275)
T ss_pred CChHHHHHHHHcCCCCEEEEcC
Confidence 4567899999999999999754
No 88
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=82.44 E-value=4.5 Score=22.58 Aligned_cols=38 Identities=16% Similarity=0.081 Sum_probs=25.8
Q ss_pred HHHHHHHHc-CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l-~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++..+.++. +.++++.. +....+...|.+|++|+++..
T Consensus 18 ~l~~~~~~~P~v~l~i~~---------------~~~~~~~~~l~~g~~D~~i~~ 56 (200)
T cd08464 18 LLAALRAEAPGVRLVFRQ---------------VDPFNVGDMLDRGEIDLAIGV 56 (200)
T ss_pred HHHHHHHHCCCcEEEEec---------------CCcccHHHHHhcCcccEEEec
Confidence 344455443 56666653 345678889999999999864
No 89
>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=82.43 E-value=6.2 Score=21.83 Aligned_cols=22 Identities=14% Similarity=0.095 Sum_probs=18.0
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~ 57 (197)
T cd08414 36 MTTAEQLEALRAGRLDVGFVRP 57 (197)
T ss_pred CChHHHHHHHHcCCccEEEEcC
Confidence 4457889999999999999643
No 90
>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=82.33 E-value=5.9 Score=22.74 Aligned_cols=22 Identities=9% Similarity=0.078 Sum_probs=18.1
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.....+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 36 VTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred CChhhHHHHHHCCCccEEEecC
Confidence 4566789999999999999743
No 91
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=82.01 E-value=7.9 Score=25.39 Aligned_cols=51 Identities=14% Similarity=0.251 Sum_probs=30.4
Q ss_pred HHHHHHHc-CCeEEEEEecCCcccceecc------CCCcchhh-HHHhhhcCCccEEEeCC
Q psy2313 4 LENIAQEL-EFDFHLYIVADGLYGTKVRE------NQKDKWNG-VVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l-~f~~~~~~~~~~~~G~~~~~------~~~~~w~g-~ig~l~~g~~D~av~~l 56 (62)
.+.|.+.. +++++++... +-|-+..+ .+.|-|.- +=.+|.+|++|+||-++
T Consensus 23 ~~~L~~~~p~~~~ei~~i~--T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVHSl 81 (295)
T PRK00072 23 KDRLKAAHPGLEVELVPIK--TKGDKILDVPLAKIGGKGLFVKELEEALLEGEIDIAVHSL 81 (295)
T ss_pred HHHHHHHCCCCeEEEEEee--ccCcccccccHHHcCCcceeHHHHHHHHHcCCCCEEEecc
Confidence 34555543 5777777543 22322211 12467764 44789999999999776
No 92
>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=81.88 E-value=7.1 Score=22.12 Aligned_cols=21 Identities=24% Similarity=0.273 Sum_probs=17.2
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+.-+.++.+|.+|++|+++..
T Consensus 37 ~~~~~~~~~l~~~~~D~~i~~ 57 (198)
T cd08485 37 MSKNRQIEALDAGTIDIGFGR 57 (198)
T ss_pred CCHHHHHHHHHcCCccEEEec
Confidence 345678999999999999864
No 93
>cd08443 PBP2_CysB The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding speci
Probab=81.84 E-value=6.6 Score=22.25 Aligned_cols=21 Identities=10% Similarity=0.121 Sum_probs=17.5
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+..+.+...|.+|++|+++..
T Consensus 36 ~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08443 36 GSPTQIAEMVSKGLVDFAIAT 56 (198)
T ss_pred CCHHHHHHHHHCCCccEEEEe
Confidence 456688999999999999964
No 94
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=81.77 E-value=7.1 Score=21.85 Aligned_cols=50 Identities=16% Similarity=0.266 Sum_probs=33.5
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
+.++..|+..|+...-++.+.+.-|.... -..|..|+..+..|++|..+.
T Consensus 22 ~~~~~~a~~~g~~i~~~~~d~~~Sg~~~~---Rp~l~~ll~~~~~g~~~~ivv 71 (148)
T smart00857 22 EALRAYAKANGWEVVRIYEDEGVSGKKAD---RPGLQRLLADLRAGDIDVLVV 71 (148)
T ss_pred HHHHHHHHHCCCEEEEEEEeCCCcCCCCC---CHHHHHHHHHHHcCCCCEEEE
Confidence 34667788889886544444434444321 146999999999999987664
No 95
>cd03087 PGM_like1 This archaeal PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=81.56 E-value=5.3 Score=26.84 Aligned_cols=52 Identities=13% Similarity=0.168 Sum_probs=34.7
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+.+++|+++..+ ..+|+.++...|+.....+..+...+...++|++++
T Consensus 179 ~~~~~l~~lg~~v~~~~~~~d~~f~~~~p~p~~~~l~~l~~~v~~~~adlgia 231 (439)
T cd03087 179 TTPYLLRELGCKVITLNANPDGFFPGRPPEPTPENLSELMELVRATGADLGIA 231 (439)
T ss_pred HHHHHHHHcCCEEEEECCcCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCEEEE
Confidence 5678888999987654 345667653333211244667777777889999885
No 96
>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=80.76 E-value=6.5 Score=22.21 Aligned_cols=17 Identities=18% Similarity=0.075 Sum_probs=15.5
Q ss_pred hHHHhhhcCCccEEEeC
Q psy2313 39 GVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 39 g~ig~l~~g~~D~av~~ 55 (62)
.++..|.+|++|+++..
T Consensus 39 ~~~~~l~~g~~D~~i~~ 55 (200)
T cd08462 39 QPHELLERGEVDLLIAP 55 (200)
T ss_pred hHHHHHhcCCeeEEEec
Confidence 89999999999999964
No 97
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=80.06 E-value=8.2 Score=21.48 Aligned_cols=22 Identities=18% Similarity=0.267 Sum_probs=18.0
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+..+.+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~~~~D~~i~~~ 57 (199)
T cd08426 36 ASTADVLEAVLSGEADIGLAFS 57 (199)
T ss_pred CCcHHHHHHHHCCCccEEEecC
Confidence 4457789999999999999754
No 98
>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=79.44 E-value=8.5 Score=21.32 Aligned_cols=22 Identities=14% Similarity=0.279 Sum_probs=17.5
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.-..+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~~~~Dl~i~~~ 57 (201)
T cd08435 36 GTSDELLEGLRAGELDLAIGRL 57 (201)
T ss_pred CCHHHHHHHHHcCCccEEEEec
Confidence 3456788899999999998643
No 99
>cd08428 PBP2_IciA_ArgP The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold. The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-
Probab=79.36 E-value=6.5 Score=21.98 Aligned_cols=21 Identities=14% Similarity=0.036 Sum_probs=16.6
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....+...|.+|++|+++..
T Consensus 35 ~~~~~~~~~l~~~~~D~~i~~ 55 (195)
T cd08428 35 DDEDRTHDLLRDGEVVGCIST 55 (195)
T ss_pred CCchhHHHHHHcCcceEEEEe
Confidence 345678899999999988753
No 100
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=79.23 E-value=12 Score=23.01 Aligned_cols=23 Identities=9% Similarity=-0.032 Sum_probs=18.3
Q ss_pred cchhhHHHhhhcCCccEEEeCCc
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~lt 57 (62)
.....++..|.+|++|+++....
T Consensus 127 ~~~~~~~~~l~~g~~Dl~i~~~~ 149 (296)
T PRK11242 127 MSQERIEALLADDELDVGIAFAP 149 (296)
T ss_pred CCHHHHHHHHHCCCCcEEEEecC
Confidence 34577889999999999997543
No 101
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=78.95 E-value=8.6 Score=24.30 Aligned_cols=21 Identities=19% Similarity=0.272 Sum_probs=18.7
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+.++.++..|.+|++|+++..
T Consensus 129 ~~~~~~~~~L~~~~~D~~i~~ 149 (309)
T PRK12683 129 GSPQEIAEMLLNGEADIGIAT 149 (309)
T ss_pred CCHHHHHHHHHcCCccEEEec
Confidence 568899999999999999864
No 102
>PRK01066 porphobilinogen deaminase; Provisional
Probab=78.65 E-value=12 Score=23.87 Aligned_cols=51 Identities=10% Similarity=0.139 Sum_probs=29.4
Q ss_pred HHHHHHHc-CCeEEEEEecCCcccceecc------CCCcchhh-HHHhhhcCCccEEEeCC
Q psy2313 4 LENIAQEL-EFDFHLYIVADGLYGTKVRE------NQKDKWNG-VVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l-~f~~~~~~~~~~~~G~~~~~------~~~~~w~g-~ig~l~~g~~D~av~~l 56 (62)
.+.|.+.. +++++++... +-|-...+ .+.|-|.- +=.+|.+|++|+||-++
T Consensus 36 ~~~L~~~~p~~~~ei~~i~--T~GD~~~~~~L~~iGgkGlFtkele~aLl~g~iDiAVHSl 94 (231)
T PRK01066 36 LRLLRSFFPKLWFQISTTT--TQGDLDQKTPLHLVENTGFFTDDVDFLVLSGQCDLAIHSA 94 (231)
T ss_pred HHHHHHhCCCCcEEEEEEe--ccCcccccccHHHcCCceeeHHHHHHHHHcCCCCEEEecC
Confidence 34555544 6677777543 22322211 11355543 55588999999999776
No 103
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=78.60 E-value=4.7 Score=25.45 Aligned_cols=20 Identities=10% Similarity=0.119 Sum_probs=16.9
Q ss_pred chhhHHHhhhcCCccEEEeC
Q psy2313 36 KWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 36 ~w~g~ig~l~~g~~D~av~~ 55 (62)
....++..|.+|++|+++..
T Consensus 65 ~~~~~~~aL~~G~iDia~~~ 84 (314)
T PRK11553 65 AGPQMLEALNVGSIDLGSTG 84 (314)
T ss_pred CcHHHHHHHHcCCCCEEccC
Confidence 34689999999999999864
No 104
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=78.56 E-value=8.1 Score=24.35 Aligned_cols=22 Identities=5% Similarity=-0.083 Sum_probs=18.2
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....++..|.+|++|+++...
T Consensus 148 ~~~~~~~~~l~~g~~Di~i~~~ 169 (314)
T PRK09508 148 SLNQNIEHQLRYQETEFVISYE 169 (314)
T ss_pred CcchhHHHHHhcCCccEEEecC
Confidence 4457789999999999999754
No 105
>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=78.27 E-value=3.2 Score=26.24 Aligned_cols=22 Identities=14% Similarity=0.154 Sum_probs=18.9
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....++..|.+|++|+++..-
T Consensus 71 ~~s~~l~~~L~~G~iDlai~~~ 92 (287)
T TIGR02136 71 AGSGTGIKALINGTVDIGNSSR 92 (287)
T ss_pred CCchHHHHHHHcCCCchhhccC
Confidence 5688999999999999988653
No 106
>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=78.25 E-value=9.6 Score=21.23 Aligned_cols=21 Identities=10% Similarity=0.021 Sum_probs=16.8
Q ss_pred chhhHHHhhhcCCccEEEeCC
Q psy2313 36 KWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 36 ~w~g~ig~l~~g~~D~av~~l 56 (62)
.-..+...|.+|++|+++...
T Consensus 37 ~~~~~~~~l~~~~~D~~i~~~ 57 (198)
T cd08433 37 LSGHLLEWLLNGRLDLALLYG 57 (198)
T ss_pred CcHHHHHHHhCCCCcEEEEeC
Confidence 346788899999999998643
No 107
>cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II. HMBS is found in all organisms except viruses.
Probab=77.85 E-value=12 Score=24.50 Aligned_cols=51 Identities=16% Similarity=0.342 Sum_probs=29.8
Q ss_pred HHHHHHHc-CCeEEEEEecCCcccceecc------CCCcchhh-HHHhhhcCCccEEEeCC
Q psy2313 4 LENIAQEL-EFDFHLYIVADGLYGTKVRE------NQKDKWNG-VVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l-~f~~~~~~~~~~~~G~~~~~------~~~~~w~g-~ig~l~~g~~D~av~~l 56 (62)
.+.|.+.. +++++++... +-|-...+ .+.|-|.- +=.+|.+|++|+||-++
T Consensus 19 ~~~L~~~~p~~~~ei~~i~--T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVHSl 77 (292)
T cd00494 19 IEKLKELCPGIEVEIVIIK--TTGDKILDKPLAKIGGKGLFTKELEEALLNGEIDLAVHSL 77 (292)
T ss_pred HHHHHHhCCCCeEEEEEEE--ecCcccccccHHHcCCcceeHHHHHHHHHcCCCCEEEecc
Confidence 34555544 5677777542 22222110 12366764 44589999999999776
No 108
>TIGR00212 hemC porphobilinogen deaminase. Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin
Probab=77.73 E-value=12 Score=24.51 Aligned_cols=51 Identities=20% Similarity=0.367 Sum_probs=30.1
Q ss_pred HHHHHHHc-CCeEEEEEecCCcccceecc------CCCcchh-hHHHhhhcCCccEEEeCC
Q psy2313 4 LENIAQEL-EFDFHLYIVADGLYGTKVRE------NQKDKWN-GVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l-~f~~~~~~~~~~~~G~~~~~------~~~~~w~-g~ig~l~~g~~D~av~~l 56 (62)
.+.|.+.. +++++++... +-|-+..+ .+.|-|. .+=.+|.+|++|+||-++
T Consensus 19 ~~~L~~~~p~~~~ei~~i~--T~GD~~~~~~L~~iGgkGlFtkele~aLl~g~iDiAVHSl 77 (292)
T TIGR00212 19 REQLKAVYPELDTEIVIIK--TTGDKIQDKPLYDIGGKGLFTKELEQALLDGEIDLAVHSL 77 (292)
T ss_pred HHHHHHhCCCceEEEEEEe--eeCcccccCcHHHcCCceeeHHHHHHHHhcCCCCEEEecc
Confidence 34555544 5777777442 22322110 1236675 455789999999999776
No 109
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=76.99 E-value=12 Score=23.54 Aligned_cols=22 Identities=9% Similarity=0.259 Sum_probs=18.7
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+..+.++..|.+|++|+++...
T Consensus 133 ~~~~~~~~~l~~g~~Dl~i~~~ 154 (312)
T PRK10341 133 AQLSSFLPAIRDGRLDFAIGTL 154 (312)
T ss_pred CCHHHHHHHHHcCCCcEEEecC
Confidence 4567899999999999999754
No 110
>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=76.45 E-value=16 Score=22.91 Aligned_cols=46 Identities=15% Similarity=0.208 Sum_probs=35.0
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
..+.+.++.+=++++...+.++. +.-..++..|..|.+|++..+..
T Consensus 18 fa~~v~e~t~G~v~i~v~~~g~l---------g~~~e~~~~v~~G~vdm~~~~~~ 63 (286)
T PF03480_consen 18 FAEEVEERTGGRVKIEVFPAGQL---------GKEAEVLEAVQDGAVDMAVVSPS 63 (286)
T ss_dssp HHHHHHHHTTTSEEEEEEETTSS---------SSHHHHHHHHHTTSSSEEEEEGG
T ss_pred HHHHHHHHcCCeEEEEEecCccc---------CCHHHHHHHHhCCCccEEeecch
Confidence 56778888888888876554443 34568999999999999987664
No 111
>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=76.14 E-value=15 Score=22.30 Aligned_cols=21 Identities=10% Similarity=0.108 Sum_probs=17.5
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....++..|.+|++|+++..
T Consensus 120 ~~~~~~~~~l~~g~~Dl~i~~ 140 (279)
T TIGR03339 120 GNSQEVLQALQSYRVDVAVSS 140 (279)
T ss_pred CCHHHHHHHHHcCCCcEEEEe
Confidence 456678899999999999964
No 112
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=75.89 E-value=12 Score=22.53 Aligned_cols=22 Identities=23% Similarity=0.285 Sum_probs=17.5
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.-..+...|.+|++|+++...
T Consensus 103 ~~~~~~~~~l~~~~~D~~i~~~ 124 (269)
T PRK11716 103 GDAADAVEKVQSGEADLAIAAK 124 (269)
T ss_pred CCHHHHHHHHHCCCccEEEEec
Confidence 3446788999999999999643
No 113
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=75.81 E-value=12 Score=23.70 Aligned_cols=21 Identities=14% Similarity=0.235 Sum_probs=17.8
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+..+.++..|.+|++|+++..
T Consensus 129 ~~~~~~~~~L~~g~~D~~i~~ 149 (313)
T PRK12684 129 GSPTQIAEMVLHGQADLAIAT 149 (313)
T ss_pred CChHHHHHHHHCCCcCEEEee
Confidence 456789999999999999964
No 114
>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=75.80 E-value=9.5 Score=25.18 Aligned_cols=39 Identities=10% Similarity=0.295 Sum_probs=27.9
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
++..-.+++|+++++.. ..|+.+...+..++.|+++.+.
T Consensus 337 ~i~~~l~~~Gi~v~~~~---------------~~~~~~~~~~~~~~~d~~~~~w 375 (457)
T cd08516 337 VIQAQLAAIGINVEIEL---------------VEWATWLDDVNKGDYDATIAGT 375 (457)
T ss_pred HHHHHHHHcCceEEEEE---------------ecHHHHHHHHhCCCcceeeecc
Confidence 34444556799888875 3577778888888999887654
No 115
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=75.61 E-value=17 Score=22.77 Aligned_cols=21 Identities=14% Similarity=0.170 Sum_probs=17.1
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....+...|.+|++|+++..
T Consensus 128 ~~~~~~~~~l~~g~~Di~i~~ 148 (305)
T PRK11233 128 NSGATLNEKLMNGQLDMAVIY 148 (305)
T ss_pred CCcHHHHHHHHCCCCCEEEEc
Confidence 345678889999999999964
No 116
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=74.39 E-value=13 Score=23.84 Aligned_cols=21 Identities=14% Similarity=0.166 Sum_probs=18.2
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+..+.++..|.+|++|+++..
T Consensus 129 ~~~~~~~~~l~~g~~Dl~i~~ 149 (327)
T PRK12680 129 AAESAALDLLGQGDADIAIVS 149 (327)
T ss_pred CChHHHHHHHHCCCCcEEEEe
Confidence 457889999999999999965
No 117
>PRK07377 hypothetical protein; Provisional
Probab=74.32 E-value=10 Score=23.37 Aligned_cols=41 Identities=15% Similarity=0.185 Sum_probs=33.2
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.++.+.+..+.+.|++..+ .-..+..+|.+|++|.+.+.-
T Consensus 97 ~~l~~~~~~y~~rlElv~y~--------------~~~~l~~aL~~~eVh~~c~~~ 137 (184)
T PRK07377 97 DQLRTILDKYHLRLELVVYP--------------DLQALEQALRDKEVHAICLES 137 (184)
T ss_pred HHHHHHHHHhCceeeEEecC--------------CHHHHHHHHhcCCccEEecCC
Confidence 45677888899999998753 467899999999999887654
No 118
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=74.10 E-value=12 Score=20.46 Aligned_cols=50 Identities=12% Similarity=0.132 Sum_probs=32.2
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
.++..|+..|+...-++.+.+.-|.... .-..|..|+..+..++.|..+.
T Consensus 22 ~~~~~a~~~g~~i~~~~~d~~~s~~~~~--~R~~~~~ll~~~~~~~~d~ivv 71 (137)
T cd00338 22 ALREYAARNGLEVVGEYEDAGSSATSLV--DRPGLQRLLADVKAGKIDVVLV 71 (137)
T ss_pred HHHHHHHHCCCEEEEEEEeCCCCccccc--CCHHHHHHHHHHHcCCCCEEEE
Confidence 4567777778876555544443332011 1246999999999999997663
No 119
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=74.06 E-value=14 Score=23.68 Aligned_cols=21 Identities=14% Similarity=0.199 Sum_probs=18.3
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+..+.++..|.+|++|+++..
T Consensus 129 ~~~~~~~~~L~~g~iDl~i~~ 149 (324)
T PRK12681 129 GSPTQIAEAAAKGNADFAIAT 149 (324)
T ss_pred CCHHHHHHHHHcCCCCEEEec
Confidence 567889999999999999964
No 120
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=73.61 E-value=19 Score=22.42 Aligned_cols=22 Identities=18% Similarity=0.271 Sum_probs=18.0
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
..-+.++..|.+|++|+++...
T Consensus 127 ~~~~~~~~~l~~g~~Dl~i~~~ 148 (305)
T PRK11151 127 AQTHQLLAQLDSGKLDCAILAL 148 (305)
T ss_pred CCHHHHHHHHHcCCccEEEEec
Confidence 3457899999999999999643
No 121
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=72.57 E-value=19 Score=22.04 Aligned_cols=21 Identities=5% Similarity=0.126 Sum_probs=17.4
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....++..|.+|++|+++..
T Consensus 125 ~~~~~~~~~l~~g~~Di~i~~ 145 (290)
T PRK10837 125 GNSQDVINAVLDFRVDIGLIE 145 (290)
T ss_pred CCHHHHHHHHHhCCceEEEec
Confidence 455678999999999999864
No 122
>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=72.16 E-value=16 Score=22.62 Aligned_cols=40 Identities=5% Similarity=0.094 Sum_probs=30.0
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
|+..+-+..|+..++... +...-+..+|.+|++|+.....
T Consensus 19 i~~~~Le~~G~~v~~~~~--------------~~~~~~~~al~~G~iD~~~~~w 58 (257)
T PF04069_consen 19 IYAQLLEAAGYVVEVVNL--------------GSTPVIFAALASGDIDIYPEEW 58 (257)
T ss_dssp HHHHHHHHTTEEEEEEEE--------------SSHHHHHHHHHTTSSSEEEEEE
T ss_pred HHHHHHHHCCCeEEEecC--------------CchHHHHHHHHCCCCeEEhhhc
Confidence 556667777998877753 3456788999999999987443
No 123
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=72.04 E-value=14 Score=22.87 Aligned_cols=21 Identities=5% Similarity=-0.029 Sum_probs=17.4
Q ss_pred chhhHHHhhhcCCccEEEeCC
Q psy2313 36 KWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 36 ~w~g~ig~l~~g~~D~av~~l 56 (62)
+....+.+|.+|++|.++++-
T Consensus 181 ~~~~~~~~l~~GrvDa~~~d~ 201 (259)
T PRK11917 181 DYPSIKAALDAKRVDAFSVDK 201 (259)
T ss_pred CHHHHHHHHHcCCCcEEEecH
Confidence 467788999999999987764
No 124
>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=72.02 E-value=13 Score=24.63 Aligned_cols=39 Identities=13% Similarity=0.399 Sum_probs=27.4
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
+..-.+++|+++++... .|+.+...+..++.|+++.+..
T Consensus 341 i~~~l~~~Gi~v~~~~~---------------~~~~~~~~~~~~~~d~~~~~~~ 379 (470)
T cd08490 341 IQAQLKKIGIDVEIRVV---------------EYDAIEEDLLDGDFDLALYSRN 379 (470)
T ss_pred HHHHHHHcCceEEEEEe---------------ehhhhhhHhhcCCccEEEeccc
Confidence 33334557999998753 4666777777888998887654
No 125
>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=71.75 E-value=15 Score=20.46 Aligned_cols=21 Identities=19% Similarity=0.245 Sum_probs=16.8
Q ss_pred chhhHHHhhhcCCccEEEeCC
Q psy2313 36 KWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 36 ~w~g~ig~l~~g~~D~av~~l 56 (62)
.-..+...|.+|++|+++...
T Consensus 37 ~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08457 37 SSSQVLEAVASGRADLGIADG 57 (196)
T ss_pred CcHHHHHHHHcCCccEEEecc
Confidence 346788889999999999754
No 126
>cd05800 PGM_like2 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four structural domains (subdomains) with a centrally located active site formed by four loops, one from each subdomain. All four subdomains are included in this alignment model.
Probab=70.48 E-value=14 Score=25.05 Aligned_cols=53 Identities=19% Similarity=0.248 Sum_probs=33.5
Q ss_pred hHHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 2 DLLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 2 dll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
.++..+-+++|+++... ..+|+.++...|+.....-..+...+....+|++++
T Consensus 187 ~~~~~il~~lg~~v~~~~~~~dg~F~~~~p~p~~~~l~~l~~~v~~~~ad~Gia 240 (461)
T cd05800 187 GYLEELLRGAGVDVEEIRAERDPLFGGIPPEPIEKNLGELAEAVKEGGADLGLA 240 (461)
T ss_pred HHHHHHHHHcCCCEEEeeCCcCCCCCCCCCCCCHHHHHHHHHHHHhcCCCEEEE
Confidence 35677888999877443 456777654433311223345666777888999875
No 127
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=70.11 E-value=17 Score=22.79 Aligned_cols=22 Identities=14% Similarity=0.238 Sum_probs=17.7
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.-+.+...|..|++|+++..-
T Consensus 129 ~~~~~~~~~l~~g~~D~~i~~~ 150 (309)
T PRK12682 129 GSPDEIARMVISGEADIGIATE 150 (309)
T ss_pred CCHHHHHHHHHcCCccEEEecC
Confidence 3446788999999999999753
No 128
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=69.76 E-value=21 Score=22.34 Aligned_cols=21 Identities=5% Similarity=0.185 Sum_probs=18.2
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....++..|.+|++|+++..
T Consensus 131 ~~~~~~~~~l~~g~~Dl~i~~ 151 (305)
T CHL00180 131 HSTRRIAWNVANGQIDIAIVG 151 (305)
T ss_pred CCHHHHHHHHHcCCccEEEEc
Confidence 457889999999999999974
No 129
>cd08507 PBP2_SgrR_like The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold. A novel family of SgrR transcriptional regulator contains a two-domain structure with an N terminal DNA-binding domain of the winged helix family and a C-terminal solute-binding domain. The C-terminal domain shows strong homology with the ABC-type oligopeptide-binding protein family, a member of the type 2 periplasmic-binding fold protein (PBP2) superfamily that also includes the C-terminal substrate-binding domain of LysR-type transcriptional regulators. SgrR (SugaR transport-related Regulator) is negatively autoregulated and activates transcription of divergent operon SgrS, which encodes a small RNA required for recovery from glucose-phosphate stress. Hence, the small RNA SgrS and SgrR, the transcription factor that controls sgrS expression, are both required for recovery f
Probab=69.18 E-value=12 Score=24.98 Aligned_cols=40 Identities=5% Similarity=0.147 Sum_probs=27.8
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
++.+..+..|+++++... .|+.+...+..|..|+.+.+.+
T Consensus 316 ~l~~~l~~~Gi~v~l~~~---------------~~~~~~~~~~~g~~d~~~~~~~ 355 (448)
T cd08507 316 WIQQRLAKHGIRLEIHIL---------------SYEELLEGDADSMADLWLGSAN 355 (448)
T ss_pred HHHHHHHHcCcEEEEEee---------------cccchhhhhhhhccCeeecccc
Confidence 455555678999999764 4566666667788888776654
No 130
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=68.93 E-value=22 Score=23.45 Aligned_cols=47 Identities=13% Similarity=0.232 Sum_probs=38.0
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCcc
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSV 58 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lti 58 (62)
+.+.+.++.|=++++..-|+++-|. =..++..|..|.+|+.+.+.+.
T Consensus 49 fa~~v~ekt~G~l~i~vfP~~qLG~---------~~~~ie~l~~G~id~~~~s~~~ 95 (332)
T COG1638 49 FAELVEEKTGGRLKIEVFPNSQLGG---------EAEMIEQLRSGTLDIGVVSLGF 95 (332)
T ss_pred HHHHHHHHhCCeEEEEECCCcccCc---------HHHHHHHHhcCCeeEEeccchh
Confidence 5678888999999999888777663 3578999999999999887643
No 131
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=68.91 E-value=17 Score=23.20 Aligned_cols=36 Identities=14% Similarity=0.194 Sum_probs=26.5
Q ss_pred HHHHH-HHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEE
Q psy2313 4 LENIA-QELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSF 53 (62)
Q Consensus 4 l~~la-~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av 53 (62)
++.+. ++.|++++++.. ..+..+..+|.+|++|+..
T Consensus 49 ~~~~l~~~~G~~Vel~~f--------------~~~~~~~~ALa~GdID~~~ 85 (271)
T PRK11063 49 AQKVAKEKYGLDVELVTF--------------NDYVLPNEALSKGDIDANA 85 (271)
T ss_pred HHHHHHHhcCCeEEEEEe--------------cCcHHHHHHHHcCCcceec
Confidence 33444 445999999864 3577888999999999854
No 132
>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=68.82 E-value=21 Score=22.71 Aligned_cols=31 Identities=10% Similarity=0.080 Sum_probs=25.2
Q ss_pred HcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 10 ELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 10 ~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
+.|++++++.. ..|..+..+|.+|++|+...
T Consensus 43 ~~G~~Ve~~~f--------------~d~~~~~~Al~~G~ID~~~~ 73 (258)
T TIGR00363 43 KYGLDVELVEF--------------NDYALPNEAVSKGDLDANAF 73 (258)
T ss_pred hcCCEEEEEEe--------------CCcHHHHHHHHcCCCCeEec
Confidence 46999999864 35888999999999998754
No 133
>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=68.49 E-value=22 Score=21.04 Aligned_cols=39 Identities=8% Similarity=0.136 Sum_probs=24.8
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcC-CccEEEeC
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTG-TAHMSFAA 55 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g-~~D~av~~ 55 (62)
+++++..++.+++++++. +.=..++..|..| ++|+.+++
T Consensus 10 ~~~~~f~~~~gi~V~~~~---------------~gs~~l~~~l~~~~~aDv~~~~ 49 (216)
T TIGR01256 10 EIAKQFEKRTGNKVVFSF---------------GSSGTLYTQIENGAPADLFISA 49 (216)
T ss_pred HHHHHHHHhhCCeEEEEe---------------CChHHHHHHHHcCCCCcEEEEC
Confidence 355666677788887764 2223455666655 59998874
No 134
>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=68.19 E-value=19 Score=23.94 Aligned_cols=38 Identities=5% Similarity=0.122 Sum_probs=27.1
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.+-.+++|+++++.. ..|+.+...+..|+.|+++.+.
T Consensus 354 i~~~l~~~Gi~v~~~~---------------~~~~~~~~~~~~~~~d~~~~~w 391 (476)
T cd08512 354 LQASLAQIGIKVEIEP---------------VPWAQLLEAARSREFDIFIGGW 391 (476)
T ss_pred HHHHHHHhCCeEEEEE---------------cCHHHHHHHhhCCCccEEEEec
Confidence 3444455788888875 3577777888888999887654
No 135
>cd08504 PBP2_OppA The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which
Probab=68.19 E-value=16 Score=24.41 Aligned_cols=40 Identities=13% Similarity=0.240 Sum_probs=28.1
Q ss_pred HHHHHHHH-cCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 3 LLENIAQE-LEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 3 ll~~la~~-l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
++....++ .|+++++... .|+.+...+..++.|+++.+..
T Consensus 362 ~i~~~l~~~iGI~v~i~~~---------------~~~~~~~~~~~~~~d~~~~~~~ 402 (498)
T cd08504 362 AIQQMWKKNLGVKVTLKNV---------------EWKVFLDRRRKGDFDIARSGWG 402 (498)
T ss_pred HHHHHHHHcCCCeEEEEec---------------chHHhhhhccCCCeeEEecccc
Confidence 45556677 8999998753 4666666677788888876553
No 136
>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=68.19 E-value=25 Score=21.73 Aligned_cols=22 Identities=14% Similarity=0.160 Sum_probs=18.0
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.....++.+|.+|++|++++..
T Consensus 129 ~~~~~~~~~l~~g~~D~~i~~~ 150 (300)
T TIGR02424 129 GPNAYLLDQLRVGALDLVVGRL 150 (300)
T ss_pred CchHHHHHHHHCCCCCEEEEec
Confidence 4557789999999999999644
No 137
>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=68.14 E-value=14 Score=23.73 Aligned_cols=38 Identities=11% Similarity=0.089 Sum_probs=27.6
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
|++.+-+.+|++++++. +.-.-+...|.+|++|+.+..
T Consensus 26 i~~~iLE~~Gy~Ve~~~---------------~~~~~~~~al~~GdiD~~~e~ 63 (290)
T TIGR03414 26 LASVLLEGLGYQPKVTL---------------LSVPVTYAGLKDGDLDVFLGN 63 (290)
T ss_pred HHHHHHHHcCCcceeEE---------------ccHHHHHHHHHcCCceEeccc
Confidence 56667777899888864 233556778889999987644
No 138
>cd06353 PBP1_BmpA_Med_like Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type I periplasmic sugar-binding protein-like fold.
Probab=68.01 E-value=18 Score=22.58 Aligned_cols=41 Identities=10% Similarity=0.070 Sum_probs=30.7
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++++++.+|.+++++.... . ...|...+.++.+..+|++++
T Consensus 23 ~~~~~~~~gv~~~~~e~~~------~----~~~~~~~i~~~~~~g~dlIi~ 63 (258)
T cd06353 23 RKAAEKALGVEVTYVENVP------E----GADAERVLRELAAQGYDLIFG 63 (258)
T ss_pred HHHHHHhcCCeEEEEecCC------c----hHhHHHHHHHHHHcCCCEEEE
Confidence 4567777899888876431 1 246889999999888999886
No 139
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=67.66 E-value=22 Score=22.11 Aligned_cols=21 Identities=10% Similarity=0.303 Sum_probs=17.8
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....+...|.+|++|+++..
T Consensus 131 ~~~~~~~~~l~~g~~Di~i~~ 151 (302)
T PRK09791 131 GQLVSMINELRQGELDFTINT 151 (302)
T ss_pred CChHHHHHHHHCCCccEEEEe
Confidence 456789999999999999874
No 140
>cd03089 PMM_PGM The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a bisphosphorylated sugar intermediate. The reaction involves two phosphoryl transfers, with an intervening 180 degree reorientation of the reaction intermediate during catalysis. Reorientation of the intermediate occurs without dissociation from the active site of the enzyme and is thus, a simple example of processivity, as defined by multiple rounds of catalysis without release of substrate. Glucose-6-phosphate and glucose-1-phosphate are known to be utilized for energy metabolism and cell surface construction, respectively. PMM/PGM belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other membe
Probab=67.17 E-value=19 Score=24.27 Aligned_cols=52 Identities=10% Similarity=0.250 Sum_probs=35.0
Q ss_pred HHHHHHHHcCCeEEE-EEecCCcccceeccCC-CcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHL-YIVADGLYGTKVRENQ-KDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~-~~~~~~~~G~~~~~~~-~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|-+++|+++.. ...+|+.++...|+.. ...+..+...+...++|++++
T Consensus 178 ~~~~ll~~lG~~v~~i~~~~d~~F~~~~p~p~~~~~l~~l~~~v~~~~adlgia 231 (443)
T cd03089 178 IAPQLLEALGCEVIPLFCEPDGTFPNHHPDPTDPENLEDLIAAVKENGADLGIA 231 (443)
T ss_pred HHHHHHHHCCCEEEEecCCCCCCCCCCCcCCCCHHHHHHHHHHHHHcCCCEEEE
Confidence 567788889997533 3557777765444311 134677788888889999885
No 141
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=66.65 E-value=28 Score=21.50 Aligned_cols=23 Identities=13% Similarity=0.001 Sum_probs=18.7
Q ss_pred cchhhHHHhhhcCCccEEEeCCc
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~lt 57 (62)
...+.++..|.+|++|+++....
T Consensus 126 ~~~~~~~~~l~~~~~D~~i~~~~ 148 (296)
T PRK09906 126 LITTQQEEKLRRGELDVGFMRHP 148 (296)
T ss_pred CCcHHHHHHHHcCCeeEEEecCC
Confidence 34678999999999999997543
No 142
>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=64.88 E-value=25 Score=23.56 Aligned_cols=38 Identities=8% Similarity=0.049 Sum_probs=26.6
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+..-.+++|+++++.. ..|+.+...+..|+.|+++.+.
T Consensus 351 i~~~l~~~Gi~v~i~~---------------~~~~~~~~~~~~~~~d~~~~~w 388 (481)
T cd08498 351 VAGMLARIGIKVNLET---------------MPKSVYFPRATKGEADFYLLGW 388 (481)
T ss_pred HHHHHHHhCceEEEEE---------------ecHHHHHHHhhCCCcCEEEEcc
Confidence 3334455788888865 3577777778888899887654
No 143
>COG2113 ProX ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]
Probab=64.58 E-value=15 Score=24.12 Aligned_cols=39 Identities=15% Similarity=0.116 Sum_probs=30.8
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+++.+-+.+|++.+++. +...-|...|.+|++|+....-
T Consensus 49 v~~~iLk~~Gy~v~~~~---------------~~~~~~~~sla~gd~D~~~~~W 87 (302)
T COG2113 49 VAKKILKGLGYTVELVT---------------LDTAVMYQSLAKGDLDVFPEAW 87 (302)
T ss_pred HHHHHHHhCCCcceeee---------------ccHHHHHHHHHcCCCcccccee
Confidence 45566699999998875 5678888899999999876544
No 144
>PRK10918 phosphate ABC transporter periplasmic substrate-binding protein PstS; Provisional
Probab=63.96 E-value=21 Score=23.74 Aligned_cols=25 Identities=16% Similarity=0.284 Sum_probs=20.1
Q ss_pred cchhhHHHhhhcCCccEEEeCCcccc
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAALSVSS 60 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ltit~ 60 (62)
|+-.| +.++.+|.+||+.++..+++
T Consensus 62 GSG~G-i~~~~~g~vd~a~ssr~l~~ 86 (346)
T PRK10918 62 GSSGG-VKQIIANTVDFGASDAPLSD 86 (346)
T ss_pred ccHHH-HHHHHhCCCcEEecCccCCH
Confidence 56566 57789999999999887764
No 145
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=63.77 E-value=10 Score=24.00 Aligned_cols=31 Identities=16% Similarity=0.191 Sum_probs=24.6
Q ss_pred HHcCC-eEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEE
Q psy2313 9 QELEF-DFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSF 53 (62)
Q Consensus 9 ~~l~f-~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av 53 (62)
++.|. .++++.. ..|...+..|..|++|+++
T Consensus 56 ~~~Gl~~v~~~~~--------------~~~~~~~~~l~~G~~D~a~ 87 (335)
T COG0715 56 KKEGLDDVELVEF--------------TGGAPVLEALAAGALDFAV 87 (335)
T ss_pred hHhCCCceEEEEc--------------CCChHHHHHHhcCCcCccc
Confidence 44566 4777763 4799999999999999994
No 146
>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=63.59 E-value=26 Score=23.38 Aligned_cols=38 Identities=3% Similarity=0.070 Sum_probs=27.2
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+..-.+++|+++++.. ..|+.+...+..++.|+++.+.
T Consensus 349 i~~~l~~iGi~v~i~~---------------~~~~~~~~~~~~~~~d~~~~~~ 386 (468)
T cd08520 349 IKEQLERVGIKVNVKS---------------LESKTLDSAVKDGDYDLAISGH 386 (468)
T ss_pred HHHHHHHcCceEEEEe---------------cChHHHHHHHhCCCeeEEEecc
Confidence 4444456899988875 3577777778888899887654
No 147
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=63.58 E-value=20 Score=22.41 Aligned_cols=22 Identities=18% Similarity=0.166 Sum_probs=18.5
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.....++..|.+|++|+++...
T Consensus 134 ~~~~~~~~~l~~g~~Dlai~~~ 155 (303)
T PRK10082 134 IDVDEAVDKLREGQSDCIFSFH 155 (303)
T ss_pred CCHHHHHHHHHCCCCCEEEEec
Confidence 4567899999999999999753
No 148
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=63.27 E-value=26 Score=22.26 Aligned_cols=22 Identities=9% Similarity=-0.005 Sum_probs=18.1
Q ss_pred chhhHHHhhhcCCccEEEeCCc
Q psy2313 36 KWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 36 ~w~g~ig~l~~g~~D~av~~lt 57 (62)
.++.++..|.+|++|+++....
T Consensus 152 ~~~~~~~~l~~g~~Dl~i~~~~ 173 (317)
T PRK11482 152 PISDAENQLSQFQTDLIIDTHS 173 (317)
T ss_pred cchhHHHHHHCCCcCEEEeccC
Confidence 4567899999999999997543
No 149
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=62.93 E-value=30 Score=21.38 Aligned_cols=22 Identities=14% Similarity=0.051 Sum_probs=18.0
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+..+.+...|.+|++|+++...
T Consensus 125 ~~~~~~~~~L~~~~~d~~i~~~ 146 (294)
T PRK13348 125 DDQDHTFALLERGEVVGCVSTQ 146 (294)
T ss_pred cchHHHHHHHhcCCeEEEEecC
Confidence 4567888999999999998654
No 150
>cd08497 PBP2_NikA_DppA_OppA_like_14 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=62.79 E-value=28 Score=23.55 Aligned_cols=39 Identities=18% Similarity=-0.009 Sum_probs=27.7
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
+..-.+++|+++++.. ..|+.+...+..|..|+++....
T Consensus 366 i~~~l~~iGi~v~i~~---------------~~~~~~~~~~~~g~~d~~~~~~~ 404 (491)
T cd08497 366 YVRNLKKLGIDASLRL---------------VDSAQYQKRLRSFDFDMITAAWG 404 (491)
T ss_pred HHHHHHhcCceEEEee---------------ccHHHHHHHhhcCCeeEEEeccC
Confidence 3444456899999875 35777777778888888876653
No 151
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=62.65 E-value=29 Score=21.96 Aligned_cols=22 Identities=18% Similarity=0.155 Sum_probs=17.6
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.-+.+...|.+|++|+++...
T Consensus 129 ~~~~~~~~~L~~g~~Dl~i~~~ 150 (316)
T PRK12679 129 GTPQEIATLLQNGEADIGIASE 150 (316)
T ss_pred CCHHHHHHHHHcCCCCEEEecc
Confidence 4456788999999999998643
No 152
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=62.07 E-value=26 Score=19.58 Aligned_cols=22 Identities=9% Similarity=-0.026 Sum_probs=17.1
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.-..+...|.+|++|+++...
T Consensus 36 ~~~~~~~~~l~~g~~Dl~i~~~ 57 (196)
T cd08458 36 VPSQTVLELVSLQHYDLGISIL 57 (196)
T ss_pred cChHHHHHHHHcCCCCEEEEec
Confidence 3455688889999999998743
No 153
>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=61.82 E-value=30 Score=23.10 Aligned_cols=39 Identities=5% Similarity=0.211 Sum_probs=26.8
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
+....++.|+++++... .|+.+...+..++.|++..+..
T Consensus 359 i~~~l~~~Gi~v~~~~~---------------~~~~~~~~~~~~~~dl~~~~~~ 397 (482)
T cd08493 359 IQADLAKVGIKVEIVTY---------------EWGEYLERTKAGEHDLYLLGWT 397 (482)
T ss_pred HHHHHHHhCCEEEEEEe---------------eHHHHHHHhhCCCCCEEEEccc
Confidence 34444668898888753 4667777777888888775543
No 154
>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=61.38 E-value=25 Score=23.39 Aligned_cols=39 Identities=10% Similarity=0.262 Sum_probs=26.5
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
+..-.+++|+++++... .|+.+...+.+++.|+++.+.+
T Consensus 364 i~~~l~~iGi~v~i~~~---------------~~~~~~~~~~~~~~d~~~~~~~ 402 (484)
T cd08492 364 IQAQLKEVGIDLQLKVL---------------DAGTLTARRASGDYDLALSYYG 402 (484)
T ss_pred HHHHHHhhCeEEEEEEe---------------chHHHHHhhhcCCceEEEEecc
Confidence 34444668999998764 4666666667788888776543
No 155
>cd05799 PGM2 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. PGM2L1 is thought to catalyze the 1,3-bisphosphoglycerate-dependent synthesis of glucose 1,6-bisphosphate and other aldose-bisphosphates that serve as cofactors for several sugar phosphomutases and possibly also as regulators of glycolytic enzymes. PGM2 and PGM2L1 belong to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/ph
Probab=60.91 E-value=21 Score=24.40 Aligned_cols=52 Identities=13% Similarity=0.054 Sum_probs=34.2
Q ss_pred hHHHHHHHHcCCe----EEEEEecCCcccc---eeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 2 DLLENIAQELEFD----FHLYIVADGLYGT---KVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 2 dll~~la~~l~f~----~~~~~~~~~~~G~---~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
.++..+.+.||++ +++...+|+.|+. ++|. ....+..+...+....+|++++
T Consensus 200 ~~~~~il~~LG~~~v~~~~~~~~~d~~F~~~~~p~p~-~~~~l~~l~~~v~~~~ad~Gia 258 (487)
T cd05799 200 KFVPRALKEAGFTNVIVVEEQAEPDPDFPTVKFPNPE-EPGALDLAIELAKKVGADLILA 258 (487)
T ss_pred HHHHHHHHHcCCCCcEEeeeccCCCcCCCCCCCCCCC-CHHHHHHHHHHHHHhCCCEEEE
Confidence 3577888899988 4444556777753 3331 0134666777777889999875
No 156
>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=60.55 E-value=41 Score=22.36 Aligned_cols=38 Identities=16% Similarity=0.262 Sum_probs=25.4
Q ss_pred HHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 5 ENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 5 ~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
+.-.+.+|+++++... .++.+...+..|+.|+++.+..
T Consensus 339 ~~~l~~~Gi~v~i~~~---------------~~~~~~~~~~~~~~di~~~~w~ 376 (467)
T cd08511 339 QAMAAEAGFTVKLRPT---------------EFATLLDRALAGDFQATLWGWS 376 (467)
T ss_pred HHHHHhcCcEeEEEEc---------------cHHHHHHHHhCCCccEEEeccc
Confidence 3334557888877653 4666667777889998876543
No 157
>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=60.48 E-value=28 Score=23.33 Aligned_cols=34 Identities=9% Similarity=0.131 Sum_probs=24.6
Q ss_pred HHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEE
Q psy2313 5 ENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSF 53 (62)
Q Consensus 5 ~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av 53 (62)
..-.+++|+++++... .|+.+...+..|..|+++
T Consensus 355 ~~~l~~~Gi~v~~~~~---------------~~~~~~~~~~~~~~d~~~ 388 (488)
T cd08489 355 QSELKKIGIDLNIIGE---------------EEQAYYDRQKDGDFDLIF 388 (488)
T ss_pred HHHHHHcCcEEEEeec---------------cHHHHHhHhhCCcccEEE
Confidence 3344557999998763 566777777888888876
No 158
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=60.31 E-value=32 Score=21.69 Aligned_cols=19 Identities=16% Similarity=0.225 Sum_probs=15.8
Q ss_pred chhhHHHhhhcCCccEEEe
Q psy2313 36 KWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 36 ~w~g~ig~l~~g~~D~av~ 54 (62)
.-..+...|.+|++|++++
T Consensus 130 ~~~~~~~~l~~g~~D~~i~ 148 (308)
T PRK10094 130 IYMGVWDSLLYEGFSLAIG 148 (308)
T ss_pred hhhhHHHHHhCCCccEEEe
Confidence 3467888999999999885
No 159
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=59.79 E-value=37 Score=21.58 Aligned_cols=20 Identities=5% Similarity=0.023 Sum_probs=16.6
Q ss_pred chhhHHHhhhcCCccEEEeC
Q psy2313 36 KWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 36 ~w~g~ig~l~~g~~D~av~~ 55 (62)
....++..|.+|++|+++..
T Consensus 136 ~~~~~~~~l~~g~~Di~i~~ 155 (310)
T PRK15092 136 RNAFMMEMLESQEVDLAVTT 155 (310)
T ss_pred CcHHHHHHHhCCCeeEEEEe
Confidence 45678889999999999864
No 160
>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=59.64 E-value=30 Score=21.97 Aligned_cols=39 Identities=15% Similarity=0.252 Sum_probs=28.8
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcch-hhHHHhhhcCCccEEEeCCc
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKW-NGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w-~g~ig~l~~g~~D~av~~lt 57 (62)
+..-.+++|+++++... .| +.....+..|+.|+++...+
T Consensus 314 l~~~l~~~Gi~v~i~~~---------------~~~~~~~~~~~~~~~d~~~~~~~ 353 (374)
T PF00496_consen 314 LQEQLKKIGIKVEIKPV---------------DFNDTYDKRLRAGDFDMALSGWS 353 (374)
T ss_dssp HHHHHHHTTEEEEEEEE---------------SHHHHHHHHHHCTSESEEEEEEE
T ss_pred HHHHHhhcceeEEEEEe---------------ChHHHHHHHhhCCCcCEEEEecC
Confidence 44444568999999874 57 56667788999999987654
No 161
>PLN02371 phosphoglucosamine mutase family protein
Probab=59.14 E-value=22 Score=25.18 Aligned_cols=52 Identities=15% Similarity=0.366 Sum_probs=34.8
Q ss_pred HHHHHHHHcCCeEE--EEEecCCcccceeccCC-CcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFH--LYIVADGLYGTKVRENQ-KDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~--~~~~~~~~~G~~~~~~~-~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|-+++|+++. +...+|+.|+...|+.. ...+..+...+...++|++++
T Consensus 278 ~~~~lL~~LG~~v~~~~~~~pDg~Fp~~~P~P~~~~~l~~l~~~v~~~~aDlGia 332 (583)
T PLN02371 278 FAEKVLEPLGADTSGSLFLEPDGMFPNHIPNPEDKAAMSATTQAVLANKADLGII 332 (583)
T ss_pred HHHHHHHHcCCCeEeeccCCCCCCCCCcCCCCCCHHHHHHHHHHHHhcCCCEEEE
Confidence 46677788998754 44557787764444311 123667777888899999885
No 162
>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=58.43 E-value=36 Score=22.68 Aligned_cols=38 Identities=11% Similarity=0.356 Sum_probs=25.6
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCC-ccEEEeCC
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGT-AHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~-~D~av~~l 56 (62)
+.+-.+++|+++++... .|+.+...+..++ .|+++.+.
T Consensus 338 i~~~l~~~GI~v~i~~~---------------~~~~~~~~~~~~~~~dl~~~~w 376 (474)
T cd08499 338 IQQQLAQIGIDVEIEVM---------------EWGAYLEETGNGEEHQMFLLGW 376 (474)
T ss_pred HHHHHHHcCceEEEEec---------------cHHHHHHHhcCCCcccEEEEec
Confidence 33334557888888753 5777777777777 88877544
No 163
>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=58.00 E-value=32 Score=22.52 Aligned_cols=32 Identities=3% Similarity=0.100 Sum_probs=23.1
Q ss_pred HHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 9 QELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 9 ~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
+..|++++++..+ .....+.++.+|++|++..
T Consensus 31 ~~~Gl~Ve~~~f~--------------~~~~~l~Al~aG~iD~~~~ 62 (328)
T TIGR03427 31 DKYGITIEVVQIN--------------DYVESINQYTAGKFDGCTM 62 (328)
T ss_pred HHcCCeEEEEECC--------------ChHHHHHHHHcCCCCEEee
Confidence 4567788887532 3567778888999998653
No 164
>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=57.77 E-value=37 Score=22.35 Aligned_cols=37 Identities=8% Similarity=0.079 Sum_probs=25.2
Q ss_pred HHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcC-CccEEEeCC
Q psy2313 5 ENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTG-TAHMSFAAL 56 (62)
Q Consensus 5 ~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g-~~D~av~~l 56 (62)
..-.+++|+++++.. ..|+.+...+..+ +.|+++...
T Consensus 336 ~~~l~~~GI~v~i~~---------------~~~~~~~~~~~~~~~~d~~~~~~ 373 (448)
T cd08494 336 ASQLAEVGITVKIEV---------------VEPATWLQRVYKGKDYDLTLIAH 373 (448)
T ss_pred HHHHHhcCcEEEEEE---------------eeHHHHHHHhccCCceeEEEecc
Confidence 333455788888875 3577777766666 889887654
No 165
>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=57.40 E-value=27 Score=23.37 Aligned_cols=39 Identities=8% Similarity=0.108 Sum_probs=26.4
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcC-CccEEEeCCc
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTG-TAHMSFAALS 57 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g-~~D~av~~lt 57 (62)
+..-.+++|+++++.. ..|+.+...+..+ ..|+++.+..
T Consensus 366 i~~~l~~iGi~v~i~~---------------~~~~~~~~~~~~~~~~d~~~~~~~ 405 (486)
T cd08501 366 IQDMLAKAGIKVTVVS---------------VPSNDFSKTLLSGGDYDAVLFGWQ 405 (486)
T ss_pred HHHHHHhcCCEEEecc---------------cCchHHhhccCCCCceEEEEeccc
Confidence 3444455799998875 3577777776666 7888876543
No 166
>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=56.47 E-value=31 Score=22.30 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=19.2
Q ss_pred cchhhHHHhhhcCCccEEEeCCcccc
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAALSVSS 60 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ltit~ 60 (62)
|+-.| +.+|.+|++|++.++-.+++
T Consensus 35 GSg~G-i~~l~~g~~dia~ssr~l~~ 59 (314)
T TIGR00975 35 GSGAG-IAQFAAGTVDFGASDAPLSE 59 (314)
T ss_pred CCHHH-HHHHHcCCCCEEecCCCCCH
Confidence 55445 67788999999999877764
No 167
>cd05803 PGM_like4 This PGM-like (phosphoglucomutase-like) domain is located C-terminal to a mannose-1-phosphate guanyltransferase domain in a protein of unknown function that is found in both prokaryotes and eukaryotes. This domain belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=56.43 E-value=41 Score=22.72 Aligned_cols=51 Identities=16% Similarity=0.292 Sum_probs=31.4
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+.+++|+++... ..+|+.+|. .|+.....-..+...+...++|++++
T Consensus 188 ~~~~ll~~lg~~v~~~~~~~d~~F~~-~p~p~~~~l~~l~~~v~~~~adlgi~ 239 (445)
T cd05803 188 LIPRLLEKLGCEVIVLNCEPTGLFPH-TPEPLPENLTQLCAAVKESGADVGFA 239 (445)
T ss_pred HHHHHHHHcCCEEEEeCCcCCCCCCC-CCCCChHHHHHHHHHHHhcCCCEEEe
Confidence 5677888899986433 456777762 33211122345566677788999875
No 168
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=56.05 E-value=23 Score=23.31 Aligned_cols=38 Identities=18% Similarity=0.295 Sum_probs=27.6
Q ss_pred HHHHHHHHcCCeE-EEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 3 LLENIAQELEFDF-HLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l~f~~-~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
+++.+-+.+|+++ +++.. .=.-+...|.+|.+|+.+..
T Consensus 47 v~~~iLe~~GY~V~e~~~~---------------~~~~~~~ala~GdiDv~~~~ 85 (331)
T PRK11119 47 LVSRALEKLGYDVNKPKEV---------------DYNVFYTSIANGDATFTAVN 85 (331)
T ss_pred HHHHHHHHcCCceeeeccc---------------CcHHHHHHHHcCCCeEehhh
Confidence 5677778889988 77643 22566778889999987644
No 169
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=55.90 E-value=40 Score=20.95 Aligned_cols=19 Identities=11% Similarity=-0.020 Sum_probs=15.7
Q ss_pred hhhHHHhhhcCCccEEEeC
Q psy2313 37 WNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 37 w~g~ig~l~~g~~D~av~~ 55 (62)
-+..+..|.+|++|+++..
T Consensus 127 ~~~~~~~l~~~~~d~~i~~ 145 (294)
T PRK03635 127 QDHTAELLRRGEVVGAVTT 145 (294)
T ss_pred cHHHHHHHhCCCceEEEec
Confidence 3568889999999999864
No 170
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=54.88 E-value=38 Score=21.11 Aligned_cols=21 Identities=29% Similarity=0.542 Sum_probs=17.3
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+....++..|.+|++|+++..
T Consensus 128 ~~~~~~~~~l~~g~~Dl~i~~ 148 (300)
T PRK11074 128 EVFNGVWDALADGRVDIAIGA 148 (300)
T ss_pred hhhhHHHHHHHCCCCCEEEec
Confidence 345678899999999999964
No 171
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=54.80 E-value=42 Score=20.67 Aligned_cols=18 Identities=11% Similarity=0.062 Sum_probs=15.1
Q ss_pred hhHHHhhhcCCccEEEeC
Q psy2313 38 NGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 38 ~g~ig~l~~g~~D~av~~ 55 (62)
..++..|.+|++|+++..
T Consensus 128 ~~~~~~l~~g~~d~~i~~ 145 (292)
T TIGR03298 128 DHTAELLRSGEVLGAVTT 145 (292)
T ss_pred hhHHHHHhCCCceEEEec
Confidence 457889999999999865
No 172
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=54.41 E-value=46 Score=20.06 Aligned_cols=21 Identities=24% Similarity=0.336 Sum_probs=17.2
Q ss_pred hhhHHHhhhcCCccEEEeCCc
Q psy2313 37 WNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 37 w~g~ig~l~~g~~D~av~~lt 57 (62)
.+.+..++.+|++|+++....
T Consensus 128 ~~~~~~~l~~~~~D~~i~~~~ 148 (297)
T COG0583 128 SDRLLEDLVEGELDLAIRAGP 148 (297)
T ss_pred hHHHHHHHHcCCCCEEEecCC
Confidence 445788999999999998764
No 173
>PRK09542 manB phosphomannomutase/phosphoglucomutase; Reviewed
Probab=54.16 E-value=46 Score=22.54 Aligned_cols=52 Identities=10% Similarity=0.076 Sum_probs=33.1
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCC-CcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQ-KDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~-~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|.+.+++++... ..+|+.|+...|+.. ......+...+...++|++++
T Consensus 179 ~~~~ll~~lg~~vv~~~~~~d~~Fp~~~p~P~~~~~l~~l~~~v~~~~adlGia 232 (445)
T PRK09542 179 TVPAVLGGLPITLLPLYFELDGTFPNHEANPLDPANLVDLQAFVRETGADIGLA 232 (445)
T ss_pred HHHHHHHhCCCEEEEEecCcCCCCCCCCcCCCCHHHHHHHHHHHHHcCCCEEEE
Confidence 5667778888775433 456777765444311 123456666778889999885
No 174
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=53.38 E-value=56 Score=20.74 Aligned_cols=20 Identities=10% Similarity=-0.037 Sum_probs=16.2
Q ss_pred hhhHHHhhhcCCccEEEeCC
Q psy2313 37 WNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 37 w~g~ig~l~~g~~D~av~~l 56 (62)
-..+...|.+|++|+++..-
T Consensus 127 ~~~~~~~L~~g~~Dl~i~~~ 146 (317)
T PRK15421 127 TFDPQPALQQGELDLVMTSD 146 (317)
T ss_pred cHHHHHHHHCCCcCEEEecC
Confidence 35678899999999999653
No 175
>cd03084 phosphohexomutase The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=53.03 E-value=55 Score=21.33 Aligned_cols=52 Identities=12% Similarity=0.185 Sum_probs=32.6
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCC-CcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQ-KDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~-~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+-+++|+++..+ ..+|+.|+...|+.. ......+...+...++|++++
T Consensus 127 ~~~~ll~~lg~~v~~~n~~~d~~F~~~~p~p~~~~~l~~l~~~v~~~~adlG~a 180 (355)
T cd03084 127 IAPQLLEKLGAEVIPLNCEPDGNFGNINPDPGSETNLKQLLAVVKAEKADFGVA 180 (355)
T ss_pred HHHHHHHHcCCcEEEEcCcCCCCCCCCCCCCCchhhHHHHHHHHHhcCCCEEEE
Confidence 4566777888766433 345666655444211 134667777888889999874
No 176
>PRK06034 hypothetical protein; Provisional
Probab=52.89 E-value=20 Score=23.44 Aligned_cols=22 Identities=14% Similarity=0.190 Sum_probs=20.5
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.++...+.+|.+|++|++|-|+
T Consensus 126 ~s~~dVf~AV~~g~adyGVVPI 147 (279)
T PRK06034 126 FSAQAVVEAVARSKGDLGLVSL 147 (279)
T ss_pred CCHHHHHHHHHcCCCCEEEEEC
Confidence 5799999999999999999888
No 177
>PLN02691 porphobilinogen deaminase
Probab=52.76 E-value=65 Score=21.81 Aligned_cols=22 Identities=9% Similarity=0.321 Sum_probs=16.9
Q ss_pred cchhh-HHHhhhcCCccEEEeCC
Q psy2313 35 DKWNG-VVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g-~ig~l~~g~~D~av~~l 56 (62)
|-|.- +=.+|.+|++|+||-++
T Consensus 102 GlFtkele~aLl~g~iDiAVHSl 124 (351)
T PLN02691 102 GLFTKEIDDALLSGRIDIAVHSM 124 (351)
T ss_pred eEeHHHHHHHHHcCCCCEEEecc
Confidence 55644 44589999999999776
No 178
>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=52.75 E-value=38 Score=22.85 Aligned_cols=35 Identities=14% Similarity=0.153 Sum_probs=23.7
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEE
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSF 53 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av 53 (62)
+....+++|+++++... .|+.+...+..|+.|+++
T Consensus 362 l~~~l~~~GI~v~i~~~---------------~~~~~~~~~~~g~~d~~~ 396 (500)
T TIGR02294 362 LQAEWRKIGIKLSLIGE---------------EEDKIAARRRDGDFDMMF 396 (500)
T ss_pred HHHHHHHcCCeEEEeec---------------ChhhHhhhhhcCCeeEEE
Confidence 44445568999999864 455556666677778765
No 179
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=52.58 E-value=21 Score=22.68 Aligned_cols=20 Identities=15% Similarity=0.180 Sum_probs=15.6
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
|+|.|++.. ..|++|+|-.-
T Consensus 26 GS~gG~~~i-~~G~adiag~h 45 (223)
T COG1910 26 GSMGGLLAI-KRGEADIAGIH 45 (223)
T ss_pred ccccchHhh-hhcccceeeee
Confidence 789887764 99999997543
No 180
>PRK15414 phosphomannomutase CpsG; Provisional
Probab=52.35 E-value=46 Score=22.68 Aligned_cols=47 Identities=13% Similarity=0.146 Sum_probs=30.0
Q ss_pred HHHcCCeEE---EEEecCCcccceeccCC-CcchhhHHHhhhcCCccEEEe
Q psy2313 8 AQELEFDFH---LYIVADGLYGTKVRENQ-KDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 8 a~~l~f~~~---~~~~~~~~~G~~~~~~~-~~~w~g~ig~l~~g~~D~av~ 54 (62)
-+++|+.++ +...+|+.|+...|+.. ......+...+...++|++++
T Consensus 193 l~~lG~~v~v~~~~~~pdg~F~~~~p~P~~~~~l~~l~~~v~~~~adlGia 243 (456)
T PRK15414 193 FKALGAPVELIKVHNTPDGNFPNGIPNPLLPECRDDTRNAVIKHGADMGIA 243 (456)
T ss_pred HHhcCCCeEEEEeecCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCEEEE
Confidence 567887444 44456777755444311 124667777888899999885
No 181
>cd03085 PGM1 Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one direction, G-1-P produced from sucrose catabolism is converted to G-6-P, the first intermediate in glycolysis. In the other direction, conversion of G-6-P to G-1-P generates a substrate for synthesis of UDP-glucose which is required for synthesis of a variety of cellular constituents including cell wall polymers and glycoproteins. The PGM1 family also includes a non-enzymatic PGM-related protein (PGM-RP) thought to play a structural role in eukaryotes, as well as pp63/parafusin, a phosphoglycoprotein that plays an important role in calcium-regulated exocytosis in ciliated protozoans. PGM1 belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl t
Probab=51.88 E-value=39 Score=23.79 Aligned_cols=52 Identities=13% Similarity=0.024 Sum_probs=32.0
Q ss_pred HHHHHHH-HcCCeE--EEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQ-ELEFDF--HLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~-~l~f~~--~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|-+ .+|++. .+...+|+.|+...|+.....-..+...+...++|++++
T Consensus 222 ~~~~lL~~~LG~~~v~~i~~~pDg~Fp~~~P~P~~~~l~~L~~~V~~~~ADlGia 276 (548)
T cd03085 222 YAKKIFVEELGAPESSVVNCTPLPDFGGGHPDPNLTYAKDLVELMKSGEPDFGAA 276 (548)
T ss_pred HHHHHHHHhcCCCceEEEeCeeCCCCCCCCCCCcHHHHHHHHHHHhccCCCEEEE
Confidence 4555664 789864 455667888765444311222345666677788999885
No 182
>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=51.87 E-value=59 Score=21.80 Aligned_cols=39 Identities=13% Similarity=0.211 Sum_probs=27.7
Q ss_pred HHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcC--CccEEEeCCcc
Q psy2313 5 ENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTG--TAHMSFAALSV 58 (62)
Q Consensus 5 ~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g--~~D~av~~lti 58 (62)
..-.+++|+++++... .|+.+...+..+ +.|+++.+...
T Consensus 353 ~~~l~~iGI~v~v~~~---------------~~~~~~~~~~~~~~~~d~~~~~~~~ 393 (472)
T cd08502 353 AQQLKAAGFNVDLQVM---------------DWATLVQRRAKPDGGWNIFITSWSG 393 (472)
T ss_pred HHHHHhcCcEEEEEEe---------------chHHHHHHHhCCCCceeEEEecccc
Confidence 3334557999888753 577888877777 88988876544
No 183
>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=51.82 E-value=18 Score=24.17 Aligned_cols=36 Identities=8% Similarity=0.350 Sum_probs=21.7
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEE
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSF 53 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av 53 (62)
++.+-.+.+|+++++... .|..+...+..|+.|+++
T Consensus 358 ~i~~~l~~~Gi~v~~~~~---------------~~~~~~~~~~~~~~d~~~ 393 (483)
T cd08514 358 IIQQQLKEIGIDVKIRVL---------------EWAAFLEKVDDKDFDAVL 393 (483)
T ss_pred HHHHHHHhcCcEEEEEEe---------------cHHHHHHHhccccHHHhh
Confidence 344445568999998864 345555555555555544
No 184
>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=51.57 E-value=58 Score=21.33 Aligned_cols=38 Identities=8% Similarity=0.200 Sum_probs=25.2
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCC-ccEEEeCC
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGT-AHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~-~D~av~~l 56 (62)
+..-.+++|+++++... .|+.+...+..++ .|+++.+.
T Consensus 343 i~~~l~~~Gi~v~~~~~---------------~~~~~~~~~~~~~~~d~~~~~~ 381 (466)
T cd00995 343 IQAQLKEIGIKVEIEPL---------------DFATLLDALDAGDDFDLFLLGW 381 (466)
T ss_pred HHHHHHHcCceEEEEEe---------------chHHHHHHhhcCcccceeeecc
Confidence 34444557888888753 4666666677777 78877554
No 185
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=51.56 E-value=58 Score=20.39 Aligned_cols=20 Identities=5% Similarity=-0.134 Sum_probs=16.1
Q ss_pred hhhHHHhhhcCCccEEEeCC
Q psy2313 37 WNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 37 w~g~ig~l~~g~~D~av~~l 56 (62)
-..+...|.+|++|+++...
T Consensus 132 ~~~~~~~l~~~~~Dl~i~~~ 151 (309)
T PRK11013 132 SPLLEEWLSAQRHDLGLTET 151 (309)
T ss_pred HHHHHHHHHcCCCCEEEEcC
Confidence 45677899999999998643
No 186
>PRK14321 glmM phosphoglucosamine mutase; Provisional
Probab=51.09 E-value=65 Score=21.88 Aligned_cols=50 Identities=12% Similarity=0.062 Sum_probs=33.2
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccc-eeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGT-KVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~-~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+.+++|+++... ..+|+.++. +.|+ ......+...+....+|++++
T Consensus 180 ~~~~il~~lg~~v~~i~~~~d~~f~~~p~p~--~~~l~~l~~~v~~~~adlGia 231 (449)
T PRK14321 180 LSPYLQRELGNKVISLNSHPSGFFVRELEPN--AKSLSMLAKTVKVLKADVGIA 231 (449)
T ss_pred HHHHHHHHcCCEEEEeCccCCCCCCCCCCCc--hhhHHHHHHHHHHCCCCEEEE
Confidence 5677888899986544 345666652 3332 245666777778888999875
No 187
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=50.59 E-value=58 Score=20.27 Aligned_cols=21 Identities=10% Similarity=0.115 Sum_probs=17.6
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
+..+.+...|.+|++|+++..
T Consensus 129 ~~~~~~~~~l~~g~~D~~i~~ 149 (296)
T PRK11062 129 STHEMLLEQLSQHKLDMILSD 149 (296)
T ss_pred CCHHHHHHHHHcCCCCEEEec
Confidence 456788899999999999964
No 188
>PTZ00150 phosphoglucomutase-2-like protein; Provisional
Probab=50.50 E-value=23 Score=24.99 Aligned_cols=52 Identities=10% Similarity=0.024 Sum_probs=32.0
Q ss_pred HHHHHHHHcCCeE----EEEEecCCcccc---eeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDF----HLYIVADGLYGT---KVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~----~~~~~~~~~~G~---~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+-+++|++. .....+|+.|+. ++|......++.+...+...++|++++
T Consensus 243 ~~~~iL~~lG~~~~~~v~~~~~pDg~Fp~~~~PnPe~~~~~l~~~~~~v~~~~adlgia 301 (584)
T PTZ00150 243 FVQKALHTVGLPNLLSVAQQAEPDPEFPTVTFPNPEEGKGALKLSMETAEAHGSTVVLA 301 (584)
T ss_pred HHHHHHHhcCCCCceEeccccccCcCCCCCCCcChhhhHHHHHHHHHHHHHhCCCEEEE
Confidence 5667778899962 223346777653 333100123666777777888999885
No 189
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.30 E-value=42 Score=22.36 Aligned_cols=40 Identities=13% Similarity=0.022 Sum_probs=29.9
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
...+++..|+++.++..+ .-.-++.+|..|++|+++..++
T Consensus 166 ~~~~~k~~Gi~~~~Vpy~--------------g~gea~taLlgg~v~a~~~~~s 205 (319)
T COG3181 166 GALFAKAAGIKITYVPYK--------------GGGEALTALLGGHVDAGSTNLS 205 (319)
T ss_pred HHHHHHHhCCceeEEeec--------------CccHHHHHHhcCceeeeecChh
Confidence 457888999988888542 2345778888999999887764
No 190
>PF06345 Drf_DAD: DRF Autoregulatory Domain; InterPro: IPR010465 This domain is found in Diaphanous-related formins (Drfs). It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of diaphanous activating domains (DAD) to mammalian cells induces actin filament formation, stabilises microtubules, and activates serum-response mediated transcription [].; PDB: 3O4X_H 3OBV_E 2BAP_C 2F31_B.
Probab=48.07 E-value=14 Score=13.48 Aligned_cols=13 Identities=31% Similarity=0.504 Sum_probs=8.8
Q ss_pred hhhHHHhhhcCCc
Q psy2313 37 WNGVVGDLVTGTA 49 (62)
Q Consensus 37 w~g~ig~l~~g~~ 49 (62)
.+.++.+|..|++
T Consensus 3 mdsllealqtg~a 15 (15)
T PF06345_consen 3 MDSLLEALQTGSA 15 (15)
T ss_dssp HHHHHHHHHHSTT
T ss_pred HHHHHHHHHccCC
Confidence 4567777777754
No 191
>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=48.01 E-value=78 Score=21.04 Aligned_cols=36 Identities=11% Similarity=0.187 Sum_probs=22.9
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcC-CccEEEe
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTG-TAHMSFA 54 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g-~~D~av~ 54 (62)
+..-.+++|+++++... .|+.+...+..+ +.|+++.
T Consensus 354 i~~~l~~iGi~v~i~~~---------------~~~~~~~~~~~~~~~d~~~~ 390 (480)
T cd08517 354 VKQALKEVGIDVELRSQ---------------DFATWLKRVYTDRDFDLAMN 390 (480)
T ss_pred HHHHHHHcCCEEEEEEe---------------cHHHHHHhhcccCCceEEEe
Confidence 33444557888888753 466666666555 7777764
No 192
>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=47.90 E-value=42 Score=20.69 Aligned_cols=23 Identities=9% Similarity=0.280 Sum_probs=18.0
Q ss_pred hhhHHHhhhcCCccEEEeCCccc
Q psy2313 37 WNGVVGDLVTGTAHMSFAALSVS 59 (62)
Q Consensus 37 w~g~ig~l~~g~~D~av~~ltit 59 (62)
-..-+.+|.+|++|+++++-.++
T Consensus 47 S~~g~~~l~~g~~di~~~sr~l~ 69 (281)
T PF12849_consen 47 SGAGIQALINGKVDIAISSRPLT 69 (281)
T ss_dssp HHHHHHHHHTTSSSEEEESSHHH
T ss_pred CHHHHHHHHhCCCEEEEeCCCCc
Confidence 35677888999999999885544
No 193
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=47.56 E-value=52 Score=21.04 Aligned_cols=37 Identities=14% Similarity=0.046 Sum_probs=26.3
Q ss_pred HHHHHHHH-cCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEE
Q psy2313 3 LLENIAQE-LEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSF 53 (62)
Q Consensus 3 ll~~la~~-l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av 53 (62)
+.+.+.++ .|++++++.. ..+.....+|.+|++|+..
T Consensus 49 ~a~~~~k~~~G~~Velv~f--------------sd~~~~n~AL~~G~ID~n~ 86 (272)
T PRK09861 49 VAKKVAKEKYGLDVELVGF--------------SGSLLPNDATNHGELDANV 86 (272)
T ss_pred HHHHHHHHcCCCeEEEEec--------------CchhhHHHHHHcCCcceeh
Confidence 45556655 4999999853 2355666899999999865
No 194
>smart00094 TR_FER Transferrin.
Probab=47.37 E-value=64 Score=21.40 Aligned_cols=20 Identities=10% Similarity=0.077 Sum_probs=17.8
Q ss_pred cchhhHHHhhhcCCccEEEe
Q psy2313 35 DKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~ 54 (62)
.+-...+..|.+|+||++..
T Consensus 35 ~s~~~Ci~~I~~g~AD~a~l 54 (332)
T smart00094 35 SSTEECIKAIQKGEADAVTL 54 (332)
T ss_pred CCHHHHHHHHHCCCCCEEEE
Confidence 46889999999999999875
No 195
>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=47.00 E-value=56 Score=20.47 Aligned_cols=22 Identities=18% Similarity=0.211 Sum_probs=18.9
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
-.|+.+...|.+|.+|-+..+.
T Consensus 161 ip~~evy~aLq~G~vDg~~~~~ 182 (286)
T PF03480_consen 161 IPWSEVYQALQQGVVDGAENSA 182 (286)
T ss_dssp -TGGGHHHHHHTTSSSEEEEEH
T ss_pred CcHHHHHHHHhcCCcCeEecCH
Confidence 4799999999999999888765
No 196
>PRK11890 phosphate acetyltransferase; Provisional
Probab=46.58 E-value=40 Score=22.28 Aligned_cols=47 Identities=15% Similarity=0.116 Sum_probs=30.6
Q ss_pred HHHHHHHHcCCe---EEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCccc
Q psy2313 3 LLENIAQELEFD---FHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALSVS 59 (62)
Q Consensus 3 ll~~la~~l~f~---~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ltit 59 (62)
-++++++.+|++ |+++.+++.. .--..-+..+..|++|+.+.+..-|
T Consensus 58 ~I~~~a~~~g~dl~~~eII~~~~~~----------~~a~~av~mV~~G~AD~lmkG~i~T 107 (312)
T PRK11890 58 RIEAVAAECGLDLSGYEIVDAPHSH----------AAAAKAVELVREGEAEALMKGSLHT 107 (312)
T ss_pred HHHHHHHHcCCCcCCCEEECCCChH----------HHHHHHHHHHHcCCCCEEecCCccc
Confidence 467788888886 5666543211 0112345688899999999887654
No 197
>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=46.19 E-value=69 Score=20.18 Aligned_cols=37 Identities=11% Similarity=0.167 Sum_probs=28.0
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEE
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSF 53 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av 53 (62)
.++..+++.|++.+++... .+...-.+|.+|++|+-+
T Consensus 16 ~v~~~~~~~Gi~vevv~f~--------------D~~~~N~AL~~G~iDaN~ 52 (237)
T PF03180_consen 16 AVKEKLKKKGIDVEVVEFS--------------DYVQPNEALADGEIDANF 52 (237)
T ss_dssp HHHHHHHHTTEEEEEEEES--------------STTHHHHHHHTTSSSEEE
T ss_pred HHHHHHHhcCCeEEEEEec--------------chhhcChHHHCCCcceec
Confidence 3456677789999998753 466777789999999754
No 198
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=46.13 E-value=16 Score=24.08 Aligned_cols=20 Identities=20% Similarity=0.371 Sum_probs=17.7
Q ss_pred hhhHHHhhhcCCccEEEeCC
Q psy2313 37 WNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 37 w~g~ig~l~~g~~D~av~~l 56 (62)
--.+..+|+.|..|++++|+
T Consensus 111 aisit~DLv~g~ld~~lSPi 130 (321)
T COG3888 111 AISITRDLVEGKLDFGLSPI 130 (321)
T ss_pred HHHHHHHHHhhhhhhcccHH
Confidence 45788999999999999987
No 199
>cd08500 PBP2_NikA_DppA_OppA_like_4 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=45.82 E-value=68 Score=21.77 Aligned_cols=39 Identities=13% Similarity=0.185 Sum_probs=26.8
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCC-ccEEEeCCc
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGT-AHMSFAALS 57 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~-~D~av~~lt 57 (62)
+..-.+++|+++++... .|+.+...+..++ .|+++.+..
T Consensus 364 i~~~l~~~Gi~v~~~~~---------------~~~~~~~~~~~~~~~d~~~~~~~ 403 (499)
T cd08500 364 IKDDWRKIGIKVNLQPI---------------DFNLLVTRLSANEDWDAILLGLT 403 (499)
T ss_pred HHHHHHHhCCceEEEec---------------cHHHHHHHHhcCCCceEEEEecc
Confidence 33444568999998853 5777777777775 888876554
No 200
>cd05805 MPG1_transferase GTP-mannose-1-phosphate guanyltransferase (MPG1 transferase), also known as GDP-mannose pyrophosphorylase, is a bifunctional enzyme with both phosphomannose isomerase (PMI) activity and GDP-mannose phosphorylase (GMP) activity. The protein contains an N-terminal NTP transferase domain, an L-beta-H domain, and a C-terminal PGM-like domain that belongs to the alpha-D-phosphohexomutase superfamily. This subfamily is limited to bacteria and archaea. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this group appear to lack conserved residues necessary for metal binding and catalytic activity. Other members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional
Probab=45.69 E-value=77 Score=21.37 Aligned_cols=51 Identities=10% Similarity=0.063 Sum_probs=31.7
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|.+++|+++..+ ..+|+.. .+.++........+...+...++|++++
T Consensus 183 ~~~~ll~~lG~~v~~i~~~~d~~~-~~~~~~~~~~l~~l~~~v~~~~adlgia 234 (441)
T cd05805 183 VLPGLLSRLGCDVVILNARLDEDA-PRTDTERQRSLDRLGRIVKALGADFGVI 234 (441)
T ss_pred HHHHHHHHcCCEEEEEecccCCcc-CCCCccchhHHHHHHHHHHhCCCCEEEE
Confidence 5677888999987643 3344431 1112111235677888888889999885
No 201
>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=44.93 E-value=66 Score=19.12 Aligned_cols=39 Identities=15% Similarity=0.187 Sum_probs=24.4
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcC-CccEEEeC
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTG-TAHMSFAA 55 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g-~~D~av~~ 55 (62)
++.+...++-+++++++.. .-..+...|..| ++|+.+++
T Consensus 15 ~l~~~f~~~~g~~v~v~~~---------------~s~~~~~~l~~g~~~Dv~~~~ 54 (230)
T PF13531_consen 15 ELAEAFEKQPGIKVEVSFG---------------GSGELVRRLQAGKKPDVFIPA 54 (230)
T ss_dssp HHHHHHHHHHCEEEEEEEE---------------CHHHHHHHHHTT-S-SEEEES
T ss_pred HHHHHHHhccCCeEEEEEC---------------ChHHHHHHHhcCCCceEEEEC
Confidence 3556666777888888863 223455555554 78887765
No 202
>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=44.59 E-value=75 Score=19.63 Aligned_cols=45 Identities=7% Similarity=0.119 Sum_probs=31.6
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.+.|.++-+=++++...+.++. +.-..++..+..|.+|++....
T Consensus 18 f~~~v~e~t~G~v~v~~~~~g~L---------g~~~e~~~~v~~G~~d~~~~~~ 62 (257)
T TIGR00787 18 FAKLVNEKTNGEIKISVFPSSQL---------GSDRAMLEALQGGALDMTAPSS 62 (257)
T ss_pred HHHHHHHHcCCeEEEEEcCCCCC---------CChHHHHHHHhCCCccEEeccc
Confidence 45677777776677665544332 3356789999999999988654
No 203
>PRK14315 glmM phosphoglucosamine mutase; Provisional
Probab=44.49 E-value=99 Score=20.98 Aligned_cols=50 Identities=10% Similarity=0.044 Sum_probs=31.3
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+-+++|+++..+ ..+|+.+....+. ...-..+...+...++|++++
T Consensus 191 ~~~~ll~~lG~~v~~i~~~~dg~~~~~~~~--~~~l~~l~~~v~~~~adlGia 241 (448)
T PRK14315 191 VAPEALWELGAEVITIGVEPNGFNINEECG--STHPEALAKKVREVRADIGIA 241 (448)
T ss_pred HHHHHHHHcCCeEEEeccCCCCCCCCCCCC--CCCHHHHHHHHHHcCCCEEEE
Confidence 4566778889876433 3455555422221 123456888888889999885
No 204
>PF11834 DUF3354: Domain of unknown function (DUF3354); InterPro: IPR021789 Potassium channels take part in important processes of higher plants, including opening and closing of stomatal pores and leaf movement. Inward rectifying potassium (K(+)in) channels play an important role in turgor regulation and ion uptake in higher plants. All of them comprise, from their N-terminal to their C-terminal ends: a short hydrophilic region, a hydrophobic region structurally analogous and partially homologous to the transmembrane domain of voltage-gated animal channels from the Shaker superfamily, a putative cyclic nucleotide-binding domain, and a conserved C-terminal KHA domain. Between these last two regions, some of them (AKT1, AKT2 and SKT1) contain an ankyrin-repeat domain with six repeats homologous to those of human erythrocyte ankyrin. This entry represents the KHA domain which is unique to plant K(+)in channels. The KHA domain contains two high-homology blocks enriched for hydrophobic and acidic residues, respectively. The KHA domain is essential for interaction of plant K(+)in channels. The KHA domain mediates tetramerization and/or stabilisation of the heteromers [, , ].
Probab=44.24 E-value=38 Score=17.48 Aligned_cols=21 Identities=19% Similarity=0.327 Sum_probs=16.4
Q ss_pred hHHHHHHHHcCCeEEEEEecC
Q psy2313 2 DLLENIAQELEFDFHLYIVAD 22 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~ 22 (62)
||++..++++++....+...|
T Consensus 30 eLl~ia~~kfg~~~~~v~~~d 50 (69)
T PF11834_consen 30 ELLKIASEKFGFSATKVLNED 50 (69)
T ss_pred HHHHHHHHHhCCCceEEEcCC
Confidence 678888999999877776544
No 205
>cd08505 PBP2_NikA_DppA_OppA_like_18 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=44.18 E-value=93 Score=21.45 Aligned_cols=38 Identities=13% Similarity=0.156 Sum_probs=25.7
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.+-.+++|+++++.. ..|+.+...+..|+.|+.....
T Consensus 400 iq~~l~~iGI~v~i~~---------------~d~~~~~~~~~~~~~d~~~~~w 437 (528)
T cd08505 400 WRKQFAKLGIQLNVRA---------------TDYNRFQDKLRKGNAQLFSWGW 437 (528)
T ss_pred HHHHHHHcCceEEEEe---------------ccHHHHHHHHhCCCCCeEEecc
Confidence 3344455788888875 3577777777778888876544
No 206
>KOG0024|consensus
Probab=43.83 E-value=29 Score=23.51 Aligned_cols=19 Identities=5% Similarity=0.216 Sum_probs=17.0
Q ss_pred CcchhhHHHhhhcCCccEE
Q psy2313 34 KDKWNGVVGDLVTGTAHMS 52 (62)
Q Consensus 34 ~~~w~g~ig~l~~g~~D~a 52 (62)
++.|...+..+.+|++|+-
T Consensus 301 ~~~y~~ai~li~sGki~~k 319 (354)
T KOG0024|consen 301 NGDYPTAIELVSSGKIDVK 319 (354)
T ss_pred cccHHHHHHHHHcCCcCch
Confidence 4789999999999999974
No 207
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=43.40 E-value=77 Score=19.41 Aligned_cols=18 Identities=6% Similarity=-0.186 Sum_probs=15.4
Q ss_pred hhhHHHhhhcCCccEEEe
Q psy2313 37 WNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 37 w~g~ig~l~~g~~D~av~ 54 (62)
-+..+..|.+|++|+++.
T Consensus 135 ~~~~~~~l~~g~~D~~i~ 152 (294)
T PRK09986 135 PSMQMAALERRELDAGIW 152 (294)
T ss_pred HHHHHHHHHcCCCCEEEe
Confidence 356888999999999995
No 208
>PRK14317 glmM phosphoglucosamine mutase; Provisional
Probab=43.28 E-value=89 Score=21.34 Aligned_cols=50 Identities=14% Similarity=0.051 Sum_probs=31.3
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|-+++|+++... ..+|+.+..+++. ......+...+...++|++++
T Consensus 203 ~~~~ll~~LG~~v~~l~~~~dg~~~~~~~~--~~~l~~l~~~v~~~~adlGia 253 (465)
T PRK14317 203 CAPEVFKALGAEVICLHDQPDGDRINVNCG--STHLEPLQAAVLEHGADMGFA 253 (465)
T ss_pred HHHHHHHHcCCeEEEEecccCCCCCCCCCc--hHhHHHHHHHHHhcCCCEEEE
Confidence 4667778899877543 3455554332221 123566777777888999875
No 209
>TIGR00067 glut_race glutamate racemase. The most closely related proteins differing in function are aspartate racemases.
Probab=43.23 E-value=30 Score=21.78 Aligned_cols=53 Identities=23% Similarity=0.201 Sum_probs=32.1
Q ss_pred HHHHHHHHcCCeEEEEEecCCc---ccceeccCCCcchhhHHHhhh-cCCccEEEeCC
Q psy2313 3 LLENIAQELEFDFHLYIVADGL---YGTKVRENQKDKWNGVVGDLV-TGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~---~G~~~~~~~~~~w~g~ig~l~-~g~~D~av~~l 56 (62)
++++|.+.+. ..++++..|.. ||.+.+..-...--.++..|. +..+|+++.+.
T Consensus 13 v~~~l~~~~p-~~~~iy~~D~~~~PYG~ks~~~i~~~~~~~~~~L~~~~g~d~ivIaC 69 (251)
T TIGR00067 13 VLKEIRKQLP-KEHYIYVGDTKRFPYGEKSPEFILEYVLELLTFLKERHNIKLLVVAC 69 (251)
T ss_pred HHHHHHHHCC-CCCEEEEecCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCEEEEeC
Confidence 5788888885 33555566653 888765211112235666777 77799776543
No 210
>PRK11899 prephenate dehydratase; Provisional
Probab=42.57 E-value=24 Score=22.85 Aligned_cols=22 Identities=9% Similarity=0.335 Sum_probs=20.3
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.++..++.+|.+|++|++|-|+
T Consensus 34 ~s~~~vf~av~~g~~d~gVvPi 55 (279)
T PRK11899 34 ATFEDAFEAVESGEADLAMIPI 55 (279)
T ss_pred CCHHHHHHHHHCCCCCEEEEEe
Confidence 4799999999999999999887
No 211
>PRK15109 antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
Probab=41.52 E-value=1e+02 Score=21.32 Aligned_cols=40 Identities=8% Similarity=0.057 Sum_probs=24.8
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
++.+..++.|+++++... .|+.....+..|+.|+++.+.+
T Consensus 399 ~iq~~l~~iGI~v~i~~~---------------~~~~~~~~~~~g~~dl~~~~w~ 438 (547)
T PRK15109 399 LIQADLAQVGVKVVIVPV---------------EGRFQEARLMDMNHDLTLSGWA 438 (547)
T ss_pred HHHHHHHHcCCEEEEEEc---------------chHHHHHHhhcCCCCeEEEccc
Confidence 344455667888888754 3444444456778888776553
No 212
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=41.38 E-value=25 Score=22.94 Aligned_cols=22 Identities=14% Similarity=0.231 Sum_probs=20.3
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.+....+.++.+|++|++|-|+
T Consensus 33 ~ti~evf~ave~g~aD~gVVPI 54 (279)
T COG0077 33 STIEDVFKAVENGEADYGVVPI 54 (279)
T ss_pred CCHHHHHHHHHcCCCceEEEEe
Confidence 5789999999999999999887
No 213
>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]
Probab=41.20 E-value=28 Score=22.00 Aligned_cols=22 Identities=27% Similarity=0.433 Sum_probs=18.1
Q ss_pred HHHHHHHHcCCeEEEEEecCCc
Q psy2313 3 LLENIAQELEFDFHLYIVADGL 24 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~ 24 (62)
|.+.||+++++...+..++++.
T Consensus 20 La~~La~~l~~~~~~E~vednp 41 (216)
T COG1428 20 LAQALAEHLGFKVFYELVEDNP 41 (216)
T ss_pred HHHHHHHHhCCceeeecccCCh
Confidence 6789999999888887777764
No 214
>PRK09755 putative ABC transporter periplasmic-binding protein; Provisional
Probab=41.06 E-value=1e+02 Score=21.29 Aligned_cols=32 Identities=16% Similarity=0.186 Sum_probs=23.5
Q ss_pred cCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 11 LEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 11 l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
+|+++++.. ..|+.+...+..|+.|+...+..
T Consensus 404 iGI~v~i~~---------------~d~~~~~~~~~~~~~d~~~~~w~ 435 (535)
T PRK09755 404 LGAQVTLRT---------------MEWKTYLDARRAGDFMLSRQSWD 435 (535)
T ss_pred hCCeeEEEe---------------ccHHHHHHHhhCCCceEEecccC
Confidence 788888875 35777777777888888765543
No 215
>cd08496 PBP2_NikA_DppA_OppA_like_9 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=41.04 E-value=1.1e+02 Score=20.38 Aligned_cols=40 Identities=3% Similarity=0.091 Sum_probs=24.3
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhh-hcCCccEEEeCCcc
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDL-VTGTAHMSFAALSV 58 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l-~~g~~D~av~~lti 58 (62)
+..-.+.+|+++++... .|+.+...+ ..++.|+++.+...
T Consensus 334 i~~~l~~iGi~v~~~~~---------------~~~~~~~~~~~~~~~d~~~~~w~~ 374 (454)
T cd08496 334 VQQQLAKVGIKVTIKPL---------------TGANAAGEFFAAEKFDLAVSGWVG 374 (454)
T ss_pred HHHHHHHcCceEEEEEe---------------chHHHHHhhccCCCccEEEeccCC
Confidence 33344557888888754 455555544 34678887766543
No 216
>KOG1879|consensus
Probab=40.62 E-value=32 Score=27.31 Aligned_cols=19 Identities=21% Similarity=0.529 Sum_probs=16.3
Q ss_pred hHHHHHHHHcCCeEEEEEe
Q psy2313 2 DLLENIAQELEFDFHLYIV 20 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~ 20 (62)
|.+..||+++||+|+++..
T Consensus 1227 e~iP~mA~eYnFeyElv~Y 1245 (1470)
T KOG1879|consen 1227 ESIPHMAKEYNFEYELVQY 1245 (1470)
T ss_pred HHHHHHHHHhCceEEEEEe
Confidence 4578899999999999963
No 217
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris
Probab=40.60 E-value=53 Score=17.92 Aligned_cols=16 Identities=6% Similarity=0.063 Sum_probs=12.7
Q ss_pred HHHhhhcCCccEEEeC
Q psy2313 40 VVGDLVTGTAHMSFAA 55 (62)
Q Consensus 40 ~ig~l~~g~~D~av~~ 55 (62)
.+.+|.+|++|+++..
T Consensus 38 ~~~~l~~g~~D~~i~~ 53 (194)
T cd08432 38 RLVDFAREGIDLAIRY 53 (194)
T ss_pred CccccccccccEEEEe
Confidence 4567889999999864
No 218
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and
Probab=40.50 E-value=14 Score=19.24 Aligned_cols=12 Identities=25% Similarity=0.728 Sum_probs=10.9
Q ss_pred HHHHHHHcCCeE
Q psy2313 4 LENIAQELEFDF 15 (62)
Q Consensus 4 l~~la~~l~f~~ 15 (62)
++.||+++||++
T Consensus 19 Wr~LA~~Lg~~~ 30 (79)
T cd08312 19 WTALAEEMGFEY 30 (79)
T ss_pred HHHHHHHcCCCH
Confidence 688999999997
No 219
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=39.80 E-value=15 Score=19.26 Aligned_cols=15 Identities=20% Similarity=0.299 Sum_probs=12.0
Q ss_pred HHHHHHHcCCeEEEE
Q psy2313 4 LENIAQELEFDFHLY 18 (62)
Q Consensus 4 l~~la~~l~f~~~~~ 18 (62)
++.||++|||++.-+
T Consensus 18 W~~LA~~LG~~~~~I 32 (77)
T cd08311 18 WRSLAGELGYEDEAI 32 (77)
T ss_pred HHHHHHHcCCCHHHH
Confidence 678999999998443
No 220
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=39.63 E-value=77 Score=20.16 Aligned_cols=29 Identities=10% Similarity=0.062 Sum_probs=19.1
Q ss_pred CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 12 EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 12 ~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
|-+++++. -....++..|.+|++|.++=.
T Consensus 136 gk~Ve~Ve---------------i~Y~q~~~~l~~g~IDA~IWN 164 (232)
T PF14503_consen 136 GKNVEFVE---------------IPYNQLLELLRSGEIDAAIWN 164 (232)
T ss_dssp TS--EEEE-----------------HHHHHHHHHHTS--EEEEE
T ss_pred CCceEEEE---------------ecHHHHHHHHHCCCccEEEEC
Confidence 55677776 368999999999999988744
No 221
>PRK14316 glmM phosphoglucosamine mutase; Provisional
Probab=39.36 E-value=1.2e+02 Score=20.51 Aligned_cols=50 Identities=18% Similarity=0.142 Sum_probs=30.6
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|.+++|+++..+ ..+|+.+....+. ...-..+...+...++|++++
T Consensus 188 ~~~~ll~~lg~~v~~in~~~dg~~~~~~~~--~~~~~~l~~~v~~~~adlGia 238 (448)
T PRK14316 188 LAPRLFADLGADVTVIGTSPDGLNINDGVG--STHPEALQELVVEKGADLGLA 238 (448)
T ss_pred HHHHHHHHcCCeEEEEccCCCCCCCCCCCC--CCCHHHHHHHHhhcCCCEEEE
Confidence 5677888899887654 3345554322221 012345777778889999875
No 222
>PRK14320 glmM phosphoglucosamine mutase; Provisional
Probab=37.79 E-value=1.1e+02 Score=20.69 Aligned_cols=50 Identities=10% Similarity=0.078 Sum_probs=30.7
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+.+++|+++..+ ..+|+.+-..++ .+.....+...+...++|++++
T Consensus 187 ~~~~ll~~lg~~v~~i~~~~dg~~~~~~~--~~~~l~~l~~~v~~~~adlGia 237 (443)
T PRK14320 187 NFEALLDKFGINYVSIASNPDGLNINVGC--GATCVSNIKKAVKEQKADLGIS 237 (443)
T ss_pred HHHHHHHHcCCcEEEECCcCCCCCCCCCC--chHhHHHHHHHHHHcCCCEEEE
Confidence 5667888899876544 334555432221 1123556777777888999875
No 223
>PRK10116 universal stress protein UspC; Provisional
Probab=37.45 E-value=72 Score=17.35 Aligned_cols=21 Identities=0% Similarity=-0.080 Sum_probs=17.3
Q ss_pred cchhhHHHhhhcCCccEEEeC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ 55 (62)
..+..++.......+|+++.+
T Consensus 89 ~~~~~I~~~a~~~~~DLiV~g 109 (142)
T PRK10116 89 ELSEHILEVCRKHHFDLVICG 109 (142)
T ss_pred CHHHHHHHHHHHhCCCEEEEc
Confidence 357889988888999998865
No 224
>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=36.89 E-value=34 Score=20.34 Aligned_cols=23 Identities=17% Similarity=0.358 Sum_probs=20.6
Q ss_pred cchhhHHHhhhcCCccEEEeCCc
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~lt 57 (62)
.+++..+.++..+++|+++-|+-
T Consensus 30 ~s~~~v~~av~~~~~d~~vvPiE 52 (181)
T PF00800_consen 30 DSFEEVFDAVEEGEADYGVVPIE 52 (181)
T ss_dssp SSHHHHHHHHHCTSSSEEEEEEE
T ss_pred CCHHHHHHHHHcCCCceEEEeEe
Confidence 47999999999999999998874
No 225
>PRK14324 glmM phosphoglucosamine mutase; Provisional
Probab=36.84 E-value=1.4e+02 Score=20.37 Aligned_cols=50 Identities=14% Similarity=0.087 Sum_probs=30.2
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|-+++|+++..+ ..+|+.+....+. ...-+.+...+...++|++++
T Consensus 190 ~~~~ll~~lG~~v~~i~~~~dg~~~~~~~~--~~~~e~l~~~v~~~~adlGia 240 (446)
T PRK14324 190 VAPTVFSELGADVIVINDEPNGFNINENCG--ALHPENLAQEVKRYRADIGFA 240 (446)
T ss_pred HHHHHHHHcCCeEEEECCCCCCCCCCCCCC--CCCHHHHHHHHHhCCCCEEEE
Confidence 4667778899876544 3455544322210 112345777788889999875
No 226
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=36.78 E-value=76 Score=17.45 Aligned_cols=17 Identities=12% Similarity=-0.013 Sum_probs=13.9
Q ss_pred HHHHHHHHcCCeEEEEE
Q psy2313 3 LLENIAQELEFDFHLYI 19 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~ 19 (62)
-++++++..|+++++..
T Consensus 20 k~k~~~~e~gi~~~i~a 36 (104)
T PRK09590 20 KTTEYLKEQGKDIEVDA 36 (104)
T ss_pred HHHHHHHHCCCceEEEE
Confidence 35788899999999875
No 227
>PF01784 NIF3: NIF3 (NGG1p interacting factor 3); InterPro: IPR002678 This family contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown [][].; PDB: 1NMO_F 1NMP_B 2GX8_C 2FYW_B 2NYD_A 3LNL_A 2YYB_A 3RXY_F.
Probab=36.57 E-value=1.1e+02 Score=19.08 Aligned_cols=52 Identities=10% Similarity=0.033 Sum_probs=32.0
Q ss_pred hHHHHHHHHcCCeE-EEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 2 DLLENIAQELEFDF-HLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 2 dll~~la~~l~f~~-~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++++.+.+.++.+. .+.-.++....+.--. .|+-..++.+.....+|+-+++
T Consensus 146 el~~~vk~~l~~~~vr~~g~~~~~v~rVav~--~GsG~~~i~~a~~~g~D~~ITG 198 (241)
T PF01784_consen 146 ELAERVKEKLGLPGVRVVGDPDKKVKRVAVC--GGSGGSFIEEAAEAGADVYITG 198 (241)
T ss_dssp HHHHHHHHHTTSS-EEEESCTTSEEEEEEEE--CSSSGGGHHHHHHTTSSEEEES
T ss_pred HHHHHHHHHcCCCcEEecCCCCCcccEEEEE--cccCccHHHHHHhCCCeEEEEc
Confidence 67889999998854 4432233322222111 2555588888888889987764
No 228
>PRK14314 glmM phosphoglucosamine mutase; Provisional
Probab=36.34 E-value=1.4e+02 Score=20.30 Aligned_cols=50 Identities=12% Similarity=0.070 Sum_probs=29.8
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+-+++|+++..+ ..+|+.+....+. ......+...+...++|++++
T Consensus 192 ~~~~il~~lg~~v~~~~~~~dg~~~~~~~~--~~~~~~l~~~v~~~~adlGia 242 (450)
T PRK14314 192 VAPAVFEELGAEVICIGVEPNGLNINAGCG--SLHPEVIAKAVIEHGADLGIA 242 (450)
T ss_pred HHHHHHHHcCCeEEEeccCCCCCCCCCCCC--CCCHHHHHHHHHhcCCCeEEE
Confidence 4566778899876533 2345444322221 123456777777889999875
No 229
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=36.27 E-value=31 Score=20.33 Aligned_cols=13 Identities=23% Similarity=0.675 Sum_probs=7.0
Q ss_pred HHHHHHHHcCCeE
Q psy2313 3 LLENIAQELEFDF 15 (62)
Q Consensus 3 ll~~la~~l~f~~ 15 (62)
+.+.||++||++|
T Consensus 15 Ia~~LA~~Lg~~~ 27 (179)
T PF13189_consen 15 IAERLAEKLGYPY 27 (179)
T ss_dssp HHHHHHHHCT--E
T ss_pred HHHHHHHHcCCcc
Confidence 5566666666655
No 230
>PF11761 CbiG_mid: Cobalamin biosynthesis central region; InterPro: IPR021745 Members of this family are involved in cobalamin synthesis. The gene encoded by P72862 from SWISSPROT has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [].
Probab=36.08 E-value=22 Score=18.28 Aligned_cols=14 Identities=29% Similarity=0.394 Sum_probs=8.6
Q ss_pred cchhhHHHhhhcCC
Q psy2313 35 DKWNGVVGDLVTGT 48 (62)
Q Consensus 35 ~~w~g~ig~l~~g~ 48 (62)
..|+.+..+|.+|+
T Consensus 19 ~~~k~vsaalv~g~ 32 (93)
T PF11761_consen 19 EAVKRVSAALVNGE 32 (93)
T ss_pred HHHHHHHHHHHCCC
Confidence 35666666666664
No 231
>cd08802 Death_UNC5B Death domain found in Uncoordinated-5B. Death Domain (DD) found in Uncoordinated-5B (UNC5B). UNC5B is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5B signaling is involved in the netrin-1-induced proliferation and migration of renal proximal tubular cells. It is also required for vascular patterning during embryonic development, and its activation inhibits sprouting angiogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activatio
Probab=35.92 E-value=19 Score=19.34 Aligned_cols=11 Identities=36% Similarity=0.495 Sum_probs=9.9
Q ss_pred HHHHHHHcCCe
Q psy2313 4 LENIAQELEFD 14 (62)
Q Consensus 4 l~~la~~l~f~ 14 (62)
++.||++|||.
T Consensus 23 W~~LAekL~ld 33 (84)
T cd08802 23 WRLLAQKLSMD 33 (84)
T ss_pred HHHHHHHcCch
Confidence 67899999998
No 232
>PF09568 RE_MjaI: MjaI restriction endonuclease; InterPro: IPR019068 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MjaI (recognises CTAG but cleavage site unknown) restriction endonuclease. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=35.70 E-value=22 Score=21.66 Aligned_cols=24 Identities=29% Similarity=0.613 Sum_probs=18.9
Q ss_pred HHHHHHHHcCCeEEEEEecCCccc
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYG 26 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G 26 (62)
+++.||+.+|.+|+.-.+++..+|
T Consensus 97 I~~~la~~~~~~~~~A~~eee~~~ 120 (170)
T PF09568_consen 97 ILKKLAEELNVKYRLATPEEESYG 120 (170)
T ss_pred HHHHHHhhcCCceeECccHHHHcC
Confidence 678999999999999876654443
No 233
>PRK15046 2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional
Probab=35.54 E-value=1.2e+02 Score=19.49 Aligned_cols=38 Identities=8% Similarity=0.041 Sum_probs=22.7
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhh----cCCccEEEeC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLV----TGTAHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~----~g~~D~av~~ 55 (62)
++....++.|++++++. +.+..++..+. +..+|+++++
T Consensus 52 ii~~Fe~~~gikV~~~~---------------~~s~~~~~kl~~~~~~~~~DVv~~~ 93 (349)
T PRK15046 52 VFPAFTKATGIKVNYVE---------------AGSGEVVNRAAKEKSNPQADVLVTL 93 (349)
T ss_pred HHHHHHhhhCcEEEEEe---------------CChHHHHHHHHhhhcCCCCCEEEeC
Confidence 45555566688777764 33445555443 3578987654
No 234
>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=35.49 E-value=1.1e+02 Score=20.35 Aligned_cols=38 Identities=8% Similarity=0.057 Sum_probs=22.4
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHh-hhcCCccEEEeCC
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGD-LVTGTAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~-l~~g~~D~av~~l 56 (62)
+..-.+++|+++++... .|..+... +..|+.|+++.+.
T Consensus 357 i~~~l~~iGi~v~~~~~---------------~~~~~~~~~~~~~~~d~~~~~~ 395 (482)
T cd08513 357 IQQQLAKIGIDVEIENV---------------PASVFFSDDPGNRKFDLALFGW 395 (482)
T ss_pred HHHHHHHcCCEEEEeeC---------------CHHHHhhhcccCCceeEEEEcc
Confidence 34444568999998763 35555443 2345677766443
No 235
>PRK14318 glmM phosphoglucosamine mutase; Provisional
Probab=35.25 E-value=1.4e+02 Score=20.20 Aligned_cols=50 Identities=14% Similarity=0.074 Sum_probs=30.5
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+-+++|+++... ..+|+.+....+. ...-..+...+....+|++++
T Consensus 190 ~~~~ll~~lG~~v~~in~~~dg~~~~~~~~--~~~l~~l~~~v~~~~adlGia 240 (448)
T PRK14318 190 VAPEAYRAAGADVIAINADPDGLNINDGCG--STHLEQLQAAVVAHGADLGLA 240 (448)
T ss_pred HHHHHHHHcCCEEEEeccCCCCCCCCCCCC--CCCHHHHHHHHHhcCCCEEEE
Confidence 5667788899986543 3345554322210 123456777778888999875
No 236
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=35.21 E-value=1.1e+02 Score=19.04 Aligned_cols=38 Identities=13% Similarity=0.186 Sum_probs=21.4
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCC-ccEEEeC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGT-AHMSFAA 55 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~-~D~av~~ 55 (62)
+.+...++.|+++++..- ++ ..+...+..|. +|+.+++
T Consensus 44 l~~~Fe~~~g~~v~~~~~--------------~S-g~l~~qi~~g~~~Dv~~~a 82 (257)
T PRK10677 44 IAAQYKKEKGVDVVSSFA--------------SS-STLARQIEQGAPADLFISA 82 (257)
T ss_pred HHHHHHhhhCCeEEEEec--------------cc-HHHHHHHHcCCCCCEEEEC
Confidence 334444555777776642 11 24555666665 8888765
No 237
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=34.57 E-value=1.2e+02 Score=19.08 Aligned_cols=17 Identities=12% Similarity=0.419 Sum_probs=14.3
Q ss_pred hHHHhhhcCCccEEEeC
Q psy2313 39 GVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 39 g~ig~l~~g~~D~av~~ 55 (62)
.....|.+|++|+++..
T Consensus 136 ~~~~~l~~g~~D~~i~~ 152 (319)
T PRK10216 136 DSLDAITRGEVDIGFTG 152 (319)
T ss_pred chHHHHhcCCccEEEec
Confidence 36889999999999863
No 238
>cd08506 PBP2_clavulanate_OppA2 The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold. Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the precursors, glyceraldehyde-3-phosphate and arginine. CA possesses a characteristic (3R,5R) stereochemistry essential for reaction with penicillin-binding proteins and beta-lactamases. Two genes (oppA1 and oppA2) in the clavulanic acid gene cluster encode oligopeptide-binding proteins that are required for CA biosynthesis. OppA1/2 is involved in the binding and transport of peptides across the cell membrane of Streptomyces clavuligerus. Most of other periplasmic binding proteins are comprised of only two globular subdomains cor
Probab=34.44 E-value=1.4e+02 Score=19.85 Aligned_cols=38 Identities=8% Similarity=0.039 Sum_probs=23.3
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcC---CccEEEeCC
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTG---TAHMSFAAL 56 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g---~~D~av~~l 56 (62)
+..-.+++|+++++... .|+.+...+..+ +.|+++...
T Consensus 338 i~~~l~~iGI~v~i~~~---------------~~~~~~~~~~~~~~~~~d~~~~~w 378 (466)
T cd08506 338 LQASLARAGIDVTLKPI---------------DSATYYDTIANPDGAAYDLFITGW 378 (466)
T ss_pred HHHHHHHcCCeEEEEEc---------------chHHHHHHhcCCCccccCeEeecc
Confidence 33444668999888753 455666655554 467766544
No 239
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=34.18 E-value=21 Score=18.87 Aligned_cols=15 Identities=27% Similarity=0.408 Sum_probs=11.6
Q ss_pred HHHHHHHcCCeEEEE
Q psy2313 4 LENIAQELEFDFHLY 18 (62)
Q Consensus 4 l~~la~~l~f~~~~~ 18 (62)
++.+|++|||++.=+
T Consensus 18 Wk~LAr~Lg~se~dI 32 (84)
T cd08804 18 WTELARELDFTEEQI 32 (84)
T ss_pred HHHHHHHcCCCHHHH
Confidence 678999999987433
No 240
>COG1109 {ManB} Phosphomannomutase [Carbohydrate transport and metabolism]
Probab=33.73 E-value=1.6e+02 Score=20.20 Aligned_cols=52 Identities=13% Similarity=0.179 Sum_probs=31.8
Q ss_pred HHHHHHHHcCCeE-EEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDF-HLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~-~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+.+.+|..+ .+...+|+.+...+|+-+...-..+...+....+|++++
T Consensus 193 ~~~~ll~~lG~~vv~~~~~pDg~fp~~~p~p~~~~~~~l~~~v~~~~aDlgia 245 (464)
T COG1109 193 VAPRLLKELGAEVVSINCDPDGLFPNINPNPGETELLDLAKAVKEHGADLGIA 245 (464)
T ss_pred HHHHHHHHcCCEEEEecCCCCCCCCCCCCCCCCccHHHHHHHHHhcCCCEEEE
Confidence 5677788888543 333467888755444322222235666667778998875
No 241
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=33.55 E-value=21 Score=18.95 Aligned_cols=12 Identities=33% Similarity=0.637 Sum_probs=10.2
Q ss_pred HHHHHHHcCCeE
Q psy2313 4 LENIAQELEFDF 15 (62)
Q Consensus 4 l~~la~~l~f~~ 15 (62)
++.||+.|||++
T Consensus 18 W~~LA~eLg~s~ 29 (84)
T cd08803 18 WTELARELNFSV 29 (84)
T ss_pred HHHHHHHcCCCH
Confidence 567999999988
No 242
>PF04509 CheC: CheC-like family; InterPro: IPR007597 The precise function of these proteins is unclear, but some of them are involved in flagella motor switch []. The region represented in this entry is found in the CheC, CheX, CheA and FliY proteins. In some cases, this region is repeated in multiple copies.; GO: 0016787 hydrolase activity; PDB: 3QTA_A 1XKO_B 1SQU_B 3HZH_B 2F9Z_B 1XKR_A.
Probab=33.28 E-value=54 Score=14.72 Aligned_cols=17 Identities=6% Similarity=0.155 Sum_probs=12.8
Q ss_pred HHHHHHHcCCeEEEEEe
Q psy2313 4 LENIAQELEFDFHLYIV 20 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~ 20 (62)
+..|++.+|++.++..|
T Consensus 18 ~~als~~~~~~i~is~P 34 (38)
T PF04509_consen 18 ATALSEMLGLEIDISPP 34 (38)
T ss_dssp HHHHHHHHTS-EEEEEE
T ss_pred HHHHHHHhCCceEcCCC
Confidence 46788889998888765
No 243
>PF01379 Porphobil_deam: Porphobilinogen deaminase, dipyromethane cofactor binding domain; InterPro: IPR022417 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the N-terminal domains 1 and 2 of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this domain consists of a duplication of two similar intertwined domains with three layers of (a/b/a) each. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A 3EQ1_B 3ECR_A.
Probab=32.58 E-value=42 Score=21.06 Aligned_cols=22 Identities=14% Similarity=0.305 Sum_probs=15.9
Q ss_pred cchh-hHHHhhhcCCccEEEeCC
Q psy2313 35 DKWN-GVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~-g~ig~l~~g~~D~av~~l 56 (62)
|-|. .+-.+|.+|++|+||-++
T Consensus 56 g~Ftkele~aLl~g~iDiAVHSl 78 (215)
T PF01379_consen 56 GLFTKELEEALLDGEIDIAVHSL 78 (215)
T ss_dssp HCCCHHHHHHHHTTS-SEEEEEG
T ss_pred cHHHHHHHHHHHcCCccEEEecc
Confidence 5554 355689999999999776
No 244
>cd08310 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function
Probab=32.53 E-value=23 Score=18.24 Aligned_cols=13 Identities=23% Similarity=0.322 Sum_probs=11.0
Q ss_pred HHHHHHHcCCeEE
Q psy2313 4 LENIAQELEFDFH 16 (62)
Q Consensus 4 l~~la~~l~f~~~ 16 (62)
++.||+++||.+-
T Consensus 15 Wr~LA~~L~~~~~ 27 (72)
T cd08310 15 WRELAQLLDLGHL 27 (72)
T ss_pred HHHHHHHcCcHHH
Confidence 6889999999864
No 245
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=32.24 E-value=41 Score=22.74 Aligned_cols=22 Identities=18% Similarity=0.388 Sum_probs=19.7
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.+|..++.+|.+|++|++|-|+
T Consensus 137 ~s~~~v~~av~~g~~d~gVvPi 158 (386)
T PRK10622 137 AKFADIFNQVETGQADYAVLPI 158 (386)
T ss_pred CCHHHHHHHHHCCCCCEEEEEE
Confidence 4688899999999999999887
No 246
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=31.98 E-value=1.2e+02 Score=18.32 Aligned_cols=47 Identities=17% Similarity=0.162 Sum_probs=30.4
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEE
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSF 53 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av 53 (62)
+.++..+...++...+....++..+..+. ..+.-|+.++..|+ |..+
T Consensus 22 ~~l~~~~~~~g~~~~~~~~~sg~~~~~~R----p~l~~ll~~i~~g~-d~lv 68 (222)
T COG1961 22 EALEAYAKNKGCEIVFEDKDSGSSSGKNR----PGLQRLLEDIEEGK-DTLV 68 (222)
T ss_pred HHHHHHHHhCCCEEEEEeecCCccCCCCC----HHHHHHHHHHHcCC-cEEE
Confidence 35677788889884444444444333212 35888999999998 7654
No 247
>PRK11898 prephenate dehydratase; Provisional
Probab=31.78 E-value=44 Score=21.53 Aligned_cols=22 Identities=14% Similarity=0.288 Sum_probs=20.1
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.++...+.+|.+|++|+++-|+
T Consensus 34 ~s~~~v~~av~~~~~d~gvvPi 55 (283)
T PRK11898 34 DSIPDVLDAVEAGEVDYAVVPI 55 (283)
T ss_pred CCHHHHHHHHHcCCCCEEEEEe
Confidence 4799999999999999999886
No 248
>PRK15104 oligopeptide ABC transporter substrate-binding protein OppA; Provisional
Probab=31.40 E-value=1.6e+02 Score=20.38 Aligned_cols=33 Identities=18% Similarity=0.278 Sum_probs=22.2
Q ss_pred HHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 9 QELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 9 ~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.+|+++++... .|..+...+..|..|+.+.+.
T Consensus 410 ~~iGI~v~l~~~---------------~~~~~~~~~~~~~~d~~~~~~ 442 (543)
T PRK15104 410 KNLGVNVKLENQ---------------EWKTFLDTRHQGTFDVARAGW 442 (543)
T ss_pred HhcCceEEEEec---------------CHHHHHHHhhcCCccEeeccc
Confidence 347888888753 466666666777788766544
No 249
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the C-terminal region of DltD.; PDB: 3BMA_C.
Probab=31.04 E-value=66 Score=18.50 Aligned_cols=20 Identities=30% Similarity=0.464 Sum_probs=14.1
Q ss_pred hHHHHHHHHcCCeEEEEEec
Q psy2313 2 DLLENIAQELEFDFHLYIVA 21 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~ 21 (62)
+|+-.++++.|.++-++.+|
T Consensus 39 ~l~L~~~k~~g~~~lfVi~P 58 (130)
T PF04914_consen 39 QLLLDVCKELGIDVLFVIQP 58 (130)
T ss_dssp HHHHHHHHHTT-EEEEEE--
T ss_pred HHHHHHHHHcCCceEEEecC
Confidence 45667889999999999876
No 250
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=30.86 E-value=1.1e+02 Score=21.72 Aligned_cols=22 Identities=23% Similarity=0.063 Sum_probs=18.8
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+....++..|.+|++|+++...
T Consensus 448 ~~s~~vl~~L~~GeiDlai~~~ 469 (633)
T PRK14498 448 VGSMGGLMALKRGEADIAGIHL 469 (633)
T ss_pred cCCHHHHHHHHcCCceEEEEcc
Confidence 5678999999999999999643
No 251
>COG0283 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=30.50 E-value=40 Score=21.40 Aligned_cols=13 Identities=23% Similarity=0.585 Sum_probs=10.1
Q ss_pred HHHHHHHHcCCeE
Q psy2313 3 LLENIAQELEFDF 15 (62)
Q Consensus 3 ll~~la~~l~f~~ 15 (62)
+.+.||++|||.|
T Consensus 20 vak~lA~~Lg~~y 32 (222)
T COG0283 20 VAKILAEKLGFHY 32 (222)
T ss_pred HHHHHHHHhCCCe
Confidence 4678888888876
No 252
>PF07833 Cu_amine_oxidN1: Copper amine oxidase N-terminal domain; InterPro: IPR012854 Amine oxidases (AO) are enzymes that catalyse the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (1.4.3.4 from EC) and copper-containing (1.4.3.6 from EC). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor []: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen [, ]. In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling []. The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access. The two N-terminal domains share a common structural fold, its core consisting of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the stalk, of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other [, ]. This entry represents a domain found at the N-terminal of certain copper amine oxidases, as well as in related proteins such as cell wall hydrolase and N-acetylmuramoyl-L-alanine amidase. This domain consists of a five-stranded antiparallel beta-sheet twisted around an alpha helix [, ]. ; PDB: 1SPU_A 2WGQ_A 2WO0_A 1JRQ_A 1QAF_B 1D6U_B 1QAL_A 2WOF_A 1OAC_B 1QAK_A ....
Probab=30.37 E-value=53 Score=16.61 Aligned_cols=15 Identities=27% Similarity=0.162 Sum_probs=11.6
Q ss_pred HHHHHHHcCCeEEEE
Q psy2313 4 LENIAQELEFDFHLY 18 (62)
Q Consensus 4 l~~la~~l~f~~~~~ 18 (62)
++.+++.+|+++++-
T Consensus 9 l~~i~~~lg~~v~~d 23 (93)
T PF07833_consen 9 LRFIAEALGAKVSWD 23 (93)
T ss_dssp HHHHHHHHT-EEEEE
T ss_pred HHHHHHHcCCEEEEE
Confidence 578899999988884
No 253
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=29.53 E-value=39 Score=17.92 Aligned_cols=13 Identities=23% Similarity=0.281 Sum_probs=10.7
Q ss_pred HHHHHHHcCCeEE
Q psy2313 4 LENIAQELEFDFH 16 (62)
Q Consensus 4 l~~la~~l~f~~~ 16 (62)
++.+|++|||++.
T Consensus 16 Wk~lar~LG~s~~ 28 (86)
T cd08777 16 WKRCARKLGFTES 28 (86)
T ss_pred HHHHHHHcCCCHH
Confidence 6789999999863
No 254
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=29.45 E-value=1.4e+02 Score=18.72 Aligned_cols=44 Identities=16% Similarity=0.369 Sum_probs=31.1
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeC
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAA 55 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~ 55 (62)
++.+.+++.+|++++....++ . ...|..+...|.+|+.=++..+
T Consensus 53 ~~~~~~~~~lG~~~~~~~~~~-----~-----~~~~~~l~~~l~~g~pv~~~~D 96 (317)
T PF14399_consen 53 DFEENLLERLGIKYEWREFSS-----P-----DEAWEELKEALDAGRPVIVWVD 96 (317)
T ss_pred HHHHHHHHHCCceEEEEecCC-----H-----HHHHHHHHHHHhCCCceEEEec
Confidence 467789999999999765321 1 1468889999999975554443
No 255
>PF11057 Cortexin: Cortexin of kidney; InterPro: IPR020066 Cortexin is a neuron-specific, 82-residue membrane protein which is found especially in vertebrate brain cortex tissue. It may mediate extracellular or intracellular signalling of cortical neurons during forebrain development. Cortexin is present at significant levels in the foetal brain, suggesting that it may be important to neurons of both the developing and adult cerebral cortex. Cortexin has a conserved single membrane-spanning region in the middle of each sequence []. In humans, there is selective expression of Cortexin 3 (CTXN3) in the kidney as well as the brain []. This entry contains Cortexins 1, 2 and 3.; GO: 0031224 intrinsic to membrane
Probab=29.14 E-value=31 Score=18.39 Aligned_cols=20 Identities=20% Similarity=0.388 Sum_probs=17.5
Q ss_pred cchhhHHHhhhcCCccEEEe
Q psy2313 35 DKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~ 54 (62)
.+|..-...+..|+.|.|++
T Consensus 62 StW~d~~eglekGqFdyaLa 81 (81)
T PF11057_consen 62 STWTDHKEGLEKGQFDYALA 81 (81)
T ss_pred chhhhhhhhhhccccccccC
Confidence 68999999999999998763
No 256
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=28.91 E-value=48 Score=19.82 Aligned_cols=15 Identities=13% Similarity=0.443 Sum_probs=12.6
Q ss_pred hHHHHHHHHcCCeEE
Q psy2313 2 DLLENIAQELEFDFH 16 (62)
Q Consensus 2 dll~~la~~l~f~~~ 16 (62)
|+|++|+++.|..++
T Consensus 49 eVLkALc~eAGw~Ve 63 (150)
T PF05687_consen 49 EVLKALCREAGWTVE 63 (150)
T ss_pred HHHHHHHHhCCEEEc
Confidence 789999999998654
No 257
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=28.75 E-value=38 Score=19.25 Aligned_cols=47 Identities=19% Similarity=0.316 Sum_probs=22.9
Q ss_pred HHHHHHHcCCeEEEEEe-cCC---cccc--eeccCCCcchhhHHHhhhcCCcc
Q psy2313 4 LENIAQELEFDFHLYIV-ADG---LYGT--KVRENQKDKWNGVVGDLVTGTAH 50 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~-~~~---~~G~--~~~~~~~~~w~g~ig~l~~g~~D 50 (62)
++++++.+|.+|--+-. -|. +.|. ......+..-..++..|.+|+++
T Consensus 52 lKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~GeIs 104 (113)
T PF09862_consen 52 LKEMEKELGISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGEIS 104 (113)
T ss_pred HHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCCCC
Confidence 56777888877743310 000 1222 00001123456677777777754
No 258
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=28.08 E-value=1.8e+02 Score=20.22 Aligned_cols=38 Identities=0% Similarity=0.131 Sum_probs=23.2
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
.++...++.|+++++... .|...... .+++|+.+++..
T Consensus 422 ~iq~~l~~~GI~v~i~~~---------------~~~~~~~~--~~~~D~~l~~~~ 459 (552)
T PRK13626 422 IMQQLLASHGVTLEIQEI---------------DYDQWHQG--EAESDIWLNSAN 459 (552)
T ss_pred HHHHHHHHhCcEEEEEEe---------------eHHHHhcC--CCCCCEEEeccc
Confidence 345555667999998754 34443332 357888776643
No 259
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=27.89 E-value=44 Score=17.61 Aligned_cols=12 Identities=25% Similarity=0.324 Sum_probs=9.6
Q ss_pred HHHHHHHcCCeE
Q psy2313 4 LENIAQELEFDF 15 (62)
Q Consensus 4 l~~la~~l~f~~ 15 (62)
++.||++|||+-
T Consensus 21 Wk~Lar~LGls~ 32 (86)
T cd08318 21 WKTLAPHLEMKD 32 (86)
T ss_pred HHHHHHHcCCCH
Confidence 678899999873
No 260
>COG4143 TbpA ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]
Probab=27.59 E-value=1.2e+02 Score=20.50 Aligned_cols=42 Identities=12% Similarity=0.188 Sum_probs=26.6
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
+.++..++.+++++|+...|+. .-.+.++-+=.+-+||++++
T Consensus 46 vk~~FE~~~~~~v~fV~~~d~v----------~llnRl~leg~~~~ADvvvG 87 (336)
T COG4143 46 VKKAFEAEYGCKVNFVALGDGV----------ELLNRLILEGKNPKADVVVG 87 (336)
T ss_pred HHHHHHHHhCceEEEEEcCcHH----------HHHHHHHHcCCCCCCcEEEe
Confidence 4667778889999999765321 12344444444557888774
No 261
>PF13847 Methyltransf_31: Methyltransferase domain; PDB: 3T0I_B 3SVZ_B 3SXJ_A 3F4K_A 3GU3_B 2GH1_A 1R8Y_E 1R8X_B 2B3T_A 1T43_A ....
Probab=26.76 E-value=97 Score=17.32 Aligned_cols=39 Identities=10% Similarity=0.127 Sum_probs=22.8
Q ss_pred hHHHHHHHHcCCe-EEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 2 DLLENIAQELEFD-FHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 2 dll~~la~~l~f~-~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.++..+++++++ ++++. +.+.. +.....+++|++++.-
T Consensus 42 ~~a~~~~~~~~~~ni~~~~---------------~d~~~-l~~~~~~~~D~I~~~~ 81 (152)
T PF13847_consen 42 EYAKKRAKELGLDNIEFIQ---------------GDIED-LPQELEEKFDIIISNG 81 (152)
T ss_dssp HHHHHHHHHTTSTTEEEEE---------------SBTTC-GCGCSSTTEEEEEEES
T ss_pred HHhhcccccccccccceEE---------------eehhc-cccccCCCeeEEEEcC
Confidence 4566667777876 66664 33444 2221117899888764
No 262
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=26.65 E-value=1.5e+02 Score=17.59 Aligned_cols=35 Identities=6% Similarity=-0.051 Sum_probs=22.1
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEE
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSF 53 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av 53 (62)
-+.++|+++|+++-++. | .+-+...+...+.|.++
T Consensus 77 ~l~~lae~~g~~v~i~~---------------G-gt~ar~~ik~~~p~~ii 111 (158)
T PF01976_consen 77 DLKKLAEKYGYKVYIAT---------------G-GTLARKIIKEYRPKAII 111 (158)
T ss_pred HHHHHHHHcCCEEEEEc---------------C-hHHHHHHHHHhCCCEEE
Confidence 36789999999865542 2 34455556666666443
No 263
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=26.51 E-value=94 Score=20.75 Aligned_cols=38 Identities=13% Similarity=0.198 Sum_probs=22.8
Q ss_pred HHHHHHH-HcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQ-ELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~-~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
|.+.+.+ ..+++++.+.. .++-.. +..+.+|++|+|+.
T Consensus 46 ia~~~~~~~~~i~~~v~~t-------------ggSv~N-l~~i~~Ge~d~alv 84 (321)
T COG2358 46 LAQLLNKDEKGIECSVVPT-------------GGSVEN-LKLLASGEADLALV 84 (321)
T ss_pred HHHHHhccCCCeEEEEeec-------------cchHHH-HHhHhcCccchhhh
Confidence 4455555 56666665542 233333 44778999999864
No 264
>PLN02307 phosphoglucomutase
Probab=26.41 E-value=1.7e+02 Score=21.01 Aligned_cols=29 Identities=21% Similarity=0.139 Sum_probs=19.3
Q ss_pred HHHHHH-HHcCCeE--EEEEecCCcccceecc
Q psy2313 3 LLENIA-QELEFDF--HLYIVADGLYGTKVRE 31 (62)
Q Consensus 3 ll~~la-~~l~f~~--~~~~~~~~~~G~~~~~ 31 (62)
++..+- +++|++. .+...+|+.|+...|+
T Consensus 239 ~~~~lL~~~lG~~~~~~i~~~pDg~Fp~~~Pn 270 (579)
T PLN02307 239 YAKRIFVEELGAPESSLLNCVPKEDFGGGHPD 270 (579)
T ss_pred HHHHHHHHhcCCCceeeecCccCCCCCCCCCC
Confidence 455666 6889865 4666788888754443
No 265
>PRK09501 potD spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed
Probab=25.71 E-value=1.9e+02 Score=18.57 Aligned_cols=39 Identities=18% Similarity=0.222 Sum_probs=24.7
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhc---CCccEEEe
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVT---GTAHMSFA 54 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~---g~~D~av~ 54 (62)
++++...++.|+++++... ++.+.++..|.. +.+|++..
T Consensus 41 ~i~~~Fe~~~gi~V~~~~~--------------~s~~~~~~kl~a~~~~~~Dvv~~ 82 (348)
T PRK09501 41 GLLEQFTKETGIKVIYSTY--------------ESNETMYAKLKTYKDGAYDLVVP 82 (348)
T ss_pred HHHHHHHHHHCCeEEEEec--------------CCHHHHHHHHhcCCCCCceEEEe
Confidence 4677788888988887642 234455555443 45788764
No 266
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=25.70 E-value=1.5e+02 Score=23.34 Aligned_cols=41 Identities=15% Similarity=0.174 Sum_probs=29.1
Q ss_pred hHHHHHHHH---cCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 2 DLLENIAQE---LEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 2 dll~~la~~---l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
|..++|++. .||+.+.+.. + -...+.....|++|+.++--+
T Consensus 349 e~aeel~e~Lr~~Gi~a~~~~a--------------~-~~~~le~F~~GeidvLVGvAs 392 (1187)
T COG1110 349 EKAEELAEYLRSHGINAELIHA--------------E-KEEALEDFEEGEVDVLVGVAS 392 (1187)
T ss_pred HHHHHHHHHHHhcCceEEEeec--------------c-chhhhhhhccCceeEEEEecc
Confidence 445566644 5899988863 2 267788889999998876543
No 267
>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=25.61 E-value=2.1e+02 Score=19.10 Aligned_cols=22 Identities=14% Similarity=0.256 Sum_probs=15.4
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
..|+.+...+..++.|+++...
T Consensus 364 ~~~~~~~~~~~~~~~d~~~~~~ 385 (469)
T cd08519 364 VEWTTYYKQLSKGAYPVYLLGW 385 (469)
T ss_pred cchHHHHHHHhcCCCCEEEEec
Confidence 3567777777788888876543
No 268
>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=25.47 E-value=1.8e+02 Score=18.22 Aligned_cols=38 Identities=8% Similarity=0.178 Sum_probs=24.4
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhc----CCccEEEe
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVT----GTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~----g~~D~av~ 54 (62)
+++...++.|++++++.. ++=..++..|.. .++|++++
T Consensus 22 ~~~~Fe~~~gi~V~~~~~--------------~s~~~l~~kl~~e~~~~~~DVv~~ 63 (309)
T TIGR01276 22 VKKAFEADCNCELKLVAL--------------EDGVSLLNRLRLEGKNSKADVVLG 63 (309)
T ss_pred HHHHHHHHHCCEEEEEec--------------CcHHHHHHHHHHcCCCCCCCEEEe
Confidence 567777888999988742 111225555543 57898765
No 269
>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=25.43 E-value=2.2e+02 Score=19.36 Aligned_cols=33 Identities=12% Similarity=0.216 Sum_probs=21.0
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCcc
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAH 50 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D 50 (62)
++..-.+++|+++++... .|+.+...+..++.|
T Consensus 371 ~lq~~l~~iGi~v~i~~~---------------~~~~~~~~~~~~~~d 403 (509)
T cd08509 371 IIAEQLKEFGIDVTVKTP---------------DFGTYWAALTKGDFD 403 (509)
T ss_pred HHHHHHHhcCeEEEEecC---------------CHHHHHHHhccCCCc
Confidence 344455668999998753 455665666666664
No 270
>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=25.36 E-value=1.8e+02 Score=18.20 Aligned_cols=38 Identities=5% Similarity=0.133 Sum_probs=23.1
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhh----cCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLV----TGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~----~g~~D~av~ 54 (62)
+.+...++-|++++++.. +....++..+. ++++|++++
T Consensus 22 i~~~Fe~~~gi~V~~~~~--------------~~~~~~~~~l~~~~~~~~~Dv~~~ 63 (304)
T TIGR01254 22 VEKAFEADCNCKVKFVAL--------------EDAGELLNRLRLEGKNPKADVVLG 63 (304)
T ss_pred HHHHHhhhcCcEEEEEEC--------------CCHHHHHHHHHhcCCCCCCCEEEE
Confidence 445556677888887652 23445655554 257898863
No 271
>cd05802 GlmM GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of UDP-N-acetylglucosamine, an essential precursor to components of the cell envelope. In order to be active, GlmM must be phosphorylated, which can occur via autophosphorylation or by the Ser/Thr kinase StkP. GlmM functions in a classical ping-pong bi-bi mechanism with glucosamine-1,6-diphosphate as an intermediate. Other members of the alpha-D-phosphohexomutase superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=25.21 E-value=2.2e+02 Score=19.16 Aligned_cols=50 Identities=14% Similarity=0.123 Sum_probs=29.9
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|.+++|+++... ..+|+.+....+. ...-..+...+....+|++++
T Consensus 184 ~~~~ll~~lg~~v~~in~~~dg~~~~~~~~--~~~~~~l~~~v~~~~adlGia 234 (434)
T cd05802 184 VAPEVFRELGAEVIVINNAPDGLNINVNCG--STHPESLQKAVLENGADLGIA 234 (434)
T ss_pred HHHHHHHHcCCeEEEecCCCCCCCCCCCCC--ccCHHHHHHHHHhcCCCEEEE
Confidence 4677888899887544 2345444322221 122345667777888999875
No 272
>cd03088 ManB ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In Mycobacterium tuberculosis, the causative agent of tuberculosis, PMM is involved in the biosynthesis of mannosylated lipoglycans that participate in the association of mycobacteria with host macrophage phagocytic receptors. ManB belongs to the the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrall
Probab=25.19 E-value=2.3e+02 Score=19.34 Aligned_cols=51 Identities=10% Similarity=-0.053 Sum_probs=29.9
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCC-cchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQK-DKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~-~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|-+++|+++.... .+..++...|.... .....+...+...++|++++
T Consensus 180 ~~~~ll~~lG~~v~~l~-~~~~~~~~~~~~~~~~~l~~l~~~v~~~~adlGia 231 (459)
T cd03088 180 LLVRILEALGAEVVPLG-RSDTFIPVDTEAVRPEDRALAAAWAAEHGLDAIVS 231 (459)
T ss_pred HHHHHHHHcCCeEEEeC-CCCCCCCCCCCcCCHHHHHHHHHHHHhcCCCEEEE
Confidence 46677788999875442 12233332221000 23566777788889999885
No 273
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=25.19 E-value=1e+02 Score=15.37 Aligned_cols=19 Identities=21% Similarity=0.240 Sum_probs=15.7
Q ss_pred HHHHHHHHcCCeEEEEEec
Q psy2313 3 LLENIAQELEFDFHLYIVA 21 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~ 21 (62)
.+++++++++..++++...
T Consensus 19 ~~~~~~~e~~~~~~~~~v~ 37 (76)
T TIGR00412 19 NVKKAVEELGIDAEFEKVT 37 (76)
T ss_pred HHHHHHHHcCCCeEEEEeC
Confidence 4688999999999988764
No 274
>PRK15118 universal stress global response regulator UspA; Provisional
Probab=25.14 E-value=1.3e+02 Score=16.43 Aligned_cols=21 Identities=5% Similarity=-0.089 Sum_probs=16.9
Q ss_pred chhhHHHhhhcCCccEEEeCC
Q psy2313 36 KWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 36 ~w~g~ig~l~~g~~D~av~~l 56 (62)
..+.++......++|+++.+-
T Consensus 91 p~~~I~~~a~~~~~DLIV~Gs 111 (144)
T PRK15118 91 LGQVLVDAIKKYDMDLVVCGH 111 (144)
T ss_pred HHHHHHHHHHHhCCCEEEEeC
Confidence 467888888889999988653
No 275
>PRK15329 chaperone protein SicP; Provisional
Probab=25.08 E-value=78 Score=18.69 Aligned_cols=16 Identities=13% Similarity=0.395 Sum_probs=12.9
Q ss_pred hHHHHHHHHcCCeEEE
Q psy2313 2 DLLENIAQELEFDFHL 17 (62)
Q Consensus 2 dll~~la~~l~f~~~~ 17 (62)
+|+..+++++|.+.++
T Consensus 6 ~lL~~~~~~lGLpL~f 21 (138)
T PRK15329 6 EWLAALGEALGLPLTF 21 (138)
T ss_pred HHHHHHHHHhCCceEE
Confidence 6889999999995554
No 276
>PF00766 ETF_alpha: Electron transfer flavoprotein FAD-binding domain; InterPro: IPR014731 Electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, "housekeeping" ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II) []. ETFs are heterodimeric proteins composed of an alpha and beta subunit, and contain an FAD cofactor and AMP [, , , , ]. ETF consists of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit. Domains I and III share an almost identical alpha-beta-alpha sandwich fold, while domain II forms an alpha-beta-alpha sandwich similar to that of bacterial flavodoxins. FAD is bound in a cleft between domains II and III, while domain III binds the AMP molecule. Interactions between domains I and III stabilise the protein, forming a shallow bowl where domain II resides. This entry represents the C-terminal domain of the alpha subunit of both Group I and Group II ETFs.; PDB: 1O96_D 3CLR_D 1O97_D 3CLT_D 3CLU_D 3CLS_D 2A1U_A 2A1T_R 1EFV_A 1EFP_C ....
Probab=24.90 E-value=72 Score=17.23 Aligned_cols=19 Identities=21% Similarity=0.288 Sum_probs=14.1
Q ss_pred ChHHHHHHHHcCCeEEEEE
Q psy2313 1 MDLLENIAQELEFDFHLYI 19 (62)
Q Consensus 1 idll~~la~~l~f~~~~~~ 19 (62)
++++++||+.+|..+=..-
T Consensus 23 ~~l~~~LA~~lga~vg~SR 41 (86)
T PF00766_consen 23 FELIEELAEALGAAVGASR 41 (86)
T ss_dssp CHHHHHHHHHHT-EEEE-H
T ss_pred HHHHHHHHHHhCCchhccH
Confidence 4689999999999887763
No 277
>COG0181 HemC Porphobilinogen deaminase [Coenzyme metabolism]
Probab=24.88 E-value=53 Score=21.84 Aligned_cols=22 Identities=14% Similarity=0.296 Sum_probs=16.2
Q ss_pred cchhh-HHHhhhcCCccEEEeCC
Q psy2313 35 DKWNG-VVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g-~ig~l~~g~~D~av~~l 56 (62)
|-|.- +=.+|.+|++|+||-+|
T Consensus 58 GlFtkEle~all~g~~DiAVHSl 80 (307)
T COG0181 58 GLFTKELEQALLEGEIDIAVHSL 80 (307)
T ss_pred EEEHHHHHHHHHcCCCCEEEeec
Confidence 55543 44478899999999876
No 278
>PF00035 dsrm: Double-stranded RNA binding motif; InterPro: IPR001159 The DsRBD domain is found in a variety of RNA-binding proteins with different structures and exhibiting a diversity of functions []. It is involved in localisation of at least five different mRNAs in the early Drosophila embryo and by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.; GO: 0003725 double-stranded RNA binding, 0005622 intracellular; PDB: 1EKZ_A 1STU_A 1QU6_A 2L2M_A 3ADJ_A 1WHN_A 3LLH_B 2B7V_A 2L3J_A 1UHZ_A ....
Probab=24.82 E-value=92 Score=14.65 Aligned_cols=19 Identities=21% Similarity=0.310 Sum_probs=15.3
Q ss_pred hHHHHHHHHcCCeEEEEEe
Q psy2313 2 DLLENIAQELEFDFHLYIV 20 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~ 20 (62)
.+|++++++.++.++++..
T Consensus 3 ~~L~e~~~~~~~~~~~~~~ 21 (67)
T PF00035_consen 3 SRLNEYCQKNKFPPPYYYI 21 (67)
T ss_dssp HHHHHHHHHCTSSEEEEEE
T ss_pred HHHHHHHHHcCCCCCEEEE
Confidence 4688899999988888754
No 279
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=24.64 E-value=95 Score=20.38 Aligned_cols=17 Identities=35% Similarity=0.716 Sum_probs=11.8
Q ss_pred HHHHHHHHcCCe---EEEEE
Q psy2313 3 LLENIAQELEFD---FHLYI 19 (62)
Q Consensus 3 ll~~la~~l~f~---~~~~~ 19 (62)
||..||++++|+ |.+++
T Consensus 181 LL~~la~~l~~~f~~y~l~P 200 (314)
T PF04111_consen 181 LLQTLAKKLNFKFQRYRLVP 200 (314)
T ss_dssp HHHHHHHHCT---SSEEEE-
T ss_pred HHHHHHHHhCCCcccceeEe
Confidence 688999999999 66665
No 280
>PLN02317 arogenate dehydratase
Probab=24.62 E-value=68 Score=21.91 Aligned_cols=22 Identities=5% Similarity=0.087 Sum_probs=19.9
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
.++...+.+|..|++|++|-|+
T Consensus 124 ~sf~~vf~AVe~g~ad~gVvPI 145 (382)
T PLN02317 124 EQFEAAFQAVELWLADRAVLPI 145 (382)
T ss_pred CCHHHHHHHHHCCCCCEEEEEE
Confidence 4789999999999999999887
No 281
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=24.58 E-value=55 Score=16.98 Aligned_cols=12 Identities=25% Similarity=0.271 Sum_probs=10.0
Q ss_pred HHHHHHHcCCeE
Q psy2313 4 LENIAQELEFDF 15 (62)
Q Consensus 4 l~~la~~l~f~~ 15 (62)
++.||++|||+.
T Consensus 18 W~~LAr~Lg~~~ 29 (84)
T cd08317 18 WPQLARELGVSE 29 (84)
T ss_pred HHHHHHHcCCCH
Confidence 577899999886
No 282
>TIGR01455 glmM phosphoglucosamine mutase. This model describes GlmM, phosphoglucosamine mutase, also designated in MrsA and YhbF E. coli, UreC in Helicobacter pylori, and femR315 or FemD in Staphlococcus aureus. It converts glucosamine-6-phosphate to glucosamine-1-phosphate as part of the pathway toward UDP-N-acetylglucosamine for peptidoglycan and lipopolysaccharides.
Probab=24.42 E-value=2.3e+02 Score=19.15 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=29.4
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..+-+++|+++..+ ..+|+.+....+. ...-..+...+...++|++++
T Consensus 187 ~~~~ll~~lg~~v~~in~~~d~~~~~~~~~--~~~l~~l~~~v~~~~adlGia 237 (443)
T TIGR01455 187 VAPHVFRELGAEVIAIGVEPDGLNINDGCG--STHLDALQKAVREHGADLGIA 237 (443)
T ss_pred HHHHHHHHcCCEEEEEccCCCCCCCCCCCC--CCCHHHHHHHHhhcCCCEEEE
Confidence 4667788889876433 2345554322211 122355666777788999875
No 283
>PRK10887 glmM phosphoglucosamine mutase; Provisional
Probab=24.20 E-value=2.4e+02 Score=19.15 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=30.0
Q ss_pred HHHHHHHHcCCeEEEE-EecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 3 LLENIAQELEFDFHLY-IVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 3 ll~~la~~l~f~~~~~-~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++..|-+++|+++..+ ..+|+.+..+.+. ...-..+...+...++|++++
T Consensus 186 ~~~~ll~~lG~~v~~~n~~~dg~~~~~~~~--~~~l~~l~~~v~~~~adlGia 236 (443)
T PRK10887 186 IAPNVFRELGAEVIAIGCEPNGLNINDECG--ATDPEALQAAVLAEKADLGIA 236 (443)
T ss_pred HHHHHHHHhCCeEEEEeccCCCCCCCCCCC--CCCHHHHHHHHHhcCCCeeeE
Confidence 4667778889876543 3345544322221 123456777777889999874
No 284
>TIGR02706 P_butyryltrans phosphate butyryltransferase. Members of this family are phosphate butyryltransferase, also called phosphotransbutyrylase. In general, this enzyme is found in butyrate-producing anaerobic bacteria, encoded next to the gene for butyrate kinase. Together, these two enzymes represent what may be the less common of two pathways for butyrate production from butyryl-CoA. The alternative is transfer of the CoA group to acetate by butyryl-CoA:acetate CoA transferase. Cutoffs for this model are set such that the homolog from Thermotoga maritima, whose activity on butyryl-CoA is only 30 % of its activity with acetyl-CoA, scores in the zone between trusted and noice cutoffs.
Probab=24.09 E-value=2.1e+02 Score=18.49 Aligned_cols=17 Identities=35% Similarity=0.378 Sum_probs=14.3
Q ss_pred HHHhhhcCCccEEEeCC
Q psy2313 40 VVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 40 ~ig~l~~g~~D~av~~l 56 (62)
.+..|.+|++|..+++.
T Consensus 79 a~~lv~~G~aD~~vsg~ 95 (294)
T TIGR02706 79 AVRLVSTGKADMLMKGL 95 (294)
T ss_pred HHHHHHCCCCCEEEeCC
Confidence 36688999999999877
No 285
>PF09140 MipZ: ATPase MipZ; InterPro: IPR015223 Cell division in bacteria is facilitated by a polymeric ring structure, the Z ring, composed of tubulin-like FtsZ protofilaments. Correct positioning of the division plane is a prerequisite for the generation of daughter cells with a normal chromosome complement. In Caulobacter crescentus MipZ, an essential protein, coordinates and regulates the assembly of the FtsZ cytokinetic ring during cell division. MipZ, forms a complex with the partitioning protein ParB near the origin of replication and localizes with the duplicated origin regions to the cell poles. MipZ also directly interferes with FtsZ polymerisation, thereby restricting FtsZ ring formation to mid-cell, the region of lowest MipZ concentration. In eukaryotes members of this entry belong to the Mrp/NBP35 ATP-binding protein family, and specifically the NUBP2/CFD1 subfamily. This includes the cytosolic Fe-S cluster assembly factor Cfd1, which is a component of the cytosolic iron-sulphur (Fe/S) protein assembly machinery. This protein is required for maturation of extra-mitochondrial Fe/S proteins. It may bind and transfer a labile 4Fe-4S cluster to target apoproteins. Cfd1 is also required for biogenesis and export of both ribosomal subunits, suggesting a role in assembly of the Fe/S clusters in RLI1, a protein which performs rRNA processing and ribosome export. ; PDB: 2XIT_B 2XJ4_A 2XJ9_A.
Probab=23.94 E-value=62 Score=21.06 Aligned_cols=17 Identities=18% Similarity=0.344 Sum_probs=12.2
Q ss_pred hHHHHHHHHcCCeEEEE
Q psy2313 2 DLLENIAQELEFDFHLY 18 (62)
Q Consensus 2 dll~~la~~l~f~~~~~ 18 (62)
+.+++|||+.||+.---
T Consensus 195 ~~l~~ls~rigfr~~~G 211 (261)
T PF09140_consen 195 EALEELSKRIGFRVAPG 211 (261)
T ss_dssp HHHHHHHHHHT-EEEE-
T ss_pred HHHHHHHHhhCceeCCC
Confidence 46889999999987543
No 286
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 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 [, ]. This entry represents a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=23.68 E-value=1.7e+02 Score=17.18 Aligned_cols=43 Identities=14% Similarity=0.216 Sum_probs=26.6
Q ss_pred HHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 4 LENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
+..+++.+|++..++...+ .......+..+...-+|+.+++..
T Consensus 92 ~~~~~~ll~~~i~~~~~~~-----------~~e~~~~i~~~~~~G~~viVGg~~ 134 (176)
T PF06506_consen 92 LESIEELLGVDIKIYPYDS-----------EEEIEAAIKQAKAEGVDVIVGGGV 134 (176)
T ss_dssp HHHHHHHHT-EEEEEEESS-----------HHHHHHHHHHHHHTT--EEEESHH
T ss_pred HHHHHHHhCCceEEEEECC-----------HHHHHHHHHHHHHcCCcEEECCHH
Confidence 4567777888877776431 134566677777777999998864
No 287
>TIGR00083 ribF riboflavin kinase/FMN adenylyltransferase. multifunctional enzyme: riboflavin kinase (EC 2.7.1.26) (flavokinase) / FMN adenylyltransferase (EC 2.7.7.2) (FAD pyrophosphorylase) (FAD synthetase).
Probab=23.52 E-value=64 Score=20.95 Aligned_cols=43 Identities=12% Similarity=0.045 Sum_probs=26.3
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEE
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMS 52 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~a 52 (62)
+.|+.+++..+|.+.+..+. ..+.+ -+-+.+-..|..|+++.|
T Consensus 119 ~~L~~~~~~~g~~v~~~~~~--~~~~~------ISST~IR~~l~~G~i~~A 161 (288)
T TIGR00083 119 LLLQLFGNTTIFCVIVKQLF--CQDIR------ISSSAIRQALKNGDLELA 161 (288)
T ss_pred HHHHHhccccCcEEEEeccc--cCCCe------ECHHHHHHHHHcCCHHHH
Confidence 56788888888877666443 22321 234556667777776644
No 288
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=23.41 E-value=61 Score=16.15 Aligned_cols=13 Identities=38% Similarity=0.728 Sum_probs=10.7
Q ss_pred hHHHHHHHHcCCe
Q psy2313 2 DLLENIAQELEFD 14 (62)
Q Consensus 2 dll~~la~~l~f~ 14 (62)
||++.+++++|..
T Consensus 21 ~l~~~v~~~l~l~ 33 (80)
T PF09379_consen 21 DLLEQVCDKLGLK 33 (80)
T ss_dssp HHHHHHHHHHTTS
T ss_pred HHHHHHHHHcCCC
Confidence 6889999998764
No 289
>TIGR00246 tRNA_RlmH_YbeA rRNA large subunit m3Psi methyltransferase RlmH. This protein, in the SPOUT methyltransferase family, previously designated YbeA in E. coli, was shown to be responsible for a further modification, a methylation, to a pseudouridine base in ribosomal large subunit RNA.
Probab=22.80 E-value=1.3e+02 Score=17.72 Aligned_cols=13 Identities=23% Similarity=0.381 Sum_probs=8.4
Q ss_pred Ccc--EEEeCCcccc
Q psy2313 48 TAH--MSFAALSVSS 60 (62)
Q Consensus 48 ~~D--~av~~ltit~ 60 (62)
++| +++++||.+.
T Consensus 114 ~a~~~lSLS~mTfpH 128 (153)
T TIGR00246 114 AAEQSWSLSKLTLPH 128 (153)
T ss_pred hcCceEEeecCCCcH
Confidence 455 6777777654
No 290
>PF04459 DUF512: Protein of unknown function (DUF512); InterPro: IPR007549 This is a domain of uncharacterised prokaryotic proteins. It is often found C-terminal to the radical SAM domain (IPR007197 from INTERPRO).
Probab=22.58 E-value=2e+02 Score=17.79 Aligned_cols=51 Identities=10% Similarity=0.225 Sum_probs=30.9
Q ss_pred HHHHHHHHc----CCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCc-cEEE
Q psy2313 3 LLENIAQEL----EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTA-HMSF 53 (62)
Q Consensus 3 ll~~la~~l----~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~-D~av 53 (62)
.++.+++++ |.+++++.+++.-||....-.+=-+-..++.+|..... |..+
T Consensus 111 ~l~~~~~~l~~~~~~~v~V~~V~N~fFG~~ItVaGLLTg~Dii~~L~~~~~~d~ll 166 (204)
T PF04459_consen 111 FLKPLVEKLNRIPGLEVEVVPVKNRFFGGTITVAGLLTGQDIIEQLKGKELGDLLL 166 (204)
T ss_pred HHHHHHHHHhccCCCeEEEEEeecCCCCCCeEEeeCccHHHHHHHhCcCCCCCEEE
Confidence 456666666 99999999999999975431100122345566654433 5444
No 291
>COG4002 Predicted phosphotransacetylase [General function prediction only]
Probab=22.40 E-value=62 Score=20.75 Aligned_cols=33 Identities=24% Similarity=0.202 Sum_probs=23.6
Q ss_pred HHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEe
Q psy2313 9 QELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFA 54 (62)
Q Consensus 9 ~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~ 54 (62)
++.++.++++..+ ..-.-++..|.+|++|-|+-
T Consensus 37 ~~~~~dvelV~~k-------------dp~k~lve~Lv~g~~daaVR 69 (256)
T COG4002 37 KEEGIDVELVDNK-------------DPEKVLVEKLVDGEIDAAVR 69 (256)
T ss_pred hhcCCceEEecCC-------------ChhHHHHHHHHccchhHHHh
Confidence 3568888887543 23356889999999997764
No 292
>cd08508 PBP2_NikA_DppA_OppA_like_1 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=22.26 E-value=2.5e+02 Score=18.78 Aligned_cols=17 Identities=12% Similarity=0.268 Sum_probs=11.5
Q ss_pred HHHHHHHcCCeEEEEEe
Q psy2313 4 LENIAQELEFDFHLYIV 20 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~ 20 (62)
++.-.+++|+++++...
T Consensus 345 l~~~l~~~Gi~v~~~~~ 361 (470)
T cd08508 345 VQAQLAEAGINLEIDVV 361 (470)
T ss_pred HHHHHHhcCcEEEEEEc
Confidence 44445667999888754
No 293
>PRK08190 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated
Probab=22.16 E-value=1.9e+02 Score=19.95 Aligned_cols=19 Identities=11% Similarity=-0.031 Sum_probs=15.2
Q ss_pred hHHHhhhcCCccEEEeCCc
Q psy2313 39 GVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 39 g~ig~l~~g~~D~av~~lt 57 (62)
..+.+|..|++|..+++..
T Consensus 241 ~a~~lv~~G~aD~~v~G~~ 259 (466)
T PRK08190 241 RAVALARAGEVEALMKGSL 259 (466)
T ss_pred HHHHHHHCCCCCEEEeCCC
Confidence 3557888999999998854
No 294
>PRK04021 hypothetical protein; Reviewed
Probab=22.14 E-value=1.2e+02 Score=16.44 Aligned_cols=17 Identities=12% Similarity=0.268 Sum_probs=14.1
Q ss_pred hHHHHHHHHcCCeEEEE
Q psy2313 2 DLLENIAQELEFDFHLY 18 (62)
Q Consensus 2 dll~~la~~l~f~~~~~ 18 (62)
+|++.||+.++...+++
T Consensus 50 ali~~LAk~l~~~I~I~ 66 (92)
T PRK04021 50 ELVKFFSKLLGAEVEII 66 (92)
T ss_pred HHHHHHHHHhCCCEEEE
Confidence 57899999999876665
No 295
>PF02621 VitK2_biosynth: Menaquinone biosynthesis; InterPro: IPR003773 This entry describes proteins of unknown function, which appear to be putative periplasmic binding proteins.; PDB: 3A3U_A 2CZL_A 1ZBM_A 2NXO_C 2I6E_E.
Probab=22.06 E-value=1.7e+02 Score=18.29 Aligned_cols=22 Identities=9% Similarity=0.054 Sum_probs=15.9
Q ss_pred cchhhHHHhhhcCCccEEEeCC
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~l 56 (62)
+.=+.+-..+.+|++|++..+.
T Consensus 31 ~~P~~Ln~~l~~g~~Dv~~iSs 52 (251)
T PF02621_consen 31 GVPSELNQMLLEGELDVALISS 52 (251)
T ss_dssp E-HHHHHHHHHTTS-SEEEEEH
T ss_pred CCHHHHHHHHHcCCCCEEEcCH
Confidence 3456788899999999987654
No 296
>PRK10222 PTS system L-ascorbate-specific transporter subunit IIB; Provisional
Probab=22.03 E-value=1.4e+02 Score=15.67 Aligned_cols=16 Identities=6% Similarity=0.198 Sum_probs=12.5
Q ss_pred HHHHHHHcCCeEEEEE
Q psy2313 4 LENIAQELEFDFHLYI 19 (62)
Q Consensus 4 l~~la~~l~f~~~~~~ 19 (62)
++.+.+++|+++++.-
T Consensus 7 Ik~~L~e~Gi~~~ve~ 22 (85)
T PRK10222 7 VDQFLTQSNIDHTVNS 22 (85)
T ss_pred HHHHHHHcCCCeEEEE
Confidence 5678889999988763
No 297
>cd08799 Death_UNC5C Death domain found in Uncoordinated-5C. Death Domain (DD) found in Uncoordinated-5C (UNC5C). UNC5C is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5C plays a critical role in the development of spinal accesory motor neurons. Methylation of the UNC5C gene is associated with early stages of colorectal carcinogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN.
Probab=21.94 E-value=60 Score=17.39 Aligned_cols=11 Identities=27% Similarity=0.507 Sum_probs=9.9
Q ss_pred HHHHHHHcCCe
Q psy2313 4 LENIAQELEFD 14 (62)
Q Consensus 4 l~~la~~l~f~ 14 (62)
++.||++|||.
T Consensus 23 Wr~LAekLgl~ 33 (84)
T cd08799 23 WRMLAHKLNLD 33 (84)
T ss_pred HHHHHHHcCCH
Confidence 68899999998
No 298
>cd00560 PanC Pantoate-beta-alanine ligase. PanC Pantoate-beta-alanine ligase, also known as pantothenate synthase, catalyzes the formation of pantothenate from pantoate and alanine. PanC belongs to a large superfamily of nucleotidyltransferases that includes , ATP sulfurylase (ATPS), phosphopantetheine adenylyltransferase (PPAT), and the amino-acyl tRNA synthetases. The enzymes of this family are structurally similar and share a dinucleotide-binding domain.
Probab=21.73 E-value=97 Score=20.09 Aligned_cols=18 Identities=6% Similarity=0.292 Sum_probs=16.1
Q ss_pred hHHHHHHHHcCCeEEEEE
Q psy2313 2 DLLENIAQELEFDFHLYI 19 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~ 19 (62)
++++.+++.++|.++++.
T Consensus 156 ~~Lk~~~~dl~~~v~ii~ 173 (277)
T cd00560 156 AVIRRMVRDLNLPVEIVG 173 (277)
T ss_pred HHHHHHHHHcCCeEEEEc
Confidence 689999999999999984
No 299
>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A ....
Probab=21.65 E-value=84 Score=16.58 Aligned_cols=13 Identities=31% Similarity=0.560 Sum_probs=11.0
Q ss_pred HHHHHHHHcCCeE
Q psy2313 3 LLENIAQELEFDF 15 (62)
Q Consensus 3 ll~~la~~l~f~~ 15 (62)
+.+.|++++|+.+
T Consensus 15 ~a~~La~~~~~~~ 27 (121)
T PF13207_consen 15 LAKELAERLGFPV 27 (121)
T ss_dssp HHHHHHHHHTCEE
T ss_pred HHHHHHHHHCCeE
Confidence 6789999999875
No 300
>PF13369 Transglut_core2: Transglutaminase-like superfamily
Probab=21.49 E-value=1.4e+02 Score=17.10 Aligned_cols=21 Identities=14% Similarity=0.082 Sum_probs=16.9
Q ss_pred HHHHHHHHcCCeEEEEEecCC
Q psy2313 3 LLENIAQELEFDFHLYIVADG 23 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~ 23 (62)
|...+|+++|+..+.+..|..
T Consensus 73 ly~~va~rlGl~~~~v~~Pgh 93 (152)
T PF13369_consen 73 LYLEVARRLGLPAEPVNFPGH 93 (152)
T ss_pred HHHHHHHHcCCeEEEEecCCE
Confidence 467899999999998876544
No 301
>TIGR00251 conserved hypothetical protein TIGR00251.
Probab=20.90 E-value=1.4e+02 Score=15.96 Aligned_cols=17 Identities=12% Similarity=0.321 Sum_probs=13.6
Q ss_pred hHHHHHHHHcCCeEEEE
Q psy2313 2 DLLENIAQELEFDFHLY 18 (62)
Q Consensus 2 dll~~la~~l~f~~~~~ 18 (62)
.|++.||+.++.+++++
T Consensus 49 ali~~La~~l~v~I~i~ 65 (87)
T TIGR00251 49 ELIKFFGEIFGVDVEIV 65 (87)
T ss_pred HHHHHHHHHhCceEEEE
Confidence 47889999999966665
No 302
>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene wh
Probab=20.78 E-value=62 Score=17.89 Aligned_cols=14 Identities=14% Similarity=0.233 Sum_probs=10.8
Q ss_pred hhhcCCccEEEeCC
Q psy2313 43 DLVTGTAHMSFAAL 56 (62)
Q Consensus 43 ~l~~g~~D~av~~l 56 (62)
++.+|++|+++...
T Consensus 44 ~l~~~~~D~~i~~~ 57 (199)
T cd08478 44 DLIERKTDVAIRIG 57 (199)
T ss_pred cchhccccEEEEec
Confidence 46789999998743
No 303
>PRK11205 tbpA thiamine transporter substrate binding subunit; Provisional
Probab=20.72 E-value=2.4e+02 Score=17.92 Aligned_cols=39 Identities=8% Similarity=0.140 Sum_probs=24.2
Q ss_pred hHHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhh----cCCccEEEe
Q psy2313 2 DLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLV----TGTAHMSFA 54 (62)
Q Consensus 2 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~----~g~~D~av~ 54 (62)
++++...++.|++++++... +=..++..+. ++++|++++
T Consensus 42 ~i~~~Fe~~tgikV~~~~~~--------------s~~~~~~kl~~e~~~~~~DV~~~ 84 (330)
T PRK11205 42 AVKKAFEAECGCELKFVALE--------------DGVSLLNRLRLEGKNSKADVVLG 84 (330)
T ss_pred HHHHHHHHHHCCEEEEEecC--------------cHHHHHHHHHhcCCCCCCCEEEE
Confidence 36677777789998887421 1123555444 467898764
No 304
>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=20.68 E-value=2.1e+02 Score=17.21 Aligned_cols=24 Identities=21% Similarity=0.242 Sum_probs=17.3
Q ss_pred cchhhHHHhhhcCCccEEEeCCccc
Q psy2313 35 DKWNGVVGDLVTGTAHMSFAALSVS 59 (62)
Q Consensus 35 ~~w~g~ig~l~~g~~D~av~~ltit 59 (62)
|+..|+. .|.+|++|+|...+...
T Consensus 19 gS~~gl~-~L~~g~~~iAg~h~~~~ 42 (193)
T PF12727_consen 19 GSRAGLS-ALARGEADIAGIHLPDP 42 (193)
T ss_pred CCHHHHH-HHHCCCceEEEecCCCC
Confidence 5665554 55799999998877543
No 305
>PF12953 DUF3842: Domain of unknown function (DUF3842); InterPro: IPR024208 This family of proteins has no known function.
Probab=20.46 E-value=39 Score=19.75 Aligned_cols=53 Identities=13% Similarity=0.315 Sum_probs=27.3
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccc--eeccCCCcchhhHHHh----hhcCCccEEEeCCcc
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGT--KVRENQKDKWNGVVGD----LVTGTAHMSFAALSV 58 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~--~~~~~~~~~w~g~ig~----l~~g~~D~av~~lti 58 (62)
+.+.|.+.+.=..+++-..-+..-. -.+ .|.=.|-.|+ ...+++|++++|+.|
T Consensus 16 iv~~lr~~~~~~~eI~AlGTNa~AT~~MlK---aGA~~gATGENaIv~n~~~aDiIvGpigI 74 (131)
T PF12953_consen 16 IVEKLRKELPEEVEIIALGTNAIATSAMLK---AGANEGATGENAIVVNARKADIIVGPIGI 74 (131)
T ss_pred HHHHHHHhCCCCcEEEEEehhHHHHHHHHH---cCCCCcccccchheeccCCCCEEECcHHH
Confidence 5677777777777777653221100 000 0111111111 235689999999875
No 306
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=20.22 E-value=1.3e+02 Score=15.04 Aligned_cols=20 Identities=10% Similarity=0.079 Sum_probs=16.3
Q ss_pred HHHHHHHcCCeEEEEEecCC
Q psy2313 4 LENIAQELEFDFHLYIVADG 23 (62)
Q Consensus 4 l~~la~~l~f~~~~~~~~~~ 23 (62)
++.+.+..|++++++..|..
T Consensus 17 ~ek~lk~~gi~~~liP~P~~ 36 (73)
T PF11823_consen 17 AEKLLKKNGIPVRLIPTPRE 36 (73)
T ss_pred HHHHHHHCCCcEEEeCCChh
Confidence 56788899999999977654
No 307
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=20.22 E-value=76 Score=16.70 Aligned_cols=11 Identities=18% Similarity=0.428 Sum_probs=8.2
Q ss_pred HHHHHHHcCCe
Q psy2313 4 LENIAQELEFD 14 (62)
Q Consensus 4 l~~la~~l~f~ 14 (62)
++.+|++|||+
T Consensus 16 Wk~laR~LGls 26 (86)
T cd08306 16 WRKLARKLGLS 26 (86)
T ss_pred HHHHHHHcCCC
Confidence 56778888865
No 308
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=20.20 E-value=1.6e+02 Score=15.60 Aligned_cols=41 Identities=7% Similarity=0.002 Sum_probs=27.5
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCC
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAAL 56 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~l 56 (62)
.+..+.++.|+++.+.... ..-+.+...+...++|++.-+.
T Consensus 19 ~la~~l~~~G~~v~~~d~~-------------~~~~~l~~~~~~~~pd~V~iS~ 59 (121)
T PF02310_consen 19 YLAAYLRKAGHEVDILDAN-------------VPPEELVEALRAERPDVVGISV 59 (121)
T ss_dssp HHHHHHHHTTBEEEEEESS-------------B-HHHHHHHHHHTTCSEEEEEE
T ss_pred HHHHHHHHCCCeEEEECCC-------------CCHHHHHHHHhcCCCcEEEEEc
Confidence 3455667779988887431 3347778888888999865443
No 309
>cd02065 B12-binding_like B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif.
Probab=20.18 E-value=1.6e+02 Score=15.61 Aligned_cols=42 Identities=10% Similarity=-0.067 Sum_probs=28.8
Q ss_pred HHHHHHHHcCCeEEEEEecCCcccceeccCCCcchhhHHHhhhcCCccEEEeCCc
Q psy2313 3 LLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGTAHMSFAALS 57 (62)
Q Consensus 3 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~~~~~w~g~ig~l~~g~~D~av~~lt 57 (62)
++..+.+..||...+.-. +.....++..+...++|+..-+.+
T Consensus 18 ~~~~~l~~~G~~v~~l~~-------------~~~~~~~~~~i~~~~pdiV~iS~~ 59 (125)
T cd02065 18 IVAIALRDNGFEVIDLGV-------------DVPPEEIVEAAKEEDADVVGLSAL 59 (125)
T ss_pred HHHHHHHHCCCEEEEcCC-------------CCCHHHHHHHHHHcCCCEEEEecc
Confidence 345566778888776532 245678888888889997664443
Done!