Query 011028
Match_columns 495
No_of_seqs 197 out of 595
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 07:17:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011028.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011028hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00272 DPH2 diphthamide bio 100.0 2E-118 4E-123 950.3 38.0 454 2-488 32-496 (496)
2 KOG2648 Diphthamide biosynthes 100.0 1E-109 3E-114 847.0 35.8 420 4-488 33-453 (453)
3 TIGR00322 diphth2_R diphthamid 100.0 2E-93 4.3E-98 728.3 34.6 328 4-376 2-330 (332)
4 TIGR03682 arCOG04112 arCOG0411 100.0 8E-86 1.7E-90 666.6 32.1 304 20-375 1-306 (308)
5 PF01866 Diphthamide_syn: Puta 100.0 6.3E-84 1.4E-88 655.5 26.4 304 28-376 1-307 (307)
6 COG1736 DPH2 Diphthamide synth 100.0 1.6E-75 3.4E-80 590.6 32.9 329 5-378 8-337 (347)
7 PF08901 DUF1847: Protein of u 83.7 1.9 4.2E-05 39.6 4.8 39 8-46 42-80 (157)
8 PRK09492 treR trehalose repres 74.8 9.7 0.00021 38.1 7.3 77 274-352 60-143 (315)
9 cd06280 PBP1_LacI_like_4 Ligan 71.4 7.5 0.00016 37.7 5.4 59 278-337 1-65 (263)
10 COG4887 Uncharacterized metal- 67.8 4.9 0.00011 36.7 2.9 39 8-46 53-91 (191)
11 cd06293 PBP1_LacI_like_11 Liga 66.8 11 0.00023 36.6 5.4 61 278-339 1-67 (269)
12 cd06289 PBP1_MalI_like Ligand- 65.5 13 0.00028 35.8 5.7 75 278-353 1-84 (268)
13 COG1609 PurR Transcriptional r 65.0 17 0.00037 37.5 6.7 63 272-335 54-122 (333)
14 PRK07188 nicotinate phosphorib 61.0 17 0.00038 38.0 5.9 42 290-331 261-307 (352)
15 cd06272 PBP1_hexuronate_repres 60.9 14 0.00029 35.7 4.9 74 278-353 1-79 (261)
16 cd06274 PBP1_FruR Ligand bindi 59.9 17 0.00038 35.0 5.5 75 278-353 1-83 (264)
17 TIGR02405 trehalos_R_Ecol treh 59.5 26 0.00057 35.1 6.9 64 273-337 56-125 (311)
18 cd06295 PBP1_CelR Ligand bindi 59.5 14 0.00031 35.9 4.8 64 275-338 2-75 (275)
19 cd06279 PBP1_LacI_like_3 Ligan 59.4 16 0.00034 36.0 5.1 61 278-339 1-68 (283)
20 cd01536 PBP1_ABC_sugar_binding 57.4 19 0.00041 34.3 5.2 75 278-354 1-86 (267)
21 PF00919 UPF0004: Uncharacteri 57.2 15 0.00032 31.2 3.8 70 261-332 21-97 (98)
22 cd06298 PBP1_CcpA_like Ligand- 55.7 23 0.00051 34.0 5.6 58 278-337 1-65 (268)
23 cd06315 PBP1_ABC_sugar_binding 55.3 16 0.00035 35.9 4.4 76 277-353 1-86 (280)
24 cd06271 PBP1_AglR_RafR_like Li 55.0 32 0.00069 33.0 6.4 77 278-354 1-88 (268)
25 cd06273 PBP1_GntR_like_1 This 54.9 16 0.00036 35.2 4.3 75 278-354 1-84 (268)
26 COG0622 Predicted phosphoester 54.6 18 0.00039 33.9 4.3 79 64-144 2-91 (172)
27 PRK10014 DNA-binding transcrip 53.0 51 0.0011 33.2 7.8 79 273-353 61-149 (342)
28 COG5136 U1 snRNP-specific prot 52.3 16 0.00036 33.6 3.5 66 260-340 29-94 (188)
29 cd06310 PBP1_ABC_sugar_binding 52.3 17 0.00036 35.3 3.9 62 278-339 1-69 (273)
30 PF00532 Peripla_BP_1: Peripla 51.8 17 0.00037 36.4 3.9 61 277-339 2-68 (279)
31 cd06277 PBP1_LacI_like_1 Ligan 51.6 41 0.00089 32.5 6.6 73 279-353 2-85 (268)
32 cd06270 PBP1_GalS_like Ligand 51.1 45 0.00097 32.2 6.7 60 278-339 1-67 (268)
33 PRK11303 DNA-binding transcrip 50.9 41 0.00088 33.8 6.6 63 273-337 58-127 (328)
34 TIGR02990 ectoine_eutA ectoine 50.8 58 0.0013 32.2 7.5 81 272-358 116-216 (239)
35 cd06281 PBP1_LacI_like_5 Ligan 50.6 29 0.00063 33.6 5.4 60 278-338 1-66 (269)
36 cd06283 PBP1_RegR_EndR_KdgR_li 50.2 48 0.001 31.7 6.8 74 278-353 1-83 (267)
37 cd06291 PBP1_Qymf_like Ligand 49.5 35 0.00077 32.8 5.7 59 278-337 1-65 (265)
38 PLN03241 magnesium chelatase s 49.3 11 0.00024 46.1 2.5 28 85-112 663-708 (1353)
39 cd01542 PBP1_TreR_like Ligand- 49.2 31 0.00067 33.0 5.2 74 278-353 1-83 (259)
40 PLN03069 magnesiumprotoporphyr 48.9 11 0.00025 45.6 2.5 28 85-112 600-645 (1220)
41 PRK14987 gluconate operon tran 48.7 40 0.00086 34.0 6.1 64 273-337 60-129 (331)
42 PRK11041 DNA-binding transcrip 48.4 60 0.0013 32.1 7.3 63 273-336 32-100 (309)
43 TIGR02417 fruct_sucro_rep D-fr 47.4 43 0.00093 33.6 6.2 62 274-336 58-125 (327)
44 cd01538 PBP1_ABC_xylose_bindin 47.1 20 0.00044 35.4 3.7 75 278-353 1-85 (288)
45 PRK12493 magnesium chelatase s 46.6 13 0.00027 45.6 2.4 28 85-112 587-632 (1310)
46 TIGR01753 flav_short flavodoxi 46.4 67 0.0015 27.9 6.6 55 279-338 1-55 (140)
47 PRK10703 DNA-binding transcrip 45.0 53 0.0011 33.2 6.4 64 272-336 55-124 (341)
48 PRK06703 flavodoxin; Provision 44.8 69 0.0015 28.6 6.5 55 278-337 3-57 (151)
49 PRK05723 flavodoxin; Provision 44.7 65 0.0014 29.4 6.3 55 278-337 2-56 (151)
50 cd06299 PBP1_LacI_like_13 Liga 44.6 62 0.0013 31.0 6.6 60 278-339 1-67 (265)
51 cd01574 PBP1_LacI Ligand-bindi 44.5 39 0.00084 32.4 5.1 62 278-339 1-68 (264)
52 cd06316 PBP1_ABC_sugar_binding 44.3 26 0.00057 34.6 4.0 75 278-352 1-85 (294)
53 PRK02126 ribonuclease Z; Provi 44.1 24 0.00052 36.7 3.7 34 62-95 241-274 (334)
54 PRK10653 D-ribose transporter 43.8 41 0.00089 33.3 5.3 63 274-337 24-92 (295)
55 PF00731 AIRC: AIR carboxylase 43.7 67 0.0014 29.5 6.1 72 278-352 2-82 (150)
56 PRK09526 lacI lac repressor; R 43.5 75 0.0016 32.0 7.3 62 274-335 61-128 (342)
57 PRK10423 transcriptional repre 43.5 81 0.0017 31.5 7.4 64 273-337 53-122 (327)
58 cd06290 PBP1_LacI_like_9 Ligan 43.3 44 0.00096 32.1 5.3 59 278-337 1-65 (265)
59 cd06297 PBP1_LacI_like_12 Liga 43.2 39 0.00084 32.9 4.9 62 278-339 1-67 (269)
60 cd06292 PBP1_LacI_like_10 Liga 43.1 55 0.0012 31.6 6.0 58 278-336 1-64 (273)
61 PRK13405 bchH magnesium chelat 42.2 17 0.00036 44.1 2.5 28 85-112 593-638 (1209)
62 TIGR02025 BchH magnesium chela 42.0 17 0.00036 44.2 2.4 28 85-112 573-618 (1216)
63 TIGR01481 ccpA catabolite cont 41.8 79 0.0017 31.7 7.1 63 274-337 57-125 (329)
64 cd06284 PBP1_LacI_like_6 Ligan 41.3 70 0.0015 30.5 6.4 58 279-337 2-65 (267)
65 cd06285 PBP1_LacI_like_7 Ligan 41.3 48 0.001 31.9 5.2 60 278-338 1-66 (265)
66 COG2984 ABC-type uncharacteriz 41.2 1E+02 0.0022 31.9 7.5 110 263-378 145-265 (322)
67 cd06286 PBP1_CcpB_like Ligand- 41.0 47 0.001 31.8 5.1 59 278-338 1-66 (260)
68 cd06282 PBP1_GntR_like_2 Ligan 41.0 52 0.0011 31.4 5.4 75 278-354 1-85 (266)
69 TIGR02257 cobalto_cobN cobalto 40.9 18 0.0004 43.5 2.5 28 85-112 535-580 (1122)
70 PRK05989 cobN cobaltochelatase 40.7 18 0.00039 44.1 2.4 28 85-112 541-586 (1244)
71 PRK09004 FMN-binding protein M 40.7 73 0.0016 28.7 5.9 53 278-337 3-55 (146)
72 COG1429 CobN Cobalamin biosynt 40.2 18 0.00039 44.5 2.4 26 87-112 554-597 (1388)
73 cd01545 PBP1_SalR Ligand-bindi 39.5 91 0.002 29.8 6.9 59 278-337 1-66 (270)
74 PRK08105 flavodoxin; Provision 39.2 69 0.0015 29.0 5.6 41 277-318 2-42 (149)
75 COG1234 ElaC Metal-dependent h 39.0 29 0.00062 35.3 3.3 29 62-94 189-217 (292)
76 PRK12321 cobN cobaltochelatase 38.7 20 0.00043 43.1 2.3 28 85-112 522-567 (1100)
77 PF02514 CobN-Mg_chel: CobN/Ma 38.5 31 0.00067 41.6 3.9 93 239-335 716-817 (1098)
78 cd06278 PBP1_LacI_like_2 Ligan 38.5 75 0.0016 30.3 6.1 61 278-338 1-65 (266)
79 cd06318 PBP1_ABC_sugar_binding 38.4 41 0.00089 32.7 4.3 75 278-353 1-85 (282)
80 TIGR00640 acid_CoA_mut_C methy 38.4 43 0.00093 29.9 3.9 70 269-341 45-119 (132)
81 cd06296 PBP1_CatR_like Ligand- 38.1 92 0.002 29.9 6.7 59 278-337 1-65 (270)
82 PF00885 DMRL_synthase: 6,7-di 37.2 76 0.0016 28.9 5.4 60 277-336 4-71 (144)
83 PRK07308 flavodoxin; Validated 37.1 1.3E+02 0.0029 26.7 7.0 57 278-339 3-59 (146)
84 COG2185 Sbm Methylmalonyl-CoA 35.7 48 0.001 30.2 3.8 55 271-326 57-112 (143)
85 cd05569 PTS_IIB_fructose PTS_I 35.5 1.2E+02 0.0027 25.2 6.1 59 279-340 2-66 (96)
86 cd01575 PBP1_GntR Ligand-bindi 35.5 70 0.0015 30.6 5.3 61 278-339 1-67 (268)
87 PF01729 QRPTase_C: Quinolinat 35.2 45 0.00097 31.2 3.7 63 269-335 92-156 (169)
88 PF00258 Flavodoxin_1: Flavodo 34.7 71 0.0015 28.0 4.8 54 281-337 1-54 (143)
89 cd06307 PBP1_uncharacterized_s 34.7 37 0.0008 33.0 3.2 76 278-353 1-88 (275)
90 PRK10339 DNA-binding transcrip 34.5 74 0.0016 32.0 5.5 58 275-336 62-123 (327)
91 PRK05569 flavodoxin; Provision 34.4 1.5E+02 0.0033 25.9 6.9 56 278-338 3-58 (141)
92 cd01571 NAPRTase_B Nicotinate 33.5 81 0.0017 32.3 5.5 55 277-331 211-270 (302)
93 TIGR00288 conserved hypothetic 33.1 1.4E+02 0.003 27.7 6.5 53 274-335 104-156 (160)
94 cd06302 PBP1_LsrB_Quorum_Sensi 32.9 75 0.0016 31.6 5.2 59 278-336 1-65 (298)
95 KOG0781 Signal recognition par 32.9 2.1E+02 0.0045 31.5 8.5 70 268-338 457-542 (587)
96 cd01473 vWA_CTRP CTRP for CS 32.3 1.3E+02 0.0027 28.4 6.3 50 276-326 108-159 (192)
97 TIGR01579 MiaB-like-C MiaB-lik 32.3 47 0.001 35.3 3.8 65 267-332 25-92 (414)
98 PRK08662 nicotinate phosphorib 32.2 70 0.0015 33.4 4.9 55 277-331 227-285 (343)
99 PF03698 UPF0180: Uncharacteri 31.8 1E+02 0.0022 25.2 4.8 56 296-358 11-72 (80)
100 COG0716 FldA Flavodoxins [Ener 31.7 1.4E+02 0.003 26.8 6.3 59 277-339 2-60 (151)
101 PF04392 ABC_sub_bind: ABC tra 31.6 1.3E+02 0.0029 30.1 6.8 113 261-378 115-237 (294)
102 cd06275 PBP1_PurR Ligand-bindi 31.5 1.5E+02 0.0033 28.3 7.0 60 278-338 1-66 (269)
103 cd06321 PBP1_ABC_sugar_binding 31.1 60 0.0013 31.3 4.1 59 278-336 1-66 (271)
104 cd02071 MM_CoA_mut_B12_BD meth 31.1 1.1E+02 0.0024 26.5 5.4 62 273-338 48-113 (122)
105 TIGR01754 flav_RNR ribonucleot 30.3 97 0.0021 27.4 4.9 57 278-337 2-59 (140)
106 PRK10936 TMAO reductase system 29.9 75 0.0016 32.6 4.7 63 275-337 45-114 (343)
107 cd01543 PBP1_XylR Ligand-bindi 29.7 88 0.0019 30.1 5.0 56 278-336 1-59 (265)
108 PRK09426 methylmalonyl-CoA mut 29.5 85 0.0018 36.2 5.4 73 269-342 625-700 (714)
109 PRK14571 D-alanyl-alanine synt 29.1 1.7E+02 0.0036 29.4 7.0 76 278-354 2-85 (299)
110 cd06319 PBP1_ABC_sugar_binding 28.9 1E+02 0.0022 29.6 5.3 74 278-353 1-85 (277)
111 PRK09271 flavodoxin; Provision 28.7 1.8E+02 0.0039 26.5 6.5 58 278-337 2-60 (160)
112 cd06312 PBP1_ABC_sugar_binding 28.1 1.1E+02 0.0024 29.6 5.4 60 278-337 1-67 (271)
113 cd06305 PBP1_methylthioribose_ 28.1 1.1E+02 0.0023 29.5 5.3 58 278-336 1-64 (273)
114 PRK08091 ribulose-phosphate 3- 28.0 1.8E+02 0.0038 28.7 6.6 59 275-333 140-206 (228)
115 cd01537 PBP1_Repressors_Sugar_ 27.9 1.2E+02 0.0027 28.3 5.6 74 278-353 1-84 (264)
116 cd06300 PBP1_ABC_sugar_binding 27.7 1.2E+02 0.0025 29.3 5.4 76 278-353 1-90 (272)
117 PRK10727 DNA-binding transcrip 27.4 2.1E+02 0.0045 28.9 7.5 63 274-337 57-125 (343)
118 cd06325 PBP1_ABC_uncharacteriz 27.3 1.4E+02 0.0031 28.7 6.0 75 278-354 1-87 (281)
119 cd06294 PBP1_ycjW_transcriptio 27.3 1.3E+02 0.0028 28.8 5.6 59 278-336 1-69 (270)
120 PRK05568 flavodoxin; Provision 27.1 2.4E+02 0.0053 24.6 7.0 56 278-338 3-58 (142)
121 cd01452 VWA_26S_proteasome_sub 26.6 1.4E+02 0.003 28.4 5.4 49 277-326 108-158 (187)
122 cd06288 PBP1_sucrose_transcrip 26.3 1.3E+02 0.0027 28.8 5.4 59 278-337 1-66 (269)
123 PRK08883 ribulose-phosphate 3- 26.2 82 0.0018 30.7 4.0 49 287-335 142-196 (220)
124 TIGR02634 xylF D-xylose ABC tr 26.0 69 0.0015 32.0 3.6 60 279-339 1-66 (302)
125 cd01540 PBP1_arabinose_binding 25.7 1E+02 0.0022 30.0 4.7 58 278-337 1-64 (289)
126 cd04502 SGNH_hydrolase_like_7 25.7 3.1E+02 0.0066 24.6 7.6 53 263-315 38-96 (171)
127 cd06306 PBP1_TorT-like TorT-li 25.6 84 0.0018 30.5 4.0 77 278-354 1-87 (268)
128 PF00205 TPP_enzyme_M: Thiamin 25.2 48 0.001 29.1 2.0 46 269-316 4-49 (137)
129 PF02514 CobN-Mg_chel: CobN/Ma 25.2 1E+02 0.0022 37.4 5.2 84 274-357 69-168 (1098)
130 PRK09701 D-allose transporter 25.2 1.7E+02 0.0036 29.4 6.2 64 272-335 20-90 (311)
131 PF02302 PTS_IIB: PTS system, 25.1 2E+02 0.0044 23.0 5.6 56 282-341 4-59 (90)
132 COG0041 PurE Phosphoribosylcar 24.8 1.9E+02 0.004 26.9 5.6 60 278-340 4-68 (162)
133 PRK10355 xylF D-xylose transpo 24.8 1.5E+02 0.0033 30.2 5.9 64 275-339 24-93 (330)
134 cd06304 PBP1_BmpA_like Peripla 24.6 1.3E+02 0.0029 29.0 5.2 57 278-336 1-65 (260)
135 TIGR01162 purE phosphoribosyla 24.6 1.4E+02 0.0031 27.6 4.9 71 279-352 1-80 (156)
136 cd06317 PBP1_ABC_sugar_binding 24.0 99 0.0022 29.7 4.2 59 278-337 1-66 (275)
137 PRK14336 (dimethylallyl)adenos 23.9 1.6E+02 0.0034 31.6 5.9 9 332-340 130-138 (418)
138 PRK00055 ribonuclease Z; Revie 23.8 84 0.0018 30.6 3.6 30 62-95 165-194 (270)
139 cd06320 PBP1_allose_binding Pe 23.5 1.4E+02 0.003 28.8 5.1 75 278-353 1-87 (275)
140 PRK09240 thiH thiamine biosynt 23.5 1.8E+02 0.0038 30.7 6.1 57 263-320 201-263 (371)
141 COG1736 DPH2 Diphthamide synth 23.5 8.8E+02 0.019 25.5 11.5 168 115-342 8-175 (347)
142 COG0052 RpsB Ribosomal protein 23.2 73 0.0016 31.7 2.9 52 93-147 14-77 (252)
143 PRK10401 DNA-binding transcrip 23.0 2.8E+02 0.006 28.0 7.4 62 274-336 57-124 (346)
144 cd05566 PTS_IIB_galactitol PTS 22.9 3E+02 0.0065 22.0 6.2 54 282-338 5-58 (89)
145 PRK14057 epimerase; Provisiona 22.8 2.2E+02 0.0047 28.6 6.2 60 275-334 154-221 (254)
146 cd01541 PBP1_AraR Ligand-bindi 22.7 1.6E+02 0.0035 28.3 5.4 55 278-334 1-62 (273)
147 cd06309 PBP1_YtfQ_like Peripla 22.6 78 0.0017 30.6 3.1 59 278-337 1-65 (273)
148 PRK14814 NADH dehydrogenase su 22.6 1.6E+02 0.0034 28.1 4.9 15 324-339 128-142 (186)
149 cd06267 PBP1_LacI_sugar_bindin 22.2 1.4E+02 0.0031 28.0 4.8 32 279-310 2-33 (264)
150 cd06322 PBP1_ABC_sugar_binding 22.2 1.1E+02 0.0023 29.4 4.0 76 278-354 1-86 (267)
151 PF02593 dTMP_synthase: Thymid 22.0 1.3E+02 0.0029 29.3 4.4 40 267-308 66-105 (217)
152 PRK00061 ribH 6,7-dimethyl-8-r 21.9 2.2E+02 0.0047 26.3 5.6 61 277-337 13-81 (154)
153 TIGR01574 miaB-methiolase tRNA 21.9 1.1E+02 0.0023 33.0 4.2 66 267-332 29-100 (438)
154 PRK15395 methyl-galactoside AB 21.8 2.1E+02 0.0046 29.0 6.2 64 274-337 22-91 (330)
155 KOG3360 Acylphosphatase [Energ 21.4 2.1E+02 0.0045 24.4 4.8 44 265-308 23-72 (98)
156 TIGR01012 Sa_S2_E_A ribosomal 21.1 2E+02 0.0044 27.6 5.4 51 93-146 14-73 (196)
157 PRK02910 light-independent pro 21.0 2.6E+02 0.0057 30.8 7.1 76 277-353 159-238 (519)
158 cd06276 PBP1_FucR_like Ligand- 20.8 1.4E+02 0.0031 28.7 4.6 56 279-337 2-62 (247)
159 cd01539 PBP1_GGBP Periplasmic 20.8 85 0.0019 31.3 3.0 59 278-337 1-67 (303)
160 cd06314 PBP1_tmGBP Periplasmic 20.5 1.4E+02 0.0031 28.8 4.5 59 278-337 1-65 (271)
161 cd06324 PBP1_ABC_sugar_binding 20.1 1.3E+02 0.0029 29.9 4.3 59 278-337 1-68 (305)
162 PRK12359 flavodoxin FldB; Prov 20.1 2.8E+02 0.0061 25.9 6.1 53 278-338 2-55 (172)
No 1
>TIGR00272 DPH2 diphthamide biosynthesis protein 2. This protein has been shown in Saccharomyces cerevisiae to be one of several required for the modification of a particular histidine residue of translation elongation factor 2 to diphthamide. This modified site can then become the target for ADP-ribosylation by diphtheria toxin.
Probab=100.00 E-value=2.1e-118 Score=950.29 Aligned_cols=454 Identities=31% Similarity=0.515 Sum_probs=372.9
Q ss_pred ccccccchHHHHHHHHhCCCcEEEEeCCccchhhHHHHHHHHHHhhccCCCCCCCCCCCCCceeEEEEcCCccccCccch
Q 011028 2 DFELNYEIASTADFIYSRKFTRVALQFPDNLLKDSIRIVRALRAKLGSLRSSDGERGVDDKDIGLFVMADTTYGSCCVDE 81 (495)
Q Consensus 2 ~~~~~yei~~~i~~I~~~~~krVaLQfPD~Ll~~s~~V~~~L~~~l~~~~~~~~~~~~~~~~~~v~IlaDtsYGsCCVDe 81 (495)
+|+..|||++|++||++++++|||||||||||++|..|++.|++++.. .++++|||||||||||||||
T Consensus 32 ~~~~~yei~~~~~~I~~~~~krVaLQFPDgLL~~a~~va~~L~~~~~~------------~~~~v~IlaDtsYGaCCVDe 99 (496)
T TIGR00272 32 DISAYYEIEPTVGYIKQGNEYQVALQFPDDLLKDSSKVVRLLQSKFPH------------GKIKFWVLADTAYSSCCVDE 99 (496)
T ss_pred HHHHHhhHHHHHHHHHHCCCCEEEEECChHHHHHHHHHHHHHHhhccc------------CCceEEEEeCCcccccccCH
Confidence 688999999999999999999999999999999999999999987521 25899999999999999999
Q ss_pred hhhcccCCcEEEEecCCCCCCCCCCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchhhhHHHHHHHHhhcc
Q 011028 82 VGASHVDADCVIHYGHTCLSPTSTLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASS 161 (495)
Q Consensus 82 vaA~hv~aD~iVHyGhsCls~~~~lpviYVf~~~~id~~~~~~~l~~~~~~~~~~v~l~~dvqy~~~l~~l~~~L~~~~~ 161 (495)
+||+|++||+|||||||||+|++++||+|||++.++|+++|++.+++.+++..++|+|++|+||.|+++++++.|++...
T Consensus 100 vaA~hv~aD~iVHyGhsCLsp~~~lPviYVf~~~~~d~~~~~~~~~~~~~~~~~kV~l~~dvqy~~~~~~l~~~L~~~~~ 179 (496)
T TIGR00272 100 VAAEHVHAEAVVHFGDACLSAIQNLPVVYVFGTPPIDLALVVENFQRAFPDLSSKICLMADAPFSKHQSQLYNILKEVLP 179 (496)
T ss_pred HHHhhcCCCEEEEeCCCCCCCCCCCCEEEEeccCCCCHHHHHHHHHHhccccCCeEEEEEchhHHHHHHHHHHHHHhhcc
Confidence 99999999999999999999999999999999999999999999987665545679999999999999999999986432
Q ss_pred CCCCCcceeeeeeccceeeecCCCCCCCCCCCCCCcccccccCcccccCCcccccceEEEEEcCCCc-hhhhhhhhcC-C
Q 011028 162 SYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNS-AFANVVLTFN-G 239 (495)
Q Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~l~~Ig~~~~-~l~~l~l~~~-~ 239 (495)
..+ ...++.+++ ..|. .....++++||+++...+ ...+++.+||||++++ +|++++|+++ .
T Consensus 180 ~~~--~~~~~~~~~-----~~~~--~~~~~~~vlGc~~~~~~~--------~~~~~~~~l~IG~~~~g~f~~l~l~~~~~ 242 (496)
T TIGR00272 180 GDL--HYTNIIYPQ-----VNTS--AVEEKFVTIGRTFHVPED--------VDQQEKNLVLFGQHSSEDLHLIHLTTYQD 242 (496)
T ss_pred ccc--cccceeccc-----cccc--cCCCCceecCccccCccc--------cccccceEEEEcCCCchhhhHhhhhcCCC
Confidence 100 011222211 1111 112236789998664421 2334667999999777 8899988644 4
Q ss_pred -ceEEEecCCCCcccccccc-HHHHHHHHHHHHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCC
Q 011028 240 -CEIVRYDATEERLLTDVSQ-PLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKP 317 (495)
Q Consensus 240 -~~v~~yDP~~~~~~~~~~~-~~r~l~rRy~~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkl 317 (495)
+++|+|||+++++..+... ++|+|||||++|+|||+|++||||||||++|+|++++++|+++|+++|||+|+|+||||
T Consensus 243 ~~~v~~~dP~~~~~~~~~~~~~~~~L~rRy~~I~kA~~A~~~GIlVgTL~~q~~~~ii~~l~~li~~~GkK~yl~~vgki 322 (496)
T TIGR00272 243 LSTVFQFVPIFDPILPESVTGPFPSLRRRYKLVHVARDAGCIGIVVGTLGVRNTRETINELRKMIKTAGKKHYLFVVGKP 322 (496)
T ss_pred CCceEEECCCCCcceecccchHHHHHHHHHHHHHHHhcCCEEEEEEecCccCCCHHHHHHHHHHHHHcCCcEEEEEeCCC
Confidence 6799999999998776645 89999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHcCCCCCcEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCcCccceeeecccccCCCC------CCCCCccc
Q 011028 318 NPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSSSP------VEGSDQAE 391 (495)
Q Consensus 318 n~aKLaNF~eID~fV~vaCPr~si~d~~~f~kPViTP~El~vAL~~~~~W~g~y~~Df~~ll~~~~------~~~~~~~~ 391 (495)
||+|||||++||+||+|||||++|+|+++|+||||||||++|||+.+.+|.++|..+|..+.+... .+..++++
T Consensus 323 npaKLaNF~eID~fV~vaCPr~sidd~~~F~KPVlTP~ElelAL~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 402 (496)
T TIGR00272 323 NPAKLANFEDIDIFVLLGCSQSGIIDSNEFYRPIVTPFELNLALSEEVTWVVDFRDSIDEIEQLLGGQDTISPSTTSDEA 402 (496)
T ss_pred CHHHHhCCCCCCEEEEccCCCcccccHhhCCCceecHHHHHHHhCCcccccchHHHHhhhhhhcccccccCCCccccccC
Confidence 999999999999999999999999999999999999999999999877899999888887764311 11122346
Q ss_pred ccccccccCcccccCCCCCCCCcchhhhhHHHHhhhhhhhhhhccCCCcceeecccchHHHHhhcCCcccCCCCCCC-CC
Q 011028 392 EARFSFLKGGYVEDVAQPETENGEEEKEGALALANAAEKALQLRDRSLDPIVKGTAKSGAEYFVSRSYHGLEMQCNS-SS 470 (495)
Q Consensus 392 ~p~fslitG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~s~~a~~l~~Rtw~GL~~~~g~-~~ 470 (495)
+|+||||||+|++++++++.....+... .....+.+++.+.+.+.+++++++|+||+||++|||||||+++|+ ++
T Consensus 403 ~p~fslitG~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~s~~a~~l~~Rtw~GL~~~~~~~~~ 478 (496)
T TIGR00272 403 APEFSLIRGKYTSTSRPLRALTHLELEA----ADNDDSKQSTTRHTASGAVIKGTVSTSASALQNRSWKGLGDDVDSTEV 478 (496)
T ss_pred CCceeccccceeecCCccchhhhccccc----cCCCCccceeecccCcceeeccccccHHHHhhcCceeCCCCCcCCCCC
Confidence 8999999999999888765222111000 001223345544443336677889999999999999999999986 45
Q ss_pred CcccccCcccccccccCC
Q 011028 471 PEPYAIGRSGKASGYDDE 488 (495)
Q Consensus 471 ~~~~~~Gr~GiA~gY~~e 488 (495)
++.++|||+||||||+++
T Consensus 479 ~a~~~eGrsGIA~gY~~~ 496 (496)
T TIGR00272 479 DAKIEEGISGIARGYGGD 496 (496)
T ss_pred cceeecCCccccccCCCC
Confidence 789999999999999864
No 2
>KOG2648 consensus Diphthamide biosynthesis protein [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-109 Score=847.04 Aligned_cols=420 Identities=37% Similarity=0.600 Sum_probs=355.9
Q ss_pred ccccchHHHHHHHHhCCCcEEEEeCCccchhhHHHHHHHHHHhhccCCCCCCCCCCCCCceeEEEEcCCccccCccchhh
Q 011028 4 ELNYEIASTADFIYSRKFTRVALQFPDNLLKDSIRIVRALRAKLGSLRSSDGERGVDDKDIGLFVMADTTYGSCCVDEVG 83 (495)
Q Consensus 4 ~~~yei~~~i~~I~~~~~krVaLQfPD~Ll~~s~~V~~~L~~~l~~~~~~~~~~~~~~~~~~v~IlaDtsYGsCCVDeva 83 (495)
.++|||++|++||++.|+|||||||||+||.||..|++.|++.+ +.++|||||||||||||||+|
T Consensus 33 ~~~fEi~ktv~~Ir~~~~kRVALQfPD~LL~~S~~I~~ile~~~---------------~~k~~VLaDttYGsCCVDeva 97 (453)
T KOG2648|consen 33 NYNFEIHKTVWFIRSLGAKRVALQFPDGLLMYSCKISDILESFT---------------GAKTFVLGDTTYGSCCVDEVA 97 (453)
T ss_pred hcchhhhhHHHHHHhCCceEEEEeCChHHhhHHHHHHHHHHHhc---------------cccEEEEecCcccccccchHH
Confidence 34799999999999999999999999999999999999999986 469999999999999999999
Q ss_pred hcccCCcEEEEecCCCCCCCCCCCe-EEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchhhhHHHHHHHHhhccC
Q 011028 84 ASHVDADCVIHYGHTCLSPTSTLPA-FFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASSS 162 (495)
Q Consensus 84 A~hv~aD~iVHyGhsCls~~~~lpv-iYVf~~~~id~~~~~~~l~~~~~~~~~~v~l~~dvqy~~~l~~l~~~L~~~~~~ 162 (495)
|+|++||+|||||||||+|++++|+ +|||++++||+++|+++|+..+++..++|+|++++||+|.++++++.|......
T Consensus 98 A~h~~ad~lVHyG~aCLsp~~~~~~~lYVf~~i~Idl~~~~~~l~~~~~~~~~~I~l~~~i~f~~~l~~~~~~L~~~~~~ 177 (453)
T KOG2648|consen 98 AEHLDADALVHYGHACLSPIDRLPVVLYVFVDIPIDLDHLVKSLQRNFPQLISQIVLLGTIQFAHSLEALATELKEELLD 177 (453)
T ss_pred HhhcCCCEEEEecccccCccccCCceEEEeecccccHHHHHHHHHhhcccccceeEEeechhhhHHHHHHHHHHhhccCc
Confidence 9999999999999999999999998 999999999999999999988876666899999999999999999999775421
Q ss_pred CCCCcceeeeeeccceeeecCCCCCCCCCCCCCCcccccccCcccccCCcccccceEEEEEcCCCchhhhhhhhcCCceE
Q 011028 163 YGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEI 242 (495)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~l~~Ig~~~~~l~~l~l~~~~~~v 242 (495)
.++ +.|+.. +.+++.++|||.+...++ .+..+++|||++++|+...|+..+..++
T Consensus 178 ------~~~---------i~Pq~~-p~s~~e~lG~t~p~~~~~---------~~~~~li~iGD~~~~le~~mi~np~~~~ 232 (453)
T KOG2648|consen 178 ------LEV---------ILPQFK-PLSPGEVLGCTSPLLEGR---------EEYDALIFIGDGRFHLESSMIANPGLPA 232 (453)
T ss_pred ------eEE---------eccCCC-CCCCccccceeccCCCCc---------cccceEEEecCCCcchhHHHHhCCCCCe
Confidence 122 234333 566899999988765432 3456899999999999888888889999
Q ss_pred EEecCCCCccccccccHHHHHHHHHHHHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH
Q 011028 243 VRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL 322 (495)
Q Consensus 243 ~~yDP~~~~~~~~~~~~~r~l~rRy~~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL 322 (495)
++|||+++++..|.+++.+|++|||++|||||+|++||||+||||+|||++++++|+++|+++|||+|+|+||||||+||
T Consensus 233 ~~ydp~s~kl~~E~y~~~~m~~rR~~~vekardA~~iGlivGTLG~qg~~~vl~~L~~~~~~~Gkk~y~l~~g~inPaKL 312 (453)
T KOG2648|consen 233 YRYDPYSKKLTRESYDHSRMLRRRYYLVEKARDARTIGLIVGTLGRQGNREVLEHLRKLLKAAGKKSYVLALGEINPAKL 312 (453)
T ss_pred EEeCCccCceeecccchHHHHHHHHHHHHHHhcCCeEEEEEecccccCCHHHHHHHHHHHHHcCCceEEEEecCCCHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCcEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCcCccceeeecccccCCCCCCCCCcccccccccccCcc
Q 011028 323 ANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSSSPVEGSDQAEEARFSFLKGGY 402 (495)
Q Consensus 323 aNF~eID~fV~vaCPr~si~d~~~f~kPViTP~El~vAL~~~~~W~g~y~~Df~~ll~~~~~~~~~~~~~p~fslitG~~ 402 (495)
|||+||||||++||||+++||+++|+||||||||+++||++. .|++.|.++|...+.+.. .+.+++. ..+|.|
T Consensus 313 AnF~eIDvfV~iaCp~lsid~s~~F~kPiltPfEa~~Al~~~-~W~~~~~~~~~~~~~~~~----~~~~~~~--~~~~d~ 385 (453)
T KOG2648|consen 313 ANFPEIDVFVQIACPRLSIDWSKEFYKPLLTPFEAEVALNPI-AWTGDYLAPFVTAIKLLL----KESEFHS--SELGDY 385 (453)
T ss_pred cCCccccEEEEEeCcccchhhhhhhccccccHHHHHHhcCcc-ccCCccccchhhHHhhhh----ccccccc--cccccC
Confidence 999999999999999999999999999999999999999986 999999999988765332 1112221 344544
Q ss_pred cccCCCCCCCCcchhhhhHHHHhhhhhhhhhhccCCCcceeecccchHHHHhhcCCcccCCCCCCCCCCcccccCccccc
Q 011028 403 VEDVAQPETENGEEEKEGALALANAAEKALQLRDRSLDPIVKGTAKSGAEYFVSRSYHGLEMQCNSSSPEPYAIGRSGKA 482 (495)
Q Consensus 403 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~s~~a~~l~~Rtw~GL~~~~g~~~~~~~~~Gr~GiA 482 (495)
.++.......... .+ .. +..... .+..++|+.||++|+||||+++.+++++++..+||||||
T Consensus 386 pm~~~~~~~~~~~--------~~------~~--~~~~~~--~~~~~~a~~~~~~rsw~gLd~~~~~~~~~~~~~Grsgia 447 (453)
T KOG2648|consen 386 PMDYYSLGSLGPP--------PA------WT--SSNDHG--AGESSPAISFLQNRSWQGLDPRLGQTPPTKLVSGRSGIA 447 (453)
T ss_pred cccccccccCCcC--------cc------cC--Cccccc--ccccccccchhccccccCCCcCCCCCCccchhccccccc
Confidence 3322211100000 00 00 000000 123356788999999999999999999999999999999
Q ss_pred ccccCC
Q 011028 483 SGYDDE 488 (495)
Q Consensus 483 ~gY~~e 488 (495)
+||.+|
T Consensus 448 ~gy~~~ 453 (453)
T KOG2648|consen 448 IGYSDE 453 (453)
T ss_pred cccCCC
Confidence 999875
No 3
>TIGR00322 diphth2_R diphthamide biosynthesis protein 2-related domain. Because archaeal species are known to have the diphthamide modification to the conserved His of archaeal and eukaryotic EF-2, it may be that the lone homolog of YKL191W in M. jannaschii, A. fulgidus, and M. thermoautotrophicum is orthologous. However, each of these is considerably shorter than YKL191W and seems more closely related to the uncharacterized protein YIL103W than to YKL191W.
Probab=100.00 E-value=2e-93 Score=728.31 Aligned_cols=328 Identities=23% Similarity=0.410 Sum_probs=296.1
Q ss_pred ccccchHHHHHHHHhCCCcEEEEeCCccchhhHHHHHHHHHHhhccCCCCCCCCCCCCCceeEEEEcCCccccCccchhh
Q 011028 4 ELNYEIASTADFIYSRKFTRVALQFPDNLLKDSIRIVRALRAKLGSLRSSDGERGVDDKDIGLFVMADTTYGSCCVDEVG 83 (495)
Q Consensus 4 ~~~yei~~~i~~I~~~~~krVaLQfPD~Ll~~s~~V~~~L~~~l~~~~~~~~~~~~~~~~~~v~IlaDtsYGsCCVDeva 83 (495)
.++||++++++||+++|+|||+||||||||.+|..|++.|++.. ++++||||||||||||||+++
T Consensus 2 ~y~~e~~~~i~~I~~~~~krV~LQfPdgLl~~a~~ia~~l~~~~---------------~~~v~IlaD~~YGaCcvdd~~ 66 (332)
T TIGR00322 2 NYNLETEKVIGNIRKYNAKRVGLQMPEGLKIRALEIAEIIEQFC---------------GVETVISGDTSFGACDIDDFT 66 (332)
T ss_pred CccccHHHHHHHHHHcCCCEEEEECCHHHHHHHHHHHHHHHhcc---------------CceEEEEcCCceecCCCCHHH
Confidence 37899999999999999999999999999999999999998742 589999999999999999999
Q ss_pred hcccCCcEEEEecCCCCCCCC-CCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchhhhHHHHHHHHhhccC
Q 011028 84 ASHVDADCVIHYGHTCLSPTS-TLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASSS 162 (495)
Q Consensus 84 A~hv~aD~iVHyGhsCls~~~-~lpviYVf~~~~id~~~~~~~l~~~~~~~~~~v~l~~dvqy~~~l~~l~~~L~~~~~~ 162 (495)
|+|++||+|||||||||+|+. ++||+|||++.++|++++++.+.+.+.. .++|+|++|+||.|.++++++.|++.++.
T Consensus 67 a~~~~aD~iVHyGHscl~~~~~~~pv~yVf~~~~~d~~~~~~~~~~~~~~-~~~i~l~~tiq~~~~~~~~~~~L~~~g~~ 145 (332)
T TIGR00322 67 ARALDVDLIVHYAHTPLVPDDVEIKVLYVPVTINIEYDHIIKTLQDNFPK-GRRIATIGTAQFNHKLHSVRDKLLNEGHE 145 (332)
T ss_pred HhhcCCCEEEEcCCCCCCcccCCCCEEEEEccCCCCHHHHHHHHHHHcCC-CCeEEEEECHHHHHHHHHHHHHHHhcCce
Confidence 999999999999999999988 9999999999999999999999876644 46799999999999999999999887542
Q ss_pred CCCCcceeeeeeccceeeecCCCCCCCCCCCCCCcccccccCcccccCCcccccceEEEEEcCCCchhhhhhhhcCCceE
Q 011028 163 YGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEI 242 (495)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~l~~Ig~~~~~l~~l~l~~~~~~v 242 (495)
+.+ ......+.++|+++||++..+.+ .+.+ .++|||+|.||+++++|. +++++
T Consensus 146 --------v~i--------~~~~~~~~~~g~vLGC~~~~~~~--------~~~d--~~l~vg~g~FH~~~~~l~-~~~~v 198 (332)
T TIGR00322 146 --------VYI--------GPPQGKPLSRGQVLGCNSEVLRG--------EQAD--AMVFIGDGRFHPLGAAIH-TEKEV 198 (332)
T ss_pred --------EEE--------ecCccCCCCCccccCCCcCCCCC--------CCCC--EEEEEcCCcchHHHHHHH-cCCcE
Confidence 222 11223456799999998765421 1232 688999999999999995 58999
Q ss_pred EEecCCCCccccccccHHHHHHHHHHHHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH
Q 011028 243 VRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL 322 (495)
Q Consensus 243 ~~yDP~~~~~~~~~~~~~r~l~rRy~~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL 322 (495)
|+|||+++++..+..+++|+|||||++|+||++|++||||+||||+|+|++++++|+++|+++|||+|+|+||+|||+||
T Consensus 199 ~~~DP~s~~~~~~~~~~~~~l~rR~~~I~ka~~A~~vGIlvgTl~~q~~~~~~~~l~~ll~~~gkk~y~i~~~~in~~kL 278 (332)
T TIGR00322 199 FKYDPYSGEFTRIGEDAKQFVKVRALAISKARKGKKFGVVLSSKGGQGRLRLAKNLKKNLEEAGKTVLIILLSNVSPAKL 278 (332)
T ss_pred EEECCCCCceeEccccHHHHHHHHHHHHHHHhcCCEEEEEEecCccCCCHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH
Confidence 99999999987777779999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCcEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCcCccceeeecc
Q 011028 323 ANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFR 376 (495)
Q Consensus 323 aNF~eID~fV~vaCPr~si~d~~~f~kPViTP~El~vAL~~~~~W~g~y~~Df~ 376 (495)
+||++||+||++||||++|||+++|+||||||||++|||+. +.|. .|+||+.
T Consensus 279 ~nf~eiD~fV~~aCPr~sidd~~~f~kPvlTP~E~e~al~~-~~~~-~y~~d~~ 330 (332)
T TIGR00322 279 LMFDQIDVFVQVACPRIAIDDGYLFNKPLLTPYEFELLLKK-RVEK-YYPMDEI 330 (332)
T ss_pred hCCCCcCEEEEecCCCceecchhhcCCccccHHHHHHHhCc-cccc-cCCCcee
Confidence 99999999999999999999999999999999999999997 4696 5999974
No 4
>TIGR03682 arCOG04112 arCOG04112 universal archaeal diphthamide biosynthesis domain protein. This family of proteins has been observed universally in archaeal genomes and contains a match to the TIGR00322 model for the diphthamide biosynthesis protein 2-related domain.
Probab=100.00 E-value=8e-86 Score=666.62 Aligned_cols=304 Identities=22% Similarity=0.394 Sum_probs=269.8
Q ss_pred CCcEEEEeCCccchhhHHHHHHHHHHhhccCCCCCCCCCCCCCceeEEEEcCCccccCcc-chhhhcccCCcEEEEecCC
Q 011028 20 KFTRVALQFPDNLLKDSIRIVRALRAKLGSLRSSDGERGVDDKDIGLFVMADTTYGSCCV-DEVGASHVDADCVIHYGHT 98 (495)
Q Consensus 20 ~~krVaLQfPD~Ll~~s~~V~~~L~~~l~~~~~~~~~~~~~~~~~~v~IlaDtsYGsCCV-DevaA~hv~aD~iVHyGhs 98 (495)
|++||+||||||||.+|..|++.|++ .++++||||||||||||| |++|++| ||+|||||||
T Consensus 1 ~~~rV~LQfPdgLl~~a~~ia~~l~~----------------~~~~v~I~gD~tYGaCcV~D~~a~~~--~D~iVH~GHs 62 (308)
T TIGR03682 1 NAKRVLLQAPEGLKRRAFEIAQKLEE----------------KGYEVIISGEPCYGACDLADDEALEL--VDLIVHFGHS 62 (308)
T ss_pred CCcEEEEECChhHHHHHHHHHHHHHh----------------CCceEEEEcCCceeeccCChHHHHhc--CCEEEEcCCC
Confidence 68999999999999999999999985 248999999999999999 8887665 9999999999
Q ss_pred CCC-CCCCCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchhhhHHHHHHHHhhccCCCCCcceeeeeeccc
Q 011028 99 CLS-PTSTLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASSSYGSGLKLEINFADVM 177 (495)
Q Consensus 99 Cls-~~~~lpviYVf~~~~id~~~~~~~l~~~~~~~~~~v~l~~dvqy~~~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~ 177 (495)
||+ +++++||+|||++.++|++++++.+.+.+. .++|+|++|+||.|.++++++.|++.++ ++.++
T Consensus 63 cl~~~~~~~pv~yV~~~~~~d~~~~~~~~~~~~~--~~~v~l~~tiq~~~~~~~v~~~L~~~g~--------~v~i~--- 129 (308)
T TIGR03682 63 PLPNVKPEIPVIFIEARSDVDVEEVIEKALEELK--GRRIGLVTTAQHVHLLEKVKEILEERGI--------EVVIG--- 129 (308)
T ss_pred CCCcccCCCCEEEEEecCCcCHHHHHHHHHHHCC--CCeEEEEEcHHhHHHHHHHHHHHHHcCc--------eEEec---
Confidence 999 488999999999999999987777765543 3689999999999999999999988764 22222
Q ss_pred eeeecCCCCCCCCCCCCCCcccccccCcccccCCcccccceEEEEEcCCCchhhhhhhhcCCceEEEecCCCCccccccc
Q 011028 178 CTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTDVS 257 (495)
Q Consensus 178 ~~~~~~~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~l~~Ig~~~~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~ 257 (495)
.....+..+|+++||++.... +.+. ..++|||+|.||+++++| ++++++|+|||+++++..+..
T Consensus 130 -----~~~~~~~~~g~vlGC~~~~~~--------~~~~--d~~~~vg~g~Fh~~~l~l-~~~~~v~~~DP~~~~~~~~~~ 193 (308)
T TIGR03682 130 -----KGDGRVTYPGQVLGCNFSAAR--------SVDA--DAFLFVGTGLFHPLGLAL-ATNKPVYAADPFSGEVEDIEA 193 (308)
T ss_pred -----CCCCCCCCCceeeCccccCCC--------CCCc--cEEEEEcCCcchHHHHHh-ccCCcEEEECCCCCceEeech
Confidence 122335679999999865432 1122 278899999999998888 789999999999999877766
Q ss_pred cHHHHHHHHHHHHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCC
Q 011028 258 QPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 337 (495)
Q Consensus 258 ~~~r~l~rRy~~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCP 337 (495)
+++|++||||++|+||++|++||||+|||++|+|++++++|+++|+++|||+|+|+||+|||+||+|| +||+||++|||
T Consensus 194 ~~~~~l~~R~~~I~ka~~A~~vGIlvgTl~~q~~~~~~~~l~~ll~~~gkk~y~i~~~~in~~kL~nf-~iD~fV~~aCP 272 (308)
T TIGR03682 194 EIDKFLRVRYARISKALDAKKFGILVSTKKGQRRPELAEELKKLLEELGKEALLILLDNISPDQLRNL-DFDAYVNTACP 272 (308)
T ss_pred hHHHHHHHHHHHHHHHhhCCeEEEEEEccCcCCCHHHHHHHHHHHHHcCCeEEEEEeCCCCHHHHhcC-CcCEEEEccCC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999 79999999999
Q ss_pred CcccccccCCCCcccCHHHHHHhhCCCCcCccceeeec
Q 011028 338 QTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEF 375 (495)
Q Consensus 338 r~si~d~~~f~kPViTP~El~vAL~~~~~W~g~y~~Df 375 (495)
|+++||+++|+||||||||+++||+. ++| |+||.
T Consensus 273 r~sidd~~~f~kPvlTP~E~~~al~~-~~~---y~~D~ 306 (308)
T TIGR03682 273 RIAIDDYARFKKPVLTPQEFEIVLGK-RSE---YVFDE 306 (308)
T ss_pred CcccccHhhCCCcccCHHHHHHHhCC-Ccc---ccCCc
Confidence 99999999999999999999999997 789 99885
No 5
>PF01866 Diphthamide_syn: Putative diphthamide synthesis protein; InterPro: IPR002728 Members of this family include Q16439 from SWISSPROT, a candidate tumour suppressor gene [], and DPH2 from yeast P32461 from SWISSPROT [], which confers resistance to diphtheria toxin and has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a posttranslationally modified histidine residue present in EF2. The exact function of the members of this family is unknown.; GO: 0017183 peptidyl-diphthamide biosynthetic process from peptidyl-histidine, 0005737 cytoplasm; PDB: 3LZD_B 3LZC_A.
Probab=100.00 E-value=6.3e-84 Score=655.51 Aligned_cols=304 Identities=40% Similarity=0.754 Sum_probs=214.5
Q ss_pred CCccchhhHHHHHHHHHHhhccCCCCCCCCCCCCCceeEEEEcCCccccCccchhhhcccCCcEEEEecCCCCCCCC-CC
Q 011028 28 FPDNLLKDSIRIVRALRAKLGSLRSSDGERGVDDKDIGLFVMADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTS-TL 106 (495)
Q Consensus 28 fPD~Ll~~s~~V~~~L~~~l~~~~~~~~~~~~~~~~~~v~IlaDtsYGsCCVDevaA~hv~aD~iVHyGhsCls~~~-~l 106 (495)
||||||++|..|++.|++. +.++||||||||||||||+++|+|++||+|||||||||++++ ++
T Consensus 1 fPdgLl~~a~~ia~~L~~~----------------~~~v~IlaDttYGaCcvD~~~a~h~~aD~IVH~Ghscl~~~~~~i 64 (307)
T PF01866_consen 1 FPDGLLPDAVEIASILEST----------------GVEVYILADTTYGACCVDEVAAEHVGADLIVHYGHSCLSPTKPRI 64 (307)
T ss_dssp -BGGGHHHHHHHHHHHHTT----------------T-EEEEE-S-B--TTS--HHHHHHTT-SEEEEEE----S----SS
T ss_pred CChhHHHHHHHHHHHHHcC----------------CceEEEEeCCcccCCCcCHHHHhhcCCcEEEECCCCCCCcccccC
Confidence 8999999999999999862 478999999999999999999999999999999999999975 99
Q ss_pred CeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchhhhHHHHHHHHhhccCCCCCcceeeeeeccceeeecCCCC
Q 011028 107 PAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKD 186 (495)
Q Consensus 107 pviYVf~~~~id~~~~~~~l~~~~~~~~~~v~l~~dvqy~~~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (495)
||+|||++.++|++++++.+.+.+.+ .++|+|++|+||.|.++++++.|++.+.. ..+ ..+..
T Consensus 65 pviyV~~~~~id~~~~~~~~~~~~~~-~~~i~l~~~vqy~~~~~~~~~~L~~~g~~------~~i----------~~~~~ 127 (307)
T PF01866_consen 65 PVIYVFVEINIDVEHLVESLKEEFKK-KKKIVLLTDVQYAHALEELKEILREKGFE------VVI----------GIPQN 127 (307)
T ss_dssp -EEEEE--B-S-HHHHHHHTHHHHHT--SEEEEEE-GGGGGGHHHHHHHHHHTT-E------EE---------------T
T ss_pred ceEEEeccCCCCHHHHHHHHHHhccC-CceEEEEEehhHHHHHHHHHHHHHHhccc------ccc----------cCCcc
Confidence 99999999999999999999887766 58999999999999999999999986431 111 12223
Q ss_pred CCCCCCCCCCcccccccCcccccCCcccccceEEEEEcCCCchhhhhhhhcCCceEEEecCCCCccccc--cccHHHHHH
Q 011028 187 HKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTD--VSQPLKILK 264 (495)
Q Consensus 187 ~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~l~~Ig~~~~~l~~l~l~~~~~~v~~yDP~~~~~~~~--~~~~~r~l~ 264 (495)
.+..+|+++||+...+... .+.+.++|||+|.||+++++|+ +++++|+|||++++...+ ..+.+|+||
T Consensus 128 ~~~~~g~vlGc~~~~~~~~---------~~~~~~l~IG~g~fh~~~l~l~-~~~~v~~~dP~~~~~~~e~~~~~~~~~l~ 197 (307)
T PF01866_consen 128 RPLSPGQVLGCTYPSADSL---------DDDDAILFIGGGRFHLLGLMLS-PGKPVYRYDPYSKTLSVEDISYDIERLLR 197 (307)
T ss_dssp T-SSTTB-BTTB-GGG-S-----------S-SEEEEESSSSHHHHHHHHH-H-SEEEEE-TT--T--EEE----THHHHH
T ss_pred ccCCcccccCCccCccccc---------ccccEEEEEcCCchHHHHHHHh-cCCCEEEeCCCcccceeecccccHHHHHH
Confidence 3467899999987765321 3456899999999999999999 899999999997766555 456899999
Q ss_pred HHHHHHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCCcccccc
Q 011028 265 RRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDS 344 (495)
Q Consensus 265 rRy~~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d~ 344 (495)
|||++|+||++|++||||+|||++|+|++++++|+++|+++|||+|+|+||+|||+||+||+|||+||++||||+++||+
T Consensus 198 ~R~~~i~ka~~a~~~GIiv~tl~~q~~~~~~~~l~~~l~~~gkk~y~~~~~~i~~~kL~nf~eid~fV~~aCPr~~idd~ 277 (307)
T PF01866_consen 198 RRYALIEKAKDAKTFGIIVGTLGGQGYLELIKRLKKLLKKAGKKSYTLSVGEINPAKLANFPEIDAFVQIACPRLSIDDS 277 (307)
T ss_dssp HHHHHHHHHTT--EEEEEEE-STTT--HHHHHHHHHHHHHTT-EEEEEEESS--GGGGTTS---SEEEE-S-THHHHT--
T ss_pred HHHHHHHHHhcCCEEEEEEecCCCCCCHHHHHHHHHHHHHcCCEEEEEEECCCCHHHHhcCcccCEEEEecCCCcccCch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCcccCHHHHHHhhCCCCcCccceeeecc
Q 011028 345 KEFLAPVITPFEAMLAFGRGTQWTGAYVMEFR 376 (495)
Q Consensus 345 ~~f~kPViTP~El~vAL~~~~~W~g~y~~Df~ 376 (495)
++|+||||||||++|||+.. .| ++|+|||.
T Consensus 278 ~~f~kPvltP~E~~~al~~~-~~-~~Y~~D~~ 307 (307)
T PF01866_consen 278 KDFYKPVLTPYELEVALNER-EW-GEYPMDEI 307 (307)
T ss_dssp S--SS-EE-HHHHHHHTTS--S---S------
T ss_pred hhcCCcccCHHHHHHHhCCc-cc-CcCCCCcC
Confidence 99999999999999999974 34 79999973
No 6
>COG1736 DPH2 Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-75 Score=590.57 Aligned_cols=329 Identities=26% Similarity=0.478 Sum_probs=294.9
Q ss_pred cccchHHHHHHHHhCCCcEEEEeCCccchhhHHHHHHHHHHhhccCCCCCCCCCCCCCceeEEEEcCCccccCccchhhh
Q 011028 5 LNYEIASTADFIYSRKFTRVALQFPDNLLKDSIRIVRALRAKLGSLRSSDGERGVDDKDIGLFVMADTTYGSCCVDEVGA 84 (495)
Q Consensus 5 ~~yei~~~i~~I~~~~~krVaLQfPD~Ll~~s~~V~~~L~~~l~~~~~~~~~~~~~~~~~~v~IlaDtsYGsCCVDevaA 84 (495)
++||++++++.|++.|++||+|||||||+.+|..|++.|++++ +++++|+|||+|||||||+.+|
T Consensus 8 ~~~e~~~iv~~ir~~~ak~V~LQ~PeGLk~~~~~ia~~le~~~---------------~~~v~i~gd~~yGACdi~~~~a 72 (347)
T COG1736 8 YNYEIEEIVREIRRLGAKRVLLQFPEGLKRYAIEIADILEANL---------------GAEVIISGDPVYGACDIDDLKA 72 (347)
T ss_pred eecchhHHHHHHHhCCCceEEEECChHHHHHHHHHHHHHHHhh---------------CceEEEeCCcccccccCCHHHH
Confidence 8999999999999999999999999999999999999999986 4899999999999999999999
Q ss_pred cccCCcEEEEecCCCCCC-CCCCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchhhhHHHHHHHHhhccCC
Q 011028 85 SHVDADCVIHYGHTCLSP-TSTLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASSSY 163 (495)
Q Consensus 85 ~hv~aD~iVHyGhsCls~-~~~lpviYVf~~~~id~~~~~~~l~~~~~~~~~~v~l~~dvqy~~~l~~l~~~L~~~~~~~ 163 (495)
+|+ ||+||||||||+++ ...+||+|||...++|+++.++.+...+....++|++++++||.|.++++++.|+..+.
T Consensus 73 ~~~-~D~iVH~GHs~l~~~~~~~~Viyv~~~~~~d~~~~~~~~~~~l~~~~r~I~li~t~q~~~~l~~~k~~L~~~g~-- 149 (347)
T COG1736 73 KDV-VDLIVHYGHSCLPPVEYELPVIYVFAFSRVDVDLVVLEATRELKKGSRRIGLITTAQHVHLLEEVKEILEGRGY-- 149 (347)
T ss_pred hhc-ccEEEEcccccCCCcCCCCcEEEeecccccchhHHHHHhhHhhccCCceEEEEecccchhHHHHHHHHhhcCCe--
Confidence 999 99999999999997 67999999999999999998877766444445679999999999999999999998764
Q ss_pred CCCcceeeeeeccceeeecCCCCCCCCCCCCCCcccccccCcccccCCcccccceEEEEEcCCCchhhhhhhhcCCceEE
Q 011028 164 GSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIV 243 (495)
Q Consensus 164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~l~~Ig~~~~~l~~l~l~~~~~~v~ 243 (495)
++. +.+.+.+...+||++||++..+.+ . +.-.++|||+|.||++++++. +.++|+
T Consensus 150 ------~v~--------i~~~~~r~~~~gqVLGC~~~~~~~--------~--~~d~~l~vg~G~FH~lg~~i~-~~~~v~ 204 (347)
T COG1736 150 ------EVV--------IGRGQTRPAYPGQVLGCNFSVLEG--------V--DADAVLYVGSGRFHPLGLAIR-TEKPVF 204 (347)
T ss_pred ------EEE--------EeCCCCcccCcceeeccccccCCc--------c--ccceEEEEcCCccChhhcccc-cCCcEE
Confidence 222 234444467899999998776532 1 223678899999998888888 889999
Q ss_pred EecCCCCccccccccHHHHHHHHHHHHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc
Q 011028 244 RYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA 323 (495)
Q Consensus 244 ~yDP~~~~~~~~~~~~~r~l~rRy~~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa 323 (495)
.|||+++.+..+...+++++++||+.|+||++|++||||+||+++|+++++++.|.++++++||++|+|+|+++||+||+
T Consensus 205 ~~dP~s~~~~~~~~~~~~~l~~R~~~i~~a~~a~~~giiv~tk~gQ~r~~~~~~l~k~~~~~g~~~~li~~~~i~p~~L~ 284 (347)
T COG1736 205 AIDPYSGKVREEDPEADRFLRKRYAAISKALDAKSFGIIVSTKGGQRRLEVARELVKLLKEAGKEVYLIVVDEISPDKLA 284 (347)
T ss_pred EEcCCCCceeecchhhhHHHHHHHHHHHHHhcCCeEEEEEecccccCcHHHHHHHHHHHHHcCCceEEEEecCCCHHHHh
Confidence 99999999877666689999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCcCccceeeecccc
Q 011028 324 NFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 378 (495)
Q Consensus 324 NF~eID~fV~vaCPr~si~d~~~f~kPViTP~El~vAL~~~~~W~g~y~~Df~~l 378 (495)
||.+||+||++||||+++||+..|.||||||+|+++||+ ..|..+|.||+-.-
T Consensus 285 ~f~~iD~~v~taCPRi~iDd~~~f~kPlLTP~E~~~~l~--~~~~~~y~~Dei~~ 337 (347)
T COG1736 285 NFDDIDAFVNTACPRIPIDDGDRFKKPLLTPYEFEIALG--WRSDERYAFDEIVG 337 (347)
T ss_pred cccceeEEEEecCCCcccchHhhhCCcccChHHHHHhhc--cCcccccccceeec
Confidence 999999999999999999999999999999999999998 22336898886443
No 7
>PF08901 DUF1847: Protein of unknown function (DUF1847); InterPro: IPR014997 This group of proteins are functionally uncharacterised. They contain 4 N-terminal cysteines that may form a zinc-binding domain.
Probab=83.70 E-value=1.9 Score=39.60 Aligned_cols=39 Identities=15% Similarity=0.319 Sum_probs=36.6
Q ss_pred chHHHHHHHHhCCCcEEEEeCCccchhhHHHHHHHHHHh
Q 011028 8 EIASTADFIYSRKFTRVALQFPDNLLKDSIRIVRALRAK 46 (495)
Q Consensus 8 ei~~~i~~I~~~~~krVaLQfPD~Ll~~s~~V~~~L~~~ 46 (495)
.++++++|-++.|||||.|=|==||...|..++++|+.+
T Consensus 42 RveEiieFak~mgykkiGiAfCiGL~~EA~~~~~iL~~~ 80 (157)
T PF08901_consen 42 RVEEIIEFAKRMGYKKIGIAFCIGLRKEARILAKILEAN 80 (157)
T ss_pred hHHHHHHHHHHcCCCeeeehhhHhHHHHHHHHHHHHHHC
Confidence 478999999999999999999999999999999999763
No 8
>PRK09492 treR trehalose repressor; Provisional
Probab=74.78 E-value=9.7 Score=38.08 Aligned_cols=77 Identities=13% Similarity=0.162 Sum_probs=50.8
Q ss_pred hcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEecCCCcccccccC
Q 011028 274 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTALLDSKE 346 (495)
Q Consensus 274 r~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~si~d~~~ 346 (495)
+..++||+|+.++.-..+..+++.+.+.++++|....++.. .-++++ |.+. .+|.+|+.++..........
T Consensus 60 ~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~~~~~-~~~~~~~~~~~~~l~~~-~vdgiIi~~~~~~~~~~l~~ 137 (315)
T PRK09492 60 QSDKVVGIIVSRLDSLSENQAVRTMLPAFYEQGYDPIIMES-QFSPEKVNEHLGVLKRR-NVDGVILFGFTGITEEMLAP 137 (315)
T ss_pred CCCCeEEEEecCCcCcccHHHHHHHHHHHHHcCCeEEEEec-CCChHHHHHHHHHHHhc-CCCEEEEeCCCcccHHHHHh
Confidence 45679999999877667789999999999999987644433 334433 2232 59999998753222222234
Q ss_pred CCCccc
Q 011028 347 FLAPVI 352 (495)
Q Consensus 347 f~kPVi 352 (495)
+.+|++
T Consensus 138 ~~~pvv 143 (315)
T PRK09492 138 WQDKLV 143 (315)
T ss_pred cCCCEE
Confidence 455665
No 9
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=71.37 E-value=7.5 Score=37.66 Aligned_cols=59 Identities=15% Similarity=0.219 Sum_probs=44.9
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaN----F--~eID~fV~vaCP 337 (495)
+||+|+..+.-..+..+++.+.+.+++.|.+.. +....-++++... + ..+|++|+.+|.
T Consensus 1 ~Ig~i~p~~~~~~~~~~~~~i~~~~~~~g~~~~-~~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (263)
T cd06280 1 TVGLIVADIRNPFFTAVSRAVEDAAYRAGLRVI-LCNTDEDPEKEAMYLELMEEERVTGVIFAPTR 65 (263)
T ss_pred CEEEEecccccccHHHHHHHHHHHHHHCCCEEE-EEeCCCCHHHHHHHHHHHHhCCCCEEEEeCCC
Confidence 589999998877888999999999999997764 4444455554322 1 269999998875
No 10
>COG4887 Uncharacterized metal-binding protein conserved in archaea [General function prediction only]
Probab=67.85 E-value=4.9 Score=36.66 Aligned_cols=39 Identities=10% Similarity=0.219 Sum_probs=35.0
Q ss_pred chHHHHHHHHhCCCcEEEEeCCccchhhHHHHHHHHHHh
Q 011028 8 EIASTADFIYSRKFTRVALQFPDNLLKDSIRIVRALRAK 46 (495)
Q Consensus 8 ei~~~i~~I~~~~~krVaLQfPD~Ll~~s~~V~~~L~~~ 46 (495)
.+++++++-+...||+|.+-|=-||-..|..++++|.+.
T Consensus 53 rlEEIae~ckrm~ykkiGiAFCigle~EAr~l~~iLsr~ 91 (191)
T COG4887 53 RLEEIAELCKRMVYKKIGIAFCIGLEEEARALCEILSRG 91 (191)
T ss_pred hHHHHHHHHHHhhhhhcceeeeeccHHHHHHHHHHHHhc
Confidence 356778888889999999999999999999999999864
No 11
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=66.76 E-value=11 Score=36.63 Aligned_cols=61 Identities=15% Similarity=0.178 Sum_probs=45.3
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCcEEEEecCCCc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCAQT 339 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaN----F--~eID~fV~vaCPr~ 339 (495)
+||+|+..+.-..+..+++.+.+.++++|....++..+ -++++... + ..+|++|+.+|+..
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~gy~v~~~~~~-~~~~~~~~~i~~~~~~~~dgiii~~~~~~ 67 (269)
T cd06293 1 TIGLVVPDIANPFFAELADAVEEEADARGLSLVLCATR-NRPERELTYLRWLDTNHVDGLIFVTNRPD 67 (269)
T ss_pred CEEEEeCCCCCCcHHHHHHHHHHHHHHCCCEEEEEeCC-CCHHHHHHHHHHHHHCCCCEEEEeCCCCC
Confidence 58999988776666799999999999999888666444 35543322 1 25999999998744
No 12
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=65.51 E-value=13 Score=35.79 Aligned_cols=75 Identities=16% Similarity=0.195 Sum_probs=52.1
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCCCcccc---cccCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQTALL---DSKEFL 348 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCPr~si~---d~~~f~ 348 (495)
+||+|+....-..+..+++.+++.+++.|.+..++ .+.-++++. .++ ..+|++++.+|...+.. ..+..-
T Consensus 1 ~I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~-~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~~~ 79 (268)
T cd06289 1 TIGLVINDLTNPFFAELAAGLEEVLEEAGYTVFLA-NSGEDVERQEQLLSTMLEHGVAGIILCPAAGTSPDLLKRLAESG 79 (268)
T ss_pred CEEEEecCCCcchHHHHHHHHHHHHHHcCCeEEEe-cCCCChHHHHHHHHHHHHcCCCEEEEeCCCCccHHHHHHHHhcC
Confidence 58999988776777789999999999999876544 445555542 222 36999999999765422 223445
Q ss_pred CcccC
Q 011028 349 APVIT 353 (495)
Q Consensus 349 kPViT 353 (495)
.|+|+
T Consensus 80 ipvV~ 84 (268)
T cd06289 80 IPVVL 84 (268)
T ss_pred CCEEE
Confidence 57775
No 13
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=64.99 E-value=17 Score=37.49 Aligned_cols=63 Identities=16% Similarity=0.258 Sum_probs=52.5
Q ss_pred HHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEec
Q 011028 272 KAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVS 335 (495)
Q Consensus 272 kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~va 335 (495)
+.+..++||+|+..+.-.-|.++++.+.+.++++|+...+...+. ++++.. ++ ..+|.+|+.+
T Consensus 54 ~~~~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~-~~~~e~~~~~~l~~~~vdGiIi~~ 122 (333)
T COG1609 54 RTGRTKTIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDD-DPEKEREYLETLLQKRVDGLILLG 122 (333)
T ss_pred HhCCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCC-CHHHHHHHHHHHHHcCCCEEEEec
Confidence 344788999999988888889999999999999999988888887 776632 22 2699999998
No 14
>PRK07188 nicotinate phosphoribosyltransferase; Provisional
Probab=60.98 E-value=17 Score=38.02 Aligned_cols=42 Identities=17% Similarity=0.360 Sum_probs=36.8
Q ss_pred CcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHHHHcCCC----CCcEE
Q 011028 290 GYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFP----ECDVF 331 (495)
Q Consensus 290 ~~~~~i~~L~~li~~~G-Kk~y~~~vgkln~aKLaNF~----eID~f 331 (495)
....+++++++.|.++| .+.-+++.|-+|+.+++.|. .||+|
T Consensus 261 ~~~~l~~~vr~~Ld~~g~~~vkI~aSgGine~~I~~~~~~g~piD~~ 307 (352)
T PRK07188 261 VNPELIKALRKALDENGGKHVKIIVSSGFDAKKIREFEAQNVPVDIY 307 (352)
T ss_pred ccHHHHHHHHHHHhhCCCCCcEEEEeCCCCHHHHHHHHHcCCCccEE
Confidence 35899999999999999 88889999999999999984 27776
No 15
>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor
Probab=60.90 E-value=14 Score=35.72 Aligned_cols=74 Identities=16% Similarity=0.247 Sum_probs=49.3
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc-CC--CCCcEEEEecCCCccc--ccccCCCCccc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA-NF--PECDVFINVSCAQTAL--LDSKEFLAPVI 352 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa-NF--~eID~fV~vaCPr~si--~d~~~f~kPVi 352 (495)
+||+++.++.-..+..+++.+++.++++|....+...+ +++... .+ ..+|+.|+.+|....- ....+...|+|
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~--~~~~~~~~l~~~~vdgii~~~~~~~~~~~~~~~~~~ipvV 78 (261)
T cd06272 1 TIGLIWPSVSRVALTELVTGINQAISKNGYNMNVSITP--SLAEAEDLFKENRFDGVIIFGESASDVEYLYKIKLAIPVV 78 (261)
T ss_pred CEEEEecCCCchhHHHHHHHHHHHHHHcCCEEEEEecc--cHHHHHHHHHHcCcCEEEEeCCCCChHHHHHHHHcCCCEE
Confidence 58999998877777899999999999999876666554 333221 22 2699999988753221 12233445665
Q ss_pred C
Q 011028 353 T 353 (495)
Q Consensus 353 T 353 (495)
+
T Consensus 79 ~ 79 (261)
T cd06272 79 S 79 (261)
T ss_pred E
Confidence 4
No 16
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=59.90 E-value=17 Score=35.02 Aligned_cols=75 Identities=13% Similarity=0.240 Sum_probs=50.0
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCcEEEEecCCCccc--ccccCCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCAQTAL--LDSKEFLA 349 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaN----F--~eID~fV~vaCPr~si--~d~~~f~k 349 (495)
+||+|+..+.-..+..+++.+.+.+++.|....++.. .-++++... + ..+|+.|+.++...+. ....+-..
T Consensus 1 ~igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~~~~i 79 (264)
T cd06274 1 TIGLIIPDLENRSFARIAKRLEALARERGYQLLIACS-DDDPETERETVETLIARQVDALIVAGSLPPDDPYYLCQKAGL 79 (264)
T ss_pred CEEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEeC-CCCHHHHHHHHHHHHHcCCCEEEEcCCCCchHHHHHHHhcCC
Confidence 4899999888777889999999999999887644433 345554322 1 1699999998864331 12223344
Q ss_pred cccC
Q 011028 350 PVIT 353 (495)
Q Consensus 350 PViT 353 (495)
|||+
T Consensus 80 pvV~ 83 (264)
T cd06274 80 PVVA 83 (264)
T ss_pred CEEE
Confidence 6654
No 17
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=59.53 E-value=26 Score=35.07 Aligned_cols=64 Identities=14% Similarity=0.156 Sum_probs=44.5
Q ss_pred HhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecCC
Q 011028 273 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 337 (495)
Q Consensus 273 ar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaCP 337 (495)
.+..++||+|+..+.---+..+++.+.+.++++|....++ ...-++++.. .+ ..+|.+|+++..
T Consensus 56 ~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~-~~~~~~~~~~~~~~~l~~~~vdGvIi~~~~ 125 (311)
T TIGR02405 56 GGSDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYDPIIM-ESQFSPQLTNEHLSVLQKRNVDGVILFGFT 125 (311)
T ss_pred cCCCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCeEEEe-cCCCChHHHHHHHHHHHhcCCCEEEEeCCC
Confidence 3456799999987655556789999999999999885544 3434554322 12 259999998653
No 18
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=59.45 E-value=14 Score=35.90 Aligned_cols=64 Identities=14% Similarity=0.254 Sum_probs=45.4
Q ss_pred cCCeEEEEEcc-------ccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC---CCCcEEEEecCCC
Q 011028 275 DANIIGVLVGT-------LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF---PECDVFINVSCAQ 338 (495)
Q Consensus 275 ~A~~~GIlvgT-------l~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF---~eID~fV~vaCPr 338 (495)
..++||||+.. ..-..+..+++.+++.+++.|.+..++..+.-...++..+ ..+|++|+.+|..
T Consensus 2 ~s~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~~~v~~~~~~~~~~~~~~l~~~~~dgiii~~~~~ 75 (275)
T cd06295 2 RTDTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYDLLLSFVSSPDRDWLARYLASGRADGVILIGQHD 75 (275)
T ss_pred CceEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCEEEEEeCCchhHHHHHHHHHhCCCCEEEEeCCCC
Confidence 46789999954 3334567899999999999999987776654323333221 2699999988753
No 19
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=59.44 E-value=16 Score=35.98 Aligned_cols=61 Identities=16% Similarity=0.195 Sum_probs=42.9
Q ss_pred eEEEEEcc-----ccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC--CCCcEEEEecCCCc
Q 011028 278 IIGVLVGT-----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF--PECDVFINVSCAQT 339 (495)
Q Consensus 278 ~~GIlvgT-----l~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF--~eID~fV~vaCPr~ 339 (495)
+||+|+-+ ..-..+..+++.+.+.+++.|....++.... ....+.++ ..+|.+++.+|+..
T Consensus 1 ~igvi~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~~~dgiii~~~~~~ 68 (283)
T cd06279 1 AVGVVLTDSLSYAFSDPVASQFLAGVAEVLDAAGVNLLLLPASS-EDSDSALVVSALVDGFIVYGVPRD 68 (283)
T ss_pred CEEEEeCCcccccccCccHHHHHHHHHHHHHHCCCEEEEecCcc-HHHHHHHHHhcCCCEEEEeCCCCC
Confidence 48999866 4445557899999999999998876665543 22333333 26999999998754
No 20
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=57.43 E-value=19 Score=34.35 Aligned_cols=75 Identities=21% Similarity=0.181 Sum_probs=49.8
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEecCCCcc----cccccC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA----LLDSKE 346 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~s----i~d~~~ 346 (495)
+||+|+....-..+..+++.+++.++++|.+.-++-.+. ++++ |.+- .+|++++.++.... +.....
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~l~~~-~vdgvi~~~~~~~~~~~~~~~l~~ 78 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDAQN-DVSKQIQQIEDLIAQ-GVDGIIISPVDSAALTPALKKANA 78 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECCCC-CHHHHHHHHHHHHHc-CCCEEEEeCCCchhHHHHHHHHHH
Confidence 589999766556778899999999999887765555543 5543 3333 69999988875332 222334
Q ss_pred CCCcccCH
Q 011028 347 FLAPVITP 354 (495)
Q Consensus 347 f~kPViTP 354 (495)
...|+|+.
T Consensus 79 ~~ip~V~~ 86 (267)
T cd01536 79 AGIPVVTV 86 (267)
T ss_pred CCCcEEEe
Confidence 45677654
No 21
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=57.20 E-value=15 Score=31.19 Aligned_cols=70 Identities=23% Similarity=0.369 Sum_probs=48.1
Q ss_pred HHHHHH-HHHHHHHhcCCeEEEEEccccccCc--HHHHHHHHHHHHHcCCcEEEEEcC---CCCHHHHcCC-CCCcEEE
Q 011028 261 KILKRR-YYLVEKAKDANIIGVLVGTLGVAGY--LHMIHQMKELITKAGKKAYTLVMG---KPNPAKLANF-PECDVFI 332 (495)
Q Consensus 261 r~l~rR-y~~I~kar~A~~~GIlvgTl~~q~~--~~~i~~L~~li~~~GKk~y~~~vg---kln~aKLaNF-~eID~fV 332 (495)
..|.++ |..++...+|+.+ |++|=++... .+++++|+++.+...+...+++.| ...+++|... |++|+|+
T Consensus 21 ~~l~~~G~~~~~~~e~AD~i--iiNTC~V~~~Ae~k~~~~i~~l~~~~~~~~~ivv~GC~aq~~~~~l~~~~p~vd~v~ 97 (98)
T PF00919_consen 21 SILQAAGYEIVDDPEEADVI--IINTCTVRESAEQKSRNRIRKLKKLKKPGAKIVVTGCMAQRYGEELKKEFPEVDLVV 97 (98)
T ss_pred HHHHhcCCeeecccccCCEE--EEEcCCCCcHHHHHHHHHHHHHHHhcCCCCEEEEEeCccccChHHHHhhCCCeEEEe
Confidence 334444 5566666789986 5555555444 688888888887764667788887 5567888765 6689885
No 22
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=55.66 E-value=23 Score=33.99 Aligned_cols=58 Identities=10% Similarity=0.147 Sum_probs=43.2
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HHcCCCCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~a-------KLaNF~eID~fV~vaCP 337 (495)
+||+|+..+.-..+..+++.+++.+++.|....+.. ..-+++ +|.+ ..+|++|+.+++
T Consensus 1 ~i~vi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~-~~vdgiii~~~~ 65 (268)
T cd06298 1 TVGVIIPDITNSYFAELARGIDDIATMYKYNIILSN-SDNDKEKELKVLNNLLA-KQVDGIIFMGGK 65 (268)
T ss_pred CEEEEECCCcchHHHHHHHHHHHHHHHcCCeEEEEe-CCCCHHHHHHHHHHHHH-hcCCEEEEeCCC
Confidence 489999888777788999999999999998765553 444443 2222 369999998765
No 23
>cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=55.25 E-value=16 Score=35.91 Aligned_cols=76 Identities=16% Similarity=0.081 Sum_probs=51.0
Q ss_pred CeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCCCccc----ccccC
Q 011028 277 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQTAL----LDSKE 346 (495)
Q Consensus 277 ~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCPr~si----~d~~~ 346 (495)
++||+|+.++.-..+..+++.+.+.+++.|....+ .-+.-++++. .+| ..+|++|++++..... ...++
T Consensus 1 ~~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~~~~-~~~~~~~~~~~~~i~~l~~~~vdgiil~~~~~~~~~~~~~~~~~ 79 (280)
T cd06315 1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRI-LDGRGSEAGQAAALNQAIALKPDGIVLGGVDAAELQAELELAQK 79 (280)
T ss_pred CeEEEEecccCCcHHHHHHHHHHHHHHHcCcEEEE-ECCCCCHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHHHHHHHHH
Confidence 57999999988777789999999999999976433 3444565543 222 2699999998653321 12233
Q ss_pred CCCcccC
Q 011028 347 FLAPVIT 353 (495)
Q Consensus 347 f~kPViT 353 (495)
...|||.
T Consensus 80 ~~iPvV~ 86 (280)
T cd06315 80 AGIPVVG 86 (280)
T ss_pred CCCCEEE
Confidence 4556654
No 24
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=54.98 E-value=32 Score=32.98 Aligned_cols=77 Identities=18% Similarity=0.171 Sum_probs=48.2
Q ss_pred eEEEEEccc----cccCcHHHHHHHHHHHHHcCCcEEEEEcCCC-CH----HHHcCCCCCcEEEEecCCCcc--cccccC
Q 011028 278 IIGVLVGTL----GVAGYLHMIHQMKELITKAGKKAYTLVMGKP-NP----AKLANFPECDVFINVSCAQTA--LLDSKE 346 (495)
Q Consensus 278 ~~GIlvgTl----~~q~~~~~i~~L~~li~~~GKk~y~~~vgkl-n~----aKLaNF~eID~fV~vaCPr~s--i~d~~~ 346 (495)
.||+|+.+. +-..+..+++.+++.+++.|....++....- +. .++.+-..+|++|+.+|.... +....+
T Consensus 1 ~igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~ 80 (268)
T cd06271 1 AIGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYDLVLLPVDPDEDPLEVYRRLVESGLVDGVIISRTRPDDPRVALLLE 80 (268)
T ss_pred CeEEEeCCcccccCCccHHHHHHHHHHHHHHCCceEEEecCCCcHHHHHHHHHHHHcCCCCEEEEecCCCCChHHHHHHh
Confidence 489999773 3466678999999999999988766665432 11 122222369999998875331 111223
Q ss_pred CCCcccCH
Q 011028 347 FLAPVITP 354 (495)
Q Consensus 347 f~kPViTP 354 (495)
-..|+|..
T Consensus 81 ~~ipvV~~ 88 (268)
T cd06271 81 RGFPFVTH 88 (268)
T ss_pred cCCCEEEE
Confidence 34576653
No 25
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=54.95 E-value=16 Score=35.16 Aligned_cols=75 Identities=19% Similarity=0.163 Sum_probs=49.9
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HHcCCCCCcEEEEecCCCcc--cccccCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQTA--LLDSKEFL 348 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~a-------KLaNF~eID~fV~vaCPr~s--i~d~~~f~ 348 (495)
+||+++..+.-..|..+++.+.+.+++.|....++ -+.-++. +|.+- .+|+++++++.... +....+-.
T Consensus 1 ~i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~-~~~~~~~~~~~~~~~l~~~-~vdgiii~~~~~~~~~~~~l~~~~ 78 (268)
T cd06273 1 TIGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVA-SSGYDLDREYAQARKLLER-GVDGLALIGLDHSPALLDLLARRG 78 (268)
T ss_pred CeEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEe-cCCCCHHHHHHHHHHHHhc-CCCEEEEeCCCCCHHHHHHHHhCC
Confidence 58999988877778899999999999999665443 3333444 33332 69999998875321 11223345
Q ss_pred CcccCH
Q 011028 349 APVITP 354 (495)
Q Consensus 349 kPViTP 354 (495)
.|+|+.
T Consensus 79 iPvv~~ 84 (268)
T cd06273 79 VPYVAT 84 (268)
T ss_pred CCEEEE
Confidence 677764
No 26
>COG0622 Predicted phosphoesterase [General function prediction only]
Probab=54.58 E-value=18 Score=33.91 Aligned_cols=79 Identities=20% Similarity=0.181 Sum_probs=49.4
Q ss_pred eeEEEEcCCccccCccchhh--hcccCCcEEEEecCCCCCCC-----C--CCCeEEEccccCCChHH--HHHHHhhhhcC
Q 011028 64 IGLFVMADTTYGSCCVDEVG--ASHVDADCVIHYGHTCLSPT-----S--TLPAFFVFGKASINTSN--CIENLSKHALT 132 (495)
Q Consensus 64 ~~v~IlaDtsYGsCCVDeva--A~hv~aD~iVHyGhsCls~~-----~--~lpviYVf~~~~id~~~--~~~~l~~~~~~ 132 (495)
.++.|++||=...|++.... ...-++|+|||-|+.=.+.+ . .-++++|+|+-..+... +=+.. .+.-
T Consensus 2 m~ilviSDtH~~~~~~~~~~~~~~~~~~d~vih~GD~~~~~~~~~l~~~~~~~i~~V~GN~D~~~~~~~~p~~~--~~~~ 79 (172)
T COG0622 2 MKILVISDTHGPLRAIEKALKIFNLEKVDAVIHAGDSTSPFTLDALEGGLAAKLIAVRGNCDGEVDQEELPEEL--VLEV 79 (172)
T ss_pred cEEEEEeccCCChhhhhHHHHHhhhcCCCEEEECCCcCCccchHHhhcccccceEEEEccCCCccccccCChhH--eEEE
Confidence 36889999999998654332 33569999999999876532 1 35678999976554321 00111 1112
Q ss_pred CCCcEEEEeccc
Q 011028 133 NGKPILVLYGLE 144 (495)
Q Consensus 133 ~~~~v~l~~dvq 144 (495)
.+.++.++-.=+
T Consensus 80 ~g~ki~l~HGh~ 91 (172)
T COG0622 80 GGVKIFLTHGHL 91 (172)
T ss_pred CCEEEEEECCCc
Confidence 345788876633
No 27
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=53.02 E-value=51 Score=33.24 Aligned_cols=79 Identities=22% Similarity=0.321 Sum_probs=53.2
Q ss_pred HhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEecCCCcc--c-c
Q 011028 273 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA--L-L 342 (495)
Q Consensus 273 ar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~s--i-~ 342 (495)
.+..++||+|+..+.-..+..+++.+.+.++++|...+++..+ -++++ |.+ ..+|++++.+..... + .
T Consensus 61 ~~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~~~-~~~~~~~~~~~~l~~-~~vdgiIi~~~~~~~~~~~~ 138 (342)
T PRK10014 61 GGQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQGG-KDGEQLAQRFSTLLN-QGVDGVVIAGAAGSSDDLRE 138 (342)
T ss_pred cCCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHh-CCCCEEEEeCCCCCcHHHHH
Confidence 3456899999988776677889999999999999776655433 34443 223 269999998765321 1 1
Q ss_pred cccCCCCcccC
Q 011028 343 DSKEFLAPVIT 353 (495)
Q Consensus 343 d~~~f~kPViT 353 (495)
...+...|+|+
T Consensus 139 ~l~~~~iPvV~ 149 (342)
T PRK10014 139 MAEEKGIPVVF 149 (342)
T ss_pred HHhhcCCCEEE
Confidence 22344567775
No 28
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=52.31 E-value=16 Score=33.61 Aligned_cols=66 Identities=21% Similarity=0.265 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCCc
Q 011028 260 LKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 339 (495)
Q Consensus 260 ~r~l~rRy~~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr~ 339 (495)
+-++++.-+.+++|+|- .+-..+..+-|+.+|-|+--..-+.+...+.-.|+.+|-+.+++||+-
T Consensus 29 ~H~~~~~dYY~~~a~di---------------~~e~~~~lr~i~~~G~kv~c~gnks~~~p~~~a~~p~d~~~nL~~p~p 93 (188)
T COG5136 29 KHGLMRKDYYMEMAEDI---------------AAEMASILRDIKTAGEKVECEGNKSTSYPPFPAFPPGDFYLNLALPEP 93 (188)
T ss_pred HHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHhhcCceEEeccCCccCCCCcccCCccchhhhccCCCC
Confidence 34677777788888741 112234555667789888888888899999989999999999999987
Q ss_pred c
Q 011028 340 A 340 (495)
Q Consensus 340 s 340 (495)
+
T Consensus 94 p 94 (188)
T COG5136 94 P 94 (188)
T ss_pred C
Confidence 6
No 29
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=52.27 E-value=17 Score=35.26 Aligned_cols=62 Identities=10% Similarity=-0.041 Sum_probs=44.2
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHHc----CC--CCCcEEEEecCCCc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLA----NF--PECDVFINVSCAQT 339 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vg-kln~aKLa----NF--~eID~fV~vaCPr~ 339 (495)
+||+|+.++.-..+..+++.+++.++++|.+..++..+ .=++++.. ++ ..+|..|+.++...
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgvii~~~~~~ 69 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQGPASETDVAGQVNLLENAIARGPDAILLAPTDAK 69 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHHcCCEEEEecCccCCCHHHHHHHHHHHHHhCCCEEEEcCCChh
Confidence 48999998876777899999999999999876555432 23554322 21 26999999877653
No 30
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=51.83 E-value=17 Score=36.38 Aligned_cols=61 Identities=20% Similarity=0.236 Sum_probs=47.8
Q ss_pred CeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH------HcCCCCCcEEEEecCCCc
Q 011028 277 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK------LANFPECDVFINVSCAQT 339 (495)
Q Consensus 277 ~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK------LaNF~eID~fV~vaCPr~ 339 (495)
++||+|+..+.-.-+.++++.+.+.++++|....++..+.= +++ |.+- .+|.+|+.+....
T Consensus 2 ~~IGvivp~~~npff~~ii~gIe~~a~~~Gy~l~l~~t~~~-~~~e~~i~~l~~~-~vDGiI~~s~~~~ 68 (279)
T PF00532_consen 2 KTIGVIVPDISNPFFAEIIRGIEQEAREHGYQLLLCNTGDD-EEKEEYIELLLQR-RVDGIILASSEND 68 (279)
T ss_dssp CEEEEEESSSTSHHHHHHHHHHHHHHHHTTCEEEEEEETTT-HHHHHHHHHHHHT-TSSEEEEESSSCT
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHHcCCEEEEecCCCc-hHHHHHHHHHHhc-CCCEEEEecccCC
Confidence 68999999998888899999999999999998877666633 332 2222 6999999955444
No 31
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=51.59 E-value=41 Score=32.45 Aligned_cols=73 Identities=19% Similarity=0.247 Sum_probs=49.9
Q ss_pred EEEEEcc---ccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEecCCCcccc-cccCC
Q 011028 279 IGVLVGT---LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTALL-DSKEF 347 (495)
Q Consensus 279 ~GIlvgT---l~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~si~-d~~~f 347 (495)
||+|+.+ ++-..+..+++.+++.+++.|.+..+...+. +.++ |.+ ..+|++|+.++...+.. ...+-
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~l~~-~~vdgiii~~~~~~~~~~~l~~~ 79 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKFVSD-EDEEEFELPSFLED-GKVDGIILLGGISTEYIKEIKEL 79 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEeCCC-ChHHHHHHHHHHHH-CCCCEEEEeCCCChHHHHHHhhc
Confidence 7999988 5666778999999999999998887776653 3321 222 26999999887654332 22333
Q ss_pred CCcccC
Q 011028 348 LAPVIT 353 (495)
Q Consensus 348 ~kPViT 353 (495)
..|+|+
T Consensus 80 ~ipvV~ 85 (268)
T cd06277 80 GIPFVL 85 (268)
T ss_pred CCCEEE
Confidence 457664
No 32
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=51.10 E-value=45 Score=32.19 Aligned_cols=60 Identities=27% Similarity=0.369 Sum_probs=45.0
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEecCCCc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQT 339 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~ 339 (495)
+||+|+..+.-..+..+++.+++.++++|.+.-++. +.-++++ |.+ ..+|++|+.+|...
T Consensus 1 ~igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~-~~~~~~~~~~~i~~~~~-~~vdgii~~~~~~~ 67 (268)
T cd06270 1 TIGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITA-GHHSAEKEREAIEFLLE-RRCDALILHSKALS 67 (268)
T ss_pred CEEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEe-CCCchHHHHHHHHHHHH-cCCCEEEEecCCCC
Confidence 489999998888889999999999999998865543 3344443 223 36999999988533
No 33
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=50.93 E-value=41 Score=33.76 Aligned_cols=63 Identities=16% Similarity=0.261 Sum_probs=45.2
Q ss_pred HhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEecCC
Q 011028 273 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCA 337 (495)
Q Consensus 273 ar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~vaCP 337 (495)
.+..++||+|+..+.-..+..+++.+.+.++++|....++..+ -++++ |.+- .+|..|+.++.
T Consensus 58 ~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~-~vdgiIi~~~~ 127 (328)
T PRK11303 58 AGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSD-DQPDNEMRCAEHLLQR-QVDALIVSTSL 127 (328)
T ss_pred cCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHHc-CCCEEEEcCCC
Confidence 3346799999987766677889999999999999887655443 23332 2222 69999997763
No 34
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=50.85 E-value=58 Score=32.16 Aligned_cols=81 Identities=17% Similarity=0.224 Sum_probs=60.6
Q ss_pred HHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEE---------EcCCCCHHHHcC------CCCCcEEEEecC
Q 011028 272 KAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTL---------VMGKPNPAKLAN------FPECDVFINVSC 336 (495)
Q Consensus 272 kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~---------~vgkln~aKLaN------F~eID~fV~vaC 336 (495)
++.++++|+|+- -+-.++-+++++-++++|.++--+ -++++.|+-+.. -++.|+.++. |
T Consensus 116 ~alg~~RIalvT-----PY~~~v~~~~~~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aDAifis-C 189 (239)
T TIGR02990 116 AALGVRRISLLT-----PYTPETSRPMAQYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDADALFLS-C 189 (239)
T ss_pred HHcCCCEEEEEC-----CCcHHHHHHHHHHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCCEEEEe-C
Confidence 555899999985 344688899999999999998666 577788887643 3578886655 9
Q ss_pred CCccccc-----ccCCCCcccCHHHHH
Q 011028 337 AQTALLD-----SKEFLAPVITPFEAM 358 (495)
Q Consensus 337 Pr~si~d-----~~~f~kPViTP~El~ 358 (495)
=.+...+ ..++-|||||.--+.
T Consensus 190 TnLrt~~vi~~lE~~lGkPVlsSNqat 216 (239)
T TIGR02990 190 TALRAATCAQRIEQAIGKPVVTSNQAT 216 (239)
T ss_pred CCchhHHHHHHHHHHHCCCEEEHHHHH
Confidence 8886443 356899999875544
No 35
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=50.63 E-value=29 Score=33.59 Aligned_cols=60 Identities=17% Similarity=0.209 Sum_probs=44.1
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQ 338 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCPr 338 (495)
+||+|+....-..+..+++.+.+.+++.|....+. ...-++++. ..+ ..+|++++.+|..
T Consensus 1 ~Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~ 66 (269)
T cd06281 1 TIGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIA-NSLNDPERELEILRSFEQRRMDGIIIAPGDE 66 (269)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHcCCEEEEE-eCCCChHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 58999988877777899999999999999885544 344455432 122 2699999999853
No 36
>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=50.18 E-value=48 Score=31.71 Aligned_cols=74 Identities=16% Similarity=0.238 Sum_probs=49.5
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEecCCCcc--cccccCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA--LLDSKEFL 348 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~s--i~d~~~f~ 348 (495)
+||+|+....-..+..+++.+++.+++.|....++. ..-+++. |.+. .+|++++.++.... +...++--
T Consensus 1 ~igvi~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~-~~dgiii~~~~~~~~~l~~~~~~~ 78 (267)
T cd06283 1 LIGVIVADITNPFSSLVLKGIEDVCRAHGYQVLVCN-SDNDPEKEKEYLESLLAY-QVDGLIVNPTGNNKELYQRLAKNG 78 (267)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEc-CCCCHHHHHHHHHHHHHc-CcCEEEEeCCCCChHHHHHHhcCC
Confidence 589999887777778999999999999997764443 3335443 3332 69999998764332 12223344
Q ss_pred CcccC
Q 011028 349 APVIT 353 (495)
Q Consensus 349 kPViT 353 (495)
.|||+
T Consensus 79 ipvV~ 83 (267)
T cd06283 79 KPVVL 83 (267)
T ss_pred CCEEE
Confidence 57665
No 37
>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription
Probab=49.51 E-value=35 Score=32.79 Aligned_cols=59 Identities=19% Similarity=0.268 Sum_probs=42.5
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC------CCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF------~eID~fV~vaCP 337 (495)
+||+|+..+..-.+..+++.+++.+++.|.+..++.. .-++++-..+ ..+|++|+.++.
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~~~~~~~dgiii~~~~ 65 (265)
T cd06291 1 LIGLIVPTISNPFFSELARAVEKELYKKGYKLILCNS-DNDPEKEREYLEMLRQNQVDGIIAGTHN 65 (265)
T ss_pred CEEEEECCCCChhHHHHHHHHHHHHHHCCCeEEEecC-CccHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 5899998887777789999999999999987654433 3344433221 158999998874
No 38
>PLN03241 magnesium chelatase subunit H; Provisional
Probab=49.32 E-value=11 Score=46.12 Aligned_cols=28 Identities=39% Similarity=0.707 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-C---------------CCCCC--CCCCCeEEEc
Q 011028 85 SHVDADCVIHYG-H---------------TCLSP--TSTLPAFFVF 112 (495)
Q Consensus 85 ~hv~aD~iVHyG-h---------------sCls~--~~~lpviYVf 112 (495)
+..+||+||||| | +|.+. +..+|.+|+|
T Consensus 663 ~~F~ADAvIHfGtHGtLEwLPGK~vGLS~~cwPd~LiGdlPniY~Y 708 (1353)
T PLN03241 663 DGYGADAVIHFGMHGTVEWLPGQPLGNDRLSWSDELLGGLPNVYVY 708 (1353)
T ss_pred cccCCCeEEEccCCcCcccCCCccccCCcccChHHHhCCCCEEEEE
No 39
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=49.15 E-value=31 Score=32.99 Aligned_cols=74 Identities=20% Similarity=0.225 Sum_probs=50.2
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEecCCCc-cc-ccccCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQT-AL-LDSKEFL 348 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~-si-~d~~~f~ 348 (495)
+||+|+....-..+..+++.+++.+++.|.+..++. ..-++++ |.+ ..+|++|++++... .+ ...++..
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~-~~~dgii~~~~~~~~~~~~~~~~~~ 78 (259)
T cd01542 1 LIGVIVPRLDSFSTSRTVKGILAALYENGYQMLLMN-TNFSIEKEIEALELLAR-QKVDGIILLATTITDEHREAIKKLN 78 (259)
T ss_pred CeEEEecCCccchHHHHHHHHHHHHHHCCCEEEEEe-CCCCHHHHHHHHHHHHh-cCCCEEEEeCCCCCHHHHHHHhcCC
Confidence 489999887766667999999999999998865543 3445554 223 37999999876432 11 2234445
Q ss_pred CcccC
Q 011028 349 APVIT 353 (495)
Q Consensus 349 kPViT 353 (495)
.|||+
T Consensus 79 ipvv~ 83 (259)
T cd01542 79 VPVVV 83 (259)
T ss_pred CCEEE
Confidence 67775
No 40
>PLN03069 magnesiumprotoporphyrin-IX chelatase subunit H; Provisional
Probab=48.86 E-value=11 Score=45.63 Aligned_cols=28 Identities=29% Similarity=0.802 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-C---------------CCCCC--CCCCCeEEEc
Q 011028 85 SHVDADCVIHYG-H---------------TCLSP--TSTLPAFFVF 112 (495)
Q Consensus 85 ~hv~aD~iVHyG-h---------------sCls~--~~~lpviYVf 112 (495)
+..+||+||||| | +|.+. +..+|.+|.|
T Consensus 600 ~~F~ADAviH~GtHGtlEwLPGK~vGLS~~cwPd~liGdlPniY~Y 645 (1220)
T PLN03069 600 KIFKADAVLHFGTHGSLEFMPGKQVGMSDACYPDSLIGNIPNVYYY 645 (1220)
T ss_pred hhcCCCEEEEcCCCCCcccCCCccccCCcccChHHHhCCCCEEeEE
No 41
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=48.66 E-value=40 Score=34.00 Aligned_cols=64 Identities=17% Similarity=0.239 Sum_probs=45.4
Q ss_pred HhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCcEEEEecCC
Q 011028 273 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 337 (495)
Q Consensus 273 ar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK----LaNF--~eID~fV~vaCP 337 (495)
.+..++||+++.++.-..+..+++.+.+.++++|.+..+...+ -++++ +.+| ..+|.+|+.++.
T Consensus 60 ~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~vdgiI~~~~~ 129 (331)
T PRK14987 60 NATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAHYG-YKPEMEQERLESMLSWNIDGLILTERT 129 (331)
T ss_pred hCCCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEecCC-CCHHHHHHHHHHHHhcCCCEEEEcCCC
Confidence 3456799999988776677899999999999999776544333 23322 2222 269999997653
No 42
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=48.39 E-value=60 Score=32.11 Aligned_cols=63 Identities=10% Similarity=0.057 Sum_probs=45.2
Q ss_pred HhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecC
Q 011028 273 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 336 (495)
Q Consensus 273 ar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaC 336 (495)
.+..++||+|+..+.-..+..+++.+++.+++.|....++.... +.++-. .+ ..+|.+++.++
T Consensus 32 ~~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~-~~~~~~~~i~~l~~~~vDgiIi~~~ 100 (309)
T PRK11041 32 RNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVLIGDCAH-QNQQEKTFVNLIITKQIDGMLLLGS 100 (309)
T ss_pred cCCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCEEEEEeCCC-ChHHHHHHHHHHHHcCCCEEEEecC
Confidence 34568999999877666778999999999999998776654332 333211 11 26999999876
No 43
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=47.39 E-value=43 Score=33.63 Aligned_cols=62 Identities=21% Similarity=0.423 Sum_probs=45.5
Q ss_pred hcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCcEEEEecC
Q 011028 274 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSC 336 (495)
Q Consensus 274 r~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK----LaNF--~eID~fV~vaC 336 (495)
+..++||+++..+.-..+..+++.+.+.++++|....+...+. ++++ +.++ ..+|..|+.++
T Consensus 58 ~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~-~~~~~~~~~~~l~~~~vdgiIi~~~ 125 (327)
T TIGR02417 58 GRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSDD-NPDQEKVVIENLLARQVDALIVASC 125 (327)
T ss_pred CCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCCC-CHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 3468999999887767788999999999999998876655543 4432 2222 26999888765
No 44
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=47.09 E-value=20 Score=35.37 Aligned_cols=75 Identities=19% Similarity=0.220 Sum_probs=48.2
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecCCCcc---c-ccccCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQTA---L-LDSKEF 347 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaCPr~s---i-~d~~~f 347 (495)
+||+|+....-..+..+++.+++.+++.|....++..+ -++++.. ++ ..+|.+|+++|.... + ...++.
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~-~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l~~~ 79 (288)
T cd01538 1 KIGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQNAN-GDPAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAADA 79 (288)
T ss_pred CeEEEEeCCCcHHHHHHHHHHHHHHHHcCCEEEEECCC-CCHHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHHHHC
Confidence 48899987765556788899999999888876655443 3555421 12 258999998875432 1 122345
Q ss_pred CCcccC
Q 011028 348 LAPVIT 353 (495)
Q Consensus 348 ~kPViT 353 (495)
-.|||+
T Consensus 80 ~ipvV~ 85 (288)
T cd01538 80 GIPVIA 85 (288)
T ss_pred CCCEEE
Confidence 567764
No 45
>PRK12493 magnesium chelatase subunit H; Provisional
Probab=46.64 E-value=13 Score=45.58 Aligned_cols=28 Identities=36% Similarity=0.878 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-C---------------CCCCC--CCCCCeEEEc
Q 011028 85 SHVDADCVIHYG-H---------------TCLSP--TSTLPAFFVF 112 (495)
Q Consensus 85 ~hv~aD~iVHyG-h---------------sCls~--~~~lpviYVf 112 (495)
+..+||+||||| | +|.+. +..+|.+|.|
T Consensus 587 ~~F~ADAviH~GtHGtlEwLPGK~vGLS~~cwPd~liG~lP~iY~Y 632 (1310)
T PRK12493 587 KVWGADAVLHFGTHGALEFMPGKQMGMSASCWPDRLIGSLPNFYYY 632 (1310)
T ss_pred hhcCCCEEEECCCCcCcccCCCccccCCcccChHHHhCCCCEEeEE
No 46
>TIGR01753 flav_short flavodoxin, short chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction.
Probab=46.37 E-value=67 Score=27.85 Aligned_cols=55 Identities=16% Similarity=0.278 Sum_probs=42.9
Q ss_pred EEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCC
Q 011028 279 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 338 (495)
Q Consensus 279 ~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr 338 (495)
|-|+.+|.. .+...+++.|.+.+++.|.++-++-+.+.++.+|.+ .|.+ ++++|-
T Consensus 1 v~Iiy~S~t-GnT~~~A~~i~~~~~~~g~~v~~~~~~~~~~~~l~~---~d~i-ilgspt 55 (140)
T TIGR01753 1 ILIVYASMT-GNTEEMANIIAEGLKEAGAEVDLLEVADADAEDLLS---YDAV-LLGCST 55 (140)
T ss_pred CEEEEECCC-cHHHHHHHHHHHHHHhcCCeEEEEEcccCCHHHHhc---CCEE-EEEcCC
Confidence 357888863 567899999999999999999999999999888865 4554 445543
No 47
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=45.01 E-value=53 Score=33.20 Aligned_cols=64 Identities=14% Similarity=0.140 Sum_probs=46.4
Q ss_pred HHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCcEEEEecC
Q 011028 272 KAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSC 336 (495)
Q Consensus 272 kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaN----F--~eID~fV~vaC 336 (495)
+.+..++||+|+..+.-..+..+++.+.+.+++.|.+.+++..+ -++++..+ + ..+|++++.+.
T Consensus 55 ~~~~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~i~~l~~~~vdgiii~~~ 124 (341)
T PRK10703 55 KVNHTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYTLILCNAW-NNLEKQRAYLSMLAQKRVDGLLVMCS 124 (341)
T ss_pred hhCCCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEEeCC-CCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 33456799999988776677889999999999999887766543 34544221 1 15899988764
No 48
>PRK06703 flavodoxin; Provisional
Probab=44.84 E-value=69 Score=28.65 Aligned_cols=55 Identities=11% Similarity=0.050 Sum_probs=42.6
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCP 337 (495)
.+.|+.+|.. -+...+++.|.+.|++.|.++-++-+.+..+..|.+ .|. |+++||
T Consensus 3 kv~IiY~S~t-GnT~~iA~~ia~~l~~~g~~v~~~~~~~~~~~~l~~---~d~-viigsp 57 (151)
T PRK06703 3 KILIAYASMS-GNTEDIADLIKVSLDAFDHEVVLQEMDGMDAEELLA---YDG-IILGSY 57 (151)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHhcCCceEEEehhhCCHHHHhc---CCc-EEEEEC
Confidence 5788999854 566899999999999999998888888887776654 454 555665
No 49
>PRK05723 flavodoxin; Provisional
Probab=44.65 E-value=65 Score=29.36 Aligned_cols=55 Identities=15% Similarity=0.205 Sum_probs=40.5
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCP 337 (495)
.++|+.||-++ +...+.++|.+.++++|.+..++ ...++..|..+ +.|.. ++.|+
T Consensus 2 ~i~I~ygS~tG-~ae~~A~~la~~l~~~g~~~~~~--~~~~~~~~~~~-~~~~l-i~~~s 56 (151)
T PRK05723 2 KVAILSGSVYG-TAEEVARHAESLLKAAGFEAWHN--PRASLQDLQAF-APEAL-LAVTS 56 (151)
T ss_pred eEEEEEEcCch-HHHHHHHHHHHHHHHCCCceeec--CcCCHhHHHhC-CCCeE-EEEEC
Confidence 68999999864 56789999999999999987653 44777788776 34543 44444
No 50
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=44.56 E-value=62 Score=30.99 Aligned_cols=60 Identities=22% Similarity=0.261 Sum_probs=43.8
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEecCCCc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQT 339 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~ 339 (495)
+||+|+....-..+..+++.+++.+++.|....++... -++++ |.+- .+|.+++.++...
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~-~vdgiIi~~~~~~ 67 (265)
T cd06299 1 TIGVIVPDIRNPYFASLATAIQDAASAAGYSTIIGNSD-ENPETENRYLDNLLSQ-RVDGIIVVPHEQS 67 (265)
T ss_pred CEEEEecCCCCccHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHhc-CCCEEEEcCCCCC
Confidence 58999987665666789999999999999887776554 24442 3332 6899999887544
No 51
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=44.50 E-value=39 Score=32.41 Aligned_cols=62 Identities=16% Similarity=0.209 Sum_probs=44.1
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCCCc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQT 339 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCPr~ 339 (495)
+||+|+.+..-..+..+++.+++.+++.|....++..+.-.+++- .++ ..+|+.++.+|...
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~ 68 (264)
T cd01574 1 TIGVVTTDLALHGPSSTLAAIESAAREAGYAVTLSMLAEADEEALRAAVRRLLAQRVDGVIVNAPLDD 68 (264)
T ss_pred CEEEEeCCCCcccHHHHHHHHHHHHHHCCCeEEEEeCCCCchHHHHHHHHHHHhcCCCEEEEeCCCCC
Confidence 589999887766678999999999999998876665554332211 112 25999999988543
No 52
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=44.32 E-value=26 Score=34.58 Aligned_cols=75 Identities=15% Similarity=0.138 Sum_probs=47.5
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecCCCcccc----cccCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQTALL----DSKEF 347 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaCPr~si~----d~~~f 347 (495)
+||+|+.++.-..+..+++.+++.+++.|....++..+.-++++.. .+ ..+|.+|+.+|.....+ ...+.
T Consensus 1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~dgiii~~~~~~~~~~~i~~~~~~ 80 (294)
T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVATTDAQFDPAKQVADIETTISQKPDIIISIPVDPVSTAAAYKKVAEA 80 (294)
T ss_pred CeEEEecCCCChHHHHHHHHHHHHHHHcCCEEEEecCCCCCHHHHHHHHHHHHHhCCCEEEEcCCCchhhhHHHHHHHHc
Confidence 4789998765444467888899999999877654434555565321 11 25899999887643222 22344
Q ss_pred CCccc
Q 011028 348 LAPVI 352 (495)
Q Consensus 348 ~kPVi 352 (495)
-.|||
T Consensus 81 ~iPvV 85 (294)
T cd06316 81 GIKLV 85 (294)
T ss_pred CCcEE
Confidence 45665
No 53
>PRK02126 ribonuclease Z; Provisional
Probab=44.15 E-value=24 Score=36.65 Aligned_cols=34 Identities=9% Similarity=0.007 Sum_probs=23.0
Q ss_pred CceeEEEEcCCccccCccchhhhcccCCcEEEEe
Q 011028 62 KDIGLFVMADTTYGSCCVDEVGASHVDADCVIHY 95 (495)
Q Consensus 62 ~~~~v~IlaDtsYGsCCVDevaA~hv~aD~iVHy 95 (495)
.+..+.++|||.|..-.......-.-+||++||=
T Consensus 241 ~g~~v~y~gDT~~~~~~~~~l~~~a~~aDlLI~E 274 (334)
T PRK02126 241 PGQKIGYVTDIGYTEENLARIVELAAGVDLLFIE 274 (334)
T ss_pred CCCEEEEECCCCCCcccHHHHHHHHcCCCEEEEE
Confidence 4578999999997643222333334589999983
No 54
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=43.75 E-value=41 Score=33.32 Aligned_cols=63 Identities=17% Similarity=0.199 Sum_probs=45.5
Q ss_pred hcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecCC
Q 011028 274 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 337 (495)
Q Consensus 274 r~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaCP 337 (495)
++.++||+|+.++.-..+..+++.+++.++++|....++..+ -++++.. ++ ..+|+.++.++.
T Consensus 24 ~~~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~~~~~~~~-~d~~~~~~~~~~l~~~~~dgiii~~~~ 92 (295)
T PRK10653 24 MAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQ-NNPAKELANVQDLTVRGTKILLINPTD 92 (295)
T ss_pred ccCCeEEEEecCCCChHHHHHHHHHHHHHHHcCCeEEEecCC-CCHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence 468899999998876678899999999999999877655433 2344332 22 258988887654
No 55
>PF00731 AIRC: AIR carboxylase; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process; PDB: 3TRH_O 2YWX_A 2NSL_A 1D7A_A 2NSJ_A 1QCZ_A 2ATE_A 2NSH_A 3RG8_C 3RGG_D ....
Probab=43.68 E-value=67 Score=29.54 Aligned_cols=72 Identities=22% Similarity=0.328 Sum_probs=46.8
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHHcCC------CCCcEEEEecCCCccccc--ccCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANF------PECDVFINVSCAQTALLD--SKEFL 348 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vg-kln~aKLaNF------~eID~fV~vaCPr~si~d--~~~f~ 348 (495)
.++||.|+ ..-+.+.+..++.|++-|..+-+-+.+ .=+|++|..| .++|+||.+|==...+-- ...-.
T Consensus 2 ~V~Ii~gs---~SD~~~~~~a~~~L~~~gi~~~~~V~saHR~p~~l~~~~~~~~~~~~~viIa~AG~~a~Lpgvva~~t~ 78 (150)
T PF00731_consen 2 KVAIIMGS---TSDLPIAEEAAKTLEEFGIPYEVRVASAHRTPERLLEFVKEYEARGADVIIAVAGMSAALPGVVASLTT 78 (150)
T ss_dssp EEEEEESS---GGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHTTTTTESEEEEEEESS--HHHHHHHHSS
T ss_pred eEEEEeCC---HHHHHHHHHHHHHHHHcCCCEEEEEEeccCCHHHHHHHHHHhccCCCEEEEEECCCcccchhhheeccC
Confidence 58899986 456788899999999999888776655 6677777655 257888887766655431 12236
Q ss_pred Cccc
Q 011028 349 APVI 352 (495)
Q Consensus 349 kPVi 352 (495)
+|||
T Consensus 79 ~PVI 82 (150)
T PF00731_consen 79 LPVI 82 (150)
T ss_dssp S-EE
T ss_pred CCEE
Confidence 6665
No 56
>PRK09526 lacI lac repressor; Reviewed
Probab=43.49 E-value=75 Score=32.04 Aligned_cols=62 Identities=11% Similarity=0.129 Sum_probs=45.5
Q ss_pred hcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCcEEEEec
Q 011028 274 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVS 335 (495)
Q Consensus 274 r~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK----LaNF--~eID~fV~va 335 (495)
+..++||+++..+.-..+..+++.+.+.+++.|....++..+.-++++ |.++ ..+|.+++.+
T Consensus 61 ~~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~~~i~~~~~~~~~~~~~~l~~l~~~~vdGiii~~ 128 (342)
T PRK09526 61 KQSLTIGLATTSLALHAPSQIAAAIKSRADQLGYSVVISMVERSGVEACQAAVNELLAQRVSGVIINV 128 (342)
T ss_pred CCCceEEEEeCCCCcccHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHHhcCCCEEEEec
Confidence 456799999998876677899999999999999887766555433322 2333 2699998863
No 57
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=43.45 E-value=81 Score=31.51 Aligned_cols=64 Identities=11% Similarity=0.151 Sum_probs=46.5
Q ss_pred HhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCcEEEEecCC
Q 011028 273 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 337 (495)
Q Consensus 273 ar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK----LaNF--~eID~fV~vaCP 337 (495)
.+..++||+|+....-..|..+++.+.+.+++.|.+..++..+ -++++ |.+| ..+|.+|+.+..
T Consensus 53 ~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~~vdGiI~~~~~ 122 (327)
T PRK10423 53 LNQTRTIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTE-GDEQRMNRNLETLMQKRVDGLLLLCTE 122 (327)
T ss_pred hCCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHHcCCCEEEEeCCC
Confidence 4567899999988776778899999999999999886554433 34433 2222 269999987654
No 58
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=43.31 E-value=44 Score=32.10 Aligned_cols=59 Identities=19% Similarity=0.229 Sum_probs=43.4
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaCP 337 (495)
+||+|+..+.-..+..+++.+.+.+++.|....++ ...-++++.. ++ ..+|.+++.+|.
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~gy~~~~~-~~~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (265)
T cd06290 1 TIGVLTQDFASPFYGRILKGMERGLNGSGYSPIIA-TGHWNQSRELEALELLKSRRVDALILLGGD 65 (265)
T ss_pred CEEEEECCCCCchHHHHHHHHHHHHHHCCCEEEEE-eCCCCHHHHHHHHHHHHHCCCCEEEEeCCC
Confidence 58999988876677889999999999999776443 3455665432 22 159999999875
No 59
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=43.17 E-value=39 Score=32.87 Aligned_cols=62 Identities=13% Similarity=0.066 Sum_probs=43.5
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH--HHHcC-CC--CCcEEEEecCCCc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLAN-FP--ECDVFINVSCAQT 339 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~--aKLaN-F~--eID~fV~vaCPr~ 339 (495)
+||+|+..+.-..+..+++.+.+.+++.|....+........ +.+.+ +. .+|.+++.++...
T Consensus 1 ~Igvi~p~~~~~~~~~~~~~i~~~~~~~gy~~~~~~~~~~~~~~~~~~~~l~~~~vdgvi~~~~~~~ 67 (269)
T cd06297 1 TISVLLPVVATEFYRRLLEGIEGALLEQRYDLALFPLLSLARLKRYLESTTLAYLTDGLLLASYDLT 67 (269)
T ss_pred CEEEEeCCCcChhHHHHHHHHHHHHHHCCCEEEEEeCCCcHHHHHHHHHHHHhcCCCEEEEecCccC
Confidence 589999877666678999999999999998877766553211 11221 21 4999999877533
No 60
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=43.09 E-value=55 Score=31.58 Aligned_cols=58 Identities=12% Similarity=0.145 Sum_probs=41.6
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 336 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaC 336 (495)
.||+|+..+.--.+..+++.+.+.+++.|....++. ..-++++-. ++ ..+|..+++++
T Consensus 1 ~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~~~vdgiIi~~~ 64 (273)
T cd06292 1 LVGLLVPELSNPIFPAFAEAIEAALAQYGYTVLLCN-TYRGGVSEADYVEDLLARGVRGVVFISS 64 (273)
T ss_pred CEEEEeCCCcCchHHHHHHHHHHHHHHCCCEEEEEe-CCCChHHHHHHHHHHHHcCCCEEEEeCC
Confidence 489999988777778999999999999998765433 333443221 22 26999999865
No 61
>PRK13405 bchH magnesium chelatase subunit H; Provisional
Probab=42.25 E-value=17 Score=44.14 Aligned_cols=28 Identities=32% Similarity=0.844 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCC--CCCCCeEEEc
Q 011028 85 SHVDADCVIHYG-HT---------------CLSP--TSTLPAFFVF 112 (495)
Q Consensus 85 ~hv~aD~iVHyG-hs---------------Cls~--~~~lpviYVf 112 (495)
+..+||+||||| |- |.+. +..+|.+|.|
T Consensus 593 ~~F~ADAviH~GtHGtlEwLPGK~vGLS~~cwPd~liGdlP~iY~Y 638 (1209)
T PRK13405 593 EDFGADAVLHFGTHGALEFMPGKQAGLSAACWPDRLIGDLPNVYLY 638 (1209)
T ss_pred hhcCCCEEEECCCCcccccCCCccccCCcccChHHHhCCCCEEEEE
No 62
>TIGR02025 BchH magnesium chelatase, H subunit. This model represents the H subunit of the magnesium chelatase complex responsible for magnesium insertion into the protoporphyrin IX ring in the biosynthesis of both chlorophyll and bacteriochlorophyll. In chlorophyll-utilizing species, this gene is known as ChlH, while in bacteriochlorophyll-utilizing spoecies it is called BchH. Subunit H is the largest (~140kDa) of the three subunits (the others being BchD/ChlD and BchI/ChlI), and is known to bind protoporphyrin IX. Subunit H is homologous to the CobN subunit of cobaltochelatase and by anology with that enzyme, subunit H is believed to also bind the magnesium ion which is inserted into the ring. In conjunction with the hydrolysis of ATP by subunits I and D, a conformation change is believed to happen in subunit H causing the magnesium ion insertion into the distorted protoporphyrin ring.
Probab=41.98 E-value=17 Score=44.19 Aligned_cols=28 Identities=36% Similarity=0.933 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCC--CCCCCeEEEc
Q 011028 85 SHVDADCVIHYG-HT---------------CLSP--TSTLPAFFVF 112 (495)
Q Consensus 85 ~hv~aD~iVHyG-hs---------------Cls~--~~~lpviYVf 112 (495)
+..+||+||||| |- |.+. +..+|.+|+|
T Consensus 573 ~~f~ADAviH~GtHGtlEwLPGK~~GLS~~cwPd~liG~lP~iY~Y 618 (1216)
T TIGR02025 573 RDFKADAVLHFGTHGSLEFMPGKQTGLTGECWPDRLLGDLPNFYIY 618 (1216)
T ss_pred hhcCCCEEEECCCCcCcccCCCccccCCcccChHHHhCCCCEEeEE
No 63
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=41.79 E-value=79 Score=31.65 Aligned_cols=63 Identities=14% Similarity=0.220 Sum_probs=44.8
Q ss_pred hcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCC
Q 011028 274 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 337 (495)
Q Consensus 274 r~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCP 337 (495)
+..++||+++..+.-..+..+++.+++.++++|....++. ..-++++. ..| ..+|.+|++++.
T Consensus 57 ~~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~~-~~~~~~~~~~~~~~l~~~~vdGiIi~~~~ 125 (329)
T TIGR01481 57 KRTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILSN-SDEDPEKEVQVLNTLLSKQVDGIIFMGGT 125 (329)
T ss_pred CCCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEEe-CCCCHHHHHHHHHHHHhCCCCEEEEeCCC
Confidence 3567999999887666678899999999999998765543 33343322 122 269999998764
No 64
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=41.29 E-value=70 Score=30.54 Aligned_cols=58 Identities=16% Similarity=0.225 Sum_probs=44.2
Q ss_pred EEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC------CCCcEEEEecCC
Q 011028 279 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 337 (495)
Q Consensus 279 ~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF------~eID~fV~vaCP 337 (495)
||+|+.+++-..+..+++.+++.++++|....++.. .-++++.... ..+|++++.+|.
T Consensus 2 i~~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~-~~~~~~~~~~~~~~~~~~vdgiii~~~~ 65 (267)
T cd06284 2 ILVLVPDIANPFFSEILKGIEDEAREAGYGVLLGDT-RSDPEREQEYLDLLRRKQADGIILLDGS 65 (267)
T ss_pred EEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecC-CCChHHHHHHHHHHHHcCCCEEEEecCC
Confidence 789999988788889999999999999988765544 3455543322 269999998764
No 65
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=41.26 E-value=48 Score=31.89 Aligned_cols=60 Identities=22% Similarity=0.218 Sum_probs=43.0
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ 338 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaCPr 338 (495)
+||+|+....-..+..+++.+.+.+++.|.+..+ ..+.-++++.. .+ ..+|..++..|..
T Consensus 1 ~igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~-~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~ 66 (265)
T cd06285 1 TIGVLVPRLTDTVMATMYEGIEEAAAERGYSTFV-ANTGDNPDAQRRAIEMLLDRRVDGLILGDARS 66 (265)
T ss_pred CEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEE-EeCCCCHHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 5899998887667789999999999999988644 34444554321 11 2589999877653
No 66
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=41.17 E-value=1e+02 Score=31.95 Aligned_cols=110 Identities=21% Similarity=0.293 Sum_probs=72.6
Q ss_pred HHHHHHHHHH-HhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH--HHHcCC-CCCcEEEEecCCC
Q 011028 263 LKRRYYLVEK-AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLANF-PECDVFINVSCAQ 338 (495)
Q Consensus 263 l~rRy~~I~k-ar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~--aKLaNF-~eID~fV~vaCPr 338 (495)
+.++-.+|.+ .=+|++||++-+. +-++...+++.|++.++++|.+.+...+.+.|. .-..+. ..+|++..- |-.
T Consensus 145 v~q~i~lik~~~Pnak~Igv~Y~p-~E~ns~~l~eelk~~A~~~Gl~vve~~v~~~ndi~~a~~~l~g~~d~i~~p-~dn 222 (322)
T COG2984 145 VAQQIELIKALLPNAKSIGVLYNP-GEANSVSLVEELKKEARKAGLEVVEAAVTSVNDIPRAVQALLGKVDVIYIP-TDN 222 (322)
T ss_pred HHHHHHHHHHhCCCCeeEEEEeCC-CCcccHHHHHHHHHHHHHCCCEEEEEecCcccccHHHHHHhcCCCcEEEEe-cch
Confidence 4555666654 4569999999975 557999999999999999999999999988873 333444 357765443 322
Q ss_pred cc------cc-cccCCCCcccCHHHHHHhhCCCCcCccceeeecccc
Q 011028 339 TA------LL-DSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 378 (495)
Q Consensus 339 ~s------i~-d~~~f~kPViTP~El~vAL~~~~~W~g~y~~Df~~l 378 (495)
+. +. -......||+++-+-.+-=|. .-.+-.|+.++
T Consensus 223 ~i~s~~~~l~~~a~~~kiPli~sd~~~V~~Ga----~aA~gvdy~~~ 265 (322)
T COG2984 223 LIVSAIESLLQVANKAKIPLIASDTSSVKEGA----LAALGVDYKDL 265 (322)
T ss_pred HHHHHHHHHHHHHHHhCCCeecCCHHHHhcCc----ceeeccCHHHH
Confidence 21 11 234567788887776664322 12344555554
No 67
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=41.04 E-value=47 Score=31.82 Aligned_cols=59 Identities=19% Similarity=0.213 Sum_probs=44.6
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH-------cCCCCCcEEEEecCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL-------ANFPECDVFINVSCAQ 338 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL-------aNF~eID~fV~vaCPr 338 (495)
+||+|+...+-.-+..+++.+++.+++.|....++. ..-++++. .+ ..+|++++.+|..
T Consensus 1 ~i~~i~~~~~~~~~~~i~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~-~~vdgiii~~~~~ 66 (260)
T cd06286 1 TIGVVLPYINHPYFSQLVDGIEKAALKHGYKVVLLQ-TNYDKEKELEYLELLKT-KQVDGLILCSREN 66 (260)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEe-CCCChHHHHHHHHHHHH-cCCCEEEEeCCCC
Confidence 589999888777788999999999999998876553 34455433 22 2699999988743
No 68
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=40.96 E-value=52 Score=31.44 Aligned_cols=75 Identities=15% Similarity=0.148 Sum_probs=49.1
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEecCCCcc---cccccCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA---LLDSKEF 347 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~s---i~d~~~f 347 (495)
+||+|+...+--.+..+++.+.+.+++.|....++..+ -++.+ |.+. .+|+.|+..+-... +....+.
T Consensus 1 ~igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~-~vdgiii~~~~~~~~~~~~~~~~~ 78 (266)
T cd06282 1 TVGVVLPSLANPVFAECVQGIQEEARAAGYSLLLATTD-YDAEREADAVETLLRQ-RVDGLILTVADAATSPALDLLDAE 78 (266)
T ss_pred CeEEEeCCCCcchHHHHHHHHHHHHHHCCCEEEEeeCC-CCHHHHHHHHHHHHhc-CCCEEEEecCCCCchHHHHHHhhC
Confidence 58999987766667789999999999988877665443 34433 3332 68999887663221 1223345
Q ss_pred CCcccCH
Q 011028 348 LAPVITP 354 (495)
Q Consensus 348 ~kPViTP 354 (495)
..|+|+.
T Consensus 79 ~ipvV~~ 85 (266)
T cd06282 79 RVPYVLA 85 (266)
T ss_pred CCCEEEE
Confidence 5677655
No 69
>TIGR02257 cobalto_cobN cobaltochelatase, CobN subunit.
Probab=40.87 E-value=18 Score=43.48 Aligned_cols=28 Identities=32% Similarity=0.752 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCC--CCCCCeEEEc
Q 011028 85 SHVDADCVIHYG-HT---------------CLSP--TSTLPAFFVF 112 (495)
Q Consensus 85 ~hv~aD~iVHyG-hs---------------Cls~--~~~lpviYVf 112 (495)
+..+||+|||+| |- |.+. +..+|.+|.|
T Consensus 535 ~~f~ADAiIH~GtHGtlEwLPGK~vgLS~~c~Pd~lig~lP~iYpy 580 (1122)
T TIGR02257 535 KVFGADAIVHVGKHGTLEWLPGKGVGLSETCFPEIVLGPLPHIYPF 580 (1122)
T ss_pred hhcCCCEEEECCCCcCcccCCCccccCCcccChHHHhCCCCEEEEE
No 70
>PRK05989 cobN cobaltochelatase subunit CobN; Reviewed
Probab=40.74 E-value=18 Score=44.12 Aligned_cols=28 Identities=36% Similarity=0.749 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCC--CCCCCeEEEc
Q 011028 85 SHVDADCVIHYG-HT---------------CLSP--TSTLPAFFVF 112 (495)
Q Consensus 85 ~hv~aD~iVHyG-hs---------------Cls~--~~~lpviYVf 112 (495)
+..+||+|||+| |- |.+. ...+|.+|.|
T Consensus 541 ~~f~ADAiIH~GtHGtlEwLPGK~vgLS~~c~Pd~llgdlP~iYpY 586 (1244)
T PRK05989 541 EGFGADAVVHVGKHGNLEWLPGKSVGLSADCYPDAALGDLPHLYPF 586 (1244)
T ss_pred hhcCCCEEEECCCCcccccCCCccccCCcccChHHHhCCCCEEEEE
No 71
>PRK09004 FMN-binding protein MioC; Provisional
Probab=40.69 E-value=73 Score=28.74 Aligned_cols=53 Identities=17% Similarity=0.088 Sum_probs=37.8
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCP 337 (495)
.+.|+.||-++ +...+.++|.+.+++.|.++.++-+. .++.| ++.|. +++.||
T Consensus 3 ~i~I~ygS~tG-nae~~A~~l~~~~~~~g~~~~~~~~~--~~~~l---~~~~~-li~~~s 55 (146)
T PRK09004 3 DITLISGSTLG-GAEYVADHLAEKLEEAGFSTETLHGP--LLDDL---SASGL-WLIVTS 55 (146)
T ss_pred eEEEEEEcCch-HHHHHHHHHHHHHHHcCCceEEeccC--CHHHh---ccCCe-EEEEEC
Confidence 68999999864 56889999999999999988765443 34444 44554 444444
No 72
>COG1429 CobN Cobalamin biosynthesis protein CobN and related Mg-chelatases [Coenzyme metabolism]
Probab=40.22 E-value=18 Score=44.52 Aligned_cols=26 Identities=31% Similarity=0.641 Sum_probs=0.0
Q ss_pred cCCcEEEEec-C---------------CCCCC--CCCCCeEEEc
Q 011028 87 VDADCVIHYG-H---------------TCLSP--TSTLPAFFVF 112 (495)
Q Consensus 87 v~aD~iVHyG-h---------------sCls~--~~~lpviYVf 112 (495)
.+||+|||+| | .|.+. +..+|.+|.|
T Consensus 554 f~ADAvVHvGtHGTlEWLPGK~vgLs~~d~P~illgdlP~iYpY 597 (1388)
T COG1429 554 FGADAVVHVGTHGTLEWLPGKEVGLSREDFPDILLGDLPNIYPY 597 (1388)
T ss_pred cCCCeEEEccCccCcccCCCccccCChhhchHHhhCCCCeEEEE
No 73
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=39.48 E-value=91 Score=29.83 Aligned_cols=59 Identities=15% Similarity=0.078 Sum_probs=44.0
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH-------HHHcCCCCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP-------AKLANFPECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~-------aKLaNF~eID~fV~vaCP 337 (495)
+||+|+....-..+..+++.+++.+++.|....++..+.-.+ ..|.+ ..+|++|++.+-
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~-~~vdgiii~~~~ 66 (270)
T cd01545 1 LIGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCDSGSPDLAERVRALLQR-SRVDGVILTPPL 66 (270)
T ss_pred CEEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCCCCchHHHHHHHHHHHH-CCCCEEEEeCCC
Confidence 589999888777788999999999999998887766654332 11222 269999998774
No 74
>PRK08105 flavodoxin; Provisional
Probab=39.24 E-value=69 Score=29.03 Aligned_cols=41 Identities=17% Similarity=0.255 Sum_probs=33.6
Q ss_pred CeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC
Q 011028 277 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN 318 (495)
Q Consensus 277 ~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln 318 (495)
+.++|+.||-++ +...++++|.+.+++.|.++-++-+..+.
T Consensus 2 ~~i~I~YgS~tG-nte~~A~~l~~~l~~~g~~~~~~~~~~~~ 42 (149)
T PRK08105 2 AKVGIFVGTVYG-NALLVAEEAEAILTAQGHEVTLFEDPELS 42 (149)
T ss_pred CeEEEEEEcCch-HHHHHHHHHHHHHHhCCCceEEechhhCC
Confidence 368999999864 56789999999999999998877766544
No 75
>COG1234 ElaC Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]
Probab=38.95 E-value=29 Score=35.32 Aligned_cols=29 Identities=31% Similarity=0.314 Sum_probs=21.7
Q ss_pred CceeEEEEcCCccccCccchhhhcccCCcEEEE
Q 011028 62 KDIGLFVMADTTYGSCCVDEVGASHVDADCVIH 94 (495)
Q Consensus 62 ~~~~v~IlaDtsYGsCCVDevaA~hv~aD~iVH 94 (495)
.+..+.++|||.| |+ +.....-+||++||
T Consensus 189 ~G~~v~ysGDT~p--~~--~~~~~a~~aDlLiH 217 (292)
T COG1234 189 KGKSVVYSGDTRP--CD--ELIDLAKGADLLIH 217 (292)
T ss_pred CCcEEEEECCCCC--CH--HHHHHhcCCCEEEE
Confidence 4579999999996 33 33333478999999
No 76
>PRK12321 cobN cobaltochelatase subunit CobN; Reviewed
Probab=38.72 E-value=20 Score=43.12 Aligned_cols=28 Identities=36% Similarity=0.763 Sum_probs=0.0
Q ss_pred cccCCcEEEEec----------------CCCCCC--CCCCCeEEEc
Q 011028 85 SHVDADCVIHYG----------------HTCLSP--TSTLPAFFVF 112 (495)
Q Consensus 85 ~hv~aD~iVHyG----------------hsCls~--~~~lpviYVf 112 (495)
+|.+||+|||+| .+|.+. +..+|.+|.|
T Consensus 522 ~~~~ADAiiH~GtHGtlEwLPGK~vgLS~~c~Pd~lig~lP~iYpy 567 (1100)
T PRK12321 522 REVGVDALIHLGAHGTLEWLPGKAVALSPACWPEALTGALPVIYPF 567 (1100)
T ss_pred hhcCCCEEEECCCCcccccCCCccccCCcccChHHHhCCCCEEEEE
No 77
>PF02514 CobN-Mg_chel: CobN/Magnesium Chelatase; InterPro: IPR003672 This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN may play a role in cobalt insertion reactions and is implicated in the conversion of precorrin-2 to cobyrinic acid in cobalamin biosynthesis []. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis as the third subunit of light-independent protochlorophyllide reductase in bacteria and plants [].; GO: 0009058 biosynthetic process
Probab=38.53 E-value=31 Score=41.60 Aligned_cols=93 Identities=18% Similarity=0.177 Sum_probs=47.8
Q ss_pred CceEEEecCCCCccc--ccc-ccHHHHHHHHHHHHHHHhcCCeEEEEE-ccccccCcHHHHHHHHHHHHHcCCcEEEEEc
Q 011028 239 GCEIVRYDATEERLL--TDV-SQPLKILKRRYYLVEKAKDANIIGVLV-GTLGVAGYLHMIHQMKELITKAGKKAYTLVM 314 (495)
Q Consensus 239 ~~~v~~yDP~~~~~~--~~~-~~~~r~l~rRy~~I~kar~A~~~GIlv-gTl~~q~~~~~i~~L~~li~~~GKk~y~~~v 314 (495)
+.++|.+||..--.. .+. ......|.+||..=+ =+--+++|+++ ||=.....-..+-.+-. --|-|..-=..
T Consensus 716 GrN~y~~Dp~~iPt~~A~~~G~~la~~ll~~y~~~~-g~yPe~v~~vlW~~~t~rt~G~~~aqil~---llGv~Pvw~~~ 791 (1098)
T PF02514_consen 716 GRNFYSFDPRKIPTPAAWEVGKKLAEQLLERYREEH-GRYPEKVAFVLWGTETMRTGGEDIAQILY---LLGVRPVWDSS 791 (1098)
T ss_pred CCcccccCcccccCHHHHHHHHHHHHHHHHHHHHhc-CCCCceeEEEEEecchhhcCCHHHHHHHH---hcCceeccCCC
Confidence 667999999864311 111 122233455564444 44457888877 33333333333333333 33544432233
Q ss_pred CCCC-----HHHHcCCCCCcEEEEec
Q 011028 315 GKPN-----PAKLANFPECDVFINVS 335 (495)
Q Consensus 315 gkln-----~aKLaNF~eID~fV~va 335 (495)
|++. |-.-.+-|.|||.|.++
T Consensus 792 grv~~~e~iPl~eL~RPRIDV~~~~s 817 (1098)
T PF02514_consen 792 GRVSGVELIPLEELGRPRIDVVVRIS 817 (1098)
T ss_pred CCCCCceeccHHHcCCCCeeEEEecc
Confidence 4332 44444678899999876
No 78
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=38.48 E-value=75 Score=30.30 Aligned_cols=61 Identities=18% Similarity=0.242 Sum_probs=41.5
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC-HH-HHcCC--CCCcEEEEecCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN-PA-KLANF--PECDVFINVSCAQ 338 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln-~a-KLaNF--~eID~fV~vaCPr 338 (495)
+||+++....-..+..+++.+.+.+++.|.+..++....-. .. -+.++ ..+|.+|+.+|..
T Consensus 1 ~I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~ 65 (266)
T cd06278 1 LIGVVVADLDNPFYSELLEALSRALQARGYQPLLINTDDDEDLDAALRQLLQYRVDGVIVTSGTL 65 (266)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 48999977665666788999999999999886555444221 11 12222 2699999988853
No 79
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=38.42 E-value=41 Score=32.67 Aligned_cols=75 Identities=17% Similarity=0.176 Sum_probs=48.4
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCcEEEEecCCCccccc----ccCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCAQTALLD----SKEF 347 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK----LaNF--~eID~fV~vaCPr~si~d----~~~f 347 (495)
+||+|+.++.-..+..+++.+.+.+++.|....+.. ..-++++ |.++ ..+|++++.++...+..+ .++.
T Consensus 1 ~igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~-~~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~~ 79 (282)
T cd06318 1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYELISTD-AQGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKAA 79 (282)
T ss_pred CeeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEc-CCCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHHC
Confidence 589999888766678999999999999998754433 3334432 2222 269999988765332211 2344
Q ss_pred CCcccC
Q 011028 348 LAPVIT 353 (495)
Q Consensus 348 ~kPViT 353 (495)
-.|||+
T Consensus 80 ~iPvV~ 85 (282)
T cd06318 80 GVPVVV 85 (282)
T ss_pred CCCEEE
Confidence 557664
No 80
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=38.39 E-value=43 Score=29.92 Aligned_cols=70 Identities=16% Similarity=0.358 Sum_probs=45.8
Q ss_pred HHHHHhc--CCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCC-CCHHHHcCCC--CCcEEEEecCCCccc
Q 011028 269 LVEKAKD--ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK-PNPAKLANFP--ECDVFINVSCAQTAL 341 (495)
Q Consensus 269 ~I~kar~--A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgk-ln~aKLaNF~--eID~fV~vaCPr~si 341 (495)
.++.|++ |..+|| +++. ..|++.+..+.+.|+++|.....+++|- +-.+..+.|. .+|.|+-.++|-..+
T Consensus 45 ~v~aa~e~~adii~i--Ssl~-~~~~~~~~~~~~~L~~~g~~~i~vivGG~~~~~~~~~l~~~Gvd~~~~~gt~~~~i 119 (132)
T TIGR00640 45 IARQAVEADVHVVGV--SSLA-GGHLTLVPALRKELDKLGRPDILVVVGGVIPPQDFDELKEMGVAEIFGPGTPIPES 119 (132)
T ss_pred HHHHHHHcCCCEEEE--cCch-hhhHHHHHHHHHHHHhcCCCCCEEEEeCCCChHhHHHHHHCCCCEEECCCCCHHHH
Confidence 3444444 555554 5554 6789999999999999998666677773 3233344443 588887777664433
No 81
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=38.13 E-value=92 Score=29.87 Aligned_cols=59 Identities=15% Similarity=0.121 Sum_probs=41.3
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCP 337 (495)
+||||+..+.-..+..+++.+++.+++.|.+..++.. .-++.+. .++ ..+|+.|++++-
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (270)
T cd06296 1 LIGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSES-GRRTSPERQWVERLSARRTDGVILVTPE 65 (270)
T ss_pred CeEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecC-CCchHHHHHHHHHHHHcCCCEEEEecCC
Confidence 5899998887777889999999999999977655443 3333222 222 258998887653
No 82
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=37.19 E-value=76 Score=28.85 Aligned_cols=60 Identities=15% Similarity=0.185 Sum_probs=43.0
Q ss_pred CeEEEEEccccccCcHHHHHHHHHHHHHcCC---cEEEEEcCCCC-----HHHHcCCCCCcEEEEecC
Q 011028 277 NIIGVLVGTLGVAGYLHMIHQMKELITKAGK---KAYTLVMGKPN-----PAKLANFPECDVFINVSC 336 (495)
Q Consensus 277 ~~~GIlvgTl~~q~~~~~i~~L~~li~~~GK---k~y~~~vgkln-----~aKLaNF~eID~fV~vaC 336 (495)
-+||||++.-...---.+++...+.|+++|- ...++.|--.. ..+|++...+|++|.+||
T Consensus 4 ~ri~IV~s~~n~~i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi~lG~ 71 (144)
T PF00885_consen 4 LRIAIVVSRFNEEITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVIALGC 71 (144)
T ss_dssp EEEEEEEESTTHHHHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEEEEEE
T ss_pred CEEEEEEEeccHHHHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEEEecc
Confidence 4789999866444444555556778888886 66777665433 467777778999999998
No 83
>PRK07308 flavodoxin; Validated
Probab=37.08 E-value=1.3e+02 Score=26.68 Aligned_cols=57 Identities=7% Similarity=0.141 Sum_probs=43.3
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCCc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 339 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr~ 339 (495)
.+-|+-+|.. -+...+++.|.+.+++.|..+-++-+.+..+..|. +.|+++ ++||-.
T Consensus 3 ~~~IvY~S~t-GnTe~iA~~ia~~l~~~g~~~~~~~~~~~~~~~l~---~~d~vi-~g~~t~ 59 (146)
T PRK07308 3 LAKIVYASMT-GNTEEIADIVADKLRELGHDVDVDECTTVDASDFE---DADIAI-VATYTY 59 (146)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHhCCCceEEEecccCCHhHhc---cCCEEE-EEeCcc
Confidence 4678888864 46689999999999999998877878777776654 456544 488765
No 84
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=35.72 E-value=48 Score=30.23 Aligned_cols=55 Identities=20% Similarity=0.332 Sum_probs=39.9
Q ss_pred HHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEc-CCCCHHHHcCCC
Q 011028 271 EKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM-GKPNPAKLANFP 326 (495)
Q Consensus 271 ~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~v-gkln~aKLaNF~ 326 (495)
..|.+...=.|.|+.+. .+|+.++..|.+.|+++|...-++++ |.|.++.+.+|.
T Consensus 57 ~aA~~~dv~vIgvSsl~-g~h~~l~~~lve~lre~G~~~i~v~~GGvip~~d~~~l~ 112 (143)
T COG2185 57 RAAVEEDVDVIGVSSLD-GGHLTLVPGLVEALREAGVEDILVVVGGVIPPGDYQELK 112 (143)
T ss_pred HHHHhcCCCEEEEEecc-chHHHHHHHHHHHHHHhCCcceEEeecCccCchhHHHHH
Confidence 33444444455666676 78999999999999999999888444 577777765554
No 85
>cd05569 PTS_IIB_fructose PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. The FruB protein (also referred to as diphosphoryl transfer protein) contains a IIA domain, a domain of unknown function, and an Hpr-like domain called FPr (fructose-inducible HPr). This familiy also includes the IIB domains of several fructose-like PTS permeases including the Frv permease encoded by the frvABXR operon, the Frw permease encoded by the frwACBD operon, the Frx permease encoded by the hrsA gene, and the Fry permease encoded by the fryABC (ypdDGH) operon. FruAB takes up exogenous fructose, releasing the 1-p
Probab=35.50 E-value=1.2e+02 Score=25.25 Aligned_cols=59 Identities=14% Similarity=0.126 Sum_probs=45.4
Q ss_pred EEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEE------cCCCCHHHHcCCCCCcEEEEecCCCcc
Q 011028 279 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV------MGKPNPAKLANFPECDVFINVSCAQTA 340 (495)
Q Consensus 279 ~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~------vgkln~aKLaNF~eID~fV~vaCPr~s 340 (495)
++|+.+.-|.....-..+.|++.++++|.+.-+-. .+.++.+.+ .+.|.+++++.....
T Consensus 2 ~~i~ac~~G~a~s~laa~~L~~aa~~~g~~~~ve~~~~~g~~~~l~~~~i---~~Ad~vi~~~~~~~~ 66 (96)
T cd05569 2 VAVTACPTGIAHTYMAAEALEKAAKKLGWEIKVETQGSLGIENELTAEDI---AEADAVILAADVPVD 66 (96)
T ss_pred EEEEECCCchhHHHHHHHHHHHHHHHCCCeEEEEEecCcCccCcCCHHHH---hhCCEEEEecCCCCc
Confidence 67788888888888899999999999999976443 334555555 457899999988743
No 86
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=35.48 E-value=70 Score=30.57 Aligned_cols=61 Identities=15% Similarity=0.213 Sum_probs=45.2
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecCCCc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQT 339 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaCPr~ 339 (495)
+||+|+.......+..+++.+.+.+++.|.+..++. ..-++++.. .+ ..+|+.+++++...
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~ 67 (268)
T cd01575 1 LVAVLVPSLSNSVFADVLQGISDVLEAAGYQLLLGN-TGYSPEREEELLRTLLSRRPAGLILTGLEHT 67 (268)
T ss_pred CEEEEeCCCcchhHHHHHHHHHHHHHHcCCEEEEec-CCCCchhHHHHHHHHHHcCCCEEEEeCCCCC
Confidence 589999888777888999999999999998876544 344554432 11 26999999887543
No 87
>PF01729 QRPTase_C: Quinolinate phosphoribosyl transferase, C-terminal domain; InterPro: IPR002638 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0009435 NAD biosynthetic process; PDB: 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 1QPN_E 1QPO_A 1QPQ_F 1QPR_E 2I14_D ....
Probab=35.19 E-value=45 Score=31.17 Aligned_cols=63 Identities=14% Similarity=0.129 Sum_probs=47.0
Q ss_pred HHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCC--CCcEEEEec
Q 011028 269 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFINVS 335 (495)
Q Consensus 269 ~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~--eID~fV~va 335 (495)
..+.|.+++.=+|.+=+.+ ++.++.+.+.++..+.+.-+.+.|.+|++.++.|. .+|++++-+
T Consensus 92 e~~ea~~~g~d~I~lD~~~----~~~~~~~v~~l~~~~~~v~ie~SGGI~~~ni~~ya~~gvD~isvg~ 156 (169)
T PF01729_consen 92 EAEEALEAGADIIMLDNMS----PEDLKEAVEELRELNPRVKIEASGGITLENIAEYAKTGVDVISVGS 156 (169)
T ss_dssp HHHHHHHTT-SEEEEES-C----HHHHHHHHHHHHHHTTTSEEEEESSSSTTTHHHHHHTT-SEEEECH
T ss_pred HHHHHHHhCCCEEEecCcC----HHHHHHHHHHHhhcCCcEEEEEECCCCHHHHHHHHhcCCCEEEcCh
Confidence 4556677888888887764 47777777777888888999999999999998885 578776544
No 88
>PF00258 Flavodoxin_1: Flavodoxin; InterPro: IPR008254 This domain is found in a number of proteins including flavodoxin and nitric-oxide synthase. Flavodoxins are electron-transfer proteins that function in various electron transport systems. They bind one FMN molecule, which serves as a redox-active prosthetic group [] and are functionally interchangeable with ferredoxins. They have been isolated from prokaryotes, cyanobacteria, and some eukaryotic algae. Nitric oxide synthase (1.14.13.39 from EC) produces nitric oxide from L-arginie and NADPH. Nitric oxide acts as a messenger molecule in the body.; GO: 0010181 FMN binding, 0016491 oxidoreductase activity; PDB: 2WC1_A 2FVX_A 2FOX_A 6NUL_A 1FVX_A 2FAX_A 1FLN_A 1FLA_A 4NLL_A 2FDX_A ....
Probab=34.72 E-value=71 Score=28.02 Aligned_cols=54 Identities=11% Similarity=0.236 Sum_probs=39.2
Q ss_pred EEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCC
Q 011028 281 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 337 (495)
Q Consensus 281 IlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCP 337 (495)
|+-+|.. .+...+++.|.+.++++|.++.++-+...+.. +..+.+-+.+ +++||
T Consensus 1 I~Y~S~t-G~te~~A~~ia~~l~~~g~~~~~~~~~~~~~~-~~~~~~~~~~-i~~~s 54 (143)
T PF00258_consen 1 IVYGSMT-GNTEKMAEAIAEGLRERGVEVRVVDLDDFDDS-PSDLSEYDLL-IFGVS 54 (143)
T ss_dssp EEEETSS-SHHHHHHHHHHHHHHHTTSEEEEEEGGGSCHH-HHHHCTTSEE-EEEEE
T ss_pred CEEECCc-hhHHHHHHHHHHHHHHcCCceeeechhhhhhh-hhhhhhhcee-eEeec
Confidence 5666665 34578999999999999999999999999966 2233334444 44454
No 89
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=34.65 E-value=37 Score=32.99 Aligned_cols=76 Identities=16% Similarity=0.123 Sum_probs=47.7
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEc---CCCCHHHH----cCCC-CCcEEEEecCCCccc----cccc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM---GKPNPAKL----ANFP-ECDVFINVSCAQTAL----LDSK 345 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~v---gkln~aKL----aNF~-eID~fV~vaCPr~si----~d~~ 345 (495)
+||+|+....-..+..+++.+.+.+++.|...++... ..-++++. .++. .+|+.|+++...... ....
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~~~~~vdgiii~~~~~~~~~~~i~~~~ 80 (275)
T cd06307 1 RLGFLLPKGSNAFYRELAAALEAAAAAFPDARIRVRIHFVESFDPAALAAALLRLGARSDGVALVAPDHPQVRAAVARLA 80 (275)
T ss_pred CeEEEeCCCCChHHHHHHHHHHHHHhhhhccCceEEEEEccCCCHHHHHHHHHHHHhcCCEEEEeCCCcHHHHHHHHHHH
Confidence 5899998877667778889999999988877665543 23344332 2332 589998877553321 1123
Q ss_pred CCCCcccC
Q 011028 346 EFLAPVIT 353 (495)
Q Consensus 346 ~f~kPViT 353 (495)
+.-.|||+
T Consensus 81 ~~~ipvV~ 88 (275)
T cd06307 81 AAGVPVVT 88 (275)
T ss_pred HCCCcEEE
Confidence 34557764
No 90
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=34.50 E-value=74 Score=31.97 Aligned_cols=58 Identities=12% Similarity=0.111 Sum_probs=40.3
Q ss_pred cCCeEEEEEc----cccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecC
Q 011028 275 DANIIGVLVG----TLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSC 336 (495)
Q Consensus 275 ~A~~~GIlvg----Tl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaC 336 (495)
...++|||+. ++.-..+..+++.+.+.++++|....+....+ .. .....+|.+++++.
T Consensus 62 ~~~~i~v~~~~~~~~~~~~f~~~l~~~i~~~~~~~g~~~~~~~~~~--~~--~~~~~vDgiI~~~~ 123 (327)
T PRK10339 62 QHHILAIYSYQQELEINDPYYLAIRHGIETQCEKLGIELTNCYEHS--GL--PDIKNVTGILIVGK 123 (327)
T ss_pred cccEEEEEEccccccccCchHHHHHHHHHHHHHHCCCEEEEeeccc--cc--cccccCCEEEEeCC
Confidence 4578899984 45555667899999999999998754432222 11 12357999999875
No 91
>PRK05569 flavodoxin; Provisional
Probab=34.40 E-value=1.5e+02 Score=25.93 Aligned_cols=56 Identities=7% Similarity=0.104 Sum_probs=41.4
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 338 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr 338 (495)
.+.|+-+|. --+...+++.+.+-+++.|-.+-++-+.+..+.++. +.|. |+++||-
T Consensus 3 ki~iiY~S~-tGnT~~iA~~i~~~~~~~g~~v~~~~~~~~~~~~~~---~~d~-iilgsPt 58 (141)
T PRK05569 3 KVSIIYWSC-GGNVEVLANTIADGAKEAGAEVTIKHVADAKVEDVL---EADA-VAFGSPS 58 (141)
T ss_pred eEEEEEECC-CCHHHHHHHHHHHHHHhCCCeEEEEECCcCCHHHHh---hCCE-EEEECCC
Confidence 577888885 346689999999999999988777777777766554 4454 5667774
No 92
>cd01571 NAPRTase_B Nicotinate phosphoribosyltransferase (NAPRTase), subgroup B. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products.
Probab=33.49 E-value=81 Score=32.29 Aligned_cols=55 Identities=18% Similarity=0.293 Sum_probs=42.6
Q ss_pred CeEEEEEccccc--cCcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHHHHcCCC--CCcEE
Q 011028 277 NIIGVLVGTLGV--AGYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFP--ECDVF 331 (495)
Q Consensus 277 ~~~GIlvgTl~~--q~~~~~i~~L~~li~~~G-Kk~y~~~vgkln~aKLaNF~--eID~f 331 (495)
+..+|.+=+.+. -...+.++.+++.++..| .+.-+.+.|.||+++++.|. .||++
T Consensus 211 ~~d~I~lDn~~~~~G~~~~~~~~~~~~l~~~g~~~~~ieaSGgI~~~~i~~~a~~gvD~i 270 (302)
T cd01571 211 KLDGVRLDTPSSRRGVFRYLIREVRWALDIRGYKHVKIFVSGGLDEEDIKELEDVGVDAF 270 (302)
T ss_pred CCcEEEECCCCCCCCCHHHHHHHHHHHHHhCCCCCeEEEEeCCCCHHHHHHHHHcCCCEE
Confidence 356788876531 225677899999999887 66788999999999999885 48866
No 93
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=33.08 E-value=1.4e+02 Score=27.75 Aligned_cols=53 Identities=19% Similarity=0.310 Sum_probs=41.4
Q ss_pred hcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEec
Q 011028 274 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVS 335 (495)
Q Consensus 274 r~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~va 335 (495)
.+..+|.|+-|- ..+..++++|+ +.||+++.+.+.+.++.-|.|= +|-||-+.
T Consensus 104 ~~iD~~vLvSgD---~DF~~Lv~~lr----e~G~~V~v~g~~~~ts~~L~~a--cd~FI~L~ 156 (160)
T TIGR00288 104 PNIDAVALVTRD---ADFLPVINKAK----ENGKETIVIGAEPGFSTALQNS--ADIAIILG 156 (160)
T ss_pred CCCCEEEEEecc---HhHHHHHHHHH----HCCCEEEEEeCCCCChHHHHHh--cCeEEeCC
Confidence 667888887764 67777776665 6799999999888899999884 77887654
No 94
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=32.91 E-value=75 Score=31.56 Aligned_cols=59 Identities=17% Similarity=0.151 Sum_probs=41.8
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 336 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaC 336 (495)
+||+|+.+.+-..+..+++.+++.+++.|.+..++.-+.-++++-. ++ ..+|+.|+++.
T Consensus 1 ~I~vi~~~~~~~f~~~i~~gi~~~a~~~g~~v~~~~~~~~d~~~~~~~i~~~~~~~~DgiIi~~~ 65 (298)
T cd06302 1 TIAFVPKVTGIPYFNRMEEGAKEAAKELGVDAIYVGPTTADAAGQVQIIEDLIAQGVDAIAVVPN 65 (298)
T ss_pred CEEEEEcCCCChHHHHHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHHhcCCCEEEEecC
Confidence 5899998877677788999999999998877655434445554332 22 25899998764
No 95
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.87 E-value=2.1e+02 Score=31.47 Aligned_cols=70 Identities=19% Similarity=0.256 Sum_probs=50.8
Q ss_pred HHHHHHhcCCeEEEEEccccc-cCcHHHHHHHHHHHHHcCCcEEEEEcCC-----CCHHHHcCCC----------CCcEE
Q 011028 268 YLVEKAKDANIIGVLVGTLGV-AGYLHMIHQMKELITKAGKKAYTLVMGK-----PNPAKLANFP----------ECDVF 331 (495)
Q Consensus 268 ~~I~kar~A~~~GIlvgTl~~-q~~~~~i~~L~~li~~~GKk~y~~~vgk-----ln~aKLaNF~----------eID~f 331 (495)
.+|+-|++-.-=-|||-|-|+ ++...++..|.++++.+ +.--+|.||+ =..+.|.+|. -||.|
T Consensus 457 ~AI~~a~~~gfDVvLiDTAGR~~~~~~lm~~l~k~~~~~-~pd~i~~vgealvg~dsv~q~~~fn~al~~~~~~r~id~~ 535 (587)
T KOG0781|consen 457 EAIQEARNQGFDVVLIDTAGRMHNNAPLMTSLAKLIKVN-KPDLILFVGEALVGNDSVDQLKKFNRALADHSTPRLIDGI 535 (587)
T ss_pred HHHHHHHhcCCCEEEEeccccccCChhHHHHHHHHHhcC-CCceEEEehhhhhCcHHHHHHHHHHHHHhcCCCccccceE
Confidence 467788887777899999996 77789999999999864 5555666654 3455554442 38888
Q ss_pred EEecCCC
Q 011028 332 INVSCAQ 338 (495)
Q Consensus 332 V~vaCPr 338 (495)
+++-|.-
T Consensus 536 ~ltk~dt 542 (587)
T KOG0781|consen 536 LLTKFDT 542 (587)
T ss_pred EEEeccc
Confidence 8887754
No 96
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=32.30 E-value=1.3e+02 Score=28.44 Aligned_cols=50 Identities=18% Similarity=0.175 Sum_probs=37.6
Q ss_pred CCeEEEEEccccccCc--HHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCC
Q 011028 276 ANIIGVLVGTLGVAGY--LHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP 326 (495)
Q Consensus 276 A~~~GIlvgTl~~q~~--~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~ 326 (495)
+..+.||+ |=|.... ..-+....+.++++|-+.|++-||..+.+.|....
T Consensus 108 ~~kv~Ill-TDG~s~~~~~~~~~~~a~~lk~~gV~i~~vGiG~~~~~el~~ia 159 (192)
T cd01473 108 APKVTMLF-TDGNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLKLLA 159 (192)
T ss_pred CCeEEEEE-ecCCCCCcchhhHHHHHHHHHHCCCEEEEEEeccccHHHHHHhc
Confidence 47888887 5555443 23455667788999999999999999988887764
No 97
>TIGR01579 MiaB-like-C MiaB-like tRNA modifying enzyme. This clade is a member of a subfamily (TIGR00089) and spans low GC Gram positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium.
Probab=32.28 E-value=47 Score=35.28 Aligned_cols=65 Identities=18% Similarity=0.325 Sum_probs=37.0
Q ss_pred HHHHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcC---CCCHHHHcCCCCCcEEE
Q 011028 267 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG---KPNPAKLANFPECDVFI 332 (495)
Q Consensus 267 y~~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vg---kln~aKLaNF~eID~fV 332 (495)
|..+....+|..++|=..|...+.-...++.++++ ++.|++..+++.| ...|+.+..++++|++|
T Consensus 25 ~~~~~~~~~aD~v~intctv~~~a~~~~~~~i~~~-k~~~p~~~vvvgGc~a~~~~ee~~~~~~vD~vv 92 (414)
T TIGR01579 25 YEVVPDEDKADVYIINTCTVTAKADSKARRAIRRA-RRQNPTAKIIVTGCYAQSNPKELADLKDVDLVL 92 (414)
T ss_pred CEECCCcccCCEEEEeccccchHHHHHHHHHHHHH-HhhCCCcEEEEECCccccCHHHHhcCCCCcEEE
Confidence 44444455677766554444332223344444433 5566666666666 34677777777888776
No 98
>PRK08662 nicotinate phosphoribosyltransferase; Reviewed
Probab=32.24 E-value=70 Score=33.43 Aligned_cols=55 Identities=16% Similarity=0.368 Sum_probs=41.8
Q ss_pred CeEEEEEccccc--cCcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHHHHcCCCC-CcEE
Q 011028 277 NIIGVLVGTLGV--AGYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFPE-CDVF 331 (495)
Q Consensus 277 ~~~GIlvgTl~~--q~~~~~i~~L~~li~~~G-Kk~y~~~vgkln~aKLaNF~e-ID~f 331 (495)
+..||.+=+.+. ..-.++++.+++.+++.| .+.-+.+.|.||++++++|.+ ||+|
T Consensus 227 ~~d~I~LDn~~~~~g~l~~~v~~vr~~ld~~g~~~v~IeaSGgI~~~ni~~ya~~vD~i 285 (343)
T PRK08662 227 RLDGVRLDTPSSRRGNFRKIVREVRWTLDIRGYEHVKIFVSGGLDPERIRELRDVVDGF 285 (343)
T ss_pred cCCEEEcCCCCCCCccHHHHHHHHHHHHHhcCCCCeEEEEeCCCCHHHHHHHHHhCCEE
Confidence 556888887763 555677788888888887 467888999999999988843 5544
No 99
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=31.85 E-value=1e+02 Score=25.25 Aligned_cols=56 Identities=20% Similarity=0.265 Sum_probs=37.9
Q ss_pred HHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCCcccc-cccCCCCccc-----CHHHHH
Q 011028 296 HQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALL-DSKEFLAPVI-----TPFEAM 358 (495)
Q Consensus 296 ~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~-d~~~f~kPVi-----TP~El~ 358 (495)
..+++.|+++|.++..+- +.+ ++..+||.|+.+=..+-+- ....+.-||| ||-|..
T Consensus 11 s~v~~~L~~~GyeVv~l~----~~~---~~~~~daiVvtG~~~n~mg~~d~~~~~pVInA~G~T~eEI~ 72 (80)
T PF03698_consen 11 SNVKEALREKGYEVVDLE----NEQ---DLQNVDAIVVTGQDTNMMGIQDTSTKVPVINASGLTAEEIV 72 (80)
T ss_pred hHHHHHHHHCCCEEEecC----Ccc---ccCCcCEEEEECCCcccccccccccCceEEecCCCCHHHHH
Confidence 478889999999865554 222 4567999999997776432 1235677885 666654
No 100
>COG0716 FldA Flavodoxins [Energy production and conversion]
Probab=31.68 E-value=1.4e+02 Score=26.83 Aligned_cols=59 Identities=10% Similarity=0.000 Sum_probs=42.3
Q ss_pred CeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCCc
Q 011028 277 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 339 (495)
Q Consensus 277 ~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr~ 339 (495)
..++|+-+|.. -+...+++.|++.|.+.|.+. .+-...-+...+. + ..|.+++.+++-.
T Consensus 2 ~ki~Ivy~S~t-GnTe~vA~~i~~~l~~~~~~~-~~~~~~~~~~~~~-~-~~d~~~~g~~t~~ 60 (151)
T COG0716 2 MKILIVYGSRT-GNTEKVAEIIAEELGADGFEV-DIDIRPGIKDDLL-E-SYDELLLGTPTWG 60 (151)
T ss_pred CeEEEEEEcCC-CcHHHHHHHHHHHhccCCceE-EEeecCCcchhhh-c-cCCEEEEEeCCCC
Confidence 36899999987 577899999999999999998 4444443333332 2 4677777776654
No 101
>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 3LFT_A 3LKV_A.
Probab=31.61 E-value=1.3e+02 Score=30.08 Aligned_cols=113 Identities=19% Similarity=0.257 Sum_probs=66.9
Q ss_pred HHHHHHHHHHHHHh-cCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH--HHHcCC-CCCcEEEEecC
Q 011028 261 KILKRRYYLVEKAK-DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLANF-PECDVFINVSC 336 (495)
Q Consensus 261 r~l~rRy~~I~kar-~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~--aKLaNF-~eID~fV~vaC 336 (495)
..+.++..++.+.. +++++|+|...- -.+....++.+++..++.|.+...+.+...+. ..+..+ ...|++++...
T Consensus 115 ~~~~~~l~l~~~l~P~~k~igvl~~~~-~~~~~~~~~~~~~~a~~~g~~l~~~~v~~~~~~~~~~~~l~~~~da~~~~~~ 193 (294)
T PF04392_consen 115 PPIEKQLELIKKLFPDAKRIGVLYDPS-EPNSVAQIEQLRKAAKKLGIELVEIPVPSSEDLEQALEALAEKVDALYLLPD 193 (294)
T ss_dssp --HHHHHHHHHHHSTT--EEEEEEETT--HHHHHHHHHHHHHHHHTT-EEEEEEESSGGGHHHHHHHHCTT-SEEEE-S-
T ss_pred cCHHHHHHHHHHhCCCCCEEEEEecCC-CccHHHHHHHHHHHHHHcCCEEEEEecCcHhHHHHHHHHhhccCCEEEEECC
Confidence 45667788888876 799999999754 35567889999999999999999888887663 233333 36898887654
Q ss_pred CCcc-----cc-cccCCCCcccCHHHHHHhhCCCCcCccceeeecccc
Q 011028 337 AQTA-----LL-DSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 378 (495)
Q Consensus 337 Pr~s-----i~-d~~~f~kPViTP~El~vAL~~~~~W~g~y~~Df~~l 378 (495)
+-.. +. -..+...||++.++..+.-| .-+-|..|+.++
T Consensus 194 ~~~~~~~~~i~~~~~~~~iPv~~~~~~~v~~G----al~~~~~~~~~~ 237 (294)
T PF04392_consen 194 NLVDSNFEAILQLANEAKIPVFGSSDFYVKAG----ALGGYSVDYYEQ 237 (294)
T ss_dssp HHHHHTHHHHHHHCCCTT--EEESSHHHHCTT-----SEEEE--HHHH
T ss_pred cchHhHHHHHHHHHHhcCCCEEECCHHHhcCC----cEEEEccCHHHH
Confidence 3210 11 13456778887777666433 224566666555
No 102
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a
Probab=31.46 E-value=1.5e+02 Score=28.26 Aligned_cols=60 Identities=13% Similarity=0.191 Sum_probs=42.1
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQ 338 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCPr 338 (495)
+||+|+.+..-..+..+++.+++.+++.|....++.. .=++++. .++ ..+|.+|+.++..
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiii~~~~~ 66 (269)
T cd06275 1 TIGMLVTTSTNPFFAEVVRGVEQYCYRQGYNLILCNT-EGDPERQRSYLRMLAQKRVDGLLVMCSEY 66 (269)
T ss_pred CEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEEeC-CCChHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 4899998876666778999999999999977654433 3355432 122 2699999988743
No 103
>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=31.09 E-value=60 Score=31.32 Aligned_cols=59 Identities=19% Similarity=0.195 Sum_probs=39.0
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEE-cCCCCHHHHcCC------CCCcEEEEecC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV-MGKPNPAKLANF------PECDVFINVSC 336 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~-vgkln~aKLaNF------~eID~fV~vaC 336 (495)
+||+|+.++.-..+..+++.+.+.+++.|..+-+++ -+.-++++.... ..+|.+|+.+.
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~dgiIi~~~ 66 (271)
T cd06321 1 KIGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVVSADYDLNKQVSQIDNFIAAKVDLILLNAV 66 (271)
T ss_pred CeEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEccCCCCHHHHHHHHHHHHHhCCCEEEEeCC
Confidence 589999888767778999999999999555443333 233344433221 25899888653
No 104
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=31.05 E-value=1.1e+02 Score=26.48 Aligned_cols=62 Identities=16% Similarity=0.317 Sum_probs=42.0
Q ss_pred HhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCC-cEEEEEcCCCCHHHH---cCCCCCcEEEEecCCC
Q 011028 273 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGK-KAYTLVMGKPNPAKL---ANFPECDVFINVSCAQ 338 (495)
Q Consensus 273 ar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GK-k~y~~~vgkln~aKL---aNF~eID~fV~vaCPr 338 (495)
..+|..++| +.+ ...+.+.++.+.+.|++.|. +..+++-|...++.. ..+ .+|.|+-.+|+-
T Consensus 48 ~~~~d~V~i--S~~-~~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~~~~~~~~~~~-G~d~~~~~~~~~ 113 (122)
T cd02071 48 QEDVDVIGL--SSL-SGGHMTLFPEVIELLRELGAGDILVVGGGIIPPEDYELLKEM-GVAEIFGPGTSI 113 (122)
T ss_pred HcCCCEEEE--ccc-chhhHHHHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHC-CCCEEECCCCCH
Confidence 345777666 333 36788888999999999988 444555555555544 344 699998887763
No 105
>TIGR01754 flav_RNR ribonucleotide reductase-associated flavodoxin, putative. This model represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulfate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation.
Probab=30.31 E-value=97 Score=27.43 Aligned_cols=57 Identities=12% Similarity=0.068 Sum_probs=35.1
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEE-EEEcCCCCHHHHcCCCCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY-TLVMGKPNPAKLANFPECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y-~~~vgkln~aKLaNF~eID~fV~vaCP 337 (495)
.+.||.+|..+ +...+++.|.+.++..|.+.- ++-+.+++.. ..++.+.|+ |+++||
T Consensus 2 ~i~IiY~S~tG-nTe~iA~~ia~~l~~~g~~v~~~~~~~~~~~~-~~~~~~~d~-iilgs~ 59 (140)
T TIGR01754 2 RILLAYLSLSG-NTEEVAFMIQDYLQKDGHEVDILHRIGTLADA-PLDPENYDL-VFLGTW 59 (140)
T ss_pred eEEEEEECCCC-hHHHHHHHHHHHHhhCCeeEEecccccccccC-cCChhhCCE-EEEEcC
Confidence 46889998653 568899999999998887653 2223332211 123445566 455554
No 106
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=29.94 E-value=75 Score=32.56 Aligned_cols=63 Identities=21% Similarity=0.071 Sum_probs=43.5
Q ss_pred cCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHH----cCC--CCCcEEEEecCC
Q 011028 275 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKL----ANF--PECDVFINVSCA 337 (495)
Q Consensus 275 ~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vg-kln~aKL----aNF--~eID~fV~vaCP 337 (495)
..++||+|+.++.-..+..+++.+++.+++.|.+.-++... .-+.++. .+| ..+|++|+.+..
T Consensus 45 ~t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~~~~~~~q~~~i~~l~~~~vdgIIl~~~~ 114 (343)
T PRK10936 45 KAWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGGYYNLAKQQQQLEQCVAWGADAILLGAVT 114 (343)
T ss_pred CCeEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCCCCCHHHHHHHHHHHHHhCCCEEEEeCCC
Confidence 47899999988765666788899999999999775554332 2333333 222 258999987644
No 107
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=29.66 E-value=88 Score=30.14 Aligned_cols=56 Identities=13% Similarity=-0.006 Sum_probs=34.1
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHH-cCCcEEEEEcCCCCHHHHcCCC--CCcEEEEecC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITK-AGKKAYTLVMGKPNPAKLANFP--ECDVFINVSC 336 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~-~GKk~y~~~vgkln~aKLaNF~--eID~fV~vaC 336 (495)
.||+|+.+ +--.+..+++.+.+.+++ .|....+. .+.. ..-+.++. .+|.+++...
T Consensus 1 ~ig~i~~~-~~~~~~~~~~gi~~~~~~~~g~~~~~~-~~~~-~~~~~~l~~~~vdGiI~~~~ 59 (265)
T cd01543 1 RVALLVET-SSSYGRGVLRGIARYAREHGPWSIYLE-PRGL-QEPLRWLKDWQGDGIIARID 59 (265)
T ss_pred CeEEEecc-cchhhHHHHHHHHHHHHhcCCeEEEEe-cccc-hhhhhhccccccceEEEECC
Confidence 48999974 344557888899988888 55554332 2221 22222332 6999988653
No 108
>PRK09426 methylmalonyl-CoA mutase; Reviewed
Probab=29.47 E-value=85 Score=36.17 Aligned_cols=73 Identities=16% Similarity=0.203 Sum_probs=47.6
Q ss_pred HHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEE-EEEcCCCCHHHHcCC--CCCcEEEEecCCCcccc
Q 011028 269 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY-TLVMGKPNPAKLANF--PECDVFINVSCAQTALL 342 (495)
Q Consensus 269 ~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y-~~~vgkln~aKLaNF--~eID~fV~vaCPr~si~ 342 (495)
.++.|++.+.=-|+++.+ -..|++.+..+.+.|+++|.+.. +++=|++-++..+.+ ..+|.|+-.+|+-..++
T Consensus 625 ~v~aa~~~~a~ivvlcs~-d~~~~e~~~~l~~~Lk~~G~~~v~vl~GG~~~~~~~~~l~~aGvD~~i~~g~d~~~~L 700 (714)
T PRK09426 625 AARQAVENDVHVVGVSSL-AAGHKTLVPALIEALKKLGREDIMVVVGGVIPPQDYDFLYEAGVAAIFGPGTVIADAA 700 (714)
T ss_pred HHHHHHHcCCCEEEEecc-chhhHHHHHHHHHHHHhcCCCCcEEEEeCCCChhhHHHHHhCCCCEEECCCCCHHHHH
Confidence 445555544333333433 27899999999999999998655 444455455433323 27999999999866554
No 109
>PRK14571 D-alanyl-alanine synthetase A; Provisional
Probab=29.07 E-value=1.7e+02 Score=29.41 Aligned_cols=76 Identities=13% Similarity=0.036 Sum_probs=52.4
Q ss_pred eEEEEEcccccc--CcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCCccccc------ccCCCC
Q 011028 278 IIGVLVGTLGVA--GYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD------SKEFLA 349 (495)
Q Consensus 278 ~~GIlvgTl~~q--~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d------~~~f~k 349 (495)
+|+||.|-.+.. -.+...+.+.+-|++.|.++..+-+.+--..++....++| +|+..|+...-.| ...+-.
T Consensus 2 ~v~v~~gg~s~e~~~sl~s~~~i~~al~~~g~~~~~i~~~~~~~~~~~~~~~~D-~v~~~~~g~~ge~~~~~~~le~~gi 80 (299)
T PRK14571 2 RVALLMGGVSREREISLRSGERVKKALEKLGYEVTVFDVDEDFLKKVDQLKSFD-VVFNVLHGTFGEDGTLQAILDFLGI 80 (299)
T ss_pred eEEEEeCCCCCCccchHHHHHHHHHHHHHcCCeEEEEccCchHHHHhhhccCCC-EEEEeCCCCCCCccHHHHHHHHcCC
Confidence 589999988854 4477888999999999999998887765556666666788 4555665431111 123567
Q ss_pred cccCH
Q 011028 350 PVITP 354 (495)
Q Consensus 350 PViTP 354 (495)
|.+.+
T Consensus 81 p~~G~ 85 (299)
T PRK14571 81 RYTGS 85 (299)
T ss_pred CccCC
Confidence 87744
No 110
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=28.92 E-value=1e+02 Score=29.64 Aligned_cols=74 Identities=16% Similarity=0.127 Sum_probs=48.0
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HHcCCCCCcEEEEecCCCc---c-cccccC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQT---A-LLDSKE 346 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~a-------KLaNF~eID~fV~vaCPr~---s-i~d~~~ 346 (495)
.||+|+..+.-..+..+++.+++.+++.|.+..++ -+.=+++ +|.+ ..+|.+|+.++... . +....+
T Consensus 1 ~i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~-~~~~~~~~~~~~i~~~~~-~~~dgiii~~~~~~~~~~~l~~~~~ 78 (277)
T cd06319 1 QIAYIVSDLRIPFWQIMGRGVKSKAKALGYDAVEL-SAENSAKKELENLRTAID-KGVSGIIISPTNSSAAVTLLKLAAQ 78 (277)
T ss_pred CeEEEeCCCCchHHHHHHHHHHHHHHhcCCeEEEe-cCCCCHHHHHHHHHHHHh-cCCCEEEEcCCchhhhHHHHHHHHH
Confidence 37889887776777889999999999988776543 3333443 2333 36999988776422 1 222345
Q ss_pred CCCcccC
Q 011028 347 FLAPVIT 353 (495)
Q Consensus 347 f~kPViT 353 (495)
...|||+
T Consensus 79 ~~ipvV~ 85 (277)
T cd06319 79 AKIPVVI 85 (277)
T ss_pred CCCCEEE
Confidence 5667775
No 111
>PRK09271 flavodoxin; Provisional
Probab=28.71 E-value=1.8e+02 Score=26.45 Aligned_cols=58 Identities=12% Similarity=0.098 Sum_probs=38.5
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-HcCCCCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-LANFPECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-LaNF~eID~fV~vaCP 337 (495)
.+.|+-+|.. -+...+++.|.+.|++.|.++-+.-+....... ...+.+.|++++ +||
T Consensus 2 kv~IvY~S~t-GnTe~~A~~ia~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~d~vil-gt~ 60 (160)
T PRK09271 2 RILLAYASLS-GNTREVAREIEERCEEAGHEVDWVETDVQTLAEYPLDPEDYDLYLL-GTW 60 (160)
T ss_pred eEEEEEEcCC-chHHHHHHHHHHHHHhCCCeeEEEecccccccccccCcccCCEEEE-ECc
Confidence 4689999976 456899999999999999887555544433222 223445666554 444
No 112
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=28.14 E-value=1.1e+02 Score=29.59 Aligned_cols=60 Identities=10% Similarity=-0.024 Sum_probs=41.7
Q ss_pred eEEEEEccc-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC------CCCcEEEEecCC
Q 011028 278 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl-~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF------~eID~fV~vaCP 337 (495)
+||+|+..+ .-..+..+++.+++.+++.|....++....-++++.... ..+|++|+.++.
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 67 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRGPETFDVADMARLIEAAIAAKPDGIVVTIPD 67 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEECCCCCCHHHHHHHHHHHHHhCCCEEEEeCCC
Confidence 478888766 555667899999999999888876655543355544221 268999887754
No 113
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=28.08 E-value=1.1e+02 Score=29.47 Aligned_cols=58 Identities=16% Similarity=-0.054 Sum_probs=40.6
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCcEEEEecC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSC 336 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaN----F--~eID~fV~vaC 336 (495)
+||+|+.++.-.-+..+++.+.+.+++.|.+..++ -..-++++-.+ + ..+|++|+.+.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~-~~~~~~~~~~~~l~~~~~~~vdgii~~~~ 64 (273)
T cd06305 1 RIAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVY-DAGGDDAKQADQIDQAIAQKVDAIIIQHG 64 (273)
T ss_pred CeEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEE-CCCCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 47899988765556788899999999998875554 34556654322 1 26899988753
No 114
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=28.00 E-value=1.8e+02 Score=28.69 Aligned_cols=59 Identities=8% Similarity=0.047 Sum_probs=39.4
Q ss_pred cCCeEEEEEcccc--ccCcH-H---HHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC--CCCcEEEE
Q 011028 275 DANIIGVLVGTLG--VAGYL-H---MIHQMKELITKAGKKAYTLVMGKPNPAKLANF--PECDVFIN 333 (495)
Q Consensus 275 ~A~~~GIlvgTl~--~q~~~-~---~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF--~eID~fV~ 333 (495)
....+=|..-..| +|.+. . -+++++++++++|.++-+-+=|.+|.+-+.-. .++|+||.
T Consensus 140 ~vD~VLiMtV~PGfgGQ~f~~~~l~KI~~lr~~~~~~~~~~~IeVDGGI~~~ti~~l~~aGaD~~V~ 206 (228)
T PRK08091 140 QIDLIQILTLDPRTGTKAPSDLILDRVIQVENRLGNRRVEKLISIDGSMTLELASYLKQHQIDWVVS 206 (228)
T ss_pred hcCEEEEEEECCCCCCccccHHHHHHHHHHHHHHHhcCCCceEEEECCCCHHHHHHHHHCCCCEEEE
Confidence 4666666655555 67665 3 45566667777787766667778998876554 35898876
No 115
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=27.95 E-value=1.2e+02 Score=28.32 Aligned_cols=74 Identities=22% Similarity=0.192 Sum_probs=46.6
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HHcCCCCCcEEEEecCCCccc---ccccCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQTAL---LDSKEF 347 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~a-------KLaNF~eID~fV~vaCPr~si---~d~~~f 347 (495)
+||++....+-..+..+++.+++.+++.|.+..++-.+ -+++ +|.+- .+|++|..+|..... ....+-
T Consensus 1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~~~-~~~~~~~~~~~~~~~~-~~d~ii~~~~~~~~~~~~~~l~~~ 78 (264)
T cd01537 1 TIGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLANSQ-NDAEKQLSALENLIAR-GVDGIIIAPSDLTAPTIVKLARKA 78 (264)
T ss_pred CeEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEeCC-CCHHHHHHHHHHHHHc-CCCEEEEecCCCcchhHHHHhhhc
Confidence 47888866545566788888888888888765444333 2432 23332 689999888876554 223344
Q ss_pred CCcccC
Q 011028 348 LAPVIT 353 (495)
Q Consensus 348 ~kPViT 353 (495)
..|+|+
T Consensus 79 ~ip~v~ 84 (264)
T cd01537 79 GIPVVL 84 (264)
T ss_pred CCCEEE
Confidence 557765
No 116
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=27.66 E-value=1.2e+02 Score=29.32 Aligned_cols=76 Identities=20% Similarity=0.192 Sum_probs=48.4
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHc---CCcE-EEEEcCCCCHHHHcCC------CCCcEEEEecCCCcccc----c
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKA---GKKA-YTLVMGKPNPAKLANF------PECDVFINVSCAQTALL----D 343 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~---GKk~-y~~~vgkln~aKLaNF------~eID~fV~vaCPr~si~----d 343 (495)
+||+++....-..+..+++.+.+.+++. |.+. .++.-+.-++++..+. ..+|++|+.++-...+. -
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~l~~ 80 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIVTSADGDVAQQIADIRNLIAQGVDAIIINPASPTALNPVIEE 80 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHHH
Confidence 4899998776666778999999999888 7753 3444455565543221 26899999876433222 1
Q ss_pred ccCCCCcccC
Q 011028 344 SKEFLAPVIT 353 (495)
Q Consensus 344 ~~~f~kPViT 353 (495)
.++...|||+
T Consensus 81 ~~~~~iPvv~ 90 (272)
T cd06300 81 ACEAGIPVVS 90 (272)
T ss_pred HHHCCCeEEE
Confidence 2344457665
No 117
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=27.44 E-value=2.1e+02 Score=28.92 Aligned_cols=63 Identities=14% Similarity=0.283 Sum_probs=43.9
Q ss_pred hcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCcEEEEecCC
Q 011028 274 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 337 (495)
Q Consensus 274 r~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK----LaNF--~eID~fV~vaCP 337 (495)
+..++||+++.++.-.-+..+++.+.+.++++|....+. -+.-++++ +.++ ..+|..++.++.
T Consensus 57 ~~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~ 125 (343)
T PRK10727 57 QSTETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFLLIG-NGYHNEQKERQAIEQLIRHRCAALVVHAKM 125 (343)
T ss_pred CCCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEE-eCCCCHHHHHHHHHHHHhcCCCEEEEecCC
Confidence 346899999988776677899999999999999765433 23333332 2222 269999988653
No 118
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=27.34 E-value=1.4e+02 Score=28.74 Aligned_cols=75 Identities=11% Similarity=0.110 Sum_probs=47.0
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCC----cEEEEEcC-CCCHH-------HHcCCCCCcEEEEecCCCccccccc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGK----KAYTLVMG-KPNPA-------KLANFPECDVFINVSCAQTALLDSK 345 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GK----k~y~~~vg-kln~a-------KLaNF~eID~fV~vaCPr~si~d~~ 345 (495)
+||+++. ..-..+..+++.+++.++++|. +.-+++.+ .-+++ +|.+- .+|.+|+++++-....-..
T Consensus 1 ~igv~~~-~~~~~~~~~~~gi~~~~~~~g~~~g~~v~l~~~~~~~~~~~~~~~~~~l~~~-~vd~iI~~~~~~~~~~~~~ 78 (281)
T cd06325 1 KVGILQL-VEHPALDAARKGFKDGLKEAGYKEGKNVKIDYQNAQGDQSNLPTIARKFVAD-KPDLIVAIATPAAQAAANA 78 (281)
T ss_pred CeEEecC-CCCcchHHHHHHHHHHHHHhCccCCceEEEEEecCCCCHHHHHHHHHHHHhc-CCCEEEEcCcHHHHHHHHc
Confidence 5899985 5555677999999999999986 33333332 33343 45553 6999999876522111122
Q ss_pred CCCCcccCH
Q 011028 346 EFLAPVITP 354 (495)
Q Consensus 346 ~f~kPViTP 354 (495)
..-.|||.+
T Consensus 79 ~~~iPvV~~ 87 (281)
T cd06325 79 TKDIPIVFT 87 (281)
T ss_pred CCCCCEEEE
Confidence 344588755
No 119
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=27.28 E-value=1.3e+02 Score=28.82 Aligned_cols=59 Identities=12% Similarity=0.200 Sum_probs=36.8
Q ss_pred eEEEEEcc-----ccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC--HHHHcCC---CCCcEEEEecC
Q 011028 278 IIGVLVGT-----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN--PAKLANF---PECDVFINVSC 336 (495)
Q Consensus 278 ~~GIlvgT-----l~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln--~aKLaNF---~eID~fV~vaC 336 (495)
+||+|+.. +.-..+..+++.+++.+++.|.+..+....... ...+.++ ..+|++|+++.
T Consensus 1 ~igli~p~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dgiii~~~ 69 (270)
T cd06294 1 TIGVVLPPSADEAFQNPFFIEVLRGISAVANENGYDISLATGKNEEELLEEVKKMIQQKRVDGFILLYS 69 (270)
T ss_pred CEEEEeCCccccCcCCCCHHHHHHHHHHHHHHCCCEEEEecCCCcHHHHHHHHHHHHHcCcCEEEEecC
Confidence 47888875 444566788999999999998775443222211 1122221 24899998764
No 120
>PRK05568 flavodoxin; Provisional
Probab=27.11 E-value=2.4e+02 Score=24.57 Aligned_cols=56 Identities=13% Similarity=0.134 Sum_probs=42.8
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 338 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr 338 (495)
.+.|+-.|.. -+...+++.+.+-+++.|-++-++-+.+.+..+|. +.|. |++++|=
T Consensus 3 ~~~IvY~S~~-GnT~~~a~~i~~~~~~~g~~v~~~~~~~~~~~~~~---~~d~-iilgsp~ 58 (142)
T PRK05568 3 KINIIYWSGT-GNTEAMANLIAEGAKENGAEVKLLNVSEASVDDVK---GADV-VALGSPA 58 (142)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHHCCCeEEEEECCCCCHHHHH---hCCE-EEEECCc
Confidence 4678888854 46689999999999999998888888888877664 4564 6666664
No 121
>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.
Probab=26.61 E-value=1.4e+02 Score=28.45 Aligned_cols=49 Identities=18% Similarity=0.204 Sum_probs=37.2
Q ss_pred CeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCC--CCHHHHcCCC
Q 011028 277 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK--PNPAKLANFP 326 (495)
Q Consensus 277 ~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgk--ln~aKLaNF~ 326 (495)
+.+=|++|+.+-..-.. +..+-+.++++|-+.+++.+|+ -|++||..|-
T Consensus 108 ~rivi~v~S~~~~d~~~-i~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~ 158 (187)
T cd01452 108 QRIVAFVGSPIEEDEKD-LVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFI 158 (187)
T ss_pred ceEEEEEecCCcCCHHH-HHHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHH
Confidence 47888999886544344 4455667788999999999995 5789998884
No 122
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=26.33 E-value=1.3e+02 Score=28.81 Aligned_cols=59 Identities=10% Similarity=0.106 Sum_probs=41.0
Q ss_pred eEEEEEccc-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCcEEEEecCC
Q 011028 278 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl-~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK----LaNF--~eID~fV~vaCP 337 (495)
+||+|+-.. .-..+..+++.+++.+++.|....++. ..-++++ +.++ ..+|+.++.++.
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~~dgiii~~~~ 66 (269)
T cd06288 1 TIGLISDEIATTPFAVEIILGAQDAAREHGYLLLVVN-TGGDDELEAEAVEALLDHRVDGIIYATMY 66 (269)
T ss_pred CeEEEeCCCCCCccHHHHHHHHHHHHHHCCCEEEEEe-CCCCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 589999876 555566899999999999997764443 4445433 2222 258999998764
No 123
>PRK08883 ribulose-phosphate 3-epimerase; Provisional
Probab=26.22 E-value=82 Score=30.66 Aligned_cols=49 Identities=14% Similarity=0.367 Sum_probs=36.1
Q ss_pred cccCcH----HHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCC--CCcEEEEec
Q 011028 287 GVAGYL----HMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFINVS 335 (495)
Q Consensus 287 ~~q~~~----~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~--eID~fV~va 335 (495)
++|.+. +-++++++++.++|...-+.+-|-+|++.+.... ++|++|+.+
T Consensus 142 gGq~fi~~~lekI~~l~~~~~~~~~~~~I~vdGGI~~eni~~l~~aGAd~vVvGS 196 (220)
T PRK08883 142 GGQSFIPHTLDKLRAVRKMIDESGRDIRLEIDGGVKVDNIREIAEAGADMFVAGS 196 (220)
T ss_pred CCceecHhHHHHHHHHHHHHHhcCCCeeEEEECCCCHHHHHHHHHcCCCEEEEeH
Confidence 356564 4567777777777877778899999988776553 589998873
No 124
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.
Probab=26.05 E-value=69 Score=32.01 Aligned_cols=60 Identities=20% Similarity=0.252 Sum_probs=42.5
Q ss_pred EEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCCCc
Q 011028 279 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQT 339 (495)
Q Consensus 279 ~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCPr~ 339 (495)
||+++.+++-.-+..+.+.+++.+++.|....+.. ..-++++. .+| ..+|++|+.++...
T Consensus 1 ig~~~~~~~~~~~~~~~~~i~~~a~~~g~~v~~~~-~~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~ 66 (302)
T TIGR02634 1 IGVSIDDLRLERWQKDRDIFVAAAESLGAKVFVQS-ANGNEAKQISQIENLIARGVDVLVIIPQNGQ 66 (302)
T ss_pred CeeecCccchhhHHHHHHHHHHHHHhcCCEEEEEe-CCCCHHHHHHHHHHHHHcCCCEEEEeCCChh
Confidence 58888888877778888999999999887765543 34455533 233 25899998877544
No 125
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=25.74 E-value=1e+02 Score=29.97 Aligned_cols=58 Identities=14% Similarity=0.078 Sum_probs=40.4
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaCP 337 (495)
+||+|+.++.-..+..+++.+.+.+++.|.+.-++ -.. ++++.. ++ ..+|.+|+.++-
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~-~~~-~~~~~~~~i~~~~~~~~dgiii~~~~ 64 (289)
T cd01540 1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKI-DVP-DGEKVLSAIDNLGAQGAKGFVICVPD 64 (289)
T ss_pred CeeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEc-cCC-CHHHHHHHHHHHHHcCCCEEEEccCc
Confidence 58999988776677889999999999988774333 233 554432 22 258999998763
No 126
>cd04502 SGNH_hydrolase_like_7 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.
Probab=25.73 E-value=3.1e+02 Score=24.57 Aligned_cols=53 Identities=6% Similarity=-0.016 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhcCCeEEEEEcccc------ccCcHHHHHHHHHHHHHcCCcEEEEEcC
Q 011028 263 LKRRYYLVEKAKDANIIGVLVGTLG------VAGYLHMIHQMKELITKAGKKAYTLVMG 315 (495)
Q Consensus 263 l~rRy~~I~kar~A~~~GIlvgTl~------~q~~~~~i~~L~~li~~~GKk~y~~~vg 315 (495)
+..|......+...+.+=|.+||=- .+.+.+-++.+-+.+++++.+.-+++++
T Consensus 38 ~~~~~~~~~~~~~p~~vvi~~G~ND~~~~~~~~~~~~~~~~lv~~i~~~~~~~~iil~~ 96 (171)
T cd04502 38 CLHYFDRLVLPYQPRRVVLYAGDNDLASGRTPEEVLRDFRELVNRIRAKLPDTPIAIIS 96 (171)
T ss_pred HHHHHHhhhccCCCCEEEEEEecCcccCCCCHHHHHHHHHHHHHHHHHHCCCCcEEEEE
Confidence 4455555545557788888888733 2334444445555555554444444444
No 127
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=25.62 E-value=84 Score=30.50 Aligned_cols=77 Identities=26% Similarity=0.218 Sum_probs=49.3
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCC-CCHH----HHcCC--CCCcEEEEecCCCccc---ccccCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK-PNPA----KLANF--PECDVFINVSCAQTAL---LDSKEF 347 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgk-ln~a----KLaNF--~eID~fV~vaCPr~si---~d~~~f 347 (495)
+||||+..+.-..+..++..+++.+++.|.+..++..+. -+++ .+.++ ..+|+.|+.+...... .....-
T Consensus 1 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~~ 80 (268)
T cd06306 1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGGYPNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVAA 80 (268)
T ss_pred CeEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHHC
Confidence 489999988777778999999999999998765554332 2332 23332 2699999887543322 222333
Q ss_pred CCcccCH
Q 011028 348 LAPVITP 354 (495)
Q Consensus 348 ~kPViTP 354 (495)
-.|||+-
T Consensus 81 giPvV~~ 87 (268)
T cd06306 81 SIPVIAL 87 (268)
T ss_pred CCCEEEe
Confidence 4577643
No 128
>PF00205 TPP_enzyme_M: Thiamine pyrophosphate enzyme, central domain; InterPro: IPR012000 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This central domain of TPP enzymes contains a 2-fold Rossman fold. ; GO: 0000287 magnesium ion binding, 0030976 thiamine pyrophosphate binding; PDB: 1OZH_C 1OZF_B 1OZG_B 2Q29_B 2Q28_A 2Q27_B 1OVM_B 1PVD_A 1PYD_B 2VK1_C ....
Probab=25.25 E-value=48 Score=29.14 Aligned_cols=46 Identities=24% Similarity=0.200 Sum_probs=35.2
Q ss_pred HHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCC
Q 011028 269 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK 316 (495)
Q Consensus 269 ~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgk 316 (495)
..+..+.|++--||+|... .+....+.+++++++.|-.+++-.++|
T Consensus 4 ~~~~L~~A~rP~il~G~g~--~~~~a~~~l~~lae~~~~Pv~~t~~~k 49 (137)
T PF00205_consen 4 AADLLSSAKRPVILAGRGA--RRSGAAEELRELAEKLGIPVATTPMGK 49 (137)
T ss_dssp HHHHHHH-SSEEEEE-HHH--HHTTCHHHHHHHHHHHTSEEEEEGGGT
T ss_pred HHHHHHhCCCEEEEEcCCc--ChhhHHHHHHHHHHHHCCCEEecCccc
Confidence 5677888999999999653 333667888899999999999888876
No 129
>PF02514 CobN-Mg_chel: CobN/Magnesium Chelatase; InterPro: IPR003672 This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN may play a role in cobalt insertion reactions and is implicated in the conversion of precorrin-2 to cobyrinic acid in cobalamin biosynthesis []. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis as the third subunit of light-independent protochlorophyllide reductase in bacteria and plants [].; GO: 0009058 biosynthetic process
Probab=25.18 E-value=1e+02 Score=37.36 Aligned_cols=84 Identities=14% Similarity=0.194 Sum_probs=60.3
Q ss_pred hcCCeEEEEEccccc-cCcHHHHHHHHHHHHHcCCcEEEEEcCC--CCHHHHcC-CC-----CCcEEEEecCCCcccc--
Q 011028 274 KDANIIGVLVGTLGV-AGYLHMIHQMKELITKAGKKAYTLVMGK--PNPAKLAN-FP-----ECDVFINVSCAQTALL-- 342 (495)
Q Consensus 274 r~A~~~GIlvgTl~~-q~~~~~i~~L~~li~~~GKk~y~~~vgk--ln~aKLaN-F~-----eID~fV~vaCPr~si~-- 342 (495)
-++.+||||+..--. .+....++.|-+.|+++|-.++.++..- -....+.. |. .||+.|.+.+=++.-.
T Consensus 69 ~~~P~VgIlfyrs~~~~g~~~~vdaLI~~LE~~G~nvipvf~~~~~~~~~~i~~~f~~~g~~~vDaIIn~~~f~l~~~~~ 148 (1098)
T PF02514_consen 69 PNRPTVGILFYRSYWLSGNTAVVDALIRALEERGLNVIPVFCSSGPDSQEAIEDYFMDDGKPRVDAIINLTGFSLGGGPA 148 (1098)
T ss_pred CCCCEEEEEeehhhhhcCCcHHHHHHHHHHHHCCCeEEEEEecCccchHHHHHHHHhhcCCCCceEEEEcCccccCCCCc
Confidence 468999999975543 5678999999999999999999988653 33333432 33 3999998888765432
Q ss_pred -----cccCCCCcccCHHHH
Q 011028 343 -----DSKEFLAPVITPFEA 357 (495)
Q Consensus 343 -----d~~~f~kPViTP~El 357 (495)
..++..-|||.+.-+
T Consensus 149 ~~~~~~L~~LnVPVlq~i~~ 168 (1098)
T PF02514_consen 149 GGAIELLKELNVPVLQAITL 168 (1098)
T ss_pred chhHHHHHHCCCCEEEeecc
Confidence 345667788776533
No 130
>PRK09701 D-allose transporter subunit; Provisional
Probab=25.17 E-value=1.7e+02 Score=29.36 Aligned_cols=64 Identities=11% Similarity=0.081 Sum_probs=44.7
Q ss_pred HHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEE-cCCCCHHH----HcCCC--CCcEEEEec
Q 011028 272 KAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV-MGKPNPAK----LANFP--ECDVFINVS 335 (495)
Q Consensus 272 kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~-vgkln~aK----LaNF~--eID~fV~va 335 (495)
.|.-|.+||+|+.++.-..+..+++.+++.+++.|....++. -+.-++++ |.+|. .+|.+|+.+
T Consensus 20 ~~~~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~ 90 (311)
T PRK09701 20 SAFAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAP 90 (311)
T ss_pred hhccCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCeEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEeC
Confidence 345577999999887656677899999999999987766553 23334433 33442 589998864
No 131
>PF02302 PTS_IIB: PTS system, Lactose/Cellobiose specific IIB subunit; InterPro: IPR003501 The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This signature is often found downstream of IPR003352 from INTERPRO.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TVM_A 2WY2_D 1IIB_A 2WWV_D 1H9C_A 1E2B_A 2L2Q_A 2KYR_A 3CZC_A 3NBM_A ....
Probab=25.13 E-value=2e+02 Score=22.95 Aligned_cols=56 Identities=16% Similarity=0.232 Sum_probs=35.7
Q ss_pred EEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCCccc
Q 011028 282 LVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTAL 341 (495)
Q Consensus 282 lvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr~si 341 (495)
++..-|.....-+.++|++.+++.|.+...............+ ++|+++.. |+...
T Consensus 4 vvC~~Gi~TS~~~~~~i~~~~~~~gi~~~~~~~~~~~~~~~~~--~~D~il~~--~~i~~ 59 (90)
T PF02302_consen 4 VVCGSGIGTSLMVANKIKKALKELGIEVEVSAGSILEVEEIAD--DADLILLT--PQIAY 59 (90)
T ss_dssp EEESSSSHHHHHHHHHHHHHHHHTTECEEEEEEETTTHHHHHT--T-SEEEEE--ESSGG
T ss_pred EECCChHHHHHHHHHHHHHHHHhccCceEEEEecccccccccC--CCcEEEEc--Cccch
Confidence 4444455555555699999999999887777777444444444 57876544 55553
No 132
>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
Probab=24.81 E-value=1.9e+02 Score=26.86 Aligned_cols=60 Identities=18% Similarity=0.299 Sum_probs=44.0
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEE-cCCCCHHHHcCCC----CCcEEEEecCCCcc
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV-MGKPNPAKLANFP----ECDVFINVSCAQTA 340 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~-vgkln~aKLaNF~----eID~fV~vaCPr~s 340 (495)
.+|||+|+. .-+++.+.--+.|++-|..+-.-+ .-+=+|++|..|. +-++=|+||..-.+
T Consensus 4 ~V~IIMGS~---SD~~~mk~Aa~~L~~fgi~ye~~VvSAHRTPe~m~~ya~~a~~~g~~viIAgAGgA 68 (162)
T COG0041 4 KVGIIMGSK---SDWDTMKKAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVKVIIAGAGGA 68 (162)
T ss_pred eEEEEecCc---chHHHHHHHHHHHHHcCCCeEEEEEeccCCHHHHHHHHHHHHHCCCeEEEecCcch
Confidence 799999985 457888888899999999987744 4588999998775 23333555555443
No 133
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=24.76 E-value=1.5e+02 Score=30.21 Aligned_cols=64 Identities=14% Similarity=0.193 Sum_probs=47.7
Q ss_pred cCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCCCc
Q 011028 275 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQT 339 (495)
Q Consensus 275 ~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCPr~ 339 (495)
++.+||+++..+.-..+..+++-+++.++++|....+.. +.-++++. .++ ..+|.+|+.++...
T Consensus 24 ~~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~~-~~~~~~~~~~~i~~l~~~~vDGiIi~~~~~~ 93 (330)
T PRK10355 24 KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQS-ANGNEETQMSQIENMINRGVDVLVIIPYNGQ 93 (330)
T ss_pred CCceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEEC-CCCCHHHHHHHHHHHHHcCCCEEEEeCCChh
Confidence 478999999988888888999999999999998766543 33455433 223 26999999876533
No 134
>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type I periplasmic sugar-binding protein-like fold.
Probab=24.63 E-value=1.3e+02 Score=29.00 Aligned_cols=57 Identities=7% Similarity=0.018 Sum_probs=38.4
Q ss_pred eEEEEEcc--ccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCcEEEEecC
Q 011028 278 IIGVLVGT--LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 336 (495)
Q Consensus 278 ~~GIlvgT--l~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLa----NF--~eID~fV~vaC 336 (495)
+||+|+.. ++-..+..+++.+++.+++.|....+.... ++++.. ++ ..+|.++++++
T Consensus 1 ~Igvi~~~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~~~~--~~~~~~~~~~~l~~~~vdgiii~~~ 65 (260)
T cd06304 1 KVALVYDGGGGDKSFNQSAYEGLEKAEKELGVEVKYVESV--EDADYEPNLRQLAAQGYDLIFGVGF 65 (260)
T ss_pred CEEEEecCCCCcchHHHHHHHHHHHHHHhcCceEEEEecC--CHHHHHHHHHHHHHcCCCEEEECCc
Confidence 47888874 555666789999999999988775554333 555432 22 14898888654
No 135
>TIGR01162 purE phosphoribosylaminoimidazole carboxylase, PurE protein. Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, an N5-CAIR mutase.
Probab=24.57 E-value=1.4e+02 Score=27.62 Aligned_cols=71 Identities=17% Similarity=0.277 Sum_probs=52.0
Q ss_pred EEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHHcCCC------CCcEEEEecCCCcccc--cccCCCC
Q 011028 279 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANFP------ECDVFINVSCAQTALL--DSKEFLA 349 (495)
Q Consensus 279 ~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vg-kln~aKLaNF~------eID~fV~vaCPr~si~--d~~~f~k 349 (495)
+|||+|+ ..-+++.+...+.|++-|..+-+-+.+ +=+|++|..|. ++++||.+|=-...+- -...-.+
T Consensus 1 V~IimGS---~SD~~~~~~a~~~L~~~gi~~dv~V~SaHRtp~~~~~~~~~a~~~g~~viIa~AG~aa~Lpgvva~~t~~ 77 (156)
T TIGR01162 1 VGIIMGS---DSDLPTMKKAADILEEFGIPYELRVVSAHRTPELMLEYAKEAEERGIKVIIAGAGGAAHLPGMVAALTPL 77 (156)
T ss_pred CEEEECc---HhhHHHHHHHHHHHHHcCCCeEEEEECcccCHHHHHHHHHHHHHCCCeEEEEeCCccchhHHHHHhccCC
Confidence 5788876 446788889999999999997665444 77899998884 5788887776666553 2445577
Q ss_pred ccc
Q 011028 350 PVI 352 (495)
Q Consensus 350 PVi 352 (495)
|||
T Consensus 78 PVI 80 (156)
T TIGR01162 78 PVI 80 (156)
T ss_pred CEE
Confidence 777
No 136
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=24.04 E-value=99 Score=29.67 Aligned_cols=59 Identities=14% Similarity=0.066 Sum_probs=37.9
Q ss_pred eEEEEEccc-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC------CCCcEEEEecCC
Q 011028 278 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl-~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF------~eID~fV~vaCP 337 (495)
+||+|+.++ .-..+..+++.+++.++++|....++ .+.-++++.... ..+|++|+.++-
T Consensus 1 ~i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~~~~~-~~~~~~~~~~~~~~~l~~~~vdgiii~~~~ 66 (275)
T cd06317 1 TIGYTQNNVGSHSYQTTYNKAFQAAAEEDGVEVIVL-DANGDVARQAAQVEDLIAQKVDGIILWPTD 66 (275)
T ss_pred CeEEEecccCCCHHHHHHHHHHHHHHHhcCCEEEEE-cCCcCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 478888776 55556788888888888888775443 333344333111 258888887764
No 137
>PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=23.88 E-value=1.6e+02 Score=31.58 Aligned_cols=9 Identities=22% Similarity=0.405 Sum_probs=5.8
Q ss_pred EEecCCCcc
Q 011028 332 INVSCAQTA 340 (495)
Q Consensus 332 V~vaCPr~s 340 (495)
|.-|||..+
T Consensus 130 i~rGC~~~C 138 (418)
T PRK14336 130 IMQGCDNFC 138 (418)
T ss_pred eccCCCCCC
Confidence 445788764
No 138
>PRK00055 ribonuclease Z; Reviewed
Probab=23.76 E-value=84 Score=30.58 Aligned_cols=30 Identities=20% Similarity=0.115 Sum_probs=20.9
Q ss_pred CceeEEEEcCCccccCccchhhhcccCCcEEEEe
Q 011028 62 KDIGLFVMADTTYGSCCVDEVGASHVDADCVIHY 95 (495)
Q Consensus 62 ~~~~v~IlaDtsYGsCCVDevaA~hv~aD~iVHy 95 (495)
.+.++++.+||.|. ++.....-++|++||=
T Consensus 165 ~g~~~~y~~Dt~~~----~~~~~~~~~~d~li~E 194 (270)
T PRK00055 165 KGRKVAYCGDTRPC----EALVELAKGADLLVHE 194 (270)
T ss_pred CCcEEEEeCCCCCc----HHHHHHhCCCCEEEEe
Confidence 35679999999983 3433333478999973
No 139
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=23.55 E-value=1.4e+02 Score=28.83 Aligned_cols=75 Identities=15% Similarity=0.123 Sum_probs=0.0
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC--------HHHHcCCCCCcEEEEecCCCcccccc----c
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN--------PAKLANFPECDVFINVSCAQTALLDS----K 345 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln--------~aKLaNF~eID~fV~vaCPr~si~d~----~ 345 (495)
.||+|+..+.--.+..+++.+++.++++|...-++....-+ ..+|.+- .+|+.|+.++....++.. +
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~~-~vdgiIi~~~~~~~~~~~~~~~~ 79 (275)
T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAAPSEGDQQGQLSIAENMINK-GYKGLLFSPISDVNLVPAVERAK 79 (275)
T ss_pred CeeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEccCCCCCHHHHHHHHHHHHHh-CCCEEEECCCChHHhHHHHHHHH
Q ss_pred CCCCcccC
Q 011028 346 EFLAPVIT 353 (495)
Q Consensus 346 ~f~kPViT 353 (495)
+...|||+
T Consensus 80 ~~~iPvV~ 87 (275)
T cd06320 80 KKGIPVVN 87 (275)
T ss_pred HCCCeEEE
No 140
>PRK09240 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=23.51 E-value=1.8e+02 Score=30.66 Aligned_cols=57 Identities=25% Similarity=0.319 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHhcCCe----EEEEEccccccC--cHHHHHHHHHHHHHcCCcEEEEEcCCCCHH
Q 011028 263 LKRRYYLVEKAKDANI----IGVLVGTLGVAG--YLHMIHQMKELITKAGKKAYTLVMGKPNPA 320 (495)
Q Consensus 263 l~rRy~~I~kar~A~~----~GIlvgTl~~q~--~~~~i~~L~~li~~~GKk~y~~~vgkln~a 320 (495)
...|...++.|++|+. .|+|+| ++... ...++.+|+.|=...++-.+.+.+..++|.
T Consensus 201 ~~~rl~~i~~a~~aG~~~v~~g~i~G-lge~~~d~~~~a~~l~~L~~~~~~~~~sv~~~~l~P~ 263 (371)
T PRK09240 201 FEYRLETPERAGRAGIRKIGLGALLG-LSDWRTDALMTALHLRYLQRKYWQAEYSISFPRLRPC 263 (371)
T ss_pred HHHHHHHHHHHHHcCCCeeceEEEec-CCccHHHHHHHHHHHHHHHHhCCCCceeeecCccccC
Confidence 5678999999999963 799998 44433 567788888888788888888888888885
No 141
>COG1736 DPH2 Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis]
Probab=23.46 E-value=8.8e+02 Score=25.48 Aligned_cols=168 Identities=16% Similarity=0.247 Sum_probs=89.3
Q ss_pred cCCChHHHHHHHhhhhcCCCCcEEEEecccchhhhHHHHHHHHhhccCCCCCcceeeeeeccceeeecCCCCCCCCCCCC
Q 011028 115 ASINTSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPA 194 (495)
Q Consensus 115 ~~id~~~~~~~l~~~~~~~~~~v~l~~dvqy~~~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 194 (495)
.++|.+.++..+++. +.++|+|-+.--..+....+.+.|++... .++.+.. .|. =
T Consensus 8 ~~~e~~~iv~~ir~~---~ak~V~LQ~PeGLk~~~~~ia~~le~~~~-------~~v~i~g------d~~---------y 62 (347)
T COG1736 8 YNYEIEEIVREIRRL---GAKRVLLQFPEGLKRYAIEIADILEANLG-------AEVIISG------DPV---------Y 62 (347)
T ss_pred eecchhHHHHHHHhC---CCceEEEECChHHHHHHHHHHHHHHHhhC-------ceEEEeC------Ccc---------c
Confidence 345667777777654 24789888887888888888888887621 2222210 010 0
Q ss_pred CCcccccccCcccccCCcccccceEEEEEcCCCchhhhhhhhcCCceEEEecCCCCccccccccHHHHHHHHHHHHHHHh
Q 011028 195 GGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAK 274 (495)
Q Consensus 195 ~gc~~~~~~~~~~~~~~~~~~~~~~l~~Ig~~~~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~l~rRy~~I~kar 274 (495)
+.|.- ... . -..+ .-.++|+|.... .+ ..++. + ..|=|....+ +...+...=-..+++
T Consensus 63 GACdi---~~~--~---a~~~-~D~iVH~GHs~l--~~--~~~~~-~-Viyv~~~~~~-----d~~~~~~~~~~~l~~-- 120 (347)
T COG1736 63 GACDI---DDL--K---AKDV-VDLIVHYGHSCL--PP--VEYEL-P-VIYVFAFSRV-----DVDLVVLEATRELKK-- 120 (347)
T ss_pred ccccC---CHH--H---Hhhc-ccEEEEcccccC--CC--cCCCC-c-EEEeeccccc-----chhHHHHHhhHhhcc--
Confidence 23411 000 0 0111 116889998752 22 11111 2 2222222221 122221111112222
Q ss_pred cCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCCcccc
Q 011028 275 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALL 342 (495)
Q Consensus 275 ~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~ 342 (495)
..+.||++.. ..+...++.+++.|+..|. .+++++.+-- .++. ..++||.-.++.
T Consensus 121 ~~r~I~li~t----~q~~~~l~~~k~~L~~~g~---~v~i~~~~~r-~~~~-----gqVLGC~~~~~~ 175 (347)
T COG1736 121 GSRRIGLITT----AQHVHLLEEVKEILEGRGY---EVVIGRGQTR-PAYP-----GQVLGCNFSVLE 175 (347)
T ss_pred CCceEEEEec----ccchhHHHHHHHHhhcCCe---EEEEeCCCCc-ccCc-----ceeeccccccCC
Confidence 5667888874 5677889999999998776 7888887765 4443 345666655554
No 142
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=23.24 E-value=73 Score=31.73 Aligned_cols=52 Identities=29% Similarity=0.493 Sum_probs=31.3
Q ss_pred EEecCCCCCCCCCCCeE--EEcccc----CCChHHHHHHHhhhh------cCCCCcEEEEecccchh
Q 011028 93 IHYGHTCLSPTSTLPAF--FVFGKA----SINTSNCIENLSKHA------LTNGKPILVLYGLEYAH 147 (495)
Q Consensus 93 VHyGhsCls~~~~lpvi--YVf~~~----~id~~~~~~~l~~~~------~~~~~~v~l~~dvqy~~ 147 (495)
|||||.--. --|=. |||+.. -||+...++.|...+ .....+|+++.+=+|.+
T Consensus 14 vHfGhqtr~---wnpkm~~fIf~~RngihIIDL~kT~~~l~~A~~~v~~~~~~~g~ILfVgTK~~a~ 77 (252)
T COG0052 14 VHFGHQTRR---WNPKMKPFIFGERNGIHIIDLQKTLERLREAYKFLRRIAANGGKILFVGTKKQAQ 77 (252)
T ss_pred ccccccccc---cCCcccccceeecCCcEEEEHHHHHHHHHHHHHHHHHHHcCCCEEEEEechHHHH
Confidence 899995422 23444 888853 356766666554321 23356788888876643
No 143
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=22.97 E-value=2.8e+02 Score=28.03 Aligned_cols=62 Identities=16% Similarity=0.150 Sum_probs=43.1
Q ss_pred hcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecC
Q 011028 274 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSC 336 (495)
Q Consensus 274 r~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaC 336 (495)
+..++||+++..+.-..+..+++.+.+.++++|....+. ...-++++. ..+ ..+|.+++++.
T Consensus 57 ~~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~-~~~~~~~~~~~~i~~l~~~~vdGiIi~~~ 124 (346)
T PRK10401 57 QVSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVLIG-NSYHEAEKERHAIEVLIRQRCNALIVHSK 124 (346)
T ss_pred CCCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE-cCCCChHHHHHHHHHHHhcCCCEEEEeCC
Confidence 356799999988776777889999999999998764432 233334332 122 25999999864
No 144
>cd05566 PTS_IIB_galactitol PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) comprise the gatCBA operon. Galactitol PTS permease takes up exogenous galactitol, releasing the phosphate ester into the cytoplasm in preparation for oxidation and further metabolism via a modified glycolytic pathway called the tagatose-6-phosphate glycolytic pathway. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include galactitol, chitobiose/lichenan, ascorbate, lactose, mannitol, fructose, and
Probab=22.86 E-value=3e+02 Score=22.03 Aligned_cols=54 Identities=17% Similarity=0.153 Sum_probs=30.3
Q ss_pred EEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCC
Q 011028 282 LVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 338 (495)
Q Consensus 282 lvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr 338 (495)
+|..-|..-..-+..+|++.+.+.|....+-.++.-.... ...++| +|+++.|-
T Consensus 5 ivC~~G~~tS~~l~~~i~~~~~~~~i~~~v~~~~~~~~~~--~~~~~D-liist~~~ 58 (89)
T cd05566 5 VACGTGVATSTVVASKVKELLKENGIDVKVEQCKIAEVPS--LLDDAD-LIVSTTKV 58 (89)
T ss_pred EECCCCccHHHHHHHHHHHHHHHCCCceEEEEecHHHhhc--ccCCCc-EEEEcCCc
Confidence 3333444445678899999998888764443323222221 234678 55555553
No 145
>PRK14057 epimerase; Provisional
Probab=22.81 E-value=2.2e+02 Score=28.57 Aligned_cols=60 Identities=15% Similarity=0.176 Sum_probs=39.4
Q ss_pred cCCeEEEEEcccc--ccCcH-H---HHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC--CCCcEEEEe
Q 011028 275 DANIIGVLVGTLG--VAGYL-H---MIHQMKELITKAGKKAYTLVMGKPNPAKLANF--PECDVFINV 334 (495)
Q Consensus 275 ~A~~~GIlvgTl~--~q~~~-~---~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF--~eID~fV~v 334 (495)
....|=|..-..| +|.+. . -++++++++.++|.++-+-+=|-+|.+.+.-. .++|+||.=
T Consensus 154 ~vD~VLvMtV~PGfgGQ~Fi~~~l~KI~~lr~~~~~~~~~~~IeVDGGI~~~ti~~l~~aGad~~V~G 221 (254)
T PRK14057 154 DVEVIQLLAVNPGYGSKMRSSDLHERVAQLLCLLGDKREGKIIVIDGSLTQDQLPSLIAQGIDRVVSG 221 (254)
T ss_pred hCCEEEEEEECCCCCchhccHHHHHHHHHHHHHHHhcCCCceEEEECCCCHHHHHHHHHCCCCEEEEC
Confidence 4555555555544 67764 3 45555567777787766667788998876544 269988873
No 146
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=22.67 E-value=1.6e+02 Score=28.31 Aligned_cols=55 Identities=15% Similarity=0.223 Sum_probs=40.0
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCcEEEEe
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINV 334 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aK-------LaNF~eID~fV~v 334 (495)
+||+++.++.-..+..+++.+.+.++++|....+... .-++.+ |.+. .+|++++.
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~-~vdgii~~ 62 (273)
T cd01541 1 NIGVITTYISDYIFPSIIRGIESVLSEKGYSLLLAST-NNDPERERKCLENMLSQ-GIDGLIIE 62 (273)
T ss_pred CeEEEeCCccchhHHHHHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHHHHHHc-CCCEEEEe
Confidence 4899998887666789999999999999988755443 445532 3332 68999885
No 147
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=22.63 E-value=78 Score=30.63 Aligned_cols=59 Identities=12% Similarity=-0.003 Sum_probs=38.7
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC------CCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF------~eID~fV~vaCP 337 (495)
+||+++=...-..+..+++.+.+.++++|.+..+..... ++++-... ..+|..|+.++-
T Consensus 1 ~~g~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~-~~~~~~~~i~~l~~~~vdgiIi~~~~ 65 (273)
T cd06309 1 TVGFSQVGAESPWRTAETKSIKDAAEKRGFDLKFADAQQ-KQENQISAIRSFIAQGVDVIILAPVV 65 (273)
T ss_pred CeeeccCCCCCHHHHHHHHHHHHHHHhcCCEEEEeCCCC-CHHHHHHHHHHHHHcCCCEEEEcCCc
Confidence 578888776655667888888888888887766654433 44333211 258888887653
No 148
>PRK14814 NADH dehydrogenase subunit B; Provisional
Probab=22.61 E-value=1.6e+02 Score=28.12 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=10.2
Q ss_pred CCCCCcEEEEecCCCc
Q 011028 324 NFPECDVFINVSCAQT 339 (495)
Q Consensus 324 NF~eID~fV~vaCPr~ 339 (495)
.+-.+|+| +=+||=.
T Consensus 128 ~vvpVDv~-IPGCPP~ 142 (186)
T PRK14814 128 RILPVDVY-VPGCPPR 142 (186)
T ss_pred ccccccEE-ecCCCCC
Confidence 33457776 7899965
No 149
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=22.21 E-value=1.4e+02 Score=28.01 Aligned_cols=32 Identities=22% Similarity=0.393 Sum_probs=17.4
Q ss_pred EEEEEccccccCcHHHHHHHHHHHHHcCCcEE
Q 011028 279 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAY 310 (495)
Q Consensus 279 ~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y 310 (495)
||+++-+.....+..+.+.+++.+++.|.+..
T Consensus 2 i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~~~ 33 (264)
T cd06267 2 IGVIVPDISNPFFAELLRGIEEAAREAGYSVL 33 (264)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 45555554444445555566666655555543
No 150
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=22.18 E-value=1.1e+02 Score=29.42 Aligned_cols=76 Identities=21% Similarity=0.249 Sum_probs=46.3
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCCCcccc----cccCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQTALL----DSKEF 347 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCPr~si~----d~~~f 347 (495)
+||+++.+..-..+..+++.+++.+++.|....+.. +.-++++- .++ ..+|++|+.++...... ..++.
T Consensus 1 ~i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~-~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~~ 79 (267)
T cd06322 1 VIGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSI-ANQDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKKA 79 (267)
T ss_pred CeeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEec-CCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHHHHC
Confidence 478899887655667889999999998887654433 33444432 111 25899998876432211 12234
Q ss_pred CCcccCH
Q 011028 348 LAPVITP 354 (495)
Q Consensus 348 ~kPViTP 354 (495)
-.|+|+.
T Consensus 80 ~ipvV~~ 86 (267)
T cd06322 80 GIPVITV 86 (267)
T ss_pred CCCEEEE
Confidence 4566654
No 151
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=21.98 E-value=1.3e+02 Score=29.33 Aligned_cols=40 Identities=28% Similarity=0.328 Sum_probs=33.8
Q ss_pred HHHHHHHhcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCc
Q 011028 267 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKK 308 (495)
Q Consensus 267 y~~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk 308 (495)
|.++.+|++++.-+|||++-... +.+.+.|++.+++.|..
T Consensus 66 ~~l~~~~~e~g~kavIvp~~~~~--~g~~~~lk~~~e~~gi~ 105 (217)
T PF02593_consen 66 YELPEIAKEAGVKAVIVPSESPK--PGLRRQLKKQLEEFGIE 105 (217)
T ss_pred HHHHHHHHHcCCCEEEEecCCCc--cchHHHHHHHHHhcCce
Confidence 67888899999999999988766 88999999999876644
No 152
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=21.88 E-value=2.2e+02 Score=26.26 Aligned_cols=61 Identities=15% Similarity=0.135 Sum_probs=39.6
Q ss_pred CeEEEEEccccccCcHHHHHHHHHHHHHcCC---cEEEEEcCCCC-----HHHHcCCCCCcEEEEecCC
Q 011028 277 NIIGVLVGTLGVAGYLHMIHQMKELITKAGK---KAYTLVMGKPN-----PAKLANFPECDVFINVSCA 337 (495)
Q Consensus 277 ~~~GIlvgTl~~q~~~~~i~~L~~li~~~GK---k~y~~~vgkln-----~aKLaNF~eID~fV~vaCP 337 (495)
-+||||++.-.-.-.-.+++...+.|++.|. ...++.|---. ..+|+.-.++|++|.+||-
T Consensus 13 ~riaIV~s~~n~~i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavIalG~V 81 (154)
T PRK00061 13 LRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIALGAV 81 (154)
T ss_pred CEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEEEEeeE
Confidence 4899999865433334566666678888883 33444333211 2467766679999999997
No 153
>TIGR01574 miaB-methiolase tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB. Hits to this model span all major groups of bacteria and eukaryotes, but not archaea, which are known to lack this particular tRNA modification. The enzyme from Thermotoga maritima has been cloned, expressed, spectroscopically characterized and shown to complement the E. coli MiaB enzyme.
Probab=21.86 E-value=1.1e+02 Score=32.97 Aligned_cols=66 Identities=17% Similarity=0.196 Sum_probs=30.3
Q ss_pred HHHHHHHhcCCeEEEEEccccccCcHHHHHHHHHH--HHHcCCcEEEEEcCC---CCHHHHc-CCCCCcEEE
Q 011028 267 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKEL--ITKAGKKAYTLVMGK---PNPAKLA-NFPECDVFI 332 (495)
Q Consensus 267 y~~I~kar~A~~~GIlvgTl~~q~~~~~i~~L~~l--i~~~GKk~y~~~vgk---ln~aKLa-NF~eID~fV 332 (495)
|..+....+|.++.|=..|..-.--.++.+.|.++ +++.+.+..+++.|- ..++++. .+++||.+|
T Consensus 29 ~~~~~~~~~aDv~iiNTC~v~~~a~~k~~~~i~~~~~~k~~~~~~~ivv~GC~a~~~~~~~~~~~~~vd~v~ 100 (438)
T TIGR01574 29 YALTEDAKEADVLLINTCSVREKAEHKVFGELGGFKKLKKKNPDLIIGVCGCMASHLGNEIFQRAPYVDFVF 100 (438)
T ss_pred cEECCCcccCCEEEEeccCeechHHHHHHHHHHHHHHHHhhCCCcEEEEeCccccccHHHHHhcCCCCcEEE
Confidence 33444445566655444444333334444444221 223333444555553 2455554 356666665
No 154
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=21.83 E-value=2.1e+02 Score=29.02 Aligned_cols=64 Identities=6% Similarity=-0.046 Sum_probs=41.1
Q ss_pred hcCCeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH----HHcCCC--CCcEEEEecCC
Q 011028 274 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA----KLANFP--ECDVFINVSCA 337 (495)
Q Consensus 274 r~A~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~a----KLaNF~--eID~fV~vaCP 337 (495)
+.-++||+++..++-..+..+++.+.+.++++|.-..++..+.-++. .+.++. .+|.+++.+++
T Consensus 22 ~~~~~Igvv~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~ 91 (330)
T PRK15395 22 AADTRIGVTIYKYDDNFMSVVRKAIEKDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVD 91 (330)
T ss_pred cCCceEEEEEecCcchHHHHHHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeccC
Confidence 34478999988776666778888888888887643333333333332 233332 58999987665
No 155
>KOG3360 consensus Acylphosphatase [Energy production and conversion]
Probab=21.40 E-value=2.1e+02 Score=24.39 Aligned_cols=44 Identities=23% Similarity=0.300 Sum_probs=37.8
Q ss_pred HHHHHHHHHhcCCeEEEEEcccc------ccCcHHHHHHHHHHHHHcCCc
Q 011028 265 RRYYLVEKAKDANIIGVLVGTLG------VAGYLHMIHQMKELITKAGKK 308 (495)
Q Consensus 265 rRy~~I~kar~A~~~GIlvgTl~------~q~~~~~i~~L~~li~~~GKk 308 (495)
-|.+....|+.....|-+.+|.- .++-++.++.++.+|..+|-.
T Consensus 23 fr~~t~~~a~~lGlrGWv~Nt~~GtvkG~leGp~~~vd~mk~wl~~~gsP 72 (98)
T KOG3360|consen 23 FRKHTLDEAKKLGLRGWVMNTSEGTVKGQLEGPPEKVDEMKEWLLTRGSP 72 (98)
T ss_pred hhHHHHHHHHhhcceEEEEecCCceEEEEEeCCHHHHHHHHHHHHhcCCh
Confidence 36778899999999999998865 478899999999999988754
No 156
>TIGR01012 Sa_S2_E_A ribosomal protein Sa(cytosolic)/S2(archaeal). TIGR01011 describes the related protein of organelles and bacteria.
Probab=21.10 E-value=2e+02 Score=27.61 Aligned_cols=51 Identities=22% Similarity=0.268 Sum_probs=29.4
Q ss_pred EEecCCCCCCCCCCCeEEEccccC-----CChHHHHHHHhhhh----cCCCCcEEEEecccch
Q 011028 93 IHYGHTCLSPTSTLPAFFVFGKAS-----INTSNCIENLSKHA----LTNGKPILVLYGLEYA 146 (495)
Q Consensus 93 VHyGhsCls~~~~lpviYVf~~~~-----id~~~~~~~l~~~~----~~~~~~v~l~~dvqy~ 146 (495)
|||||.-.+|-- -| |+|++.+ +|+++..+.|+... .-..+.|+++.+-.+.
T Consensus 14 vH~Gh~~~np~M-~~--yI~~~r~~gi~IIdL~kT~~~L~~A~~~i~~i~~~~ILfVgtk~~~ 73 (196)
T TIGR01012 14 VHIGTQNKTKDM-EK--FIYKVRSDGLYVLDLRKTDERLRVAAKFLVRIEPEDILVVSARIYG 73 (196)
T ss_pred eecCCCcCCCCC-cc--ceeeecCCCCEEEcHHHHHHHHHHHHHHHHHhhCCeEEEEecCHHH
Confidence 899997443321 12 7887653 57776666555421 1114578888775543
No 157
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=21.04 E-value=2.6e+02 Score=30.84 Aligned_cols=76 Identities=16% Similarity=0.130 Sum_probs=55.7
Q ss_pred CeEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCcEEEEecCCCcccc--c--ccCCCCccc
Q 011028 277 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALL--D--SKEFLAPVI 352 (495)
Q Consensus 277 ~~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~--d--~~~f~kPVi 352 (495)
+.|-||=.+..+-+...=+..|+++|+.-|-+.-.+.-+.-+.+.|.+.++.++= ++-||+.+.. . .++|-.|.+
T Consensus 159 ~~VNIiG~~~l~f~~~~D~~EikrlL~~~Gi~vn~v~p~g~s~~di~~l~~A~~n-ivl~~~~g~~~A~~Lee~fGiP~i 237 (519)
T PRK02910 159 PSVNLLGPTALGFHHRDDLTELRRLLATLGIDVNVVAPLGASPADLKRLPAAWFN-VVLYREIGESAARYLEREFGQPYV 237 (519)
T ss_pred CeEEEEecCccCCCChhHHHHHHHHHHHcCCeEEEEeCCCCCHHHHHhcccCcEE-EEeCHHHHHHHHHHHHHHhCCccc
Confidence 4566665554334445666779999999999998888889999999999877654 3449986543 1 356888877
Q ss_pred C
Q 011028 353 T 353 (495)
Q Consensus 353 T 353 (495)
.
T Consensus 238 ~ 238 (519)
T PRK02910 238 K 238 (519)
T ss_pred c
Confidence 4
No 158
>cd06276 PBP1_FucR_like Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. FcuR acts as an inducer of fucRRIAK and as a corepressor of another locus that regulates production of fucosylated glycans. FcuR and its close homologs in this group are a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes t
Probab=20.83 E-value=1.4e+02 Score=28.70 Aligned_cols=56 Identities=9% Similarity=0.070 Sum_probs=38.2
Q ss_pred EEEEEccccccCcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHH-HH---cCCCCCcEEEEecCC
Q 011028 279 IGVLVGTLGVAGYLHMIHQMKELITKAG-KKAYTLVMGKPNPA-KL---ANFPECDVFINVSCA 337 (495)
Q Consensus 279 ~GIlvgTl~~q~~~~~i~~L~~li~~~G-Kk~y~~~vgkln~a-KL---aNF~eID~fV~vaCP 337 (495)
+.||++.+ -..+..++..|.+.++++| ....+...+. ... .+ .+ ..+|.+|++++.
T Consensus 2 ~~~~~~~~-~~~~~~~~~~i~~~l~~~g~~~l~~~~~~~-~~~~~~~~~~~-~~vdGvIi~~~~ 62 (247)
T cd06276 2 ILLLLNKL-SSFKEIIYNSFVNTLGKNAQVDLYFHHYNE-DLFKNIISNTK-GKYSGYVVMPHF 62 (247)
T ss_pred EEEEEecC-chHHHHHHHHHHHHHHhcCcEEEEEEcCch-HHHHHHHHHHh-cCCCEEEEecCC
Confidence 67888888 4566789999999999999 5544433433 221 11 12 369999998865
No 159
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=20.75 E-value=85 Score=31.28 Aligned_cols=59 Identities=10% Similarity=0.050 Sum_probs=37.5
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHH--cCCcEEEEEcCCCCHHH----HcCC--CCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITK--AGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~--~GKk~y~~~vgkln~aK----LaNF--~eID~fV~vaCP 337 (495)
+||+|+..+.-..+..+++.+.+.+++ .|.+..++ -+.-++++ |.++ ..+|.+|+.++.
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~-~~~~~~~~q~~~i~~l~~~~vdgiii~~~~ 67 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFY-DAKNNQSTQNEQIDTALAKGVDLLAVNLVD 67 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEe-cCCCCHHHHHHHHHHHHHcCCCEEEEecCc
Confidence 478888877666667888889988888 45443322 33334432 2222 268998887654
No 160
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=20.52 E-value=1.4e+02 Score=28.79 Aligned_cols=59 Identities=10% Similarity=-0.024 Sum_probs=36.5
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCcEEEEecCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~eID~fV~vaCP 337 (495)
+||+|+.. .--.+..+++.+.+.+++.|.+..++....-++++. .++ ..+|.+++.++-
T Consensus 1 ~i~~v~~~-~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~ 65 (271)
T cd06314 1 TIAVVTNG-ASPFWKIAEAGVKAAGKELGVDVEFVVPQQGTVNAQLRMLEDLIAEGVDGIAISPID 65 (271)
T ss_pred CeEEEcCC-CcHHHHHHHHHHHHHHHHcCCeEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEecCC
Confidence 47888753 334467888888888888887755443233233322 222 258988887653
No 161
>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=20.10 E-value=1.3e+02 Score=29.88 Aligned_cols=59 Identities=10% Similarity=-0.017 Sum_probs=37.5
Q ss_pred eEEEEEccc-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--C--CCcEEEEecCC
Q 011028 278 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--P--ECDVFINVSCA 337 (495)
Q Consensus 278 ~~GIlvgTl-~~q~~~~~i~~L~~li~~~GKk~y~~~vgkln~aKL----aNF--~--eID~fV~vaCP 337 (495)
.||+|+..+ .-..+..+++.+++.+++.|....+...+ -++.+- .+| . .+|++|+.+..
T Consensus 1 ~Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~~~~-~~~~~~~~~i~~~~~~~~~vdgiIi~~~~ 68 (305)
T cd06324 1 SVVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVLYAE-RDRFLMLQQARTILQRPDKPDALIFTNEK 68 (305)
T ss_pred CeEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEEeCC-CCHHHHHHHHHHHHHhccCCCEEEEcCCc
Confidence 378888776 54556788888888888888776554333 233322 122 2 68888886543
No 162
>PRK12359 flavodoxin FldB; Provisional
Probab=20.08 E-value=2.8e+02 Score=25.87 Aligned_cols=53 Identities=13% Similarity=0.252 Sum_probs=38.6
Q ss_pred eEEEEEccccccCcHHHHHHHHHHHHHcCC-cEEEEEcCCCCHHHHcCCCCCcEEEEecCCC
Q 011028 278 IIGVLVGTLGVAGYLHMIHQMKELITKAGK-KAYTLVMGKPNPAKLANFPECDVFINVSCAQ 338 (495)
Q Consensus 278 ~~GIlvgTl~~q~~~~~i~~L~~li~~~GK-k~y~~~vgkln~aKLaNF~eID~fV~vaCPr 338 (495)
.+||+-+|.+ -+...+++.|++.+ |. .+-++-+.+..+..|.++ | +|+++||=
T Consensus 2 ki~I~Y~S~T-GNTe~vAe~I~~~l---g~~~v~v~~i~~~~~~~l~~y---D-~iIlG~pT 55 (172)
T PRK12359 2 KIGLFYGSST-CYTEMAAEKIRDII---GEELVDLHNLKDDPPKLMEQY---D-VLILGIPT 55 (172)
T ss_pred eEEEEEECCC-CHHHHHHHHHHHHh---CCCeEEEEEcccCChhHHccC---C-EEEEEecc
Confidence 5799999886 46678888888766 43 356677777777776654 4 67788885
Done!