Query psy11925
Match_columns 458
No_of_seqs 230 out of 678
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 22:28:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11925.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11925hhsearch_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 8.9E-85 1.9E-89 660.2 27.4 310 99-430 1-328 (332)
2 PF00405 Transferrin: Transfer 100.0 1.7E-83 3.7E-88 652.1 21.5 303 99-430 1-326 (330)
3 COG3221 PhnD ABC-type phosphat 99.8 4.4E-18 9.6E-23 171.0 14.5 193 123-381 64-260 (299)
4 PF12974 Phosphonate-bd: ABC t 99.5 4.5E-15 9.7E-20 143.9 4.6 188 125-380 28-218 (243)
5 smart00094 TR_FER Transferrin. 99.2 3.1E-11 6.6E-16 123.4 6.7 83 3-93 240-331 (332)
6 TIGR01098 3A0109s03R phosphate 99.1 1.5E-09 3.2E-14 105.2 15.6 215 97-378 32-253 (254)
7 PF00405 Transferrin: Transfer 99.1 4.3E-11 9.3E-16 122.4 2.4 84 4-93 236-329 (330)
8 TIGR03431 PhnD phosphonate ABC 99.0 9.3E-09 2E-13 102.2 14.1 221 125-425 58-282 (288)
9 TIGR01729 taurine_ABC_bnd taur 97.7 0.00065 1.4E-08 67.9 13.4 132 126-298 27-160 (300)
10 TIGR01728 SsuA_fam ABC transpo 97.6 0.00069 1.5E-08 66.0 12.1 130 127-298 30-161 (288)
11 PRK11480 tauA taurine transpor 97.2 0.0042 9E-08 63.0 12.0 130 126-298 51-182 (320)
12 PRK11553 alkanesulfonate trans 97.1 0.0045 9.8E-08 62.2 12.0 130 127-297 57-188 (314)
13 PF09084 NMT1: NMT1/THI5 like; 97.1 0.0016 3.5E-08 61.3 8.2 95 127-227 22-117 (216)
14 TIGR02122 TRAP_TAXI TRAP trans 97.1 0.0094 2E-07 59.5 13.3 237 96-385 29-287 (320)
15 cd00134 PBPb Bacterial peripla 96.9 0.03 6.6E-07 50.4 14.0 121 126-299 38-160 (218)
16 smart00062 PBPb Bacterial peri 96.7 0.059 1.3E-06 48.3 14.3 121 126-299 39-161 (219)
17 COG2358 Imp TRAP-type uncharac 95.3 0.052 1.1E-06 55.6 7.7 119 97-227 26-162 (321)
18 TIGR03427 ABC_peri_uca ABC tra 95.2 0.072 1.6E-06 54.8 8.3 93 127-227 36-130 (328)
19 COG0715 TauA ABC-type nitrate/ 94.6 0.1 2.2E-06 52.6 7.4 98 127-228 62-162 (335)
20 PF13379 NMT1_2: NMT1-like fam 94.3 0.38 8.3E-06 46.8 10.7 130 127-298 36-183 (252)
21 PRK09495 glnH glutamine ABC tr 93.5 1.1 2.4E-05 43.1 12.1 69 128-207 65-137 (247)
22 PRK11917 bifunctional adhesin/ 92.8 2.6 5.7E-05 41.3 13.7 69 127-206 82-153 (259)
23 PRK10859 membrane-bound lytic 91.8 2.8 6.1E-05 45.2 13.4 73 125-207 79-155 (482)
24 PF03401 TctC: Tripartite tric 88.9 2.7 5.9E-05 41.9 9.7 141 182-380 79-230 (274)
25 COG4521 TauA ABC-type taurine 88.8 0.81 1.8E-05 45.3 5.5 94 128-227 59-154 (334)
26 PRK00489 hisG ATP phosphoribos 85.5 2.1 4.6E-05 43.0 6.7 75 126-206 44-118 (287)
27 COG3181 Uncharacterized protei 84.1 6.5 0.00014 40.5 9.4 216 95-380 26-273 (319)
28 PRK11063 metQ DL-methionine tr 82.7 9.2 0.0002 38.3 9.8 120 98-229 32-156 (271)
29 cd08414 PBP2_LTTR_aromatics_li 82.0 34 0.00074 29.8 13.4 71 128-210 31-106 (197)
30 PRK15010 ABC transporter lysin 81.7 4 8.7E-05 39.6 6.7 63 134-206 72-138 (260)
31 TIGR00363 lipoprotein, YaeC fa 80.3 3.7 8E-05 40.9 5.9 93 127-229 47-143 (258)
32 TIGR01256 modA molybdenum ABC 78.1 10 0.00022 35.7 8.0 132 127-297 22-161 (216)
33 PRK10797 glutamate and asparta 76.2 6.3 0.00014 39.7 6.3 69 127-206 87-158 (302)
34 PRK15437 histidine ABC transpo 75.9 6.2 0.00013 38.3 6.0 69 127-206 66-138 (259)
35 cd05466 PBP2_LTTR_substrate Th 75.6 39 0.00086 28.8 10.6 71 127-209 30-105 (197)
36 CHL00180 rbcR LysR transcripti 73.5 76 0.0016 31.4 13.3 56 95-154 93-151 (305)
37 cd08436 PBP2_LTTR_like_3 The C 70.7 55 0.0012 28.3 10.4 73 127-210 30-107 (194)
38 PRK11151 DNA-binding transcrip 70.3 1E+02 0.0022 30.4 13.3 101 95-207 89-194 (305)
39 TIGR01096 3A0103s03R lysine-ar 70.3 7.3 0.00016 37.0 5.0 119 127-299 64-187 (250)
40 TIGR02995 ectoine_ehuB ectoine 70.3 21 0.00046 34.9 8.4 115 131-298 76-199 (275)
41 PRK09959 hybrid sensory histid 69.1 15 0.00033 43.8 8.2 124 124-299 94-219 (1197)
42 PF03466 LysR_substrate: LysR 68.2 45 0.00098 29.5 9.5 113 96-223 5-123 (209)
43 PF12727 PBP_like: PBP superfa 66.6 66 0.0014 30.4 10.5 134 127-298 12-157 (193)
44 PRK11260 cystine transporter s 66.4 13 0.00027 36.3 5.8 69 127-206 81-154 (266)
45 cd08469 PBP2_PnbR The C-termin 66.3 87 0.0019 28.3 11.1 100 99-210 2-105 (221)
46 PRK09861 cytoplasmic membrane 65.6 16 0.00034 36.7 6.4 94 126-229 60-157 (272)
47 cd08448 PBP2_LTTR_aromatics_li 65.3 91 0.002 27.0 13.4 70 127-208 30-104 (197)
48 cd08412 PBP2_PAO1_like The C-t 65.1 94 0.002 27.0 12.4 71 127-209 30-105 (198)
49 PF00497 SBP_bac_3: Bacterial 64.6 7 0.00015 35.7 3.4 118 128-299 40-166 (225)
50 cd08467 PBP2_SyrM The C-termin 62.5 1.1E+02 0.0024 27.1 11.3 72 127-210 30-105 (200)
51 TIGR00787 dctP tripartite ATP- 60.7 8.1 0.00018 37.8 3.3 71 135-205 42-140 (257)
52 cd08449 PBP2_XapR The C-termin 60.1 1.2E+02 0.0025 26.4 12.6 73 127-209 30-107 (197)
53 TIGR03870 ABC_MoxJ methanol ox 56.8 29 0.00063 33.5 6.4 23 277-299 155-177 (246)
54 cd08437 PBP2_MleR The substrat 52.1 1.6E+02 0.0035 25.7 10.2 75 126-209 27-107 (198)
55 PRK15007 putative ABC transpor 51.3 31 0.00067 32.6 5.5 66 134-207 67-132 (243)
56 cd08420 PBP2_CysL_like C-termi 49.8 1.7E+02 0.0037 25.2 9.8 70 128-209 31-105 (201)
57 PF02621 VitK2_biosynth: Menaq 49.2 8 0.00017 38.1 1.1 79 125-213 23-104 (251)
58 cd08463 PBP2_DntR_like_4 The C 45.7 2.2E+02 0.0048 25.4 11.3 70 127-207 30-104 (203)
59 cd08417 PBP2_Nitroaromatics_li 45.3 1.6E+02 0.0034 25.7 8.9 71 127-209 30-104 (200)
60 cd08461 PBP2_DntR_like_3 The C 44.0 2.2E+02 0.0047 24.8 11.3 30 125-154 26-56 (198)
61 cd08438 PBP2_CidR The C-termin 43.9 2.1E+02 0.0046 24.6 9.6 99 99-209 2-105 (197)
62 PRK11242 DNA-binding transcrip 43.4 2.1E+02 0.0045 27.8 10.2 103 95-210 89-198 (296)
63 cd08446 PBP2_Chlorocatechol Th 43.4 2.2E+02 0.0048 24.7 10.7 98 98-209 2-106 (198)
64 TIGR00070 hisG ATP phosphoribo 42.3 70 0.0015 30.3 6.2 80 137-227 50-129 (182)
65 cd08425 PBP2_CynR The C-termin 41.9 2.3E+02 0.0051 24.5 10.0 98 98-209 2-107 (197)
66 cd08415 PBP2_LysR_opines_like 40.0 2E+02 0.0043 24.8 8.6 70 128-209 31-105 (196)
67 PRK10837 putative DNA-binding 39.9 3.5E+02 0.0075 26.1 11.1 103 95-210 87-194 (290)
68 cd08428 PBP2_IciA_ArgP The C-t 37.9 2.7E+02 0.0059 24.2 10.7 100 98-211 1-107 (195)
69 cd08435 PBP2_GbpR The C-termin 36.4 2.8E+02 0.0061 23.9 10.1 73 127-209 30-107 (201)
70 cd08456 PBP2_LysR The C-termin 35.7 2.9E+02 0.0063 23.8 10.2 27 127-154 30-56 (196)
71 cd08421 PBP2_LTTR_like_1 The C 35.1 2.3E+02 0.0049 24.6 8.2 79 127-219 30-113 (198)
72 TIGR03871 ABC_peri_MoxJ_2 quin 35.0 2E+02 0.0043 26.8 8.3 71 126-208 35-111 (232)
73 PRK09986 DNA-binding transcrip 34.8 3.7E+02 0.0079 26.0 10.4 103 95-209 95-204 (294)
74 PRK14498 putative molybdopteri 34.5 1.1E+02 0.0025 34.2 7.4 77 126-210 439-532 (633)
75 smart00079 PBPe Eukaryotic hom 34.5 35 0.00077 29.1 2.7 55 132-191 50-105 (134)
76 PRK11074 putative DNA-binding 34.4 2.1E+02 0.0045 28.1 8.6 58 95-155 90-149 (300)
77 cd08423 PBP2_LTTR_like_6 The C 33.7 3.1E+02 0.0067 23.6 10.1 74 127-209 30-110 (200)
78 PF14503 YhfZ_C: YhfZ C-termin 33.1 24 0.00052 34.8 1.6 63 127-192 138-201 (232)
79 TIGR02424 TF_pcaQ pca operon t 32.8 4E+02 0.0086 25.9 10.3 104 95-210 91-201 (300)
80 COG0834 HisJ ABC-type amino ac 32.3 80 0.0017 30.1 5.1 71 129-206 79-151 (275)
81 cd08453 PBP2_IlvR The C-termin 32.1 3.4E+02 0.0074 23.6 12.5 75 127-210 30-109 (200)
82 cd08468 PBP2_Pa0477 The C-term 31.6 3.6E+02 0.0078 23.7 10.3 30 125-154 26-56 (202)
83 cd08462 PBP2_NodD The C-termin 31.1 3.6E+02 0.0079 23.6 11.1 70 127-209 30-103 (200)
84 cd08442 PBP2_YofA_SoxR_like Th 30.6 3.5E+02 0.0075 23.2 9.7 71 127-209 30-101 (193)
85 cd08451 PBP2_BudR The C-termin 30.4 3.3E+02 0.0071 23.5 8.4 72 127-209 31-107 (199)
86 PRK09791 putative DNA-binding 29.8 4E+02 0.0087 26.0 9.8 100 95-208 93-199 (302)
87 cd08460 PBP2_DntR_like_1 The C 29.2 3.9E+02 0.0084 23.3 10.2 70 127-209 30-103 (200)
88 cd08433 PBP2_Nac The C-teminal 29.2 3.8E+02 0.0082 23.2 9.6 70 128-209 31-105 (198)
89 PF13531 SBP_bac_11: Bacterial 29.1 78 0.0017 29.8 4.4 106 111-226 12-128 (230)
90 cd08466 PBP2_LeuO The C-termin 28.3 3.9E+02 0.0085 23.1 9.3 27 127-154 30-56 (200)
91 cd08447 PBP2_LTTR_aromatics_li 28.2 3.9E+02 0.0085 23.0 13.0 72 126-208 27-104 (198)
92 cd08419 PBP2_CbbR_RubisCO_like 26.6 4.1E+02 0.0089 22.7 10.1 69 127-207 29-102 (197)
93 PF04069 OpuAC: Substrate bind 25.4 1.2E+02 0.0025 29.6 5.0 87 127-216 30-131 (257)
94 cd08465 PBP2_ToxR The C-termin 24.9 4.8E+02 0.01 22.9 10.9 73 126-209 27-104 (200)
95 cd08426 PBP2_LTTR_like_5 The C 24.6 4.6E+02 0.0099 22.6 9.6 72 126-208 27-104 (199)
96 PRK12682 transcriptional regul 24.4 6.8E+02 0.015 24.5 12.9 102 95-209 91-199 (309)
97 PRK10216 DNA-binding transcrip 24.3 7E+02 0.015 24.6 11.6 58 95-154 94-152 (319)
98 PRK12684 transcriptional regul 24.1 6E+02 0.013 25.1 9.9 103 95-208 91-198 (313)
99 PRK11482 putative DNA-binding 23.8 4.9E+02 0.011 25.9 9.3 95 95-203 115-213 (317)
100 cd08439 PBP2_LrhA_like The C-t 23.7 4.8E+02 0.01 22.5 8.3 30 125-154 26-56 (185)
101 cd08434 PBP2_GltC_like The sub 23.7 4.6E+02 0.0099 22.3 10.4 68 128-207 31-103 (195)
102 cd08464 PBP2_DntR_like_2 The C 23.3 4.9E+02 0.011 22.4 9.7 71 127-209 30-104 (200)
103 PF00497 SBP_bac_3: Bacterial 22.2 1E+02 0.0022 27.9 3.6 53 99-158 111-163 (225)
104 PF01634 HisG: ATP phosphoribo 21.6 1.2E+02 0.0026 28.2 4.0 81 137-226 4-86 (163)
105 cd08459 PBP2_DntR_NahR_LinR_li 21.6 2.6E+02 0.0057 24.4 6.1 71 128-210 31-105 (201)
106 PRK10677 modA molybdate transp 21.4 4.9E+02 0.011 25.5 8.5 80 125-210 53-145 (257)
107 cd08411 PBP2_OxyR The C-termin 21.0 5.5E+02 0.012 22.2 10.4 73 126-209 28-106 (200)
108 PRK12683 transcriptional regul 20.6 8.3E+02 0.018 24.1 12.3 114 95-223 91-211 (309)
109 TIGR03339 phn_lysR aminoethylp 20.5 2.8E+02 0.006 26.4 6.5 97 95-209 85-189 (279)
110 COG1910 Periplasmic molybdate- 20.5 5E+02 0.011 25.5 7.9 116 139-291 30-156 (223)
111 cd08485 PBP2_ClcR The C-termin 20.3 5.9E+02 0.013 22.3 12.0 73 125-208 27-105 (198)
112 cd08457 PBP2_OccR The C-termin 20.2 5.7E+02 0.012 22.1 8.8 71 127-209 30-105 (196)
No 1
>smart00094 TR_FER Transferrin.
Probab=100.00 E-value=8.9e-85 Score=660.25 Aligned_cols=310 Identities=36% Similarity=0.656 Sum_probs=280.9
Q ss_pred eEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCC
Q psy11925 99 IRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNE 178 (458)
Q Consensus 99 vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~ 178 (458)
|||||+|+.|++||++|+.++.+. .+|+|+|+.++|+.+||++|++|+||++++|++++|+|++.++|+||++|.|+.+
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 VRWCAVSNAEKSKCDQWSVNSRGR-DVPALECVSASSTEECIKAIQKGEADAVTLDGGDVYTAGKPYNLVPVFAENYGSE 79 (332)
T ss_pred CEEecCCHHHHHHHHHHHHHHhhC-CCCceEEEEcCCHHHHHHHHHCCCCCEEEECcHHHHhhcccCCceEEEEEeeccC
Confidence 799999999999999999876443 3899999999999999999999999999999999999988899999999999753
Q ss_pred c---ce-EEEEEEecCCCccChhhhcCCceeeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCc
Q psy11925 179 K---DL-LAVAVVNKNSKVKSLEELKGLKSCHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDE 254 (458)
Q Consensus 179 ~---~~-~aVAVVkk~s~~~~l~dLkGkksChtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~ 254 (458)
. .. |+||||||+|++.+|+||||||+||||+++|+||++|++.|+++|+|+..+|+..++|++||+ +||+||++.
T Consensus 80 ~~~~~~Y~aVaVVkk~S~i~sl~dLkGKksChtg~~stsGw~iP~~~L~~~g~i~~~~~~~~~avs~fFs-~sC~PG~~~ 158 (332)
T smart00094 80 EEPETGYYAVAVVKKGSAIFTWNQLRGKKSCHTGVGRTAGWNIPMGLLYNKLVIRPPNCPFEKAVSKFFS-ASCAPGADK 158 (332)
T ss_pred CCCCceeEEEEEEECCCCCCCHHHhCCCceecCCCCCcchhHHHHHHHHHcCCCCCCCCcHHHHHHHHhh-ccccCCCCC
Confidence 2 24 999999999999999999999999999999999999999999999999999988889999998 999999976
Q ss_pred cccCCCchhhhhCCCCCCC---------Chh-hhhhcccCCCcEEEEechhhhhhhhcccccccchhhhccCCCCCCCCC
Q psy11925 255 EEKDAPASLEKICPKATRV---------TYT-PLQCLKSGDGDVAFIKQVKVNKAIEEGLFKTDEIEYLCSKGGRAPVSK 324 (458)
Q Consensus 255 ~~~~~~~~LC~lC~g~~~C---------Gy~-A~rCL~eg~GDVAFvk~~tv~~~~~~~~~~~~g~~~~~~~~~wa~~~~ 324 (458)
+ +++++||+||.|+++| ||+ |||||+||+||||||||+||.++ ++|+ ++++|++++.
T Consensus 159 ~--~~~~~LC~lC~g~~~C~~~~~e~Y~Gy~GA~rCL~eg~GdVAFvk~~tv~~~-------~~~~----~~~~wa~~~~ 225 (332)
T smart00094 159 P--DPNSNLCALCAGDNKCACSSHEPYYGYSGAFRCLAEGAGDVAFVKHSTVFEN-------TDGK----NGADWAKNLK 225 (332)
T ss_pred C--CCchhhHhhcCCCCccCCCCCCcccCcchhheeeccCCccEEEEecccHHhh-------cCCC----CccccccccC
Confidence 5 3468999999998888 999 99999999999999999999998 7887 8899999999
Q ss_pred CCCcccccccCCCCccccccCccccccccCCceEEEcCCCChhHHHHHHHHHHHHHHHhcCC-CccccccccCCCCCCcc
Q psy11925 325 AGDYEIEYLCSKGGRAPVSKAADCNLGVVPPHMVVTSNSKSNVEIDTIRHAILSAADLFSKK-PEIFKLFGSFMGKPDVL 403 (458)
Q Consensus 325 ~~dy~~~LLCpdg~r~~v~~~~~C~l~~vP~~aVv~r~~~~~~~~~~i~~~l~~~~~~fg~~-~~~F~lF~s~~~~kdll 403 (458)
++||+ ||||||+|+||++|++|||+++|+|+||+|++.. ..+++.|+..+++||++ .+.|+||+|+. +||||
T Consensus 226 ~~dy~--lLC~dg~r~pi~~~~~C~la~~P~~~vv~~~~~~----~~~~~~ll~~~~~~g~~~~~~f~lf~s~~-~kdLl 298 (332)
T smart00094 226 RDDYE--LLCLDGTRKPVTEYKNCHLARVPSHAVVARKDKK----EDVIWELLNQQQKFGKDKPSLFQLFGSPT-GKDLL 298 (332)
T ss_pred ccceE--EECCCCCcCCCccCCcceeeeccCCeEEecccch----HHHHHHHHHHHHHhccCCCCccccccCCC-CCcce
Confidence 99999 9999999999999999999999999999999742 34566667777799876 57799999985 49999
Q ss_pred ccCCCCcceeCC-CCCHHHHH--HHHHhhh
Q psy11925 404 FLNPATGVEVLP-DQATDVET--NYSNNML 430 (458)
Q Consensus 404 F~D~t~~l~~v~-~~~~~~~~--~y~~~~~ 430 (458)
|+|+|++|+.|| ..+|+.|. +|...+.
T Consensus 299 FkD~t~~l~~i~~~~~~~~~lg~~y~~~~~ 328 (332)
T smart00094 299 FKDSAKCLAKIPPKTDYELYLGEEYVTAIQ 328 (332)
T ss_pred eeccccchhhCCCCCchhhhcCHHHHHHHH
Confidence 999999999998 56898884 6766664
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=1.7e-83 Score=652.11 Aligned_cols=303 Identities=42% Similarity=0.719 Sum_probs=270.7
Q ss_pred eEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEec-cCCCceEEEEEeecC
Q psy11925 99 IRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGR-KNLNLRPILKEKYGN 177 (458)
Q Consensus 99 vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~-~~~~L~pil~E~y~~ 177 (458)
|||||+|+.|++||++|+.++.+.+ .|.|+||++.|++|||++|++|+||++++|++++|+|+ +.|+|+||++|.|+.
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 VRWCVVSEAELKKCERMSKAFSSAG-RPEISCVRATSREDCMRRIKKGEADAVTLDGGDVYIAGLRKYNLKPIAAEVYGS 79 (330)
T ss_dssp EEEEEESHHHHHHHHHHHHHHTHTS-STSEEEEEESSHHHHHHHHHTTSSSBEEEEHHHHHHHHSTTTTEEEEEEEEESS
T ss_pred CEEeecChHHHHHHHHHHHHhhhcC-CCCceeEeCCCHHHHHHHHhhccCCEEEeCchhhhhhhccccCCEEeeeeeccc
Confidence 7999999999999999999877666 89999999999999999999999999999999999999 899999999999984
Q ss_pred Cc---ce-EEEEEEecCCCccChhhhcCCceeeCCCCCCCchHHHHHHHHHcCCCCC--CCCccccccccccccCcccCC
Q psy11925 178 EK---DL-LAVAVVNKNSKVKSLEELKGLKSCHTAYMRTTGWVAPVYNLLEKGLIKK--DSCPYYKGVAEFFTGGSCVPG 251 (458)
Q Consensus 178 ~~---~~-~aVAVVkk~s~~~~l~dLkGkksChtg~~~taGw~~Pv~~L~~~~~i~~--~~c~~~~~~~~FFsg~sC~pG 251 (458)
.. .. |+||||||++.+ +|+||||||+||||+++++||++||+.|+++++|+. ..|++.+++++||+ +||+||
T Consensus 80 ~~~~~~~y~aVAVVkk~s~~-~l~~LrGkksCHtG~g~~aGW~~Pv~~L~~~~~i~~~~~~~~~~~avs~FF~-~sC~PG 157 (330)
T PF00405_consen 80 EEEPEASYYAVAVVKKSSNI-TLKDLRGKKSCHTGYGRTAGWNIPVGYLLEKGVIPWTGPDCDVEKAVSDFFS-KSCVPG 157 (330)
T ss_dssp SSSEESEEEEEEEEETTSS--SGGGGTTSEEEESSTTTTTTTHHHHHHHHHHHHCCSSSTTSSHHHHHHHHSS-EEE-TT
T ss_pred cccccceeEEEEEEecCCCc-chhhhcCCCCCCcCcCCcccccccchhhhhcCcCCcccccchhhhHHhhhhc-Cccccc
Confidence 32 24 999999999987 699999999999999999999999999999999987 46888999999998 999999
Q ss_pred CCccccCCCchhhhhCCC--CCCC---------Chh-hhhhcccCCCcEEEEechhhhhhhhcccccccchhhhccCCCC
Q psy11925 252 IDEEEKDAPASLEKICPK--ATRV---------TYT-PLQCLKSGDGDVAFIKQVKVNKAIEEGLFKTDEIEYLCSKGGR 319 (458)
Q Consensus 252 ~~~~~~~~~~~LC~lC~g--~~~C---------Gy~-A~rCL~eg~GDVAFvk~~tv~~~~~~~~~~~~g~~~~~~~~~w 319 (458)
++. .++++||+||.| .++| ||. |||||+||.||||||+|+||.++ ++++
T Consensus 158 a~~---~~~~~LC~lC~g~~~~~C~~~~~e~y~G~~GAlrCL~eg~GDVAFv~~~tv~~~-------~~~~--------- 218 (330)
T PF00405_consen 158 ADK---KNYSNLCSLCKGDGESKCSCSSNEPYYGYEGALRCLVEGKGDVAFVKHTTVFEN-------TDGN--------- 218 (330)
T ss_dssp SST---TTTSGGGTTSTSSTTSTTTSSTTSTTSHHHHHHHHHHTTSSSEEEEETTHHHHH-------STSS---------
T ss_pred ccc---ccCCcccccccCCCCCcCCCCCcccCCCCCcceEEEecCCCcEEEEeccchhhh-------cccc---------
Confidence 975 357899999999 4567 899 99999999999999999999998 4432
Q ss_pred CCCCCCCCcccccccCCCCccccccCccccccccCCceEEEcCCCChhHHHHHHHHHHHHHHHhcCC-CccccccccCCC
Q psy11925 320 APVSKAGDYEIEYLCSKGGRAPVSKAADCNLGVVPPHMVVTSNSKSNVEIDTIRHAILSAADLFSKK-PEIFKLFGSFMG 398 (458)
Q Consensus 320 a~~~~~~dy~~~LLCpdg~r~~v~~~~~C~l~~vP~~aVv~r~~~~~~~~~~i~~~l~~~~~~fg~~-~~~F~lF~s~~~ 398 (458)
...+||+ ||||||+|+||++|++|||+++|+|+||+|++.+ .+++|+++|.+++++||.+ .+.|+||+|+.+
T Consensus 219 ---~~~~dy~--lLCpdG~~~~v~~~~~C~l~~~p~~~vv~r~~~~--~~~~i~~~L~~~~~~fg~~~~~~f~lF~s~~~ 291 (330)
T PF00405_consen 219 ---NQADDYE--LLCPDGTRAPVSNYKPCNLGKVPWHAVVTRSDTS--KKDEIYNLLLKAQQLFGSNKSDDFQLFGSFSY 291 (330)
T ss_dssp ---SHSGGEE--EEETTSEEEEGGGGGGSSSEEEESEEEEEESSSS--GHHHHHHHHHHHHHHHSTTSTSSS-TTSSSTT
T ss_pred ---cccccEE--EEcCCCCccCcCCCCceeeeEecCceEEEcCccc--cHHHHHHHHHHHHHhhhcccccccccccccCC
Confidence 2358999 9999999999999999999999999999998765 3478999999999999987 667999999987
Q ss_pred CCCccccCCCCcceeCC-CCCHHHHH--HHHHhhh
Q psy11925 399 KPDVLFLNPATGVEVLP-DQATDVET--NYSNNML 430 (458)
Q Consensus 399 ~kdllF~D~t~~l~~v~-~~~~~~~~--~y~~~~~ 430 (458)
.+||||+|+|++|++|| ..+|+.|. +|...|.
T Consensus 292 ~~dllF~D~t~~L~~i~~~~~~~~~lg~~y~~~~~ 326 (330)
T PF00405_consen 292 GKDLLFKDSTKCLVPIPSSTDYQEYLGPDYYRAMK 326 (330)
T ss_dssp SSSSSSBTTEEEEEE-TTTSSHHHHHHHHHHHHHH
T ss_pred CCccccccccceeEECCCCCCHHHhcCHHHHHHHH
Confidence 89999999999999999 56899997 6666654
No 3
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=99.77 E-value=4.4e-18 Score=171.02 Aligned_cols=193 Identities=19% Similarity=0.256 Sum_probs=159.0
Q ss_pred CCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCC-CceEEEEEeecCCcce-EEEEEEecCCCccChhhhc
Q psy11925 123 DIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNL-NLRPILKEKYGNEKDL-LAVAVVNKNSKVKSLEELK 200 (458)
Q Consensus 123 ~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~-~L~pil~E~y~~~~~~-~aVAVVkk~s~~~~l~dLk 200 (458)
.++.+++=+.++++..-+|++++|++|++.+.+..+..|.+.. ...|++.-...++... |++.||+++|++++++|||
T Consensus 64 ~lG~~V~~~~a~dy~~vieal~~g~~D~A~~~~~a~~~a~~~~~~~e~~~~~~~~dg~~~Y~S~~i~~~ds~i~sl~dlk 143 (299)
T COG3221 64 ELGIPVEFFVATDYAAVIEALRAGQVDIAWLGPSAYVEAVDRALAGEPLAQTVQKDGSPGYYSVIIVRADSPIKSLEDLK 143 (299)
T ss_pred HhCCceEEEecccHHHHHHHHhCCCeeEEecCchhHHHHHhhcccccceeeeeccCCCcceeEEEEEeCCCCcchHHHhc
Confidence 3566799999999999999999999999999999888887766 7888887654444445 9999999999999999999
Q ss_pred CCceeeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhh
Q psy11925 201 GLKSCHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQ 279 (458)
Q Consensus 201 GkksChtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~r 279 (458)
|||.+++.+.+|+|+++|...|.++|.+. ..+||+ ..=.-| ||+ |+-
T Consensus 144 gk~~af~d~~StSG~l~P~~~L~~~g~~d---------~~~~f~-~v~~~G----------------------~H~~a~~ 191 (299)
T COG3221 144 GKRFAFGDPDSTSGYLFPLYYLAKEGGID---------PDKFFG-EVIFSG----------------------GHDAAVL 191 (299)
T ss_pred CCeEeccCCCcchhhHhHHHHHHHhcCCC---------hhhhhc-eeeccC----------------------hHHHHHH
Confidence 99999999999999999999999998542 257886 422222 599 999
Q ss_pred hcccCCCcEEEEechhhhhhhhcccccccchhhhccCCCCCCCC-CCCCcccccccCCCCccccccCccccccccCCceE
Q psy11925 280 CLKSGDGDVAFIKQVKVNKAIEEGLFKTDEIEYLCSKGGRAPVS-KAGDYEIEYLCSKGGRAPVSKAADCNLGVVPPHMV 358 (458)
Q Consensus 280 CL~eg~GDVAFvk~~tv~~~~~~~~~~~~g~~~~~~~~~wa~~~-~~~dy~~~LLCpdg~r~~v~~~~~C~l~~vP~~aV 358 (458)
.+++|+.|||.+..+++.... ... .. ..++.+ +|+.. ..+|++.+
T Consensus 192 aV~nG~vDva~~~~~~~~~~~------~~~------------~~~~~~~l~--vi~~S--------------~~iP~~pi 237 (299)
T COG3221 192 AVANGQVDVAAVNSSARGLLK------KAA------------PEGVAEKLR--VIWKS--------------PLIPNDPI 237 (299)
T ss_pred HHHcCCceEEeccHHHHhhhh------hcc------------cccchhhce--EEEec--------------CCCCCCCE
Confidence 999999999999998877641 110 11 235677 66533 67999999
Q ss_pred EEcCCCChhHHHHHHHHHHHHHH
Q psy11925 359 VTSNSKSNVEIDTIRHAILSAAD 381 (458)
Q Consensus 359 v~r~~~~~~~~~~i~~~l~~~~~ 381 (458)
++|++.+++.+++|+++|+++.+
T Consensus 238 ~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 238 AVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred EEeCCCCHHHHHHHHHHHHhcCc
Confidence 99999999999999999999765
No 4
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=99.53 E-value=4.5e-15 Score=143.87 Aligned_cols=188 Identities=21% Similarity=0.253 Sum_probs=137.4
Q ss_pred CCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcce-EEEEEEecCCCccChhhhcCCc
Q psy11925 125 RPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDL-LAVAVVNKNSKVKSLEELKGLK 203 (458)
Q Consensus 125 ~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~-~aVAVVkk~s~~~~l~dLkGkk 203 (458)
+-+++-+...++.+-++++++|++|++.+++..+..+.+..+++|++.-....+... .++.||++++++++++||||||
T Consensus 28 g~~v~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds~i~~l~dL~Gk~ 107 (243)
T PF12974_consen 28 GVPVELVPADDYAEFIEALRSGEIDLAFMGPLPYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADSPITSLADLKGKR 107 (243)
T ss_dssp TSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTSS--SHHHHGGSE
T ss_pred CCCEEEEEcCCHHHHHHHHHcCCccEEEECcHHHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCCCCCChhhcCCCE
Confidence 346888999999999999999999999999999888876679999998765333334 8999999999999999999999
Q ss_pred eeeCCCCCCCchHHHHHHH-HHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhc
Q psy11925 204 SCHTAYMRTTGWVAPVYNL-LEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCL 281 (458)
Q Consensus 204 sChtg~~~taGw~~Pv~~L-~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL 281 (458)
.++++.++++||.+|...| .+.|+- ..+||. .. .-| .++ +++-|
T Consensus 108 v~~~~~~s~sg~l~~~~~L~~~~Gl~----------~~~~~~-~~-~~~----------------------~~~~~~~~l 153 (243)
T PF12974_consen 108 VAFPDPSSTSGYLIPRYELLREAGLD----------PGDDFK-QV-FVG----------------------SHDAVLEAL 153 (243)
T ss_dssp EEEE-TT-TTTTHHHHHHTCCCCT------------HHHHSS-EE-EEE-----------------------HHHHHHHH
T ss_pred EEEecCCccHHHHHHHHHHHHHcCCC----------hhHcee-EE-EeC----------------------CHHHHHHHH
Confidence 9999999999999999998 466742 234554 22 111 266 99999
Q ss_pred ccCCCcEEEEechhhhhhhhcccccccchhhhccCCCCCCCCCCCCcccccccCCCCccccccCccccccccCCceEEEc
Q psy11925 282 KSGDGDVAFIKQVKVNKAIEEGLFKTDEIEYLCSKGGRAPVSKAGDYEIEYLCSKGGRAPVSKAADCNLGVVPPHMVVTS 361 (458)
Q Consensus 282 ~eg~GDVAFvk~~tv~~~~~~~~~~~~g~~~~~~~~~wa~~~~~~dy~~~LLCpdg~r~~v~~~~~C~l~~vP~~aVv~r 361 (458)
.+|..|+|++...++..... .|. ...++++ +|. + ...+|.+.++++
T Consensus 154 ~~G~~Da~~~~~~~~~~~~~------~~~------------~~~~~~r--vl~-----------~---s~~~p~~~~~~~ 199 (243)
T PF12974_consen 154 LNGKADAAAIPSDAFERLEA------EGP------------DIPSQLR--VLW-----------T---SPPYPNWPLVAS 199 (243)
T ss_dssp HTTSSSEEEEEHHHHHHHHH------H-H------------HHHTTEE--EEE-----------E---EEEEE--EEEEE
T ss_pred HcCCccEEEEechhHHHHHH------ccC------------cccccEE--EEE-----------E---eCCCCCcEEEEe
Confidence 99999999999988877521 110 1234566 553 1 256899999999
Q ss_pred CCCChhHHHHHHHHHHHHH
Q psy11925 362 NSKSNVEIDTIRHAILSAA 380 (458)
Q Consensus 362 ~~~~~~~~~~i~~~l~~~~ 380 (458)
++.+++.+++|+++|+++.
T Consensus 200 ~~~~~~~~~~l~~al~~~~ 218 (243)
T PF12974_consen 200 PDLPPELRQRLRDALLSLS 218 (243)
T ss_dssp TTS-HHHHHHHHHHHHHTT
T ss_pred CCCCHHHHHHHHHHHHcCC
Confidence 9999999999999999865
No 5
>smart00094 TR_FER Transferrin.
Probab=99.17 E-value=3.1e-11 Score=123.38 Aligned_cols=83 Identities=14% Similarity=0.114 Sum_probs=65.3
Q ss_pred CCCCCCCceeeecCCCeEEecCCcccccccHHHHHHHHHHHhhc--------CCCCCccccccceeeeccccccc-CCCC
Q psy11925 3 LLQSETPCTWAARPWPGFVANDRIEVNTQDLTQLRNYISQLNKL--------GESSGNDWLINVLGIDSNSTAVD-NKKT 73 (458)
Q Consensus 3 ~~~~~~~C~wa~~Pw~aVvar~d~~~~~~~v~~i~~~L~~~~~~--------g~~sS~~~~~k~LlF~Dst~~v~-~~~~ 73 (458)
-++.+++||||++|||+||+|++.. .+.|+.+|.+++.+ ..++|+. +|||||+|+|..|. .+..
T Consensus 240 pi~~~~~C~la~~P~~~vv~~~~~~-----~~~~~~ll~~~~~~g~~~~~~f~lf~s~~--~kdLlFkD~t~~l~~i~~~ 312 (332)
T smart00094 240 PVTEYKNCHLARVPSHAVVARKDKK-----EDVIWELLNQQQKFGKDKPSLFQLFGSPT--GKDLLFKDSAKCLAKIPPK 312 (332)
T ss_pred CCccCCcceeeeccCCeEEecccch-----HHHHHHHHHHHHHhccCCCCccccccCCC--CCcceeeccccchhhCCCC
Confidence 4567799999999999999999743 45688888777653 3456664 49999999999753 4556
Q ss_pred CChhhhhccccchhhhccCC
Q psy11925 74 LHPTQYLQKANYEDVIGRVV 93 (458)
Q Consensus 74 ~~~~~YLg~a~Y~~ai~~~~ 93 (458)
+++.+||| .+|+++|+++.
T Consensus 313 ~~~~~~lg-~~y~~~~~~l~ 331 (332)
T smart00094 313 TDYELYLG-EEYVTAIQNLR 331 (332)
T ss_pred CchhhhcC-HHHHHHHHHhc
Confidence 78999999 78999998754
No 6
>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=99.12 E-value=1.5e-09 Score=105.21 Aligned_cols=215 Identities=17% Similarity=0.208 Sum_probs=142.1
Q ss_pred CceEEEeCChhHHhH----HHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEE
Q psy11925 97 KPIRWCVSSPEGMSK----CLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILK 172 (458)
Q Consensus 97 ~~vrwCv~s~~E~~K----C~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~ 172 (458)
.++|+++........ -..+..... ...+.+++++...+..+++++++.|++|++..++..+..+....+..++..
T Consensus 32 ~~l~vg~~~~~~~~~~~~~~~~l~~~l~-~~~g~~v~~~~~~~~~~~~~~l~~g~~Di~~~~~~~~~~~~~~~~~~~~~~ 110 (254)
T TIGR01098 32 KELNFGILPGENASNLTRRWEPLADYLE-KKLGIKVQLFVATDYSAVIEAMRFGRVDIAWFGPSSYVLAHYRANAEVFAL 110 (254)
T ss_pred CceEEEECCCCCHHHHHHHHHHHHHHHH-HHhCCcEEEEeCCCHHHHHHHHHcCCccEEEECcHHHHHHHHhcCCceEEe
Confidence 468888877554222 223443322 234567999988899999999999999999988776544323345555544
Q ss_pred Eee-cCCcce-EEEEEEecCCCccChhhhcCCceeeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccC
Q psy11925 173 EKY-GNEKDL-LAVAVVNKNSKVKSLEELKGLKSCHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVP 250 (458)
Q Consensus 173 E~y-~~~~~~-~aVAVVkk~s~~~~l~dLkGkksChtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~p 250 (458)
... ..+... +.+.||++++++++++||+|||.+.++.+.+++|.++...|.+.+.+... +++. . +.
T Consensus 111 ~~~~~~~~~~~~~~lvv~~d~~i~~~~dL~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~---------~~~~-~--i~ 178 (254)
T TIGR01098 111 TAVSTDGSPGYYSVIIVKADSPIKSLKDLKGKTFAFGDPASTSGYLVPRYQLKKEGGLDAD---------GFFS-E--VV 178 (254)
T ss_pred eccccCCCCceEEEEEEECCCCCCChHHhcCCEEEeeCCCCccchHhHHHHHHHhcCCChH---------Hhhh-h--ee
Confidence 322 112122 56888999999999999999999998887778899988888776433211 0110 0 00
Q ss_pred CCCccccCCCchhhhhCCCCCCCChh-hhhhcccCCCcEEEEechhhhhhhhcccccccchhhhccCCCCCCCCCCCCcc
Q psy11925 251 GIDEEEKDAPASLEKICPKATRVTYT-PLQCLKSGDGDVAFIKQVKVNKAIEEGLFKTDEIEYLCSKGGRAPVSKAGDYE 329 (458)
Q Consensus 251 G~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~eg~GDVAFvk~~tv~~~~~~~~~~~~g~~~~~~~~~wa~~~~~~dy~ 329 (458)
-. . ++. +++.|..|+.|++|+...++..... .+ .....+|+
T Consensus 179 ~~-------~-------------~~~~~~~al~~G~~Da~~~~~~~~~~~~~------~~------------~~~~~~~~ 220 (254)
T TIGR01098 179 FS-------G-------------SHDASALAVANGKVDAATNNSSAIGRLKK------RG------------PSDMKKVR 220 (254)
T ss_pred ec-------C-------------chHHHHHHHHcCCCCeEEecHHHHHHHHH------hC------------ccchhheE
Confidence 00 0 245 8999999999999998887765421 11 01124566
Q ss_pred cccccCCCCccccccCccccccccCCceEEEcCCCChhHHHHHHHHHHH
Q psy11925 330 IEYLCSKGGRAPVSKAADCNLGVVPPHMVVTSNSKSNVEIDTIRHAILS 378 (458)
Q Consensus 330 ~~LLCpdg~r~~v~~~~~C~l~~vP~~aVv~r~~~~~~~~~~i~~~l~~ 378 (458)
++-.. ...|..++++|++..+..++.|.++|..
T Consensus 221 --~~~~~--------------~~~~~~~~~~~~~~~~~l~~~i~~~l~~ 253 (254)
T TIGR01098 221 --VIWKS--------------PLIPNDPIAVRKDLPPELKEKIRDAFLT 253 (254)
T ss_pred --EEEec--------------CCCCCCCEEEECCCCHHHHHHHHHHHhh
Confidence 55321 2355678999999887888888888764
No 7
>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=99.07 E-value=4.3e-11 Score=122.40 Aligned_cols=84 Identities=13% Similarity=0.281 Sum_probs=66.8
Q ss_pred CCCCCCceeeecCCCeEEecCCcccccccHHHHHHHHHHHhh-cC--------CCCCccccccceeeecccccc-cCCCC
Q psy11925 4 LQSETPCTWAARPWPGFVANDRIEVNTQDLTQLRNYISQLNK-LG--------ESSGNDWLINVLGIDSNSTAV-DNKKT 73 (458)
Q Consensus 4 ~~~~~~C~wa~~Pw~aVvar~d~~~~~~~v~~i~~~L~~~~~-~g--------~~sS~~~~~k~LlF~Dst~~v-~~~~~ 73 (458)
++.+++|||+++|||+||+|++.. ..+.|+++|.++++ || .++|+.+. +||||+|+|+.| +.++.
T Consensus 236 v~~~~~C~l~~~p~~~vv~r~~~~----~~~~i~~~L~~~~~~fg~~~~~~f~lF~s~~~~-~dllF~D~t~~L~~i~~~ 310 (330)
T PF00405_consen 236 VSNYKPCNLGKVPWHAVVTRSDTS----KKDEIYNLLLKAQQLFGSNKSDDFQLFGSFSYG-KDLLFKDSTKCLVPIPSS 310 (330)
T ss_dssp GGGGGGSSSEEEESEEEEEESSSS----GHHHHHHHHHHHHHHHSTTSTSSS-TTSSSTTS-SSSSSBTTEEEEEE-TTT
T ss_pred cCCCCceeeeEecCceEEEcCccc----cHHHHHHHHHHHHHhhhcccccccccccccCCC-CccccccccceeEECCCC
Confidence 456689999999999999998653 35678899998886 43 45666644 999999999974 45666
Q ss_pred CChhhhhccccchhhhccCC
Q psy11925 74 LHPTQYLQKANYEDVIGRVV 93 (458)
Q Consensus 74 ~~~~~YLg~a~Y~~ai~~~~ 93 (458)
++++.||| .+|+.+|++++
T Consensus 311 ~~~~~~lg-~~y~~~~~~l~ 329 (330)
T PF00405_consen 311 TDYQEYLG-PDYYRAMKSLR 329 (330)
T ss_dssp SSHHHHHH-HHHHHHHHHHH
T ss_pred CCHHHhcC-HHHHHHHHHhc
Confidence 89999999 78999998653
No 8
>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=98.96 E-value=9.3e-09 Score=102.17 Aligned_cols=221 Identities=18% Similarity=0.202 Sum_probs=139.7
Q ss_pred CCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcce-EEEEEEecCCCccChhhhcCCc
Q psy11925 125 RPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDL-LAVAVVNKNSKVKSLEELKGLK 203 (458)
Q Consensus 125 ~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~-~aVAVVkk~s~~~~l~dLkGkk 203 (458)
+.+++.+...+..++++++..|++|++..++..+..+.+..+.+++....+...... +.+.||++++++++++||+|||
T Consensus 58 g~~v~~~~~~~~~~~~~al~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~lvv~~ds~i~sl~DL~Gk~ 137 (288)
T TIGR03431 58 GVKVKLFFATDYAGVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAFAIEVNADGSTGYYSVLIVKKDSPIKSLEDLKGKT 137 (288)
T ss_pred CCcEEEEeCCCHHHHHHHHHcCCccEEEEChHHHHHHHHhcCCeEEEEeccCCCCCceEEEEEEeCCCCCCcHHHhCCCE
Confidence 457888888899999999999999999988776544433455566655433222222 5688889999999999999999
Q ss_pred eeeCCCCCCCchHHHHHHHHHc-CCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhc
Q psy11925 204 SCHTAYMRTTGWVAPVYNLLEK-GLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCL 281 (458)
Q Consensus 204 sChtg~~~taGw~~Pv~~L~~~-~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL 281 (458)
.+.++.++++++.++...+.+. |+ ...+||. ..=.+| ++. ++.-|
T Consensus 138 v~~~~~~s~~~~~~~~~~l~~~~g~----------~~~~~~~-~v~~~~----------------------~~~~~~~al 184 (288)
T TIGR03431 138 FGFVDPNSTSGFLVPSYYLFKKNGI----------KPKEYFK-KVTFSG----------------------SHEAAILAV 184 (288)
T ss_pred EEeeCCCcchhhHHHHHHHHHhcCC----------ChHHhHH-hheecC----------------------chHHHHHHH
Confidence 9999888889999887666443 31 1123332 100011 144 88899
Q ss_pred ccCCCcEEEEechhhhhhhhcccccccchhhhccCCCCCCCCCC-CCcccccccCCCCccccccCccccccccCCceEEE
Q psy11925 282 KSGDGDVAFIKQVKVNKAIEEGLFKTDEIEYLCSKGGRAPVSKA-GDYEIEYLCSKGGRAPVSKAADCNLGVVPPHMVVT 360 (458)
Q Consensus 282 ~eg~GDVAFvk~~tv~~~~~~~~~~~~g~~~~~~~~~wa~~~~~-~dy~~~LLCpdg~r~~v~~~~~C~l~~vP~~aVv~ 360 (458)
.+|..|++++...++...+. +|. ... .+++ ++-. ....|...+++
T Consensus 185 ~~G~vDa~~~~~~~~~~~~~------~~~------------~~~~~~~~--~~~~--------------~~~~~~~~~~~ 230 (288)
T TIGR03431 185 ANGTVDAATTNDENLDRMIR------KGQ------------PDAMEDLR--IIWK--------------SPLIPNGPIVY 230 (288)
T ss_pred HcCCCCeEeccHHHHHHHHH------cCC------------CCchhheE--EEEE--------------cCCCCCCcEEE
Confidence 99999999998777665421 110 011 2344 3311 02345566888
Q ss_pred cCCCChhHHHHHHHHHHHHHHHhcCCCccccccccCCCCCCccccCCCCcceeCCCCCHHHHHHH
Q psy11925 361 SNSKSNVEIDTIRHAILSAADLFSKKPEIFKLFGSFMGKPDVLFLNPATGVEVLPDQATDVETNY 425 (458)
Q Consensus 361 r~~~~~~~~~~i~~~l~~~~~~fg~~~~~F~lF~s~~~~kdllF~D~t~~l~~v~~~~~~~~~~y 425 (458)
+++.....++.|..+|.++.+ .+.++ +-+.+.--..+|.++.+.+|.-.++.
T Consensus 231 ~~~~~~~~~~~v~~~l~~~~~-----~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~ 282 (288)
T TIGR03431 231 RKDLPADLKAKIRKAFLNYHK-----TDKAC--------FEKIAGGDLKGFVAASDKDYDPIRDL 282 (288)
T ss_pred eCCCCHHHHHHHHHHHHhcCC-----CcHHH--------HHhhhcccccCeEECCHHHhHHHHHH
Confidence 888777777788887776543 11122 11121212378887755566655543
No 9
>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=97.68 E-value=0.00065 Score=67.86 Aligned_cols=132 Identities=12% Similarity=0.104 Sum_probs=85.8
Q ss_pred CCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEe-ccCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCce
Q psy11925 126 PPFECNREKSSKVCLKLIADGAADVITLDATEAVLG-RKNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKS 204 (458)
Q Consensus 126 p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A-~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkks 204 (458)
-.++-+.-.+..+.++++..|++|++......+..+ .+...++.++...+.. .....||++++++++++||||||.
T Consensus 27 l~Ve~~~~~~~~~~~~al~~G~iD~~~~~~~~~~~a~~~g~~~~~v~~~~~~~---~~~~lv~~~~s~I~s~~DLkGK~I 103 (300)
T TIGR01729 27 ATIDWRKFDSGADISTALASGNVPIGVIGSSPLAAAASRGVPIELFWILDNIG---KSEALVAREGSGIEKPEDLKGKNV 103 (300)
T ss_pred CeeEEEecCcHHHHHHHHHcCCCCEeccCCCHHHHHHHCCCCeEEEEEeccCC---ccceEEecCCCCCCChhHcCCCEE
Confidence 357777788889999999999999998766555444 2334444444333211 134667889999999999999998
Q ss_pred eeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhccc
Q psy11925 205 CHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCLKS 283 (458)
Q Consensus 205 Chtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~e 283 (458)
..+.. +++..+-...|.+.|+-+ .+ + ++.. . +.. ++..|.+
T Consensus 104 gv~~~--s~~~~~l~~~L~~~Gl~~-~d------v-~~v~----~------------------------~~~~~~~al~~ 145 (300)
T TIGR01729 104 AVPFV--STTHYSLLAALKHWKTDP-RE------V-NILN----L------------------------KPPQIVAAWQR 145 (300)
T ss_pred EeCCC--CcHHHHHHHHHHHcCCCh-hh------e-EEEe----c------------------------CcHHHHHHHHc
Confidence 77532 334444455666666422 11 1 1111 0 122 7788999
Q ss_pred CCCcEEEEechhhhh
Q psy11925 284 GDGDVAFIKQVKVNK 298 (458)
Q Consensus 284 g~GDVAFvk~~tv~~ 298 (458)
|..|.+++....+.+
T Consensus 146 G~vDa~~~~~p~~~~ 160 (300)
T TIGR01729 146 GDIDAAYVWPPALSE 160 (300)
T ss_pred CCcCEEEEecHHHHH
Confidence 999999998776554
No 10
>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=97.60 E-value=0.00069 Score=65.99 Aligned_cols=130 Identities=17% Similarity=0.166 Sum_probs=82.2
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEec-cCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCcee
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGR-KNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKSC 205 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~-~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkksC 205 (458)
.++-+...+..++++++.+|++|++.+.......+. +..+++.+..... . ...+.||++++++++++||+|||..
T Consensus 30 ~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~--~--~~~~~v~~~~~~i~s~~dL~Gk~i~ 105 (288)
T TIGR01728 30 KVEWVEFPAGPPALEALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSD--N--KATAIVVIKGSPIRTVADLKGKRIA 105 (288)
T ss_pred eEEEEecCCCcHHHHHHhcCCccccccCCcHHHHHHhcCCCEEEEEEecC--C--CceEEEECCCCCCCCHHHcCCCEEE
Confidence 566667677789999999999999987665433332 2234554433221 1 1445567888899999999999987
Q ss_pred eCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhcccC
Q psy11925 206 HTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCLKSG 284 (458)
Q Consensus 206 htg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~eg 284 (458)
.+. + ++...+....|...|+ +.. .+.-.+. ++. +...|.+|
T Consensus 106 ~~~-~-~~~~~~~~~~l~~~G~-~~~------~v~~~~~-----------------------------~~~~~~~al~~g 147 (288)
T TIGR01728 106 VPK-G-GSGHDLLLRALLKAGL-SGD------DVTILYL-----------------------------GPSDARAAFAAG 147 (288)
T ss_pred ecC-C-ccHHHHHHHHHHHcCC-Ccc------ceeEEec-----------------------------CcHHHHHHHHCC
Confidence 753 2 3445554455555564 211 1111111 233 77899999
Q ss_pred CCcEEEEechhhhh
Q psy11925 285 DGDVAFIKQVKVNK 298 (458)
Q Consensus 285 ~GDVAFvk~~tv~~ 298 (458)
..|++++.......
T Consensus 148 ~vda~~~~~p~~~~ 161 (288)
T TIGR01728 148 QVDAWAIWEPWGSA 161 (288)
T ss_pred CCCEEEeccchHhH
Confidence 99999997665544
No 11
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=97.17 E-value=0.0042 Score=63.05 Aligned_cols=130 Identities=17% Similarity=0.183 Sum_probs=83.6
Q ss_pred CCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEec-cCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCce
Q psy11925 126 PPFECNREKSSKVCLKLIADGAADVITLDATEAVLGR-KNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKS 204 (458)
Q Consensus 126 p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~-~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkks 204 (458)
-.|+-+...+..+.++++..|++|++.+....+..+. +...++.++...+.. .-.+.|+++ ++++++||||||.
T Consensus 51 l~Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~~~a~~~g~~~~~v~~~~~~~---~~~~lv~~~--~I~s~~DLkGK~I 125 (320)
T PRK11480 51 ATVDWRKFDSGASIVRALASGDVQIGNLGSSPLAVAASQQVPIEVFLLASKLG---NSEALVVKK--TISKPEDLIGKRI 125 (320)
T ss_pred CeeEEEEeCCHHHHHHHHHCCCCCEECcCchHHHHHHHCCCCeEEEEeeccCC---cceEEEecC--CCCChHHcCCCEE
Confidence 4677778888999999999999999988777665542 334555444333221 112334553 4889999999999
Q ss_pred eeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhccc
Q psy11925 205 CHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCLKS 283 (458)
Q Consensus 205 Chtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~e 283 (458)
-.+.. ++ ++.+....|.+.|+-+ . .+ ++.. . +.. +...|.+
T Consensus 126 av~~~-s~-~~~~l~~~L~~~Gl~~-~------dv-~~v~----~------------------------~~~~~~~Al~~ 167 (320)
T PRK11480 126 AVPFI-ST-THYSLLAALKHWGIKP-G------QV-EIVN----L------------------------QPPAIIAAWQR 167 (320)
T ss_pred ecCCC-Cc-hHHHHHHHHHHcCCCH-h------he-EEEE----C------------------------CcHHHHHHHHc
Confidence 88643 23 3444556677767422 1 11 1111 1 122 6778899
Q ss_pred CCCcEEEEechhhhh
Q psy11925 284 GDGDVAFIKQVKVNK 298 (458)
Q Consensus 284 g~GDVAFvk~~tv~~ 298 (458)
|..|++++....+.+
T Consensus 168 G~VDAa~~~~p~~~~ 182 (320)
T PRK11480 168 GDIDGAYVWAPAVNA 182 (320)
T ss_pred CCcCEEEEcchHHHH
Confidence 999999987765544
No 12
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=97.15 E-value=0.0045 Score=62.23 Aligned_cols=130 Identities=16% Similarity=0.143 Sum_probs=79.9
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEe-ccCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCcee
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLG-RKNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKSC 205 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A-~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkksC 205 (458)
+++=+...+..+.++++.+|++|++.........+ .....++.+..+.+... ..+.||++++++.+++||+||+..
T Consensus 57 ~ie~~~~~~~~~~~~aL~~G~iDia~~~~~~~~~~~~~g~~~~~v~~~~~~~~---~~~lvv~~~s~i~s~~dL~Gk~I~ 133 (314)
T PRK11553 57 KISWVEFPAGPQMLEALNVGSIDLGSTGDIPPIFAQAAGADLVYVGVEPPKPK---AEVILVAENSPIKTVADLKGHKVA 133 (314)
T ss_pred eeEEEECCCcHHHHHHHHcCCCCEEccCCHHHHHHHhCCCCEEEEEEecCCCc---ceEEEEeCCCCCCCHHHhCCCEEe
Confidence 45545555667999999999999998754322222 12345566655544221 457788999999999999999988
Q ss_pred eCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhcccC
Q psy11925 206 HTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCLKSG 284 (458)
Q Consensus 206 htg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~eg 284 (458)
.+. +++. ..+-...|.+.|+- .. .+.-.+ . ++. ++..|.+|
T Consensus 134 ~~~-gs~~-~~~l~~~l~~~g~~-~~------dv~~v~-----~------------------------~~~~~~~al~~G 175 (314)
T PRK11553 134 FQK-GSSS-HNLLLRALRKAGLK-FT------DIQPTY-----L------------------------TPADARAAFQQG 175 (314)
T ss_pred ecC-CCcH-HHHHHHHHHHcCCC-HH------HeEEEe-----c------------------------ChHHHHHHHHcC
Confidence 743 4332 23323344444431 11 111001 0 233 77889999
Q ss_pred CCcEEEEechhhh
Q psy11925 285 DGDVAFIKQVKVN 297 (458)
Q Consensus 285 ~GDVAFvk~~tv~ 297 (458)
..|++++....+.
T Consensus 176 ~vDa~~~~ep~~~ 188 (314)
T PRK11553 176 NVDAWAIWDPYYS 188 (314)
T ss_pred CCCEEEEcCcHHH
Confidence 9999998765444
No 13
>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=97.14 E-value=0.0016 Score=61.30 Aligned_cols=95 Identities=22% Similarity=0.187 Sum_probs=67.1
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEec-cCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCcee
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGR-KNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKSC 205 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~-~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkksC 205 (458)
.++-+...+..+++++|..|++|++..+...+..+. +...++-|....... ....|+++++.+++++||||||.-
T Consensus 22 ~ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~----~~~l~~~~~s~i~~~~DLkGK~i~ 97 (216)
T PF09084_consen 22 DVEIVFFGGGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSS----PNALVVRKDSGIKSPADLKGKKIG 97 (216)
T ss_dssp EEEEEEESSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEEC----CEEEEEETTTS-SSGGGGTTSEEE
T ss_pred EEEEEEecChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCC----ceEEEEeccCCCCCHHHhCCCEEE
Confidence 567777788899999999999999998888777554 445666665443221 334567788889999999999998
Q ss_pred eCCCCCCCchHHHHHHHHHcCC
Q psy11925 206 HTAYMRTTGWVAPVYNLLEKGL 227 (458)
Q Consensus 206 htg~~~taGw~~Pv~~L~~~~~ 227 (458)
-+. ++ .++..-...|.+.|+
T Consensus 98 v~~-~s-~~~~~~~~~l~~~g~ 117 (216)
T PF09084_consen 98 VSR-GS-SSEYFLRALLKKNGI 117 (216)
T ss_dssp EST-TS-HHHHHHHHHHHHTTT
T ss_pred Eec-Cc-chhHHHHHHHHHhcc
Confidence 776 43 344444445555564
No 14
>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=97.06 E-value=0.0094 Score=59.51 Aligned_cols=237 Identities=18% Similarity=0.146 Sum_probs=120.4
Q ss_pred CCceEEEeCChhHH--hHHHHHHHHHhcCCCC-CCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEec---cC-----
Q psy11925 96 IKPIRWCVSSPEGM--SKCLAFKDAAFSRDIR-PPFECNREKSSKVCLKLIADGAADVITLDATEAVLGR---KN----- 164 (458)
Q Consensus 96 ~~~vrwCv~s~~E~--~KC~~l~~~~~~~~~~-p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~---~~----- 164 (458)
..++|+.+.+.... .--..+...... ... ..++-+...+..+-++++++|++|++.......+.+. ..
T Consensus 29 ~~~l~Ig~~~~~~~~~~~~~~la~~~~~-~~~~i~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~~ 107 (320)
T TIGR02122 29 PTFVTIGTGGTGGVYYPIGGAIAQLINK-KSGKLRVRVQSTGGSVENVNLLEAGEADLAIVQSDVAYYAYEGDGEFEFEG 107 (320)
T ss_pred CceEEEEeCCCCCChHHHHHHHHHHHhc-cCCCeeEEEEeCcchHHHHHHHhCCCCcEEEEcchhHHHHhcCcCccccCC
Confidence 45688888764332 112334433211 111 3455555567788999999999999988754432111 11
Q ss_pred --CCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCceeeCCCCCCCchHHHHHHHHHc-CCCCCCCCcccccccc
Q psy11925 165 --LNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKSCHTAYMRTTGWVAPVYNLLEK-GLIKKDSCPYYKGVAE 241 (458)
Q Consensus 165 --~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkksChtg~~~taGw~~Pv~~L~~~-~~i~~~~c~~~~~~~~ 241 (458)
-+++++. ..+. ...+.||++++++++++||+||+...... +++....+..++++ |+ .. .+
T Consensus 108 ~~~~~~~v~-~~~~----~~~~lvv~~d~~i~sl~dL~gk~v~~~~~--~s~~~~~~~~~l~~~G~-~~---------~~ 170 (320)
T TIGR02122 108 PVEKLRALA-SLYP----EYIQIVVRKDSGIKTVADLKGKRVAVGAP--GSGTELNARAVLKAAGL-TY---------DD 170 (320)
T ss_pred CCccHHhHH-Hhcc----ccEEEEEECCCCCCcHHHcCCCEEecCCC--CcchHHHHHHHHHHcCC-CH---------HH
Confidence 1222221 0111 14567889999999999999999877533 34455444444443 42 11 11
Q ss_pred ccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhcccCCCcEEEEech----hhhhhhhcccc---cccchhhh
Q psy11925 242 FFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCLKSGDGDVAFIKQV----KVNKAIEEGLF---KTDEIEYL 313 (458)
Q Consensus 242 FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~eg~GDVAFvk~~----tv~~~~~~~~~---~~~g~~~~ 313 (458)
++. ++- . |+. ++.-|.+|..|+++.... .+.+....+-+ ...+.++
T Consensus 171 ~~~----v~~--------~-------------~~~~~~~al~~G~vDa~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~- 224 (320)
T TIGR02122 171 VKK----VEY--------L-------------GYAEAADALKDGKIDAAFYTAGTPTAAITELATSLDIRIVPISGEKV- 224 (320)
T ss_pred ccc----hhc--------C-------------CHHHHHHHHHCCCccEEEEecCCChHHHHHHHhcCCeEEEeCCHHHH-
Confidence 110 000 0 345 888899999999998722 45544221100 0000000
Q ss_pred ccCCCCCCCCCCCCcccccccCCCCccccccCccccccccCCceEEEcCCCChhHHHHHHHHHHHHHHHhcC
Q psy11925 314 CSKGGRAPVSKAGDYEIEYLCSKGGRAPVSKAADCNLGVVPPHMVVTSNSKSNVEIDTIRHAILSAADLFSK 385 (458)
Q Consensus 314 ~~~~~wa~~~~~~dy~~~LLCpdg~r~~v~~~~~C~l~~vP~~aVv~r~~~~~~~~~~i~~~l~~~~~~fg~ 385 (458)
..+.+.. .-|. +.-=|-|+-.... .... ...-+..++++++.+++.+.++..+|.+..+.|..
T Consensus 225 ---~~~~~~~--p~~~-~~~ip~g~~~~~~--~~~~-~~~~~~~~~~~~~~p~~~v~~l~~a~~e~~~~~~~ 287 (320)
T TIGR02122 225 ---EKLREKY--PFYR-KGVIPAGTYPGQD--EDVP-TLAVPAALVTSSDVPEDLVYQITKAIFENLDELKD 287 (320)
T ss_pred ---HHHHHhC--CceE-eeeccCCCCCCCC--CCcc-eEEEEEEEEEcCCCCHHHHHHHHHHHHhCHHHHHH
Confidence 0000000 0000 0000001000000 0000 13344688899999999999999999887665543
No 15
>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=96.90 E-value=0.03 Score=50.44 Aligned_cols=121 Identities=21% Similarity=0.277 Sum_probs=73.9
Q ss_pred CCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCce-EEEEEeecCCcceEEEEEEecCCCccChhhhcCCce
Q psy11925 126 PPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLR-PILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKS 204 (458)
Q Consensus 126 p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~-pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkks 204 (458)
.+++-+... ..++++.+++|++|++.............+... |+.. ...+.||++++++.+++||+|++.
T Consensus 38 ~~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~dl~g~~i 108 (218)
T cd00134 38 VKVKFVEVD-WDGLITALKSGKVDLIAAGMTITPERAKQVDFSDPYYK--------SGQVILVKKGSPIKSVKDLKGKKV 108 (218)
T ss_pred CeEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCHHHHhhccCccccee--------ccEEEEEECCCCCCChHHhCCCEE
Confidence 356666665 789999999999999987762111111111111 1110 056778899988889999999999
Q ss_pred eeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhccc
Q psy11925 205 CHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCLKS 283 (458)
Q Consensus 205 Chtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~e 283 (458)
+.. . |+... .++.+- .. . .. -..+. +++ ++.-|..
T Consensus 109 ~~~-~----~~~~~--~~~~~~-~~--~----~~-~~~~~-----------------------------~~~~~~~~l~~ 144 (218)
T cd00134 109 AVQ-K----GSTAE--KYLKKA-LP--E----AK-VVSYD-----------------------------DNAEALAALEN 144 (218)
T ss_pred EEE-c----CchHH--HHHHHh-CC--c----cc-EEEeC-----------------------------CHHHHHHHHHc
Confidence 986 2 22221 122211 00 0 00 00111 345 8999999
Q ss_pred CCCcEEEEechhhhhh
Q psy11925 284 GDGDVAFIKQVKVNKA 299 (458)
Q Consensus 284 g~GDVAFvk~~tv~~~ 299 (458)
|.+|++++....+...
T Consensus 145 g~~d~~~~~~~~~~~~ 160 (218)
T cd00134 145 GRADAVIVDEIALAAL 160 (218)
T ss_pred CCccEEEeccHHHHHH
Confidence 9999999988877654
No 16
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=96.71 E-value=0.059 Score=48.30 Aligned_cols=121 Identities=26% Similarity=0.229 Sum_probs=73.9
Q ss_pred CCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCC-ceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCce
Q psy11925 126 PPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLN-LRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKS 204 (458)
Q Consensus 126 p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~-L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkks 204 (458)
-+++.+.. +..++++.+.+|++|++.............+. -.|+.. ...+.|+++++++.+++||+||+.
T Consensus 39 ~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~dL~g~~i 109 (219)
T smart00062 39 LKVEFVEV-SFDNLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYK--------SGQVILVRKDSPIKSLEDLKGKKV 109 (219)
T ss_pred CeEEEEec-cHHHHHHHHHCCcccEEeccccCCHHHHhheeeccceee--------ceeEEEEecCCCCCChHHhCCCEE
Confidence 46777777 88999999999999999865431100001010 112211 134667888888999999999999
Q ss_pred eeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhccc
Q psy11925 205 CHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCLKS 283 (458)
Q Consensus 205 Chtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~e 283 (458)
+-.. |+... ..+...+ + . .--.+++ +.. ++..|..
T Consensus 110 ~~~~-----g~~~~-~~~~~~~--~--~-----~~~~~~~-----------------------------~~~~~~~~l~~ 145 (219)
T smart00062 110 AVVA-----GTTGE-ELLKKLY--P--E-----AKIVSYD-----------------------------SQAEALAALKA 145 (219)
T ss_pred EEec-----CccHH-HHHHHhC--C--C-----ceEEEcC-----------------------------CHHHHHHHhhc
Confidence 8754 33222 2222211 0 0 0001111 234 8899999
Q ss_pred CCCcEEEEechhhhhh
Q psy11925 284 GDGDVAFIKQVKVNKA 299 (458)
Q Consensus 284 g~GDVAFvk~~tv~~~ 299 (458)
|.+|++++....+...
T Consensus 146 g~~d~~~~~~~~~~~~ 161 (219)
T smart00062 146 GRADAAVADAPALAAL 161 (219)
T ss_pred CcccEEEeccHHHHHH
Confidence 9999999988866543
No 17
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=95.34 E-value=0.052 Score=55.58 Aligned_cols=119 Identities=25% Similarity=0.226 Sum_probs=76.7
Q ss_pred CceEEEeCC------hhHHhHHHHHHHHHhcCCCCCCeEEEe--cCCHHHHHHHHHcCCccEEEeCCcceEEec----cC
Q psy11925 97 KPIRWCVSS------PEGMSKCLAFKDAAFSRDIRPPFECNR--EKSSKVCLKLIADGAADVITLDATEAVLGR----KN 164 (458)
Q Consensus 97 ~~vrwCv~s------~~E~~KC~~l~~~~~~~~~~p~v~Cv~--~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~----~~ 164 (458)
..|+|=|=| ..-..=|+.+.+. .+.++|.. .....+=|+.|.+|++|+..+-..-.|.|. ..
T Consensus 26 ~~itigTG~~~G~YY~ig~~ia~~~~~~------~~~i~~~v~~tggSv~Nl~~i~~Ge~d~alvq~d~a~~ay~G~g~f 99 (321)
T COG2358 26 KFITIGTGSTGGVYYPIGGGLAQLLNKD------EKGIECSVVPTGGSVENLKLLASGEADLALVQSDVAYEAYNGTGSF 99 (321)
T ss_pred eEEEEeecCCCceeeehHHHHHHHHhcc------CCCeEEEEeeccchHHHHHhHhcCccchhhhhHHHHHHHHhCcccc
Confidence 346664433 2345556655541 23366654 445788899999999999988776555441 11
Q ss_pred C------CceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCceeeCCCCCCCchHHHHHHHHHcCC
Q psy11925 165 L------NLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKSCHTAYMRTTGWVAPVYNLLEKGL 227 (458)
Q Consensus 165 ~------~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkksChtg~~~taGw~~Pv~~L~~~~~ 227 (458)
. +|+.+.. .|. .+.-.|+|+++.|++|.||+|||.--...++..+-++.+ .|-..|+
T Consensus 100 ~~~~~~~~lr~v~~-lyp----e~~~vv~r~d~~Ikti~DL~GKrV~iG~~gSgt~~~a~~-il~a~Gi 162 (321)
T COG2358 100 EGKGKDENLRAVAA-LYP----EPFHVVTRKDAGIKTIADLKGKRVAIGPPGSGTEATARQ-ILEALGI 162 (321)
T ss_pred cccccccchhhhee-ccc----ceEEEEEecCCCcceehhcCCCEEeecCCCCccHHHHHH-HHHHcCC
Confidence 1 2222221 111 178889999999999999999999988888877777664 3333454
No 18
>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=95.19 E-value=0.072 Score=54.79 Aligned_cols=93 Identities=18% Similarity=0.195 Sum_probs=60.3
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcce-EE-eccCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCce
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEA-VL-GRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKS 204 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~-y~-A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkks 204 (458)
.++-+.-.+..+.|+++..|+.|++.+..... .. +.....++-++...+..+ ....||++ +++++||||||.
T Consensus 36 ~Ve~~~f~~~~~~l~Al~aG~iD~~~~g~~~~~~~~~a~g~~~~iv~v~~~~~g---~~~ivv~~---i~svaDLKGKkI 109 (328)
T TIGR03427 36 TIEVVQINDYVESINQYTAGKFDGCTMTNMDALTIPAAGGVDTTALIVGDFSNG---NDGIVLKG---GKSLADLKGQKV 109 (328)
T ss_pred eEEEEECCChHHHHHHHHcCCCCEEeecCHHHHHHHHhCCCCeEEEEEEccCCC---ceEEEECC---CCCHHHcCCCEE
Confidence 58888888899999999999999977654332 22 223344555554443221 23345554 789999999999
Q ss_pred eeCCCCCCCchHHHHHHHHHcCC
Q psy11925 205 CHTAYMRTTGWVAPVYNLLEKGL 227 (458)
Q Consensus 205 Chtg~~~taGw~~Pv~~L~~~~~ 227 (458)
..+. + +.+-.+-...|.+.|+
T Consensus 110 av~~-g-s~~~~ll~~aL~~aGL 130 (328)
T TIGR03427 110 NLVE-L-SVSHYLLARALESVGL 130 (328)
T ss_pred eccC-C-ChHHHHHHHHHHHcCC
Confidence 7643 3 3444455566777775
No 19
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=94.56 E-value=0.1 Score=52.59 Aligned_cols=98 Identities=20% Similarity=0.155 Sum_probs=67.3
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceE--Eec-cCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCc
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAV--LGR-KNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLK 203 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y--~A~-~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkk 203 (458)
.++-+...+-.+.++++..|.+|++....+..+ .++ +...++-+.....+. .-...++++++++++++||||||
T Consensus 62 ~v~~~~~~~~~~~~~~l~~G~~D~a~~~~~~~~~~~~~~~g~pv~~va~~~~~~---~~~~i~~~~~~~i~~~adlkGk~ 138 (335)
T COG0715 62 DVELVEFTGGAPVLEALAAGALDFAVYYTGDTPLIAAGAAGAPVKVVAALVQNG---NGIALLVLKDSGIKSVADLKGKK 138 (335)
T ss_pred ceEEEEcCCChHHHHHHhcCCcCccccccCchHHHHhhccCCCeEEeeecccCC---ceeEEEeccCCCcccccCCCCce
Confidence 588889999999999999999999975555554 332 111233333332221 14556677888999999999999
Q ss_pred eeeCCCCCCCchHHHHHHHHHcCCC
Q psy11925 204 SCHTAYMRTTGWVAPVYNLLEKGLI 228 (458)
Q Consensus 204 sChtg~~~taGw~~Pv~~L~~~~~i 228 (458)
...+..+++.-+.+ ...|.+.|+-
T Consensus 139 vg~~~~~~~~~~~l-~~~L~~~Gl~ 162 (335)
T COG0715 139 VGVPFGGSTSDFLL-RYALAKAGLD 162 (335)
T ss_pred EEEeCCCchHHHHH-HHHHHHcCCC
Confidence 99998876443333 4466666753
No 20
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=94.35 E-value=0.38 Score=46.79 Aligned_cols=130 Identities=22% Similarity=0.184 Sum_probs=79.4
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccC-C-----CceEEEEEeecCCcceEEEEEEecC----CCccCh
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKN-L-----NLRPILKEKYGNEKDLLAVAVVNKN----SKVKSL 196 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~-~-----~L~pil~E~y~~~~~~~aVAVVkk~----s~~~~l 196 (458)
.++-+...+..+-++++..|++|++.+ ......+... - .++-+.. .. .. -...||+++ +.++++
T Consensus 36 ~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~~~~~~~~~~~~~-~~---~~-g~~lvv~~~~~~~~~~~~~ 109 (252)
T PF13379_consen 36 DVEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGAGGPDVDIVVLAG-LS---QN-GNALVVRNDLKDASDIKSL 109 (252)
T ss_dssp CEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTTTT----EEEEEE-CS---BS-SEEEEECGGGTTCSTTCCG
T ss_pred EEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCCCCcccceEEeec-cC---CC-ceEEEEcCccccCCCccCH
Confidence 477777788999999999999999999 5554443221 1 2222211 11 11 345667776 788999
Q ss_pred hhh-------cCCceeeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCC
Q psy11925 197 EEL-------KGLKSCHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPK 269 (458)
Q Consensus 197 ~dL-------kGkksChtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g 269 (458)
+|| ||||.--+..++ ..+.+-...|.+.|+-+..+- .+ .+++
T Consensus 110 ~dl~~~~~~~kGk~i~~~~~gs-~~~~~l~~~l~~~Gl~~~~dv----~~-~~~~------------------------- 158 (252)
T PF13379_consen 110 ADLIKKRKAQKGKKIAVPFPGS-THDMLLRYLLKKAGLDPKDDV----TL-VNVP------------------------- 158 (252)
T ss_dssp HHHHHTCCSCSTEEEEESSTTS-HHHHHHHHHHHHTT--TTTSS----EE-EE---------------------------
T ss_pred HHHHhhhcccCCcEEEEcCCCC-HHHHHHHHHHHhCCCCcccce----EE-EecC-------------------------
Confidence 999 999998766653 233333334556675331111 00 1111
Q ss_pred CCCCChh-hhhhcccCCCcEEEEechhhhh
Q psy11925 270 ATRVTYT-PLQCLKSGDGDVAFIKQVKVNK 298 (458)
Q Consensus 270 ~~~CGy~-A~rCL~eg~GDVAFvk~~tv~~ 298 (458)
.. +...|.+|++|.+++..-....
T Consensus 159 -----~~~~~~al~~g~iDa~~~~eP~~~~ 183 (252)
T PF13379_consen 159 -----PPEMVAALRAGEIDAAVLWEPFASQ 183 (252)
T ss_dssp -----GHHHHHHHHTTS-SEEEEETTHHHH
T ss_pred -----HHHHHHHHhCCCcCEEEecCCHHHH
Confidence 13 7889999999999998776554
No 21
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=93.53 E-value=1.1 Score=43.12 Aligned_cols=69 Identities=13% Similarity=0.191 Sum_probs=41.9
Q ss_pred eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEecc--CCCc-eEEEEEeecCCcceEEEEEEecCCC-ccChhhhcCCc
Q psy11925 128 FECNREKSSKVCLKLIADGAADVITLDATEAVLGRK--NLNL-RPILKEKYGNEKDLLAVAVVNKNSK-VKSLEELKGLK 203 (458)
Q Consensus 128 v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~--~~~L-~pil~E~y~~~~~~~aVAVVkk~s~-~~~l~dLkGkk 203 (458)
++-+. .+..++++.+.+|++|++..... +...+ .+.. .|++. ...+.++++++. +.+++||+||+
T Consensus 65 ~~~~~-~~~~~~~~~l~~G~vDi~~~~~~--~t~~R~~~~~fs~p~~~--------~~~~~~~~~~~~~~~~~~dL~g~~ 133 (247)
T PRK09495 65 YTLKP-MDFSGIIPALQTKNVDLALAGIT--ITDERKKAIDFSDGYYK--------SGLLVMVKANNNDIKSVKDLDGKV 133 (247)
T ss_pred eEEEe-CCHHHHHHHHhCCCcCEEEecCc--cCHHHHhhccccchhee--------cceEEEEECCCCCCCChHHhCCCE
Confidence 44443 46899999999999999753321 12212 1111 12211 122335666654 88999999999
Q ss_pred eeeC
Q psy11925 204 SCHT 207 (458)
Q Consensus 204 sCht 207 (458)
.|..
T Consensus 134 I~v~ 137 (247)
T PRK09495 134 VAVK 137 (247)
T ss_pred EEEe
Confidence 9874
No 22
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=92.82 E-value=2.6 Score=41.28 Aligned_cols=69 Identities=20% Similarity=0.271 Sum_probs=41.8
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccC--CCc-eEEEEEeecCCcceEEEEEEecCCCccChhhhcCCc
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKN--LNL-RPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLK 203 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~--~~L-~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkk 203 (458)
+++-+.. +....+.++++|++|++.-.-. +...|. +.. .|++.. ..+.||++++++.+++||+||+
T Consensus 82 ~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~--~t~eR~~~~~fs~py~~~--------~~~lvv~~~~~~~s~~dL~g~~ 150 (259)
T PRK11917 82 KIKLVAV-NAKTRGPLLDNGSVDAVIATFT--ITPERKRIYNFSEPYYQD--------AIGLLVLKEKNYKSLADMKGAN 150 (259)
T ss_pred cEEEEEc-ChhhHHHHHHCCCccEEEeccc--CChhhhheeeeccCceee--------ceEEEEECCCCCCCHHHhCCCe
Confidence 3443333 4566778999999999863211 111111 111 122111 4456788888899999999999
Q ss_pred eee
Q psy11925 204 SCH 206 (458)
Q Consensus 204 sCh 206 (458)
.+-
T Consensus 151 V~v 153 (259)
T PRK11917 151 IGV 153 (259)
T ss_pred EEE
Confidence 877
No 23
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=91.77 E-value=2.8 Score=45.25 Aligned_cols=73 Identities=16% Similarity=0.191 Sum_probs=46.1
Q ss_pred CCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccC--CCc-eEEEEEeecCCcceEEEEEEecCC-CccChhhhc
Q psy11925 125 RPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKN--LNL-RPILKEKYGNEKDLLAVAVVNKNS-KVKSLEELK 200 (458)
Q Consensus 125 ~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~--~~L-~pil~E~y~~~~~~~aVAVVkk~s-~~~~l~dLk 200 (458)
+-+++-+...+..+++.++++|++|++...- .++..+. +.. .|++. ...+.|+++++ .+.+++||+
T Consensus 79 Gv~~e~v~~~~~~~ll~aL~~G~iDi~~~~l--t~T~eR~~~~~FS~Py~~--------~~~~lv~r~~~~~i~~l~dL~ 148 (482)
T PRK10859 79 GVKLEIKVRDNISQLFDALDKGKADLAAAGL--TYTPERLKQFRFGPPYYS--------VSQQLVYRKGQPRPRSLGDLK 148 (482)
T ss_pred CCcEEEEecCCHHHHHHHHhCCCCCEEeccC--cCChhhhccCcccCCcee--------eeEEEEEeCCCCCCCCHHHhC
Confidence 3456666778899999999999999875321 1122121 111 12211 14455677664 468899999
Q ss_pred CCceeeC
Q psy11925 201 GLKSCHT 207 (458)
Q Consensus 201 GkksCht 207 (458)
||+.+-.
T Consensus 149 Gk~I~V~ 155 (482)
T PRK10859 149 GGTLTVA 155 (482)
T ss_pred CCeEEEE
Confidence 9998764
No 24
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=88.92 E-value=2.7 Score=41.92 Aligned_cols=141 Identities=23% Similarity=0.164 Sum_probs=79.1
Q ss_pred EEEEEEecCCCccChhhh----c---C-CceeeCCCCCCCchHHHHHHHHHc-CCCCCCCCccccccccccccCcccCCC
Q psy11925 182 LAVAVVNKNSKVKSLEEL----K---G-LKSCHTAYMRTTGWVAPVYNLLEK-GLIKKDSCPYYKGVAEFFTGGSCVPGI 252 (458)
Q Consensus 182 ~aVAVVkk~s~~~~l~dL----k---G-kksChtg~~~taGw~~Pv~~L~~~-~~i~~~~c~~~~~~~~FFsg~sC~pG~ 252 (458)
..|.||+++++++||+|| | | -+.-++|.+ +.+.+....|.+. |+ .. +. +| .
T Consensus 79 ~~vl~v~~dsp~~t~~eli~~ak~~p~~~~~g~~g~g--~~~hl~~~~l~~~~G~-~~------~~----------Vp-y 138 (274)
T PF03401_consen 79 PNVLVVRADSPYKTLEELIEYAKANPGKLTFGSSGPG--SSDHLAAALLAKAAGI-KF------TH----------VP-Y 138 (274)
T ss_dssp EEEEEEETTSS-SSHHHHHHHHHCSCCC-EEEESSTT--SHHHHHHHHHHHHHT----------EE----------EE--
T ss_pred ceEEEEeCCCccccHHHHHHHHHhCCCCeEEEecCCC--chHHHHHHHHHHHhCC-ce------EE----------EE-e
Confidence 667788999999999998 2 2 244555554 4567776666654 42 10 01 22 0
Q ss_pred CccccCCCchhhhhCCCCCCCChh-hhhhcccCCCcEEEEechhhhhhhhcccccccchhhhccCCCCCCCCCCCCcccc
Q psy11925 253 DEEEKDAPASLEKICPKATRVTYT-PLQCLKSGDGDVAFIKQVKVNKAIEEGLFKTDEIEYLCSKGGRAPVSKAGDYEIE 331 (458)
Q Consensus 253 ~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~eg~GDVAFvk~~tv~~~~~~~~~~~~g~~~~~~~~~wa~~~~~~dy~~~ 331 (458)
. |-. ++..|..|..|++|.....+..++..|-+.. |+.. . ..+...|
T Consensus 139 ~--------------------G~~~~~~allgG~vd~~~~~~~~~~~~~~~G~~k~-----Lav~---~-~~r~~~~--- 186 (274)
T PF03401_consen 139 D--------------------GGAEALTALLGGHVDAAFGSPGEALPYVEAGDLKP-----LAVF---S-DERSPAL--- 186 (274)
T ss_dssp S--------------------SHHHHHHHHHTTSSSEEEEEHHHHHHHHHTTSEEE-----EEEC---S-SS-BTTC---
T ss_pred C--------------------CccHHHHHHhCCeeeEEeecHHHHHHHHhCCCceE-----EEEe---c-Ccccccc---
Confidence 0 333 8899999999999999888887754332110 0000 0 0011111
Q ss_pred cccCCCC-ccccccCccccccccCCceEEEcCCCChhHHHHHHHHHHHHH
Q psy11925 332 YLCSKGG-RAPVSKAADCNLGVVPPHMVVTSNSKSNVEIDTIRHAILSAA 380 (458)
Q Consensus 332 LLCpdg~-r~~v~~~~~C~l~~vP~~aVv~r~~~~~~~~~~i~~~l~~~~ 380 (458)
||-. .++. .+. .+....+++++++++.+++.++++..+|.++.
T Consensus 187 ---pdvPT~~E~-G~~--d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~ 230 (274)
T PF03401_consen 187 ---PDVPTFKEQ-GYP--DIVFGSWRGLFAPKGTPDEIVDKLADAIKKAL 230 (274)
T ss_dssp ---TTS-BTTTT-T-T--TG--EEEEEEEEETTS-HHHHHHHHHHHHHHH
T ss_pred ---CCCCCHHHh-Ccc--ceeeeeeeeeecCCCCCHHHHHHHHHHHHHHh
Confidence 1210 0010 011 13445678999999999998888888887764
No 25
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=88.81 E-value=0.81 Score=45.30 Aligned_cols=94 Identities=18% Similarity=0.246 Sum_probs=67.3
Q ss_pred eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEe-ccCCCceEEEEE-eecCCcceEEEEEEecCCCccChhhhcCCcee
Q psy11925 128 FECNREKSSKVCLKLIADGAADVITLDATEAVLG-RKNLNLRPILKE-KYGNEKDLLAVAVVNKNSKVKSLEELKGLKSC 205 (458)
Q Consensus 128 v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A-~~~~~L~pil~E-~y~~~~~~~aVAVVkk~s~~~~l~dLkGkksC 205 (458)
+.=.+-+|-.+.+.++..|..++..+++..+-.| .++--++.++.- ..+. ----|||++|.|...+||.|||..
T Consensus 59 iDWRkFdSG~~vv~AlASGdvqiG~iGSsplaaAaSr~vpie~f~~~~~ig~----sEALVvr~gsgI~kpeDL~GK~ia 134 (334)
T COG4521 59 IDWRKFDSGASIVRALASGDVQIGNIGSSPLAAAASRQVPIEVFLLASQIGN----SEALVVRKGSGIEKPEDLIGKRIA 134 (334)
T ss_pred cchhhcCchhHHHHHHhcCCccccccCCchhhHHhhcCCceEEeehhhhcCc----cceeeeecCCCcCChHHhccCeec
Confidence 3334556678999999999999999988877665 365555555432 2221 123478999999999999999999
Q ss_pred eCCCCCCCchHHHHHHHHHcCC
Q psy11925 206 HTAYMRTTGWVAPVYNLLEKGL 227 (458)
Q Consensus 206 htg~~~taGw~~Pv~~L~~~~~ 227 (458)
-|=+ +|+.|.+- ..|..-++
T Consensus 135 vPFv-STtHysLL-aaLkhw~i 154 (334)
T COG4521 135 VPFV-STTHYSLL-AALKHWGI 154 (334)
T ss_pred ccee-ehhHHHHH-HHHHHcCC
Confidence 8855 68888874 45666553
No 26
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=85.49 E-value=2.1 Score=42.96 Aligned_cols=75 Identities=20% Similarity=0.229 Sum_probs=49.4
Q ss_pred CCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCcee
Q psy11925 126 PPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKSC 205 (458)
Q Consensus 126 p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkksC 205 (458)
.+++.+...+ .+-+..+.+|++|+++..-..... +.-.+..+..-.|. . ...+.+|++++++.+++||+||+..
T Consensus 44 ~~ie~~~~~~-~~i~~~L~sG~vDlgi~g~~~~~e--r~~~v~~~~~l~~~--~-~~lvvvvp~~~~i~sl~DL~Gk~ia 117 (287)
T PRK00489 44 NPIEVLFLRP-DDIPGYVADGVVDLGITGEDLLEE--SGADVEELLDLGFG--K-CRLVLAVPEDSDWQGVEDLAGKRIA 117 (287)
T ss_pred CCEEEEEECc-HHHHHHHHcCCCCEEEcchHHHHH--CCCCceEeeeccCC--c-eEEEEEEECCCCCCChHHhCCCEEE
Confidence 4577777665 799999999999999865332211 11122222211122 1 1677788999999999999999766
Q ss_pred e
Q psy11925 206 H 206 (458)
Q Consensus 206 h 206 (458)
-
T Consensus 118 ~ 118 (287)
T PRK00489 118 T 118 (287)
T ss_pred E
Confidence 5
No 27
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.06 E-value=6.5 Score=40.49 Aligned_cols=216 Identities=18% Similarity=0.188 Sum_probs=117.6
Q ss_pred CCCceEEEeCChh---HHhHHHHHHHHHhcCCCCCCeEEEecC--CHHHHHHHHHc---CCccEEEeCCcceEEec----
Q psy11925 95 PIKPIRWCVSSPE---GMSKCLAFKDAAFSRDIRPPFECNREK--SSKVCLKLIAD---GAADVITLDATEAVLGR---- 162 (458)
Q Consensus 95 p~~~vrwCv~s~~---E~~KC~~l~~~~~~~~~~p~v~Cv~~~--s~~~Ci~~I~~---g~AD~~~ld~~~~y~A~---- 162 (458)
|.++|++-|.-.. --.-|+.++...... +.-++...... +=.-=+..+.+ |....+...++..+...
T Consensus 26 P~~~it~Ivp~~~GGg~D~~aR~~~~~l~k~-lg~~v~V~N~pGagG~ia~~~va~a~pG~t~~l~~~~~~~~~~~~~~~ 104 (319)
T COG3181 26 PERPITIIVPAAAGGGTDQTARALAESLSKE-LGQPVVVDNKPGAGGAIAAGAVAKAAPGYTILLIAGSTPALLLPILGG 104 (319)
T ss_pred CCCCeEEEEecCCCChHHHHHHHHHHHHHHH-hCCCEEEEecCCCcchHHHHHHHhcCCCCceEEEecCcccccchhhcc
Confidence 6666776665432 233466666543332 54445444433 22222222222 45566665554443321
Q ss_pred ----cCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhc-------CCceeeCCCCCCCchHHHHHHHHHc-CCCCC
Q psy11925 163 ----KNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELK-------GLKSCHTAYMRTTGWVAPVYNLLEK-GLIKK 230 (458)
Q Consensus 163 ----~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLk-------GkksChtg~~~taGw~~Pv~~L~~~-~~i~~ 230 (458)
+.-++.||+.-.+. +.+.||+++++.+|++||- |...+-++-..+..|..-. .|.+. | +..
T Consensus 105 ~~~~~~~D~~pva~v~~~-----p~~l~v~~~s~~~t~~dlv~~~k~~p~~v~~~~~g~Gs~dhl~~~-~~~k~~G-i~~ 177 (319)
T COG3181 105 LPYYKLKDFTPVASLVSD-----PGVLVVRADSPYKTLKDLVAYAKADPGSVIGGGSGLGSADHLAGA-LFAKAAG-IKI 177 (319)
T ss_pred CCCCchhhceehhheecc-----cceEEEeCCCCcccHHHHHHHHHhCCCeEEecCCCCCcHHHHHHH-HHHHHhC-Cce
Confidence 11245566433211 7889999999999999973 4344443333344554322 22222 3 211
Q ss_pred CCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhcccCCCcEEEEechhhhhhhhcccccccc
Q psy11925 231 DSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCLKSGDGDVAFIKQVKVNKAIEEGLFKTDE 309 (458)
Q Consensus 231 ~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~eg~GDVAFvk~~tv~~~~~~~~~~~~g 309 (458)
. | +| ++|-. |+..|..|..|+++...+.....
T Consensus 178 ~----------~------Vp---------------------y~g~gea~taLlgg~v~a~~~~~se~~~~---------- 210 (319)
T COG3181 178 T----------Y------VP---------------------YKGGGEALTALLGGHVDAGSTNLSELLSQ---------- 210 (319)
T ss_pred e----------E------Ee---------------------ecCccHHHHHHhcCceeeeecChhhhhhh----------
Confidence 0 0 11 11333 99999999999999988776654
Q ss_pred hhhhccCCCCCCCCCCCCcccccccCCCCcc-cc-ccCcccc-----ccccCCceEEEcCCCChhHHHHHHHHHHHHH
Q psy11925 310 IEYLCSKGGRAPVSKAGDYEIEYLCSKGGRA-PV-SKAADCN-----LGVVPPHMVVTSNSKSNVEIDTIRHAILSAA 380 (458)
Q Consensus 310 ~~~~~~~~~wa~~~~~~dy~~~LLCpdg~r~-~v-~~~~~C~-----l~~vP~~aVv~r~~~~~~~~~~i~~~l~~~~ 380 (458)
.++.+.+ +||-...-+ +. -+-.+|. .-..-+++|++.+..+.+.+.++..+|.++.
T Consensus 211 -------------vksG~lr--~Lav~s~eRl~~~pdvPT~~E~G~~~~~~~wrgvfap~g~~~e~~~~~~~a~kk~l 273 (319)
T COG3181 211 -------------VKSGTLR--LLAVFSEERLPGLPDVPTLKEQGYDVVMSIWRGVFAPAGTPDEIIAKLSAALKKAL 273 (319)
T ss_pred -------------hccCceE--EEEeechhhcCCCCCCCChHhcCCceeeeeeeEEEeCCCCCHHHHHHHHHHHHHHh
Confidence 2344566 666544322 11 0001110 1256789999999999998888888887764
No 28
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=82.66 E-value=9.2 Score=38.28 Aligned_cols=120 Identities=17% Similarity=0.134 Sum_probs=69.9
Q ss_pred ceEEEeCChhHHhHHHHHH-HHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEe---ccCCCceEEEEE
Q psy11925 98 PIRWCVSSPEGMSKCLAFK-DAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLG---RKNLNLRPILKE 173 (458)
Q Consensus 98 ~vrwCv~s~~E~~KC~~l~-~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A---~~~~~L~pil~E 173 (458)
+||+=++.-.+... -.+. ...... .+-.++-+.-++..+..+++.+|++|+.......++.+ ....+|+++..
T Consensus 32 ~I~IG~~~~~~~~~-~~~~~~~l~~~-~G~~Vel~~f~~~~~~~~ALa~GdID~~~~qh~~~l~~~~~~~g~~l~~~~~- 108 (271)
T PRK11063 32 HIKVGVIVGAEQQV-AEVAQKVAKEK-YGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLVAVGN- 108 (271)
T ss_pred cEEEEeCCCChHHH-HHHHHHHHHHh-cCCeEEEEEecCcHHHHHHHHcCCcceecccCHHHHHHHHHHcCCcEEEEeE-
Confidence 47777764333322 1111 111222 12368888878889999999999999987555444321 12344544411
Q ss_pred eecCCcceEEEEEEecCCCccChhhhc-CCceeeCCCCCCCchHHHHHHHHHcCCCC
Q psy11925 174 KYGNEKDLLAVAVVNKNSKVKSLEELK-GLKSCHTAYMRTTGWVAPVYNLLEKGLIK 229 (458)
Q Consensus 174 ~y~~~~~~~aVAVVkk~s~~~~l~dLk-GkksChtg~~~taGw~~Pv~~L~~~~~i~ 229 (458)
. +++-..--+..+++++||+ |||..-+.-..+.+=. +..|.+.|+|.
T Consensus 109 ~-------~vvp~~~ys~~i~si~DL~~Gk~IAip~d~~n~~r~--L~lL~~~Gli~ 156 (271)
T PRK11063 109 T-------FVYPIAGYSKKIKSLDELQDGSQVAVPNDPTNLGRS--LLLLQKVGLIK 156 (271)
T ss_pred E-------EEEEeeccccCCCCHHHhcCCCEEEecCCCccHHHH--HHHHHHCCCEE
Confidence 0 2222222234689999998 9999887644333333 33477889875
No 29
>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=81.96 E-value=34 Score=29.80 Aligned_cols=71 Identities=20% Similarity=0.185 Sum_probs=42.4
Q ss_pred eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcCC
Q psy11925 128 FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKGL 202 (458)
Q Consensus 128 v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkGk 202 (458)
++... .+..+.++.+.+|++|++....... ...+.-.|+..+ ..+.|+.++.+ ..+++||..-
T Consensus 31 i~i~~-~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~~~~l~~~--------~~~~v~~~~~~l~~~~~~~~~~L~~~ 98 (197)
T cd08414 31 LELRE-MTTAEQLEALRAGRLDVGFVRPPPD---PPGLASRPLLRE--------PLVVALPADHPLAARESVSLADLADE 98 (197)
T ss_pred EEEec-CChHHHHHHHHcCCccEEEEcCCCC---CCCeeEEEEeec--------cEEEEecCCCccccCCccCHHHhccC
Confidence 44433 3578999999999999998643321 122223344322 33455555442 2468899988
Q ss_pred ceeeCCCC
Q psy11925 203 KSCHTAYM 210 (458)
Q Consensus 203 ksChtg~~ 210 (458)
+......+
T Consensus 99 ~~i~~~~~ 106 (197)
T cd08414 99 PFVLFPRE 106 (197)
T ss_pred CEEEecCC
Confidence 88775443
No 30
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=81.73 E-value=4 Score=39.61 Aligned_cols=63 Identities=13% Similarity=0.215 Sum_probs=39.6
Q ss_pred CCHHHHHHHHHcCCccEEEeCCcceEEecc--CCCc-eEEEEEeecCCcceEEEEEEecCCCcc-ChhhhcCCceee
Q psy11925 134 KSSKVCLKLIADGAADVITLDATEAVLGRK--NLNL-RPILKEKYGNEKDLLAVAVVNKNSKVK-SLEELKGLKSCH 206 (458)
Q Consensus 134 ~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~--~~~L-~pil~E~y~~~~~~~aVAVVkk~s~~~-~l~dLkGkksCh 206 (458)
.+...++++++.|++|++..... +...| .+.. .|++.+ -.+.|+++++++. +++||+||+.+-
T Consensus 72 ~~~~~~~~~l~~g~~Di~~~~~~--~t~eR~~~~~fs~p~~~~--------~~~~~~~~~~~~~~~~~dl~g~~Igv 138 (260)
T PRK15010 72 SDFDALIPSLKAKKIDAIISSLS--ITDKRQQEIAFSDKLYAA--------DSRLIAAKGSPIQPTLDSLKGKHVGV 138 (260)
T ss_pred CCHHHHHHHHHCCCCCEEEecCc--CCHHHHhhcccccceEec--------cEEEEEECCCCCCCChhHcCCCEEEE
Confidence 46789999999999998763211 11212 1221 344321 2355667776654 799999999876
No 31
>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=80.28 E-value=3.7 Score=40.88 Aligned_cols=93 Identities=18% Similarity=0.202 Sum_probs=60.3
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEe---ccCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhc-CC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLG---RKNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELK-GL 202 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A---~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLk-Gk 202 (458)
.++-+.-.+..+.++++.+|++|+..+.-..+..+ ...+.|+++..- +.+-+..-++.+++++||| ||
T Consensus 47 ~Ve~~~f~d~~~~~~Al~~G~ID~~~~q~~~~l~~~~~~~g~~lv~v~~~--------~~~p~~~ys~~~~sl~dlk~G~ 118 (258)
T TIGR00363 47 DVELVEFNDYALPNEAVSKGDLDANAFQHKPYLDQDAKAKGYKLVAVGNT--------FVYPLAGYSKKIKNVNELQDGA 118 (258)
T ss_pred EEEEEEeCCcHHHHHHHHcCCCCeEecCCHHHHHHHHHhCCCcEEEEeee--------EEecccccCcCCCCHHHcCCCC
Confidence 57777878899999999999999987655544332 234556555311 2222233346789999997 99
Q ss_pred ceeeCCCCCCCchHHHHHHHHHcCCCC
Q psy11925 203 KSCHTAYMRTTGWVAPVYNLLEKGLIK 229 (458)
Q Consensus 203 ksChtg~~~taGw~~Pv~~L~~~~~i~ 229 (458)
|..-+.-....+-. +..|.+.|+|.
T Consensus 119 ~IAip~d~~n~~ra--L~~L~~aGLi~ 143 (258)
T TIGR00363 119 KVAVPNDPTNLGRA--LLLLQKQGLIK 143 (258)
T ss_pred EEEEeCCcchHHHH--HHHHHHcCCce
Confidence 99886332222222 23577779874
No 32
>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=78.10 E-value=10 Score=35.66 Aligned_cols=132 Identities=19% Similarity=0.106 Sum_probs=72.7
Q ss_pred CeEEEecCCHHHHHHHHHcCC-ccEEEeCCcceE-EeccCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhc----
Q psy11925 127 PFECNREKSSKVCLKLIADGA-ADVITLDATEAV-LGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELK---- 200 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~-AD~~~ld~~~~y-~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLk---- 200 (458)
.|+-+ ..+..+.+++|.+|. +|++.......+ .+....-+.|.-...+... ..|.+++++..+.+|+||+
T Consensus 22 ~V~~~-~~gs~~l~~~l~~~~~aDv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~---~~~l~~~~~~~~~s~~dL~~~~~ 97 (216)
T TIGR01256 22 KVVFS-FGSSGTLYTQIENGAPADLFISADNKWPKKLVDKGLVVAGSRFTYAGN---KLVLISPKNRVVDDLDILKKWVA 97 (216)
T ss_pred eEEEE-eCChHHHHHHHHcCCCCcEEEECCHHHHHHHHHCCCCCCCchheEEcc---EEEEEEECCCCcCcHHHHhhccc
Confidence 45533 445678999999874 999998655332 2212112333322112111 5566677776668899994
Q ss_pred CCceeeCCCCC-CCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hh
Q psy11925 201 GLKSCHTAYMR-TTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PL 278 (458)
Q Consensus 201 GkksChtg~~~-taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~ 278 (458)
+.|.-.+++.. ..|... +..|...|+... +.+.+ -++. +.. ++
T Consensus 98 ~~~i~~~~P~~~~~g~~~-~~~~~~~g~~~~----l~~n~-~~~~-----------------------------~~~~~~ 142 (216)
T TIGR01256 98 DKRVAIGDPKHAPYGAAA-KEVLQKLGLWET----LKKKL-VYGE-----------------------------DVRQAL 142 (216)
T ss_pred CCeEEecCCCcCcChHHH-HHHHHHCCChhh----hhhhe-eecC-----------------------------cHHHHH
Confidence 45777777653 345544 334433342210 00011 0110 122 67
Q ss_pred hhcccCCCcEEEEechhhh
Q psy11925 279 QCLKSGDGDVAFIKQVKVN 297 (458)
Q Consensus 279 rCL~eg~GDVAFvk~~tv~ 297 (458)
+.|.+|..|++|+..+.+.
T Consensus 143 ~~~~~Ge~~~~~~~~~~~~ 161 (216)
T TIGR01256 143 QFVETGNAPAGIVALSDVI 161 (216)
T ss_pred HHHHcCCCCEEeeehhhhc
Confidence 7888999999999776544
No 33
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=76.21 E-value=6.3 Score=39.71 Aligned_cols=69 Identities=14% Similarity=0.126 Sum_probs=41.8
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccC--CCc-eEEEEEeecCCcceEEEEEEecCCCccChhhhcCCc
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKN--LNL-RPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLK 203 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~--~~L-~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkk 203 (458)
+++=+.. +...-+.++..|++|++.-.- .+...|. +.. .|+... ..+.+|++++.+.+++||+||+
T Consensus 87 ~~~~v~~-~~~~~i~~L~~G~~Di~~~~~--~~t~eR~~~~~fS~Py~~~--------~~~lv~r~~~~i~sl~dL~Gk~ 155 (302)
T PRK10797 87 QVKLIPI-TSQNRIPLLQNGTFDFECGST--TNNLERQKQAAFSDTIFVV--------GTRLLTKKGGDIKDFADLKGKA 155 (302)
T ss_pred eEEEEEc-ChHhHHHHHHCCCccEEecCC--ccCcchhhcceecccEeec--------cEEEEEECCCCCCChHHcCCCE
Confidence 3444443 345688999999999975221 1122221 211 132211 3455678888899999999999
Q ss_pred eee
Q psy11925 204 SCH 206 (458)
Q Consensus 204 sCh 206 (458)
.+-
T Consensus 156 V~v 158 (302)
T PRK10797 156 VVV 158 (302)
T ss_pred EEE
Confidence 875
No 34
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=75.86 E-value=6.2 Score=38.28 Aligned_cols=69 Identities=16% Similarity=0.217 Sum_probs=41.0
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEecc--CCCc-eEEEEEeecCCcceEEEEEEecCCCcc-ChhhhcCC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRK--NLNL-RPILKEKYGNEKDLLAVAVVNKNSKVK-SLEELKGL 202 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~--~~~L-~pil~E~y~~~~~~~aVAVVkk~s~~~-~l~dLkGk 202 (458)
+++=+. .+...+++++++|++|++.-... +...| .+.. .|++. .-.+.++++++++. +++||+|+
T Consensus 66 ~i~~~~-~pw~~~~~~l~~g~~D~~~~~~~--~t~eR~~~~~fs~p~~~--------~~~~~~~~~~~~~~~~~~dl~g~ 134 (259)
T PRK15437 66 QCTFVE-NPLDALIPSLKAKKIDAIMSSLS--ITEKRQQEIAFTDKLYA--------ADSRLVVAKNSDIQPTVESLKGK 134 (259)
T ss_pred ceEEEe-CCHHHHHHHHHCCCCCEEEecCC--CCHHHhhhccccchhhc--------CceEEEEECCCCCCCChHHhCCC
Confidence 344333 45899999999999997753211 11111 1121 23221 13345567777664 79999999
Q ss_pred ceee
Q psy11925 203 KSCH 206 (458)
Q Consensus 203 ksCh 206 (458)
+.+-
T Consensus 135 ~Igv 138 (259)
T PRK15437 135 RVGV 138 (259)
T ss_pred EEEE
Confidence 9765
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=75.60 E-value=39 Score=28.76 Aligned_cols=71 Identities=17% Similarity=0.185 Sum_probs=43.1
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCc-----cChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKV-----KSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~-----~~l~dLkG 201 (458)
.++.... +..+.++.+.+|++|+++..... -......+++..+ ..+.|+.++.+. .+++||++
T Consensus 30 ~i~~~~~-~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~~~~l~~~--------~~~~~~~~~~~~~~~~~~~~~~l~~ 97 (197)
T cd05466 30 ELSLVEG-GSSELLEALLEGELDLAIVALPV---DDPGLESEPLFEE--------PLVLVVPPDHPLAKRKSVTLADLAD 97 (197)
T ss_pred EEEEEEC-ChHHHHHHHHcCCceEEEEcCCC---CCCcceEeeeecc--------ceEEEecCCCCcccCcEecHHHHcC
Confidence 4666554 45799999999999999865443 1112222333221 334455555432 36899999
Q ss_pred CceeeCCC
Q psy11925 202 LKSCHTAY 209 (458)
Q Consensus 202 kksChtg~ 209 (458)
.+......
T Consensus 98 ~~~i~~~~ 105 (197)
T cd05466 98 EPLILFER 105 (197)
T ss_pred CCEEEecC
Confidence 88776544
No 36
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=73.51 E-value=76 Score=31.37 Aligned_cols=56 Identities=14% Similarity=0.053 Sum_probs=35.4
Q ss_pred CCCceEEEeCChhHHhH-HHHHHHHHhcCCCCCC--eEEEecCCHHHHHHHHHcCCccEEEeC
Q psy11925 95 PIKPIRWCVSSPEGMSK-CLAFKDAAFSRDIRPP--FECNREKSSKVCLKLIADGAADVITLD 154 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~K-C~~l~~~~~~~~~~p~--v~Cv~~~s~~~Ci~~I~~g~AD~~~ld 154 (458)
+.+++|+.+.......- -..+.. +... .|. ++.... +..++++.+.+|++|++...
T Consensus 93 ~~g~l~ig~~~~~~~~~~~~~l~~-~~~~--~P~v~i~~~~~-~~~~~~~~l~~g~~Dl~i~~ 151 (305)
T CHL00180 93 QRGTLIIGASQTTGTYLMPRLIGL-FRQR--YPQINVQLQVH-STRRIAWNVANGQIDIAIVG 151 (305)
T ss_pred cCceEEEEEcCcchHhHHHHHHHH-HHHH--CCCceEEEEeC-CHHHHHHHHHcCCccEEEEc
Confidence 56789999987653322 222222 2221 254 455433 57999999999999999864
No 37
>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=70.65 E-value=55 Score=28.34 Aligned_cols=73 Identities=19% Similarity=0.150 Sum_probs=42.1
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkG 201 (458)
.++.... +..+.++.+.+|++|++...... .....+.-+++..+ ..+.|+.++.+ ..++++|.+
T Consensus 30 ~i~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~~~~~l~~~--------~~~~~~~~~~~l~~~~~~~~~~L~~ 98 (194)
T cd08436 30 DIRLRQA-GSDDLLAAVREGRLDLAFVGLPE--RRPPGLASRELARE--------PLVAVVAPDHPLAGRRRVALADLAD 98 (194)
T ss_pred EEEEecC-CHHHHHHHHHcCCccEEEEecCC--CCCCCcEEEEeecc--------eEEEEecCCCcccCCCccCHHHHhC
Confidence 3444433 57889999999999999864322 01111222333221 23444555432 247899999
Q ss_pred CceeeCCCC
Q psy11925 202 LKSCHTAYM 210 (458)
Q Consensus 202 kksChtg~~ 210 (458)
.+......+
T Consensus 99 ~~~i~~~~~ 107 (194)
T cd08436 99 EPFVDFPPG 107 (194)
T ss_pred CCeEEecCc
Confidence 988875443
No 38
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=70.31 E-value=1e+02 Score=30.36 Aligned_cols=101 Identities=11% Similarity=0.039 Sum_probs=53.8
Q ss_pred CCCceEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEe
Q psy11925 95 PIKPIRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEK 174 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~ 174 (458)
..+++|+++.......-=..+-..+....-...+.+... +..+.++.+.+|++|+++...... .. .+..+.
T Consensus 89 ~~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~-~~~~~~~~l~~g~~Dl~i~~~~~~-----~~---~l~~~~ 159 (305)
T PRK11151 89 MSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEA-QTHQLLAQLDSGKLDCAILALVKE-----SE---AFIEVP 159 (305)
T ss_pred CCceEEEEecchhHHHHHHHHHHHHHHHCCCcEEEEEeC-CHHHHHHHHHcCCccEEEEecCCC-----CC---CeEEEE
Confidence 346799999876432211111111111111224566554 468999999999999999653221 11 122232
Q ss_pred ecCCcceEEEEEEecCCC-----ccChhhhcCCceeeC
Q psy11925 175 YGNEKDLLAVAVVNKNSK-----VKSLEELKGLKSCHT 207 (458)
Q Consensus 175 y~~~~~~~aVAVVkk~s~-----~~~l~dLkGkksCht 207 (458)
...+ ..+.|+.++.+ ..+++||.+...=..
T Consensus 160 l~~~---~~~~~~~~~hpl~~~~~i~~~~L~~~~~i~~ 194 (305)
T PRK11151 160 LFDE---PMLLAVYEDHPWANRDRVPMSDLAGEKLLML 194 (305)
T ss_pred eccC---cEEEEecCCCCcccCCccCHHHhcCCCeEee
Confidence 2221 33444555443 247888888776554
No 39
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=70.28 E-value=7.3 Score=37.03 Aligned_cols=119 Identities=18% Similarity=0.246 Sum_probs=68.3
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEecc--CCCc-eEEEEEeecCCcceEEEEEEecCCCc-cChhhhcCC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRK--NLNL-RPILKEKYGNEKDLLAVAVVNKNSKV-KSLEELKGL 202 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~--~~~L-~pil~E~y~~~~~~~aVAVVkk~s~~-~~l~dLkGk 202 (458)
+++=+. .+..+++..+.+|++|++... . .+...+ .+.. .|+.. ...+.+++++++. .+++||+|+
T Consensus 64 ~~~~~~-~~~~~~~~~l~~G~~D~~~~~-~-~~~~~r~~~~~~s~p~~~--------~~~~~~~~~~~~~~~~~~dl~g~ 132 (250)
T TIGR01096 64 KCKFVE-QNFDGLIPSLKAKKVDAIMAT-M-SITPKRQKQIDFSDPYYA--------TGQGFVVKKGSDLAKTLEDLDGK 132 (250)
T ss_pred eEEEEe-CCHHHHHHHHhCCCcCEEEec-C-ccCHHHhhccccccchhc--------CCeEEEEECCCCcCCChHHcCCC
Confidence 455444 568999999999999998631 1 111111 1111 12211 1345566776543 579999999
Q ss_pred ceeeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhc
Q psy11925 203 KSCHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCL 281 (458)
Q Consensus 203 ksChtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL 281 (458)
+.|.. .|+...- .|.+. .+. +- .+.. |. +.+ +++-|
T Consensus 133 ~i~~~-----~g~~~~~-~l~~~--~~~-~~----~~~~-~~-----------------------------s~~~~~~~L 169 (250)
T TIGR01096 133 TVGVQ-----SGTTHEQ-YLKDY--FKP-GV----DIVE-YD-----------------------------SYDNANMDL 169 (250)
T ss_pred EEEEe-----cCchHHH-HHHHh--ccC-Cc----EEEE-cC-----------------------------CHHHHHHHH
Confidence 99873 3454432 22221 110 00 0111 11 244 99999
Q ss_pred ccCCCcEEEEechhhhhh
Q psy11925 282 KSGDGDVAFIKQVKVNKA 299 (458)
Q Consensus 282 ~eg~GDVAFvk~~tv~~~ 299 (458)
.+|..|++++....+...
T Consensus 170 ~~g~vD~~v~~~~~~~~~ 187 (250)
T TIGR01096 170 KAGRIDAVFTDASVLAEG 187 (250)
T ss_pred HcCCCCEEEeCHHHHHHH
Confidence 999999999987766543
No 40
>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=70.26 E-value=21 Score=34.95 Aligned_cols=115 Identities=16% Similarity=0.216 Sum_probs=66.6
Q ss_pred EecCCHHHHHHHHHcCCccEEEeCCcceEEecc--CCCc-eEEEEEeecCCcceEEEEEEecCCC--ccChhhhc---CC
Q psy11925 131 NREKSSKVCLKLIADGAADVITLDATEAVLGRK--NLNL-RPILKEKYGNEKDLLAVAVVNKNSK--VKSLEELK---GL 202 (458)
Q Consensus 131 v~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~--~~~L-~pil~E~y~~~~~~~aVAVVkk~s~--~~~l~dLk---Gk 202 (458)
+...+...++..+++|++|++..+.. +...+ .+.. .|++.+ ..+.++++++. +.+++||+ |+
T Consensus 76 ~~~~~w~~~~~~l~~G~~Di~~~~~~--~t~eR~~~~~fs~py~~~--------~~~~~~~~~~~~~i~~~~dl~~~~g~ 145 (275)
T TIGR02995 76 ASITEYGALIPGLQAGRFDAIAAGLF--IKPERCKQVAFTQPILCD--------AEALLVKKGNPKGLKSYKDIAKNPDA 145 (275)
T ss_pred eccCCHHHHHHHHHCCCcCEEeeccc--CCHHHHhccccccceeec--------ceeEEEECCCCCCCCCHHHhccCCCc
Confidence 45567889999999999999764321 11111 1111 233221 23466777653 56888886 67
Q ss_pred ceeeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhc
Q psy11925 203 KSCHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCL 281 (458)
Q Consensus 203 ksChtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL 281 (458)
+.+- ..||.. ...|.+.++.. . .+. .+. +++ +++.|
T Consensus 146 ~Igv-----~~g~~~-~~~l~~~~~~~-~------~i~-~~~-----------------------------~~~~~i~~L 182 (275)
T TIGR02995 146 KIAA-----PGGGTE-EKLAREAGVKR-E------QII-VVP-----------------------------DGQSGLKMV 182 (275)
T ss_pred eEEE-----eCCcHH-HHHHHHcCCCh-h------hEE-EeC-----------------------------CHHHHHHHH
Confidence 7764 445542 33444433210 0 000 111 245 99999
Q ss_pred ccCCCcEEEEechhhhh
Q psy11925 282 KSGDGDVAFIKQVKVNK 298 (458)
Q Consensus 282 ~eg~GDVAFvk~~tv~~ 298 (458)
.+|..|++++....+..
T Consensus 183 ~~grvDa~i~d~~~~~~ 199 (275)
T TIGR02995 183 QDGRADAYSLTVLTIND 199 (275)
T ss_pred HcCCCCEEecChHHHHH
Confidence 99999999887765544
No 41
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=69.14 E-value=15 Score=43.82 Aligned_cols=124 Identities=10% Similarity=0.141 Sum_probs=73.7
Q ss_pred CCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcce-EEEEEEecCCCccChhhhcCC
Q psy11925 124 IRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDL-LAVAVVNKNSKVKSLEELKGL 202 (458)
Q Consensus 124 ~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~-~aVAVVkk~s~~~~l~dLkGk 202 (458)
++-+++=+...+..++++++++|++|++.-.. .....+...+ ....-| -. ..++||++++.+.++.+|+||
T Consensus 94 lG~~~e~v~~~~~~~~l~~l~~g~iDl~~~~~--~~~~~r~~~~--~fs~py----~~~~~~~v~~~~~~~~~~~~l~~~ 165 (1197)
T PRK09959 94 LNIKLTLREYADHQKAMDALEEGEVDIVLSHL--VASPPLNDDI--AATKPL----IITFPALVTTLHDSMRPLTSSKPV 165 (1197)
T ss_pred cCCceEEEeCCCHHHHHHHHHcCCCcEecCcc--ccccccccch--hcCCCc----cCCCceEEEeCCCCCCCcccccCe
Confidence 34578888888999999999999999974110 0111111000 000001 01 677888888888899999999
Q ss_pred ceeeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhc
Q psy11925 203 KSCHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCL 281 (458)
Q Consensus 203 ksChtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL 281 (458)
+..... ||.. ...+.+. .|. . .+ .+|. ... |++.|
T Consensus 166 ~i~~~~-----g~~~-~~~~~~~--~p~-----~-~i-~~~~-----------------------------s~~~al~av 201 (1197)
T PRK09959 166 NIARVA-----NYPP-DEVIHQS--FPK-----A-TI-ISFT-----------------------------NLYQALASV 201 (1197)
T ss_pred EEEEeC-----CCCC-HHHHHHh--CCC-----C-EE-EeCC-----------------------------CHHHHHHHH
Confidence 976643 4432 1222221 110 0 00 1121 245 99999
Q ss_pred ccCCCcEEEEechhhhhh
Q psy11925 282 KSGDGDVAFIKQVKVNKA 299 (458)
Q Consensus 282 ~eg~GDVAFvk~~tv~~~ 299 (458)
.+|..|+++....++...
T Consensus 202 ~~G~~Da~i~~~~~~~~~ 219 (1197)
T PRK09959 202 SAGQNDYFIGSNIITSSM 219 (1197)
T ss_pred HcCCCCEEEccHHHHHHH
Confidence 999999988876655543
No 42
>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=68.20 E-value=45 Score=29.54 Aligned_cols=113 Identities=16% Similarity=0.078 Sum_probs=65.4
Q ss_pred CCceEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEe-cCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEe
Q psy11925 96 IKPIRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNR-EKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEK 174 (458)
Q Consensus 96 ~~~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~-~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~ 174 (458)
.+++|+.+.......-=..+-..+.. ..|.+.... ..+..+.++++.+|++|+++..... ....+.-+|+..|
T Consensus 5 ~~~l~Ig~~~~~~~~~l~~~l~~~~~--~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~~~~l~~~- 78 (209)
T PF03466_consen 5 RGTLRIGASPSFASSLLPPLLAEFRE--RHPNIRIEIREGDSDELIEALRSGELDLAITFGPP---PPPGLESEPLGEE- 78 (209)
T ss_dssp EEEEEEEEEHHHHHHTHHHHHHHHHH--HSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSS---SSTTEEEEEEEEE-
T ss_pred ceEEEEEEEhHHHHHHHHHHHHHHHH--HCCCcEEEEEeccchhhhHHHhcccccEEEEEeec---cccccccccccce-
Confidence 34688887755432211111111111 236665544 3456899999999999999876655 1122334555543
Q ss_pred ecCCcceEEEEEEecCCC-----ccChhhhcCCceeeCCCCCCCchHHHHHHHH
Q psy11925 175 YGNEKDLLAVAVVNKNSK-----VKSLEELKGLKSCHTAYMRTTGWVAPVYNLL 223 (458)
Q Consensus 175 y~~~~~~~aVAVVkk~s~-----~~~l~dLkGkksChtg~~~taGw~~Pv~~L~ 223 (458)
.-+.|+.++.+ ..+++||++-...+...+. +|.-.+....
T Consensus 79 -------~~~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~--~~~~~~~~~~ 123 (209)
T PF03466_consen 79 -------PLVLVVSPDHPLAQKKPITLEDLADYPLILLSPGS--PYRDQLDRWL 123 (209)
T ss_dssp -------EEEEEEETTSGGGTTSSSSGGGGTTSEEEEESTTT--SHHHHHHHHH
T ss_pred -------eeeeeeeccccccccccchhhhhhhcccccccccc--cccccccccc
Confidence 34666677653 2478999999988865543 3444444433
No 43
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=66.56 E-value=66 Score=30.42 Aligned_cols=134 Identities=19% Similarity=0.207 Sum_probs=72.6
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCce----------EEEEEeecCCcceEEEEEEecCC-CccC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLR----------PILKEKYGNEKDLLAVAVVNKNS-KVKS 195 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~----------pil~E~y~~~~~~~aVAVVkk~s-~~~~ 195 (458)
.+..... +..+=+.++.+|++|++.+.-.+- ....|++. -++...+.. ...++|-+.+. .+.+
T Consensus 12 ~v~~~~~-gS~~gl~~L~~g~~~iAg~h~~~~--~~~~~n~~~~~~~l~g~~~v~v~~~~r---~~Gl~v~~~np~~i~~ 85 (193)
T PF12727_consen 12 RVAVQYT-GSRAGLSALARGEADIAGIHLPDP--ESGEYNIPFVRRLLPGIEVVLVRLARR---EQGLIVRPGNPKGITS 85 (193)
T ss_pred eEEEEec-CCHHHHHHHHCCCceEEEecCCCC--cccccchHHHHHhcCCCcEEEEeeeEE---eeeEEEeCCCCccCCC
Confidence 4554444 446678899999999998743221 01112221 122222110 04444444332 4789
Q ss_pred hhhhcCCceeeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCCh
Q psy11925 196 LEELKGLKSCHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTY 275 (458)
Q Consensus 196 l~dLkGkksChtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy 275 (458)
|+||..++.-+-+-...+|=.+-+-.++...-|++. . ++|.... .+ .|
T Consensus 86 ~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~------~----------i~gy~~~-----~~-----------th 133 (193)
T PF12727_consen 86 LEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPE------D----------IPGYAQE-----AN-----------TH 133 (193)
T ss_pred HHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChh------h----------CCCcccc-----cc-----------Ch
Confidence 999955555554455567766666666654223211 1 2332111 00 35
Q ss_pred h-hhhhcccCCCcEEEEechhhhh
Q psy11925 276 T-PLQCLKSGDGDVAFIKQVKVNK 298 (458)
Q Consensus 276 ~-A~rCL~eg~GDVAFvk~~tv~~ 298 (458)
. +-..+.+|.+||+|.-...-.+
T Consensus 134 ~~vA~aVa~G~AD~G~g~~~~A~~ 157 (193)
T PF12727_consen 134 LAVAAAVASGKADAGIGIRAAAEE 157 (193)
T ss_pred HHHHHHHHcCCCCEEeehHHHHHh
Confidence 5 7788999999999976554443
No 44
>PRK11260 cystine transporter subunit; Provisional
Probab=66.41 E-value=13 Score=36.28 Aligned_cols=69 Identities=19% Similarity=0.197 Sum_probs=41.4
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEecc--CCCc-eEEEEEeecCCcceEEEEEEecCC--CccChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRK--NLNL-RPILKEKYGNEKDLLAVAVVNKNS--KVKSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~--~~~L-~pil~E~y~~~~~~~aVAVVkk~s--~~~~l~dLkG 201 (458)
+++=+.. +..++++++++|++|++..... +...+ .+.. .|++.. .-+.+++++. .+.+++||+|
T Consensus 81 ~~e~~~~-~~~~~~~~l~~G~~D~~~~~~~--~~~~r~~~~~fs~p~~~~--------~~~~~~~~~~~~~~~~~~dL~g 149 (266)
T PRK11260 81 KASLKPT-KWDGMLASLDSKRIDVVINQVT--ISDERKKKYDFSTPYTVS--------GIQALVKKGNEGTIKTAADLKG 149 (266)
T ss_pred eEEEEeC-CHHHHHHHHhcCCCCEEEeccc--cCHHHHhccccCCceeec--------ceEEEEEcCCcCCCCCHHHcCC
Confidence 3444443 5789999999999999863211 11111 1111 233211 2245667653 4678999999
Q ss_pred Cceee
Q psy11925 202 LKSCH 206 (458)
Q Consensus 202 kksCh 206 (458)
++.+-
T Consensus 150 ~~Igv 154 (266)
T PRK11260 150 KKVGV 154 (266)
T ss_pred CEEEE
Confidence 99874
No 45
>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=66.30 E-value=87 Score=28.26 Aligned_cols=100 Identities=10% Similarity=-0.023 Sum_probs=54.4
Q ss_pred eEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCC
Q psy11925 99 IRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNE 178 (458)
Q Consensus 99 vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~ 178 (458)
+|+++.......--..+-..+....-...++.... +..++++.+.+|++|+++...... ......+|+..|
T Consensus 2 ~~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~i~~~-~~~~~~~~l~~g~~Di~i~~~~~~---~~~l~~~~l~~~----- 72 (221)
T cd08469 2 FVIAANDYVTAVLLPALVRRLETEAPGIDLRIRPV-TRLDLAEQLDLGRIDLVIGIFEQI---PPRFRRRTLFDE----- 72 (221)
T ss_pred EEEEEChHHHHHHHHHHHHHHHHHCCCcEEEEeeC-ChhhHHHHHHCCCccEEEecCCCC---Cccceeeeeecc-----
Confidence 56666655433222222222222211234666554 577999999999999999743221 122233344322
Q ss_pred cceEEEEEEecCCC----ccChhhhcCCceeeCCCC
Q psy11925 179 KDLLAVAVVNKNSK----VKSLEELKGLKSCHTAYM 210 (458)
Q Consensus 179 ~~~~aVAVVkk~s~----~~~l~dLkGkksChtg~~ 210 (458)
..++|+.++.+ ..+++||.+.+.-....+
T Consensus 73 ---~~~~v~~~~~pl~~~~~~~~dL~~~~~i~~~~~ 105 (221)
T cd08469 73 ---DEVWVMRKDHPAARGALTIETLARYPHIVVSLG 105 (221)
T ss_pred ---ceEEEEeCCCcCCCCCCCHHHHHhCCeEEEecC
Confidence 34555665543 246889988877654443
No 46
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=65.55 E-value=16 Score=36.67 Aligned_cols=94 Identities=14% Similarity=0.102 Sum_probs=58.3
Q ss_pred CCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEec---cCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhc-C
Q psy11925 126 PPFECNREKSSKVCLKLIADGAADVITLDATEAVLGR---KNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELK-G 201 (458)
Q Consensus 126 p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~---~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLk-G 201 (458)
-.++-+..++.....+++.+|+.|+..+.-..++.+. ..++|+++.. . +++-..-=++++++++||+ |
T Consensus 60 ~~Velv~fsd~~~~n~AL~~G~ID~n~~qh~~yl~~~~~~~g~~lv~~~~-~-------~~~P~~~Ys~~iksl~DL~~G 131 (272)
T PRK09861 60 LDVELVGFSGSLLPNDATNHGELDANVFQHRPFLEQDNQAHGYKLVAVGN-T-------FVFPMAGYSKKIKTVAQIKEG 131 (272)
T ss_pred CeEEEEecCchhhHHHHHHcCCcceehhhhHHHHHHHHHhcCCCeEEEeE-E-------EEEeeeccccCCCCHHHcCCC
Confidence 3566668888999999999999999886554444332 2334444311 0 1111111156789999999 9
Q ss_pred CceeeCCCCCCCchHHHHHHHHHcCCCC
Q psy11925 202 LKSCHTAYMRTTGWVAPVYNLLEKGLIK 229 (458)
Q Consensus 202 kksChtg~~~taGw~~Pv~~L~~~~~i~ 229 (458)
+|..-+.- .+.+---+..|...|+|.
T Consensus 132 a~IAipnd--~~n~~ral~lL~~agli~ 157 (272)
T PRK09861 132 ATVAIPND--PTNLGRALLLLQKEKLIT 157 (272)
T ss_pred CEEEEeCC--CccHHHHHHHHHHCCCEE
Confidence 99998632 223333344566778775
No 47
>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=65.34 E-value=91 Score=26.98 Aligned_cols=70 Identities=17% Similarity=0.155 Sum_probs=40.3
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkG 201 (458)
.++.+.. +..+.++.+.+|++|+++...... ...+.-+++..|. + +.|+.++.+ ..+++||++
T Consensus 30 ~i~i~~~-~~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~l~~~~-------~-~~~~~~~hpl~~~~~~~~~~L~~ 97 (197)
T cd08448 30 EVALHEM-SSAEQIEALLRGELDLGFVHSRRL---PAGLSARLLHREP-------F-VCCLPAGHPLAARRRIDLRELAG 97 (197)
T ss_pred eEEEEeC-CHHHHHHHHHcCCcceEEEeCCCC---CcCceEEEEecCc-------E-EEEeeCCCCCcCCCCcCHHHhCC
Confidence 3444433 568899999999999988643211 1122223332221 2 334555542 246889998
Q ss_pred CceeeCC
Q psy11925 202 LKSCHTA 208 (458)
Q Consensus 202 kksChtg 208 (458)
.+.....
T Consensus 98 ~~~i~~~ 104 (197)
T cd08448 98 EPFVLFS 104 (197)
T ss_pred CcEEeeC
Confidence 8876543
No 48
>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=65.14 E-value=94 Score=27.03 Aligned_cols=71 Identities=8% Similarity=0.051 Sum_probs=42.4
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkG 201 (458)
.++... .+..+.++.+.+|++|++....... ......+|+..+ ..+.|+.++.+ ..++++|++
T Consensus 30 ~l~i~~-~~~~~~~~~l~~~~~D~~i~~~~~~---~~~~~~~~l~~~--------~~~~~~~~~~~l~~~~~~~~~~l~~ 97 (198)
T cd08412 30 EVRVVE-GNQEELEEGLRSGELDLALTYDLDL---PEDIAFEPLARL--------PPYVWLPADHPLAGKDEVSLADLAA 97 (198)
T ss_pred EEEEEE-CCHHHHHHHHHcCCCcEEEEcCCCC---Ccccceeeeecc--------ceEEEecCCCCCCCCCcCCHHHHcC
Confidence 355543 3578999999999999998643321 122233444322 22334444432 246899999
Q ss_pred CceeeCCC
Q psy11925 202 LKSCHTAY 209 (458)
Q Consensus 202 kksChtg~ 209 (458)
.+....+.
T Consensus 98 ~~~i~~~~ 105 (198)
T cd08412 98 EPLILLDL 105 (198)
T ss_pred CcEEecCc
Confidence 98877543
No 49
>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=64.64 E-value=7 Score=35.73 Aligned_cols=118 Identities=20% Similarity=0.266 Sum_probs=66.6
Q ss_pred eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccC--CCc-eEEEEEeecCCcceEEEEEEecCC-----CccChhhh
Q psy11925 128 FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKN--LNL-RPILKEKYGNEKDLLAVAVVNKNS-----KVKSLEEL 199 (458)
Q Consensus 128 v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~--~~L-~pil~E~y~~~~~~~aVAVVkk~s-----~~~~l~dL 199 (458)
++=+.. +...+++.+.+|++|++... -.+...+. +.. .|++.. ..+.|+++++ .+.+++||
T Consensus 40 ~~~~~~-~~~~~~~~l~~g~~D~~~~~--~~~~~~r~~~~~~s~p~~~~--------~~~~~~~~~~~~~~~~~~~~~dl 108 (225)
T PF00497_consen 40 IEFVPM-PWSRLLEMLENGKADIIIGG--LSITPERAKKFDFSDPYYSS--------PYVLVVRKGDAPPIKTIKSLDDL 108 (225)
T ss_dssp EEEEEE-EGGGHHHHHHTTSSSEEESS--EB-BHHHHTTEEEESESEEE--------EEEEEEETTSTCSTSSHSSGGGG
T ss_pred cceeec-cccccccccccccccccccc--ccccccccccccccccccch--------hheeeeccccccccccccchhhh
Confidence 444444 78999999999999998721 11122121 111 122111 5566777553 34566799
Q ss_pred cCCceeeCCCCCCCchHHHHHHHHHcCCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hh
Q psy11925 200 KGLKSCHTAYMRTTGWVAPVYNLLEKGLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PL 278 (458)
Q Consensus 200 kGkksChtg~~~taGw~~Pv~~L~~~~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~ 278 (458)
+|+|.|...-. . +.-.+......+ + .+.. +. ..+ ++
T Consensus 109 ~~~~i~~~~g~--~-~~~~l~~~~~~~-~---------~~~~-~~-----------------------------~~~~~~ 145 (225)
T PF00497_consen 109 KGKRIGVVRGS--S-YADYLKQQYPSN-I---------NIVE-VD-----------------------------SPEEAL 145 (225)
T ss_dssp TTSEEEEETTS--H-HHHHHHHHTHHT-S---------EEEE-ES-----------------------------SHHHHH
T ss_pred cCcccccccch--h-HHHHhhhhccch-h---------hhcc-cc-----------------------------cHHHHH
Confidence 99999874332 1 111121111111 0 1111 11 244 99
Q ss_pred hhcccCCCcEEEEechhhhhh
Q psy11925 279 QCLKSGDGDVAFIKQVKVNKA 299 (458)
Q Consensus 279 rCL~eg~GDVAFvk~~tv~~~ 299 (458)
+-|..|..|++++...++...
T Consensus 146 ~~l~~g~~d~~i~~~~~~~~~ 166 (225)
T PF00497_consen 146 EALLSGRIDAFIVDESTAEYL 166 (225)
T ss_dssp HHHHTTSSSEEEEEHHHHHHH
T ss_pred HHHhcCCeeeeeccchhhhhh
Confidence 999999999999988887765
No 50
>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=62.49 E-value=1.1e+02 Score=27.06 Aligned_cols=72 Identities=11% Similarity=0.146 Sum_probs=41.5
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCc----cChhhhcCC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKV----KSLEELKGL 202 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~----~~l~dLkGk 202 (458)
.++.... +..+.++.+.+|++|+++...... . ....-.++..+. + ++|+.++.+. .+++||.+.
T Consensus 30 ~l~~~~~-~~~~~~~~l~~g~~D~~i~~~~~~-~--~~~~~~~l~~~~-------~-~~v~~~~h~l~~~~~~~~dL~~~ 97 (200)
T cd08467 30 DLRLCPI-GDDLAERGLEQGTIDLAVGRFAVP-P--DGLVVRRLYDDG-------F-ACLVRHGHPALAQEWTLDDFATL 97 (200)
T ss_pred EEEEecC-CcccHHHHhhCCCcCEEEecCCCC-C--ccceeEEeeecc-------E-EEEEcCCCccccCCCCHHHHhCC
Confidence 4555544 456899999999999998532110 0 111222332221 3 3444544332 478999999
Q ss_pred ceeeCCCC
Q psy11925 203 KSCHTAYM 210 (458)
Q Consensus 203 ksChtg~~ 210 (458)
+......+
T Consensus 98 ~~i~~~~~ 105 (200)
T cd08467 98 RHVAIAPP 105 (200)
T ss_pred CCEEEcCC
Confidence 88876544
No 51
>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=60.68 E-value=8.1 Score=37.81 Aligned_cols=71 Identities=23% Similarity=0.261 Sum_probs=43.1
Q ss_pred CHHHHHHHHHcCCccEEEeCCcceEEeccCCCc--eEEEEEeecC------C-----------cc-------e--EEEEE
Q psy11925 135 SSKVCLKLIADGAADVITLDATEAVLGRKNLNL--RPILKEKYGN------E-----------KD-------L--LAVAV 186 (458)
Q Consensus 135 s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L--~pil~E~y~~------~-----------~~-------~--~aVAV 186 (458)
+..+.+++|+.|.+|+....++.+-..-..+++ -|.+...+.. . .. . -...+
T Consensus 42 ~~~e~~~~v~~G~~d~~~~~~~~~~~~~p~~~~~~lP~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~~~g~~~~ 121 (257)
T TIGR00787 42 SDRAMLEALQGGALDMTAPSSSKFGPLVPELAVFDLPFLFRDYNHVHKVLDGEVGKALKKSLEKKGLKGLAYWDNGFRQF 121 (257)
T ss_pred ChHHHHHHHhCCCccEEecccccccccCcchhhccCCeecCCHHHHHHHHcCHHHHHHHHHHHHcCcEEEeecCCceeEe
Confidence 578999999999999999776544221122222 2555422210 0 00 0 11234
Q ss_pred EecCCCccChhhhcCCcee
Q psy11925 187 VNKNSKVKSLEELKGLKSC 205 (458)
Q Consensus 187 Vkk~s~~~~l~dLkGkksC 205 (458)
+.++.++.+++||+|+|.=
T Consensus 122 ~~~~~~i~s~~Dl~G~kir 140 (257)
T TIGR00787 122 TSSKKPITKPEDLKGLKIR 140 (257)
T ss_pred eeCCCccCChHHhCCCEEe
Confidence 5556789999999999983
No 52
>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=60.13 E-value=1.2e+02 Score=26.40 Aligned_cols=73 Identities=10% Similarity=0.069 Sum_probs=43.3
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkG 201 (458)
.++.+. .+..+.++.+.+|++|++........ ....+.-+|+..+ --++|+.++.+ ..+++||.+
T Consensus 30 ~i~~~~-~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~~~~l~~~--------~~~~v~~~~~~~~~~~~~~~~~L~~ 99 (197)
T cd08449 30 TVRFHE-LSPEAQKAALLSKRIDLGFVRFADTL-NDPPLASELLWRE--------PMVVALPEEHPLAGRKSLTLADLRD 99 (197)
T ss_pred EEEEEE-CCHHHHHHHHhCCCccEEEecccccC-CCCCceEEEEEEe--------eEEEEecCCCCCCCCCCCCHHHHCC
Confidence 345543 36788999999999999985322110 0112223344332 23445555432 247899999
Q ss_pred CceeeCCC
Q psy11925 202 LKSCHTAY 209 (458)
Q Consensus 202 kksChtg~ 209 (458)
.+..+...
T Consensus 100 ~~~i~~~~ 107 (197)
T cd08449 100 EPFVFLRL 107 (197)
T ss_pred CCEEEecC
Confidence 99988654
No 53
>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=56.78 E-value=29 Score=33.47 Aligned_cols=23 Identities=17% Similarity=0.218 Sum_probs=19.4
Q ss_pred hhhhcccCCCcEEEEechhhhhh
Q psy11925 277 PLQCLKSGDGDVAFIKQVKVNKA 299 (458)
Q Consensus 277 A~rCL~eg~GDVAFvk~~tv~~~ 299 (458)
+++.|..|..|+++....++..+
T Consensus 155 ~~~aL~~GrvDa~i~~~~~~~~~ 177 (246)
T TIGR03870 155 LVSEVATGKADLAVAFAPEVARY 177 (246)
T ss_pred HHHHHHcCCCCEEEeeHHhHHHH
Confidence 89999999999999987665543
No 54
>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=52.08 E-value=1.6e+02 Score=25.67 Aligned_cols=75 Identities=16% Similarity=0.145 Sum_probs=41.8
Q ss_pred CCeEEEe-cCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhh
Q psy11925 126 PPFECNR-EKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEEL 199 (458)
Q Consensus 126 p~v~Cv~-~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dL 199 (458)
|.++-.. ..+..+.++.+.+|++|++......-... ....-+++..| ..++|+.++.+ ..+++||
T Consensus 27 P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~-~~l~~~~l~~~--------~~~~~~~~~hpl~~~~~i~~~dL 97 (198)
T cd08437 27 LMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLEN-SALHSKIIKTQ--------HFMIIVSKDHPLAKAKKVNFADL 97 (198)
T ss_pred CceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCCc-ccceEEEeecc--------eEEEEecCCCcccccCcccHHHH
Confidence 5444333 24688999999999999998643111111 11122222211 33344444432 2478999
Q ss_pred cCCceeeCCC
Q psy11925 200 KGLKSCHTAY 209 (458)
Q Consensus 200 kGkksChtg~ 209 (458)
.+.+.-....
T Consensus 98 ~~~~~i~~~~ 107 (198)
T cd08437 98 KKENFILLNE 107 (198)
T ss_pred cCCCeEEecc
Confidence 9988876543
No 55
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=51.29 E-value=31 Score=32.63 Aligned_cols=66 Identities=14% Similarity=0.178 Sum_probs=37.2
Q ss_pred CCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCceeeC
Q psy11925 134 KSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKSCHT 207 (458)
Q Consensus 134 ~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkksCht 207 (458)
.+..+++++++.|++|++... -.+...+.-.+ ....-|-.. ..+.|++++ .+.+++||+|++.+..
T Consensus 67 ~~~~~~~~~l~~g~~D~~~~~--~~~~~~r~~~~--~fs~p~~~~---~~~~v~~~~-~~~~~~dL~g~~Igv~ 132 (243)
T PRK15007 67 QAFDSLIPSLKFRRVEAVMAG--MDITPEREKQV--LFTTPYYDN---SALFVGQQG-KYTSVDQLKGKKVGVQ 132 (243)
T ss_pred CCHHHHhHHHhCCCcCEEEEc--CccCHHHhccc--ceecCcccc---ceEEEEeCC-CCCCHHHhCCCeEEEe
Confidence 457889999999999987432 11111111111 001111000 234444544 5788999999998774
No 56
>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=49.79 E-value=1.7e+02 Score=25.19 Aligned_cols=70 Identities=16% Similarity=0.131 Sum_probs=39.9
Q ss_pred eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcCC
Q psy11925 128 FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKGL 202 (458)
Q Consensus 128 v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkGk 202 (458)
+.... .+..++++++.+|++|+++.....- ...+.-.|+..| ..+.|+.++.+ ..+++||++.
T Consensus 31 l~~~~-~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~~~~l~~~--------~~~~v~~~~~~~~~~~~i~~~~l~~~ 98 (201)
T cd08420 31 VSLTI-GNTEEIAERVLDGEIDLGLVEGPVD---HPDLIVEPFAED--------ELVLVVPPDHPLAGRKEVTAEELAAE 98 (201)
T ss_pred EEEEe-CCcHHHHHHHHCCCccEEEecCCCC---CcceEEEeecCc--------cEEEEecCCCCccccCccCHHHHhcC
Confidence 44443 4678999999999999988643211 111112222111 33445555543 2357889888
Q ss_pred ceeeCCC
Q psy11925 203 KSCHTAY 209 (458)
Q Consensus 203 ksChtg~ 209 (458)
+......
T Consensus 99 ~~i~~~~ 105 (201)
T cd08420 99 PWILREP 105 (201)
T ss_pred CEEEecC
Confidence 7765433
No 57
>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=49.24 E-value=8 Score=38.14 Aligned_cols=79 Identities=22% Similarity=0.235 Sum_probs=56.3
Q ss_pred CCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceE--EEEEeecCCcce-EEEEEEecCCCccChhhhcC
Q psy11925 125 RPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRP--ILKEKYGNEKDL-LAVAVVNKNSKVKSLEELKG 201 (458)
Q Consensus 125 ~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~p--il~E~y~~~~~~-~aVAVVkk~s~~~~l~dLkG 201 (458)
.+.++-+.+ +...|-+++.+|++|+..++...+.....+|.+.| -++- . .. ++|.++.+. .+++|+|
T Consensus 23 ~~~~~~~~~-~P~~Ln~~l~~g~~Dv~~iSs~~y~~~~~~y~ilp~~~i~s-~----g~v~Sv~l~s~~----p~~~l~~ 92 (251)
T PF02621_consen 23 PFDFEIVRG-VPSELNQMLLEGELDVALISSIEYARNADDYLILPDLSISS-D----GPVYSVLLFSKV----PIEELDG 92 (251)
T ss_dssp SCCEEEEEE--HHHHHHHHHTTS-SEEEEEHHHHCTCTTTEEEESCECEEE-C----CSSSSEEEEESS-----CCC-TT
T ss_pred CCceEEEEC-CHHHHHHHHHcCCCCEEEcCHHHHHHhhhhheecCCcEEEE-c----CCccceEEEECC----ChHHcCC
Confidence 345665554 68999999999999999999988877556677766 2221 1 12 788888854 3778999
Q ss_pred CceeeCCCCCCC
Q psy11925 202 LKSCHTAYMRTT 213 (458)
Q Consensus 202 kksChtg~~~ta 213 (458)
++..-|+-.+|+
T Consensus 93 ~~ial~~~S~TS 104 (251)
T PF02621_consen 93 KKIALTGESTTS 104 (251)
T ss_dssp SEEEESTTTSHH
T ss_pred CeEEcCCCCHHH
Confidence 999999988775
No 58
>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=45.71 E-value=2.2e+02 Score=25.41 Aligned_cols=70 Identities=14% Similarity=0.221 Sum_probs=41.4
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCc-----cChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKV-----KSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~-----~~l~dLkG 201 (458)
.++.....+..+.++.+.+|++|+++...... ......+|+..| ..+.|+.++.+. .++++|.+
T Consensus 30 ~v~~~~~~~~~~l~~~L~~g~lDl~i~~~~~~---~~~l~~~~l~~~--------~~~lv~~~~h~l~~~~~i~~~~l~~ 98 (203)
T cd08463 30 RLEIHPLGPDFDYERALASGELDLVIGNWPEP---PEHLHLSPLFSD--------EIVCLMRADHPLARRGLMTLDDYLE 98 (203)
T ss_pred EEEEEeCCcchhHHHHHhcCCeeEEEeccccC---CCCcEEeEeecC--------ceEEEEeCCCCcccCCCCCHHHHhh
Confidence 45555445568899999999999999743221 011222333211 334555665432 36788888
Q ss_pred CceeeC
Q psy11925 202 LKSCHT 207 (458)
Q Consensus 202 kksCht 207 (458)
-+.-..
T Consensus 99 ~~~i~~ 104 (203)
T cd08463 99 APHLAP 104 (203)
T ss_pred CCcEEE
Confidence 876553
No 59
>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=45.33 E-value=1.6e+02 Score=25.68 Aligned_cols=71 Identities=14% Similarity=0.112 Sum_probs=41.4
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC----ccChhhhcCC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK----VKSLEELKGL 202 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~----~~~l~dLkGk 202 (458)
.+++.. .+..+.++.+.+|++|+++...... .......|+..| -.++|+.++.+ ..+++||++.
T Consensus 30 ~l~~~~-~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~~~~l~~~--------~~~~v~~~~~~~~~~~~~~~~L~~~ 97 (200)
T cd08417 30 RLRFVP-LDRDDLEEALESGEIDLAIGVFPEL---PPGLRSQPLFED--------RFVCVARKDHPLAGGPLTLEDYLAA 97 (200)
T ss_pred EEEecc-CCHHHHHHHHHcCCCCEEEeecccC---CCccchhhhhcC--------ceEEEecCCCcccccccCHHHHhCC
Confidence 355544 3568999999999999998643211 112223333222 23344444432 2468899998
Q ss_pred ceeeCCC
Q psy11925 203 KSCHTAY 209 (458)
Q Consensus 203 ksChtg~ 209 (458)
+......
T Consensus 98 ~~i~~~~ 104 (200)
T cd08417 98 PHVLVSP 104 (200)
T ss_pred CeEEecc
Confidence 8776443
No 60
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=43.97 E-value=2.2e+02 Score=24.78 Aligned_cols=30 Identities=13% Similarity=0.122 Sum_probs=22.3
Q ss_pred CCCeEEEecC-CHHHHHHHHHcCCccEEEeC
Q psy11925 125 RPPFECNREK-SSKVCLKLIADGAADVITLD 154 (458)
Q Consensus 125 ~p~v~Cv~~~-s~~~Ci~~I~~g~AD~~~ld 154 (458)
.|.+.....+ +..+.++.+.+|++|+++..
T Consensus 26 ~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~ 56 (198)
T cd08461 26 APGVRVAIRDLESDNLEAQLERGEVDLALTT 56 (198)
T ss_pred CCCcEEEEeeCCcccHHHHHhcCCCcEEEec
Confidence 3665555533 45789999999999999864
No 61
>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=43.93 E-value=2.1e+02 Score=24.62 Aligned_cols=99 Identities=17% Similarity=0.079 Sum_probs=51.1
Q ss_pred eEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCC
Q psy11925 99 IRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNE 178 (458)
Q Consensus 99 vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~ 178 (458)
+|+++....-..--..+-..+....-...++... .+..+.++.+.+|++|++...... . ...+.-+|+..+
T Consensus 2 l~Ig~~~~~~~~~l~~~l~~~~~~~p~v~i~i~~-~~~~~~~~~L~~~~~Dl~i~~~~~--~-~~~~~~~~l~~~----- 72 (197)
T cd08438 2 LRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVE-YGGKKVEQAVLNGELDVGITVLPV--D-EEEFDSQPLCNE----- 72 (197)
T ss_pred eEEEecchhhhhhcHHHHHHHHHHCcCeEEEEEE-cCcHHHHHHHHcCCCCEEEEeccc--c-cCCceeEEeccc-----
Confidence 5566655433323223322222221112344443 367899999999999999864321 0 111222333211
Q ss_pred cceEEEEEEecCCC-----ccChhhhcCCceeeCCC
Q psy11925 179 KDLLAVAVVNKNSK-----VKSLEELKGLKSCHTAY 209 (458)
Q Consensus 179 ~~~~aVAVVkk~s~-----~~~l~dLkGkksChtg~ 209 (458)
..+.|+.++.+ ..+++||.+.+.-..+.
T Consensus 73 ---~~~~v~~~~~~l~~~~~~~~~~l~~~~~i~~~~ 105 (197)
T cd08438 73 ---PLVAVLPRGHPLAGRKTVSLADLADEPFILFNE 105 (197)
T ss_pred ---cEEEEecCCCChhhccccCHHHHcCCCeEEECC
Confidence 23444555543 23688999888776543
No 62
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=43.43 E-value=2.1e+02 Score=27.75 Aligned_cols=103 Identities=18% Similarity=0.056 Sum_probs=56.6
Q ss_pred CCCceEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEe-cCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEE
Q psy11925 95 PIKPIRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNR-EKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKE 173 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~-~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E 173 (458)
..++||+|+.......-=..+-..+.. -.|.+.... ..+..++++.+.+|++|+++..... . ..-+..+
T Consensus 89 ~~~~i~I~~~~~~~~~~l~~~l~~~~~--~~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~-----~---~~~l~~~ 158 (296)
T PRK11242 89 SRGSLRLAMTPTFTAYLIGPLIDAFHA--RYPGITLTIREMSQERIEALLADDELDVGIAFAPV-----H---SPEIEAQ 158 (296)
T ss_pred CeeEEEEEeccchhhhhhHHHHHHHHH--HCCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecCC-----C---CcceeEE
Confidence 346799998765422111111111111 135654444 3456889999999999999864321 1 1112222
Q ss_pred eecCCcceEEEEEEecCCCc------cChhhhcCCceeeCCCC
Q psy11925 174 KYGNEKDLLAVAVVNKNSKV------KSLEELKGLKSCHTAYM 210 (458)
Q Consensus 174 ~y~~~~~~~aVAVVkk~s~~------~~l~dLkGkksChtg~~ 210 (458)
....+ -.++|+.++.+. .+++||+.-..-++..+
T Consensus 159 ~l~~~---~~~~~~~~~~pl~~~~~~i~~~~L~~~~~i~~~~~ 198 (296)
T PRK11242 159 PLFTE---TLALVVGRHHPLAARRKALTLDELADEPLVLLSAE 198 (296)
T ss_pred Eeeec---cEEEEEcCCCcccccCCCcCHHHHhCCCcEeeCCC
Confidence 22211 335566665432 47889998888876554
No 63
>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=43.38 E-value=2.2e+02 Score=24.71 Aligned_cols=98 Identities=10% Similarity=0.035 Sum_probs=52.2
Q ss_pred ceEEEeCChhHHhHHHHHHHHHhcCCCCCC--eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEee
Q psy11925 98 PIRWCVSSPEGMSKCLAFKDAAFSRDIRPP--FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKY 175 (458)
Q Consensus 98 ~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~--v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y 175 (458)
++|+.+........-..+-..+.. ..|. ++...+ +..+.++.+.+|++|++...... ....+.-+++..+
T Consensus 2 ~l~ig~~~~~~~~~l~~~i~~~~~--~~P~v~l~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~~~~l~~~-- 73 (198)
T cd08446 2 ELDVGYFGSAILDTVPRLLRAFLT--ARPDVTVSLHNM-TKDEQIEALRAGRIHIGFGRFYP---VEPDIAVENVAQE-- 73 (198)
T ss_pred eEEEEechHHHHHHHHHHHHHHHH--HCCCeEEEEeeC-CHHHHHHHHHCCCccEEEEecCC---CCCCceeEEeeec--
Confidence 356655554433332222222221 2354 445443 56789999999999999853221 1112222333322
Q ss_pred cCCcceEEEEEEecCCC-----ccChhhhcCCceeeCCC
Q psy11925 176 GNEKDLLAVAVVNKNSK-----VKSLEELKGLKSCHTAY 209 (458)
Q Consensus 176 ~~~~~~~aVAVVkk~s~-----~~~l~dLkGkksChtg~ 209 (458)
..++|+.++.+ ..+++||++.+.-+...
T Consensus 74 ------~~~~v~~~~~pl~~~~~~~~~~l~~~~~i~~~~ 106 (198)
T cd08446 74 ------RLYLAVPKSHPLAARPAVSLADLRNEPLILFPR 106 (198)
T ss_pred ------cEEEEEeCCCCcccCCccCHHHHcCCCEEEecc
Confidence 33455555543 24689999998887543
No 64
>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=42.29 E-value=70 Score=30.32 Aligned_cols=80 Identities=23% Similarity=0.230 Sum_probs=48.3
Q ss_pred HHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhcCCceeeCCCCCCCchH
Q psy11925 137 KVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELKGLKSCHTAYMRTTGWV 216 (458)
Q Consensus 137 ~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLkGkksChtg~~~taGw~ 216 (458)
.|.-..+..|.||+.+.+-+-+... ..++.-++- .+-+...++||+ ++++.+.+.++|+|+|..---+ +
T Consensus 50 ~Dip~yV~~G~aDlGI~G~D~l~E~--~~~v~~~~d--L~fg~crl~vA~-p~~~~~~~~~~l~~~rIATkyp------~ 118 (182)
T TIGR00070 50 QDIPTYVEHGAADLGITGYDVLLES--GADVYELLD--LGFGKCRLVLAV-PQESDISSVEDLKGKRIATKYP------N 118 (182)
T ss_pred chhHHHHhCCCccEEEecchhhhhC--CCCEEEEee--cCcCceEEEEEE-ECCCCCCChHHhCCCEEEECCH------H
Confidence 6788899999999997665555332 223332221 111111155655 5566788999999998754333 2
Q ss_pred HHHHHHHHcCC
Q psy11925 217 APVYNLLEKGL 227 (458)
Q Consensus 217 ~Pv~~L~~~~~ 227 (458)
+--.+|.++|+
T Consensus 119 i~~~~f~~~Gi 129 (182)
T TIGR00070 119 LARRYFEKKGI 129 (182)
T ss_pred HHHHHHHHcCC
Confidence 44556667674
No 65
>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=41.87 E-value=2.3e+02 Score=24.54 Aligned_cols=98 Identities=13% Similarity=0.094 Sum_probs=51.1
Q ss_pred ceEEEeCChhHHhHHHHHHHHHhcCCCCCC--eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEee
Q psy11925 98 PIRWCVSSPEGMSKCLAFKDAAFSRDIRPP--FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKY 175 (458)
Q Consensus 98 ~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~--v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y 175 (458)
++|+++........=..+-..+.. ..|. ++... .+..+.++.+.+|++|+++...... ...+.-+++..|
T Consensus 2 ~l~Ig~~~~~~~~~l~~~l~~~~~--~~P~v~i~i~~-~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~~~~l~~~-- 73 (197)
T cd08425 2 SLRLAMTPTFTAYLIGPLIDRFHA--RYPGIALSLRE-MPQERIEAALADDRLDLGIAFAPVR---SPDIDAQPLFDE-- 73 (197)
T ss_pred eEEEEechhhhhhhhHHHHHHHHH--HCCCcEEEEEE-CcHHHHHHHHHcCCccEEEEecCCC---CCCcEEEEeccc--
Confidence 466766654433332222222222 1344 44444 3567899999999999998533211 011222333222
Q ss_pred cCCcceEEEEEEecCCC------ccChhhhcCCceeeCCC
Q psy11925 176 GNEKDLLAVAVVNKNSK------VKSLEELKGLKSCHTAY 209 (458)
Q Consensus 176 ~~~~~~~aVAVVkk~s~------~~~l~dLkGkksChtg~ 209 (458)
--+.|+.++.+ ..+++||+..+.-....
T Consensus 74 ------~~~~v~~~~~pl~~~~~~~~~~dL~~~~~i~~~~ 107 (197)
T cd08425 74 ------RLALVVGATHPLAQRRTALTLDDLAAEPLALLSP 107 (197)
T ss_pred ------cEEEEecCCCchhHhcccCCHHHHhcCCcEecCC
Confidence 22344554432 14788999887766443
No 66
>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=39.99 E-value=2e+02 Score=24.82 Aligned_cols=70 Identities=19% Similarity=0.169 Sum_probs=40.7
Q ss_pred eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcCC
Q psy11925 128 FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKGL 202 (458)
Q Consensus 128 v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkGk 202 (458)
++.... +..+.++.+.+|++|++....... ...+.-+|+..| ..+.|+.++.+ ..++++|.+.
T Consensus 31 l~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~~~~l~~~--------~~~~v~~~~~~l~~~~~~~~~~l~~~ 98 (196)
T cd08415 31 ISLHTL-SSSTVVEAVLSGQADLGLASLPLD---HPGLESEPLASG--------RAVCVLPPGHPLARKDVVTPADLAGE 98 (196)
T ss_pred EEEEec-chHHHHHHHHcCCccEEEEeCCCC---CCcceeeeeccc--------ceEEEEcCCCChHhcCccCHHHhcCC
Confidence 444443 567899999999999998643211 111222333222 23445555543 2468899988
Q ss_pred ceeeCCC
Q psy11925 203 KSCHTAY 209 (458)
Q Consensus 203 ksChtg~ 209 (458)
+......
T Consensus 99 ~~i~~~~ 105 (196)
T cd08415 99 PLISLGR 105 (196)
T ss_pred cEEEeCC
Confidence 8876533
No 67
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=39.89 E-value=3.5e+02 Score=26.09 Aligned_cols=103 Identities=17% Similarity=0.063 Sum_probs=55.0
Q ss_pred CCCceEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEe-cCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEE
Q psy11925 95 PIKPIRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNR-EKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKE 173 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~-~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E 173 (458)
..+.+|+++....-..-=..+-..+.. --|.+.... ..+..+.++.+.+|++|++...+..- .....-.|+..+
T Consensus 87 ~~g~l~i~~~~~~~~~~~~~~l~~~~~--~~P~i~i~v~~~~~~~~~~~l~~g~~Di~i~~~~~~---~~~~~~~~l~~~ 161 (290)
T PRK10837 87 DNGALRIYASSTIGNYILPAMIARYRR--DYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCH---SPELISEPWLED 161 (290)
T ss_pred hCCeEEEEecchhHhhhhHHHHHHHHH--HCCCceEEEEECCHHHHHHHHHhCCceEEEecCCCC---CCceeEEEeecc
Confidence 456799999875422110011111111 125443332 23678999999999999998642210 011111222111
Q ss_pred eecCCcceEEEEEEecCCCc----cChhhhcCCceeeCCCC
Q psy11925 174 KYGNEKDLLAVAVVNKNSKV----KSLEELKGLKSCHTAYM 210 (458)
Q Consensus 174 ~y~~~~~~~aVAVVkk~s~~----~~l~dLkGkksChtg~~ 210 (458)
..+.|+.++.+. .++++|++.+......+
T Consensus 162 --------~~~lv~~~~hpl~~~~i~~~~L~~~~~i~~~~~ 194 (290)
T PRK10837 162 --------ELVVFAAPDSPLARGPVTLEQLAAAPWILRERG 194 (290)
T ss_pred --------eEEEEEcCCChhhcCCCCHHHHhcCCeEEecCC
Confidence 344555555432 47899999988886654
No 68
>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=37.95 E-value=2.7e+02 Score=24.19 Aligned_cols=100 Identities=9% Similarity=-0.011 Sum_probs=51.6
Q ss_pred ceEEEeCChhHHhHHHH-HHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeec
Q psy11925 98 PIRWCVSSPEGMSKCLA-FKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYG 176 (458)
Q Consensus 98 ~vrwCv~s~~E~~KC~~-l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~ 176 (458)
++|+|+....-..-... +.. +...- ...++... .+..+..+.+.+|++|+++..... .. ..+...++..+.
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~-f~~~~-~v~l~l~~-~~~~~~~~~l~~~~~D~~i~~~~~--~~-~~~~~~~l~~~~-- 72 (195)
T cd08428 1 TLPVAVNADSLATWFLPALAP-VLKRE-RILLDLIV-DDEDRTHDLLRDGEVVGCISTQAQ--PM-QGCRSDYLGSMD-- 72 (195)
T ss_pred CEEEEechhHHHHHhHHHHHH-HHhCc-CeEEEEEe-CCchhHHHHHHcCcceEEEEecCC--CC-CCceeEEeeeee--
Confidence 46777775322222222 222 22221 33455554 457789999999999976642211 00 112233343221
Q ss_pred CCcceEEEEEEecCC------CccChhhhcCCceeeCCCCC
Q psy11925 177 NEKDLLAVAVVNKNS------KVKSLEELKGLKSCHTAYMR 211 (458)
Q Consensus 177 ~~~~~~aVAVVkk~s------~~~~l~dLkGkksChtg~~~ 211 (458)
..++ +.++. ...+++||++.+..+...+.
T Consensus 73 -----~~~~-~~~~~~~~~~~~~i~~~~L~~~~~i~~~~~~ 107 (195)
T cd08428 73 -----YLLV-ASPDFAARYFPNGLTREALLKAPAVAFNRKD 107 (195)
T ss_pred -----EEEE-ECCcchhhcCCCCCCHHHHhcCcEEEEcCCC
Confidence 3333 33221 12478999999999865543
No 69
>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=36.36 E-value=2.8e+02 Score=23.89 Aligned_cols=73 Identities=14% Similarity=0.075 Sum_probs=41.1
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkG 201 (458)
.++... .+..++++.+.+|++|++......-. ....+.-+|+..| -.+.|+.++.+ ..+++||.+
T Consensus 30 ~i~i~~-~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~~~~l~~~--------~~~~~~~~~~~l~~~~~~~~~dL~~ 99 (201)
T cd08435 30 TVRVVE-GTSDELLEGLRAGELDLAIGRLADDE-QPPDLASEELADE--------PLVVVARPGHPLARRARLTLADLAD 99 (201)
T ss_pred EEEEEe-CCHHHHHHHHHcCCccEEEEecCccc-CCCCcEEEEcccC--------cEEEEEeCCCcCcccCCcCHHHHhc
Confidence 355543 46899999999999999985321100 0011112222211 23344554432 246889999
Q ss_pred CceeeCCC
Q psy11925 202 LKSCHTAY 209 (458)
Q Consensus 202 kksChtg~ 209 (458)
.+....+.
T Consensus 100 ~~~i~~~~ 107 (201)
T cd08435 100 YPWVLPPP 107 (201)
T ss_pred CCEEecCC
Confidence 88877544
No 70
>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=35.72 E-value=2.9e+02 Score=23.84 Aligned_cols=27 Identities=7% Similarity=0.096 Sum_probs=21.5
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLD 154 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld 154 (458)
.++.... +..+.++.+.+|++|+++..
T Consensus 30 ~~~i~~~-~~~~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08456 30 TISIHTR-DSPTVEQWLSAQQCDLGLVS 56 (196)
T ss_pred EEEEEeC-CHHHHHHHHHcCCccEEEEe
Confidence 5666654 56789999999999999854
No 71
>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=35.15 E-value=2.3e+02 Score=24.59 Aligned_cols=79 Identities=14% Similarity=0.144 Sum_probs=44.8
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkG 201 (458)
.++... .+..+.++.+.+|++|++...... ......-+|+..| -.+.|+.++.+ ..++++|.+
T Consensus 30 ~i~~~~-~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~~~~l~~~--------~~~~v~~~~~pl~~~~~~~~~~l~~ 97 (198)
T cd08421 30 RIDLEE-RLSADIVRAVAEGRADLGIVAGNV---DAAGLETRPYRTD--------RLVVVVPRDHPLAGRASVAFADTLD 97 (198)
T ss_pred eEEEEe-cCcHHHHHHHhcCCceEEEEecCC---CCCCcEEEEeecC--------cEEEEeCCCCCccccCCCCHHHhcC
Confidence 344443 356889999999999998864322 1122223344322 23344455432 247889998
Q ss_pred CceeeCCCCCCCchHHHH
Q psy11925 202 LKSCHTAYMRTTGWVAPV 219 (458)
Q Consensus 202 kksChtg~~~taGw~~Pv 219 (458)
-+......+ .+|.-.+
T Consensus 98 ~~~i~~~~~--~~~~~~~ 113 (198)
T cd08421 98 HDFVGLPAG--SALHTFL 113 (198)
T ss_pred CceEeecCC--cchHHHH
Confidence 887765433 3454433
No 72
>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=34.98 E-value=2e+02 Score=26.78 Aligned_cols=71 Identities=27% Similarity=0.230 Sum_probs=41.0
Q ss_pred CCeEEEecC-CHHHHHHHHHcCCccEEEeCCcceEEeccCCCc-eEEEEEeecCCcceEEEEEEecCC--CccChhh--h
Q psy11925 126 PPFECNREK-SSKVCLKLIADGAADVITLDATEAVLGRKNLNL-RPILKEKYGNEKDLLAVAVVNKNS--KVKSLEE--L 199 (458)
Q Consensus 126 p~v~Cv~~~-s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L-~pil~E~y~~~~~~~aVAVVkk~s--~~~~l~d--L 199 (458)
-+++.+... .....+..++.|++|++.-.+. .. +.+.. .|++. .-.+.|+++++ .+++++| |
T Consensus 35 ~~i~~~~~~~~~~~~~~~l~~g~~Di~~~~~~---r~-~~~~fs~py~~--------~~~~lv~~~~~~~~~~~~~d~~l 102 (232)
T TIGR03871 35 LPLEYTWFPQRRGFVRNTLNAGRCDVVIGVPA---GY-EMVLTTRPYYR--------STYVFVTRKDSLLDVKSLDDPRL 102 (232)
T ss_pred CceEEEecCcchhhHHHHHhcCCccEEEeccC---cc-ccccccCCcEe--------eeEEEEEeCCCcccccchhhhhh
Confidence 345665443 3556788999999999864211 11 11111 12211 13455667763 5678887 9
Q ss_pred cCCceeeCC
Q psy11925 200 KGLKSCHTA 208 (458)
Q Consensus 200 kGkksChtg 208 (458)
+|++.+-..
T Consensus 103 ~g~~V~v~~ 111 (232)
T TIGR03871 103 KKLRIGVFA 111 (232)
T ss_pred cCCeEEEEc
Confidence 999987743
No 73
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=34.80 E-value=3.7e+02 Score=25.98 Aligned_cols=103 Identities=8% Similarity=0.033 Sum_probs=55.5
Q ss_pred CCCceEEEeCChhHHhHHHHHHHHHhcCCCCCC--eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEE
Q psy11925 95 PIKPIRWCVSSPEGMSKCLAFKDAAFSRDIRPP--FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILK 172 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~--v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~ 172 (458)
..+++|+.+........-..+-..+... .|. +..+. .+..+.++.+.+|++|+++.....-- ....+.-.|+..
T Consensus 95 ~~~~l~I~~~~~~~~~~l~~~l~~f~~~--~p~i~l~i~~-~~~~~~~~~l~~g~~D~~i~~~~~~~-~~~~l~~~~l~~ 170 (294)
T PRK09986 95 EAGRIEIGIVGTALWGRLRPAMRHFLKE--NPNVEWLLRE-LSPSMQMAALERRELDAGIWRMADLE-PNPGFTSRRLHE 170 (294)
T ss_pred CcceEEEEEehHHhHHHHHHHHHHHHHh--CCCeEEEEEe-CCHHHHHHHHHcCCCCEEEecCCccC-CCCCeEEEEeec
Confidence 4567999876543322222222222222 344 55543 35689999999999999986322100 001122233322
Q ss_pred EeecCCcceEEEEEEecCCCc-----cChhhhcCCceeeCCC
Q psy11925 173 EKYGNEKDLLAVAVVNKNSKV-----KSLEELKGLKSCHTAY 209 (458)
Q Consensus 173 E~y~~~~~~~aVAVVkk~s~~-----~~l~dLkGkksChtg~ 209 (458)
| ..+.|+.++.+. .+++||.+-..-+...
T Consensus 171 ~--------~~~~v~~~~~~l~~~~~~~~~dL~~~~~i~~~~ 204 (294)
T PRK09986 171 S--------AFAVAVPEEHPLASRSSVPLKALRNEYFITLPF 204 (294)
T ss_pred c--------cEEEEEcCCCCcccCCccCHHHHcCCCEEecCC
Confidence 1 445566655432 3789999888766443
No 74
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=34.54 E-value=1.1e+02 Score=34.15 Aligned_cols=77 Identities=16% Similarity=0.130 Sum_probs=47.3
Q ss_pred CCeEEEe-cCCHHHHHHHHHcCCccEEEeCCcceEEe------------ccCCCceEEEEEeecCCcceEEEEEEecCCC
Q psy11925 126 PPFECNR-EKSSKVCLKLIADGAADVITLDATEAVLG------------RKNLNLRPILKEKYGNEKDLLAVAVVNKNSK 192 (458)
Q Consensus 126 p~v~Cv~-~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A------------~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~ 192 (458)
|.++... ..+..+.++++++|++|++.+.....-.. .......|+..| ..++||+++++
T Consensus 439 P~v~i~v~~~~s~~vl~~L~~GeiDlai~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~d--------~lvlvvp~~hP 510 (633)
T PRK14498 439 RGLRLRSLHVGSMGGLMALKRGEADIAGIHLLDPETGEYNIPYIKKYLLGEDAVLVKGYRR--------EQGLVVRKGNP 510 (633)
T ss_pred cCCceeEEecCCHHHHHHHHcCCceEEEEcccCcccccccHHHHHhhcCCCCEEEEEEEEE--------eEEEEECCCCC
Confidence 5544433 24678999999999999998642210000 001122333222 56777888764
Q ss_pred --ccChhhhcCC--ceeeCCCC
Q psy11925 193 --VKSLEELKGL--KSCHTAYM 210 (458)
Q Consensus 193 --~~~l~dLkGk--ksChtg~~ 210 (458)
..+|+||++. +..-...+
T Consensus 511 l~~isl~dL~~~~~plI~~~~g 532 (633)
T PRK14498 511 KGIEGIEDLVRKDVRFVNRQRG 532 (633)
T ss_pred CCCCCHHHhccCCcEEEecCCC
Confidence 3589999999 88776544
No 75
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=34.53 E-value=35 Score=29.13 Aligned_cols=55 Identities=18% Similarity=0.125 Sum_probs=33.6
Q ss_pred ecCCHHHHHHHHHcCCccEEEeCCcce-EEeccCCCceEEEEEeecCCcceEEEEEEecCC
Q psy11925 132 REKSSKVCLKLIADGAADVITLDATEA-VLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNS 191 (458)
Q Consensus 132 ~~~s~~~Ci~~I~~g~AD~~~ld~~~~-y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s 191 (458)
.-.+..+|+.+++.|+ |+++.|...+ |...+..+++ ++.+.+... .|++||- |++
T Consensus 50 ~~~~~~~~~~~l~~g~-da~v~d~~~~~~~~~~~~~~~-~~~~~~~~~--~~~ia~~-k~~ 105 (134)
T smart00079 50 FVKSYAEGVQRVRVSN-YAFLMESTYLDYELSQNCDLM-TVGENFGRK--GYGIAFP-KGS 105 (134)
T ss_pred CCCCHHHHHHHHHcCC-CEEEeehHhHHHHHhCCCCeE-EcCcccCCC--ceEEEec-CCC
Confidence 4568899999999999 9999986544 2222333333 222223211 1888875 444
No 76
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=34.38 E-value=2.1e+02 Score=28.14 Aligned_cols=58 Identities=9% Similarity=-0.031 Sum_probs=36.8
Q ss_pred CCCceEEEeCChhHHhHHHHHHHHHhcCCCCCC--eEEEecCCHHHHHHHHHcCCccEEEeCC
Q psy11925 95 PIKPIRWCVSSPEGMSKCLAFKDAAFSRDIRPP--FECNREKSSKVCLKLIADGAADVITLDA 155 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~--v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~ 155 (458)
..+++|+.+.......--..+-..+.. .-|. |.... .+..++++++.+|++|+++...
T Consensus 90 ~~g~l~Ig~~~~~~~~~l~~~l~~~~~--~~p~i~i~i~~-~~~~~~~~~l~~g~~Dl~i~~~ 149 (300)
T PRK11074 90 WRGQLSIAVDNIVRPDRTRQLIVDFYR--HFDDVELIIRQ-EVFNGVWDALADGRVDIAIGAT 149 (300)
T ss_pred CCceEEEEEcCccchhHHHHHHHHHHH--hCCCceEEEEe-hhhhHHHHHHHCCCCCEEEecC
Confidence 457899998766543333333322221 1244 44443 3578899999999999999643
No 77
>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=33.74 E-value=3.1e+02 Score=23.59 Aligned_cols=74 Identities=12% Similarity=0.070 Sum_probs=41.3
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcce--EEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhh
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEA--VLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEEL 199 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~--y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dL 199 (458)
.+++... +..+.++.+.+|++|+++...... ......+..+++..+ ..+.|+.++.+ ..+++||
T Consensus 30 ~i~~~~~-~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~~~~l~~~--------~~~~~~~~~~p~~~~~~~~~~~l 100 (200)
T cd08423 30 EVRLREA-EPPESLDALRAGELDLAVVFDYPVTPPPDDPGLTRVPLLDD--------PLDLVLPADHPLAGREEVALADL 100 (200)
T ss_pred eEEEEeC-CHHHHHHHHhcCCccEEEEeccccccCCCCCCcEEEEeccC--------cEEEEecCCCCccccCCCCHHHh
Confidence 4666544 568999999999999988643210 000011222333211 23344444432 2478999
Q ss_pred cCCceeeCCC
Q psy11925 200 KGLKSCHTAY 209 (458)
Q Consensus 200 kGkksChtg~ 209 (458)
.+-+.-....
T Consensus 101 ~~~~~i~~~~ 110 (200)
T cd08423 101 ADEPWIAGCP 110 (200)
T ss_pred cCCceEEecC
Confidence 9887766443
No 78
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=33.06 E-value=24 Score=34.76 Aligned_cols=63 Identities=24% Similarity=0.249 Sum_probs=34.0
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcce-EEEEEEecCCC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDL-LAVAVVNKNSK 192 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~-~aVAVVkk~s~ 192 (458)
+++=|. -++.+|++.|.+|++|+++-..+++ ..+..+|.++--......... -||.||+++..
T Consensus 138 ~Ve~Ve-i~Y~q~~~~l~~g~IDA~IWN~d~i--~~~~~~l~~~~l~~~~~~~~~seAVivi~~~~~ 201 (232)
T PF14503_consen 138 NVEFVE-IPYNQLLELLRSGEIDAAIWNYDEI--EDKNFGLKYVPLKDDPMSKDASEAVIVIRKDNE 201 (232)
T ss_dssp --EEEE---HHHHHHHHHHTS--EEEEE--HH--CCHHCTEEEEE--SSCHHHHTT-EEEEEETT-H
T ss_pred ceEEEE-ecHHHHHHHHHCCCccEEEECCccc--ccccCCeeEEeCCchHHHHhcCeeEEEEeCCCH
Confidence 455444 4699999999999999998776633 224467776533321111112 89999999863
No 79
>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=32.84 E-value=4e+02 Score=25.92 Aligned_cols=104 Identities=13% Similarity=0.043 Sum_probs=56.8
Q ss_pred CCCceEEEeCChhHHhH-HHHHHHHHhcCCCCCCeEEEec-CCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEE
Q psy11925 95 PIKPIRWCVSSPEGMSK-CLAFKDAAFSRDIRPPFECNRE-KSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILK 172 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~K-C~~l~~~~~~~~~~p~v~Cv~~-~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~ 172 (458)
..+++|+++.......- -..+.. +.. -.|.+..... .+..+.++.+.+|++|++....... .....+..+|+..
T Consensus 91 ~~~~l~I~~~~~~~~~~~~~~l~~-~~~--~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~-~~~~~~~~~~l~~ 166 (300)
T TIGR02424 91 EGPTVRIGALPTVAARLMPEVVKR-FLA--RAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAP-ETMQGLSFEHLYN 166 (300)
T ss_pred CCceEEEecccHHHHhhhHHHHHH-HHH--hCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCc-ccccceeeeeecC
Confidence 45679999886432211 122222 111 2366544433 3678999999999999999533211 0111222233322
Q ss_pred EeecCCcceEEEEEEecCCCc-----cChhhhcCCceeeCCCC
Q psy11925 173 EKYGNEKDLLAVAVVNKNSKV-----KSLEELKGLKSCHTAYM 210 (458)
Q Consensus 173 E~y~~~~~~~aVAVVkk~s~~-----~~l~dLkGkksChtg~~ 210 (458)
| ..+.++.++.+. .+++||.+-+......+
T Consensus 167 ~--------~~~~~~~~~hpl~~~~~i~~~dL~~~~~i~~~~~ 201 (300)
T TIGR02424 167 E--------PVVFVVRAGHPLLAAPSLPVASLADYPVLLPPEG 201 (300)
T ss_pred C--------ceEEEEcCCCccccCCCCCHHHHhCCCEEecCCC
Confidence 2 234555555432 37889998887765543
No 80
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=32.28 E-value=80 Score=30.05 Aligned_cols=71 Identities=24% Similarity=0.196 Sum_probs=41.3
Q ss_pred EEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC--ccChhhhcCCceee
Q psy11925 129 ECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK--VKSLEELKGLKSCH 206 (458)
Q Consensus 129 ~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~--~~~l~dLkGkksCh 206 (458)
.-....+...-+.++..|++|++.-.-...- . +. ..... .+-|.. .-.+.+|++++. +.+++||+||+.+=
T Consensus 79 ~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~-e-r~-~~~~f-s~py~~---~~~~~~~~~~~~~~~~~~~DL~gk~v~v 151 (275)
T COG0834 79 VEFVPVAWDGLIPALKAGKVDIIIAGMTITP-E-RK-KKVDF-SDPYYY---SGQVLLVKKDSDIGIKSLEDLKGKKVGV 151 (275)
T ss_pred eEEeccchhhhhHHHhcCCcCEEEeccccCH-H-Hh-ccccc-cccccc---cCeEEEEECCCCcCcCCHHHhCCCEEEE
Confidence 3445557899999999999999986612111 1 10 01111 122211 123445555544 46899999998875
No 81
>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=32.06 E-value=3.4e+02 Score=23.58 Aligned_cols=75 Identities=17% Similarity=0.130 Sum_probs=42.5
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCc-----cChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKV-----KSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~-----~~l~dLkG 201 (458)
.++.... +..+-++.+.+|++|++.......-.....+.-+|+..| -.++|+.++.+. .++++|++
T Consensus 30 ~l~i~~~-~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~~~l~~~--------~~~~v~~~~hp~~~~~~i~~~~L~~ 100 (200)
T cd08453 30 ELQLREA-TSDVQLEALLAGEIDAGIVIPPPGASAPPALAYRPLLSE--------PLVLAVPAAWAAEGGAPLALAAVAA 100 (200)
T ss_pred eEEEEeC-CHHHHHHHHHcCCCCEEEEecCcccCCCcceeEEEeeeC--------ceEEEEECCCccccCCCCCHHHhcc
Confidence 3555544 466789999999999987532210000111223344332 224555655432 47899999
Q ss_pred CceeeCCCC
Q psy11925 202 LKSCHTAYM 210 (458)
Q Consensus 202 kksChtg~~ 210 (458)
.+......+
T Consensus 101 ~~~i~~~~~ 109 (200)
T cd08453 101 EPLVIFPRR 109 (200)
T ss_pred CCEEeccCC
Confidence 887765443
No 82
>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=31.59 E-value=3.6e+02 Score=23.68 Aligned_cols=30 Identities=20% Similarity=0.156 Sum_probs=22.0
Q ss_pred CCCeEEEec-CCHHHHHHHHHcCCccEEEeC
Q psy11925 125 RPPFECNRE-KSSKVCLKLIADGAADVITLD 154 (458)
Q Consensus 125 ~p~v~Cv~~-~s~~~Ci~~I~~g~AD~~~ld 154 (458)
.|.++.... .+..+.++.+.+|++|+++..
T Consensus 26 ~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (202)
T cd08468 26 APSVRLNLVHAEQKLPLDALLAGEIDFALGY 56 (202)
T ss_pred CCCCEEEEEECChHhHHHHHHCCCccEEEec
Confidence 355444333 357899999999999998863
No 83
>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=31.11 E-value=3.6e+02 Score=23.60 Aligned_cols=70 Identities=16% Similarity=0.167 Sum_probs=40.6
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCc----cChhhhcCC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKV----KSLEELKGL 202 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~----~~l~dLkGk 202 (458)
.++.+.. +. +.++.+.+|++|+++...... .....-+|+..+ --+.|+.++.+. .++++|.+-
T Consensus 30 ~l~i~~~-~~-~~~~~l~~g~~D~~i~~~~~~---~~~~~~~~l~~~--------~~~~v~~~~hpl~~~~~~~~~l~~~ 96 (200)
T cd08462 30 RFELLPP-DD-QPHELLERGEVDLLIAPERFM---SDGHPSEPLFEE--------EFVCVVWADNPLVGGELTAEQYFSA 96 (200)
T ss_pred EEEEecC-Ch-hHHHHHhcCCeeEEEecCCCC---CCCceeeeeecc--------ceEEEEcCCCCccCCCCCHHHHhhC
Confidence 4666654 44 999999999999998643211 011222333222 334455555432 467888877
Q ss_pred ceeeCCC
Q psy11925 203 KSCHTAY 209 (458)
Q Consensus 203 ksChtg~ 209 (458)
+......
T Consensus 97 ~~i~~~~ 103 (200)
T cd08462 97 GHVVVRF 103 (200)
T ss_pred CCEEEec
Confidence 6665444
No 84
>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=30.58 E-value=3.5e+02 Score=23.18 Aligned_cols=71 Identities=15% Similarity=0.179 Sum_probs=42.1
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCc-cChhhhcCCcee
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKV-KSLEELKGLKSC 205 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~-~~l~dLkGkksC 205 (458)
.+++... +..+-++.+.+|++|++....... .....-+++..| --++|+.++.+. .++++|+....-
T Consensus 30 ~l~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~~~~l~~~--------~~~~v~~~~~~~~~~~~~l~~~~~i 97 (193)
T cd08442 30 DLSLSTG-TTGALIQAVLEGRLDGAFVAGPVE---HPRLEQEPVFQE--------ELVLVSPKGHPPVSRAEDLAGSTLL 97 (193)
T ss_pred eEEEEeC-CcHHHHHHHHCCCccEEEEeCCCC---CCCcEEEEeecC--------cEEEEecCCCcccccHHHhCCCceE
Confidence 4666543 678899999999999988643211 011112222211 345566666543 467888888776
Q ss_pred eCCC
Q psy11925 206 HTAY 209 (458)
Q Consensus 206 htg~ 209 (458)
....
T Consensus 98 ~~~~ 101 (193)
T cd08442 98 AFRA 101 (193)
T ss_pred EecC
Confidence 6443
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=30.38 E-value=3.3e+02 Score=23.47 Aligned_cols=72 Identities=14% Similarity=0.107 Sum_probs=41.1
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkG 201 (458)
.++... .+..+.++.+.+|++|+++....... .....-.++..| .-+.|+.++.+ ..+++||.+
T Consensus 31 ~l~i~~-~~~~~~~~~l~~g~~Dl~i~~~~~~~--~~~~~~~~l~~~--------~~~~v~~~~~~l~~~~~~~~~dL~~ 99 (199)
T cd08451 31 ELTLEE-ANTAELLEALREGRLDAAFVRPPVAR--SDGLVLELLLEE--------PMLVALPAGHPLARERSIPLAALAD 99 (199)
T ss_pred EEEEec-CChHHHHHHHHCCCccEEEEecCCCC--CCceeEEEeecc--------cEEEEecCCCCCcccCccCHHHhcC
Confidence 344443 35688999999999999986432110 011222333222 22344444432 247899999
Q ss_pred CceeeCCC
Q psy11925 202 LKSCHTAY 209 (458)
Q Consensus 202 kksChtg~ 209 (458)
.+..+...
T Consensus 100 ~~~i~~~~ 107 (199)
T cd08451 100 EPFILFPR 107 (199)
T ss_pred CCEEEecC
Confidence 99887543
No 86
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=29.83 E-value=4e+02 Score=26.03 Aligned_cols=100 Identities=8% Similarity=0.035 Sum_probs=53.0
Q ss_pred CCCceEEEeCChhH-HhHHHHHHHHHhcCCCCCC--eEEEecCCHHHHHHHHHcCCccEEEeCC-cceEEeccCCCceEE
Q psy11925 95 PIKPIRWCVSSPEG-MSKCLAFKDAAFSRDIRPP--FECNREKSSKVCLKLIADGAADVITLDA-TEAVLGRKNLNLRPI 170 (458)
Q Consensus 95 p~~~vrwCv~s~~E-~~KC~~l~~~~~~~~~~p~--v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~-~~~y~A~~~~~L~pi 170 (458)
...++|+.++...- .--...+... ... .|. ++... .+..+-++.+.+|++|+++... +..+. ..+..+|+
T Consensus 93 ~~g~l~I~~~~~~~~~~l~~~l~~~-~~~--~p~i~~~~~~-~~~~~~~~~l~~g~~Di~i~~~~~~~~~--~~~~~~~l 166 (302)
T PRK09791 93 LAGQINIGMGASIARSLMPAVISRF-HQQ--HPQVKVRIME-GQLVSMINELRQGELDFTINTYYQGPYD--HEFTFEKL 166 (302)
T ss_pred cceEEEEEechHHHHhhhHHHHHHH-HHH--CCCeEEEEEe-CChHHHHHHHHCCCccEEEEecCCcccc--cceeEEEe
Confidence 45779999887542 2233333331 211 244 44443 3568889999999999988631 11111 12233344
Q ss_pred EEEeecCCcceEEEEEEecCCCc---cChhhhcCCceeeCC
Q psy11925 171 LKEKYGNEKDLLAVAVVNKNSKV---KSLEELKGLKSCHTA 208 (458)
Q Consensus 171 l~E~y~~~~~~~aVAVVkk~s~~---~~l~dLkGkksChtg 208 (458)
..| ..|.|+.++.+. .++++|..-......
T Consensus 167 ~~~--------~~~l~~~~~~~~~~~~~~~~l~~~~~i~~~ 199 (302)
T PRK09791 167 LEK--------QFAVFCRPGHPAIGARSLKQLLDYSWTMPT 199 (302)
T ss_pred ccc--------eEEEEEcCCCCcCCCCCHHHHhcCCeecCC
Confidence 322 334455555432 346777766655443
No 87
>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=29.23 E-value=3.9e+02 Score=23.34 Aligned_cols=70 Identities=11% Similarity=0.142 Sum_probs=38.3
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCc----cChhhhcCC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKV----KSLEELKGL 202 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~----~~l~dLkGk 202 (458)
.++..... . +.++.+.+|++|++...... .. ....-.|+..+ ..+.|+.++.+. .+++||..-
T Consensus 30 ~v~l~~~~-~-~~~~~l~~g~~D~~i~~~~~--~~-~~~~~~~l~~~--------~~~~v~~~~hpl~~~~~~l~dl~~~ 96 (200)
T cd08460 30 RLRFVPES-D-KDVDALREGRIDLEIGVLGP--TG-PEIRVQTLFRD--------RFVGVVRAGHPLARGPITPERYAAA 96 (200)
T ss_pred EEEEecCc-h-hHHHHHHCCCccEEEecCCC--CC-cchheeeeecc--------ceEEEEeCCCCCCCCCCCHHHHhcC
Confidence 35554443 3 88999999999999863321 01 11222333222 233444544432 367888777
Q ss_pred ceeeCCC
Q psy11925 203 KSCHTAY 209 (458)
Q Consensus 203 ksChtg~ 209 (458)
+......
T Consensus 97 ~~i~~~~ 103 (200)
T cd08460 97 PHVSVSR 103 (200)
T ss_pred CCEEEec
Confidence 7665433
No 88
>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=29.17 E-value=3.8e+02 Score=23.18 Aligned_cols=70 Identities=20% Similarity=0.162 Sum_probs=40.1
Q ss_pred eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcCC
Q psy11925 128 FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKGL 202 (458)
Q Consensus 128 v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkGk 202 (458)
++... .+..++++.+.+|++|+++...... ...+.-+|+..| .-+.|+.++.+ ..+++||.+.
T Consensus 31 i~~~~-~~~~~~~~~l~~~~~D~~i~~~~~~---~~~~~~~~l~~~--------~~~~~~~~~~~~~~~~~~~~~~l~~~ 98 (198)
T cd08433 31 LRIVE-GLSGHLLEWLLNGRLDLALLYGPPP---IPGLSTEPLLEE--------DLFLVGPADAPLPRGAPVPLAELARL 98 (198)
T ss_pred EEEEe-cCcHHHHHHHhCCCCcEEEEeCCCC---CCCeeEEEeccc--------cEEEEecCCCccccCCCCCHHHhCCC
Confidence 44443 4678999999999999998532211 011122233222 22344444432 2468999999
Q ss_pred ceeeCCC
Q psy11925 203 KSCHTAY 209 (458)
Q Consensus 203 ksChtg~ 209 (458)
+.-....
T Consensus 99 ~~i~~~~ 105 (198)
T cd08433 99 PLILPSR 105 (198)
T ss_pred ceEEcCC
Confidence 8877543
No 89
>PF13531 SBP_bac_11: Bacterial extracellular solute-binding protein; PDB: 2HXW_B 3FJG_C 3FJM_B 3FJ7_B 3FIR_B 3AXF_C 1WOD_A 1AMF_A 3R26_A 1SBP_A ....
Probab=29.09 E-value=78 Score=29.78 Aligned_cols=106 Identities=16% Similarity=0.127 Sum_probs=61.5
Q ss_pred HHHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcC-CccEEEeCCcceEEeccCCCc------eEEEEEeecCCcceEE
Q psy11925 111 KCLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADG-AADVITLDATEAVLGRKNLNL------RPILKEKYGNEKDLLA 183 (458)
Q Consensus 111 KC~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g-~AD~~~ld~~~~y~A~~~~~L------~pil~E~y~~~~~~~a 183 (458)
-+..+...+ ...-+..++++.+. ..+.+.+|..| .+|+++.+.......-...|+ .|++. ...
T Consensus 12 ~~~~l~~~f-~~~~g~~v~v~~~~-s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~--------~~~ 81 (230)
T PF13531_consen 12 ALEELAEAF-EKQPGIKVEVSFGG-SGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLAR--------SPL 81 (230)
T ss_dssp HHHHHHHHH-HHHHCEEEEEEEEC-HHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEE--------EEE
T ss_pred HHHHHHHHH-HhccCCeEEEEECC-hHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCccccccc--------Cce
Confidence 344555543 22222457777774 57799999987 899999887533221111111 12211 167
Q ss_pred EEEEecCC--CccChhhhcCC--ceeeCCCCCCCchHHHHHHHHHcC
Q psy11925 184 VAVVNKNS--KVKSLEELKGL--KSCHTAYMRTTGWVAPVYNLLEKG 226 (458)
Q Consensus 184 VAVVkk~s--~~~~l~dLkGk--ksChtg~~~taGw~~Pv~~L~~~~ 226 (458)
|.+++++. .+.+|+||... |.-++.+..+.+-..-...|.+.|
T Consensus 82 vl~~~~~~~~~~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~~g 128 (230)
T PF13531_consen 82 VLAVPKGNPKGIRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAAAG 128 (230)
T ss_dssp EEEEETTSTTSTTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHHHT
T ss_pred EEEeccCcccccCCHHHHhhccCEEEecCcccChhhHHHHHHHHHcc
Confidence 78888876 57899999765 888988865444445555555555
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=28.33 E-value=3.9e+02 Score=23.11 Aligned_cols=27 Identities=7% Similarity=-0.023 Sum_probs=20.2
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLD 154 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld 154 (458)
.++...+ +..+.++.+.+|++|+++..
T Consensus 30 ~l~~~~~-~~~~~~~~l~~g~~Dl~i~~ 56 (200)
T cd08466 30 SLRESPS-SEEDLFEDLRLQEVDLVIDY 56 (200)
T ss_pred EEEEecC-chHhHHHHHHcCCccEEEec
Confidence 3444443 56789999999999999853
No 91
>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=28.19 E-value=3.9e+02 Score=23.02 Aligned_cols=72 Identities=19% Similarity=0.139 Sum_probs=39.8
Q ss_pred CCeEEEe-cCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhh
Q psy11925 126 PPFECNR-EKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEEL 199 (458)
Q Consensus 126 p~v~Cv~-~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dL 199 (458)
|.+.-.. ..+..+.++.+.+|++|++...+... .-+ +.++..... -.+.|+.++.+ ..+++||
T Consensus 27 P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~-----~~~---~~~~~l~~~---~~~~v~~~~~pl~~~~~~~~~~l 95 (198)
T cd08447 27 PDVDLVLREMVTTDQIEALESGRIDLGLLRPPFA-----RPG---LETRPLVRE---PLVAAVPAGHPLAGAERLTLEDL 95 (198)
T ss_pred CCeEEEEEeCCHHHHHHHHHcCCceEEEecCCCC-----CCC---eeEEEeecC---ceEEEecCCCchhhcCcccHHHh
Confidence 5544433 23678999999999999998643211 111 222221111 22344455432 2468889
Q ss_pred cCCceeeCC
Q psy11925 200 KGLKSCHTA 208 (458)
Q Consensus 200 kGkksChtg 208 (458)
.+.+.-...
T Consensus 96 ~~~~~i~~~ 104 (198)
T cd08447 96 DGQPFIMYS 104 (198)
T ss_pred CCCeEEEeC
Confidence 887776543
No 92
>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=26.63 E-value=4.1e+02 Score=22.73 Aligned_cols=69 Identities=16% Similarity=0.149 Sum_probs=39.3
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkG 201 (458)
.+++... +..+.++.+.+|++|++...... .......+++..| -.+.|+.++.+ ..+++||.+
T Consensus 29 ~l~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~~~~l~~~--------~~~~~~~~~~~l~~~~~~~~~~l~~ 96 (197)
T cd08419 29 EVSLRVG-NREQVLERLADNEDDLAIMGRPP---EDLDLVAEPFLDN--------PLVVIAPPDHPLAGQKRIPLERLAR 96 (197)
T ss_pred eEEEEEC-CHHHHHHHHhcCCccEEEecCCC---CCCCeEEEEeccC--------CEEEEecCCCCCcCCCCcCHHHHhC
Confidence 4566554 67889999999999999854321 0011112233221 23344454432 236888888
Q ss_pred CceeeC
Q psy11925 202 LKSCHT 207 (458)
Q Consensus 202 kksCht 207 (458)
.+....
T Consensus 97 ~~~i~~ 102 (197)
T cd08419 97 EPFLLR 102 (197)
T ss_pred CCcEEe
Confidence 777653
No 93
>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=25.41 E-value=1.2e+02 Score=29.56 Aligned_cols=87 Identities=23% Similarity=0.224 Sum_probs=52.8
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEE---eCCc-ceEEec--cCCCceEEEEEeecCCcceEEEEEEecC---CCccChh
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVIT---LDAT-EAVLGR--KNLNLRPILKEKYGNEKDLLAVAVVNKN---SKVKSLE 197 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~---ld~~-~~y~A~--~~~~L~pil~E~y~~~~~~~aVAVVkk~---s~~~~l~ 197 (458)
.++-+...+.....+++.+|++|+.. ++.. ..|... .+.++. ++...+. +. .++.+|-+.- .++.|++
T Consensus 30 ~v~~~~~~~~~~~~~al~~G~iD~~~~~w~~~~~~~~~~~~~~~~~~~-~l~~~~~-~~-~~g~~Vp~~~ae~~~i~si~ 106 (257)
T PF04069_consen 30 VVEVVNLGSTPVIFAALASGDIDIYPEEWTPTTYEAYKKALEEKLGVV-WLGPLGA-GN-TYGWAVPKYVAEKPGIKSIS 106 (257)
T ss_dssp EEEEEEESSHHHHHHHHHTTSSSEEEEEEETTTHHHHHHHHHHHHEEE-EEEEEEE-EE-EEEEEEEHHHHHHHT-SBGG
T ss_pred eEEEecCCchHHHHHHHHCCCCeEEhhhcCchhHHHHHHhhhhcCccc-cCCcccc-CC-EEEEEEecccccccCcccHH
Confidence 67777888889999999999999998 4332 112211 011121 1111111 11 1666665432 3789999
Q ss_pred hhcCCce----eeCC--CCCCCchH
Q psy11925 198 ELKGLKS----CHTA--YMRTTGWV 216 (458)
Q Consensus 198 dLkGkks----Chtg--~~~taGw~ 216 (458)
||++.+. +..+ +++..||.
T Consensus 107 dL~~~~~~~~~~~~~~~~~~~~g~~ 131 (257)
T PF04069_consen 107 DLAKPAEDLEFGGKGEFYGRPDGWG 131 (257)
T ss_dssp GGGTCGGGCEEEETTEEECSSTTHH
T ss_pred HHhhcccccccCCCCceeeCCCCcc
Confidence 9987776 5555 57788998
No 94
>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=24.88 E-value=4.8e+02 Score=22.93 Aligned_cols=73 Identities=19% Similarity=0.203 Sum_probs=41.1
Q ss_pred CCeEEEe-cCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC----ccChhhhc
Q psy11925 126 PPFECNR-EKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK----VKSLEELK 200 (458)
Q Consensus 126 p~v~Cv~-~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~----~~~l~dLk 200 (458)
|.++... ..+..+.++.+.+|++|++....... .....-.|+..| ..+.|++++.. ..++++|.
T Consensus 27 P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~~~~l~~~--------~~~lv~~~~h~~~~~~i~~~~l~ 95 (200)
T cd08465 27 PGIDLAVSQASREAMLAQVADGEIDLALGVFPEL---PEELHAETLFEE--------RFVCLADRATLPASGGLSLDAWL 95 (200)
T ss_pred CCcEEEEecCChHhHHHHHHCCCccEEEeccccC---CcCeeEEEeeec--------cEEEEEeCCCCccCCCcCHHHHh
Confidence 5544333 24678899999999999998643221 011222333221 33455555542 24678888
Q ss_pred CCceeeCCC
Q psy11925 201 GLKSCHTAY 209 (458)
Q Consensus 201 GkksChtg~ 209 (458)
+.+......
T Consensus 96 ~~~~i~~~~ 104 (200)
T cd08465 96 ARPHVLVAM 104 (200)
T ss_pred hCCcEEEec
Confidence 876555443
No 95
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=24.62 E-value=4.6e+02 Score=22.60 Aligned_cols=72 Identities=17% Similarity=0.126 Sum_probs=39.9
Q ss_pred CCeEEEec-CCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhh
Q psy11925 126 PPFECNRE-KSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEEL 199 (458)
Q Consensus 126 p~v~Cv~~-~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dL 199 (458)
|.++.... .+..+.++.+.+|++|++...... .......+++..+ ..+.|+.++.+ ..++++|
T Consensus 27 P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~~~~l~~~--------~~~~v~~~~hpl~~~~~~~~~~l 95 (199)
T cd08426 27 PGVFFTVDVASTADVLEAVLSGEADIGLAFSPP---PEPGIRVHSRQPA--------PIGAVVPPGHPLARQPSVTLAQL 95 (199)
T ss_pred CCeEEEEEeCCcHHHHHHHHCCCccEEEecCCC---CCCCeEEEeeccC--------cEEEEecCCCCcccCCccCHHHH
Confidence 54443332 356889999999999998853221 0011111222111 23444555432 2468899
Q ss_pred cCCceeeCC
Q psy11925 200 KGLKSCHTA 208 (458)
Q Consensus 200 kGkksChtg 208 (458)
++.+.....
T Consensus 96 ~~~~~i~~~ 104 (199)
T cd08426 96 AGYPLALPP 104 (199)
T ss_pred hCCCeEecC
Confidence 988877643
No 96
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=24.44 E-value=6.8e+02 Score=24.55 Aligned_cols=102 Identities=12% Similarity=0.048 Sum_probs=54.8
Q ss_pred CCCceEEEeCChhHHh-HHHHHHHHHhcCCCCCCeEEEe-cCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEE
Q psy11925 95 PIKPIRWCVSSPEGMS-KCLAFKDAAFSRDIRPPFECNR-EKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILK 172 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~-KC~~l~~~~~~~~~~p~v~Cv~-~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~ 172 (458)
+.+.+|+++....... =.+.+.. +.. -.|.+.-.. ..+..+.++.+.+|++|+++...... ......-.|+..
T Consensus 91 ~~g~l~Ig~~~~~~~~~l~~~l~~-~~~--~~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~l~~~~l~~ 165 (309)
T PRK12682 91 DSGTLTIATTHTQARYVLPRVVAA-FRK--RYPKVNLSLHQGSPDEIARMVISGEADIGIATESLA--DDPDLATLPCYD 165 (309)
T ss_pred CCCeEEEeeCchHHHHHHHHHHHH-HHH--hCCCeEEEEecCCHHHHHHHHHcCCccEEEecCccc--CCCcceEEEeee
Confidence 4567999998764322 1222332 111 236555544 33578999999999999998532110 011122233322
Q ss_pred EeecCCcceEEEEEEecCCC-----ccChhhhcCCceeeCCC
Q psy11925 173 EKYGNEKDLLAVAVVNKNSK-----VKSLEELKGLKSCHTAY 209 (458)
Q Consensus 173 E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkGkksChtg~ 209 (458)
+ -.+.|+.++.+ ..+++||.+-+.-+...
T Consensus 166 ~--------~~~~~~~~~~pl~~~~~~~~~~L~~~~~i~~~~ 199 (309)
T PRK12682 166 W--------QHAVIVPPDHPLAQEERITLEDLAEYPLITYHP 199 (309)
T ss_pred e--------eEEEEecCCCccccCCCcCHHHHhcCCceeeCC
Confidence 2 22334444432 24678888777766543
No 97
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=24.29 E-value=7e+02 Score=24.64 Aligned_cols=58 Identities=17% Similarity=0.121 Sum_probs=32.3
Q ss_pred CCC-ceEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeC
Q psy11925 95 PIK-PIRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLD 154 (458)
Q Consensus 95 p~~-~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld 154 (458)
+.. ++|+++.......-=..+-..+. ...|.+.........+.++.+.+|++|++++.
T Consensus 94 ~~~~~l~I~~~~~~~~~~~~~~l~~f~--~~~P~v~v~i~~~~~~~~~~l~~g~~D~~i~~ 152 (319)
T PRK10216 94 PRGLKFELAAESPLMMIMLNALSKRIY--QRYPQATIKLRNWDYDSLDAITRGEVDIGFTG 152 (319)
T ss_pred ccCCEEEEEecchhHHHHHHHHHHHHH--HHCCCCEEEEEeCCcchHHHHhcCCccEEEec
Confidence 445 69999887642211111112122 12354333333222357999999999998874
No 98
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=24.12 E-value=6e+02 Score=25.14 Aligned_cols=103 Identities=15% Similarity=0.044 Sum_probs=54.1
Q ss_pred CCCceEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEe
Q psy11925 95 PIKPIRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEK 174 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~ 174 (458)
+.+++|+++....-..-=..+...+....-...+.... .+..++++.+.+|++|++........ ...+.-.|+..+
T Consensus 91 ~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~l~~~~-~~~~~~~~~L~~g~~D~~i~~~~~~~--~~~l~~~~l~~~- 166 (313)
T PRK12684 91 DQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQ-GSPTQIAEMVLHGQADLAIATEAIAD--YKELVSLPCYQW- 166 (313)
T ss_pred CCCeEEEEechHHHHHHhHHHHHHHHHHCCCceEEEEe-CChHHHHHHHHCCCcCEEEeecCCCC--CCCceEEEeccc-
Confidence 45679999987653332112222222211112344433 46899999999999999986421100 011112222111
Q ss_pred ecCCcceEEEEEEecCCCc-----cChhhhcCCceeeCC
Q psy11925 175 YGNEKDLLAVAVVNKNSKV-----KSLEELKGLKSCHTA 208 (458)
Q Consensus 175 y~~~~~~~aVAVVkk~s~~-----~~l~dLkGkksChtg 208 (458)
..+.|+.++.+. .+++||.+-+.-...
T Consensus 167 -------~~~~v~~~~~pl~~~~~i~~~dL~~~~~i~~~ 198 (313)
T PRK12684 167 -------NHCVVVPPDHPLLERKPLTLEDLAQYPLITYD 198 (313)
T ss_pred -------eEEEEeCCCCccccCCCcCHHHHhcCCcEecC
Confidence 234556665532 367888887766543
No 99
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=23.84 E-value=4.9e+02 Score=25.93 Aligned_cols=95 Identities=11% Similarity=0.081 Sum_probs=52.8
Q ss_pred CCCceEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEe
Q psy11925 95 PIKPIRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEK 174 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~ 174 (458)
+.++||+++.......-=..+-..+ ....|.+.+... ...+.++.|.+|++|+++..... ....+.-+|+..|
T Consensus 115 ~~~~l~Ig~~~~~~~~~l~~~l~~f--~~~~P~i~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~~~~l~~~- 187 (317)
T PRK11482 115 KQRTITIATTPSVGALVMPVIYQAI--KTHYPQLLLRNI-PISDAENQLSQFQTDLIIDTHSC---SNRTIQHHVLFTD- 187 (317)
T ss_pred CCceEEEEecHHHHHHHHHHHHHHH--HHHCCCCEEEEe-cchhHHHHHHCCCcCEEEeccCC---CCCceEEEEEecC-
Confidence 3467999999865442111111111 123477887544 34689999999999999854321 1122223343221
Q ss_pred ecCCcceEEEEEEecCCC----ccChhhhcCCc
Q psy11925 175 YGNEKDLLAVAVVNKNSK----VKSLEELKGLK 203 (458)
Q Consensus 175 y~~~~~~~aVAVVkk~s~----~~~l~dLkGkk 203 (458)
-.+.|+.++.+ ..+++||++-+
T Consensus 188 -------~~~lv~~~~hpl~~~~~~~~dL~~~~ 213 (317)
T PRK11482 188 -------NVVLVCRQGHPLLSLEDDEETLDNAE 213 (317)
T ss_pred -------cEEEEEeCCCCccCCCCCHHHHhhCC
Confidence 23445565543 24788888754
No 100
>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=23.68 E-value=4.8e+02 Score=22.48 Aligned_cols=30 Identities=13% Similarity=0.295 Sum_probs=22.0
Q ss_pred CCCeEEEec-CCHHHHHHHHHcCCccEEEeC
Q psy11925 125 RPPFECNRE-KSSKVCLKLIADGAADVITLD 154 (458)
Q Consensus 125 ~p~v~Cv~~-~s~~~Ci~~I~~g~AD~~~ld 154 (458)
.|.++.... .+..++++.+.+|++|++...
T Consensus 26 ~P~v~i~~~~~~~~~~~~~l~~~~~Dl~i~~ 56 (185)
T cd08439 26 YPRLAIEVVCKRTPRLMEMLERGEVDLALIT 56 (185)
T ss_pred CCCeEEEEEECChHHHHHHHHCCCCcEEEEe
Confidence 355444433 357899999999999998864
No 101
>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=23.66 E-value=4.6e+02 Score=22.29 Aligned_cols=68 Identities=22% Similarity=0.258 Sum_probs=38.7
Q ss_pred eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcCC
Q psy11925 128 FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKGL 202 (458)
Q Consensus 128 v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkGk 202 (458)
++.... +..+.++.+.+|++|+++...... .....-.++..+ ..+.|+.++.+ ..+++||.+.
T Consensus 31 i~i~~~-~~~~~~~~l~~~~~Dl~i~~~~~~---~~~l~~~~l~~~--------~~~~v~~~~~~l~~~~~~~~~~l~~~ 98 (195)
T cd08434 31 FELHQG-STDELLDDLKNGELDLALCSPVPD---EPDIEWIPLFTE--------ELVLVVPKDHPLAGRDSVDLAELADE 98 (195)
T ss_pred EEEecC-cHHHHHHHHHcCCccEEEEccCCC---CCCeeEEEeecc--------eEEEEecCCCccccCCccCHHHhcCC
Confidence 444433 467899999999999998643221 111222233222 23444555442 2378889887
Q ss_pred ceeeC
Q psy11925 203 KSCHT 207 (458)
Q Consensus 203 ksCht 207 (458)
+....
T Consensus 99 ~~i~~ 103 (195)
T cd08434 99 PFVLL 103 (195)
T ss_pred ceEEe
Confidence 76654
No 102
>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=23.29 E-value=4.9e+02 Score=22.44 Aligned_cols=71 Identities=11% Similarity=0.063 Sum_probs=39.7
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC----ccChhhhcCC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK----VKSLEELKGL 202 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~----~~~l~dLkGk 202 (458)
.++.+. .+..+.++.+.+|++|++..-+... ...+...++..|. + +.|+.++.+ ..++++|.+.
T Consensus 30 ~l~i~~-~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~~~~l~~~~-------~-~~v~~~~~~~~~~~~~~~~l~~~ 97 (200)
T cd08464 30 RLVFRQ-VDPFNVGDMLDRGEIDLAIGVFGEL---PAWLKREVLYTEG-------Y-ACLFDPQQLSLSAPLTLEDYVAR 97 (200)
T ss_pred EEEEec-CCcccHHHHHhcCcccEEEecCCCC---cccceeeeecccc-------e-EEEEeCCCccccCCCCHHHHhcC
Confidence 355544 3567899999999999998643221 1222333343221 3 344444432 2467888877
Q ss_pred ceeeCCC
Q psy11925 203 KSCHTAY 209 (458)
Q Consensus 203 ksChtg~ 209 (458)
.......
T Consensus 98 ~~i~~~~ 104 (200)
T cd08464 98 PHVLVSY 104 (200)
T ss_pred CcEEecC
Confidence 6654433
No 103
>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=22.15 E-value=1e+02 Score=27.94 Aligned_cols=53 Identities=19% Similarity=0.141 Sum_probs=36.1
Q ss_pred eEEEeCChhHHhHHHHHHHHHhcCCCCCCeEEEecCCHHHHHHHHHcCCccEEEeCCcce
Q psy11925 99 IRWCVSSPEGMSKCLAFKDAAFSRDIRPPFECNREKSSKVCLKLIADGAADVITLDATEA 158 (458)
Q Consensus 99 vrwCv~s~~E~~KC~~l~~~~~~~~~~p~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~ 158 (458)
.|+|++...-. -..+...... .++-+...|.+++++++.+|++|++..+...+
T Consensus 111 ~~i~~~~g~~~--~~~l~~~~~~-----~~~~~~~~~~~~~~~~l~~g~~d~~i~~~~~~ 163 (225)
T PF00497_consen 111 KRIGVVRGSSY--ADYLKQQYPS-----NINIVEVDSPEEALEALLSGRIDAFIVDESTA 163 (225)
T ss_dssp SEEEEETTSHH--HHHHHHHTHH-----TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHH
T ss_pred cccccccchhH--HHHhhhhccc-----hhhhcccccHHHHHHHHhcCCeeeeeccchhh
Confidence 58998876432 2223321100 34455678999999999999999999877655
No 104
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=21.60 E-value=1.2e+02 Score=28.18 Aligned_cols=81 Identities=27% Similarity=0.279 Sum_probs=49.4
Q ss_pred HHHHHHHHcCCccEEEeCCcceEEec-cCCCceEEEEEeecCCcceEEEEEEecCCCccChhhhc-CCceeeCCCCCCCc
Q psy11925 137 KVCLKLIADGAADVITLDATEAVLGR-KNLNLRPILKEKYGNEKDLLAVAVVNKNSKVKSLEELK-GLKSCHTAYMRTTG 214 (458)
Q Consensus 137 ~~Ci~~I~~g~AD~~~ld~~~~y~A~-~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~~~l~dLk-GkksChtg~~~taG 214 (458)
.|--.-+..|.+|+.+.+-+-+...+ ...++.-++- .+-+....+|| |+++..+.+++||+ |+|..- .|
T Consensus 4 ~DIp~yV~~G~~DlGI~G~D~l~E~~~~~~~v~~~~d--L~fg~crl~vA-vp~~~~~~~~~~l~~~~rIAT-ky----- 74 (163)
T PF01634_consen 4 QDIPTYVEDGIADLGITGKDVLLESGLGRADVEELLD--LGFGKCRLVVA-VPEDWPYKSVEDLKAGLRIAT-KY----- 74 (163)
T ss_dssp GHHHHHHHTTSSSEEEEEHHHHHHHTHH-SSEEEEEE--ESCSEEEEEEE-EETTSCGCCGGGGSSTEEEEE-S------
T ss_pred HHHHHHHHCCCCcEEEeehheeccCCCCccceEEEee--cccccEEEEEE-EECCcCCCCHHHhccCCEEEE-CC-----
Confidence 45667889999999998877665553 1123333332 22222226666 67777788999999 777643 23
Q ss_pred hHHHHHHHHHcC
Q psy11925 215 WVAPVYNLLEKG 226 (458)
Q Consensus 215 w~~Pv~~L~~~~ 226 (458)
.++--.+|.++|
T Consensus 75 p~l~~~yf~~~g 86 (163)
T PF01634_consen 75 PNLTRRYFAEKG 86 (163)
T ss_dssp HHHHHHHHHHCT
T ss_pred HHHHHHHHHHcC
Confidence 344455666666
No 105
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=21.59 E-value=2.6e+02 Score=24.38 Aligned_cols=71 Identities=14% Similarity=0.126 Sum_probs=41.1
Q ss_pred eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCCc----cChhhhcCCc
Q psy11925 128 FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSKV----KSLEELKGLK 203 (458)
Q Consensus 128 v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~~----~~l~dLkGkk 203 (458)
++.... +..+-++.+.+|++|++....... .....-+|+..+ -.+.|+.++.+. .+++||++.+
T Consensus 31 v~i~~~-~~~~~~~~l~~g~~D~~i~~~~~~---~~~l~~~~l~~~--------~~~~v~~~~~~l~~~~i~~~~L~~~~ 98 (201)
T cd08459 31 IETVRL-PVDELEEALESGEIDLAIGYLPDL---GAGFFQQRLFRE--------RYVCLVRKDHPRIGSTLTLEQFLAAR 98 (201)
T ss_pred EEEEec-CccCHHHHhhCCCceEEEEcCCCC---cccceEEEeecC--------ceEEEEcCCCccccCCcCHHHHhhCC
Confidence 444433 345778999999999998643211 112222333322 234455555432 3789999988
Q ss_pred eeeCCCC
Q psy11925 204 SCHTAYM 210 (458)
Q Consensus 204 sChtg~~ 210 (458)
......+
T Consensus 99 ~i~~~~~ 105 (201)
T cd08459 99 HVVVSAS 105 (201)
T ss_pred cEEEccC
Confidence 8876543
No 106
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=21.37 E-value=4.9e+02 Score=25.47 Aligned_cols=80 Identities=16% Similarity=0.021 Sum_probs=45.0
Q ss_pred CCCeEEEecCCHHHHHHHHHcCC-ccEEEeCCcc-eEEeccCCCce-EEEEEeecCCcce-EEEEEEecCCCc-------
Q psy11925 125 RPPFECNREKSSKVCLKLIADGA-ADVITLDATE-AVLGRKNLNLR-PILKEKYGNEKDL-LAVAVVNKNSKV------- 193 (458)
Q Consensus 125 ~p~v~Cv~~~s~~~Ci~~I~~g~-AD~~~ld~~~-~y~A~~~~~L~-pil~E~y~~~~~~-~aVAVVkk~s~~------- 193 (458)
+..|.-..+.|- .-++.|.+|. +|++..+... +..+.. -++. +.-...+. . ..|.+|+++++.
T Consensus 53 g~~v~~~~~~Sg-~l~~qi~~g~~~Dv~~~a~~~~~~~l~~-~gl~~~~~~~~~a----~n~lvl~~~~~~~~~~i~~~~ 126 (257)
T PRK10677 53 GVDVVSSFASSS-TLARQIEQGAPADLFISADQKWMDYAVD-KKAIDTATRYTLL----GNSLVVVAPKASEQKDFTIDK 126 (257)
T ss_pred CCeEEEEecccH-HHHHHHHcCCCCCEEEECCHHHHHHHHH-CCCCCCcchheee----cCEEEEEEECCCccccccccC
Confidence 346776666654 7778888887 9999877632 222211 2221 21000111 1 557777887532
Q ss_pred -cChhhh-cCCceeeCCCC
Q psy11925 194 -KSLEEL-KGLKSCHTAYM 210 (458)
Q Consensus 194 -~~l~dL-kGkksChtg~~ 210 (458)
.+|+|| ++.|...+++.
T Consensus 127 ~~~~~dLl~~~~iai~dP~ 145 (257)
T PRK10677 127 KTDWKSLLNGGRLAVGDPD 145 (257)
T ss_pred ccCHHHhcCCCeEEEcCCC
Confidence 368887 45567777765
No 107
>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=20.96 E-value=5.5e+02 Score=22.17 Aligned_cols=73 Identities=18% Similarity=0.206 Sum_probs=40.9
Q ss_pred CCeEEEec-CCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhh
Q psy11925 126 PPFECNRE-KSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEEL 199 (458)
Q Consensus 126 p~v~Cv~~-~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dL 199 (458)
|.+.-... .+..+.++.+.+|++|++...+... ...+.-+++..| .-+.|+.++.+ ..+++||
T Consensus 28 P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~~~~l~~~--------~~~~v~~~~~pl~~~~~~~~~~l 96 (200)
T cd08411 28 PKLRLYLREDQTERLLEKLRSGELDAALLALPVD---EPGLEEEPLFDE--------PFLLAVPKDHPLAKRKSVTPEDL 96 (200)
T ss_pred CCcEEEEEeCcHHHHHHHHHcCCccEEEEeccCC---CCCceEEEeecc--------ceEEEecCCCCccccCccCHHHH
Confidence 55443333 3678999999999999998533211 011222333222 23444455432 2478899
Q ss_pred cCCceeeCCC
Q psy11925 200 KGLKSCHTAY 209 (458)
Q Consensus 200 kGkksChtg~ 209 (458)
.+.+.-....
T Consensus 97 ~~~~~i~~~~ 106 (200)
T cd08411 97 AGERLLLLEE 106 (200)
T ss_pred cCCceEecCC
Confidence 8887665433
No 108
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=20.57 E-value=8.3e+02 Score=24.11 Aligned_cols=114 Identities=11% Similarity=0.024 Sum_probs=58.9
Q ss_pred CCCceEEEeCChhHHhHHHHHHHHHhcCCCCCC--eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEE
Q psy11925 95 PIKPIRWCVSSPEGMSKCLAFKDAAFSRDIRPP--FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILK 172 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~KC~~l~~~~~~~~~~p~--v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~ 172 (458)
..+++|+++.......-=..+-..+.. ..|. +++.. .+..+.++++.+|++|++......... ....-.|+..
T Consensus 91 ~~g~l~Ig~~~~~~~~~l~~~i~~f~~--~~P~i~l~~~~-~~~~~~~~~L~~~~~D~~i~~~~~~~~--~~l~~~~l~~ 165 (309)
T PRK12683 91 DSGHLTVATTHTQARYALPKVVRQFKE--VFPKVHLALRQ-GSPQEIAEMLLNGEADIGIATEALDRE--PDLVSFPYYS 165 (309)
T ss_pred CCceEEEEeccchHHHHHHHHHHHHHH--HCCCceEEEEe-CCHHHHHHHHHcCCccEEEecCCCCCC--CCceEEEccc
Confidence 456799999764321111111111211 1254 55544 368999999999999998753211000 1111122221
Q ss_pred EeecCCcceEEEEEEecCCCc-----cChhhhcCCceeeCCCCCCCchHHHHHHHH
Q psy11925 173 EKYGNEKDLLAVAVVNKNSKV-----KSLEELKGLKSCHTAYMRTTGWVAPVYNLL 223 (458)
Q Consensus 173 E~y~~~~~~~aVAVVkk~s~~-----~~l~dLkGkksChtg~~~taGw~~Pv~~L~ 223 (458)
+ ..+.|+.++.+. .++++|++-+.-.... ..+...++..+.
T Consensus 166 ~--------~~~~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~--~~~~~~~~~~~~ 211 (309)
T PRK12683 166 W--------HHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQ--GFTGRSRIDQAF 211 (309)
T ss_pred C--------eEEEEecCCCCcccCCccCHHHHhcCCeEeccC--CCcHHHHHHHHH
Confidence 1 335566766543 4688888777665433 334444444333
No 109
>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=20.55 E-value=2.8e+02 Score=26.45 Aligned_cols=97 Identities=20% Similarity=0.155 Sum_probs=52.2
Q ss_pred CCCceEEEeCChhHHhHHHHHHHHHhc-CCCCCC--eEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEE
Q psy11925 95 PIKPIRWCVSSPEGMSKCLAFKDAAFS-RDIRPP--FECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPIL 171 (458)
Q Consensus 95 p~~~vrwCv~s~~E~~KC~~l~~~~~~-~~~~p~--v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil 171 (458)
..+++|+++.... .+...... ....|. ++... .+..+.++.+.+|++|++...... ....+..+|+.
T Consensus 85 ~~~~l~ig~~~~~------~~~~~l~~~~~~~p~v~l~i~~-~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~~~~l~ 154 (279)
T TIGR03339 85 REGSLRIAATAPY------YVLDLVARFRQRYPGIEVSVRI-GNSQEVLQALQSYRVDVAVSSEVV---DDPRLDRVVLG 154 (279)
T ss_pred cceEEEEeCchHH------HHHHHHHHHHHHCCCcEEEEEE-CCHHHHHHHHHcCCCcEEEEeccc---CCCceEEEEcC
Confidence 4467999987432 22221111 012354 44443 367899999999999999863221 11112223332
Q ss_pred EEeecCCcceEEEEEEecCCC-----ccChhhhcCCceeeCCC
Q psy11925 172 KEKYGNEKDLLAVAVVNKNSK-----VKSLEELKGLKSCHTAY 209 (458)
Q Consensus 172 ~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkGkksChtg~ 209 (458)
.+ ..+.|+.++.+ ..+++||++.+.-....
T Consensus 155 ~~--------~~~lv~s~~~pl~~~~~i~~~~L~~~~~i~~~~ 189 (279)
T TIGR03339 155 ND--------PLVAVVHRQHPLAERESVTLEELAGQPLLMREP 189 (279)
T ss_pred Cc--------eEEEEECCCCccccCCCcCHHHHhCCCeEEecC
Confidence 22 23334444432 24788999887766443
No 110
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=20.46 E-value=5e+02 Score=25.54 Aligned_cols=116 Identities=22% Similarity=0.235 Sum_probs=65.8
Q ss_pred HHHHHHcCCccEEEe---CCcc-eEEe--ccCCCce-EEEEEeecCCcceEEEEEEecCC--CccChhhhcCCceeeCCC
Q psy11925 139 CLKLIADGAADVITL---DATE-AVLG--RKNLNLR-PILKEKYGNEKDLLAVAVVNKNS--KVKSLEELKGLKSCHTAY 209 (458)
Q Consensus 139 Ci~~I~~g~AD~~~l---d~~~-~y~A--~~~~~L~-pil~E~y~~~~~~~aVAVVkk~s--~~~~l~dLkGkksChtg~ 209 (458)
=+-+|+.|+||++.+ |.+. .|-. -+++... .++.--|.. ...+.| +++. ++.+|+||.++..=+-.-
T Consensus 30 G~~~i~~G~adiag~hlld~~~g~ynip~v~~~~~~~~~LI~g~~R---e~Gl~v-~~gnpk~i~~~edl~~~d~~fVNR 105 (223)
T COG1910 30 GLLAIKRGEADIAGIHLLDNESGTYNIPYVKKYLPGEAVLIRGYLR---EQGLMV-QKGNPKNISSLEDLLRKDLRFVNR 105 (223)
T ss_pred chHhhhhcccceeeeeeccCCCCceehhhhhhcCCCceEEEeeeee---eeeeEE-ecCCCCccccHHHHhhcCcEEEec
Confidence 356788999999863 3311 1111 0222221 111111110 044444 4444 358999999998888777
Q ss_pred CCCCchHHHHHHHHHc-CCCCCCCCccccccccccccCcccCCCCccccCCCchhhhhCCCCCCCChh-hhhhcccCCCc
Q psy11925 210 MRTTGWVAPVYNLLEK-GLIKKDSCPYYKGVAEFFTGGSCVPGIDEEEKDAPASLEKICPKATRVTYT-PLQCLKSGDGD 287 (458)
Q Consensus 210 ~~taGw~~Pv~~L~~~-~~i~~~~c~~~~~~~~FFsg~sC~pG~~~~~~~~~~~LC~lC~g~~~CGy~-A~rCL~eg~GD 287 (458)
+|.+|=.+-+-.++.+ ++++ . + ++|+.... + .|. +=+.++.|+.|
T Consensus 106 ~rGSGTR~LlD~~L~~~~~~~-~--------------~--I~GY~~e~-----~-----------th~avA~aVa~G~AD 152 (223)
T COG1910 106 NRGSGTRILLDELLGELNILP-D--------------S--IKGYSDEA-----T-----------THDAVASAVASGRAD 152 (223)
T ss_pred CCCccHHHHHHHHHHHcCcCc-h--------------h--cCCccccc-----c-----------ccHHHHHHHHcCCCC
Confidence 8889988877666654 3222 1 1 55653321 0 355 66788899999
Q ss_pred EEEE
Q psy11925 288 VAFI 291 (458)
Q Consensus 288 VAFv 291 (458)
+.+-
T Consensus 153 ~GvG 156 (223)
T COG1910 153 AGVG 156 (223)
T ss_pred cccc
Confidence 9887
No 111
>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=20.26 E-value=5.9e+02 Score=22.28 Aligned_cols=73 Identities=12% Similarity=0.059 Sum_probs=40.3
Q ss_pred CCCeEEEec-CCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhh
Q psy11925 125 RPPFECNRE-KSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEE 198 (458)
Q Consensus 125 ~p~v~Cv~~-~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~d 198 (458)
.|.++.... .+..+.++.+++|++|+++..+... .....-+++..+. +. +|+.++.+ ..+++|
T Consensus 27 ~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~~~~~---~~~l~~~~l~~~~-------~~-~~~~~~~~~~~~~~v~~~~ 95 (198)
T cd08485 27 APSATVSLTQMSKNRQIEALDAGTIDIGFGRFYPY---QEGVVVRNVTNER-------LF-LGAQKSRARSFGEQVHCSA 95 (198)
T ss_pred CCCcEEEEEECCHHHHHHHHHcCCccEEEecCCCC---CCCeEEEEeeccc-------eE-EEeCCCCccccCCCcCHHH
Confidence 365444332 3667899999999999988653211 1111222332211 22 33443322 146889
Q ss_pred hcCCceeeCC
Q psy11925 199 LKGLKSCHTA 208 (458)
Q Consensus 199 LkGkksChtg 208 (458)
|++.+.....
T Consensus 96 L~~~~~i~~~ 105 (198)
T cd08485 96 LRNEPLILFP 105 (198)
T ss_pred HhcCCeEecC
Confidence 9988877643
No 112
>cd08457 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant h
Probab=20.20 E-value=5.7e+02 Score=22.09 Aligned_cols=71 Identities=20% Similarity=0.091 Sum_probs=39.4
Q ss_pred CeEEEecCCHHHHHHHHHcCCccEEEeCCcceEEeccCCCceEEEEEeecCCcceEEEEEEecCCC-----ccChhhhcC
Q psy11925 127 PFECNREKSSKVCLKLIADGAADVITLDATEAVLGRKNLNLRPILKEKYGNEKDLLAVAVVNKNSK-----VKSLEELKG 201 (458)
Q Consensus 127 ~v~Cv~~~s~~~Ci~~I~~g~AD~~~ld~~~~y~A~~~~~L~pil~E~y~~~~~~~aVAVVkk~s~-----~~~l~dLkG 201 (458)
.++.... +..+.++.+.+|++|+++.....- ......+++..+ . +. .++.++.+ ..+++||++
T Consensus 30 ~l~~~~~-~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~~~~l~~~-----~--~~-~~~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08457 30 HLSLMGL-SSSQVLEAVASGRADLGIADGPLE---ERQGFLIETRSL-----P--AV-VAVPMGHPLAQLDVVSPQDLAG 97 (196)
T ss_pred EEEEEec-CcHHHHHHHHcCCccEEEeccCCC---CCCcEEEEeccC-----C--eE-EEeeCCCccccCCccCHHHhCC
Confidence 3555443 457888999999999998643210 111112222111 1 33 33333322 247899999
Q ss_pred CceeeCCC
Q psy11925 202 LKSCHTAY 209 (458)
Q Consensus 202 kksChtg~ 209 (458)
.+..+...
T Consensus 98 ~~~i~~~~ 105 (196)
T cd08457 98 ERIITLEN 105 (196)
T ss_pred CceEecCC
Confidence 98887544
Done!