Query 044324
Match_columns 291
No_of_seqs 142 out of 578
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 13:32:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044324.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044324hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00094 TR_FER Transferrin. 100.0 9E-66 1.9E-70 490.4 18.8 218 65-290 1-229 (332)
2 PF00405 Transferrin: Transfer 100.0 1E-64 2.2E-69 482.8 12.3 205 65-278 1-219 (330)
3 COG3221 PhnD ABC-type phosphat 99.2 2.2E-11 4.9E-16 115.4 8.1 145 89-273 66-212 (299)
4 PF12974 Phosphonate-bd: ABC t 99.1 2.1E-10 4.6E-15 103.2 6.0 144 89-273 28-172 (243)
5 TIGR01098 3A0109s03R phosphate 98.5 1.1E-06 2.5E-11 78.6 11.1 171 62-273 31-209 (254)
6 TIGR03431 PhnD phosphonate ABC 98.3 3E-06 6.4E-11 78.1 8.7 101 89-193 58-158 (288)
7 PF09084 NMT1: NMT1/THI5 like; 97.1 0.0012 2.7E-08 57.5 6.8 98 88-196 19-117 (216)
8 TIGR01729 taurine_ABC_bnd taur 96.4 0.012 2.6E-07 54.5 7.9 99 89-197 26-125 (300)
9 TIGR01728 SsuA_fam ABC transpo 96.4 0.01 2.2E-07 53.2 7.0 96 90-196 29-125 (288)
10 PRK11480 tauA taurine transpor 95.9 0.03 6.5E-07 52.8 7.9 98 89-198 50-148 (320)
11 PRK11553 alkanesulfonate trans 95.5 0.048 1E-06 50.8 7.3 78 91-176 57-135 (314)
12 TIGR03427 ABC_peri_uca ABC tra 94.9 0.12 2.6E-06 49.7 8.6 98 87-197 32-131 (328)
13 cd00134 PBPb Bacterial peripla 94.3 0.12 2.6E-06 42.7 6.1 74 89-176 37-111 (218)
14 smart00062 PBPb Bacterial peri 94.3 0.13 2.8E-06 42.3 6.2 75 89-177 38-113 (219)
15 COG0715 TauA ABC-type nitrate/ 94.1 0.17 3.8E-06 47.2 7.3 103 88-199 58-164 (335)
16 COG2358 Imp TRAP-type uncharac 93.7 0.1 2.2E-06 50.6 5.0 115 60-187 23-154 (321)
17 TIGR02122 TRAP_TAXI TRAP trans 92.0 0.67 1.5E-05 42.7 7.8 120 61-193 28-162 (320)
18 PF03466 LysR_substrate: LysR 87.0 7.5 0.00016 32.0 9.7 120 61-195 4-127 (209)
19 PRK15010 ABC transporter lysin 86.9 2.2 4.7E-05 38.5 6.8 72 89-175 64-138 (260)
20 PF00497 SBP_bac_3: Bacterial 82.8 1.9 4.1E-05 36.5 4.3 79 89-177 37-117 (225)
21 PRK00489 hisG ATP phosphoribos 82.7 3.3 7.1E-05 38.9 6.2 75 90-175 44-118 (287)
22 PRK09495 glnH glutamine ABC tr 82.3 3.4 7.4E-05 36.8 5.9 72 89-176 62-137 (247)
23 PRK15437 histidine ABC transpo 81.6 3.8 8.2E-05 36.9 6.0 73 89-175 64-138 (259)
24 PF13379 NMT1_2: NMT1-like fam 81.2 3.6 7.8E-05 37.1 5.7 103 88-198 33-148 (252)
25 TIGR01096 3A0103s03R lysine-ar 80.9 3.9 8.5E-05 36.0 5.7 72 89-175 62-136 (250)
26 PRK11260 cystine transporter s 80.9 4.5 9.7E-05 36.6 6.2 75 89-175 79-154 (266)
27 PRK11917 bifunctional adhesin/ 80.8 2.1 4.5E-05 39.1 4.1 71 91-175 82-153 (259)
28 PRK11063 metQ DL-methionine tr 80.2 13 0.00029 34.8 9.3 116 64-195 32-153 (271)
29 TIGR00363 lipoprotein, YaeC fa 79.3 3.9 8.5E-05 38.2 5.4 98 64-176 19-123 (258)
30 PRK10859 membrane-bound lytic 78.0 5.9 0.00013 39.9 6.6 74 89-176 79-155 (482)
31 PRK10797 glutamate and asparta 77.2 4.8 0.0001 37.8 5.4 69 91-175 87-158 (302)
32 COG4521 TauA ABC-type taurine 76.4 4.2 9.1E-05 38.7 4.6 98 91-198 58-156 (334)
33 cd08436 PBP2_LTTR_like_3 The C 75.4 18 0.00039 29.0 7.8 76 91-178 30-106 (194)
34 cd08414 PBP2_LTTR_aromatics_li 75.0 31 0.00068 27.6 9.1 101 65-179 2-106 (197)
35 cd05466 PBP2_LTTR_substrate Th 68.2 36 0.00077 26.7 7.8 75 90-177 29-104 (197)
36 cd08449 PBP2_XapR The C-termin 67.5 63 0.0014 25.9 9.8 78 90-178 29-107 (197)
37 cd08469 PBP2_PnbR The C-termin 64.4 41 0.00089 28.1 7.9 98 65-176 2-102 (221)
38 TIGR02995 ectoine_ehuB ectoine 62.9 18 0.00039 32.9 5.8 69 95-174 76-148 (275)
39 cd08437 PBP2_MleR The substrat 61.3 58 0.0013 26.4 8.1 76 91-177 30-106 (198)
40 TIGR00787 dctP tripartite ATP- 61.0 8.1 0.00018 35.2 3.1 32 90-121 30-64 (257)
41 cd08446 PBP2_Chlorocatechol Th 60.3 79 0.0017 25.5 8.7 100 64-177 2-105 (198)
42 PRK09959 hybrid sensory histid 60.1 17 0.00037 40.1 5.9 75 89-175 95-169 (1197)
43 cd08438 PBP2_CidR The C-termin 59.5 44 0.00094 26.8 6.9 99 65-177 2-104 (197)
44 cd08467 PBP2_SyrM The C-termin 59.0 97 0.0021 25.4 9.1 77 90-179 29-105 (200)
45 cd08420 PBP2_CysL_like C-termi 58.5 43 0.00094 26.7 6.7 28 91-119 30-57 (201)
46 cd08468 PBP2_Pa0477 The C-term 58.5 59 0.0013 26.7 7.7 27 91-118 30-56 (202)
47 cd08440 PBP2_LTTR_like_4 TThe 58.4 69 0.0015 25.4 7.9 73 91-176 30-103 (197)
48 cd08434 PBP2_GltC_like The sub 57.6 79 0.0017 25.1 8.1 72 91-175 30-102 (195)
49 cd08411 PBP2_OxyR The C-termin 56.2 78 0.0017 25.6 8.0 99 64-176 2-104 (200)
50 PRK11074 putative DNA-binding 54.8 49 0.0011 30.3 7.2 57 61-119 90-149 (300)
51 TIGR03871 ABC_peri_MoxJ_2 quin 54.2 61 0.0013 28.1 7.4 74 88-176 33-110 (232)
52 cd08425 PBP2_CynR The C-termin 52.9 66 0.0014 25.9 7.0 101 64-178 2-107 (197)
53 PRK11242 DNA-binding transcrip 52.2 76 0.0016 28.6 7.9 106 61-179 89-198 (296)
54 PRK15007 putative ABC transpor 51.7 21 0.00046 31.3 4.1 66 95-174 64-130 (243)
55 PF00497 SBP_bac_3: Bacterial 51.2 16 0.00034 30.8 3.1 52 65-122 111-163 (225)
56 cd08453 PBP2_IlvR The C-termin 50.8 83 0.0018 25.5 7.3 80 90-179 29-109 (200)
57 CHL00180 rbcR LysR transcripti 49.7 88 0.0019 28.7 8.0 55 61-118 93-151 (305)
58 cd08448 PBP2_LTTR_aromatics_li 49.4 1.3E+02 0.0028 24.0 8.1 73 91-176 30-103 (197)
59 cd08439 PBP2_LrhA_like The C-t 49.1 1.3E+02 0.0027 24.2 8.1 27 91-118 30-56 (185)
60 cd08465 PBP2_ToxR The C-termin 49.1 1.5E+02 0.0032 24.3 8.8 76 91-179 30-105 (200)
61 cd08485 PBP2_ClcR The C-termin 48.3 1.5E+02 0.0033 24.2 9.3 74 91-177 31-105 (198)
62 cd08445 PBP2_BenM_CatM_CatR Th 48.0 1.5E+02 0.0033 24.1 9.0 99 64-176 2-105 (203)
63 TIGR02424 TF_pcaQ pca operon t 47.9 87 0.0019 28.4 7.6 103 60-178 90-200 (300)
64 cd08463 PBP2_DntR_like_4 The C 47.6 1E+02 0.0022 25.6 7.5 75 90-176 29-104 (203)
65 cd08412 PBP2_PAO1_like The C-t 47.0 1.2E+02 0.0026 24.2 7.7 75 91-178 30-105 (198)
66 PRK14498 putative molybdopteri 46.4 44 0.00095 34.9 6.0 75 91-179 442-532 (633)
67 PRK11482 putative DNA-binding 45.1 93 0.002 29.0 7.5 57 61-119 115-172 (317)
68 PRK09861 cytoplasmic membrane 44.1 38 0.00083 31.8 4.7 73 89-177 59-138 (272)
69 cd08415 PBP2_LysR_opines_like 43.8 90 0.002 24.9 6.4 74 90-176 29-103 (196)
70 cd08435 PBP2_GbpR The C-termin 42.4 1.7E+02 0.0037 23.3 7.9 76 91-177 30-106 (201)
71 PF14503 YhfZ_C: YhfZ C-termin 42.4 15 0.00034 34.1 1.8 108 42-155 88-199 (232)
72 cd08421 PBP2_LTTR_like_1 The C 42.1 71 0.0015 25.7 5.6 84 91-189 30-114 (198)
73 PRK10216 DNA-binding transcrip 42.1 1.4E+02 0.0031 27.6 8.2 53 64-119 98-153 (319)
74 smart00079 PBPe Eukaryotic hom 42.0 34 0.00073 27.2 3.5 55 95-155 49-104 (134)
75 cd08462 PBP2_NodD The C-termin 42.0 1.9E+02 0.0041 23.5 8.5 75 90-178 29-103 (200)
76 cd08423 PBP2_LTTR_like_6 The C 41.9 1.8E+02 0.0038 23.2 7.9 79 90-178 29-110 (200)
77 cd08460 PBP2_DntR_like_1 The C 39.6 2E+02 0.0044 23.2 8.4 74 90-177 29-102 (200)
78 cd08417 PBP2_Nitroaromatics_li 39.6 1.3E+02 0.0028 24.2 6.8 75 90-177 29-103 (200)
79 cd08452 PBP2_AlsR The C-termin 39.2 1.5E+02 0.0031 24.2 7.1 77 90-179 29-106 (197)
80 PF02621 VitK2_biosynth: Menaq 38.2 27 0.00059 32.1 2.7 81 90-182 24-104 (251)
81 cd08433 PBP2_Nac The C-teminal 38.0 71 0.0015 25.8 5.0 74 91-177 30-104 (198)
82 cd08464 PBP2_DntR_like_2 The C 37.1 2.1E+02 0.0046 22.8 7.7 73 90-175 29-101 (200)
83 TIGR03870 ABC_MoxJ methanol ox 36.6 1.1E+02 0.0024 27.3 6.4 26 248-273 153-178 (246)
84 PRK11151 DNA-binding transcrip 36.2 1.7E+02 0.0036 26.7 7.6 57 61-119 89-148 (305)
85 cd08451 PBP2_BudR The C-termin 36.0 1.3E+02 0.0028 24.0 6.2 75 91-177 31-106 (199)
86 cd08442 PBP2_YofA_SoxR_like Th 35.4 1.7E+02 0.0038 23.1 6.9 70 90-176 29-99 (193)
87 cd08486 PBP2_CbnR The C-termin 35.3 2.5E+02 0.0054 23.0 8.6 76 89-176 27-104 (198)
88 PRK10837 putative DNA-binding 35.0 2.3E+02 0.0051 25.3 8.3 102 61-178 87-193 (290)
89 cd08456 PBP2_LysR The C-termin 34.8 2.3E+02 0.005 22.6 7.5 28 90-118 29-56 (196)
90 cd08466 PBP2_LeuO The C-termin 34.3 2.4E+02 0.0053 22.6 7.7 28 90-118 29-56 (200)
91 PRK09906 DNA-binding transcrip 33.8 3.6E+02 0.0077 24.3 9.5 103 63-179 90-196 (296)
92 PRK12683 transcriptional regul 33.4 1.9E+02 0.0041 26.7 7.6 116 61-191 91-210 (309)
93 PRK09986 DNA-binding transcrip 33.1 3E+02 0.0065 24.6 8.7 105 61-177 95-203 (294)
94 COG0834 HisJ ABC-type amino ac 32.3 69 0.0015 28.2 4.3 70 94-175 80-151 (275)
95 COG1638 DctP TRAP-type C4-dica 30.2 53 0.0012 31.8 3.4 86 90-175 61-172 (332)
96 COG0834 HisJ ABC-type amino ac 30.0 1.2E+02 0.0026 26.6 5.4 55 65-124 147-202 (275)
97 TIGR01256 modA molybdenum ABC 30.0 1.4E+02 0.0031 25.7 5.9 89 82-179 12-107 (216)
98 TIGR00070 hisG ATP phosphoribo 29.8 1.4E+02 0.0029 26.8 5.7 79 101-196 50-129 (182)
99 cd08419 PBP2_CbbR_RubisCO_like 29.3 1.3E+02 0.0028 24.0 5.1 28 90-118 28-55 (197)
100 TIGR01096 3A0103s03R lysine-ar 27.3 69 0.0015 28.0 3.4 53 64-122 131-184 (250)
101 cd08447 PBP2_LTTR_aromatics_li 27.2 3.2E+02 0.007 21.7 7.9 27 91-118 30-56 (198)
102 TIGR03339 phn_lysR aminoethylp 26.2 1.2E+02 0.0025 26.9 4.7 99 61-176 85-187 (279)
103 cd08428 PBP2_IciA_ArgP The C-t 25.7 3.5E+02 0.0076 21.7 9.1 104 64-180 1-107 (195)
104 TIGR03871 ABC_peri_MoxJ_2 quin 24.8 1.3E+02 0.0027 26.1 4.6 25 98-122 141-165 (232)
105 PF11623 DUF3252: Protein of u 24.7 37 0.00081 24.6 0.9 24 240-263 13-36 (53)
106 cd08457 PBP2_OccR The C-termin 24.5 2.8E+02 0.0061 22.3 6.4 76 90-178 29-105 (196)
107 PRK12684 transcriptional regul 24.0 3.2E+02 0.0069 25.2 7.4 56 60-118 90-149 (313)
108 PF15071 TMEM220: Transmembran 23.4 27 0.00058 28.3 -0.0 15 32-46 76-90 (104)
109 cd08432 PBP2_GcdR_TrpI_HvrB_Am 23.0 97 0.0021 24.7 3.3 71 90-176 29-99 (194)
110 cd08413 PBP2_CysB_like The C-t 22.7 2.6E+02 0.0057 22.7 5.9 77 90-178 29-106 (198)
111 PF04069 OpuAC: Substrate bind 20.7 2.5E+02 0.0054 25.4 5.8 99 82-185 21-131 (257)
112 TIGR02136 ptsS_2 phosphate bin 20.3 1.8E+02 0.0039 26.9 4.8 56 62-119 35-92 (287)
No 1
>smart00094 TR_FER Transferrin.
Probab=100.00 E-value=9e-66 Score=490.42 Aligned_cols=218 Identities=32% Similarity=0.643 Sum_probs=194.7
Q ss_pred eEEEecc-chHHHHHHHHHHhhcC-CCcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCC
Q 044324 65 IKWCAVR-DQYEDCEYLVSIISQS-EDYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDH 142 (291)
Q Consensus 65 vRwCv~S-~E~~KC~~l~~~a~~~-~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~ 142 (291)
|||||+| .|++||++| +.++.. .++.|+||.+.|+.+||++|++|+||+++||++++|+|++.++|+||++|.|..+
T Consensus 1 vrwCv~s~~e~~KC~~~-~~~~~~~~~~~v~Cv~~~s~~~Ci~~I~~g~AD~a~ldg~~~y~A~~~~~l~pi~~E~~~~~ 79 (332)
T smart00094 1 VRWCAVSNAEKSKCDQW-SVNSRGRDVPALECVSASSTEECIKAIQKGEADAVTLDGGDVYTAGKPYNLVPVFAENYGSE 79 (332)
T ss_pred CEEecCCHHHHHHHHHH-HHHHhhCCCCceEEEEcCCHHHHHHHHHCCCCCEEEECcHHHHhhcccCCceEEEEEeeccC
Confidence 7999999 999999999 655433 3599999999999999999999999999999999999998899999999999752
Q ss_pred C---ceeEEEEEEecCccccCCCCCcccCCCCcccCCCCCCCCCchhHHHHHHhCCCCCCCCCCchhhhhhccccccCCC
Q 044324 143 A---QSYDAVAVINRKVCQENGGINLMDFKGHKSCHGSYSTAAGWNYPVNHIKGSTPTFDSGKISDIEIASSFFSEVCAP 219 (291)
Q Consensus 143 ~---~~Y~aVAVVkK~~~~~S~~~~l~dLkGKksCHtG~~~taGW~iPvg~L~~~~~~c~~~~~~~~~~~s~FFs~SCvP 219 (291)
+ ..||+||||||+ |++.+|+||||||+||||+++++||++|++.|++++++...+.-.++++ ++||++||+|
T Consensus 80 ~~~~~~Y~aVaVVkk~----S~i~sl~dLkGKksChtg~~stsGw~iP~~~L~~~g~i~~~~~~~~~av-s~fFs~sC~P 154 (332)
T smart00094 80 EEPETGYYAVAVVKKG----SAIFTWNQLRGKKSCHTGVGRTAGWNIPMGLLYNKLVIRPPNCPFEKAV-SKFFSASCAP 154 (332)
T ss_pred CCCCceeEEEEEEECC----CCCCCHHHhCCCceecCCCCCcchhHHHHHHHHHcCCCCCCCCcHHHHH-HHHhhccccC
Confidence 2 489999999999 8889999999999999999999999999999999985321111114567 9999999999
Q ss_pred CCCC---CCCCCcCCCCCCCCCC--CCCCccCccccccccccCCCcEEEEechhhhhhhcCCCCCccccccc-cccc
Q 044324 220 GEFE---GTGMCSGCGIENGSCH--SNSLYFGDSGAFRCLVEELGDIAFVRGDTALLYSKEGPQNQSWSSKS-VRDF 290 (291)
Q Consensus 220 G~~~---~~~LC~lC~g~~~~C~--~~e~Y~Gy~GAlrCL~eg~GDVAFVk~~tV~~~~~dg~~~~~Wa~~~-~~~~ 290 (291)
|++. ++|||+||.|+ .+|. ++|+||||.||||||+||+||||||||+||.+++ +|+|.++||++. .+||
T Consensus 155 G~~~~~~~~~LC~lC~g~-~~C~~~~~e~Y~Gy~GA~rCL~eg~GdVAFvk~~tv~~~~-~~~~~~~wa~~~~~~dy 229 (332)
T smart00094 155 GADKPDPNSNLCALCAGD-NKCACSSHEPYYGYSGAFRCLAEGAGDVAFVKHSTVFENT-DGKNGADWAKNLKRDDY 229 (332)
T ss_pred CCCCCCCchhhHhhcCCC-CccCCCCCCcccCcchhheeeccCCccEEEEecccHHhhc-CCCCccccccccCccce
Confidence 9998 78999999985 7895 8999999999999999999999999999999999 999999999887 4555
No 2
>PF00405 Transferrin: Transferrin; InterPro: IPR001156 Transferrins are eukaryotic iron-binding glycoproteins that control the level of free iron in biological fluids []. The proteins have arisen by duplication of a domain, each duplicated domain binding one iron atom. Members of the family include blood serotransferrin (siderophilin); milk lactotransferrin (lactoferrin); egg white ovotransferrin (conalbumin); and membrane-associated melanotransferrin. Additional members of this family include inhibitor of carbonic anhydrase (ICA; mammals), major yolk protein (sea urchins), saxiphilin (frog), pacifastin (crayfish), and TTF-1 (algae). Most family members contain two transferrin-like domains of around 340 amino acids, the result of an ancient duplication event []. Each of the duplicated domains can be further divided into two subdomains that form a cleft inside of which the iron atom is bound in iron-transporting transferrin []. The iron-coordinating residues consist of an aspartic acid, two tyrosines and a histidine, as well as an arginine that coordinates a requisite anion. In addition to iron and anion liganding residues, the transferrin-like domain contains conserved cysteine residues involved in disulphide bond formation. Human lactoferrin is a serine peptidase belonging to MEROPS peptidase family S60, clan SR. It is found at high concentrations in all human secretions, where it plays a major role in mucosal defence. Lactoferrin cleaves IgA1 protease at an arginine-rich region defined by amino acids RRSRRSVR and digests Hap at a similar arginine-rich sequence (VRSRRAAR). Ser259 and Lys73 form a catalytic dyad, reminiscent of a number of bacterial serine proteases. ; GO: 0008199 ferric iron binding, 0006826 iron ion transport, 0006879 cellular iron ion homeostasis, 0005576 extracellular region; PDB: 1JNF_A 1TFD_A 1JW1_A 1DTZ_A 2J4U_X 1I6Q_A 1BIY_A 1CE2_A 1H76_A 1F9B_A ....
Probab=100.00 E-value=1e-64 Score=482.81 Aligned_cols=205 Identities=37% Similarity=0.698 Sum_probs=181.1
Q ss_pred eEEEecc-chHHHHHHHHHHhhcCC-CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeec-ccCCcEEEEEEeecC
Q 044324 65 IKWCAVR-DQYEDCEYLVSIISQSE-DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAF-LNFSMKAIANEVYCD 141 (291)
Q Consensus 65 vRwCv~S-~E~~KC~~l~~~a~~~~-~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~-~~~~L~PIl~E~y~~ 141 (291)
|||||+| .|++||++| +.++... .|.|+||++.|++|||++|++|+||+++||++++|+|+ ++|+|+||++|.|..
T Consensus 1 VRwCv~s~~E~~KC~~~-~~~~~~~~~~~i~Cv~~~s~~dCm~~I~~g~AD~v~ld~~~~y~A~~~~~~L~pi~~E~y~~ 79 (330)
T PF00405_consen 1 VRWCVVSEAELKKCERM-SKAFSSAGRPEISCVRATSREDCMRRIKKGEADAVTLDGGDVYIAGLRKYNLKPIAAEVYGS 79 (330)
T ss_dssp EEEEEESHHHHHHHHHH-HHHHTHTSSTSEEEEEESSHHHHHHHHHTTSSSBEEEEHHHHHHHHSTTTTEEEEEEEEESS
T ss_pred CEEeecChHHHHHHHHH-HHHhhhcCCCCceeEeCCCHHHHHHHHhhccCCEEEeCchhhhhhhccccCCEEeeeeeccc
Confidence 7999999 999999999 6666544 49999999999999999999999999999999999999 899999999999984
Q ss_pred C---CceeEEEEEEecCccccCCCCCcccCCCCcccCCCCCCCCCchhHHHHHHhCCCCCC---CCCCchhhhhhccccc
Q 044324 142 H---AQSYDAVAVINRKVCQENGGINLMDFKGHKSCHGSYSTAAGWNYPVNHIKGSTPTFD---SGKISDIEIASSFFSE 215 (291)
Q Consensus 142 ~---~~~Y~aVAVVkK~~~~~S~~~~l~dLkGKksCHtG~~~taGW~iPvg~L~~~~~~c~---~~~~~~~~~~s~FFs~ 215 (291)
. ...||+||||||+ + .++|+||||||+||||+++++||++||++|++++.+.. ...+ .+++ ++||++
T Consensus 80 ~~~~~~~y~aVAVVkk~----s-~~~l~~LrGkksCHtG~g~~aGW~~Pv~~L~~~~~i~~~~~~~~~-~~av-s~FF~~ 152 (330)
T PF00405_consen 80 EEEPEASYYAVAVVKKS----S-NITLKDLRGKKSCHTGYGRTAGWNIPVGYLLEKGVIPWTGPDCDV-EKAV-SDFFSK 152 (330)
T ss_dssp SSSEESEEEEEEEEETT----S-S-SGGGGTTSEEEESSTTTTTTTHHHHHHHHHHHHCCSSSTTSSH-HHHH-HHHSSE
T ss_pred cccccceeEEEEEEecC----C-CcchhhhcCCCCCCcCcCCcccccccchhhhhcCcCCcccccchh-hhHH-hhhhcC
Confidence 2 2489999999999 7 46899999999999999999999999999998874332 1122 3577 999999
Q ss_pred cCCCCCCC--CCCCCcCCCC-CCCCCC--CCCCccCccccccccccCCCcEEEEechhhhhhhcCCCC
Q 044324 216 VCAPGEFE--GTGMCSGCGI-ENGSCH--SNSLYFGDSGAFRCLVEELGDIAFVRGDTALLYSKEGPQ 278 (291)
Q Consensus 216 SCvPG~~~--~~~LC~lC~g-~~~~C~--~~e~Y~Gy~GAlrCL~eg~GDVAFVk~~tV~~~~~dg~~ 278 (291)
||+||+.. +++||+||.| ...+|. ++|+||||.||||||+||+||||||+|+||++++ ++++
T Consensus 153 sC~PGa~~~~~~~LC~lC~g~~~~~C~~~~~e~y~G~~GAlrCL~eg~GDVAFv~~~tv~~~~-~~~~ 219 (330)
T PF00405_consen 153 SCVPGADKKNYSNLCSLCKGDGESKCSCSSNEPYYGYEGALRCLVEGKGDVAFVKHTTVFENT-DGNN 219 (330)
T ss_dssp EE-TTSSTTTTSGGGTTSTSSTTSTTTSSTTSTTSHHHHHHHHHHTTSSSEEEEETTHHHHHS-TSSS
T ss_pred ccccccccccCCcccccccCCCCCcCCCCCcccCCCCCcceEEEecCCCcEEEEeccchhhhc-cccc
Confidence 99999987 7999999999 346787 7899999999999999999999999999999999 7754
No 3
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=99.23 E-value=2.2e-11 Score=115.42 Aligned_cols=145 Identities=18% Similarity=0.255 Sum_probs=121.4
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccC-CcEEEEEEeecCCCceeEEEEEEecCccccCCCCCccc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNF-SMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMD 167 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~-~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~d 167 (291)
+..++=+.++|+..-++++++|++|++.+.+.....|.+.. +..|++.-...++...|+++.||+++ |++.+++|
T Consensus 66 G~~V~~~~a~dy~~vieal~~g~~D~A~~~~~a~~~a~~~~~~~e~~~~~~~~dg~~~Y~S~~i~~~d----s~i~sl~d 141 (299)
T COG3221 66 GIPVEFFVATDYAAVIEALRAGQVDIAWLGPSAYVEAVDRALAGEPLAQTVQKDGSPGYYSVIIVRAD----SPIKSLED 141 (299)
T ss_pred CCceEEEecccHHHHHHHHhCCCeeEEecCchhHHHHHhhcccccceeeeeccCCCcceeEEEEEeCC----CCcchHHH
Confidence 46799999999999999999999999999999655565545 77888766566666699999999999 99999999
Q ss_pred CCCCcccCCCCCCCCCchhHHHHHHhCCCCCCCCCCchhhhhhccccccCCCCCCCCCCCCcCCCCCCCCCCCCCCccC-
Q 044324 168 FKGHKSCHGSYSTAAGWNYPVNHIKGSTPTFDSGKISDIEIASSFFSEVCAPGEFEGTGMCSGCGIENGSCHSNSLYFG- 246 (291)
Q Consensus 168 LkGKksCHtG~~~taGW~iPvg~L~~~~~~c~~~~~~~~~~~s~FFs~SCvPG~~~~~~LC~lC~g~~~~C~~~e~Y~G- 246 (291)
|||||.+++...+++|+++|+..|..++.+ .. .+||+ .-.|.|
T Consensus 142 lkgk~~af~d~~StSG~l~P~~~L~~~g~~---------d~-~~~f~--------------------------~v~~~G~ 185 (299)
T COG3221 142 LKGKRFAFGDPDSTSGYLFPLYYLAKEGGI---------DP-DKFFG--------------------------EVIFSGG 185 (299)
T ss_pred hcCCeEeccCCCcchhhHhHHHHHHHhcCC---------Ch-hhhhc--------------------------eeeccCh
Confidence 999999999999999999999999998731 11 46674 233556
Q ss_pred ccccccccccCCCcEEEEechhhhhhh
Q 044324 247 DSGAFRCLVEELGDIAFVRGDTALLYS 273 (291)
Q Consensus 247 y~GAlrCL~eg~GDVAFVk~~tV~~~~ 273 (291)
|.-++-=+.+|.-|||.+...++...-
T Consensus 186 H~~a~~aV~nG~vDva~~~~~~~~~~~ 212 (299)
T COG3221 186 HDAAVLAVANGQVDVAAVNSSARGLLK 212 (299)
T ss_pred HHHHHHHHHcCCceEEeccHHHHhhhh
Confidence 888899999999999999988875543
No 4
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=99.06 E-value=2.1e-10 Score=103.15 Aligned_cols=144 Identities=19% Similarity=0.215 Sum_probs=110.4
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccC
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDF 168 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dL 168 (291)
+..++-+...++.+-++++++|++|++.+.+.....+.+..+++||+.-....+...|.++.||+++ +++.+++||
T Consensus 28 g~~v~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~d----s~i~~l~dL 103 (243)
T PF12974_consen 28 GVPVELVPADDYAEFIEALRSGEIDLAFMGPLPYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRAD----SPITSLADL 103 (243)
T ss_dssp TSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETT----SS--SHHHH
T ss_pred CCCEEEEEcCCHHHHHHHHHcCCccEEEECcHHHHHHhhcCcEEEEEEecccCCCcceeEEEEEECC----CCCCChhhc
Confidence 3578889999999999999999999999999988777766799999987775555689999999999 889999999
Q ss_pred CCCcccCCCCCCCCCchhHHHHH-HhCCCCCCCCCCchhhhhhccccccCCCCCCCCCCCCcCCCCCCCCCCCCCCccCc
Q 044324 169 KGHKSCHGSYSTAAGWNYPVNHI-KGSTPTFDSGKISDIEIASSFFSEVCAPGEFEGTGMCSGCGIENGSCHSNSLYFGD 247 (291)
Q Consensus 169 kGKksCHtG~~~taGW~iPvg~L-~~~~~~c~~~~~~~~~~~s~FFs~SCvPG~~~~~~LC~lC~g~~~~C~~~e~Y~Gy 247 (291)
||||..++..++++||.+|...| .+.|+. . .+||... ....+
T Consensus 104 ~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~----------~-~~~~~~~--------------------------~~~~~ 146 (243)
T PF12974_consen 104 KGKRVAFPDPSSTSGYLIPRYELLREAGLD----------P-GDDFKQV--------------------------FVGSH 146 (243)
T ss_dssp GGSEEEEE-TT-TTTTHHHHHHTCCCCT------------H-HHHSSEE--------------------------EEE-H
T ss_pred CCCEEEEecCCccHHHHHHHHHHHHHcCCC----------h-hHceeEE--------------------------EeCCH
Confidence 99999999999999999999999 467752 2 4555311 11245
Q ss_pred cccccccccCCCcEEEEechhhhhhh
Q 044324 248 SGAFRCLVEELGDIAFVRGDTALLYS 273 (291)
Q Consensus 248 ~GAlrCL~eg~GDVAFVk~~tV~~~~ 273 (291)
..+++=|..|.-|+|++...+.....
T Consensus 147 ~~~~~~l~~G~~Da~~~~~~~~~~~~ 172 (243)
T PF12974_consen 147 DAVLEALLNGKADAAAIPSDAFERLE 172 (243)
T ss_dssp HHHHHHHHTTSSSEEEEEHHHHHHHH
T ss_pred HHHHHHHHcCCccEEEEechhHHHHH
Confidence 67888999999999999998887765
No 5
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=98.50 E-value=1.1e-06 Score=78.60 Aligned_cols=171 Identities=14% Similarity=0.129 Sum_probs=115.5
Q ss_pred CCceEEEecc-chHHH----HHHHHHHhhc-CCCcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEE
Q 044324 62 EATIKWCAVR-DQYED----CEYLVSIISQ-SEDYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIA 135 (291)
Q Consensus 62 ~~~vRwCv~S-~E~~K----C~~l~~~a~~-~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl 135 (291)
..++||++.. ..... -..| ...+. ..+.+++++...+..+.+++++.|++|++..+...+..+....+..++.
T Consensus 31 ~~~l~vg~~~~~~~~~~~~~~~~l-~~~l~~~~g~~v~~~~~~~~~~~~~~l~~g~~Di~~~~~~~~~~~~~~~~~~~~~ 109 (254)
T TIGR01098 31 PKELNFGILPGENASNLTRRWEPL-ADYLEKKLGIKVQLFVATDYSAVIEAMRFGRVDIAWFGPSSYVLAHYRANAEVFA 109 (254)
T ss_pred CCceEEEECCCCCHHHHHHHHHHH-HHHHHHHhCCcEEEEeCCCHHHHHHHHHcCCccEEEECcHHHHHHHHhcCCceEE
Confidence 4579999888 44222 2234 22222 2357899998889999999999999999998876654332234555554
Q ss_pred EEeec-CCCceeEEEEEEecCccccCCCCCcccCCCCcccCCCCCCCCCchhHHHHHHhCCC-CCCCCCCchhhhhhccc
Q 044324 136 NEVYC-DHAQSYDAVAVINRKVCQENGGINLMDFKGHKSCHGSYSTAAGWNYPVNHIKGSTP-TFDSGKISDIEIASSFF 213 (291)
Q Consensus 136 ~E~y~-~~~~~Y~aVAVVkK~~~~~S~~~~l~dLkGKksCHtG~~~taGW~iPvg~L~~~~~-~c~~~~~~~~~~~s~FF 213 (291)
..... ++...|+.+.||+++ +++.+++||+|||.+.++.+.+.+|.++...|.+.+. .. .+++
T Consensus 110 ~~~~~~~~~~~~~~~lvv~~d----~~i~~~~dL~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~-----------~~~~ 174 (254)
T TIGR01098 110 LTAVSTDGSPGYYSVIIVKAD----SPIKSLKDLKGKTFAFGDPASTSGYLVPRYQLKKEGGLDA-----------DGFF 174 (254)
T ss_pred eeccccCCCCceEEEEEEECC----CCCCChHHhcCCEEEeeCCCCccchHhHHHHHHHhcCCCh-----------HHhh
Confidence 43222 222356778889999 8899999999999999887777788888888876532 11 0001
Q ss_pred cccCCCCCCCCCCCCcCCCCCCCCCCCCCCccCccccccccccCCCcEEEEechhhhhhh
Q 044324 214 SEVCAPGEFEGTGMCSGCGIENGSCHSNSLYFGDSGAFRCLVEELGDIAFVRGDTALLYS 273 (291)
Q Consensus 214 s~SCvPG~~~~~~LC~lC~g~~~~C~~~e~Y~Gy~GAlrCL~eg~GDVAFVk~~tV~~~~ 273 (291)
. .-..+.++.-+++-|..|..|++|+...+...+.
T Consensus 175 ~-------------------------~i~~~~~~~~~~~al~~G~~Da~~~~~~~~~~~~ 209 (254)
T TIGR01098 175 S-------------------------EVVFSGSHDASALAVANGKVDAATNNSSAIGRLK 209 (254)
T ss_pred h-------------------------heeecCchHHHHHHHHcCCCCeEEecHHHHHHHH
Confidence 0 0001123456788999999999999988876654
No 6
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=98.28 E-value=3e-06 Score=78.11 Aligned_cols=101 Identities=19% Similarity=0.184 Sum_probs=78.5
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccC
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDF 168 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dL 168 (291)
+.+++.+...+..+++++++.|++|++..++..+..+....+.+++....+......|+.+.||+++ +++.+++||
T Consensus 58 g~~v~~~~~~~~~~~~~al~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~lvv~~d----s~i~sl~DL 133 (288)
T TIGR03431 58 GVKVKLFFATDYAGVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAFAIEVNADGSTGYYSVLIVKKD----SPIKSLEDL 133 (288)
T ss_pred CCcEEEEeCCCHHHHHHHHHcCCccEEEEChHHHHHHHHhcCCeEEEEeccCCCCCceEEEEEEeCC----CCCCcHHHh
Confidence 4688888888999999999999999999887655433233455566554443334467788889999 889999999
Q ss_pred CCCcccCCCCCCCCCchhHHHHHHh
Q 044324 169 KGHKSCHGSYSTAAGWNYPVNHIKG 193 (291)
Q Consensus 169 kGKksCHtG~~~taGW~iPvg~L~~ 193 (291)
+|||.+.++.+++.++.++...+.+
T Consensus 134 ~Gk~v~~~~~~s~~~~~~~~~~l~~ 158 (288)
T TIGR03431 134 KGKTFGFVDPNSTSGFLVPSYYLFK 158 (288)
T ss_pred CCCEEEeeCCCcchhhHHHHHHHHH
Confidence 9999999888888889888766644
No 7
>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=97.13 E-value=0.0012 Score=57.53 Aligned_cols=98 Identities=18% Similarity=0.141 Sum_probs=69.7
Q ss_pred CCcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeec-ccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcc
Q 044324 88 EDYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAF-LNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLM 166 (291)
Q Consensus 88 ~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~-~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~ 166 (291)
.+-+++=+...+..+++++|..|++|++......+..+. +...++-|+...... ....|++++ +.+.++.
T Consensus 19 ~gl~ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~-----~~~l~~~~~----s~i~~~~ 89 (216)
T PF09084_consen 19 EGLDVEIVFFGGGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSS-----PNALVVRKD----SGIKSPA 89 (216)
T ss_dssp TTEEEEEEEESSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEEC-----CEEEEEETT----TS-SSGG
T ss_pred CeEEEEEEEecChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCC-----ceEEEEecc----CCCCCHH
Confidence 356788888899999999999999999998888776555 456666555433321 224556777 7799999
Q ss_pred cCCCCcccCCCCCCCCCchhHHHHHHhCCC
Q 044324 167 DFKGHKSCHGSYSTAAGWNYPVNHIKGSTP 196 (291)
Q Consensus 167 dLkGKksCHtG~~~taGW~iPvg~L~~~~~ 196 (291)
||||||.--+. ++. ++.+-...|.+.|+
T Consensus 90 DLkGK~i~v~~-~s~-~~~~~~~~l~~~g~ 117 (216)
T PF09084_consen 90 DLKGKKIGVSR-GSS-SEYFLRALLKKNGI 117 (216)
T ss_dssp GGTTSEEEEST-TSH-HHHHHHHHHHHTTT
T ss_pred HhCCCEEEEec-Ccc-hhHHHHHHHHHhcc
Confidence 99999997766 433 44444555666665
No 8
>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=96.42 E-value=0.012 Score=54.53 Aligned_cols=99 Identities=12% Similarity=-0.016 Sum_probs=65.3
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeec-ccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCccc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAF-LNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMD 167 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~-~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~d 167 (291)
+..++-+.-.+..+.++++..|++|++.+....+..+. +...++-++...+.. .....|++++ +++.+++|
T Consensus 26 Gl~Ve~~~~~~~~~~~~al~~G~iD~~~~~~~~~~~a~~~g~~~~~v~~~~~~~----~~~~lv~~~~----s~I~s~~D 97 (300)
T TIGR01729 26 GATIDWRKFDSGADISTALASGNVPIGVIGSSPLAAAASRGVPIELFWILDNIG----KSEALVAREG----SGIEKPED 97 (300)
T ss_pred CCeeEEEecCcHHHHHHHHHcCCCCEeccCCCHHHHHHHCCCCeEEEEEeccCC----ccceEEecCC----CCCCChhH
Confidence 45778888888899999999999999987655543332 334455444333221 1235677888 88999999
Q ss_pred CCCCcccCCCCCCCCCchhHHHHHHhCCCC
Q 044324 168 FKGHKSCHGSYSTAAGWNYPVNHIKGSTPT 197 (291)
Q Consensus 168 LkGKksCHtG~~~taGW~iPvg~L~~~~~~ 197 (291)
|||||.-.+.. +++..+-+..|.+.|+.
T Consensus 98 LkGK~Igv~~~--s~~~~~l~~~L~~~Gl~ 125 (300)
T TIGR01729 98 LKGKNVAVPFV--STTHYSLLAALKHWKTD 125 (300)
T ss_pred cCCCEEEeCCC--CcHHHHHHHHHHHcCCC
Confidence 99999765432 23344445566666643
No 9
>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=96.38 E-value=0.01 Score=53.21 Aligned_cols=96 Identities=15% Similarity=0.148 Sum_probs=61.2
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeec-ccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAF-LNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDF 168 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~-~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dL 168 (291)
..++=+...+..+.++++.+|++|++.+.......+. +...++.+..-.. . ...+.|++++ +++.+++||
T Consensus 29 l~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~--~---~~~~~v~~~~----~~i~s~~dL 99 (288)
T TIGR01728 29 TKVEWVEFPAGPPALEALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSD--N---KATAIVVIKG----SPIRTVADL 99 (288)
T ss_pred ceEEEEecCCCcHHHHHHhcCCccccccCCcHHHHHHhcCCCEEEEEEecC--C---CceEEEECCC----CCCCCHHHc
Confidence 4677777777889999999999999887665432222 2234554432221 1 2345566888 779999999
Q ss_pred CCCcccCCCCCCCCCchhHHHHHHhCCC
Q 044324 169 KGHKSCHGSYSTAAGWNYPVNHIKGSTP 196 (291)
Q Consensus 169 kGKksCHtG~~~taGW~iPvg~L~~~~~ 196 (291)
+|||...+. + +....+....|.+.|+
T Consensus 100 ~Gk~i~~~~-~-~~~~~~~~~~l~~~G~ 125 (288)
T TIGR01728 100 KGKRIAVPK-G-GSGHDLLLRALLKAGL 125 (288)
T ss_pred CCCEEEecC-C-ccHHHHHHHHHHHcCC
Confidence 999987653 2 3334444445555554
No 10
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=95.91 E-value=0.03 Score=52.81 Aligned_cols=98 Identities=13% Similarity=0.030 Sum_probs=65.1
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeec-ccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCccc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAF-LNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMD 167 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~-~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~d 167 (291)
+.+++=+...+..+.++++..|++|++.+....+..+. +...++.++...+... . .+.|++++ +.+++|
T Consensus 50 Gl~Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~~~a~~~g~~~~~v~~~~~~~~--~--~~lv~~~~------I~s~~D 119 (320)
T PRK11480 50 GATVDWRKFDSGASIVRALASGDVQIGNLGSSPLAVAASQQVPIEVFLLASKLGN--S--EALVVKKT------ISKPED 119 (320)
T ss_pred CCeeEEEEeCCHHHHHHHHHCCCCCEECcCchHHHHHHHCCCCeEEEEeeccCCc--c--eEEEecCC------CCChHH
Confidence 46788888889999999999999999988777654443 3345554443333211 1 13344544 889999
Q ss_pred CCCCcccCCCCCCCCCchhHHHHHHhCCCCC
Q 044324 168 FKGHKSCHGSYSTAAGWNYPVNHIKGSTPTF 198 (291)
Q Consensus 168 LkGKksCHtG~~~taGW~iPvg~L~~~~~~c 198 (291)
|||||.-.+.. ++ ++.+....|.+.|+..
T Consensus 120 LkGK~Iav~~~-s~-~~~~l~~~L~~~Gl~~ 148 (320)
T PRK11480 120 LIGKRIAVPFI-ST-THYSLLAALKHWGIKP 148 (320)
T ss_pred cCCCEEecCCC-Cc-hHHHHHHHHHHcCCCH
Confidence 99999987643 23 3444456777777543
No 11
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=95.45 E-value=0.048 Score=50.84 Aligned_cols=78 Identities=15% Similarity=0.090 Sum_probs=54.6
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeee-cccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTA-FLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A-~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
+++=+...+..+.++++..|++|++.........+ ...+.++.|..+.+.. ...+.||+++ +++.+++||+
T Consensus 57 ~ie~~~~~~~~~~~~aL~~G~iDia~~~~~~~~~~~~~g~~~~~v~~~~~~~----~~~~lvv~~~----s~i~s~~dL~ 128 (314)
T PRK11553 57 KISWVEFPAGPQMLEALNVGSIDLGSTGDIPPIFAQAAGADLVYVGVEPPKP----KAEVILVAEN----SPIKTVADLK 128 (314)
T ss_pred eeEEEECCCcHHHHHHHHcCCCCEEccCCHHHHHHHhCCCCEEEEEEecCCC----cceEEEEeCC----CCCCCHHHhC
Confidence 55556655667999999999999998763322222 2335666665554432 2357778888 8899999999
Q ss_pred CCcccCC
Q 044324 170 GHKSCHG 176 (291)
Q Consensus 170 GKksCHt 176 (291)
||+...+
T Consensus 129 Gk~I~~~ 135 (314)
T PRK11553 129 GHKVAFQ 135 (314)
T ss_pred CCEEeec
Confidence 9998764
No 12
>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=94.94 E-value=0.12 Score=49.71 Aligned_cols=98 Identities=16% Similarity=0.136 Sum_probs=63.1
Q ss_pred CCCcceEEEecCCHHHHHHHHhccCCcEEEeCCcee-ee-ecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCC
Q 044324 87 SEDYTWKCVKRDTAQECLDSARKGEADIINLEAGLA-YT-AFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGIN 164 (291)
Q Consensus 87 ~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~i-y~-A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~ 164 (291)
..+..++-+.-.+..+.|+++..|+.|+..+..... .. +.....++-|+...+..+ ..++ || +. +.+
T Consensus 32 ~~Gl~Ve~~~f~~~~~~l~Al~aG~iD~~~~g~~~~~~~~~a~g~~~~iv~v~~~~~g---~~~i-vv-~~------i~s 100 (328)
T TIGR03427 32 KYGITIEVVQINDYVESINQYTAGKFDGCTMTNMDALTIPAAGGVDTTALIVGDFSNG---NDGI-VL-KG------GKS 100 (328)
T ss_pred HcCCeEEEEECCChHHHHHHHHcCCCCEEeecCHHHHHHHHhCCCCeEEEEEEccCCC---ceEE-EE-CC------CCC
Confidence 335678889988999999999999999987755443 22 223345555554444322 2333 44 44 689
Q ss_pred cccCCCCcccCCCCCCCCCchhHHHHHHhCCCC
Q 044324 165 LMDFKGHKSCHGSYSTAAGWNYPVNHIKGSTPT 197 (291)
Q Consensus 165 l~dLkGKksCHtG~~~taGW~iPvg~L~~~~~~ 197 (291)
++||||||...+. +++ +-.+-...|.+.|+.
T Consensus 101 vaDLKGKkIav~~-gs~-~~~ll~~aL~~aGL~ 131 (328)
T TIGR03427 101 LADLKGQKVNLVE-LSV-SHYLLARALESVGLS 131 (328)
T ss_pred HHHcCCCEEeccC-CCh-HHHHHHHHHHHcCCC
Confidence 9999999997543 333 334445667777753
No 13
>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=94.34 E-value=0.12 Score=42.67 Aligned_cols=74 Identities=16% Similarity=0.211 Sum_probs=50.7
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcE-EEEEEeecCCCceeEEEEEEecCccccCCCCCccc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMK-AIANEVYCDHAQSYDAVAVINRKVCQENGGINLMD 167 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~-PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~d 167 (291)
+.+++-+... ..++++.+++|++|++.............+... |+ + ....+.|++++ +++.+++|
T Consensus 37 g~~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~~~----~-----~~~~~~~~~~~----~~~~~~~d 102 (218)
T cd00134 37 GVKVKFVEVD-WDGLITALKSGKVDLIAAGMTITPERAKQVDFSDPY----Y-----KSGQVILVKKG----SPIKSVKD 102 (218)
T ss_pred CCeEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCHHHHhhccCcccc----e-----eccEEEEEECC----CCCCChHH
Confidence 4567777776 789999999999999987762211111111111 11 1 23457788988 77889999
Q ss_pred CCCCcccCC
Q 044324 168 FKGHKSCHG 176 (291)
Q Consensus 168 LkGKksCHt 176 (291)
|+||+.+..
T Consensus 103 l~g~~i~~~ 111 (218)
T cd00134 103 LKGKKVAVQ 111 (218)
T ss_pred hCCCEEEEE
Confidence 999999886
No 14
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=94.29 E-value=0.13 Score=42.27 Aligned_cols=75 Identities=13% Similarity=0.166 Sum_probs=50.6
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCc-EEEEEEeecCCCceeEEEEEEecCccccCCCCCccc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSM-KAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMD 167 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~d 167 (291)
+..++.+.. +..++++.+++|++|++.............+.. .|+. ....+.|++++ +++.+++|
T Consensus 38 g~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~----~~~~~~~d 103 (219)
T smart00062 38 GLKVEFVEV-SFDNLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYY---------KSGQVILVRKD----SPIKSLED 103 (219)
T ss_pred CCeEEEEec-cHHHHHHHHHCCcccEEeccccCCHHHHhheeecccee---------eceeEEEEecC----CCCCChHH
Confidence 467888888 889999999999999998754321111011111 1221 12346778888 77899999
Q ss_pred CCCCcccCCC
Q 044324 168 FKGHKSCHGS 177 (291)
Q Consensus 168 LkGKksCHtG 177 (291)
|+||+.+...
T Consensus 104 L~g~~i~~~~ 113 (219)
T smart00062 104 LKGKKVAVVA 113 (219)
T ss_pred hCCCEEEEec
Confidence 9999988654
No 15
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=94.08 E-value=0.17 Score=47.17 Aligned_cols=103 Identities=16% Similarity=0.053 Sum_probs=69.4
Q ss_pred CCc-ceEEEecCCHHHHHHHHhccCCcEEEeCCceee--eec-ccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCC
Q 044324 88 EDY-TWKCVKRDTAQECLDSARKGEADIINLEAGLAY--TAF-LNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGI 163 (291)
Q Consensus 88 ~~p-~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy--~A~-~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~ 163 (291)
.+. .++=+...+-.+.++.+..|.+|+.....++.+ .++ ....++-+...... ..-...+++++ +++.
T Consensus 58 ~Gl~~v~~~~~~~~~~~~~~l~~G~~D~a~~~~~~~~~~~~~~~g~pv~~va~~~~~----~~~~~i~~~~~----~~i~ 129 (335)
T COG0715 58 EGLDDVELVEFTGGAPVLEALAAGALDFAVYYTGDTPLIAAGAAGAPVKVVAALVQN----GNGIALLVLKD----SGIK 129 (335)
T ss_pred hCCCceEEEEcCCChHHHHHHhcCCcCccccccCchHHHHhhccCCCeEEeeecccC----CceeEEEeccC----CCcc
Confidence 345 699999999999999999999999976555544 333 11233333322222 11334555666 7789
Q ss_pred CcccCCCCcccCCCCCCCCCchhHHHHHHhCCCCCC
Q 044324 164 NLMDFKGHKSCHGSYSTAAGWNYPVNHIKGSTPTFD 199 (291)
Q Consensus 164 ~l~dLkGKksCHtG~~~taGW~iPvg~L~~~~~~c~ 199 (291)
+++||||||...+..+++. ..+-...|.+.|+..+
T Consensus 130 ~~adlkGk~vg~~~~~~~~-~~~l~~~L~~~Gl~~~ 164 (335)
T COG0715 130 SVADLKGKKVGVPFGGSTS-DFLLRYALAKAGLDPD 164 (335)
T ss_pred cccCCCCceEEEeCCCchH-HHHHHHHHHHcCCCcc
Confidence 9999999999999987643 3333566777776543
No 16
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=93.69 E-value=0.1 Score=50.56 Aligned_cols=115 Identities=18% Similarity=0.186 Sum_probs=73.0
Q ss_pred CCCCceEEEecc-------chHHHHHHHHHHhhcCCCcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccC---
Q 044324 60 GSEATIKWCAVR-------DQYEDCEYLVSIISQSEDYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNF--- 129 (291)
Q Consensus 60 ~~~~~vRwCv~S-------~E~~KC~~l~~~a~~~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~--- 129 (291)
..+..|+|=|=+ .-..-|+.+ ... ..+.+++=+......+=|+.|.+|++|+..+-..-.|.|.+--
T Consensus 23 ~~~~~itigTG~~~G~YY~ig~~ia~~~-~~~--~~~i~~~v~~tggSv~Nl~~i~~Ge~d~alvq~d~a~~ay~G~g~f 99 (321)
T COG2358 23 AEPKFITIGTGSTGGVYYPIGGGLAQLL-NKD--EKGIECSVVPTGGSVENLKLLASGEADLALVQSDVAYEAYNGTGSF 99 (321)
T ss_pred cCceEEEEeecCCCceeeehHHHHHHHH-hcc--CCCeEEEEeeccchHHHHHhHhcCccchhhhhHHHHHHHHhCcccc
Confidence 345677774433 345567666 321 1123444455557788899999999999998877555443211
Q ss_pred -------CcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCCCCcccCCCCCCCCCchhH
Q 044324 130 -------SMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFKGHKSCHGSYSTAAGWNYP 187 (291)
Q Consensus 130 -------~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLkGKksCHtG~~~taGW~iP 187 (291)
+|+-+. -.|. . +.-.|+|++ +.+++|.||+|||.--.-.++....+..
T Consensus 100 ~~~~~~~~lr~v~-~lyp----e-~~~vv~r~d----~~Ikti~DL~GKrV~iG~~gSgt~~~a~ 154 (321)
T COG2358 100 EGKGKDENLRAVA-ALYP----E-PFHVVTRKD----AGIKTIADLKGKRVAIGPPGSGTEATAR 154 (321)
T ss_pred cccccccchhhhe-eccc----c-eEEEEEecC----CCcceehhcCCCEEeecCCCCccHHHHH
Confidence 333221 1221 1 445677899 8899999999999988777776655553
No 17
>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=91.98 E-value=0.67 Score=42.69 Aligned_cols=120 Identities=15% Similarity=0.201 Sum_probs=70.3
Q ss_pred CCCceEEEecc-chH--HHHHHHHHHhhcCC-C-cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeec---cc----
Q 044324 61 SEATIKWCAVR-DQY--EDCEYLVSIISQSE-D-YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAF---LN---- 128 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~--~KC~~l~~~a~~~~-~-p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~---~~---- 128 (291)
...++|+.+.+ ... .--..| ...+... . ..++=+...+..+-++++++|++|++.+.....+.+. ..
T Consensus 28 ~~~~l~Ig~~~~~~~~~~~~~~l-a~~~~~~~~~i~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~ 106 (320)
T TIGR02122 28 EPTFVTIGTGGTGGVYYPIGGAI-AQLINKKSGKLRVRVQSTGGSVENVNLLEAGEADLAIVQSDVAYYAYEGDGEFEFE 106 (320)
T ss_pred CCceEEEEeCCCCCChHHHHHHH-HHHHhccCCCeeEEEEeCcchHHHHHHHhCCCCcEEEEcchhHHHHhcCcCccccC
Confidence 34589999876 332 223344 3333232 2 4555565567788999999999999988755432211 11
Q ss_pred ---CCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCCCCcccCCCCCCCCCchhHHHHHHh
Q 044324 129 ---FSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFKGHKSCHGSYSTAAGWNYPVNHIKG 193 (291)
Q Consensus 129 ---~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLkGKksCHtG~~~taGW~iPvg~L~~ 193 (291)
-+++++. ..+ ....+.||+++ +++.+++||+||+...... +++...-+..+++
T Consensus 107 ~~~~~~~~v~-~~~-----~~~~~lvv~~d----~~i~sl~dL~gk~v~~~~~--~s~~~~~~~~~l~ 162 (320)
T TIGR02122 107 GPVEKLRALA-SLY-----PEYIQIVVRKD----SGIKTVADLKGKRVAVGAP--GSGTELNARAVLK 162 (320)
T ss_pred CCCccHHhHH-Hhc-----cccEEEEEECC----CCCCcHHHcCCCEEecCCC--CcchHHHHHHHHH
Confidence 1122111 111 12345778888 8889999999999877533 2344444444443
No 18
>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=87.02 E-value=7.5 Score=31.95 Aligned_cols=120 Identities=13% Similarity=0.058 Sum_probs=68.1
Q ss_pred CCCceEEEecc-chHHHHHHHHHHhhcCCCcceEEEe-cCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEe
Q 044324 61 SEATIKWCAVR-DQYEDCEYLVSIISQSEDYTWKCVK-RDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEV 138 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~~KC~~l~~~a~~~~~p~l~CV~-~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~ 138 (291)
..+++|+.+.. ....-=..+ -..+....|.+.-.. ..+..+.++++++|++|++...... ....+..+++..|.
T Consensus 4 ~~~~l~Ig~~~~~~~~~l~~~-l~~~~~~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~~~~l~~~~ 79 (209)
T PF03466_consen 4 ERGTLRIGASPSFASSLLPPL-LAEFRERHPNIRIEIREGDSDELIEALRSGELDLAITFGPP---PPPGLESEPLGEEP 79 (209)
T ss_dssp SEEEEEEEEEHHHHHHTHHHH-HHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSS---SSTTEEEEEEEEEE
T ss_pred cceEEEEEEEhHHHHHHHHHH-HHHHHHHCCCcEEEEEeccchhhhHHHhcccccEEEEEeec---ccccccccccccee
Confidence 34578888876 332221222 112222235544432 3466899999999999999886665 11223345565333
Q ss_pred ecCCCceeEEEEEEecCc-cccCCCCCcccCCCCcccCCCCCCCCCchhHHHH-HHhCC
Q 044324 139 YCDHAQSYDAVAVINRKV-CQENGGINLMDFKGHKSCHGSYSTAAGWNYPVNH-IKGST 195 (291)
Q Consensus 139 y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dLkGKksCHtG~~~taGW~iPvg~-L~~~~ 195 (291)
+ |.|+.++. .+.....+++||++-+......+.. |...+.. +.+.+
T Consensus 80 ~---------~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~--~~~~~~~~~~~~~ 127 (209)
T PF03466_consen 80 L---------VLVVSPDHPLAQKKPITLEDLADYPLILLSPGSP--YRDQLDRWLREHG 127 (209)
T ss_dssp E---------EEEEETTSGGGTTSSSSGGGGTTSEEEEESTTTS--HHHHHHHHHHHTT
T ss_pred e---------eeeeeccccccccccchhhhhhhccccccccccc--ccccccccccccc
Confidence 3 77777772 1111246899999988888644333 4444443 34444
No 19
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=86.86 E-value=2.2 Score=38.53 Aligned_cols=72 Identities=11% Similarity=0.086 Sum_probs=42.1
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeec-ccCCc-EEEEEEeecCCCceeEEEEEEecCccccCCCC-Cc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAF-LNFSM-KAIANEVYCDHAQSYDAVAVINRKVCQENGGI-NL 165 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~-~~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~-~l 165 (291)
+.+++=+. .+-.+++++++.|++|++...-..- ..+ +.+.. .|++.+ ..+.|++++ +.+. ++
T Consensus 64 g~~~~~~~-~~~~~~~~~l~~g~~Di~~~~~~~t-~eR~~~~~fs~p~~~~---------~~~~~~~~~----~~~~~~~ 128 (260)
T PRK15010 64 QVKCTWVA-SDFDALIPSLKAKKIDAIISSLSIT-DKRQQEIAFSDKLYAA---------DSRLIAAKG----SPIQPTL 128 (260)
T ss_pred CCceEEEe-CCHHHHHHHHHCCCCCEEEecCcCC-HHHHhhcccccceEec---------cEEEEEECC----CCCCCCh
Confidence 33444444 4678999999999999876422111 011 11222 244311 235667777 5443 79
Q ss_pred ccCCCCcccC
Q 044324 166 MDFKGHKSCH 175 (291)
Q Consensus 166 ~dLkGKksCH 175 (291)
+||+||+.+-
T Consensus 129 ~dl~g~~Igv 138 (260)
T PRK15010 129 DSLKGKHVGV 138 (260)
T ss_pred hHcCCCEEEE
Confidence 9999999766
No 20
>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=82.81 E-value=1.9 Score=36.47 Aligned_cols=79 Identities=19% Similarity=0.108 Sum_probs=43.2
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcE-EEEEEeecCCCceeEEEEEEecCcc-ccCCCCCcc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMK-AIANEVYCDHAQSYDAVAVINRKVC-QENGGINLM 166 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~-PIl~E~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~ 166 (291)
+..++=+.. +..++++.+++|++|++...-..-..-.+.+... |++ ....+.|++++.. .-..+.++.
T Consensus 37 g~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~~~s~p~~---------~~~~~~~~~~~~~~~~~~~~~~~ 106 (225)
T PF00497_consen 37 GIKIEFVPM-PWSRLLEMLENGKADIIIGGLSITPERAKKFDFSDPYY---------SSPYVLVVRKGDAPPIKTIKSLD 106 (225)
T ss_dssp TCEEEEEEE-EGGGHHHHHHTTSSSEEESSEB-BHHHHTTEEEESESE---------EEEEEEEEETTSTCSTSSHSSGG
T ss_pred ccccceeec-cccccccccccccccccccccccccccccccccccccc---------chhheeeeccccccccccccchh
Confidence 335666665 7899999999999999873211110000111111 222 2344677775500 001134566
Q ss_pred cCCCCcccCCC
Q 044324 167 DFKGHKSCHGS 177 (291)
Q Consensus 167 dLkGKksCHtG 177 (291)
||+|+|.+...
T Consensus 107 dl~~~~i~~~~ 117 (225)
T PF00497_consen 107 DLKGKRIGVVR 117 (225)
T ss_dssp GGTTSEEEEET
T ss_pred hhcCccccccc
Confidence 99999988643
No 21
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=82.73 E-value=3.3 Score=38.86 Aligned_cols=75 Identities=8% Similarity=0.032 Sum_probs=49.8
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
..++-+...+ .+-+..+..|++|++...-..+...+ -.+.-+..-.|. .+..+.+|+++ +++.+++||+
T Consensus 44 ~~ie~~~~~~-~~i~~~L~sG~vDlgi~g~~~~~er~--~~v~~~~~l~~~----~~~lvvvvp~~----~~i~sl~DL~ 112 (287)
T PRK00489 44 NPIEVLFLRP-DDIPGYVADGVVDLGITGEDLLEESG--ADVEELLDLGFG----KCRLVLAVPED----SDWQGVEDLA 112 (287)
T ss_pred CCEEEEEECc-HHHHHHHHcCCCCEEEcchHHHHHCC--CCceEeeeccCC----ceEEEEEEECC----CCCCChHHhC
Confidence 4677777765 79999999999999987543332221 122222211121 34667788888 7789999999
Q ss_pred CCcccC
Q 044324 170 GHKSCH 175 (291)
Q Consensus 170 GKksCH 175 (291)
||+...
T Consensus 113 Gk~ia~ 118 (287)
T PRK00489 113 GKRIAT 118 (287)
T ss_pred CCEEEE
Confidence 996554
No 22
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=82.26 E-value=3.4 Score=36.77 Aligned_cols=72 Identities=8% Similarity=0.021 Sum_probs=42.6
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeec--ccCCc-EEEEEEeecCCCceeEEEEEEecCccccC-CCCC
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAF--LNFSM-KAIANEVYCDHAQSYDAVAVINRKVCQEN-GGIN 164 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~--~~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S-~~~~ 164 (291)
+.+++=+. .+..++++.+++|++|++...-. +... +.+.. .|++. ..+ +.+++++ + .+.+
T Consensus 62 g~~~~~~~-~~~~~~~~~l~~G~vDi~~~~~~--~t~~R~~~~~fs~p~~~--------~~~-~~~~~~~----~~~~~~ 125 (247)
T PRK09495 62 KLDYTLKP-MDFSGIIPALQTKNVDLALAGIT--ITDERKKAIDFSDGYYK--------SGL-LVMVKAN----NNDIKS 125 (247)
T ss_pred CCceEEEe-CCHHHHHHHHhCCCcCEEEecCc--cCHHHHhhccccchhee--------cce-EEEEECC----CCCCCC
Confidence 33444444 46889999999999999753321 1111 11111 12210 112 3356766 4 3789
Q ss_pred cccCCCCcccCC
Q 044324 165 LMDFKGHKSCHG 176 (291)
Q Consensus 165 l~dLkGKksCHt 176 (291)
++||+||+.|..
T Consensus 126 ~~dL~g~~I~v~ 137 (247)
T PRK09495 126 VKDLDGKVVAVK 137 (247)
T ss_pred hHHhCCCEEEEe
Confidence 999999999864
No 23
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=81.56 E-value=3.8 Score=36.93 Aligned_cols=73 Identities=11% Similarity=0.136 Sum_probs=42.0
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCc-EEEEEEeecCCCceeEEEEEEecCccccCCCC-Ccc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSM-KAIANEVYCDHAQSYDAVAVINRKVCQENGGI-NLM 166 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~-~l~ 166 (291)
+.+++=+. .+-..+++++++|++|++...-..--.-.+.+.. .|++ .+..+.+++++ +++. +++
T Consensus 64 g~~i~~~~-~pw~~~~~~l~~g~~D~~~~~~~~t~eR~~~~~fs~p~~---------~~~~~~~~~~~----~~~~~~~~ 129 (259)
T PRK15437 64 NTQCTFVE-NPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLY---------AADSRLVVAKN----SDIQPTVE 129 (259)
T ss_pred CCceEEEe-CCHHHHHHHHHCCCCCEEEecCCCCHHHhhhccccchhh---------cCceEEEEECC----CCCCCChH
Confidence 33455444 4689999999999999775322110000011222 2332 12335567777 5444 799
Q ss_pred cCCCCcccC
Q 044324 167 DFKGHKSCH 175 (291)
Q Consensus 167 dLkGKksCH 175 (291)
||+|++.+-
T Consensus 130 dl~g~~Igv 138 (259)
T PRK15437 130 SLKGKRVGV 138 (259)
T ss_pred HhCCCEEEE
Confidence 999998765
No 24
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=81.24 E-value=3.6 Score=37.12 Aligned_cols=103 Identities=17% Similarity=0.093 Sum_probs=62.0
Q ss_pred CCcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccC------CcEEEEEEeecCCCceeEEEEEEecCccccCC
Q 044324 88 EDYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNF------SMKAIANEVYCDHAQSYDAVAVINRKVCQENG 161 (291)
Q Consensus 88 ~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~------~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~ 161 (291)
.+..++=+...+-.+=++++..|++|+..+ ...+..+.... .++-+. -... + -...||+++....+.
T Consensus 33 ~G~~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~~~~~~~~~~~~-~~~~-~----g~~lvv~~~~~~~~~ 105 (252)
T PF13379_consen 33 EGLDVEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGAGGPDVDIVVLA-GLSQ-N----GNALVVRNDLKDASD 105 (252)
T ss_dssp TTSCEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTTTT----EEEEE-ECSB-S----SEEEEECGGGTTCST
T ss_pred cCCEEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCCCCcccceEEee-ccCC-C----ceEEEEcCccccCCC
Confidence 456688888889999999999999999999 55443333211 233222 1111 1 124566653111124
Q ss_pred CCCcccC-------CCCcccCCCCCCCCCchhHHHHHHhCCCCC
Q 044324 162 GINLMDF-------KGHKSCHGSYSTAAGWNYPVNHIKGSTPTF 198 (291)
Q Consensus 162 ~~~l~dL-------kGKksCHtG~~~taGW~iPvg~L~~~~~~c 198 (291)
+.+++|| ||||.--+..+++ .+.+--..|.+.|+..
T Consensus 106 ~~~~~dl~~~~~~~kGk~i~~~~~gs~-~~~~l~~~l~~~Gl~~ 148 (252)
T PF13379_consen 106 IKSLADLIKKRKAQKGKKIAVPFPGST-HDMLLRYLLKKAGLDP 148 (252)
T ss_dssp TCCGHHHHHTCCSCSTEEEEESSTTSH-HHHHHHHHHHHTT--T
T ss_pred ccCHHHHHhhhcccCCcEEEEcCCCCH-HHHHHHHHHHhCCCCc
Confidence 8999999 9999887766654 3343334555667644
No 25
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=80.86 E-value=3.9 Score=36.00 Aligned_cols=72 Identities=13% Similarity=0.090 Sum_probs=43.2
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeec-ccCCc-EEEEEEeecCCCceeEEEEEEecCccccCC-CCCc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAF-LNFSM-KAIANEVYCDHAQSYDAVAVINRKVCQENG-GINL 165 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~-~~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~-~~~l 165 (291)
+.+++=+. .+..+++..+++|++|++...-. .-..+ ..+.+ .|+. ....+.|++++ ++ ..++
T Consensus 62 g~~~~~~~-~~~~~~~~~l~~G~~D~~~~~~~-~~~~r~~~~~~s~p~~---------~~~~~~~~~~~----~~~~~~~ 126 (250)
T TIGR01096 62 KAKCKFVE-QNFDGLIPSLKAKKVDAIMATMS-ITPKRQKQIDFSDPYY---------ATGQGFVVKKG----SDLAKTL 126 (250)
T ss_pred CCeEEEEe-CCHHHHHHHHhCCCcCEEEecCc-cCHHHhhccccccchh---------cCCeEEEEECC----CCcCCCh
Confidence 34566555 57899999999999999864111 00111 11221 1221 11335566776 43 3578
Q ss_pred ccCCCCcccC
Q 044324 166 MDFKGHKSCH 175 (291)
Q Consensus 166 ~dLkGKksCH 175 (291)
+||+|++.|.
T Consensus 127 ~dl~g~~i~~ 136 (250)
T TIGR01096 127 EDLDGKTVGV 136 (250)
T ss_pred HHcCCCEEEE
Confidence 9999999986
No 26
>PRK11260 cystine transporter subunit; Provisional
Probab=80.85 E-value=4.5 Score=36.58 Aligned_cols=75 Identities=11% Similarity=0.021 Sum_probs=42.7
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCc-EEEEEEeecCCCceeEEEEEEecCccccCCCCCccc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSM-KAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMD 167 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~d 167 (291)
+.+++=+.. +..++++.+++|++|++......-......+.. .|++. ...+.|++++.. ..+.+++|
T Consensus 79 g~~~e~~~~-~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~~~fs~p~~~---------~~~~~~~~~~~~--~~~~~~~d 146 (266)
T PRK11260 79 GVKASLKPT-KWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTV---------SGIQALVKKGNE--GTIKTAAD 146 (266)
T ss_pred CCeEEEEeC-CHHHHHHHHhcCCCCEEEeccccCHHHHhccccCCceee---------cceEEEEEcCCc--CCCCCHHH
Confidence 335555554 678999999999999986321110000011221 23321 112556676511 23678999
Q ss_pred CCCCcccC
Q 044324 168 FKGHKSCH 175 (291)
Q Consensus 168 LkGKksCH 175 (291)
|+||+.+-
T Consensus 147 L~g~~Igv 154 (266)
T PRK11260 147 LKGKKVGV 154 (266)
T ss_pred cCCCEEEE
Confidence 99998774
No 27
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=80.81 E-value=2.1 Score=39.09 Aligned_cols=71 Identities=13% Similarity=0.032 Sum_probs=40.3
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCc-EEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSM-KAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
+++-+.- +....+.++++|++|++.-.-..--.-...+.. .|++ ....+.|++++ +++.+++||+
T Consensus 82 ~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~t~eR~~~~~fs~py~---------~~~~~lvv~~~----~~~~s~~dL~ 147 (259)
T PRK11917 82 KIKLVAV-NAKTRGPLLDNGSVDAVIATFTITPERKRIYNFSEPYY---------QDAIGLLVLKE----KNYKSLADMK 147 (259)
T ss_pred cEEEEEc-ChhhHHHHHHCCCccEEEecccCChhhhheeeeccCce---------eeceEEEEECC----CCCCCHHHhC
Confidence 3444333 345667899999999985321100000011111 1221 11236677887 6688999999
Q ss_pred CCcccC
Q 044324 170 GHKSCH 175 (291)
Q Consensus 170 GKksCH 175 (291)
||+.+-
T Consensus 148 g~~V~v 153 (259)
T PRK11917 148 GANIGV 153 (259)
T ss_pred CCeEEE
Confidence 999876
No 28
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=80.19 E-value=13 Score=34.75 Aligned_cols=116 Identities=9% Similarity=0.031 Sum_probs=68.5
Q ss_pred ceEEEecc-chHHHHHHHHHHhh-cCCCcceEEEecCCHHHHHHHHhccCCcEEEeCCceee---eecccCCcEEEEEEe
Q 044324 64 TIKWCAVR-DQYEDCEYLVSIIS-QSEDYTWKCVKRDTAQECLDSARKGEADIINLEAGLAY---TAFLNFSMKAIANEV 138 (291)
Q Consensus 64 ~vRwCv~S-~E~~KC~~l~~~a~-~~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy---~A~~~~~L~PIl~E~ 138 (291)
+||+=++. .+... -.+..... ...+.+++-+.-.+..+.++++.+|+.|+..+.-...+ ...+.++|+.+.
T Consensus 32 ~I~IG~~~~~~~~~-~~~~~~~l~~~~G~~Vel~~f~~~~~~~~ALa~GdID~~~~qh~~~l~~~~~~~g~~l~~~~--- 107 (271)
T PRK11063 32 HIKVGVIVGAEQQV-AEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLVAVG--- 107 (271)
T ss_pred cEEEEeCCCChHHH-HHHHHHHHHHhcCCeEEEEEecCcHHHHHHHHcCCcceecccCHHHHHHHHHHcCCcEEEEe---
Confidence 58888876 55433 22212222 22367899999889999999999999999765444332 122345555442
Q ss_pred ecCCCceeEEEEEEecCccccCCCCCcccCC-CCcccCCCCCCCCCchhHHHHHHhCC
Q 044324 139 YCDHAQSYDAVAVINRKVCQENGGINLMDFK-GHKSCHGSYSTAAGWNYPVNHIKGST 195 (291)
Q Consensus 139 y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk-GKksCHtG~~~taGW~iPvg~L~~~~ 195 (291)
..++|-..--+ ..+.+++||+ |||.--+.-..+.+=. +..|.+.|
T Consensus 108 ------~~~vvp~~~ys----~~i~si~DL~~Gk~IAip~d~~n~~r~--L~lL~~~G 153 (271)
T PRK11063 108 ------NTFVYPIAGYS----KKIKSLDELQDGSQVAVPNDPTNLGRS--LLLLQKVG 153 (271)
T ss_pred ------EEEEEEeeccc----cCCCCHHHhcCCCEEEecCCCccHHHH--HHHHHHCC
Confidence 11222121122 3489999998 9999887643332222 22355655
No 29
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=79.30 E-value=3.9 Score=38.16 Aligned_cols=98 Identities=12% Similarity=0.091 Sum_probs=61.9
Q ss_pred ceEEEecc---chHHHHHHHHHHhhcCCCcceEEEecCCHHHHHHHHhccCCcEEEeCCceee---eecccCCcEEEEEE
Q 044324 64 TIKWCAVR---DQYEDCEYLVSIISQSEDYTWKCVKRDTAQECLDSARKGEADIINLEAGLAY---TAFLNFSMKAIANE 137 (291)
Q Consensus 64 ~vRwCv~S---~E~~KC~~l~~~a~~~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy---~A~~~~~L~PIl~E 137 (291)
+||+=+.. .++-+-- . ..++...+..++-+.-.+..+.++++..|+.|+..+.-.... ...+.+.|+++..
T Consensus 19 ~l~vG~~~~~~~~~~~~~-~-~~~~~~~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~q~~~~l~~~~~~~g~~lv~v~~- 95 (258)
T TIGR00363 19 HIKVGVISGAEQQVAEVA-A-KVAKEKYGLDVELVEFNDYALPNEAVSKGDLDANAFQHKPYLDQDAKAKGYKLVAVGN- 95 (258)
T ss_pred cEEEEeCCCChHHHHHHH-H-HHHHHhcCCEEEEEEeCCcHHHHHHHHcCCCCeEecCCHHHHHHHHHhCCCcEEEEee-
Confidence 68887754 2222211 1 222333467899999999999999999999999876555422 2234566665541
Q ss_pred eecCCCceeEEEEEEecCccccCCCCCcccCC-CCcccCC
Q 044324 138 VYCDHAQSYDAVAVINRKVCQENGGINLMDFK-GHKSCHG 176 (291)
Q Consensus 138 ~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk-GKksCHt 176 (291)
.+.+-+..-+ +.+.+++||| |||.--+
T Consensus 96 --------~~~~p~~~ys----~~~~sl~dlk~G~~IAip 123 (258)
T TIGR00363 96 --------TFVYPLAGYS----KKIKNVNELQDGAKVAVP 123 (258)
T ss_pred --------eEEecccccC----cCCCCHHHcCCCCEEEEe
Confidence 1112122223 4589999997 9999875
No 30
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=78.03 E-value=5.9 Score=39.88 Aligned_cols=74 Identities=22% Similarity=0.205 Sum_probs=46.2
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecc--cCCc-EEEEEEeecCCCceeEEEEEEecCccccCCCCCc
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFL--NFSM-KAIANEVYCDHAQSYDAVAVINRKVCQENGGINL 165 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~--~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l 165 (291)
+.+++-+...+..+.+.++++|++|++...-. +...+ .+.. .|++ ....+.|++++. ..+.++
T Consensus 79 Gv~~e~v~~~~~~~ll~aL~~G~iDi~~~~lt--~T~eR~~~~~FS~Py~---------~~~~~lv~r~~~---~~i~~l 144 (482)
T PRK10859 79 GVKLEIKVRDNISQLFDALDKGKADLAAAGLT--YTPERLKQFRFGPPYY---------SVSQQLVYRKGQ---PRPRSL 144 (482)
T ss_pred CCcEEEEecCCHHHHHHHHhCCCCCEEeccCc--CChhhhccCcccCCce---------eeeEEEEEeCCC---CCCCCH
Confidence 45677777788999999999999998753211 11111 1111 1221 123456777761 236789
Q ss_pred ccCCCCcccCC
Q 044324 166 MDFKGHKSCHG 176 (291)
Q Consensus 166 ~dLkGKksCHt 176 (291)
+||+||+....
T Consensus 145 ~dL~Gk~I~V~ 155 (482)
T PRK10859 145 GDLKGGTLTVA 155 (482)
T ss_pred HHhCCCeEEEE
Confidence 99999997763
No 31
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=77.22 E-value=4.8 Score=37.80 Aligned_cols=69 Identities=13% Similarity=0.048 Sum_probs=40.7
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecc--cCCcE-EEEEEeecCCCceeEEEEEEecCccccCCCCCccc
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFL--NFSMK-AIANEVYCDHAQSYDAVAVINRKVCQENGGINLMD 167 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~--~~~L~-PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~d 167 (291)
+++=+.. +..+-+..++.|++|++.-.-. +...+ .+... |++.. ..+.|++++ +.+.+++|
T Consensus 87 ~~~~v~~-~~~~~i~~L~~G~~Di~~~~~~--~t~eR~~~~~fS~Py~~~---------~~~lv~r~~----~~i~sl~d 150 (302)
T PRK10797 87 QVKLIPI-TSQNRIPLLQNGTFDFECGSTT--NNLERQKQAAFSDTIFVV---------GTRLLTKKG----GDIKDFAD 150 (302)
T ss_pred eEEEEEc-ChHhHHHHHHCCCccEEecCCc--cCcchhhcceecccEeec---------cEEEEEECC----CCCCChHH
Confidence 3444443 3456799999999999653211 11111 12221 33211 234567887 66889999
Q ss_pred CCCCcccC
Q 044324 168 FKGHKSCH 175 (291)
Q Consensus 168 LkGKksCH 175 (291)
|+||+.+-
T Consensus 151 L~Gk~V~v 158 (302)
T PRK10797 151 LKGKAVVV 158 (302)
T ss_pred cCCCEEEE
Confidence 99999775
No 32
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=76.41 E-value=4.2 Score=38.67 Aligned_cols=98 Identities=12% Similarity=0.073 Sum_probs=66.9
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeec-ccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAF-LNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~-~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
.+.=.+-.|-.+-++++..|..+|..+++.-+-.|. ++--++.++.-..- + ---.-|||++ |+|...+||.
T Consensus 58 tiDWRkFdSG~~vv~AlASGdvqiG~iGSsplaaAaSr~vpie~f~~~~~i-g---~sEALVvr~g----sgI~kpeDL~ 129 (334)
T COG4521 58 TIDWRKFDSGASIVRALASGDVQIGNIGSSPLAAAASRQVPIEVFLLASQI-G---NSEALVVRKG----SGIEKPEDLI 129 (334)
T ss_pred ccchhhcCchhHHHHHHhcCCccccccCCchhhHHhhcCCceEEeehhhhc-C---ccceeeeecC----CCcCChHHhc
Confidence 444455567789999999999999999988765553 44444433311111 1 1115688999 8899999999
Q ss_pred CCcccCCCCCCCCCchhHHHHHHhCCCCC
Q 044324 170 GHKSCHGSYSTAAGWNYPVNHIKGSTPTF 198 (291)
Q Consensus 170 GKksCHtG~~~taGW~iPvg~L~~~~~~c 198 (291)
|||..-|=+ +|+.|.+ +..|..-+++.
T Consensus 130 GK~iavPFv-STtHysL-LaaLkhw~idp 156 (334)
T COG4521 130 GKRIAVPFV-STTHYSL-LAALKHWGIDP 156 (334)
T ss_pred cCeecccee-ehhHHHH-HHHHHHcCCCc
Confidence 999998876 5667776 55665555433
No 33
>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=75.45 E-value=18 Score=28.98 Aligned_cols=76 Identities=14% Similarity=0.118 Sum_probs=42.9
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCcc-ccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVC-QENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~dLk 169 (291)
.++.... +..+.++.+.+|++|++....... ....+...++..+ ..+.|+.++.- +.....+++||.
T Consensus 30 ~i~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~~--~~~~~~~~~l~~~---------~~~~~~~~~~~l~~~~~~~~~~L~ 97 (194)
T cd08436 30 DIRLRQA-GSDDLLAAVREGRLDLAFVGLPER--RPPGLASRELARE---------PLVAVVAPDHPLAGRRRVALADLA 97 (194)
T ss_pred EEEEecC-CHHHHHHHHHcCCccEEEEecCCC--CCCCcEEEEeecc---------eEEEEecCCCcccCCCccCHHHHh
Confidence 5555543 578899999999999998654320 1111222333211 22455666510 001135788999
Q ss_pred CCcccCCCC
Q 044324 170 GHKSCHGSY 178 (291)
Q Consensus 170 GKksCHtG~ 178 (291)
+.+......
T Consensus 98 ~~~~i~~~~ 106 (194)
T cd08436 98 DEPFVDFPP 106 (194)
T ss_pred CCCeEEecC
Confidence 988776443
No 34
>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=75.04 E-value=31 Score=27.61 Aligned_cols=101 Identities=13% Similarity=0.039 Sum_probs=53.5
Q ss_pred eEEEecc-chHHHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecC
Q 044324 65 IKWCAVR-DQYEDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCD 141 (291)
Q Consensus 65 vRwCv~S-~E~~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~ 141 (291)
+|+++.. ....--..+ -..+....| .++.... +..+.++.+.+|++|++....... ...+.-.++..|
T Consensus 2 l~Ig~~~~~~~~~l~~~-l~~~~~~~p~i~i~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~~~~l~~~---- 72 (197)
T cd08414 2 LRIGFVGSALYGLLPRL-LRRFRARYPDVELELREM-TTAEQLEALRAGRLDVGFVRPPPD---PPGLASRPLLRE---- 72 (197)
T ss_pred EEEEeeHHHHHHHHHHH-HHHHHHHCCCcEEEEecC-ChHHHHHHHHcCCccEEEEcCCCC---CCCeeEEEEeec----
Confidence 5565555 333333333 223333234 4554443 678999999999999998654321 112233344322
Q ss_pred CCceeEEEEEEecCcc-ccCCCCCcccCCCCcccCCCCC
Q 044324 142 HAQSYDAVAVINRKVC-QENGGINLMDFKGHKSCHGSYS 179 (291)
Q Consensus 142 ~~~~Y~aVAVVkK~~~-~~S~~~~l~dLkGKksCHtG~~ 179 (291)
..+.|+.++.- +.....+++||...+......+
T Consensus 73 -----~~~~v~~~~~~l~~~~~~~~~~L~~~~~i~~~~~ 106 (197)
T cd08414 73 -----PLVVALPADHPLAARESVSLADLADEPFVLFPRE 106 (197)
T ss_pred -----cEEEEecCCCccccCCccCHHHhccCCEEEecCC
Confidence 23566666510 0011357788988777765443
No 35
>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=68.16 E-value=36 Score=26.65 Aligned_cols=75 Identities=15% Similarity=0.108 Sum_probs=43.0
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCcccc-CCCCCcccC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQE-NGGINLMDF 168 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~-S~~~~l~dL 168 (291)
..++.... +..+.++.+.+|++|++...... ....+..+++..+ ..+.|+.++.-.. ....+++||
T Consensus 29 i~i~~~~~-~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~~~~l~~~---------~~~~~~~~~~~~~~~~~~~~~~l 95 (197)
T cd05466 29 VELSLVEG-GSSELLEALLEGELDLAIVALPV---DDPGLESEPLFEE---------PLVLVVPPDHPLAKRKSVTLADL 95 (197)
T ss_pred CEEEEEEC-ChHHHHHHHHcCCceEEEEcCCC---CCCcceEeeeecc---------ceEEEecCCCCcccCcEecHHHH
Confidence 35666555 55799999999999999875543 1111222333211 2245556651100 012478899
Q ss_pred CCCcccCCC
Q 044324 169 KGHKSCHGS 177 (291)
Q Consensus 169 kGKksCHtG 177 (291)
++.+.....
T Consensus 96 ~~~~~i~~~ 104 (197)
T cd05466 96 ADEPLILFE 104 (197)
T ss_pred cCCCEEEec
Confidence 888766543
No 36
>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=67.52 E-value=63 Score=25.89 Aligned_cols=78 Identities=8% Similarity=-0.020 Sum_probs=45.2
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCcc-ccCCCCCcccC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVC-QENGGINLMDF 168 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~dL 168 (291)
..+..+.. +..+-++.+.+|++|++......... ...+.-+++..| .-++|+.++.- ......+++||
T Consensus 29 i~i~~~~~-~~~~~~~~l~~~~~Dl~i~~~~~~~~-~~~~~~~~l~~~---------~~~~v~~~~~~~~~~~~~~~~~L 97 (197)
T cd08449 29 VTVRFHEL-SPEAQKAALLSKRIDLGFVRFADTLN-DPPLASELLWRE---------PMVVALPEEHPLAGRKSLTLADL 97 (197)
T ss_pred eEEEEEEC-CHHHHHHHHhCCCccEEEecccccCC-CCCceEEEEEEe---------eEEEEecCCCCCCCCCCCCHHHH
Confidence 35566543 67889999999999998853321100 112233344322 22556666510 00113588999
Q ss_pred CCCcccCCCC
Q 044324 169 KGHKSCHGSY 178 (291)
Q Consensus 169 kGKksCHtG~ 178 (291)
.+.+......
T Consensus 98 ~~~~~i~~~~ 107 (197)
T cd08449 98 RDEPFVFLRL 107 (197)
T ss_pred CCCCEEEecC
Confidence 9999887654
No 37
>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=64.44 E-value=41 Score=28.06 Aligned_cols=98 Identities=11% Similarity=-0.017 Sum_probs=52.7
Q ss_pred eEEEecc-chHHHHHHHHHHhhcCCC--cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecC
Q 044324 65 IKWCAVR-DQYEDCEYLVSIISQSED--YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCD 141 (291)
Q Consensus 65 vRwCv~S-~E~~KC~~l~~~a~~~~~--p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~ 141 (291)
+|+++.. .....=..+ -..+.... ..+..... +..+.++++.+|++|++....... ...+..+|+.
T Consensus 2 ~~Ig~~~~~~~~~l~~~-l~~f~~~~P~v~l~i~~~-~~~~~~~~l~~g~~Di~i~~~~~~---~~~l~~~~l~------ 70 (221)
T cd08469 2 FVIAANDYVTAVLLPAL-VRRLETEAPGIDLRIRPV-TRLDLAEQLDLGRIDLVIGIFEQI---PPRFRRRTLF------ 70 (221)
T ss_pred EEEEEChHHHHHHHHHH-HHHHHHHCCCcEEEEeeC-ChhhHHHHHHCCCccEEEecCCCC---Cccceeeeee------
Confidence 5666666 333222222 22233322 46776654 677999999999999998743321 1223333443
Q ss_pred CCceeEEEEEEecCccccCCCCCcccCCCCcccCC
Q 044324 142 HAQSYDAVAVINRKVCQENGGINLMDFKGHKSCHG 176 (291)
Q Consensus 142 ~~~~Y~aVAVVkK~~~~~S~~~~l~dLkGKksCHt 176 (291)
.+..++|+.++.-......+++||.+.+.=..
T Consensus 71 ---~~~~~~v~~~~~pl~~~~~~~~dL~~~~~i~~ 102 (221)
T cd08469 71 ---DEDEVWVMRKDHPAARGALTIETLARYPHIVV 102 (221)
T ss_pred ---ccceEEEEeCCCcCCCCCCCHHHHHhCCeEEE
Confidence 22346667776110011356778877766543
No 38
>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=62.94 E-value=18 Score=32.93 Aligned_cols=69 Identities=10% Similarity=0.058 Sum_probs=38.4
Q ss_pred EecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCc-EEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC---C
Q 044324 95 VKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSM-KAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK---G 170 (291)
Q Consensus 95 V~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk---G 170 (291)
+...+..+++..+++|++|++..+...--.-...+.. .|++.+ ..+.+++++.. ..+.+++||+ |
T Consensus 76 ~~~~~w~~~~~~l~~G~~Di~~~~~~~t~eR~~~~~fs~py~~~---------~~~~~~~~~~~--~~i~~~~dl~~~~g 144 (275)
T TIGR02995 76 ASITEYGALIPGLQAGRFDAIAAGLFIKPERCKQVAFTQPILCD---------AEALLVKKGNP--KGLKSYKDIAKNPD 144 (275)
T ss_pred eccCCHHHHHHHHHCCCcCEEeecccCCHHHHhccccccceeec---------ceeEEEECCCC--CCCCCHHHhccCCC
Confidence 4556788999999999999976432210000011222 244311 22466777711 1246788886 6
Q ss_pred Cccc
Q 044324 171 HKSC 174 (291)
Q Consensus 171 KksC 174 (291)
++.+
T Consensus 145 ~~Ig 148 (275)
T TIGR02995 145 AKIA 148 (275)
T ss_pred ceEE
Confidence 6655
No 39
>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=61.31 E-value=58 Score=26.36 Aligned_cols=76 Identities=14% Similarity=0.145 Sum_probs=41.9
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCc-cccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKV-CQENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dLk 169 (291)
.++.+. .+..+.++.+.+|++|++.......+.. ..+.-+++.. ...+.|+.++. .+.....+++||.
T Consensus 30 ~i~~~~-~~~~~~~~~l~~g~~Dl~i~~~~~~~~~-~~l~~~~l~~---------~~~~~~~~~~hpl~~~~~i~~~dL~ 98 (198)
T cd08437 30 QIDTYE-GGSAELLEQLLQGDLDIALLGSLTPLEN-SALHSKIIKT---------QHFMIIVSKDHPLAKAKKVNFADLK 98 (198)
T ss_pred EEEEEE-cCHHHHHHHHHcCCCCEEEecCCCCCCc-ccceEEEeec---------ceEEEEecCCCcccccCcccHHHHc
Confidence 455544 3688999999999999998643211111 1122223321 12344555551 0101136788999
Q ss_pred CCcccCCC
Q 044324 170 GHKSCHGS 177 (291)
Q Consensus 170 GKksCHtG 177 (291)
+.+.-...
T Consensus 99 ~~~~i~~~ 106 (198)
T cd08437 99 KENFILLN 106 (198)
T ss_pred CCCeEEec
Confidence 88876543
No 40
>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=61.04 E-value=8.1 Score=35.22 Aligned_cols=32 Identities=9% Similarity=0.161 Sum_probs=24.0
Q ss_pred cceEEEecC---CHHHHHHHHhccCCcEEEeCCce
Q 044324 90 YTWKCVKRD---TAQECLDSARKGEADIINLEAGL 121 (291)
Q Consensus 90 p~l~CV~~~---s~~dCm~~I~~g~ADiv~ld~~~ 121 (291)
..++=..+. +..+.+++|+.|.+|+..+....
T Consensus 30 v~v~~~~~g~Lg~~~e~~~~v~~G~~d~~~~~~~~ 64 (257)
T TIGR00787 30 IKISVFPSSQLGSDRAMLEALQGGALDMTAPSSSK 64 (257)
T ss_pred EEEEEcCCCCCCChHHHHHHHhCCCccEEeccccc
Confidence 445544432 67899999999999999877654
No 41
>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=60.30 E-value=79 Score=25.48 Aligned_cols=100 Identities=11% Similarity=-0.006 Sum_probs=53.2
Q ss_pred ceEEEecc-chHHHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeec
Q 044324 64 TIKWCAVR-DQYEDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYC 140 (291)
Q Consensus 64 ~vRwCv~S-~E~~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~ 140 (291)
++|+.+.. .....=..+ -..+....| .++.+.+ +..+.++.+.+|++|++...... . ...+.-+++..|
T Consensus 2 ~l~ig~~~~~~~~~l~~~-i~~~~~~~P~v~l~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~-~--~~~~~~~~l~~~--- 73 (198)
T cd08446 2 ELDVGYFGSAILDTVPRL-LRAFLTARPDVTVSLHNM-TKDEQIEALRAGRIHIGFGRFYP-V--EPDIAVENVAQE--- 73 (198)
T ss_pred eEEEEechHHHHHHHHHH-HHHHHHHCCCeEEEEeeC-CHHHHHHHHHCCCccEEEEecCC-C--CCCceeEEeeec---
Confidence 45665555 433333333 222322234 5666554 66789999999999999853221 1 111223344321
Q ss_pred CCCceeEEEEEEecCcc-ccCCCCCcccCCCCcccCCC
Q 044324 141 DHAQSYDAVAVINRKVC-QENGGINLMDFKGHKSCHGS 177 (291)
Q Consensus 141 ~~~~~Y~aVAVVkK~~~-~~S~~~~l~dLkGKksCHtG 177 (291)
..+.|+.++.- ......+++||++.+.-+..
T Consensus 74 ------~~~~v~~~~~pl~~~~~~~~~~l~~~~~i~~~ 105 (198)
T cd08446 74 ------RLYLAVPKSHPLAARPAVSLADLRNEPLILFP 105 (198)
T ss_pred ------cEEEEEeCCCCcccCCccCHHHHcCCCEEEec
Confidence 23566666511 00113578899998887643
No 42
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=60.07 E-value=17 Score=40.15 Aligned_cols=75 Identities=16% Similarity=0.062 Sum_probs=46.4
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccC
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDF 168 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dL 168 (291)
+.+++=|...+..+.++++++|++|++.-.-. ....+...+. ...-| ..-..++||+++ +.+.++.+|
T Consensus 95 G~~~e~v~~~~~~~~l~~l~~g~iDl~~~~~~--~~~~r~~~~~--fs~py----~~~~~~~v~~~~----~~~~~~~~l 162 (1197)
T PRK09959 95 NIKLTLREYADHQKAMDALEEGEVDIVLSHLV--ASPPLNDDIA--ATKPL----IITFPALVTTLH----DSMRPLTSS 162 (1197)
T ss_pred CCceEEEeCCCHHHHHHHHHcCCCcEecCccc--cccccccchh--cCCCc----cCCCceEEEeCC----CCCCCcccc
Confidence 56888888889999999999999998731100 0000100000 00000 011347777887 668899999
Q ss_pred CCCcccC
Q 044324 169 KGHKSCH 175 (291)
Q Consensus 169 kGKksCH 175 (291)
+||+...
T Consensus 163 ~~~~i~~ 169 (1197)
T PRK09959 163 KPVNIAR 169 (1197)
T ss_pred cCeEEEE
Confidence 9998554
No 43
>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=59.49 E-value=44 Score=26.76 Aligned_cols=99 Identities=14% Similarity=0.035 Sum_probs=51.0
Q ss_pred eEEEecc-chHHHHHHHHHHhhcCCC--cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecC
Q 044324 65 IKWCAVR-DQYEDCEYLVSIISQSED--YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCD 141 (291)
Q Consensus 65 vRwCv~S-~E~~KC~~l~~~a~~~~~--p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~ 141 (291)
+|+.+.. ....--..+ -..+.... ..|+.+. .+..+.++.+.+|++|++....... ...+...++..|
T Consensus 2 l~Ig~~~~~~~~~l~~~-l~~~~~~~p~v~i~i~~-~~~~~~~~~L~~~~~Dl~i~~~~~~---~~~~~~~~l~~~---- 72 (197)
T cd08438 2 LRLGLPPLGGSLLFAPL-LAAFRQRYPNIELELVE-YGGKKVEQAVLNGELDVGITVLPVD---EEEFDSQPLCNE---- 72 (197)
T ss_pred eEEEecchhhhhhcHHH-HHHHHHHCcCeEEEEEE-cCcHHHHHHHHcCCCCEEEEecccc---cCCceeEEeccc----
Confidence 5666655 333333333 22333322 3555554 3678899999999999988643221 111222333211
Q ss_pred CCceeEEEEEEecCc-cccCCCCCcccCCCCcccCCC
Q 044324 142 HAQSYDAVAVINRKV-CQENGGINLMDFKGHKSCHGS 177 (291)
Q Consensus 142 ~~~~Y~aVAVVkK~~-~~~S~~~~l~dLkGKksCHtG 177 (291)
..+.|+.++. .+.....+++||++.+.-..+
T Consensus 73 -----~~~~v~~~~~~l~~~~~~~~~~l~~~~~i~~~ 104 (197)
T cd08438 73 -----PLVAVLPRGHPLAGRKTVSLADLADEPFILFN 104 (197)
T ss_pred -----cEEEEecCCCChhhccccCHHHHcCCCeEEEC
Confidence 2245556651 000113577888887766543
No 44
>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=59.03 E-value=97 Score=25.36 Aligned_cols=77 Identities=6% Similarity=0.013 Sum_probs=42.9
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
.+++.+.. +..+.++++.+|++|++....... . ..+...++..| ..++|+.++.--.....+++||+
T Consensus 29 i~l~~~~~-~~~~~~~~l~~g~~D~~i~~~~~~-~--~~~~~~~l~~~---------~~~~v~~~~h~l~~~~~~~~dL~ 95 (200)
T cd08467 29 LDLRLCPI-GDDLAERGLEQGTIDLAVGRFAVP-P--DGLVVRRLYDD---------GFACLVRHGHPALAQEWTLDDFA 95 (200)
T ss_pred CEEEEecC-CcccHHHHhhCCCcCEEEecCCCC-C--ccceeEEeeec---------cEEEEEcCCCccccCCCCHHHHh
Confidence 45666655 556899999999999988532111 0 11222233211 12455565510001135788999
Q ss_pred CCcccCCCCC
Q 044324 170 GHKSCHGSYS 179 (291)
Q Consensus 170 GKksCHtG~~ 179 (291)
+.+......+
T Consensus 96 ~~~~i~~~~~ 105 (200)
T cd08467 96 TLRHVAIAPP 105 (200)
T ss_pred CCCCEEEcCC
Confidence 8888776544
No 45
>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=58.54 E-value=43 Score=26.69 Aligned_cols=28 Identities=18% Similarity=0.170 Sum_probs=21.6
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEA 119 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~ 119 (291)
.+.... .+..+.++++.+|++|++....
T Consensus 30 ~l~~~~-~~~~~~~~~l~~g~~D~~i~~~ 57 (201)
T cd08420 30 RVSLTI-GNTEEIAERVLDGEIDLGLVEG 57 (201)
T ss_pred eEEEEe-CCcHHHHHHHHCCCccEEEecC
Confidence 455544 4678999999999999988643
No 46
>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=58.46 E-value=59 Score=26.67 Aligned_cols=27 Identities=22% Similarity=0.096 Sum_probs=20.8
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLE 118 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld 118 (291)
.++.+. .+..+.++.+.+|++|++...
T Consensus 30 ~i~~~~-~~~~~~~~~l~~g~~Dl~i~~ 56 (202)
T cd08468 30 RLNLVH-AEQKLPLDALLAGEIDFALGY 56 (202)
T ss_pred EEEEEE-CChHhHHHHHHCCCccEEEec
Confidence 444443 367899999999999998864
No 47
>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=58.43 E-value=69 Score=25.41 Aligned_cols=73 Identities=12% Similarity=0.105 Sum_probs=39.1
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCc-cccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKV-CQENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dLk 169 (291)
.++.... +..+-++.+.+|++|++....... ...+...++..|. .+.|+.++. .+.....+++||+
T Consensus 30 ~i~i~~~-~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~~~~l~~~~---------~~~~~~~~~pl~~~~~~~~~~l~ 96 (197)
T cd08440 30 RVRLRDV-SAEQVIEAVRSGEVDFGIGSEPEA---DPDLEFEPLLRDP---------FVLVCPKDHPLARRRSVTWAELA 96 (197)
T ss_pred EEEEEeC-ChHHHHHHHHcCCccEEEEeCCCC---CCCeeEEEeeccc---------EEEEecCCCCcccCCccCHHHHc
Confidence 4444433 568899999999999998643321 1112223333221 134455541 0001135678888
Q ss_pred CCcccCC
Q 044324 170 GHKSCHG 176 (291)
Q Consensus 170 GKksCHt 176 (291)
+.+.-..
T Consensus 97 ~~~~i~~ 103 (197)
T cd08440 97 GYPLIAL 103 (197)
T ss_pred cCCEEec
Confidence 7766553
No 48
>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=57.56 E-value=79 Score=25.07 Aligned_cols=72 Identities=15% Similarity=0.199 Sum_probs=39.7
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCc-cccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKV-CQENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dLk 169 (291)
+++.... +..+.++.|.+|++|++....... ...+.-.++..+ ..+.|+.++. .+.....+++||.
T Consensus 30 ~i~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~~---~~~l~~~~l~~~---------~~~~v~~~~~~l~~~~~~~~~~l~ 96 (195)
T cd08434 30 TFELHQG-STDELLDDLKNGELDLALCSPVPD---EPDIEWIPLFTE---------ELVLVVPKDHPLAGRDSVDLAELA 96 (195)
T ss_pred EEEEecC-cHHHHHHHHHcCCccEEEEccCCC---CCCeeEEEeecc---------eEEEEecCCCccccCCccCHHHhc
Confidence 4555543 567889999999999998643321 111222233211 2355666651 0001134778888
Q ss_pred CCcccC
Q 044324 170 GHKSCH 175 (291)
Q Consensus 170 GKksCH 175 (291)
+.+.-.
T Consensus 97 ~~~~i~ 102 (195)
T cd08434 97 DEPFVL 102 (195)
T ss_pred CCceEE
Confidence 776544
No 49
>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=56.19 E-value=78 Score=25.56 Aligned_cols=99 Identities=11% Similarity=0.032 Sum_probs=48.9
Q ss_pred ceEEEecc-chHHHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeec
Q 044324 64 TIKWCAVR-DQYEDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYC 140 (291)
Q Consensus 64 ~vRwCv~S-~E~~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~ 140 (291)
++|+.+.. ....-=..+ -..+....| .++-+. .+..+.++.+.+|++|++....... ...+..+++..|
T Consensus 2 ~l~I~~~~~~~~~~l~~~-l~~~~~~~P~i~i~i~~-~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~~~~l~~~--- 73 (200)
T cd08411 2 PLRLGVIPTIAPYLLPRL-LPALRQAYPKLRLYLRE-DQTERLLEKLRSGELDAALLALPVD---EPGLEEEPLFDE--- 73 (200)
T ss_pred eEEEEecHHHHhhhhHHH-HHHHHHHCCCcEEEEEe-CcHHHHHHHHHcCCccEEEEeccCC---CCCceEEEeecc---
Confidence 46776665 322221222 122322234 344443 3678999999999999998643211 011222333311
Q ss_pred CCCceeEEEEEEecCcc-ccCCCCCcccCCCCcccCC
Q 044324 141 DHAQSYDAVAVINRKVC-QENGGINLMDFKGHKSCHG 176 (291)
Q Consensus 141 ~~~~~Y~aVAVVkK~~~-~~S~~~~l~dLkGKksCHt 176 (291)
.-+.|+.++.- +.....+++||.+.+.-..
T Consensus 74 ------~~~~v~~~~~pl~~~~~~~~~~l~~~~~i~~ 104 (200)
T cd08411 74 ------PFLLAVPKDHPLAKRKSVTPEDLAGERLLLL 104 (200)
T ss_pred ------ceEEEecCCCCccccCccCHHHHcCCceEec
Confidence 22455565510 0011357788887665443
No 50
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=54.79 E-value=49 Score=30.32 Aligned_cols=57 Identities=9% Similarity=-0.065 Sum_probs=37.4
Q ss_pred CCCceEEEecc-chHHHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeCC
Q 044324 61 SEATIKWCAVR-DQYEDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLEA 119 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld~ 119 (291)
..+++|+.+.. ....--..+ -..+....| .|..... +..++++++.+|++|++....
T Consensus 90 ~~g~l~Ig~~~~~~~~~l~~~-l~~~~~~~p~i~i~i~~~-~~~~~~~~l~~g~~Dl~i~~~ 149 (300)
T PRK11074 90 WRGQLSIAVDNIVRPDRTRQL-IVDFYRHFDDVELIIRQE-VFNGVWDALADGRVDIAIGAT 149 (300)
T ss_pred CCceEEEEEcCccchhHHHHH-HHHHHHhCCCceEEEEeh-hhhHHHHHHHCCCCCEEEecC
Confidence 45789999877 544443444 223333234 4555543 678899999999999999744
No 51
>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=54.19 E-value=61 Score=28.12 Aligned_cols=74 Identities=9% Similarity=-0.117 Sum_probs=41.3
Q ss_pred CCcceEEEecC-CHHHHHHHHhccCCcEEEeCCceeeeecccCCc-EEEEEEeecCCCceeEEEEEEecCccccCCCCCc
Q 044324 88 EDYTWKCVKRD-TAQECLDSARKGEADIINLEAGLAYTAFLNFSM-KAIANEVYCDHAQSYDAVAVINRKVCQENGGINL 165 (291)
Q Consensus 88 ~~p~l~CV~~~-s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l 165 (291)
.+.+++.+... .+...+..++.|++|++.-.++. . ..+.. .|++ .-..+.|++++.. ..+.++
T Consensus 33 ~g~~i~~~~~~~~~~~~~~~l~~g~~Di~~~~~~r---~-~~~~fs~py~---------~~~~~lv~~~~~~--~~~~~~ 97 (232)
T TIGR03871 33 LGLPLEYTWFPQRRGFVRNTLNAGRCDVVIGVPAG---Y-EMVLTTRPYY---------RSTYVFVTRKDSL--LDVKSL 97 (232)
T ss_pred cCCceEEEecCcchhhHHHHHhcCCccEEEeccCc---c-ccccccCCcE---------eeeEEEEEeCCCc--ccccch
Confidence 34567777554 34557789999999998542211 1 11111 1111 1123566777610 235678
Q ss_pred cc--CCCCcccCC
Q 044324 166 MD--FKGHKSCHG 176 (291)
Q Consensus 166 ~d--LkGKksCHt 176 (291)
+| |+|++.+..
T Consensus 98 ~d~~l~g~~V~v~ 110 (232)
T TIGR03871 98 DDPRLKKLRIGVF 110 (232)
T ss_pred hhhhhcCCeEEEE
Confidence 87 999997763
No 52
>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=52.95 E-value=66 Score=25.92 Aligned_cols=101 Identities=8% Similarity=-0.075 Sum_probs=52.3
Q ss_pred ceEEEecc-chHHHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeec
Q 044324 64 TIKWCAVR-DQYEDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYC 140 (291)
Q Consensus 64 ~vRwCv~S-~E~~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~ 140 (291)
++|+.+.. .....=..+ -..+....| .++.+.. +..+.++.+.+|++|++....... ...+..+++..|
T Consensus 2 ~l~Ig~~~~~~~~~l~~~-l~~~~~~~P~v~i~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~~~~l~~~--- 73 (197)
T cd08425 2 SLRLAMTPTFTAYLIGPL-IDRFHARYPGIALSLREM-PQERIEAALADDRLDLGIAFAPVR---SPDIDAQPLFDE--- 73 (197)
T ss_pred eEEEEechhhhhhhhHHH-HHHHHHHCCCcEEEEEEC-cHHHHHHHHHcCCccEEEEecCCC---CCCcEEEEeccc---
Confidence 46776665 433333333 223333234 4555543 667899999999999998643211 011222333221
Q ss_pred CCCceeEEEEEEecCc-cccCC-CCCcccCCCCcccCCCC
Q 044324 141 DHAQSYDAVAVINRKV-CQENG-GINLMDFKGHKSCHGSY 178 (291)
Q Consensus 141 ~~~~~Y~aVAVVkK~~-~~~S~-~~~l~dLkGKksCHtG~ 178 (291)
.-+.|+.++. .+... ..+++||+..+.-....
T Consensus 74 ------~~~~v~~~~~pl~~~~~~~~~~dL~~~~~i~~~~ 107 (197)
T cd08425 74 ------RLALVVGATHPLAQRRTALTLDDLAAEPLALLSP 107 (197)
T ss_pred ------cEEEEecCCCchhHhcccCCHHHHhcCCcEecCC
Confidence 2245555551 00011 26788998877765433
No 53
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=52.24 E-value=76 Score=28.58 Aligned_cols=106 Identities=9% Similarity=-0.088 Sum_probs=54.9
Q ss_pred CCCceEEEecc-chHHHHHHHHHHhhcCCCcceEEEe-cCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEe
Q 044324 61 SEATIKWCAVR-DQYEDCEYLVSIISQSEDYTWKCVK-RDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEV 138 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~~KC~~l~~~a~~~~~p~l~CV~-~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~ 138 (291)
..++||+++.. ....-=..+ -..+....|.+.-.. ..+..+.++.+.+|++|++...... ... + +..+.
T Consensus 89 ~~~~i~I~~~~~~~~~~l~~~-l~~~~~~~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~---~~~--~---l~~~~ 159 (296)
T PRK11242 89 SRGSLRLAMTPTFTAYLIGPL-IDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPV---HSP--E---IEAQP 159 (296)
T ss_pred CeeEEEEEeccchhhhhhHHH-HHHHHHHCCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecCC---CCc--c---eeEEE
Confidence 34679999877 432111111 111212224443333 3466889999999999999864321 111 1 22222
Q ss_pred ecCCCceeEEEEEEecCc-cccCCC-CCcccCCCCcccCCCCC
Q 044324 139 YCDHAQSYDAVAVINRKV-CQENGG-INLMDFKGHKSCHGSYS 179 (291)
Q Consensus 139 y~~~~~~Y~aVAVVkK~~-~~~S~~-~~l~dLkGKksCHtG~~ 179 (291)
...+ .-++|+.++. .+.... .+++||+..+.-+...+
T Consensus 160 l~~~----~~~~~~~~~~pl~~~~~~i~~~~L~~~~~i~~~~~ 198 (296)
T PRK11242 160 LFTE----TLALVVGRHHPLAARRKALTLDELADEPLVLLSAE 198 (296)
T ss_pred eeec----cEEEEEcCCCcccccCCCcCHHHHhCCCcEeeCCC
Confidence 2221 2356677761 001112 67788888777765443
No 54
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=51.71 E-value=21 Score=31.27 Aligned_cols=66 Identities=8% Similarity=0.011 Sum_probs=0.0
Q ss_pred EecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCc-EEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCCCCcc
Q 044324 95 VKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSM-KAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFKGHKS 173 (291)
Q Consensus 95 V~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L-~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLkGKks 173 (291)
+...+..++++.+++|++|++...-..--.-...+.. .|++.... +.|++++ . +.+++||+|++.
T Consensus 64 ~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~~fs~p~~~~~~---------~~v~~~~----~-~~~~~dL~g~~I 129 (243)
T PRK15007 64 FSNQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPYYDNSA---------LFVGQQG----K-YTSVDQLKGKKV 129 (243)
T ss_pred EEeCCHHHHhHHHhCCCcCEEEEcCccCHHHhcccceecCccccce---------EEEEeCC----C-CCCHHHhCCCeE
Q ss_pred c
Q 044324 174 C 174 (291)
Q Consensus 174 C 174 (291)
+
T Consensus 130 g 130 (243)
T PRK15007 130 G 130 (243)
T ss_pred E
No 55
>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=51.22 E-value=16 Score=30.78 Aligned_cols=52 Identities=25% Similarity=0.364 Sum_probs=35.1
Q ss_pred eEEEecc-chHHHHHHHHHHhhcCCCcceEEEecCCHHHHHHHHhccCCcEEEeCCcee
Q 044324 65 IKWCAVR-DQYEDCEYLVSIISQSEDYTWKCVKRDTAQECLDSARKGEADIINLEAGLA 122 (291)
Q Consensus 65 vRwCv~S-~E~~KC~~l~~~a~~~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~i 122 (291)
.|++++. .... ..| ...... .+.=+...|..+++++|.+|++|++..+...+
T Consensus 111 ~~i~~~~g~~~~--~~l-~~~~~~---~~~~~~~~~~~~~~~~l~~g~~d~~i~~~~~~ 163 (225)
T PF00497_consen 111 KRIGVVRGSSYA--DYL-KQQYPS---NINIVEVDSPEEALEALLSGRIDAFIVDESTA 163 (225)
T ss_dssp SEEEEETTSHHH--HHH-HHHTHH---TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHH
T ss_pred cccccccchhHH--HHh-hhhccc---hhhhcccccHHHHHHHHhcCCeeeeeccchhh
Confidence 4888888 3322 223 221110 34445678999999999999999999987754
No 56
>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=50.82 E-value=83 Score=25.47 Aligned_cols=80 Identities=11% Similarity=0.013 Sum_probs=43.6
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccc-cCCCCCcccC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQ-ENGGINLMDF 168 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~-~S~~~~l~dL 168 (291)
..++.+.. +..+-++.+.+|++|++.......-.....+.-+++..|.+ ++|+.++.-. .....++++|
T Consensus 29 i~l~i~~~-~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~~~l~~~~~---------~~v~~~~hp~~~~~~i~~~~L 98 (200)
T cd08453 29 VELQLREA-TSDVQLEALLAGEIDAGIVIPPPGASAPPALAYRPLLSEPL---------VLAVPAAWAAEGGAPLALAAV 98 (200)
T ss_pred ceEEEEeC-CHHHHHHHHHcCCCCEEEEecCcccCCCcceeEEEeeeCce---------EEEEECCCccccCCCCCHHHh
Confidence 35666654 45678999999999998753321100011123334442222 4566666100 0113578899
Q ss_pred CCCcccCCCCC
Q 044324 169 KGHKSCHGSYS 179 (291)
Q Consensus 169 kGKksCHtG~~ 179 (291)
++.+.-....+
T Consensus 99 ~~~~~i~~~~~ 109 (200)
T cd08453 99 AAEPLVIFPRR 109 (200)
T ss_pred ccCCEEeccCC
Confidence 99887665433
No 57
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=49.68 E-value=88 Score=28.69 Aligned_cols=55 Identities=9% Similarity=-0.010 Sum_probs=35.0
Q ss_pred CCCceEEEecc-chH-HHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeC
Q 044324 61 SEATIKWCAVR-DQY-EDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLE 118 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~-~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld 118 (291)
...++|+.+.. ... ---..+ .. +....| .+..... +..+.++++.+|++|++...
T Consensus 93 ~~g~l~ig~~~~~~~~~~~~~l-~~-~~~~~P~v~i~~~~~-~~~~~~~~l~~g~~Dl~i~~ 151 (305)
T CHL00180 93 QRGTLIIGASQTTGTYLMPRLI-GL-FRQRYPQINVQLQVH-STRRIAWNVANGQIDIAIVG 151 (305)
T ss_pred cCceEEEEEcCcchHhHHHHHH-HH-HHHHCCCceEEEEeC-CHHHHHHHHHcCCccEEEEc
Confidence 45689998887 433 222233 22 222224 4555443 57999999999999999874
No 58
>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=49.41 E-value=1.3e+02 Score=23.97 Aligned_cols=73 Identities=14% Similarity=0.093 Sum_probs=40.6
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCcc-ccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVC-QENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~dLk 169 (291)
.++.+.. ...+-++.+.+|++|++....... ...+.-.++..| ..+.|+.++.- +.....+++||+
T Consensus 30 ~i~i~~~-~~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~l~~~---------~~~~~~~~~hpl~~~~~~~~~~L~ 96 (197)
T cd08448 30 EVALHEM-SSAEQIEALLRGELDLGFVHSRRL---PAGLSARLLHRE---------PFVCCLPAGHPLAARRRIDLRELA 96 (197)
T ss_pred eEEEEeC-CHHHHHHHHHcCCcceEEEeCCCC---CcCceEEEEecC---------cEEEEeeCCCCCcCCCCcCHHHhC
Confidence 5555543 568899999999999987643211 111222333211 12345666510 001135788898
Q ss_pred CCcccCC
Q 044324 170 GHKSCHG 176 (291)
Q Consensus 170 GKksCHt 176 (291)
+.+.-..
T Consensus 97 ~~~~i~~ 103 (197)
T cd08448 97 GEPFVLF 103 (197)
T ss_pred CCcEEee
Confidence 8776653
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=49.15 E-value=1.3e+02 Score=24.24 Aligned_cols=27 Identities=15% Similarity=0.311 Sum_probs=20.7
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLE 118 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld 118 (291)
.++...+ +..+.++.+.+|++|++...
T Consensus 30 ~i~~~~~-~~~~~~~~l~~~~~Dl~i~~ 56 (185)
T cd08439 30 AIEVVCK-RTPRLMEMLERGEVDLALIT 56 (185)
T ss_pred EEEEEEC-ChHHHHHHHHCCCCcEEEEe
Confidence 4444443 57899999999999998764
No 60
>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=49.10 E-value=1.5e+02 Score=24.32 Aligned_cols=76 Identities=12% Similarity=0.118 Sum_probs=43.1
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFKG 170 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLkG 170 (291)
.++.+. .+..+-++.+.+|++|++....... . ..+...++.. ...+.|++++--......++++|.+
T Consensus 30 ~l~i~~-~~~~~~~~~L~~g~~Dl~i~~~~~~--~-~~~~~~~l~~---------~~~~lv~~~~h~~~~~~i~~~~l~~ 96 (200)
T cd08465 30 DLAVSQ-ASREAMLAQVADGEIDLALGVFPEL--P-EELHAETLFE---------ERFVCLADRATLPASGGLSLDAWLA 96 (200)
T ss_pred EEEEec-CChHhHHHHHHCCCccEEEeccccC--C-cCeeEEEeee---------ccEEEEEeCCCCccCCCcCHHHHhh
Confidence 344443 3678899999999999988643321 0 1122223321 2346677776211112367888888
Q ss_pred CcccCCCCC
Q 044324 171 HKSCHGSYS 179 (291)
Q Consensus 171 KksCHtG~~ 179 (291)
.+......+
T Consensus 97 ~~~i~~~~~ 105 (200)
T cd08465 97 RPHVLVAMR 105 (200)
T ss_pred CCcEEEecC
Confidence 776554443
No 61
>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=48.31 E-value=1.5e+02 Score=24.22 Aligned_cols=74 Identities=8% Similarity=-0.017 Sum_probs=40.2
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCcccc-CCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQE-NGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~-S~~~~l~dLk 169 (291)
.++.+.. +..+.++.+++|++|++...+... ...+.-+++..| ..++|+.++-... ....+++||+
T Consensus 31 ~l~~~~~-~~~~~~~~l~~~~~D~~i~~~~~~---~~~l~~~~l~~~---------~~~~~~~~~~~~~~~~~v~~~~L~ 97 (198)
T cd08485 31 TVSLTQM-SKNRQIEALDAGTIDIGFGRFYPY---QEGVVVRNVTNE---------RLFLGAQKSRARSFGEQVHCSALR 97 (198)
T ss_pred EEEEEEC-CHHHHHHHHHcCCccEEEecCCCC---CCCeEEEEeecc---------ceEEEeCCCCccccCCCcCHHHHh
Confidence 3444433 667899999999999988643211 111222233211 1234455551110 1136788999
Q ss_pred CCcccCCC
Q 044324 170 GHKSCHGS 177 (291)
Q Consensus 170 GKksCHtG 177 (291)
+.+.-...
T Consensus 98 ~~~~i~~~ 105 (198)
T cd08485 98 NEPLILFP 105 (198)
T ss_pred cCCeEecC
Confidence 88777643
No 62
>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=48.05 E-value=1.5e+02 Score=24.12 Aligned_cols=99 Identities=10% Similarity=0.001 Sum_probs=50.1
Q ss_pred ceEEEecc-chHHHHHHHHHHhhcCCCcc--eEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeec
Q 044324 64 TIKWCAVR-DQYEDCEYLVSIISQSEDYT--WKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYC 140 (291)
Q Consensus 64 ~vRwCv~S-~E~~KC~~l~~~a~~~~~p~--l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~ 140 (291)
.+|+.+.. ....--..+ -..+...-|. ++.+.. +..+.++.+.+|++|++...... . . ....-.++..|
T Consensus 2 ~l~Ig~~~~~~~~~l~~~-l~~~~~~~P~i~l~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~-~-~-~~~~~~~l~~~--- 73 (203)
T cd08445 2 TFSIGFVPSTLYGLLPEL-IRRFRQAAPDVEIELIEM-TTVQQIEALKEGRIDVGFGRLRI-E-D-PAIRRIVLREE--- 73 (203)
T ss_pred eEEEEEehHHHHhHHHHH-HHHHHHHCCCeEEEEEeC-ChHHHHHHHHcCCCcEEEecCCC-C-C-CCceeEEEEec---
Confidence 56666655 332222222 1222222354 444443 57899999999999998853211 0 0 11222233211
Q ss_pred CCCceeEEEEEEecCc-cccCC-CCCcccCCCCcccCC
Q 044324 141 DHAQSYDAVAVINRKV-CQENG-GINLMDFKGHKSCHG 176 (291)
Q Consensus 141 ~~~~~Y~aVAVVkK~~-~~~S~-~~~l~dLkGKksCHt 176 (291)
..+.|+.++. .+... ..+++||++-+....
T Consensus 74 ------~~~~v~~~~hpl~~~~~~i~~~dL~~~~~i~~ 105 (203)
T cd08445 74 ------PLVVALPAGHPLAQEKAPLTLAQLADEPLILY 105 (203)
T ss_pred ------cEEEEeeCCCCCccCCCCcCHHHhcCCCEEec
Confidence 2355556651 01111 357889988877763
No 63
>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=47.87 E-value=87 Score=28.39 Aligned_cols=103 Identities=15% Similarity=0.089 Sum_probs=55.3
Q ss_pred CCCCceEEEecc-chH-HHHHHHHHHhhcCCCcceEEEec-CCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEE
Q 044324 60 GSEATIKWCAVR-DQY-EDCEYLVSIISQSEDYTWKCVKR-DTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIAN 136 (291)
Q Consensus 60 ~~~~~vRwCv~S-~E~-~KC~~l~~~a~~~~~p~l~CV~~-~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~ 136 (291)
...+++|+++.. ... ---..+ . .+...-|.+..... .+..+.++.+.+|++|++......- .....+...|+..
T Consensus 90 ~~~~~l~I~~~~~~~~~~~~~~l-~-~~~~~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~-~~~~~~~~~~l~~ 166 (300)
T TIGR02424 90 GEGPTVRIGALPTVAARLMPEVV-K-RFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAP-ETMQGLSFEHLYN 166 (300)
T ss_pred CCCceEEEecccHHHHhhhHHHH-H-HHHHhCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCc-ccccceeeeeecC
Confidence 346689998876 322 222223 2 22222355433332 3778999999999999998533211 0111222233331
Q ss_pred EeecCCCceeEEEEEEecCccccCC-----CCCcccCCCCcccCCCC
Q 044324 137 EVYCDHAQSYDAVAVINRKVCQENG-----GINLMDFKGHKSCHGSY 178 (291)
Q Consensus 137 E~y~~~~~~Y~aVAVVkK~~~~~S~-----~~~l~dLkGKksCHtG~ 178 (291)
| ..+.|+.++ .+ ..+++||.+-+......
T Consensus 167 ~---------~~~~~~~~~----hpl~~~~~i~~~dL~~~~~i~~~~ 200 (300)
T TIGR02424 167 E---------PVVFVVRAG----HPLLAAPSLPVASLADYPVLLPPE 200 (300)
T ss_pred C---------ceEEEEcCC----CccccCCCCCHHHHhCCCEEecCC
Confidence 1 224556665 32 24778888887765443
No 64
>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=47.61 E-value=1e+02 Score=25.60 Aligned_cols=75 Identities=9% Similarity=0.043 Sum_probs=42.8
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCcc-ccCCCCCcccC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVC-QENGGINLMDF 168 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~dL 168 (291)
..++.+...+..+.++.+.+|++|++....... . ..+..+++.. ...+.|+.++.- +.....++++|
T Consensus 29 ~~v~~~~~~~~~~l~~~L~~g~lDl~i~~~~~~--~-~~l~~~~l~~---------~~~~lv~~~~h~l~~~~~i~~~~l 96 (203)
T cd08463 29 ARLEIHPLGPDFDYERALASGELDLVIGNWPEP--P-EHLHLSPLFS---------DEIVCLMRADHPLARRGLMTLDDY 96 (203)
T ss_pred CEEEEEeCCcchhHHHHHhcCCeeEEEeccccC--C-CCcEEeEeec---------CceEEEEeCCCCcccCCCCCHHHH
Confidence 356666555668899999999999998753321 0 1122233321 123556676611 00113567888
Q ss_pred CCCcccCC
Q 044324 169 KGHKSCHG 176 (291)
Q Consensus 169 kGKksCHt 176 (291)
.+-+.-..
T Consensus 97 ~~~~~i~~ 104 (203)
T cd08463 97 LEAPHLAP 104 (203)
T ss_pred hhCCcEEE
Confidence 88776543
No 65
>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=47.04 E-value=1.2e+02 Score=24.20 Aligned_cols=75 Identities=12% Similarity=0.061 Sum_probs=43.7
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCc-cccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKV-CQENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dLk 169 (291)
.++... .+..+-++.+.+|++|++....... ...+..+++..| ..+.|+.++. .......++++|+
T Consensus 30 ~l~i~~-~~~~~~~~~l~~~~~D~~i~~~~~~---~~~~~~~~l~~~---------~~~~~~~~~~~l~~~~~~~~~~l~ 96 (198)
T cd08412 30 EVRVVE-GNQEELEEGLRSGELDLALTYDLDL---PEDIAFEPLARL---------PPYVWLPADHPLAGKDEVSLADLA 96 (198)
T ss_pred EEEEEE-CCHHHHHHHHHcCCCcEEEEcCCCC---Ccccceeeeecc---------ceEEEecCCCCCCCCCcCCHHHHc
Confidence 466554 3678999999999999988644321 122333444322 2244555541 0011235789999
Q ss_pred CCcccCCCC
Q 044324 170 GHKSCHGSY 178 (291)
Q Consensus 170 GKksCHtG~ 178 (291)
+.+.-....
T Consensus 97 ~~~~i~~~~ 105 (198)
T cd08412 97 AEPLILLDL 105 (198)
T ss_pred CCcEEecCc
Confidence 988776543
No 66
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=46.37 E-value=44 Score=34.89 Aligned_cols=75 Identities=13% Similarity=0.036 Sum_probs=47.0
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeee-------e-----cccCCcEEEEEEeecCCCceeEEEEEEecCccc
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYT-------A-----FLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQ 158 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~-------A-----~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~ 158 (291)
.++.... +..+.++++++|++|+..+.....-. + ...+...|+. ....++|++++
T Consensus 442 ~i~v~~~-~s~~vl~~L~~GeiDlai~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~---------~d~lvlvvp~~--- 508 (633)
T PRK14498 442 RLRSLHV-GSMGGLMALKRGEADIAGIHLLDPETGEYNIPYIKKYLLGEDAVLVKGY---------RREQGLVVRKG--- 508 (633)
T ss_pred ceeEEec-CCHHHHHHHHcCCceEEEEcccCcccccccHHHHHhhcCCCCEEEEEEE---------EEeEEEEECCC---
Confidence 4555554 77899999999999999864321100 0 0012222332 22457888888
Q ss_pred cCC--CCCcccCCCC--cccCCCCC
Q 044324 159 ENG--GINLMDFKGH--KSCHGSYS 179 (291)
Q Consensus 159 ~S~--~~~l~dLkGK--ksCHtG~~ 179 (291)
++ ..+|+||++. +......+
T Consensus 509 -hPl~~isl~dL~~~~~plI~~~~g 532 (633)
T PRK14498 509 -NPKGIEGIEDLVRKDVRFVNRQRG 532 (633)
T ss_pred -CCCCCCCHHHhccCCcEEEecCCC
Confidence 53 4789999999 87776544
No 67
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=45.11 E-value=93 Score=29.04 Aligned_cols=57 Identities=7% Similarity=-0.107 Sum_probs=37.3
Q ss_pred CCCceEEEecc-chHHHHHHHHHHhhcCCCcceEEEecCCHHHHHHHHhccCCcEEEeCC
Q 044324 61 SEATIKWCAVR-DQYEDCEYLVSIISQSEDYTWKCVKRDTAQECLDSARKGEADIINLEA 119 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~~KC~~l~~~a~~~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~ 119 (291)
..+++|+++.. ....-=..+ -..+....|.+.+... ...+.++.|.+|++|++....
T Consensus 115 ~~~~l~Ig~~~~~~~~~l~~~-l~~f~~~~P~i~i~~~-~~~~~~~~l~~g~~Dl~i~~~ 172 (317)
T PRK11482 115 KQRTITIATTPSVGALVMPVI-YQAIKTHYPQLLLRNI-PISDAENQLSQFQTDLIIDTH 172 (317)
T ss_pred CCceEEEEecHHHHHHHHHHH-HHHHHHHCCCCEEEEe-cchhHHHHHHCCCcCEEEecc
Confidence 35689999988 544322222 2233333478886544 446899999999999998643
No 68
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=44.15 E-value=38 Score=31.80 Aligned_cols=73 Identities=14% Similarity=0.050 Sum_probs=49.9
Q ss_pred CcceEEEecCCHHHHHHHHhccCCcEEEeCCcee---eeecccCCcEEEEEEeecCCCceeEEEEEEec---CccccCCC
Q 044324 89 DYTWKCVKRDTAQECLDSARKGEADIINLEAGLA---YTAFLNFSMKAIANEVYCDHAQSYDAVAVINR---KVCQENGG 162 (291)
Q Consensus 89 ~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~i---y~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK---~~~~~S~~ 162 (291)
+..++=+...+...-++++.+|+.|+..+.-... |.....++|+.+.. +-++.. + +++
T Consensus 59 G~~Velv~fsd~~~~n~AL~~G~ID~n~~qh~~yl~~~~~~~g~~lv~~~~------------~~~~P~~~Ys----~~i 122 (272)
T PRK09861 59 GLDVELVGFSGSLLPNDATNHGELDANVFQHRPFLEQDNQAHGYKLVAVGN------------TFVFPMAGYS----KKI 122 (272)
T ss_pred CCeEEEEecCchhhHHHHHHcCCcceehhhhHHHHHHHHHhcCCCeEEEeE------------EEEEeeeccc----cCC
Confidence 5788888888999999999999999988644432 22223444544321 111222 3 558
Q ss_pred CCcccCC-CCcccCCC
Q 044324 163 INLMDFK-GHKSCHGS 177 (291)
Q Consensus 163 ~~l~dLk-GKksCHtG 177 (291)
.+++||+ |+|.--+-
T Consensus 123 ksl~DL~~Ga~IAipn 138 (272)
T PRK09861 123 KTVAQIKEGATVAIPN 138 (272)
T ss_pred CCHHHcCCCCEEEEeC
Confidence 9999999 99998873
No 69
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=43.76 E-value=90 Score=24.92 Aligned_cols=74 Identities=14% Similarity=0.106 Sum_probs=41.7
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCc-cccCCCCCcccC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKV-CQENGGINLMDF 168 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dL 168 (291)
..+..... +..+.++.+.+|++|++....... ...+..+++..| ..+.|+.++. .+.....++++|
T Consensus 29 i~l~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~~~~l~~~---------~~~~v~~~~~~l~~~~~~~~~~l 95 (196)
T cd08415 29 VRISLHTL-SSSTVVEAVLSGQADLGLASLPLD---HPGLESEPLASG---------RAVCVLPPGHPLARKDVVTPADL 95 (196)
T ss_pred cEEEEEec-chHHHHHHHHcCCccEEEEeCCCC---CCcceeeeeccc---------ceEEEEcCCCChHhcCccCHHHh
Confidence 34555554 567899999999999998643211 111222333321 2255566651 000113578888
Q ss_pred CCCcccCC
Q 044324 169 KGHKSCHG 176 (291)
Q Consensus 169 kGKksCHt 176 (291)
.+.+....
T Consensus 96 ~~~~~i~~ 103 (196)
T cd08415 96 AGEPLISL 103 (196)
T ss_pred cCCcEEEe
Confidence 88877764
No 70
>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=42.45 E-value=1.7e+02 Score=23.27 Aligned_cols=76 Identities=18% Similarity=0.134 Sum_probs=41.3
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCcc-ccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVC-QENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~dLk 169 (291)
.++... .+..+.++.+.+|++|++........ ....+.-.++.. ...+.|+.++.- +.....+++||.
T Consensus 30 ~i~i~~-~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~~~~l~~---------~~~~~~~~~~~~l~~~~~~~~~dL~ 98 (201)
T cd08435 30 TVRVVE-GTSDELLEGLRAGELDLAIGRLADDE-QPPDLASEELAD---------EPLVVVARPGHPLARRARLTLADLA 98 (201)
T ss_pred EEEEEe-CCHHHHHHHHHcCCccEEEEecCccc-CCCCcEEEEccc---------CcEEEEEeCCCcCcccCCcCHHHHh
Confidence 566554 46899999999999999885422110 001122223321 123455565510 001135778888
Q ss_pred CCcccCCC
Q 044324 170 GHKSCHGS 177 (291)
Q Consensus 170 GKksCHtG 177 (291)
+.+.-...
T Consensus 99 ~~~~i~~~ 106 (201)
T cd08435 99 DYPWVLPP 106 (201)
T ss_pred cCCEEecC
Confidence 88766643
No 71
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=42.37 E-value=15 Score=34.08 Aligned_cols=108 Identities=19% Similarity=0.110 Sum_probs=54.8
Q ss_pred cccCCccccCCCcccccCCCCCc----eEEEeccchHHHHHHHHHHhhcCCCcceEEEecCCHHHHHHHHhccCCcEEEe
Q 044324 42 EEFGDHVVPSGEVGDDEEGSEAT----IKWCAVRDQYEDCEYLVSIISQSEDYTWKCVKRDTAQECLDSARKGEADIINL 117 (291)
Q Consensus 42 ~~~~~~~~~~~~~~~~~~~~~~~----vRwCv~S~E~~KC~~l~~~a~~~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~l 117 (291)
-+||.|+-.+..+=.+....... .|+=+=+.-..-+ .|....+. +.+++-|.- ++.+|++.|.+|+.|+++-
T Consensus 88 ~~fG~~sYvs~Hvli~~~~~~~~i~dGmRVGiD~~S~Dq~-~LT~~~~~--gk~Ve~Vei-~Y~q~~~~l~~g~IDA~IW 163 (232)
T PF14503_consen 88 LEFGPGSYVSEHVLIFRDGEKKEIEDGMRVGIDPSSIDQK-ILTEAEFE--GKNVEFVEI-PYNQLLELLRSGEIDAAIW 163 (232)
T ss_dssp EE--TTSSS--EEEEEETT-GGG-----EEEE-TT-HHHH-HHHHHHHT--TS--EEEE---HHHHHHHHHHTS--EEEE
T ss_pred EeeCCCCcccceEEEEecCCccceeeeeEeecCCCCccHH-HHHHHHhC--CCceEEEEe-cHHHHHHHHHCCCccEEEE
Confidence 47999998888777765543322 3544433222222 33244444 346666655 6899999999999999988
Q ss_pred CCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecC
Q 044324 118 EAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRK 155 (291)
Q Consensus 118 d~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~ 155 (291)
.-+++-. +..+|.++-..........-.||.||+|+
T Consensus 164 N~d~i~~--~~~~l~~~~l~~~~~~~~~seAVivi~~~ 199 (232)
T PF14503_consen 164 NYDEIED--KNFGLKYVPLKDDPMSKDASEAVIVIRKD 199 (232)
T ss_dssp E--HHCC--HHCTEEEEE--SSCHHHHTT-EEEEEETT
T ss_pred CCccccc--ccCCeeEEeCCchHHHHhcCeeEEEEeCC
Confidence 7773322 34777765433321111145899999998
No 72
>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=42.10 E-value=71 Score=25.68 Aligned_cols=84 Identities=10% Similarity=0.102 Sum_probs=46.2
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCcc-ccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVC-QENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~dLk 169 (291)
.++... .+..+.++.+.+|++|++....... ...+..+++..| ..+.|+.++.- ......+++||.
T Consensus 30 ~i~~~~-~~~~~~~~~l~~~~~D~~i~~~~~~---~~~~~~~~l~~~---------~~~~v~~~~~pl~~~~~~~~~~l~ 96 (198)
T cd08421 30 RIDLEE-RLSADIVRAVAEGRADLGIVAGNVD---AAGLETRPYRTD---------RLVVVVPRDHPLAGRASVAFADTL 96 (198)
T ss_pred eEEEEe-cCcHHHHHHHhcCCceEEEEecCCC---CCCcEEEEeecC---------cEEEEeCCCCCccccCCCCHHHhc
Confidence 455554 3568899999999999988643221 122223344322 22555566510 001135788898
Q ss_pred CCcccCCCCCCCCCchhHHH
Q 044324 170 GHKSCHGSYSTAAGWNYPVN 189 (291)
Q Consensus 170 GKksCHtG~~~taGW~iPvg 189 (291)
+.+......+ .+|.-.+.
T Consensus 97 ~~~~i~~~~~--~~~~~~~~ 114 (198)
T cd08421 97 DHDFVGLPAG--SALHTFLR 114 (198)
T ss_pred CCceEeecCC--cchHHHHH
Confidence 8777664432 34544343
No 73
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=42.05 E-value=1.4e+02 Score=27.56 Aligned_cols=53 Identities=21% Similarity=0.018 Sum_probs=31.5
Q ss_pred ceEEEecc-chHHHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeCC
Q 044324 64 TIKWCAVR-DQYEDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLEA 119 (291)
Q Consensus 64 ~vRwCv~S-~E~~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld~ 119 (291)
++|+++.. ....-=..+ -..+....| .++-... + .+.++++.+|++|++.+..
T Consensus 98 ~l~I~~~~~~~~~~~~~~-l~~f~~~~P~v~v~i~~~-~-~~~~~~l~~g~~D~~i~~~ 153 (319)
T PRK10216 98 KFELAAESPLMMIMLNAL-SKRIYQRYPQATIKLRNW-D-YDSLDAITRGEVDIGFTGR 153 (319)
T ss_pred EEEEEecchhHHHHHHHH-HHHHHHHCCCCEEEEEeC-C-cchHHHHhcCCccEEEecC
Confidence 79999887 433222222 223333234 4554443 3 3579999999999988743
No 74
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=42.03 E-value=34 Score=27.21 Aligned_cols=55 Identities=15% Similarity=0.116 Sum_probs=34.6
Q ss_pred EecCCHHHHHHHHhccCCcEEEeCCcee-eeecccCCcEEEEEEeecCCCceeEEEEEEecC
Q 044324 95 VKRDTAQECLDSARKGEADIINLEAGLA-YTAFLNFSMKAIANEVYCDHAQSYDAVAVINRK 155 (291)
Q Consensus 95 V~~~s~~dCm~~I~~g~ADiv~ld~~~i-y~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~ 155 (291)
+.-.+..+++.+++.|+ |+++.|...+ |...+..+++ ++.+.+. ..+|++|| +|+
T Consensus 49 ~~~~~~~~~~~~l~~g~-da~v~d~~~~~~~~~~~~~~~-~~~~~~~---~~~~~ia~-~k~ 104 (134)
T smart00079 49 VFVKSYAEGVQRVRVSN-YAFLMESTYLDYELSQNCDLM-TVGENFG---RKGYGIAF-PKG 104 (134)
T ss_pred CCCCCHHHHHHHHHcCC-CEEEeehHhHHHHHhCCCCeE-EcCcccC---CCceEEEe-cCC
Confidence 34468999999999999 9999997644 3332323333 2323232 24578877 455
No 75
>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=42.03 E-value=1.9e+02 Score=23.53 Aligned_cols=75 Identities=8% Similarity=0.088 Sum_probs=42.2
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
..++.+.. +. +-++.+.+|++|++....... . ..+.-.|+.. ..-|.|+.++--......++++|.
T Consensus 29 i~l~i~~~-~~-~~~~~l~~g~~D~~i~~~~~~--~-~~~~~~~l~~---------~~~~~v~~~~hpl~~~~~~~~~l~ 94 (200)
T cd08462 29 VRFELLPP-DD-QPHELLERGEVDLLIAPERFM--S-DGHPSEPLFE---------EEFVCVVWADNPLVGGELTAEQYF 94 (200)
T ss_pred CEEEEecC-Ch-hHHHHHhcCCeeEEEecCCCC--C-CCceeeeeec---------cceEEEEcCCCCccCCCCCHHHHh
Confidence 46777664 45 999999999999998743211 1 1122333331 133566676610001135677777
Q ss_pred CCcccCCCC
Q 044324 170 GHKSCHGSY 178 (291)
Q Consensus 170 GKksCHtG~ 178 (291)
+-+......
T Consensus 95 ~~~~i~~~~ 103 (200)
T cd08462 95 SAGHVVVRF 103 (200)
T ss_pred hCCCEEEec
Confidence 766655443
No 76
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=41.86 E-value=1.8e+02 Score=23.17 Aligned_cols=79 Identities=14% Similarity=0.056 Sum_probs=43.2
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCcee--eeecccCCcEEEEEEeecCCCceeEEEEEEecCcc-ccCCCCCcc
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLA--YTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVC-QENGGINLM 166 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~i--y~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~ 166 (291)
..++.... +..+-++.+.+|++|++....... ......+..+++.. ...+.|+.++.- ......+++
T Consensus 29 i~i~~~~~-~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~~~~l~~---------~~~~~~~~~~~p~~~~~~~~~~ 98 (200)
T cd08423 29 LEVRLREA-EPPESLDALRAGELDLAVVFDYPVTPPPDDPGLTRVPLLD---------DPLDLVLPADHPLAGREEVALA 98 (200)
T ss_pred CeEEEEeC-CHHHHHHHHhcCCccEEEEeccccccCCCCCCcEEEEecc---------CcEEEEecCCCCccccCCCCHH
Confidence 46777654 568899999999999988643210 00011122233321 123455555510 001146889
Q ss_pred cCCCCcccCCCC
Q 044324 167 DFKGHKSCHGSY 178 (291)
Q Consensus 167 dLkGKksCHtG~ 178 (291)
||.+-+.-....
T Consensus 99 ~l~~~~~i~~~~ 110 (200)
T cd08423 99 DLADEPWIAGCP 110 (200)
T ss_pred HhcCCceEEecC
Confidence 998877665433
No 77
>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=39.62 E-value=2e+02 Score=23.24 Aligned_cols=74 Identities=15% Similarity=0.153 Sum_probs=39.9
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
..++.+.+. . +.++.+.+|++|++....... . ......++..| ..+.|+.++--......+++||+
T Consensus 29 v~v~l~~~~-~-~~~~~l~~g~~D~~i~~~~~~--~-~~~~~~~l~~~---------~~~~v~~~~hpl~~~~~~l~dl~ 94 (200)
T cd08460 29 VRLRFVPES-D-KDVDALREGRIDLEIGVLGPT--G-PEIRVQTLFRD---------RFVGVVRAGHPLARGPITPERYA 94 (200)
T ss_pred CEEEEecCc-h-hHHHHHHCCCccEEEecCCCC--C-cchheeeeecc---------ceEEEEeCCCCCCCCCCCHHHHh
Confidence 356665553 3 889999999999988633210 1 11222333211 23556666510001124678887
Q ss_pred CCcccCCC
Q 044324 170 GHKSCHGS 177 (291)
Q Consensus 170 GKksCHtG 177 (291)
.-+.-...
T Consensus 95 ~~~~i~~~ 102 (200)
T cd08460 95 AAPHVSVS 102 (200)
T ss_pred cCCCEEEe
Confidence 77766543
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=39.58 E-value=1.3e+02 Score=24.17 Aligned_cols=75 Identities=13% Similarity=0.078 Sum_probs=41.9
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
..+..... +..+.++.+.+|++|++....... ...+...++..| ..++|+.++.-......+++||+
T Consensus 29 i~l~~~~~-~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~~~~l~~~---------~~~~v~~~~~~~~~~~~~~~~L~ 95 (200)
T cd08417 29 VRLRFVPL-DRDDLEEALESGEIDLAIGVFPEL---PPGLRSQPLFED---------RFVCVARKDHPLAGGPLTLEDYL 95 (200)
T ss_pred eEEEeccC-CHHHHHHHHHcCCCCEEEeecccC---CCccchhhhhcC---------ceEEEecCCCcccccccCHHHHh
Confidence 35666553 678999999999999998643211 111222333211 23555666511001134678888
Q ss_pred CCcccCCC
Q 044324 170 GHKSCHGS 177 (291)
Q Consensus 170 GKksCHtG 177 (291)
+.+.-...
T Consensus 96 ~~~~i~~~ 103 (200)
T cd08417 96 AAPHVLVS 103 (200)
T ss_pred CCCeEEec
Confidence 87766543
No 79
>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=39.25 E-value=1.5e+02 Score=24.16 Aligned_cols=77 Identities=10% Similarity=0.146 Sum_probs=43.0
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCc-cccCCCCCcccC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKV-CQENGGINLMDF 168 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dL 168 (291)
..++.+.+ +..+.++.+.+|++|++....... ...+.-.++..| ..+.|+.++- .+.....++++|
T Consensus 29 v~i~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~~~~l~~~---------~~~lv~~~~hpl~~~~~~~~~~L 95 (197)
T cd08452 29 VKVELREL-SSPDQVEELLKGRIDIGFLHPPIQ---HTALHIETVQSS---------PCVLALPKQHPLASKEEITIEDL 95 (197)
T ss_pred cEEEEEec-ChHHHHHHHHCCCccEEEeeCCCC---CCCeeEEEeeec---------cEEEEEeCCCccccCCCCCHHHh
Confidence 46777654 678899999999999988643211 011222222211 1244555551 000113578888
Q ss_pred CCCcccCCCCC
Q 044324 169 KGHKSCHGSYS 179 (291)
Q Consensus 169 kGKksCHtG~~ 179 (291)
.+-+.-+...+
T Consensus 96 ~~~~~i~~~~~ 106 (197)
T cd08452 96 RDEPIITVARE 106 (197)
T ss_pred cCCCEEeccCC
Confidence 88887765443
No 80
>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=38.15 E-value=27 Score=32.12 Aligned_cols=81 Identities=14% Similarity=0.125 Sum_probs=54.4
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
..++-+.+ +...|-+++.+|+.|+..++.-........|.+.|-+.= ...+ .-++|.++.+. .+++|+
T Consensus 24 ~~~~~~~~-~P~~Ln~~l~~g~~Dv~~iSs~~y~~~~~~y~ilp~~~i-~s~g--~v~Sv~l~s~~--------p~~~l~ 91 (251)
T PF02621_consen 24 FDFEIVRG-VPSELNQMLLEGELDVALISSIEYARNADDYLILPDLSI-SSDG--PVYSVLLFSKV--------PIEELD 91 (251)
T ss_dssp CCEEEEEE--HHHHHHHHHTTS-SEEEEEHHHHCTCTTTEEEESCECE-EECC--SSSSEEEEESS---------CCC-T
T ss_pred CceEEEEC-CHHHHHHHHHcCCCCEEEcCHHHHHHhhhhheecCCcEE-EEcC--CccceEEEECC--------ChHHcC
Confidence 45675555 789999999999999999988876654455666661100 1111 12557777765 578999
Q ss_pred CCcccCCCCCCCC
Q 044324 170 GHKSCHGSYSTAA 182 (291)
Q Consensus 170 GKksCHtG~~~ta 182 (291)
|++.--++-..|+
T Consensus 92 ~~~ial~~~S~TS 104 (251)
T PF02621_consen 92 GKKIALTGESTTS 104 (251)
T ss_dssp TSEEEESTTTSHH
T ss_pred CCeEEcCCCCHHH
Confidence 9999999998875
No 81
>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=38.01 E-value=71 Score=25.76 Aligned_cols=74 Identities=15% Similarity=0.088 Sum_probs=41.2
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccc-cCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQ-ENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~-~S~~~~l~dLk 169 (291)
.+.... .+..++++.+.+|++|++....... ...+.-+++..| ..+.|+.++.-. .....+++||+
T Consensus 30 ~i~~~~-~~~~~~~~~l~~~~~D~~i~~~~~~---~~~~~~~~l~~~---------~~~~~~~~~~~~~~~~~~~~~~l~ 96 (198)
T cd08433 30 RLRIVE-GLSGHLLEWLLNGRLDLALLYGPPP---IPGLSTEPLLEE---------DLFLVGPADAPLPRGAPVPLAELA 96 (198)
T ss_pred EEEEEe-cCcHHHHHHHhCCCCcEEEEeCCCC---CCCeeEEEeccc---------cEEEEecCCCccccCCCCCHHHhC
Confidence 455544 4678999999999999988633211 111222333322 224555555110 01235788998
Q ss_pred CCcccCCC
Q 044324 170 GHKSCHGS 177 (291)
Q Consensus 170 GKksCHtG 177 (291)
+.+.-...
T Consensus 97 ~~~~i~~~ 104 (198)
T cd08433 97 RLPLILPS 104 (198)
T ss_pred CCceEEcC
Confidence 88777644
No 82
>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=37.10 E-value=2.1e+02 Score=22.85 Aligned_cols=73 Identities=11% Similarity=0.034 Sum_probs=39.9
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
..+..+.. +..+.++.+.+|++|++..-.... ...+...++..| ..+.|+.++.-......++++|.
T Consensus 29 v~l~i~~~-~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~~~~l~~~---------~~~~v~~~~~~~~~~~~~~~~l~ 95 (200)
T cd08464 29 VRLVFRQV-DPFNVGDMLDRGEIDLAIGVFGEL---PAWLKREVLYTE---------GYACLFDPQQLSLSAPLTLEDYV 95 (200)
T ss_pred cEEEEecC-CcccHHHHHhcCcccEEEecCCCC---cccceeeeeccc---------ceEEEEeCCCccccCCCCHHHHh
Confidence 45666553 567899999999999998643321 112333334321 22556666511101124667777
Q ss_pred CCcccC
Q 044324 170 GHKSCH 175 (291)
Q Consensus 170 GKksCH 175 (291)
+.+...
T Consensus 96 ~~~~i~ 101 (200)
T cd08464 96 ARPHVL 101 (200)
T ss_pred cCCcEE
Confidence 665543
No 83
>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=36.58 E-value=1.1e+02 Score=27.34 Aligned_cols=26 Identities=12% Similarity=0.052 Sum_probs=19.2
Q ss_pred cccccccccCCCcEEEEechhhhhhh
Q 044324 248 SGAFRCLVEELGDIAFVRGDTALLYS 273 (291)
Q Consensus 248 ~GAlrCL~eg~GDVAFVk~~tV~~~~ 273 (291)
.-+++-|..|.-|+++....++..+.
T Consensus 153 ~~~~~aL~~GrvDa~i~~~~~~~~~~ 178 (246)
T TIGR03870 153 RKLVSEVATGKADLAVAFAPEVARYV 178 (246)
T ss_pred HHHHHHHHcCCCCEEEeeHHhHHHHH
Confidence 45678888888888888766665555
No 84
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=36.22 E-value=1.7e+02 Score=26.71 Aligned_cols=57 Identities=7% Similarity=-0.082 Sum_probs=35.7
Q ss_pred CCCceEEEecc-chHHHHHHHHHHhhcCCC--cceEEEecCCHHHHHHHHhccCCcEEEeCC
Q 044324 61 SEATIKWCAVR-DQYEDCEYLVSIISQSED--YTWKCVKRDTAQECLDSARKGEADIINLEA 119 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~~KC~~l~~~a~~~~~--p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~ 119 (291)
..+.+|+++.. ....-=..+ -..+.... ..|.++.. +..+.++++.+|++|++....
T Consensus 89 ~~g~l~i~~~~~~~~~~~~~~-l~~~~~~~P~v~i~~~~~-~~~~~~~~l~~g~~Dl~i~~~ 148 (305)
T PRK11151 89 MSGPLHIGLIPTVGPYLLPHI-IPMLHQTFPKLEMYLHEA-QTHQLLAQLDSGKLDCAILAL 148 (305)
T ss_pred CCceEEEEecchhHHHHHHHH-HHHHHHHCCCcEEEEEeC-CHHHHHHHHHcCCccEEEEec
Confidence 34689999977 432111111 11122222 46777665 468999999999999998754
No 85
>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=35.98 E-value=1.3e+02 Score=24.04 Aligned_cols=75 Identities=12% Similarity=0.088 Sum_probs=41.8
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCc-cccCCCCCcccCC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKV-CQENGGINLMDFK 169 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dLk 169 (291)
.++.+.. +..+.++.+.+|++|++........ ...+...++..| .-+.|+.++. .......+++||.
T Consensus 31 ~l~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~~~--~~~~~~~~l~~~---------~~~~v~~~~~~l~~~~~~~~~dL~ 98 (199)
T cd08451 31 ELTLEEA-NTAELLEALREGRLDAAFVRPPVAR--SDGLVLELLLEE---------PMLVALPAGHPLARERSIPLAALA 98 (199)
T ss_pred EEEEecC-ChHHHHHHHHCCCccEEEEecCCCC--CCceeEEEeecc---------cEEEEecCCCCCcccCccCHHHhc
Confidence 5555543 6688999999999999986432110 011222333311 2244555541 0001135789999
Q ss_pred CCcccCCC
Q 044324 170 GHKSCHGS 177 (291)
Q Consensus 170 GKksCHtG 177 (291)
+.+..+..
T Consensus 99 ~~~~i~~~ 106 (199)
T cd08451 99 DEPFILFP 106 (199)
T ss_pred CCCEEEec
Confidence 98887654
No 86
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=35.39 E-value=1.7e+02 Score=23.14 Aligned_cols=70 Identities=11% Similarity=0.052 Sum_probs=41.0
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCC-CCCcccC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENG-GINLMDF 168 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~-~~~l~dL 168 (291)
..+.++.+ +..+-++.+.+|++|++....... ...+..+++..| ..++|+.++ .+ ..+++||
T Consensus 29 i~l~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~~~~l~~~---------~~~~v~~~~----~~~~~~~~~l 91 (193)
T cd08442 29 VDLSLSTG-TTGALIQAVLEGRLDGAFVAGPVE---HPRLEQEPVFQE---------ELVLVSPKG----HPPVSRAEDL 91 (193)
T ss_pred ceEEEEeC-CcHHHHHHHHCCCccEEEEeCCCC---CCCcEEEEeecC---------cEEEEecCC----CcccccHHHh
Confidence 45677654 678899999999999988643221 111222233211 235667776 32 2356777
Q ss_pred CCCcccCC
Q 044324 169 KGHKSCHG 176 (291)
Q Consensus 169 kGKksCHt 176 (291)
+..+.-..
T Consensus 92 ~~~~~i~~ 99 (193)
T cd08442 92 AGSTLLAF 99 (193)
T ss_pred CCCceEEe
Confidence 77766543
No 87
>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=35.32 E-value=2.5e+02 Score=22.96 Aligned_cols=76 Identities=14% Similarity=0.015 Sum_probs=41.0
Q ss_pred CcceEEEe-cCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCcc-ccCCCCCcc
Q 044324 89 DYTWKCVK-RDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVC-QENGGINLM 166 (291)
Q Consensus 89 ~p~l~CV~-~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~ 166 (291)
.|.++... .....+.++.+.+|++|++....... ...+.-.++..| ..+.|+.++-- +.....+++
T Consensus 27 ~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~---~~~~~~~~l~~~---------~~~lv~~~~h~l~~~~~i~~~ 94 (198)
T cd08486 27 TPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPR---HPGIEIVNIAQE---------DLYLAVHRSQSGKFGKTCKLA 94 (198)
T ss_pred CCCeEEEEEECCHHHHHHHHHcCCceEEEecCCCC---CCceEEEEEeec---------cEEEEecCCCccccCCcccHH
Confidence 36554432 24678999999999999998643211 111222233321 22445555410 001135778
Q ss_pred cCCCCcccCC
Q 044324 167 DFKGHKSCHG 176 (291)
Q Consensus 167 dLkGKksCHt 176 (291)
||.+-..-..
T Consensus 95 dL~~~~~i~~ 104 (198)
T cd08486 95 DLRAVELTLF 104 (198)
T ss_pred HHcCCCeEee
Confidence 8888765543
No 88
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=35.00 E-value=2.3e+02 Score=25.29 Aligned_cols=102 Identities=8% Similarity=-0.033 Sum_probs=54.6
Q ss_pred CCCceEEEecc-chHHHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCc--EEEE
Q 044324 61 SEATIKWCAVR-DQYEDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSM--KAIA 135 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L--~PIl 135 (291)
....+|+.+.. .-..-=..+ -..+...-| .|+... .+..+.++.+.+|++|++......- ..++ .++.
T Consensus 87 ~~g~l~i~~~~~~~~~~~~~~-l~~~~~~~P~i~i~v~~-~~~~~~~~~l~~g~~Di~i~~~~~~-----~~~~~~~~l~ 159 (290)
T PRK10837 87 DNGALRIYASSTIGNYILPAM-IARYRRDYPQLPLELSV-GNSQDVINAVLDFRVDIGLIEGPCH-----SPELISEPWL 159 (290)
T ss_pred hCCeEEEEecchhHhhhhHHH-HHHHHHHCCCceEEEEE-CCHHHHHHHHHhCCceEEEecCCCC-----CCceeEEEee
Confidence 35689998887 332111111 111211124 455444 3778999999999999998643211 1122 2222
Q ss_pred EEeecCCCceeEEEEEEecCccccCCCCCcccCCCCcccCCCC
Q 044324 136 NEVYCDHAQSYDAVAVINRKVCQENGGINLMDFKGHKSCHGSY 178 (291)
Q Consensus 136 ~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLkGKksCHtG~ 178 (291)
....+.|+.++.-......+++||++.+......
T Consensus 160 ---------~~~~~lv~~~~hpl~~~~i~~~~L~~~~~i~~~~ 193 (290)
T PRK10837 160 ---------EDELVVFAAPDSPLARGPVTLEQLAAAPWILRER 193 (290)
T ss_pred ---------cceEEEEEcCCChhhcCCCCHHHHhcCCeEEecC
Confidence 1234666666611001235788888887776554
No 89
>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=34.80 E-value=2.3e+02 Score=22.56 Aligned_cols=28 Identities=11% Similarity=-0.016 Sum_probs=22.6
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLE 118 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld 118 (291)
..++.+.. +..+.++.+.+|++|++...
T Consensus 29 i~~~i~~~-~~~~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08456 29 VTISIHTR-DSPTVEQWLSAQQCDLGLVS 56 (196)
T ss_pred cEEEEEeC-CHHHHHHHHHcCCccEEEEe
Confidence 46777765 56789999999999999864
No 90
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=34.33 E-value=2.4e+02 Score=22.57 Aligned_cols=28 Identities=11% Similarity=0.154 Sum_probs=21.4
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLE 118 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld 118 (291)
..++.+.+ +..+.++.+.+|++|++...
T Consensus 29 v~l~~~~~-~~~~~~~~l~~g~~Dl~i~~ 56 (200)
T cd08466 29 ISLRESPS-SEEDLFEDLRLQEVDLVIDY 56 (200)
T ss_pred CEEEEecC-chHhHHHHHHcCCccEEEec
Confidence 35555554 56788999999999998863
No 91
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=33.76 E-value=3.6e+02 Score=24.28 Aligned_cols=103 Identities=12% Similarity=0.045 Sum_probs=57.8
Q ss_pred CceEEEecc-chHHHHHHHHHHhhcCCCcce--EEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEee
Q 044324 63 ATIKWCAVR-DQYEDCEYLVSIISQSEDYTW--KCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVY 139 (291)
Q Consensus 63 ~~vRwCv~S-~E~~KC~~l~~~a~~~~~p~l--~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y 139 (291)
..+|+.+.. ....-...+ -..+....|.+ ..... +..+.++.+.+|+.|++.+.... . ...+.-+|+..|
T Consensus 90 ~~l~Ig~~~~~~~~~l~~~-~~~~~~~~p~v~i~~~~~-~~~~~~~~l~~~~~D~~i~~~~~-~--~~~l~~~~l~~~-- 162 (296)
T PRK09906 90 RQLTIGFVPSAEVNLLPKV-LPMFRLRHPDTLIELVSL-ITTQQEEKLRRGELDVGFMRHPV-Y--SDEIDYLELLDE-- 162 (296)
T ss_pred CcEEEEEecchhhhHHHHH-HHHHHHHCCCeEEEEEeC-CcHHHHHHHHcCCeeEEEecCCC-C--CCCceEEEEecc--
Confidence 458888877 554444444 22333333544 44443 46889999999999999975542 1 112223344322
Q ss_pred cCCCceeEEEEEEecCcc-ccCCCCCcccCCCCcccCCCCC
Q 044324 140 CDHAQSYDAVAVINRKVC-QENGGINLMDFKGHKSCHGSYS 179 (291)
Q Consensus 140 ~~~~~~Y~aVAVVkK~~~-~~S~~~~l~dLkGKksCHtG~~ 179 (291)
..+.|++++.- +.....+++||++-..-+...+
T Consensus 163 -------~~~~v~~~~~pl~~~~~i~~~~L~~~~~i~~~~~ 196 (296)
T PRK09906 163 -------PLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPA 196 (296)
T ss_pred -------cEEEEecCCCccccCCCcCHHHHcCCCEEeccCC
Confidence 22555666510 0011357899998888765543
No 92
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=33.44 E-value=1.9e+02 Score=26.70 Aligned_cols=116 Identities=9% Similarity=-0.032 Sum_probs=58.8
Q ss_pred CCCceEEEecc-chHHHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEE
Q 044324 61 SEATIKWCAVR-DQYEDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANE 137 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E 137 (291)
..+++|+++.. ....-=..+ -..+....| .+.+... +..+.++++.+|++|++......... ......|+.
T Consensus 91 ~~g~l~Ig~~~~~~~~~l~~~-i~~f~~~~P~i~l~~~~~-~~~~~~~~L~~~~~D~~i~~~~~~~~--~~l~~~~l~-- 164 (309)
T PRK12683 91 DSGHLTVATTHTQARYALPKV-VRQFKEVFPKVHLALRQG-SPQEIAEMLLNGEADIGIATEALDRE--PDLVSFPYY-- 164 (309)
T ss_pred CCceEEEEeccchHHHHHHHH-HHHHHHHCCCceEEEEeC-CHHHHHHHHHcCCccEEEecCCCCCC--CCceEEEcc--
Confidence 45789998876 432211112 122322224 5665553 78999999999999998753211111 111122222
Q ss_pred eecCCCceeEEEEEEecCcc-ccCCCCCcccCCCCcccCCCCCCCCCchhHHHHH
Q 044324 138 VYCDHAQSYDAVAVINRKVC-QENGGINLMDFKGHKSCHGSYSTAAGWNYPVNHI 191 (291)
Q Consensus 138 ~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~dLkGKksCHtG~~~taGW~iPvg~L 191 (291)
. +..+.|+.++.- +.....+++||++-+.-.... ..+....+..+
T Consensus 165 ---~----~~~~~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~--~~~~~~~~~~~ 210 (309)
T PRK12683 165 ---S----WHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQ--GFTGRSRIDQA 210 (309)
T ss_pred ---c----CeEEEEecCCCCcccCCccCHHHHhcCCeEeccC--CCcHHHHHHHH
Confidence 1 233566777610 001135678888776654333 33344444433
No 93
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=33.12 E-value=3e+02 Score=24.64 Aligned_cols=105 Identities=8% Similarity=-0.009 Sum_probs=55.8
Q ss_pred CCCceEEEecc-chHHHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEE
Q 044324 61 SEATIKWCAVR-DQYEDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANE 137 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E 137 (291)
...++|+.+.. .....-..+ -..+....| .+..+.. +..+.++.+.+|++|++.+....... ...+.-.|+..|
T Consensus 95 ~~~~l~I~~~~~~~~~~l~~~-l~~f~~~~p~i~l~i~~~-~~~~~~~~l~~g~~D~~i~~~~~~~~-~~~l~~~~l~~~ 171 (294)
T PRK09986 95 EAGRIEIGIVGTALWGRLRPA-MRHFLKENPNVEWLLREL-SPSMQMAALERRELDAGIWRMADLEP-NPGFTSRRLHES 171 (294)
T ss_pred CcceEEEEEehHHhHHHHHHH-HHHHHHhCCCeEEEEEeC-CHHHHHHHHHcCCCCEEEecCCccCC-CCCeEEEEeecc
Confidence 35678887765 433222222 223333334 4566543 67899999999999999863321100 112222334311
Q ss_pred eecCCCceeEEEEEEecCcc-ccCCCCCcccCCCCcccCCC
Q 044324 138 VYCDHAQSYDAVAVINRKVC-QENGGINLMDFKGHKSCHGS 177 (291)
Q Consensus 138 ~y~~~~~~Y~aVAVVkK~~~-~~S~~~~l~dLkGKksCHtG 177 (291)
..+.|+.++.- ......+++||.+...-+..
T Consensus 172 ---------~~~~v~~~~~~l~~~~~~~~~dL~~~~~i~~~ 203 (294)
T PRK09986 172 ---------AFAVAVPEEHPLASRSSVPLKALRNEYFITLP 203 (294)
T ss_pred ---------cEEEEEcCCCCcccCCccCHHHHcCCCEEecC
Confidence 23566666510 00113578999888766543
No 94
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=32.31 E-value=69 Score=28.18 Aligned_cols=70 Identities=16% Similarity=0.142 Sum_probs=40.6
Q ss_pred EEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCC--CCCcccCCCC
Q 044324 94 CVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENG--GINLMDFKGH 171 (291)
Q Consensus 94 CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~--~~~l~dLkGK 171 (291)
-+....-..-+..++.|+.|++.-.-...- .+. -.+. . .+-|. ....+.+|+++ +. +.+++||+||
T Consensus 80 ~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~-er~-~~~~-f-s~py~----~~~~~~~~~~~----~~~~~~~~~DL~gk 147 (275)
T COG0834 80 EFVPVAWDGLIPALKAGKVDIIIAGMTITP-ERK-KKVD-F-SDPYY----YSGQVLLVKKD----SDIGIKSLEDLKGK 147 (275)
T ss_pred EEeccchhhhhHHHhcCCcCEEEeccccCH-HHh-cccc-c-ccccc----ccCeEEEEECC----CCcCcCCHHHhCCC
Confidence 344447799999999999999987722222 110 0000 1 11121 11235555555 32 4689999998
Q ss_pred cccC
Q 044324 172 KSCH 175 (291)
Q Consensus 172 ksCH 175 (291)
+.+-
T Consensus 148 ~v~v 151 (275)
T COG0834 148 KVGV 151 (275)
T ss_pred EEEE
Confidence 8765
No 95
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=30.19 E-value=53 Score=31.83 Aligned_cols=86 Identities=15% Similarity=0.103 Sum_probs=55.2
Q ss_pred cceEEEecC---CHHHHHHHHhccCCcEEEeCCceeeeecccCCc--EEEEEEeecC-----C------------CceeE
Q 044324 90 YTWKCVKRD---TAQECLDSARKGEADIINLEAGLAYTAFLNFSM--KAIANEVYCD-----H------------AQSYD 147 (291)
Q Consensus 90 p~l~CV~~~---s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L--~PIl~E~y~~-----~------------~~~Y~ 147 (291)
..|+-.... +..+=|+.++.|..|++..+.+.+=.-...+++ -|.+...+.+ + ...+.
T Consensus 61 l~i~vfP~~qLG~~~~~ie~l~~G~id~~~~s~~~l~~~~P~~~v~~lPflf~d~~~~~~~~~~~~g~~l~~~~e~~g~~ 140 (332)
T COG1638 61 LKIEVFPNSQLGGEAEMIEQLRSGTLDIGVVSLGFLAGLVPEFGVFDLPFLFRDEEHARRVLDSEFGEELLKSLEAKGLK 140 (332)
T ss_pred EEEEECCCcccCcHHHHHHHHhcCCeeEEeccchhhcccCCcceeecCCeeeCCHHHHHHHHccHHHHHHHHHHHHcCCE
Confidence 444444433 678999999999999999987754222244555 3777655532 1 12566
Q ss_pred EEEEEecCc---cccC-CCCCcccCCCCcccC
Q 044324 148 AVAVINRKV---CQEN-GGINLMDFKGHKSCH 175 (291)
Q Consensus 148 aVAVVkK~~---~~~S-~~~~l~dLkGKksCH 175 (291)
.+++-..+. ..+. ++.+.+||||.|.=-
T Consensus 141 ~l~~~~~G~R~~t~~k~PI~~peDlkGlkiRv 172 (332)
T COG1638 141 GLAFWENGFRQFTSNKRPIKTPEDLKGLKIRV 172 (332)
T ss_pred EEEEecCceeeeecCCCCCCChHHhCCCeeec
Confidence 666666332 2112 688999999999743
No 96
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=29.96 E-value=1.2e+02 Score=26.64 Aligned_cols=55 Identities=16% Similarity=0.084 Sum_probs=37.4
Q ss_pred eEEEecc-chHHHHHHHHHHhhcCCCcceEEEecCCHHHHHHHHhccCCcEEEeCCceeee
Q 044324 65 IKWCAVR-DQYEDCEYLVSIISQSEDYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYT 124 (291)
Q Consensus 65 vRwCv~S-~E~~KC~~l~~~a~~~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~ 124 (291)
.|..|.. -. ... ........+.+.=+.-.+..+.++++++|++|++..|...+..
T Consensus 147 k~v~v~~gt~----~~~-~~~~~~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d~~~~~~ 202 (275)
T COG0834 147 KKVGVQLGTT----DEA-EEKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSDSAVLAG 202 (275)
T ss_pred CEEEEEcCcc----hhH-HHHHhhccCCceEEeeCCHHHHHHHHHcCCccEEEcchHhhhh
Confidence 6778877 43 111 1111112245666777778999999999999999999886544
No 97
>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=29.96 E-value=1.4e+02 Score=25.71 Aligned_cols=89 Identities=10% Similarity=-0.049 Sum_probs=47.6
Q ss_pred HHhhcCC-CcceEEEecCCHHHHHHHHhccC-CcEEEeCCceee-eecccCCcEEEEEEeecCCCceeEEEEEEecCccc
Q 044324 82 SIISQSE-DYTWKCVKRDTAQECLDSARKGE-ADIINLEAGLAY-TAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQ 158 (291)
Q Consensus 82 ~~a~~~~-~p~l~CV~~~s~~dCm~~I~~g~-ADiv~ld~~~iy-~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~ 158 (291)
..+|... +..+.=+ .....+.+++|.+|. +|++.......+ ......-+.|.....+.. -..|.+++++
T Consensus 12 ~~~f~~~~gi~V~~~-~~gs~~l~~~l~~~~~aDv~~~~~~~~~~~l~~~g~~~~~~~~~~~~----~~~~l~~~~~--- 83 (216)
T TIGR01256 12 AKQFEKRTGNKVVFS-FGSSGTLYTQIENGAPADLFISADNKWPKKLVDKGLVVAGSRFTYAG----NKLVLISPKN--- 83 (216)
T ss_pred HHHHHHhhCCeEEEE-eCChHHHHHHHHcCCCCcEEEECCHHHHHHHHHCCCCCCCchheEEc----cEEEEEEECC---
Confidence 3344432 3456544 345667899999875 999998665322 221212223322111211 1345566776
Q ss_pred cCCCCCcccCC----CCcccCCCCC
Q 044324 159 ENGGINLMDFK----GHKSCHGSYS 179 (291)
Q Consensus 159 ~S~~~~l~dLk----GKksCHtG~~ 179 (291)
..+.+++||+ +.|.-.+.+.
T Consensus 84 -~~~~s~~dL~~~~~~~~i~~~~P~ 107 (216)
T TIGR01256 84 -RVVDDLDILKKWVADKRVAIGDPK 107 (216)
T ss_pred -CCcCcHHHHhhcccCCeEEecCCC
Confidence 4467899984 3455555543
No 98
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=29.82 E-value=1.4e+02 Score=26.77 Aligned_cols=79 Identities=13% Similarity=0.024 Sum_probs=46.7
Q ss_pred HHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCC-CceeEEEEEEecCccccCCCCCcccCCCCcccCCCCC
Q 044324 101 QECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDH-AQSYDAVAVINRKVCQENGGINLMDFKGHKSCHGSYS 179 (291)
Q Consensus 101 ~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~-~~~Y~aVAVVkK~~~~~S~~~~l~dLkGKksCHtG~~ 179 (291)
.|.-..|..|.||+.+.+-+-+...+ .++. |...-+ +..-.+||+ +++ +.+.+.++|+|+|..---.+
T Consensus 50 ~Dip~yV~~G~aDlGI~G~D~l~E~~--~~v~----~~~dL~fg~crl~vA~-p~~----~~~~~~~~l~~~rIATkyp~ 118 (182)
T TIGR00070 50 QDIPTYVEHGAADLGITGYDVLLESG--ADVY----ELLDLGFGKCRLVLAV-PQE----SDISSVEDLKGKRIATKYPN 118 (182)
T ss_pred chhHHHHhCCCccEEEecchhhhhCC--CCEE----EEeecCcCceEEEEEE-ECC----CCCCChHHhCCCEEEECCHH
Confidence 67888999999999976655554332 2333 222211 224456665 555 44788999999885432111
Q ss_pred CCCCchhHHHHHHhCCC
Q 044324 180 TAAGWNYPVNHIKGSTP 196 (291)
Q Consensus 180 ~taGW~iPvg~L~~~~~ 196 (291)
+--.++.++|+
T Consensus 119 ------i~~~~f~~~Gi 129 (182)
T TIGR00070 119 ------LARRYFEKKGI 129 (182)
T ss_pred ------HHHHHHHHcCC
Confidence 22345666665
No 99
>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=29.28 E-value=1.3e+02 Score=23.97 Aligned_cols=28 Identities=11% Similarity=0.100 Sum_probs=22.4
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLE 118 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld 118 (291)
..++.... +..+.++.+.+|++|++...
T Consensus 28 i~l~i~~~-~~~~~~~~l~~g~~Dl~i~~ 55 (197)
T cd08419 28 VEVSLRVG-NREQVLERLADNEDDLAIMG 55 (197)
T ss_pred ceEEEEEC-CHHHHHHHHhcCCccEEEec
Confidence 35666654 67889999999999999864
No 100
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=27.34 E-value=69 Score=28.00 Aligned_cols=53 Identities=15% Similarity=0.100 Sum_probs=35.4
Q ss_pred ceEEEecc-chHHHHHHHHHHhhcCCCcceEEEecCCHHHHHHHHhccCCcEEEeCCcee
Q 044324 64 TIKWCAVR-DQYEDCEYLVSIISQSEDYTWKCVKRDTAQECLDSARKGEADIINLEAGLA 122 (291)
Q Consensus 64 ~vRwCv~S-~E~~KC~~l~~~a~~~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~i 122 (291)
..|+|++. .... +.+ ...+.. .+.=+...+..++++++.+|++|+++.+...+
T Consensus 131 g~~i~~~~g~~~~--~~l-~~~~~~---~~~~~~~~s~~~~~~~L~~g~vD~~v~~~~~~ 184 (250)
T TIGR01096 131 GKTVGVQSGTTHE--QYL-KDYFKP---GVDIVEYDSYDNANMDLKAGRIDAVFTDASVL 184 (250)
T ss_pred CCEEEEecCchHH--HHH-HHhccC---CcEEEEcCCHHHHHHHHHcCCCCEEEeCHHHH
Confidence 34788877 3222 334 322211 34445667899999999999999999987743
No 101
>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=27.20 E-value=3.2e+02 Score=21.72 Aligned_cols=27 Identities=11% Similarity=0.122 Sum_probs=20.5
Q ss_pred ceEEEecCCHHHHHHHHhccCCcEEEeC
Q 044324 91 TWKCVKRDTAQECLDSARKGEADIINLE 118 (291)
Q Consensus 91 ~l~CV~~~s~~dCm~~I~~g~ADiv~ld 118 (291)
.++... .+..+-++.+.+|++|++...
T Consensus 30 ~v~~~~-~~~~~~~~~l~~g~~D~~i~~ 56 (198)
T cd08447 30 DLVLRE-MVTTDQIEALESGRIDLGLLR 56 (198)
T ss_pred EEEEEe-CCHHHHHHHHHcCCceEEEec
Confidence 344333 367889999999999999864
No 102
>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=26.21 E-value=1.2e+02 Score=26.90 Aligned_cols=99 Identities=15% Similarity=0.122 Sum_probs=52.3
Q ss_pred CCCceEEEecc-chHHHHHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEE
Q 044324 61 SEATIKWCAVR-DQYEDCEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANE 137 (291)
Q Consensus 61 ~~~~vRwCv~S-~E~~KC~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E 137 (291)
..+++|+++.. .-.... + . .+....| .+..+.. +..+.++++.+|++|++...... ....+..+|+..|
T Consensus 85 ~~~~l~ig~~~~~~~~~~--l-~-~~~~~~p~v~l~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~~~~l~~~ 156 (279)
T TIGR03339 85 REGSLRIAATAPYYVLDL--V-A-RFRQRYPGIEVSVRIG-NSQEVLQALQSYRVDVAVSSEVV---DDPRLDRVVLGND 156 (279)
T ss_pred cceEEEEeCchHHHHHHH--H-H-HHHHHCCCcEEEEEEC-CHHHHHHHHHcCCCcEEEEeccc---CCCceEEEEcCCc
Confidence 44688998876 322111 1 1 1222224 4555544 78899999999999999863321 1112233344321
Q ss_pred eecCCCceeEEEEEEecCc-cccCCCCCcccCCCCcccCC
Q 044324 138 VYCDHAQSYDAVAVINRKV-CQENGGINLMDFKGHKSCHG 176 (291)
Q Consensus 138 ~y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dLkGKksCHt 176 (291)
..+.|+.++. .+.....+++||++.+.-..
T Consensus 157 ---------~~~lv~s~~~pl~~~~~i~~~~L~~~~~i~~ 187 (279)
T TIGR03339 157 ---------PLVAVVHRQHPLAERESVTLEELAGQPLLMR 187 (279)
T ss_pred ---------eEEEEECCCCccccCCCcCHHHHhCCCeEEe
Confidence 2345555551 11112357888887665543
No 103
>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=25.74 E-value=3.5e+02 Score=21.65 Aligned_cols=104 Identities=10% Similarity=-0.027 Sum_probs=52.1
Q ss_pred ceEEEecc-chHHHHHHHHHHhhcCCCcceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCC
Q 044324 64 TIKWCAVR-DQYEDCEYLVSIISQSEDYTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDH 142 (291)
Q Consensus 64 ~vRwCv~S-~E~~KC~~l~~~a~~~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~ 142 (291)
++|+++.. .-..--..............++... .+..+.++.+++|+.|++..... .- . ..+...++..+
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~~v~l~l~~-~~~~~~~~~l~~~~~D~~i~~~~-~~-~-~~~~~~~l~~~----- 71 (195)
T cd08428 1 TLPVAVNADSLATWFLPALAPVLKRERILLDLIV-DDEDRTHDLLRDGEVVGCISTQA-QP-M-QGCRSDYLGSM----- 71 (195)
T ss_pred CEEEEechhHHHHHhHHHHHHHHhCcCeEEEEEe-CCchhHHHHHHcCcceEEEEecC-CC-C-CCceeEEeeee-----
Confidence 46777764 2222222221222222234566554 46778999999999997654221 00 0 11222333311
Q ss_pred CceeEEEEEEecCcccc--CCCCCcccCCCCcccCCCCCC
Q 044324 143 AQSYDAVAVINRKVCQE--NGGINLMDFKGHKSCHGSYST 180 (291)
Q Consensus 143 ~~~Y~aVAVVkK~~~~~--S~~~~l~dLkGKksCHtG~~~ 180 (291)
..+.|+.++.-.. ....+++||++.+..+...+.
T Consensus 72 ----~~~~~~~~~~~~~~~~~~i~~~~L~~~~~i~~~~~~ 107 (195)
T cd08428 72 ----DYLLVASPDFAARYFPNGLTREALLKAPAVAFNRKD 107 (195)
T ss_pred ----eEEEEECCcchhhcCCCCCCHHHHhcCcEEEEcCCC
Confidence 1233344431110 024678999999988765443
No 104
>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=24.77 E-value=1.3e+02 Score=26.09 Aligned_cols=25 Identities=16% Similarity=0.234 Sum_probs=21.4
Q ss_pred CCHHHHHHHHhccCCcEEEeCCcee
Q 044324 98 DTAQECLDSARKGEADIINLEAGLA 122 (291)
Q Consensus 98 ~s~~dCm~~I~~g~ADiv~ld~~~i 122 (291)
.+..++++++..|++|++..+...+
T Consensus 141 ~~~~~~~~~l~~G~~Da~i~~~~~~ 165 (232)
T TIGR03871 141 SPPGRMVEDLAAGEIDVAIVWGPIA 165 (232)
T ss_pred CCHHHHHHHHHcCCcCEEEeccHHH
Confidence 3789999999999999999986543
No 105
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=24.71 E-value=37 Score=24.59 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=18.1
Q ss_pred CCCCccCccccccccccCCCcEEE
Q 044324 240 SNSLYFGDSGAFRCLVEELGDIAF 263 (291)
Q Consensus 240 ~~e~Y~Gy~GAlrCL~eg~GDVAF 263 (291)
.++.||||.|-.+=+.+|+.-|-|
T Consensus 13 ~~~~Y~~y~G~VQRvsdgkaaVLF 36 (53)
T PF11623_consen 13 PNDIYYGYEGFVQRVSDGKAAVLF 36 (53)
T ss_dssp TTSTTTT-EEEEEEEETTEEEEEE
T ss_pred CCCccchheEEEEEeeCCeEEEEe
Confidence 478999999999988887655544
No 106
>cd08457 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant h
Probab=24.46 E-value=2.8e+02 Score=22.25 Aligned_cols=76 Identities=11% Similarity=0.043 Sum_probs=41.2
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCc-cccCCCCCcccC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKV-CQENGGINLMDF 168 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dL 168 (291)
..+..+.. ...+-++.+.+|++|++......- ...+...++. .+ . + +.++.++. .......+++||
T Consensus 29 i~l~~~~~-~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~~~~l~-----~~--~-~-~~~~~~~~~l~~~~~~~~~~l 95 (196)
T cd08457 29 LHLSLMGL-SSSQVLEAVASGRADLGIADGPLE---ERQGFLIETR-----SL--P-A-VVAVPMGHPLAQLDVVSPQDL 95 (196)
T ss_pred eEEEEEec-CcHHHHHHHHcCCccEEEeccCCC---CCCcEEEEec-----cC--C-e-EEEeeCCCccccCCccCHHHh
Confidence 35666654 457888999999999998643211 1111222222 11 1 2 33444441 111113578999
Q ss_pred CCCcccCCCC
Q 044324 169 KGHKSCHGSY 178 (291)
Q Consensus 169 kGKksCHtG~ 178 (291)
++.+..+...
T Consensus 96 ~~~~~i~~~~ 105 (196)
T cd08457 96 AGERIITLEN 105 (196)
T ss_pred CCCceEecCC
Confidence 9888777543
No 107
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=24.02 E-value=3.2e+02 Score=25.20 Aligned_cols=56 Identities=5% Similarity=0.032 Sum_probs=35.1
Q ss_pred CCCCceEEEecc-chHHH-HHHHHHHhhcCCCc--ceEEEecCCHHHHHHHHhccCCcEEEeC
Q 044324 60 GSEATIKWCAVR-DQYED-CEYLVSIISQSEDY--TWKCVKRDTAQECLDSARKGEADIINLE 118 (291)
Q Consensus 60 ~~~~~vRwCv~S-~E~~K-C~~l~~~a~~~~~p--~l~CV~~~s~~dCm~~I~~g~ADiv~ld 118 (291)
.....+|+.+.. .-... -..+ . .+....| .+.... .+..++++.+.+|++|++...
T Consensus 90 ~~~g~l~Ig~~~~~~~~~l~~~l-~-~~~~~~p~i~l~~~~-~~~~~~~~~L~~g~~D~~i~~ 149 (313)
T PRK12684 90 QDQGNLTIATTHTQARYALPAAI-K-EFKKRYPKVRLSILQ-GSPTQIAEMVLHGQADLAIAT 149 (313)
T ss_pred cCCCeEEEEechHHHHHHhHHHH-H-HHHHHCCCceEEEEe-CChHHHHHHHHCCCcCEEEee
Confidence 345689999877 43322 2222 2 2222223 445443 468999999999999999764
No 108
>PF15071 TMEM220: Transmembrane family 220, helix
Probab=23.37 E-value=27 Score=28.34 Aligned_cols=15 Identities=47% Similarity=0.625 Sum_probs=12.0
Q ss_pred CCCcchhhhhcccCC
Q 044324 32 PAPLTVEEGREEFGD 46 (291)
Q Consensus 32 ~~~~~~~~~~~~~~~ 46 (291)
.-.+..|||||-+|-
T Consensus 76 ~~~~~~EegRE~~GL 90 (104)
T PF15071_consen 76 SEKPHIEEGREFFGL 90 (104)
T ss_pred ccchhHHHHHHHHhH
Confidence 446689999999984
No 109
>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=23.05 E-value=97 Score=24.69 Aligned_cols=71 Identities=13% Similarity=0.090 Sum_probs=35.9
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCccccCCCCCcccCC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKVCQENGGINLMDFK 169 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~~~~S~~~~l~dLk 169 (291)
..++.+... -++.+.+|++|++....... ...+.-.++..| ..+.|+.++.-......+++||+
T Consensus 29 v~i~~~~~~----~~~~l~~g~~D~~i~~~~~~---~~~~~~~~l~~~---------~~~~v~~~~~~~~~~~i~~~~l~ 92 (194)
T cd08432 29 IDLRLSTSD----RLVDFAREGIDLAIRYGDGD---WPGLEAERLMDE---------ELVPVCSPALLAGLPLLSPADLA 92 (194)
T ss_pred eEEEEEecC----CccccccccccEEEEecCCC---CCCcceEEccCC---------cEEEecCHHHHHhcCCCCHHHhh
Confidence 355555442 47889999999987532211 111222233211 12445555411111235788888
Q ss_pred CCcccCC
Q 044324 170 GHKSCHG 176 (291)
Q Consensus 170 GKksCHt 176 (291)
+-+.-..
T Consensus 93 ~~~~i~~ 99 (194)
T cd08432 93 RHTLLHD 99 (194)
T ss_pred cCceEEe
Confidence 7765543
No 110
>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=22.72 E-value=2.6e+02 Score=22.68 Aligned_cols=77 Identities=14% Similarity=0.139 Sum_probs=42.7
Q ss_pred cceEEEecCCHHHHHHHHhccCCcEEEeCCceeeeecccCCcEEEEEEeecCCCceeEEEEEEecCc-cccCCCCCcccC
Q 044324 90 YTWKCVKRDTAQECLDSARKGEADIINLEAGLAYTAFLNFSMKAIANEVYCDHAQSYDAVAVINRKV-CQENGGINLMDF 168 (291)
Q Consensus 90 p~l~CV~~~s~~dCm~~I~~g~ADiv~ld~~~iy~A~~~~~L~PIl~E~y~~~~~~Y~aVAVVkK~~-~~~S~~~~l~dL 168 (291)
..++.+.. +..+.++.|.+|++|++..-.... ....+.-.++.. ...+.|+.++. .+.....+++||
T Consensus 29 i~v~~~~~-~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~~~~~l~~---------~~~~~v~~~~hpl~~~~~i~~~~l 96 (198)
T cd08413 29 VKLSLHQG-TPSQIAEMVLKGEADIAIATEALD--DHPDLVTLPCYR---------WNHCVIVPPGHPLADLGPLTLEDL 96 (198)
T ss_pred eEEEEEeC-CHHHHHHHHHcCCCCEEEEccCCC--CCCCcEEEEeee---------eeEEEEecCCCcccccCCCCHHHH
Confidence 35666654 567899999999999988632110 001122233321 23356666651 000113578888
Q ss_pred CCCcccCCCC
Q 044324 169 KGHKSCHGSY 178 (291)
Q Consensus 169 kGKksCHtG~ 178 (291)
++.+.-....
T Consensus 97 ~~~~~i~~~~ 106 (198)
T cd08413 97 AQYPLITYDF 106 (198)
T ss_pred hcCCEEECCC
Confidence 8888766443
No 111
>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=20.68 E-value=2.5e+02 Score=25.38 Aligned_cols=99 Identities=15% Similarity=0.201 Sum_probs=59.2
Q ss_pred HHhhcCCCcceEEEecCCHHHHHHHHhccCCcEEE---eCCc-eeeeecc--cCCcEEEEEEeecCCCceeEEEEEEecC
Q 044324 82 SIISQSEDYTWKCVKRDTAQECLDSARKGEADIIN---LEAG-LAYTAFL--NFSMKAIANEVYCDHAQSYDAVAVINRK 155 (291)
Q Consensus 82 ~~a~~~~~p~l~CV~~~s~~dCm~~I~~g~ADiv~---ld~~-~iy~A~~--~~~L~PIl~E~y~~~~~~Y~aVAVVkK~ 155 (291)
...+...+..++=+...++....+++.+|++|++. +... ..|...- ...+. ++..... ...++.+|-+.-
T Consensus 21 ~~~Le~~G~~v~~~~~~~~~~~~~al~~G~iD~~~~~w~~~~~~~~~~~~~~~~~~~-~l~~~~~---~~~~g~~Vp~~~ 96 (257)
T PF04069_consen 21 AQLLEAAGYVVEVVNLGSTPVIFAALASGDIDIYPEEWTPTTYEAYKKALEEKLGVV-WLGPLGA---GNTYGWAVPKYV 96 (257)
T ss_dssp HHHHHHTTEEEEEEEESSHHHHHHHHHTTSSSEEEEEEETTTHHHHHHHHHHHHEEE-EEEEEEE---EEEEEEEEEHHH
T ss_pred HHHHHHCCCeEEEecCCchHHHHHHHHCCCCeEEhhhcCchhHHHHHHhhhhcCccc-cCCcccc---CCEEEEEEeccc
Confidence 44444446678888888889999999999999998 4332 2232211 11222 1122221 134666664432
Q ss_pred ccccCCCCCcccCCCCcc----cCCC--CCCCCCch
Q 044324 156 VCQENGGINLMDFKGHKS----CHGS--YSTAAGWN 185 (291)
Q Consensus 156 ~~~~S~~~~l~dLkGKks----CHtG--~~~taGW~ 185 (291)
-+..++.+|+||++.+. ...+ +++..||.
T Consensus 97 -ae~~~i~si~dL~~~~~~~~~~~~~~~~~~~~g~~ 131 (257)
T PF04069_consen 97 -AEKPGIKSISDLAKPAEDLEFGGKGEFYGRPDGWG 131 (257)
T ss_dssp -HHHHT-SBGGGGGTCGGGCEEEETTEEECSSTTHH
T ss_pred -ccccCcccHHHHhhcccccccCCCCceeeCCCCcc
Confidence 11135899999988877 5555 57788998
No 112
>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=20.29 E-value=1.8e+02 Score=26.94 Aligned_cols=56 Identities=14% Similarity=-0.053 Sum_probs=33.9
Q ss_pred CCceEEEecc-chHHHHHHHHHHhhcCCCcceEEEec-CCHHHHHHHHhccCCcEEEeCC
Q 044324 62 EATIKWCAVR-DQYEDCEYLVSIISQSEDYTWKCVKR-DTAQECLDSARKGEADIINLEA 119 (291)
Q Consensus 62 ~~~vRwCv~S-~E~~KC~~l~~~a~~~~~p~l~CV~~-~s~~dCm~~I~~g~ADiv~ld~ 119 (291)
...+|+.++. ...- =..+ -..|....|.+.-... .+..++++++.+|++|++.+..
T Consensus 35 ~~~lrig~s~s~~~~-lp~~-l~~f~~~~P~i~v~i~~~~s~~l~~~L~~G~iDlai~~~ 92 (287)
T TIGR02136 35 SSTITIDGSTTVAPL-AEAA-AEEFQKIHPGVSVTVQGAGSGTGIKALINGTVDIGNSSR 92 (287)
T ss_pred cceEEEeccchHHHH-HHHH-HHHHHhhCCCceEEEccCCchHHHHHHHcCCCchhhccC
Confidence 4588888877 3211 1111 2234333354333332 3789999999999999987653
Done!