Query 028588
Match_columns 207
No_of_seqs 138 out of 1050
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 13:52:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028588.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028588hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02615 arginase 100.0 1.3E-54 2.8E-59 372.4 23.9 207 1-207 132-338 (338)
2 KOG2964 Arginase family protei 100.0 7.3E-53 1.6E-57 344.4 18.5 204 2-207 141-357 (361)
3 COG0010 SpeB Arginase/agmatina 100.0 5.1E-50 1.1E-54 340.6 23.7 204 2-207 89-303 (305)
4 TIGR01229 rocF_arginase argina 100.0 5.8E-50 1.2E-54 339.9 22.6 201 2-204 70-297 (300)
5 PRK13774 formimidoylglutamase; 100.0 9.8E-50 2.1E-54 339.7 22.9 194 2-202 107-310 (311)
6 PRK01722 formimidoylglutamase; 100.0 1.2E-49 2.5E-54 340.8 23.3 203 2-207 104-318 (320)
7 TIGR01227 hutG formimidoylglut 100.0 1.1E-49 2.4E-54 339.1 22.9 198 2-202 98-306 (307)
8 PF00491 Arginase: Arginase fa 100.0 6.7E-50 1.4E-54 336.1 20.5 200 2-202 67-276 (277)
9 PRK13775 formimidoylglutamase; 100.0 1.5E-49 3.3E-54 340.8 22.9 203 2-207 110-326 (328)
10 TIGR01230 agmatinase agmatinas 100.0 3.1E-49 6.8E-54 331.7 22.7 192 2-203 80-274 (275)
11 PRK13776 formimidoylglutamase; 100.0 2.6E-48 5.6E-53 331.8 22.6 197 2-203 104-316 (318)
12 PRK13773 formimidoylglutamase; 100.0 3.4E-48 7.4E-53 331.9 23.1 200 2-206 106-320 (324)
13 PRK02190 agmatinase; Provision 100.0 4.6E-48 1E-52 328.3 22.0 195 2-206 97-296 (301)
14 PRK13772 formimidoylglutamase; 100.0 6.5E-48 1.4E-52 328.9 22.1 196 2-202 103-314 (314)
15 KOG2965 Arginase [Amino acid t 100.0 5E-43 1.1E-47 282.5 20.1 198 2-202 89-312 (318)
16 PF12640 UPF0489: UPF0489 doma 96.7 0.012 2.5E-07 45.6 8.3 63 25-87 6-92 (162)
17 cd06831 PLPDE_III_ODC_like_AZI 79.3 45 0.00097 29.5 11.8 103 66-177 66-172 (394)
18 cd06843 PLPDE_III_PvsE_like Ty 78.7 44 0.00095 29.1 14.5 108 69-177 59-172 (377)
19 KOG1384 tRNA delta(2)-isopente 72.1 5.6 0.00012 34.5 3.9 31 4-35 85-115 (348)
20 COG0019 LysA Diaminopimelate d 70.8 77 0.0017 28.2 15.2 115 65-185 81-205 (394)
21 KOG0622 Ornithine decarboxylas 55.5 1.6E+02 0.0035 26.6 12.9 130 64-202 107-240 (448)
22 cd06839 PLPDE_III_Btrk_like Ty 55.0 1.4E+02 0.0031 25.8 11.7 107 70-177 65-177 (382)
23 PF03698 UPF0180: Uncharacteri 54.1 67 0.0015 21.9 7.1 71 85-166 4-77 (80)
24 COG0135 TrpF Phosphoribosylant 53.7 34 0.00074 27.7 5.2 52 130-184 139-193 (208)
25 PF02784 Orn_Arg_deC_N: Pyrido 52.2 43 0.00092 27.3 5.7 111 65-180 49-166 (251)
26 KOG4518 Hydroxypyruvate isomer 51.9 32 0.00069 27.9 4.6 45 141-188 206-252 (264)
27 TIGR00287 cas1 CRISPR-associat 51.7 19 0.00042 30.9 3.7 34 19-55 37-70 (323)
28 cd06285 PBP1_LacI_like_7 Ligan 51.7 38 0.00082 27.1 5.3 51 5-55 163-216 (265)
29 PF08645 PNK3P: Polynucleotide 50.1 1.1E+02 0.0024 23.3 7.4 101 3-111 33-158 (159)
30 PRK03094 hypothetical protein; 48.0 87 0.0019 21.3 7.0 71 85-166 4-77 (80)
31 TIGR03099 dCO2ase_PEP1 pyridox 47.5 1.9E+02 0.0042 25.2 11.2 92 80-175 94-191 (398)
32 PF01867 Cas_Cas1: CRISPR asso 46.5 26 0.00056 29.4 3.6 34 19-55 37-70 (282)
33 TIGR03638 cas1_ECOLI CRISPR-as 46.3 28 0.0006 29.2 3.8 32 19-53 47-78 (269)
34 PRK14334 (dimethylallyl)adenos 44.7 1.9E+02 0.004 26.0 9.0 87 75-182 242-329 (440)
35 PF01715 IPPT: IPP transferase 44.4 20 0.00043 29.8 2.6 32 3-35 44-75 (253)
36 cd06270 PBP1_GalS_like Ligand 42.0 82 0.0018 25.2 5.9 18 20-37 180-197 (268)
37 cd06840 PLPDE_III_Bif_AspK_Dap 41.9 2.4E+02 0.0051 24.6 11.5 109 66-180 65-181 (368)
38 TIGR03641 cas1_HMARI CRISPR-as 40.7 35 0.00076 29.4 3.6 34 19-55 36-69 (322)
39 PRK13586 1-(5-phosphoribosyl)- 40.7 2E+02 0.0043 23.5 8.6 120 43-177 46-169 (232)
40 COG3623 SgaU Putative L-xylulo 40.5 23 0.0005 29.4 2.3 26 150-180 13-38 (287)
41 cd01575 PBP1_GntR Ligand-bindi 40.0 85 0.0019 24.9 5.7 12 79-90 204-215 (268)
42 COG3319 Thioesterase domains o 38.9 78 0.0017 26.4 5.3 53 2-54 49-104 (257)
43 TIGR03640 cas1_DVULG CRISPR-as 38.3 41 0.00089 29.1 3.7 32 20-54 42-73 (340)
44 COG0065 LeuC 3-isopropylmalate 38.1 17 0.00038 32.2 1.3 18 20-37 117-135 (423)
45 cd01543 PBP1_XylR Ligand-bindi 37.6 1.1E+02 0.0024 24.4 6.1 50 5-54 159-211 (265)
46 cd06281 PBP1_LacI_like_5 Ligan 35.9 1E+02 0.0022 24.7 5.6 10 79-88 203-212 (269)
47 PLN02748 tRNA dimethylallyltra 35.6 31 0.00068 31.4 2.6 33 3-36 99-131 (468)
48 cd01541 PBP1_AraR Ligand-bindi 34.8 1.1E+02 0.0024 24.5 5.6 11 79-89 210-220 (273)
49 cd02068 radical_SAM_B12_BD B12 34.5 49 0.0011 23.9 3.1 9 5-13 28-36 (127)
50 COG0324 MiaA tRNA delta(2)-iso 34.2 29 0.00062 29.9 2.0 33 3-36 80-112 (308)
51 cd06297 PBP1_LacI_like_12 Liga 33.8 1.3E+02 0.0027 24.3 5.8 12 79-90 207-218 (269)
52 PF09936 Methyltrn_RNA_4: SAM- 33.0 98 0.0021 24.6 4.6 48 2-50 88-140 (185)
53 cd06283 PBP1_RegR_EndR_KdgR_li 32.9 1.2E+02 0.0026 24.0 5.4 11 79-89 205-215 (267)
54 cd06322 PBP1_ABC_sugar_binding 32.6 1.5E+02 0.0033 23.5 6.1 21 69-90 194-214 (267)
55 PF01202 SKI: Shikimate kinase 32.0 75 0.0016 23.9 3.9 45 6-55 53-97 (158)
56 PRK01222 N-(5'-phosphoribosyl) 31.7 87 0.0019 25.1 4.4 32 149-182 157-191 (210)
57 PRK13337 putative lipid kinase 31.5 1.1E+02 0.0023 25.9 5.1 42 5-47 47-89 (304)
58 PF02310 B12-binding: B12 bind 31.4 64 0.0014 22.7 3.2 28 4-31 68-95 (121)
59 PF04951 Peptidase_M55: D-amin 31.4 58 0.0013 27.4 3.3 35 129-165 2-36 (265)
60 PRK11914 diacylglycerol kinase 31.3 89 0.0019 26.3 4.6 42 5-48 54-95 (306)
61 cd01540 PBP1_arabinose_binding 31.3 1.5E+02 0.0032 24.0 5.8 12 80-91 221-232 (289)
62 PLN02840 tRNA dimethylallyltra 31.2 45 0.00098 30.0 2.8 33 3-36 98-130 (421)
63 cd06296 PBP1_CatR_like Ligand- 30.6 1.7E+02 0.0037 23.3 6.0 19 20-38 181-199 (270)
64 PF09837 DUF2064: Uncharacteri 30.5 61 0.0013 23.7 3.0 38 2-40 47-85 (122)
65 cd06278 PBP1_LacI_like_2 Ligan 30.2 1.7E+02 0.0038 23.0 6.0 9 80-88 203-211 (266)
66 cd06828 PLPDE_III_DapDC Type I 30.1 3.6E+02 0.0077 23.2 15.2 107 69-177 61-175 (373)
67 cd06289 PBP1_MalI_like Ligand- 30.0 1.6E+02 0.0034 23.3 5.7 12 79-90 205-216 (268)
68 COG3365 Uncharacterized protei 29.7 97 0.0021 22.4 3.7 33 152-184 39-76 (118)
69 PRK14729 miaA tRNA delta(2)-is 29.6 48 0.001 28.4 2.6 33 3-36 80-112 (300)
70 cd06279 PBP1_LacI_like_3 Ligan 29.3 1.5E+02 0.0033 24.0 5.6 8 80-87 223-230 (283)
71 PRK14340 (dimethylallyl)adenos 29.3 4.3E+02 0.0092 23.8 10.4 149 2-182 181-340 (445)
72 cd06314 PBP1_tmGBP Periplasmic 29.2 2E+02 0.0043 23.0 6.2 16 75-90 200-215 (271)
73 PRK10727 DNA-binding transcrip 29.0 1.5E+02 0.0032 25.0 5.6 12 79-90 264-275 (343)
74 cd06290 PBP1_LacI_like_9 Ligan 29.0 1.6E+02 0.0034 23.4 5.5 12 79-90 203-214 (265)
75 PLN02363 phosphoribosylanthran 28.8 93 0.002 25.9 4.2 31 150-182 203-236 (256)
76 cd06324 PBP1_ABC_sugar_binding 28.5 1.7E+02 0.0038 24.1 5.9 28 79-107 229-256 (305)
77 TIGR00174 miaA tRNA isopenteny 28.4 50 0.0011 28.1 2.5 33 3-36 76-108 (287)
78 cd08663 DAP_dppA_1 Peptidase M 28.4 80 0.0017 26.6 3.7 31 129-164 2-35 (266)
79 PRK10423 transcriptional repre 28.1 1.6E+02 0.0034 24.4 5.6 12 79-90 262-273 (327)
80 PF14529 Exo_endo_phos_2: Endo 28.1 53 0.0011 22.8 2.3 23 3-25 16-38 (119)
81 PRK10703 DNA-binding transcrip 28.1 1.8E+02 0.004 24.3 6.0 11 79-89 266-276 (341)
82 PRK06849 hypothetical protein; 28.0 88 0.0019 27.3 4.1 36 16-54 4-39 (389)
83 cd08770 DAP_dppA_3 Peptidase M 27.9 93 0.002 26.1 4.0 29 129-162 2-33 (263)
84 PRK10401 DNA-binding transcrip 27.4 1.7E+02 0.0037 24.6 5.7 11 79-89 264-274 (346)
85 cd03377 TPP_PFOR_PNO Thiamine 27.3 4.4E+02 0.0095 23.3 8.9 84 18-111 153-239 (365)
86 cd06272 PBP1_hexuronate_repres 27.2 2E+02 0.0043 22.8 5.9 12 79-90 199-210 (261)
87 PLN02537 diaminopimelate decar 27.0 4.4E+02 0.0095 23.2 15.7 106 69-177 76-190 (410)
88 cd06275 PBP1_PurR Ligand-bindi 27.0 1.9E+02 0.004 23.0 5.7 9 79-87 205-213 (269)
89 PF08013 Tagatose_6_P_K: Tagat 26.7 1.4E+02 0.003 26.9 5.0 87 4-92 67-178 (424)
90 PRK14338 (dimethylallyl)adenos 26.6 4.8E+02 0.01 23.5 9.8 150 2-182 187-347 (459)
91 cd01544 PBP1_GalR Ligand-bindi 26.5 2E+02 0.0044 23.0 5.8 11 79-89 206-216 (270)
92 cd06841 PLPDE_III_MccE_like Ty 26.5 4.3E+02 0.0093 22.9 11.7 90 69-167 67-157 (379)
93 PF09949 DUF2183: Uncharacteri 26.3 2.4E+02 0.0051 19.9 5.6 43 7-49 54-97 (100)
94 cd06271 PBP1_AglR_RafR_like Li 26.3 2.2E+02 0.0047 22.5 5.9 13 79-91 208-220 (268)
95 TIGR01663 PNK-3'Pase polynucle 26.2 4.6E+02 0.0099 24.4 8.5 102 3-112 201-332 (526)
96 cd02065 B12-binding_like B12 b 26.1 79 0.0017 22.3 3.0 12 18-29 81-92 (125)
97 cd08769 DAP_dppA_2 Peptidase M 25.8 1E+02 0.0022 26.0 3.8 31 129-164 2-35 (270)
98 PRK11865 pyruvate ferredoxin o 25.5 4.3E+02 0.0093 22.6 10.1 135 17-167 92-230 (299)
99 PRK10653 D-ribose transporter 24.9 2.2E+02 0.0048 23.3 5.8 20 70-90 223-242 (295)
100 TIGR00147 lipid kinase, YegS/R 24.9 1.5E+02 0.0034 24.5 4.9 41 8-49 50-91 (293)
101 PRK11024 colicin uptake protei 24.7 1.5E+02 0.0032 22.0 4.3 36 4-39 90-125 (141)
102 cd06273 PBP1_GntR_like_1 This 24.6 2E+02 0.0044 22.7 5.5 12 79-90 205-216 (268)
103 COG2040 MHT1 Homocysteine/sele 24.3 4.1E+02 0.009 22.8 7.1 75 96-182 141-218 (300)
104 cd06293 PBP1_LacI_like_11 Liga 24.0 2.3E+02 0.005 22.5 5.7 11 79-89 204-214 (269)
105 PRK14325 (dimethylallyl)adenos 23.9 5.2E+02 0.011 23.1 8.4 89 2-100 179-279 (444)
106 cd06280 PBP1_LacI_like_4 Ligan 23.9 2.4E+02 0.0052 22.4 5.8 11 79-89 199-209 (263)
107 PRK13054 lipid kinase; Reviewe 23.8 1.9E+02 0.0042 24.2 5.3 43 5-48 46-91 (300)
108 cd06267 PBP1_LacI_sugar_bindin 23.7 2.7E+02 0.0059 21.6 6.0 10 80-89 205-214 (264)
109 PRK14333 (dimethylallyl)adenos 23.6 3.9E+02 0.0085 24.0 7.5 82 80-182 265-347 (448)
110 PF00781 DAGK_cat: Diacylglyce 23.4 97 0.0021 22.3 3.0 22 17-39 56-77 (130)
111 cd06842 PLPDE_III_Y4yA_like Ty 23.4 5.3E+02 0.011 22.9 13.2 99 69-177 70-175 (423)
112 cd06313 PBP1_ABC_sugar_binding 23.0 2.9E+02 0.0063 22.2 6.1 20 71-91 200-219 (272)
113 TIGR02417 fruct_sucro_rep D-fr 22.9 2.4E+02 0.0052 23.4 5.8 11 79-89 264-274 (327)
114 TIGR03639 cas1_NMENI CRISPR-as 22.8 1.1E+02 0.0023 25.8 3.5 33 19-54 37-70 (278)
115 cd06316 PBP1_ABC_sugar_binding 22.8 2.8E+02 0.0061 22.5 6.1 30 69-99 201-230 (294)
116 cd06303 PBP1_LuxPQ_Quorum_Sens 22.6 2.2E+02 0.0048 23.0 5.4 34 69-103 205-238 (280)
117 PRK06806 fructose-bisphosphate 22.5 2E+02 0.0043 24.3 5.1 44 5-52 63-106 (281)
118 cd00458 SugarP_isomerase Sugar 22.2 3E+02 0.0066 20.9 5.8 49 3-52 7-59 (169)
119 cd06321 PBP1_ABC_sugar_binding 22.2 2.8E+02 0.006 22.1 5.9 18 73-91 200-217 (271)
120 PRK13055 putative lipid kinase 22.1 1.8E+02 0.0039 25.0 4.9 41 6-47 50-91 (334)
121 PRK11303 DNA-binding transcrip 22.1 2.5E+02 0.0054 23.3 5.7 20 70-89 254-275 (328)
122 PRK15408 autoinducer 2-binding 22.1 3E+02 0.0064 23.6 6.2 24 80-104 234-257 (336)
123 cd00281 DAP_dppA Peptidase M55 22.1 1.4E+02 0.003 25.1 4.0 29 129-162 2-33 (265)
124 PRK11267 biopolymer transport 21.9 1.8E+02 0.0038 21.7 4.2 37 3-39 85-121 (141)
125 PRK11864 2-ketoisovalerate fer 21.9 5.1E+02 0.011 22.2 8.1 81 18-107 94-176 (300)
126 PRK09920 acetyl-CoA:acetoacety 21.7 4.4E+02 0.0095 21.4 9.6 45 4-51 8-54 (219)
127 cd06309 PBP1_YtfQ_like Peripla 21.7 2.8E+02 0.0061 22.1 5.8 28 79-107 212-239 (273)
128 TIGR02803 ExbD_1 TonB system t 21.5 2.3E+02 0.005 20.3 4.7 36 4-39 72-107 (122)
129 PLN03028 pyrophosphate--fructo 21.4 4.9E+02 0.011 24.8 7.8 46 4-49 162-208 (610)
130 cd06295 PBP1_CelR Ligand bindi 21.3 3E+02 0.0066 21.9 5.9 9 80-88 214-222 (275)
131 cd01400 6PGL 6PGL: 6-Phosphogl 21.3 2.5E+02 0.0055 22.4 5.3 50 3-53 10-62 (219)
132 COG0703 AroK Shikimate kinase 21.3 2.1E+02 0.0046 22.4 4.6 45 6-55 63-107 (172)
133 PRK10014 DNA-binding transcrip 20.8 2.8E+02 0.0062 23.1 5.8 10 81-90 281-290 (342)
134 PRK14336 (dimethylallyl)adenos 20.7 6E+02 0.013 22.6 9.2 89 2-100 156-254 (418)
135 PRK07534 methionine synthase I 20.6 5.6E+02 0.012 22.2 8.1 59 97-166 139-200 (336)
136 TIGR00264 alpha-NAC-related pr 20.6 81 0.0018 23.1 2.0 24 152-175 3-29 (116)
137 cd06308 PBP1_sensor_kinase_lik 20.5 3.1E+02 0.0068 21.8 5.8 21 70-90 198-218 (270)
138 PF00532 Peripla_BP_1: Peripla 20.5 54 0.0012 27.2 1.3 49 4-52 167-224 (279)
139 TIGR02429 pcaI_scoA_fam 3-oxoa 20.3 2E+02 0.0042 23.5 4.4 48 3-53 8-57 (222)
140 COG1518 CRISPR-associated prot 20.3 1.4E+02 0.003 25.9 3.7 32 19-53 41-72 (327)
141 cd01545 PBP1_SalR Ligand-bindi 20.2 3.1E+02 0.0068 21.6 5.7 11 79-89 206-216 (270)
142 TIGR02634 xylF D-xylose ABC tr 20.1 2.8E+02 0.0062 22.9 5.6 30 69-99 199-228 (302)
143 cd06810 PLPDE_III_ODC_DapDC_li 20.0 5.6E+02 0.012 21.9 13.8 105 70-176 59-169 (368)
No 1
>PLN02615 arginase
Probab=100.00 E-value=1.3e-54 Score=372.40 Aligned_cols=207 Identities=93% Similarity=1.396 Sum_probs=187.3
Q ss_pred ChhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCCCC
Q 028588 1 MNVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGYAR 80 (207)
Q Consensus 1 ~~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~~~ 80 (207)
+++++++++.++++++.+||+||||||+|||.++|+.++++++++|||||||+|+++++.|+.++||||++++++.+..+
T Consensus 132 ~~~i~~~v~~ll~~~~~~Pi~LGGDHsit~~~iral~~~~~~~v~vI~fDAH~Dl~~~~~g~~~shgs~~rr~~e~~~~~ 211 (338)
T PLN02615 132 MNVISESVKLVMEEEPLRPLVLGGDHSISYPVVRAVSEKLGGPVDILHLDAHPDIYHAFEGNKYSHASSFARIMEGGYAR 211 (338)
T ss_pred HHHHHHHHHHHHhcCCCceEEECcchHhhHHHHHHHHHHhCCCeEEEEEecCcCCCCCCCCCCcCchhHHHHHhhCCCcC
Confidence 36789999999986467999999999999999999998876689999999999999988899999999999999987778
Q ss_pred cEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCCCCCCCCCHHHH
Q 028588 81 RLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHIEPGGLSFRDV 160 (207)
Q Consensus 81 ~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~pgGl~~~e~ 160 (207)
+++|+|+|++.++|+++++++|++++++.++.+..++++.++...+.++||||||+|||||+++|||++|+||||+++|+
T Consensus 212 ~~vqiGiR~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vYiS~DiDvlDpa~aPGtgtpepgGLt~~e~ 291 (338)
T PLN02615 212 RLLQVGIRSITKEGREQGKRFGVEQYEMRTFSKDREKLENLKLGEGVKGVYISIDVDCLDPAFAPGVSHIEPGGLSFRDV 291 (338)
T ss_pred cEEEEeecCCCHHHHHHHHHCCCEEEEeeHhhhHHHHHHHHHhccCCCeEEEEEeeCccCHhhCCCCCCCCCCCCCHHHH
Confidence 99999999999999999999999999998886545566666433355679999999999999999999999999999999
Q ss_pred HHHHHhhcCCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHHHHhhC
Q 028588 161 LNILHNLQADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELTAKISK 207 (207)
Q Consensus 161 ~~~l~~i~~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~~~~~~ 207 (207)
+++++.+..+++|+||+|++|.+|..+++|+.+||+++++++..|.|
T Consensus 292 l~il~~l~~~vvG~DvvEv~P~~D~~~~~Ta~laA~li~e~l~~~~~ 338 (338)
T PLN02615 292 LNILHNLQGDVVGADVVEFNPQRDTVDGMTAMVAAKLVRELTAKMSK 338 (338)
T ss_pred HHHHHHhhCCEEEEEEEEECCCCCCCCChHHHHHHHHHHHHHHhhcC
Confidence 99999997799999999999999953579999999999999999987
No 2
>KOG2964 consensus Arginase family protein [Amino acid transport and metabolism]
Probab=100.00 E-value=7.3e-53 Score=344.35 Aligned_cols=204 Identities=47% Similarity=0.727 Sum_probs=184.5
Q ss_pred hhHHHHHHHHHhc------CCcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHh
Q 028588 2 NVITESVKLVMEE------DPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIME 75 (207)
Q Consensus 2 ~~i~~~v~~~~~~------~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~ 75 (207)
+++++.+-+++.+ +...|+++||||+|+||+++|+.++|+ ++++||||||+|++++.+|+.++||+.|+++++
T Consensus 141 ~q~~~~y~~l~~rkg~a~~~~~~PltLGGDHtI~yPilRAvs~k~G-PV~ilH~DaH~Dt~d~~~g~~~~Hgs~F~r~~~ 219 (361)
T KOG2964|consen 141 DQIEEAYISLLARKGVAKDGPVLPLTLGGDHTIVYPILRAVSRKYG-PVSILHFDAHLDTWDPKEGGKINHGSYFYRASQ 219 (361)
T ss_pred HHHHHHHHHHHHhhhhccCCceeeeeecCCceeeHHHHHHHHHhhC-CceEEEeccCccccCccccCccccchHHHHHhh
Confidence 3445554444443 347899999999999999999999995 999999999999999999999999999999999
Q ss_pred cCCCCc--EEEEcccCCChh--HHHHHHHcCceEEEcccccch--HHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCC
Q 028588 76 GGYARR--LLQVGIRSITKE--GREQGKRFGVEQYEMRTFSRD--RQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSH 149 (207)
Q Consensus 76 ~~~~~~--vv~iG~r~~~~~--~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~ 149 (207)
+|..++ .+|+|+|+...+ .|+.-++.|++++.++++.+. ..++++++...+...||+|||+|||||+++|||++
T Consensus 220 eGl~~~~~~iq~GIRt~~s~~~~ye~d~~~Gf~~ieare~~~~gi~~i~e~ir~~~G~k~vYiSiDID~LDPafAPgtgt 299 (361)
T KOG2964|consen 220 EGLASNDRNIQAGIRTILSGLSDYEQDKRCGFEIIEAREIDKIGIDPIVERIRQRVGDKLVYISIDIDVLDPAFAPGTGT 299 (361)
T ss_pred cccccCCceeeeeeeecccCcCchhhccccCeEEEEeeehhhhhhHHHHHHHHHhcCCceEEEEEeecccCcccCCCCCC
Confidence 998876 999999997544 677778899999999999886 67888898778899999999999999999999999
Q ss_pred CCCCCCCHHHHHHHHHhhcC-CeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHHHHhhC
Q 028588 150 IEPGGLSFRDVLNILHNLQA-DVVAADVVEFNPQRDTVDGMTAMVAAKLVRELTAKISK 207 (207)
Q Consensus 150 p~pgGl~~~e~~~~l~~i~~-~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~~~~~~ 207 (207)
||+||+|++|++.+|+.+-+ +++|+|++|++|.|| .++.|+++||++++|+++.|+|
T Consensus 300 pE~gGlt~re~l~ILrglqGl~lVGaDvVEvsP~yD-~ae~Tal~AA~llfEi~s~m~K 357 (361)
T KOG2964|consen 300 PETGGLTTREMLNILRGLQGLNLVGADVVEVSPPYD-VAEMTALAAADLLFEILSKMVK 357 (361)
T ss_pred CCCCCcCHHHHHHHHhhCccccccccceEEecCccc-hhhhHHHHHHHHHHHHHHhccc
Confidence 99999999999999999976 999999999999999 5899999999999999999987
No 3
>COG0010 SpeB Arginase/agmatinase/formimionoglutamate hydrolase, arginase family [Amino acid transport and metabolism]
Probab=100.00 E-value=5.1e-50 Score=340.63 Aligned_cols=204 Identities=39% Similarity=0.661 Sum_probs=177.4
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCC---
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGY--- 78 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~--- 78 (207)
+++++.+.+++.+ +.+||++|||||+|+|+++|+.++++.+++|||||||+|++++++|++++||||++++++++.
T Consensus 89 ~~~~~~~~~~~~~-~~~pi~lGGDHsit~~~~~a~~~~~~~~~gvI~iDAH~Dl~~~~~g~~~~Hg~p~r~~~e~~~~~~ 167 (305)
T COG0010 89 DAIEEAVAELLSA-GAFPIVLGGDHSITLGTVRALARKYGGPLGVIWIDAHADLRTPYSGSGNSHGTPLRRALEEGLIDG 167 (305)
T ss_pred HHHHHHHHHHHhc-CCeeEEECCcchhhHHHHHHHHHhhCCceEEEEEecCccCCCCCCCCCCcccCHHHHHHhccccCC
Confidence 4678888889986 589999999999999999999988755799999999999999888899999999999998763
Q ss_pred -CCcEEEEcccCCChhH-HHHHHHcCceEEEcccccch---HHHHHHhhc-cCCcceEEEEEeccCCCCCCCCCCCCCCC
Q 028588 79 -ARRLLQVGIRSITKEG-REQGKRFGVEQYEMRTFSRD---RQFLENLKL-GEGVKGVYISVDVDCLDPAFAPGVSHIEP 152 (207)
Q Consensus 79 -~~~vv~iG~r~~~~~~-~~~~~~~~~~~~~~~~~~~~---~~~l~~~~~-~~~~~~vylsiDiDvldp~~~pg~~~p~p 152 (207)
+++++++|+|+.+++| .+.+++.|++++++.++... ....+.++. ....+++|||||+|||||+++|||++|+|
T Consensus 168 ~p~~~v~iGiR~~~~~e~~~~~~~~gi~~~~~~~v~~~~~~~~~~~~i~~~~~~~~~vylSiDiD~lDPa~aPgvgtp~~ 247 (305)
T COG0010 168 GPENVVQIGIRSVDPEERAAVARERGIRVLTARDVDELGLVDVIEEAIDELKGDGDPVYLSIDLDVLDPAFAPGVGTPEP 247 (305)
T ss_pred CcceEEEEEeccCChHHHHHHHHhcCCEEEEHHHHHHhcCHHHHHHHHHHhhCCCCeEEEEEecCCcCcccCCCCCCCCC
Confidence 3689999999999888 56888999999999988662 223333331 12456799999999999999999999999
Q ss_pred CCCCHHHHHHHHHhhc--CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHHHHhhC
Q 028588 153 GGLSFRDVLNILHNLQ--ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELTAKISK 207 (207)
Q Consensus 153 gGl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~~~~~~ 207 (207)
||++++|++.+++.+. .+++|+||+|+||.+|. +++|+.+|++++++++..+.+
T Consensus 248 gGlt~~e~~~~~~~l~~~~~vvg~DvvEv~P~~D~-~~~Ta~~aa~l~~~ll~~~~~ 303 (305)
T COG0010 248 GGLTFRELLDLLERLLKSGKVVGFDVVEVNPALDI-SGRTARLAARLIAELLGKRAL 303 (305)
T ss_pred CCCCHHHHHHHHHHHhccCCEEEEEEEEECCCCCC-CccHHHHHHHHHHHHHHHhhc
Confidence 9999999999998884 49999999999999995 689999999999999988653
No 4
>TIGR01229 rocF_arginase arginase. This model helps resolve arginases from known and putative agmatinases, formiminoglutamases, and other related proteins of unknown specifity. The pathway from arginine to the polyamine putrescine may procede by hydrolysis to remove urea (arginase) followed by decarboxylation (ornithine decarboxylase), or by decarboxylation first (arginine decarboxylase) followed by removal of urea (agmatinase).
Probab=100.00 E-value=5.8e-50 Score=339.86 Aligned_cols=201 Identities=32% Similarity=0.424 Sum_probs=174.2
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCC-CeEEEEEccCCCCCCCCC-CCccCCccHHHHHHhcC--
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGG-PVDVLHLDAHPDIYDAFE-GNKYSHASSFARIMEGG-- 77 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~-~~~vI~~DAH~D~~~~~~-g~~~~~g~~~~~~~~~~-- 77 (207)
+++++.|+.++++ +.+||+||||||+++|.++|+.+.+++ +++|||||||+|+++++. +++++||||++++++.+
T Consensus 70 ~~i~~~v~~~~~~-g~~pi~lGGdHsi~~~~~~a~~~~~~~~~~gvI~~DAH~D~~~~~~~~s~~~hG~p~~~~~~~~~~ 148 (300)
T TIGR01229 70 EQLAPKVYEVFEE-GRFPLVLGGDHSIAIGTISGTARVHPDKKLGVLWLDAHADINTPETTTSGNLHGMPVAFLLGRLKS 148 (300)
T ss_pred HHHHHHHHHHHhC-CCeeEEEcCcchhhhhhHHHHHHhcCCCceEEEEEecCcccCCCCCCCCCCcccCHHHHHhcccCc
Confidence 5678999999996 789999999999999999999998742 599999999999999875 57789999999998621
Q ss_pred ---------------CCCcEEEEcccCCChhHHHHHHHcCceEEEcccccch--HHHHHHhh-c-cCCcceEEEEEeccC
Q 028588 78 ---------------YARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRD--RQFLENLK-L-GEGVKGVYISVDVDC 138 (207)
Q Consensus 78 ---------------~~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~-~-~~~~~~vylsiDiDv 138 (207)
.++++++||+|+++++|+++++++|++++++.++++. +++++.+. . ...+.++|||||+||
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~v~iGiR~~~~~e~~~~~~~gi~~~~~~~i~~~g~~~v~~~~~~~l~~~~~~vyvS~DiDv 228 (300)
T TIGR01229 149 EFPDSPGLGWVAPEISPKNLVYIGLRSVDPGERKILKELGIKVFSMHEIDELGIGKVVEETLEYLKAEDGPIHLSLDVDG 228 (300)
T ss_pred cccccccccccCCccCcccEEEEecCCCChHHHHHHHHcCCeEEEHHHHhhhhHHHHHHHHHHHHhcCCCeEEEEEeccc
Confidence 2469999999999999999999999999999998653 33444332 1 122338999999999
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHhhc--CCeeEEEEeeecCCCC--CCCCHHHHHHHHHHHHHHHH
Q 028588 139 LDPAFAPGVSHIEPGGLSFRDVLNILHNLQ--ADVVAADVVEFNPQRD--TVDGMTAMVAAKLVRELTAK 204 (207)
Q Consensus 139 ldp~~~pg~~~p~pgGl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d--~~~~~t~~~aa~li~~~~~~ 204 (207)
|||+++|||++|+||||+++|++.+++.+. .+++|+||+|+||.+| . +++|+.+|++++++++..
T Consensus 229 lDps~aPgv~tp~pgGl~~~e~~~~l~~i~~~~~v~g~DivE~~P~~D~~~-~~~Ta~laa~li~~~lg~ 297 (300)
T TIGR01229 229 LDPSLAPATGTPVVGGLTFREGLLIMEMLYETGLLTALDVVEVNPTLDIKH-VNRTIKTAVEIVRSLLGS 297 (300)
T ss_pred cCcccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCEEEEEEEEECccccccc-ccHHHHHHHHHHHHHhcc
Confidence 999999999999999999999999999984 5899999999999999 6 689999999999999864
No 5
>PRK13774 formimidoylglutamase; Provisional
Probab=100.00 E-value=9.8e-50 Score=339.69 Aligned_cols=194 Identities=23% Similarity=0.325 Sum_probs=170.7
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcC-CCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCCCC
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLG-GPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGYAR 80 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~-~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~~~ 80 (207)
++++++|..++++ +.+||+||||||+|||+++|+.+.++ ++++|||||||+|+++++. .+||++++++++.+...
T Consensus 107 ~~i~~~v~~i~~~-g~~pivlGGdHsit~g~~~a~~~~~~~~~igvI~~DAH~Dlr~~~~---~~~g~~~~~i~e~~~~~ 182 (311)
T PRK13774 107 KEFAMLAAKSIAN-HRQTFLLGGGHDIAYAQYLATRKVYPTQSIGVINIDAHFDTRAEQQ---STSGTSFRQILEEDENT 182 (311)
T ss_pred HHHHHHHHHHHHC-CCeEEEEcCchHHHHHHHHHHHhhcCCCceEEEEeCCCCCCCCCCC---CCCChHHHHHHhcCCCC
Confidence 6789999999996 79999999999999999999998864 3699999999999999864 37999999999876668
Q ss_pred cEEEEcccCC--ChhHHHHHHHcCceEEEcccccch-----HHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCCCCCC
Q 028588 81 RLLQVGIRSI--TKEGREQGKRFGVEQYEMRTFSRD-----RQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHIEPG 153 (207)
Q Consensus 81 ~vv~iG~r~~--~~~~~~~~~~~~~~~~~~~~~~~~-----~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~pg 153 (207)
+++++|+|++ .++++++++++|++++++.++++. .+.++.+. .+.+++|||||+|+|||+++|||++|+||
T Consensus 183 ~~~~iGir~~~~~~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~l~~~~--~~~~~vyvS~DiD~lDps~aPGtgtP~pg 260 (311)
T PRK13774 183 DYLVLGIAQGGNTQSLFDYAKEKKIDYVFADELLSHVSPTIKDMIERFI--HEHDVIMFTICMDVIDSAFAPGVSAPAVL 260 (311)
T ss_pred CEEEEeeCCCCCCHHHHHHHHHcCCEEEEHHHhhhhhHHHHHHHHHHHH--hcCCeEEEEEeeCCcChhhCCCCCCCCCC
Confidence 9999999997 467899999999999999998652 23333332 23568999999999999999999999999
Q ss_pred CCCHHHHHHHHHhhc--CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHH
Q 028588 154 GLSFRDVLNILHNLQ--ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELT 202 (207)
Q Consensus 154 Gl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~ 202 (207)
||+++|++++++.+. .+++|+||+|+||.+|. +++|+.+||+++++++
T Consensus 261 GLt~~e~l~il~~l~~~~~v~g~DivE~nP~~D~-~~~Ta~laa~li~~~l 310 (311)
T PRK13774 261 GLYPHTVLELAKRIIPSDKVSSVSIAEMNPTYDA-DNRTAKLVANLVHHFL 310 (311)
T ss_pred CCCHHHHHHHHHHHHhcCCEEEEEEEEECCCCCC-CChHHHHHHHHHHHHh
Confidence 999999999999983 59999999999999996 6899999999999987
No 6
>PRK01722 formimidoylglutamase; Provisional
Probab=100.00 E-value=1.2e-49 Score=340.81 Aligned_cols=203 Identities=28% Similarity=0.474 Sum_probs=175.8
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhc-CCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcC---
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL-GGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGG--- 77 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~-~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~--- 77 (207)
+++++.|++++++ +.+||+||||||+|+|.++|+.+.+ .++++|||||||+|+++++.+ +++||||++++++.+
T Consensus 104 ~~i~~~v~~~~~~-g~~pi~lGGdHsit~~~~~al~~~~~~~~i~vI~~DAH~Dl~~~~~~-~~~hg~~~~~l~~~~~~~ 181 (320)
T PRK01722 104 QALADTVGHCLRP-NMRTIVLGGGHEIAFGSFAGVADAFPKGKVGIINFDAHHDLRNLEDG-GPSSGTPFRQLLEYCDAQ 181 (320)
T ss_pred HHHHHHHHHHHhC-CCeeEEEcCchHHHHHHHHHHHhhccCCcEEEEEEecCccCCCCCCC-CCCCChHHHHHhhhhhcc
Confidence 5789999999996 7999999999999999999998732 368999999999999998766 789999999999842
Q ss_pred -CCCcEEEEcccCC--ChhHHHHHHHcCceEEEcccccch--HHHHHHhh-ccCCcceEEEEEeccCCCCCCCCCCCCCC
Q 028588 78 -YARRLLQVGIRSI--TKEGREQGKRFGVEQYEMRTFSRD--RQFLENLK-LGEGVKGVYISVDVDCLDPAFAPGVSHIE 151 (207)
Q Consensus 78 -~~~~vv~iG~r~~--~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~-~~~~~~~vylsiDiDvldp~~~pg~~~p~ 151 (207)
.+++++++|+|++ ++++++++++.|+.++++.++... ...++.+. .....++||||||+|||||+++|||++|+
T Consensus 182 ~~~~~~~~iGiR~~~~~~~~~~~~~~~g~~~~~~~~i~~~g~~~~~~~~~~~i~~~~~vyvS~DiDvlDps~aPgtgtp~ 261 (320)
T PRK01722 182 IRGFHYACIGVSRASNTQALWEEAKELGVTVVTDLDVRERGLKDILTELQEFIDQVDYIYLTIDLDVLPAAEAPGVSAPA 261 (320)
T ss_pred CCCCCEEEEEecCCCCCHHHHHHHHHCCCEEEEHHHhhhcCHHHHHHHHHHHHhcCCeEEEEEEecCcChhhCCCCCCCc
Confidence 3579999999997 467889999999999999988642 33444432 11235789999999999999999999999
Q ss_pred CCCCCHHHHHHHHHhhc--CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHHHHhhC
Q 028588 152 PGGLSFRDVLNILHNLQ--ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELTAKISK 207 (207)
Q Consensus 152 pgGl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~~~~~~ 207 (207)
||||+++|++++++.+. .+++|+||+|++|.+|. +++|+.+||+++++++.++++
T Consensus 262 pgGls~~e~~~il~~l~~~~~vvg~DivE~~P~~D~-~~~Ta~laa~li~~~l~~~~~ 318 (320)
T PRK01722 262 AGGVPLETLLRAIEPICRSGKLQAADLVEYNPTFDF-DDMTARVAARLIWQIAHAWRT 318 (320)
T ss_pred CCCCCHHHHHHHHHHHHhcCCEEEEEEEEECCCCCC-CCcHHHHHHHHHHHHHHHhhc
Confidence 99999999999999983 59999999999999996 689999999999999988764
No 7
>TIGR01227 hutG formimidoylglutamase. Formiminoglutamase, the fourth enzyme of histidine degradation, is similar to arginases and agmatinases. It is often encoded near other enzymes of the histidine degredation pathway: histidine ammonia-lyase, urocanate hydratase, and imidazolonepropionase.
Probab=100.00 E-value=1.1e-49 Score=339.13 Aligned_cols=198 Identities=28% Similarity=0.467 Sum_probs=172.0
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCC-C-eEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCC-
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGG-P-VDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGY- 78 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~-~-~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~- 78 (207)
++++++|++++++ +.+||+||||||+|||+++|+.+++++ + ++|||||||+|+++++. +.++||||++++++.+.
T Consensus 98 ~~i~~~v~~~~~~-g~~Pi~lGGdHsit~~~~~al~~~~~~~~~vgvi~~DAH~D~~~~~~-~~~~~g~~~~~~~~~~~~ 175 (307)
T TIGR01227 98 HEIAQTAAALLAD-HRVPVILGGGHSIAYATFAALAQHYKGTTAIGVINFDAHFDLRATED-GGPTSGTPFRQILDECQI 175 (307)
T ss_pred HHHHHHHHHHHhc-CCeEEEECCcchhHHHHHHHHHHhcCCCCeEEEEEEccCcCCCCCCC-CCCCCchHHHHHhhccCC
Confidence 5789999999996 699999999999999999999998743 4 99999999999999864 46789999999998764
Q ss_pred -CCcEEEEcccCC--ChhHHHHHHHcCceEEEcccccch--HHHHHHhh-ccCCcceEEEEEeccCCCCCCCCCCCCCCC
Q 028588 79 -ARRLLQVGIRSI--TKEGREQGKRFGVEQYEMRTFSRD--RQFLENLK-LGEGVKGVYISVDVDCLDPAFAPGVSHIEP 152 (207)
Q Consensus 79 -~~~vv~iG~r~~--~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~-~~~~~~~vylsiDiDvldp~~~pg~~~p~p 152 (207)
.++++++|+|++ .++++++++++|++++++.+++.. ..+.+.+. ...+.+++|||||+|||||+++|||++|+|
T Consensus 176 ~~~~~~~iGiR~~~~~~~~~~~~~~~g~~~~~~~~i~~~~~~~i~~~~~~~~~~~~~vyvs~DiDvlDps~aPgtg~p~p 255 (307)
T TIGR01227 176 EDFHYAVLGIRRFSNTQALFDYAKKLGVRYVTDDALRPGLLPTIKDILPVFLDKVDHIYLTVDMDVLDAAHAPGVSAPAP 255 (307)
T ss_pred CCCcEEEEEecCCCCCHHHHHHHHHCCCEEEEHHHhhhcCHHHHHHHHHHHHhCCCeEEEEEEecccChhhCCCCCCCCC
Confidence 468999999998 457899999999999999988652 22333332 123457899999999999999999999999
Q ss_pred CCCCHHHHHHHHHhhc--CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHH
Q 028588 153 GGLSFRDVLNILHNLQ--ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELT 202 (207)
Q Consensus 153 gGl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~ 202 (207)
|||+++|++++++.+. .+++|+||+|++|.+|. +++|+++||+++++++
T Consensus 256 gGLt~~e~~~il~~l~~~~~vvg~DvvE~~P~~D~-~~~Ta~laa~li~~~l 306 (307)
T TIGR01227 256 GGLYPDELLELVKRIAASDKVRGAEIAEVNPTLDF-DQRTARAAARLVLHFL 306 (307)
T ss_pred CCCCHHHHHHHHHHHhcCCCEEEEEEEEECCCCCC-CCcHHHHHHHHHHHHh
Confidence 9999999999999983 48999999999999996 6899999999999986
No 8
>PF00491 Arginase: Arginase family; InterPro: IPR006035 The ureohydrolase superfamily includes arginase (3.5.3.1 from EC), agmatinase (3.5.3.11 from EC), formiminoglutamase (3.5.3.8 from EC) and proclavaminate amidinohydrolase (3.5.3.22 from EC) []. These enzymes share a 3-layer alpha-beta-alpha structure [, , ], and play important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways. Arginase, which catalyses the conversion of arginine to urea and ornithine, is one of the five members of the urea cycle enzymes that convert ammonia to urea as the principal product of nitrogen excretion []. There are several arginase isozymes that differ in catalytic, molecular and immunological properties. Deficiency in the liver isozyme leads to argininemia, which is usually associated with hyperammonemia. Agmatinase hydrolyses agmatine to putrescine, the precursor for the biosynthesis of higher polyamines, spermidine and spermine. In addition, agmatine may play an important regulatory role in mammals. Formiminoglutamase catalyses the fourth step in histidine degradation, acting to hydrolyse N-formimidoyl-L-glutamate to L-glutamate and formamide. Proclavaminate amidinohydrolase is involved in clavulanic acid biosynthesis. Clavulanic acid acts as an inhibitor of a wide range of beta-lactamase enzymes that are used by various microorganisms to resist beta-lactam antibiotics. As a result, this enzyme improves the effectiveness of beta-lactamase antibiotics [].; GO: 0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines, 0046872 metal ion binding; PDB: 4DZ4_A 3SL0_A 3MMR_A 3SL1_A 2EF5_D 2EIV_K 2EF4_A 3NIO_F 3THH_A 1WVA_A ....
Probab=100.00 E-value=6.7e-50 Score=336.08 Aligned_cols=200 Identities=42% Similarity=0.696 Sum_probs=168.6
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCCCCCC-CCCccCCccHHHHHHhcCC--
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDIYDAF-EGNKYSHASSFARIMEGGY-- 78 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~~~~~-~g~~~~~g~~~~~~~~~~~-- 78 (207)
+++++++++++++ +.+||+||||||+|||.++|+++.+++++++||||||+|++++. +++.++||||++++++.+.
T Consensus 67 ~~l~~~v~~~~~~-g~~pi~lGGdhsis~~~~~~l~~~~~~~i~vI~~DAH~D~~~~~~~~~~~~~g~~~~~~~~~~~~~ 145 (277)
T PF00491_consen 67 ERLAEAVAEVLEA-GAFPIVLGGDHSISYGTIAALARAYGGPIGVIWFDAHPDLRTPETSGSGNSHGMPLRRALEEPLLD 145 (277)
T ss_dssp HHHHHHHHHHHHT-TEEEEEEESSGGGHHHHHHHHHHHHTTTEEEEEESSS----STTTTTSSSGTTSHHHHHHHTTSSE
T ss_pred HHHHHHHHHhhcC-CCEEEecCCCchhHHHhHHHHHhhcCCCeeEEEecCccCCCcccccCCCCCCCChhhhhcccCCcC
Confidence 5789999999996 79999999999999999999999887799999999999999988 6788999999999997654
Q ss_pred CCcEEEEcccCCChh-HHHHHHHcCceEEEcccccch--HHHHHHhh--ccCCcceEEEEEeccCCCCCCCCCCCCCCCC
Q 028588 79 ARRLLQVGIRSITKE-GREQGKRFGVEQYEMRTFSRD--RQFLENLK--LGEGVKGVYISVDVDCLDPAFAPGVSHIEPG 153 (207)
Q Consensus 79 ~~~vv~iG~r~~~~~-~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~--~~~~~~~vylsiDiDvldp~~~pg~~~p~pg 153 (207)
+++++++|+|++.++ |++++++.|++++++.+++.. .++++++. ...+++++|||||+|||||+++||+++|+||
T Consensus 146 ~~~~v~iG~r~~~~~~e~~~~~~~~i~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~vylsiDiDvlDp~~~pg~~~p~pg 225 (277)
T PF00491_consen 146 PENVVQIGIRSFDNESEYEYLKELGIKIFSADEIREDGIDAVLEEILEALGSGTDPVYLSIDIDVLDPAFAPGVGTPEPG 225 (277)
T ss_dssp GGGEEEEEE-STTHHHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTTSTSEEEEEEEGGGBBTTTSTSBSS-BSS
T ss_pred cCcEEEEecccccchHHHHHHHHcCCEEEehhHhhhhhhhhHHHHHHHHHhcCCCeEEEEEehhhcChhhCCCcCCCcCC
Confidence 489999999999988 999999999999999998764 23444442 1235689999999999999999999999999
Q ss_pred CCCHHHHHHHHHhhc--CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHH
Q 028588 154 GLSFRDVLNILHNLQ--ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELT 202 (207)
Q Consensus 154 Gl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~ 202 (207)
||+++|++++++.+. .+++|+||+|++|.+|..+++|+++++++++++|
T Consensus 226 Gl~~~e~~~~l~~l~~~~~vvg~di~E~~P~~D~~~~~ta~~aa~li~~~~ 276 (277)
T PF00491_consen 226 GLSPRELLQLLRALARSGKVVGLDIVEYNPDLDPDGEQTARLAARLIWEFI 276 (277)
T ss_dssp -B-HHHHHHHHHHHHHHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHcccCCeEEEEEEEECCCcCcchHHHHHHHHHHHHHHh
Confidence 999999999999994 6999999999999999633599999999999974
No 9
>PRK13775 formimidoylglutamase; Provisional
Probab=100.00 E-value=1.5e-49 Score=340.79 Aligned_cols=203 Identities=24% Similarity=0.409 Sum_probs=172.6
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhc--CCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCC-
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL--GGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGY- 78 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~--~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~- 78 (207)
++++++|+.++++ +.+||+||||||+|||+++|+.+++ +++++|||||||+|+++ +.++.++||++++++++++.
T Consensus 110 ~~l~~~v~~~~~~-g~~PivlGGdHsit~g~~~g~~~~~~~~~~~gvI~~DAH~Dlr~-~~~~~~shg~~~~~~~~~~~~ 187 (328)
T PRK13775 110 NSLSKAIKRMCDL-NLKPIVLGGGHETAYGHYLGLRQSLSPSDDLAVINMDAHFDLRP-YDQTGPNSGTGFRQMFDDAVA 187 (328)
T ss_pred HHHHHHHHHHHhC-CCeEEEEcCcHHHHHHHHHHHHHhcccCCCeEEEEeccCcCCCC-CCCCCCCCCcHHHHHHHhhcc
Confidence 5789999999996 7999999999999999999999875 25899999999999996 45667899999999887542
Q ss_pred ---CCcEEEEcccCCCh--hHHHHH-HHcCceEEEcccccch--HHHHHHhh-ccCCcceEEEEEeccCCCCCCCCCCCC
Q 028588 79 ---ARRLLQVGIRSITK--EGREQG-KRFGVEQYEMRTFSRD--RQFLENLK-LGEGVKGVYISVDVDCLDPAFAPGVSH 149 (207)
Q Consensus 79 ---~~~vv~iG~r~~~~--~~~~~~-~~~~~~~~~~~~~~~~--~~~l~~~~-~~~~~~~vylsiDiDvldp~~~pg~~~ 149 (207)
..+++++|+|+... ++++++ ++.|+.++++.++++. ..+++.+. ...+.+++|||||+|+|||+++|||++
T Consensus 188 ~~~~~~~~~iGiR~~~~~~~~~~~~~~~~gi~~~~~~~i~~~g~~~v~~~~~~~~~~~~~vyvS~DiD~lDps~aPGtgt 267 (328)
T PRK13775 188 DKRLFKYFVLGIQEHNNNLFLFDFVAKSKGIQFLTGQDIYQMGHQKVCRAIDRFLEGQERVYLTIDMDCFSVGAAPGVSA 267 (328)
T ss_pred cCCCceEEEEEEeCCCCCHHHHHHHHHHcCCEEEEHHHhhhcCHHHHHHHHHHHHhcCCeEEEEEEcCccCcccCCCCCC
Confidence 34799999999754 577764 4589999999998552 33444442 112456899999999999999999999
Q ss_pred CCCCCCCHHHHHHHHHhhc--CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHHHHhhC
Q 028588 150 IEPGGLSFRDVLNILHNLQ--ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELTAKISK 207 (207)
Q Consensus 150 p~pgGl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~~~~~~ 207 (207)
|+||||+++|++.+++.+. .+++|+||+|++|.+|. +++|+.+||+++++++..|+|
T Consensus 268 P~pgGLt~~e~~~il~~l~~~~~vvg~DivEv~P~~D~-~~~Ta~laa~li~~~l~~~~~ 326 (328)
T PRK13775 268 IQSLGVDPNLAVLVLQHIAASGKLVGFDVVEVSPPHDI-DNHTANLAATFIFYLVQIMAQ 326 (328)
T ss_pred CCCCCCCHHHHHHHHHHHHhCCCEEEEEEEEECCCCCC-CCcHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999983 48999999999999996 689999999999999998864
No 10
>TIGR01230 agmatinase agmatinase. Note: a history of early misannotation of members of this family is detailed in PUBMED:10931887.
Probab=100.00 E-value=3.1e-49 Score=331.68 Aligned_cols=192 Identities=38% Similarity=0.649 Sum_probs=170.2
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCCCCc
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGYARR 81 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~~~~ 81 (207)
+++++++++++++ +.+||+||||||+|+|+++|+.+++ ++++|||||||+|+++++.|..++||||++++++.+ .+
T Consensus 80 ~~i~~~v~~~~~~-~~~pi~lGGdHsis~~~i~al~~~~-~~~~vI~~DAH~D~~~~~~g~~~~~~~~~~~~~~~~--~~ 155 (275)
T TIGR01230 80 EKIQEHAEEFLEE-GKFPVAIGGEHSITLPVIRAMAKKF-GKFAVVHFDAHTDLRDEFDGGTLNHACPMRRVIELG--LN 155 (275)
T ss_pred HHHHHHHHHHHhc-CCeEEEecCcchhhHHHHHHHHHhc-CCeEEEEEecccccccccCCCccccHhHHHHHhhCC--CC
Confidence 5788999999986 6899999999999999999999876 589999999999999988888889999999999864 59
Q ss_pred EEEEcccCCChhHHHHHHHcCceEEEcccccch-HHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCCCCCCCCCHHHH
Q 028588 82 LLQVGIRSITKEGREQGKRFGVEQYEMRTFSRD-RQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHIEPGGLSFRDV 160 (207)
Q Consensus 82 vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~pgGl~~~e~ 160 (207)
++++|+|+++++|+++++++|+.+++ .++... .++++.+ +..+||||||+|||||+++|||++|+||||+++|+
T Consensus 156 iv~iGiR~~~~~e~~~~~~~~~~~~~-~~i~~~~~~~l~~~----~~~~vyis~DiDvlDps~aPg~~~p~pgGl~~~e~ 230 (275)
T TIGR01230 156 VVQFGIRSGFKEENDFARENNIQVLK-REVDDVIAEVKQKV----GDKPVYVTIDIDVLDPAFAPGTGTPEPGGLTSDEL 230 (275)
T ss_pred EEEEEeCCCChHHHHHHHHcCCEEEe-hHHHHHHHHHHHHh----CCCceEEEEeccccCcccCCCCCCCCCCCCCHHHH
Confidence 99999999999999999999999999 766442 2333332 34679999999999999999999999999999999
Q ss_pred HHHHHhh-c-CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHHH
Q 028588 161 LNILHNL-Q-ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELTA 203 (207)
Q Consensus 161 ~~~l~~i-~-~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~~ 203 (207)
+++++.+ . .+++|+||||++|.+|. +++|+.+||+++++++.
T Consensus 231 ~~~~~~~~~~~~v~g~DivE~~P~~D~-~~~t~~~aa~li~~~l~ 274 (275)
T TIGR01230 231 INFFVRALKDDNVVGFDVVEVAPVYDQ-SEVTALTAAKIALEMLL 274 (275)
T ss_pred HHHHHHHhcCCCEEEEEEEEeCCCCCC-cchHHHHHHHHHHHHhc
Confidence 9988876 3 49999999999999996 68999999999999874
No 11
>PRK13776 formimidoylglutamase; Provisional
Probab=100.00 E-value=2.6e-48 Score=331.76 Aligned_cols=197 Identities=27% Similarity=0.406 Sum_probs=171.4
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhc-----CCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhc
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL-----GGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEG 76 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~-----~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~ 76 (207)
+++++.++.++++ +.+||+||||||+|+|+++|+.+++ +++++|||||||+|++++ ..++||+++++++++
T Consensus 104 ~~i~~~v~~i~~~-g~~Pi~lGGdHsit~g~~~a~~~~~~~~~~~~~vgvI~~DAH~D~~~~---~~~~~g~~~r~~~e~ 179 (318)
T PRK13776 104 SRYAQRVHDLLDR-GHLPIGLGGGHEIAWASFQGLARHLARSAPLPRIGIINFDAHFDLRKG---ERGSSGTPFRQIAEY 179 (318)
T ss_pred HHHHHHHHHHHhC-CCeEEEEcCchHHHHHhHHHHHHHhhcccCCCceEEEEeCCcccCCCC---CCCCCCCHHHHHHHH
Confidence 5788999999996 7999999999999999999999876 148999999999999954 346899999999974
Q ss_pred ----CCCCcEEEEcccCC--ChhHHHHHHHcCceEEEcccccch--HHHHHHhh-ccCCcceEEEEEeccCCCCCCCCCC
Q 028588 77 ----GYARRLLQVGIRSI--TKEGREQGKRFGVEQYEMRTFSRD--RQFLENLK-LGEGVKGVYISVDVDCLDPAFAPGV 147 (207)
Q Consensus 77 ----~~~~~vv~iG~r~~--~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~-~~~~~~~vylsiDiDvldp~~~pg~ 147 (207)
+.+.+++++|+|++ .+++++++++.|+.++++.++++. ..+++.+. ...+.+++|||||+|||||+++|||
T Consensus 180 ~~~~g~~~~~~~iGir~~~~~~~~~~~~~~~g~~~~~~~ei~~~g~~~v~~~~~~~~~~~~~vyvS~DiD~lDps~aPGt 259 (318)
T PRK13776 180 CAAKGWPFHYCCLGVSRFSNTAALFERAKQLGVRYLSDEDMYEWSLARILAFLDDFIANVDHIYLTICLDVLPAAVAPGV 259 (318)
T ss_pred HhhcCCcceEEEEccCCCCCCHHHHHHHHHcCCEEEEHHHhhhcCHHHHHHHHHHHHhcCCeEEEEEEeCCcCcccCCCC
Confidence 44678999999998 467889999999999999998653 34555443 1124578999999999999999999
Q ss_pred CCCCCCCCCHHHHHHHHHhhc--CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHHH
Q 028588 148 SHIEPGGLSFRDVLNILHNLQ--ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELTA 203 (207)
Q Consensus 148 ~~p~pgGl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~~ 203 (207)
++|+||||+++|++++++.+. .+++|+||+|++|.+|. +++|+.+||+++++++.
T Consensus 260 gtP~pgGLt~~e~~~il~~l~~~~~vvg~DvvEv~P~~D~-~~~Ta~laa~li~~~l~ 316 (318)
T PRK13776 260 SAPAARGVSLWVIEPLVKRIIASGKLRLADIAELNPPLDI-DQRTARVAARLVAELVD 316 (318)
T ss_pred CCCCCCCCCHHHHHHHHHHHHccCCEEEEEEEEECCCCCC-CCcHHHHHHHHHHHHHh
Confidence 999999999999999999983 58999999999999996 68999999999999984
No 12
>PRK13773 formimidoylglutamase; Provisional
Probab=100.00 E-value=3.4e-48 Score=331.92 Aligned_cols=200 Identities=26% Similarity=0.364 Sum_probs=171.8
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhc----CCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhc-
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL----GGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEG- 76 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~----~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~- 76 (207)
++++++|++++++ +.+||+||||||+|||+++|+.+.+ +++++|||||||+|++++ ..++||||++++++.
T Consensus 106 ~~i~~~v~~~~~~-g~~PivLGGdHsit~g~~~a~~~~~~~~~~~~vgvI~~DAH~D~~~~---~~~~~G~p~~~~~~~~ 181 (324)
T PRK13773 106 ERLGDAVSALLDA-GHLPVVLGGGHETAFGSYLGVAGSERRRPGKRLGILNLDAHFDLRAA---PVPSSGTPFRQIARAE 181 (324)
T ss_pred HHHHHHHHHHHHC-CCeeEEECCchHHHHHhHHHHHHhhhcccCCceEEEEeCCCccCCCC---CCCCCChHHHHHhhcc
Confidence 5789999999996 7999999999999999999999876 248999999999999986 246899999999984
Q ss_pred ---CCCCcEEEEcccCC--ChhHHHHHHHcCceEEEcccccch--HHHHHHhh-ccCCcceEEEEEeccCCCCCCCCCCC
Q 028588 77 ---GYARRLLQVGIRSI--TKEGREQGKRFGVEQYEMRTFSRD--RQFLENLK-LGEGVKGVYISVDVDCLDPAFAPGVS 148 (207)
Q Consensus 77 ---~~~~~vv~iG~r~~--~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~-~~~~~~~vylsiDiDvldp~~~pg~~ 148 (207)
+...+++++|+|+. .++++++++++|+.++++.+++.. ..+.+.+. ...+.+++|||||+|||||+++|||+
T Consensus 182 ~~~~~~~~~~~iGir~~~~~~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~~~~l~~~~~vylS~DiD~lDps~aPGtg 261 (324)
T PRK13773 182 EAAGRTFQYSVLGISEPNNTRALFDTARELGVRYLLDEECQVMDRAAVRVFVADFLADVDVIYLTIDLDVLPAAVAPGVS 261 (324)
T ss_pred cccCCCccEEEeecCcccccHHHHHHHHHcCCEEEEHHHhhhcCHHHHHHHHHHHHhcCCeEEEEEeeCcCCcccCCCCC
Confidence 23468999999996 567889999999999999998542 22333332 11244789999999999999999999
Q ss_pred CCCCCCCCHHHHHHHHHhhc--CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHHHHhh
Q 028588 149 HIEPGGLSFRDVLNILHNLQ--ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELTAKIS 206 (207)
Q Consensus 149 ~p~pgGl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~~~~~ 206 (207)
+|+||||+++|++.+++.+. .+++|+||+|++|.+|. +++|+.+||+++++++..+.
T Consensus 262 tP~pgGlt~~E~~~ll~~l~~~~~vvg~DvvE~~P~~D~-~~~Ta~laa~li~~~l~~~~ 320 (324)
T PRK13773 262 APAAYGVPLEVIQAVCDRVAASGKLALVDVAELNPRFDI-DNRTARVAARLIHTIVTAHL 320 (324)
T ss_pred CCCCCCCCHHHHHHHHHHHHhcCCEEEEEEEEECCccCC-CCCHHHHHHHHHHHHHHhhc
Confidence 99999999999999999983 58999999999999996 68999999999999998763
No 13
>PRK02190 agmatinase; Provisional
Probab=100.00 E-value=4.6e-48 Score=328.33 Aligned_cols=195 Identities=32% Similarity=0.554 Sum_probs=168.8
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCC--C
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGY--A 79 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~--~ 79 (207)
+++++.++.++++ +.+||+||||||+|+|+++++.+++ ++++|||||||+|+++++. +.++||||++++++.+. +
T Consensus 97 ~~i~~~v~~~~~~-g~~pi~lGGdHsit~~~~~a~~~~~-~~~~vi~~DAH~D~~~~~~-~~~~hg~~~~~~~~~~~v~~ 173 (301)
T PRK02190 97 EALEAHAEKILAA-GKRMLTLGGDHFITLPLLRAHAKHF-GPLALVHFDAHTDTWADGG-SRIDHGTMFYHAPKEGLIDP 173 (301)
T ss_pred HHHHHHHHHHHhC-CCeEEEECCcchhhHHHHHHHHHHc-CCeEEEEEecCCCCCCCcc-CCCCCchHHHHHhcCCCcCC
Confidence 5788999999995 6899999999999999999999887 4899999999999999875 66899999999998764 5
Q ss_pred CcEEEEcccCCChhHHHHHHHcCceEEEcccccch--HHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCCCCCCCCCH
Q 028588 80 RRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRD--RQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHIEPGGLSF 157 (207)
Q Consensus 80 ~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~pgGl~~ 157 (207)
++++++|+|+ ++.+++|++++++.++++. .++++.+....+..+||||||+|||||+++|||++|+||||++
T Consensus 174 ~~vv~iGiR~------~~~~~~gi~~~~~~~~~~~g~~~~~~~~~~~l~~~~vyiSiDiDvlDps~aPg~~~p~pgGl~~ 247 (301)
T PRK02190 174 AHSVQIGIRT------EYDKDNGFTVLDARQVNDRGVDAIIAQIKQIVGDMPVYLTFDIDCLDPAFAPGTGTPVIGGLTS 247 (301)
T ss_pred CcEEEEECCC------chHHHCCCEEEEHHHhhccCHHHHHHHHHHHhCCCEEEEEEeecccCcccCCCCCCCCCCCcCH
Confidence 8999999998 2456789999999887552 3444444322245789999999999999999999999999999
Q ss_pred HHHHHHHHhhc-CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHHHHhh
Q 028588 158 RDVLNILHNLQ-ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELTAKIS 206 (207)
Q Consensus 158 ~e~~~~l~~i~-~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~~~~~ 206 (207)
+|++.+++.+. .+++|+||||++|.+|. +++|+.+||+++++++..++
T Consensus 248 ~e~~~il~~i~~~~vvg~DivE~~P~~D~-~~~Ta~laa~li~~~l~~~~ 296 (301)
T PRK02190 248 AQALKILRGLKGLNIVGMDVVEVAPAYDH-AEITALAAATLALEMLCLQA 296 (301)
T ss_pred HHHHHHHHHHhcCCeEEEEeeeecCCCCC-CCcHHHHHHHHHHHHHHHHH
Confidence 99999999885 48999999999999996 68999999999999997643
No 14
>PRK13772 formimidoylglutamase; Provisional
Probab=100.00 E-value=6.5e-48 Score=328.90 Aligned_cols=196 Identities=31% Similarity=0.438 Sum_probs=168.2
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhc-----CCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhc
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL-----GGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEG 76 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~-----~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~ 76 (207)
++++++++.++++ +.+||+||||||+|||+++|+.+.. .++++|||||||+|++++. .++||++++++++.
T Consensus 103 ~~i~~~v~~~~~~-g~~PivlGGdHsit~g~~~a~~~~~~~~~~~~~~gvI~~DAH~D~r~~~---~~~~Gs~~rri~e~ 178 (314)
T PRK13772 103 AALAEVVAEVLAA-GARPLVLGGGHEVAWGTWQGLRAHLDAQGDRGRVLIINLDAHFDLRTSR---PASSGTPFDQIAED 178 (314)
T ss_pred HHHHHHHHHHHHC-CCEEEEEcCchHHHHhhHHHHHHHhhhcccCCceEEEEecccccCCCCC---CCCCCCHHHHHHHH
Confidence 6789999999996 7999999999999999999997642 1489999999999999763 36899999999984
Q ss_pred ----CCCCcEEEEcccCC--ChhHHHHHHHcCceEEEcccccch--HHHHHHhh-ccCCcceEEEEEeccCCCCCCCCCC
Q 028588 77 ----GYARRLLQVGIRSI--TKEGREQGKRFGVEQYEMRTFSRD--RQFLENLK-LGEGVKGVYISVDVDCLDPAFAPGV 147 (207)
Q Consensus 77 ----~~~~~vv~iG~r~~--~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~-~~~~~~~vylsiDiDvldp~~~pg~ 147 (207)
+.+.+++++|+|++ .+++++++++.|+.++++.++... ..+++.+. ....++++|||||+|+|||+++|||
T Consensus 179 ~~~~g~~~~~~~iGir~~~~~~~~~~~~~~~g~~~~~~~e~~~~g~~~~~~~i~~~l~~~~~vylS~DiD~lDps~aPGv 258 (314)
T PRK13772 179 CAARGQPFDYACLGVSRLSNTPALFARADALGVRYVEDVDMQERHLDARLAELDALLDAADHVYLTIDLDVLPAAVAPGV 258 (314)
T ss_pred HHhcCCcceEEEEecCCCCCChhHHHHHHhCCeEEEEhhhhhhcCHHHHHHHHHHHHhcCCeEEEEEEecCcCcccCCCC
Confidence 34568999999997 577888999999999999888552 33444443 1123578999999999999999999
Q ss_pred CCCCCCCCCHHHHHHHHHhhc--CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHH
Q 028588 148 SHIEPGGLSFRDVLNILHNLQ--ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELT 202 (207)
Q Consensus 148 ~~p~pgGl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~ 202 (207)
++|+||||+++|++++++.+. .+++|+||+|++|.+|. +++|+.+||+++++++
T Consensus 259 gtP~pgGlt~~e~~~il~~l~~~~~v~g~DvvEv~P~~D~-~~~Ta~laa~li~~~l 314 (314)
T PRK13772 259 SAPAAYGVPLPVVEEIVLHVRASGKLRVADLAEYNPQYDR-DRRTARVAARLAYRLL 314 (314)
T ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCeeEEEEEEECCCCCC-CCCHHHHHHHHHHHhC
Confidence 999999999999999999983 48999999999999996 6899999999999975
No 15
>KOG2965 consensus Arginase [Amino acid transport and metabolism]
Probab=100.00 E-value=5e-43 Score=282.55 Aligned_cols=198 Identities=26% Similarity=0.390 Sum_probs=167.7
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCCCCCCC-CCccCCccHHHHHHhcCC--
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDIYDAFE-GNKYSHASSFARIMEGGY-- 78 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~~~~~~-g~~~~~g~~~~~~~~~~~-- 78 (207)
+++.+.|++++++ +.+++++|||||+++|++.|.++.|+ +++|||+|||.|.++|.+ .++..||||++.++++..
T Consensus 89 rqla~~v~~vve~-~r~~l~lGGDHSlAIGTvsgva~~~~-D~gvlWvDAHaDinTp~ts~SgNLHG~PvSflLg~~~p~ 166 (318)
T KOG2965|consen 89 RQLANEVSQVVEN-GRILLVLGGDHSLAIGTVSGVARVYP-DAGVLWVDAHADINTPDTSPSGNLHGCPVSFLLGELKPL 166 (318)
T ss_pred HHHHHHHHHHHhc-CeEEEEecCcceEEEeeehhhHhhCC-CccEEEEecccccCCCCCCCCCCcCCCcHHHHHhccCCC
Confidence 4788999999996 68999999999999999999999995 899999999999999863 355589999999998641
Q ss_pred ------------CCcEEEEcccCCChhHHHHHHHcCceEEEcccccch--HHHHHHh---hccCCcceEEEEEeccCCCC
Q 028588 79 ------------ARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRD--RQFLENL---KLGEGVKGVYISVDVDCLDP 141 (207)
Q Consensus 79 ------------~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~---~~~~~~~~vylsiDiDvldp 141 (207)
++++++||+|++++.|.++++++||.+|+|.++.+. ++++|.. .......|+++|||+|.+||
T Consensus 167 ~~~f~w~~p~i~~~~l~yIGLRDvdp~E~~iLk~lgI~~fsm~~Vdk~GI~~Vme~a~~~v~~~~~rpihlSfDvDg~Dp 246 (318)
T KOG2965|consen 167 PEGFSWVKPCISPKRLAYIGLRDVDPGEHAILKELGIAAFSMHEVDKYGIQKVMEMAMELVNPGTRRPIHLSFDVDGFDP 246 (318)
T ss_pred CccccccccccChhheEEEecccCChHHHHHHHhcCcceEeehhhHhhhHHHHHHHHHHHhcCCCccceeEEEecCCcCc
Confidence 578999999999999999999999999999999875 3444432 12223478999999999999
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHhhc--CCeeEEEEeeecCCCCCCCCH----HHHHHHHHHHHHH
Q 028588 142 AFAPGVSHIEPGGLSFRDVLNILHNLQ--ADVVAADVVEFNPQRDTVDGM----TAMVAAKLVRELT 202 (207)
Q Consensus 142 ~~~pg~~~p~pgGl~~~e~~~~l~~i~--~~vvg~di~E~~P~~d~~~~~----t~~~aa~li~~~~ 202 (207)
+++|+|++|++||||++|.+.+++.+. ++++++||+|+||.++. .+. |..+|..+++..+
T Consensus 247 ~~aPAtGTpv~gGLt~rE~myi~e~i~~Tg~LiAldvvEvnP~l~~-t~eea~~tv~~av~ii~~~~ 312 (318)
T KOG2965|consen 247 SYAPATGTPVVGGLTYREGMYICEEIAETGLLIALDVVEVNPLLGN-TEEEAKTTVSLAVAIIRTSL 312 (318)
T ss_pred cccCCCCCcCCCcccHHHHHHHHHHHHhcCCeeEEEEEEeccccCC-cHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999999999994 69999999999999985 333 4445555554443
No 16
>PF12640 UPF0489: UPF0489 domain; InterPro: IPR024131 This entry describes a family of uncharacterised proteins found in metazoa.
Probab=96.71 E-value=0.012 Score=45.58 Aligned_cols=63 Identities=21% Similarity=0.371 Sum_probs=37.9
Q ss_pred CccchHHHH-HHHHHhc-CCCeEEEEEccCCCCCCCCC--------C--------------CccCCccHHHHHHhcCCCC
Q 028588 25 DHSISFPVI-RAVSEKL-GGPVDVLHLDAHPDIYDAFE--------G--------------NKYSHASSFARIMEGGYAR 80 (207)
Q Consensus 25 dhs~s~~~~-~~~~~~~-~~~~~vI~~DAH~D~~~~~~--------g--------------~~~~~g~~~~~~~~~~~~~ 80 (207)
||.-++... +++.++. +.+..+||||+|+|+..|.. . ..++.++++.-++..|..+
T Consensus 6 ~H~~al~~w~~~~~~~~l~~~~~lvHiD~H~Dl~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~l~idn~I~pa~~~g~i~ 85 (162)
T PF12640_consen 6 DHNEALPFWYRAIGRGKLPSPNSLVHIDSHPDLRIPFDMSADPIFEKLLDLPDELTFEYTNELLNIDNFILPAVYAGHIS 85 (162)
T ss_pred ChHHHHHHHHHHHhcCCCCCCCeEEEEeCCCCCCcccccchhhhhhhccccccccchhhhhhcCCHHHHHHHHHhhcccC
Confidence 455544444 3443321 35789999999999987631 1 1234555666666666667
Q ss_pred cEEEEcc
Q 028588 81 RLLQVGI 87 (207)
Q Consensus 81 ~vv~iG~ 87 (207)
+++.+--
T Consensus 86 ~v~~i~~ 92 (162)
T PF12640_consen 86 DVIWIHP 92 (162)
T ss_pred eEEEEec
Confidence 7666643
No 17
>cd06831 PLPDE_III_ODC_like_AZI Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase-like Antizyme Inhibitor. Antizyme inhibitor (AZI) is homologous to the fold type III PLP-dependent enzyme ODC but does not retain any decarboxylase activity. Like ODC, AZI is presumed to exist as a homodimer. Antizyme is a regulatory protein that binds directly to the ODC monomer to block its active site, leading to its degradation by the 26S proteasome. AZI binds to Antizyme with a higher affinity than ODC, preventing the formation of the Antizyme-ODC complex. Thus, AZI blocks the ability of Antizyme to promote ODC degradation, which leads to increased ODC enzymatic activity and polyamine levels. AZI also prevents the degradation of other proteins regulated by Antizyme, such as cyclin D1.
Probab=79.31 E-value=45 Score=29.55 Aligned_cols=103 Identities=9% Similarity=0.092 Sum_probs=65.8
Q ss_pred CccHHHHHHhcC-CCCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCCC
Q 028588 66 HASSFARIMEGG-YARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFA 144 (207)
Q Consensus 66 ~g~~~~~~~~~~-~~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~~ 144 (207)
+..-+..++..| .+++++.-|.- .+.++.+.+.+.|+..+..+.+.....+.+. ....++.+-+-.+ ....
T Consensus 66 S~gEl~~al~~G~~~~~Iif~gp~-K~~~~l~~a~~~Gv~~i~vDS~~El~~i~~~----~~~~~v~lRi~~~---~~~~ 137 (394)
T cd06831 66 SKNEMALVQELGVSPENIIYTNPC-KQASQIKYAAKVGVNIMTCDNEIELKKIARN----HPNAKLLLHIATE---DNIG 137 (394)
T ss_pred CHHHHHHHHhcCCCcCCEEEeCCC-CCHHHHHHHHHCCCCEEEECCHHHHHHHHHh----CCCCcEEEEEecc---CCCC
Confidence 444566666654 46788888864 4667888888899988877665433322221 1234688887764 1111
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhc---CCeeEEEEe
Q 028588 145 PGVSHIEPGGLSFRDVLNILHNLQ---ADVVAADVV 177 (207)
Q Consensus 145 pg~~~p~pgGl~~~e~~~~l~~i~---~~vvg~di~ 177 (207)
. .......|++.+++.++++.+. -+++|+.+-
T Consensus 138 ~-~~~~~KFGi~~~~~~~~l~~~~~~~l~~~Gih~H 172 (394)
T cd06831 138 G-EEMNMKFGTTLKNCRHLLECAKELDVQIVGVKFH 172 (394)
T ss_pred C-CccCCCCCCCHHHHHHHHHHHHHCCCeEEEEEEE
Confidence 1 1124689999999999888763 277887775
No 18
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity.
Probab=78.73 E-value=44 Score=29.12 Aligned_cols=108 Identities=16% Similarity=0.104 Sum_probs=61.5
Q ss_pred HHHHHHhcCCCCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCCCC-CC
Q 028588 69 SFARIMEGGYARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAP-GV 147 (207)
Q Consensus 69 ~~~~~~~~~~~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~~p-g~ 147 (207)
-+..+.+.+...+++..|. ...+++.+.+.++|+..+..+.+.....+.+..+......++++-+|.++-..+... +.
T Consensus 59 E~~~~~~~~~~~~I~~~gp-~k~~~~l~~a~~~gi~~i~vds~~el~~l~~~a~~~~~~~~v~lRi~~~~~~~~~~~~~~ 137 (377)
T cd06843 59 EIAHVRAAVPDAPLIFGGP-GKTDSELAQALAQGVERIHVESELELRRLNAVARRAGRTAPVLLRVNLALPDLPSSTLTM 137 (377)
T ss_pred HHHHHHhcCCCCeEEEeCC-CCCHHHHHHHHHcCCCEEEeCCHHHHHHHHHHHHHcCCCceEEEEECCCCCCCCCcceec
Confidence 3444444443567777665 345677888888898766555444332222211111122478888887653222111 11
Q ss_pred -CCCCCCCCCHHHHHHHHHhhc---C-CeeEEEEe
Q 028588 148 -SHIEPGGLSFRDVLNILHNLQ---A-DVVAADVV 177 (207)
Q Consensus 148 -~~p~pgGl~~~e~~~~l~~i~---~-~vvg~di~ 177 (207)
+.+...|+++.|+.++++.+. . ++.|+..-
T Consensus 138 ~~~~srfG~~~~~~~~~~~~~~~~~~l~~~Glh~H 172 (377)
T cd06843 138 GGQPTPFGIDEADLPDALELLRDLPNIRLRGFHFH 172 (377)
T ss_pred CCCCCCCCcCHHHHHHHHHHHHhCCCccEEEEEEE
Confidence 234678999999988887763 2 66777554
No 19
>KOG1384 consensus tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=72.11 E-value=5.6 Score=34.48 Aligned_cols=31 Identities=16% Similarity=0.346 Sum_probs=24.5
Q ss_pred HHHHHHHHHhcCCcceEEEcCCccchHHHHHH
Q 028588 4 ITESVKLVMEEDPLHPLVLGGDHSISFPVIRA 35 (207)
Q Consensus 4 i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~ 35 (207)
...+++.+.++ |..||+.||.|+---+.+..
T Consensus 85 a~~aie~I~~r-gk~PIv~GGs~~yi~al~~~ 115 (348)
T KOG1384|consen 85 ASRAIEEIHSR-GKLPIVVGGSNSYLQALLSK 115 (348)
T ss_pred HHHHHHHHHhC-CCCCEEeCCchhhHHHHhhc
Confidence 35678889986 68999999999876665544
No 20
>COG0019 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism]
Probab=70.82 E-value=77 Score=28.19 Aligned_cols=115 Identities=16% Similarity=0.200 Sum_probs=76.6
Q ss_pred CCccHHHHHHhcCC-CCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCC--cceEEEEEeccCCC-
Q 028588 65 SHASSFARIMEGGY-ARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEG--VKGVYISVDVDCLD- 140 (207)
Q Consensus 65 ~~g~~~~~~~~~~~-~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~vylsiDiDvld- 140 (207)
.+..-+++++..|. +++++.-|. ..+.+|.+++-+.|+..+..+.+.. ++.+..... ..+|++-+..|+-.
T Consensus 81 ~S~gEl~~al~aG~~~~~I~f~g~-~ks~~ei~~a~e~gi~~i~vdS~~E----l~~l~~~a~~~~~~v~lRInP~~~~~ 155 (394)
T COG0019 81 ASLGELELALAAGFPPERIVFSGP-AKSEEEIAFALELGIKLINVDSEEE----LERLSAIAPGLVARVSLRINPGVSAG 155 (394)
T ss_pred cCHHHHHHHHHcCCChhhEEECCC-CCCHHHHHHHHHcCCcEEEeCCHHH----HHHHHHhccccCceEEEEECCCCCCc
Confidence 44556666666653 456666554 5678899999999999787765543 333321122 25799999988754
Q ss_pred --CCCCCCCCCCCCCCCCHHHHHHHHHhh----cCCeeEEEEeeecCCCCC
Q 028588 141 --PAFAPGVSHIEPGGLSFRDVLNILHNL----QADVVAADVVEFNPQRDT 185 (207)
Q Consensus 141 --p~~~pg~~~p~pgGl~~~e~~~~l~~i----~~~vvg~di~E~~P~~d~ 185 (207)
+...+| ....-.|+++.++.+.++.+ .-+++|+++---+-..|.
T Consensus 156 th~~~~tg-~~~sKFG~~~~~a~~~~~~~~~~~~l~~~Glh~HiGSq~~d~ 205 (394)
T COG0019 156 THEYIATG-GKSSKFGISPEEALDVLERAAKLLGLELVGLHFHIGSQITDL 205 (394)
T ss_pred cCccccCC-ccccccCCCHHHHHHHHHHHHhcCCCceEEEEEeecCCCCCc
Confidence 333343 23477899999977777655 249999999888777664
No 21
>KOG0622 consensus Ornithine decarboxylase [Amino acid transport and metabolism]
Probab=55.46 E-value=1.6e+02 Score=26.56 Aligned_cols=130 Identities=13% Similarity=0.089 Sum_probs=79.6
Q ss_pred cCCccHHHHHHhcC-CCCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCC
Q 028588 64 YSHASSFARIMEGG-YARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPA 142 (207)
Q Consensus 64 ~~~g~~~~~~~~~~-~~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~ 142 (207)
..+.+-+..+++.+ .|++++..+. .......+++.+.|+...+.+ . +..+.++...-...++-+.|-.|.=. +
T Consensus 107 caSk~E~~lvl~~gv~P~riIyanp-cK~~s~IkyAa~~gV~~~tfD---n-e~el~kv~~~hP~a~llLrIatdds~-a 180 (448)
T KOG0622|consen 107 CASKNELDLVLSLGVSPERIIYANP-CKQVSQIKYAAKHGVSVMTFD---N-EEELEKVAKSHPNANLLLRIATDDST-A 180 (448)
T ss_pred ecChHHHHHHHhcCCChHHeEecCC-CccHHHHHHHHHcCCeEEeec---C-HHHHHHHHHhCCCceEEEEEccCCCc-c
Confidence 34455677777665 4688988875 334567788889999888742 2 23344443233456788888777531 1
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhc---CCeeEEEEeeecCCCCCCCCHHHHHHHHHHHHHH
Q 028588 143 FAPGVSHIEPGGLSFRDVLNILHNLQ---ADVVAADVVEFNPQRDTVDGMTAMVAAKLVRELT 202 (207)
Q Consensus 143 ~~pg~~~p~pgGl~~~e~~~~l~~i~---~~vvg~di~E~~P~~d~~~~~t~~~aa~li~~~~ 202 (207)
-.| --.+.|-+.+++..+|..+. -+++|..+-=-+-..|.+..++|..-|+-+++..
T Consensus 181 ~~~---l~~KFG~~~~~~~~lLd~ak~l~lnvvGvsfHvGSgc~d~~~y~~Ai~dAr~vfd~g 240 (448)
T KOG0622|consen 181 TCR---LNLKFGCSLDNCRHLLDMAKELELNVVGVSFHVGSGCTDLQAYRDAISDARNVFDMG 240 (448)
T ss_pred ccc---ccCccCCCHHHHHHHHHHHHHcCceEEEEEEEecCCCCCHHHHHHHHHHHHHHHHHH
Confidence 111 24788999999888888763 3888887732223333323445555555555443
No 22
>cd06839 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase. This subfamily is composed of Bacillus circulans BtrK decarboxylase and similar proteins. These proteins are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases, eukaryotic ornithine decarboxylases and diaminopimelate decarboxylases. BtrK is presumed to function as a PLP-dependent decarboxylase involved in the biosynthesis of the aminoglycoside antibiotic butirosin. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity.
Probab=55.00 E-value=1.4e+02 Score=25.82 Aligned_cols=107 Identities=11% Similarity=0.094 Sum_probs=61.0
Q ss_pred HHHHHhcCC-CCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCC-CCCCC
Q 028588 70 FARIMEGGY-ARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPA-FAPGV 147 (207)
Q Consensus 70 ~~~~~~~~~-~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~-~~pg~ 147 (207)
+..+...|. +.+++..|.- ..+++.+.+-+.|+..+..+.+...+.+.+..+.....-++++-+|.++-... -+.-.
T Consensus 65 ~~~~~~~G~~~~~I~~~~~~-k~~~~l~~a~~~g~~~i~vds~~el~~l~~~a~~~~~~~~v~lRin~~~~~~~~g~~~~ 143 (382)
T cd06839 65 LALALEAGVPPEKILFAGPG-KSDAELRRAIEAGIGTINVESLEELERIDALAEEHGVVARVALRINPDFELKGSGMKMG 143 (382)
T ss_pred HHHHHHcCCCHHHEEEeCCC-CCHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHhcCCCCeEEEEECCCCCCCCCccccC
Confidence 344444443 3578877752 46677777778886566666554432222222211122467888876542111 01112
Q ss_pred CCCCCCCCCHHHHHHHHHhhc--C--CeeEEEEe
Q 028588 148 SHIEPGGLSFRDVLNILHNLQ--A--DVVAADVV 177 (207)
Q Consensus 148 ~~p~pgGl~~~e~~~~l~~i~--~--~vvg~di~ 177 (207)
+.+...|++.+++.++++.+. . ++.|+.+.
T Consensus 144 ~~~sKfG~~~~~~~~~~~~~~~~~~l~l~Glh~h 177 (382)
T cd06839 144 GGPSQFGIDVEELPAVLARIAALPNLRFVGLHIY 177 (382)
T ss_pred CCCCCcCCCHHHHHHHHHHHHhCCCCcEEEEEEe
Confidence 334678999999989888773 2 78888663
No 23
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=54.09 E-value=67 Score=21.85 Aligned_cols=71 Identities=10% Similarity=0.170 Sum_probs=43.8
Q ss_pred EcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEE-EeccCCCCCCCCCCCCC--CCCCCCHHHHH
Q 028588 85 VGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYIS-VDVDCLDPAFAPGVSHI--EPGGLSFRDVL 161 (207)
Q Consensus 85 iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vyls-iDiDvldp~~~pg~~~p--~pgGl~~~e~~ 161 (207)
|++...-..-.+.+++.|+.+.++++-.+. .+++.+-++ .|-+++-.+... +..| +..|+|++|++
T Consensus 4 IAVE~~Ls~v~~~L~~~GyeVv~l~~~~~~----------~~~daiVvtG~~~n~mg~~d~~-~~~pVInA~G~T~eEI~ 72 (80)
T PF03698_consen 4 IAVEEGLSNVKEALREKGYEVVDLENEQDL----------QNVDAIVVTGQDTNMMGIQDTS-TKVPVINASGLTAEEIV 72 (80)
T ss_pred EEecCCchHHHHHHHHCCCEEEecCCcccc----------CCcCEEEEECCCcccccccccc-cCceEEecCCCCHHHHH
Confidence 344443345567889999999998744311 233444444 566666443322 2334 67799999999
Q ss_pred HHHHh
Q 028588 162 NILHN 166 (207)
Q Consensus 162 ~~l~~ 166 (207)
.-++.
T Consensus 73 ~~v~~ 77 (80)
T PF03698_consen 73 QEVEE 77 (80)
T ss_pred HHHHH
Confidence 98864
No 24
>COG0135 TrpF Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism]
Probab=53.66 E-value=34 Score=27.67 Aligned_cols=52 Identities=19% Similarity=0.116 Sum_probs=36.1
Q ss_pred EEEEEeccCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCeeEEEEe---eecCCCC
Q 028588 130 VYISVDVDCLDPAFAPGVSHIEPGGLSFRDVLNILHNLQADVVAADVV---EFNPQRD 184 (207)
Q Consensus 130 vylsiDiDvldp~~~pg~~~p~pgGl~~~e~~~~l~~i~~~vvg~di~---E~~P~~d 184 (207)
--.+||++.+.+- .......-.|||+++.+...++.. +..|+|+. |-+|..-
T Consensus 139 tG~~fDW~~l~~~-~~~~~~~LAGGL~p~NV~~ai~~~--~p~gvDvSSGVE~~pG~K 193 (208)
T COG0135 139 TGQTFDWNLLPKL-RLSKPVMLAGGLNPDNVAEAIALG--PPYGVDVSSGVESSPGIK 193 (208)
T ss_pred CCcEECHHHhccc-cccCCEEEECCCCHHHHHHHHHhc--CCceEEeccccccCCCCC
Confidence 3456777777654 122224478999999999998864 46889986 8888653
No 25
>PF02784 Orn_Arg_deC_N: Pyridoxal-dependent decarboxylase, pyridoxal binding domain; InterPro: IPR022644 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region [].; GO: 0003824 catalytic activity; PDB: 2OO0_A 2ON3_A 1D7K_B 3VAB_A 2J66_A 3C5Q_A 2QGH_A 1TWI_B 1TUF_A 3N2O_A ....
Probab=52.18 E-value=43 Score=27.34 Aligned_cols=111 Identities=12% Similarity=0.120 Sum_probs=68.8
Q ss_pred CCccHHHHHHhcC-CCCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCC
Q 028588 65 SHASSFARIMEGG-YARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAF 143 (207)
Q Consensus 65 ~~g~~~~~~~~~~-~~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~ 143 (207)
.+..-+..++..+ .+.+++.-|. ..++++.+.+.+.++..+..+...... .+..+. ...++-+-+..++-..+.
T Consensus 49 ~S~~El~~a~~~g~~~~~Ii~~gp-~k~~~~l~~a~~~~~~~i~vDs~~el~-~l~~~~---~~~~v~lRin~~~~~~~~ 123 (251)
T PF02784_consen 49 ASPGELELALKAGFPPDRIIFTGP-GKSDEELEEAIENGVATINVDSLEELE-RLAELA---PEARVGLRINPGIGAGSH 123 (251)
T ss_dssp SSHHHHHHHHHTTTTGGGEEEECS-S--HHHHHHHHHHTESEEEESSHHHHH-HHHHHH---CTHEEEEEBE-SESTTTS
T ss_pred ecccchHHHHhhhccccceeEecC-cccHHHHHHHHhCCceEEEeCCHHHHH-HHhccC---CCceeeEEEeeccccccc
Confidence 3455666666654 4678998887 557788888888888888776554432 233332 112788877776433332
Q ss_pred CC-CC-CCCCCCCCCHHH-HHHHHHhhc--C-CeeEEEEeeec
Q 028588 144 AP-GV-SHIEPGGLSFRD-VLNILHNLQ--A-DVVAADVVEFN 180 (207)
Q Consensus 144 ~p-g~-~~p~pgGl~~~e-~~~~l~~i~--~-~vvg~di~E~~ 180 (207)
.. .+ +.+...|+++++ +.++++.+. + +++|+.+-=-+
T Consensus 124 ~~~~~g~~~skFGi~~~~~~~~~l~~~~~~~l~l~GlH~H~gS 166 (251)
T PF02784_consen 124 PKISTGGKDSKFGIDIEEEAEEALERAKELGLRLVGLHFHVGS 166 (251)
T ss_dssp CHHCSSSHTSSSSBEGGGHHHHHHHHHHHTTEEEEEEEE-HCS
T ss_pred cccCCCCCCCcCCcChHHHHHHHHHhhccceEEEEEeeeeecc
Confidence 21 11 235789999999 999998873 3 68888876333
No 26
>KOG4518 consensus Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]
Probab=51.87 E-value=32 Score=27.85 Aligned_cols=45 Identities=27% Similarity=0.513 Sum_probs=36.5
Q ss_pred CCCCCCCCCC-CCCCCCHHHHHHHHHhhc-CCeeEEEEeeecCCCCCCCC
Q 028588 141 PAFAPGVSHI-EPGGLSFRDVLNILHNLQ-ADVVAADVVEFNPQRDTVDG 188 (207)
Q Consensus 141 p~~~pg~~~p-~pgGl~~~e~~~~l~~i~-~~vvg~di~E~~P~~d~~~~ 188 (207)
-+..|+-+.| .+|.+.+.-+.+.|+.++ .-++| |||-|..|.+.+
T Consensus 206 vAQVP~Rgepd~~GEldy~fiF~~l~~~gy~g~iG---cEYkPk~dtveg 252 (264)
T KOG4518|consen 206 VAQVPNRGEPDTRGELDYHFIFDELRSIGYSGVIG---CEYKPKLDTVEG 252 (264)
T ss_pred eeecCCCCCCCCCCccccHHHHHHHHHhCCCceee---eeeccCcCcccc
Confidence 3567888877 789999999999999986 46777 689999986543
No 27
>TIGR00287 cas1 CRISPR-associated endonuclease Cas1. This model identifies CRISPR-associated protein Cas1, the most universal CRISPR system protein. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, a system for heritable host defense by prokaryotic cells against phage and other foreign DNA. Cas1 is a metal-dependent DNA-specific endonuclease.
Probab=51.74 E-value=19 Score=30.85 Aligned_cols=34 Identities=29% Similarity=0.432 Sum_probs=28.3
Q ss_pred eEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCC
Q 028588 19 PLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDI 55 (207)
Q Consensus 19 pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~ 55 (207)
-|+++|.+++|-++++.+.++ ++.|+++|.+.-.
T Consensus 37 ~I~i~g~~~lst~~l~~l~~~---~I~v~f~~~~g~~ 70 (323)
T TIGR00287 37 CIVLFGGVSISSAAIRELAKR---GIDIVFLGGDGNY 70 (323)
T ss_pred EEEEECCCCcCHHHHHHHHHC---CCeEEEECCCCcE
Confidence 466778899999999999864 6999999977653
No 28
>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=51.72 E-value=38 Score=27.15 Aligned_cols=51 Identities=10% Similarity=0.169 Sum_probs=33.1
Q ss_pred HHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhc---CCCeEEEEEccCCCC
Q 028588 5 TESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL---GGPVDVLHLDAHPDI 55 (207)
Q Consensus 5 ~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~---~~~~~vI~~DAH~D~ 55 (207)
.+.++.++++++....++..+-.++.++++++.+.. ++++.++-||.-...
T Consensus 163 ~~~~~~~l~~~~~~~ai~~~~d~~a~g~~~~l~~~g~~~p~di~iig~d~~~~~ 216 (265)
T cd06285 163 EAAAEKLLRSDSPPTAIFAVNDFAAIGVMGAARDRGLRVPDDVALVGYNDIPLV 216 (265)
T ss_pred HHHHHHHHcCCCCCCEEEEcCcHHHHHHHHHHHHcCCCCCcceEEEeecCcHHH
Confidence 455666665433445667777777888888887642 356788888865543
No 29
>PF08645 PNK3P: Polynucleotide kinase 3 phosphatase; InterPro: IPR013954 Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin []. ; PDB: 2FPW_A 2FPR_A 2FPX_A 2FPS_A 2FPU_B 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B 3U7G_A ....
Probab=50.07 E-value=1.1e+02 Score=23.28 Aligned_cols=101 Identities=13% Similarity=0.172 Sum_probs=53.4
Q ss_pred hHHHHHHHHHhcCCcceEEEc---CCc----cchHHHH----HHHHHhcCCCeEEEEEccCCC-CCCCCCCCccCCccHH
Q 028588 3 VITESVKLVMEEDPLHPLVLG---GDH----SISFPVI----RAVSEKLGGPVDVLHLDAHPD-IYDAFEGNKYSHASSF 70 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iG---Gdh----s~s~~~~----~~~~~~~~~~~~vI~~DAH~D-~~~~~~g~~~~~g~~~ 70 (207)
.+-++++.+.++ |...+++- |-. ..++..+ ..+.+..+-++ .+.+=-|.| +|.| .-|||.
T Consensus 33 ~v~~~L~~l~~~-Gy~IvIvTNQ~gi~~~~~~~~~~~~~~ki~~il~~l~ip~-~~~~a~~~d~~RKP------~~GM~~ 104 (159)
T PF08645_consen 33 GVPEALRELHKK-GYKIVIVTNQSGIGRGMGEKDLENFHEKIENILKELGIPI-QVYAAPHKDPCRKP------NPGMWE 104 (159)
T ss_dssp THHHHHHHHHHT-TEEEEEEEE-CCCCCTBTCCHHHHHHHHHHHHHHHCTS-E-EEEECGCSSTTSTT------SSHHHH
T ss_pred hHHHHHHHHHhc-CCeEEEEeCccccccccccchHHHHHHHHHHHHHHcCCce-EEEecCCCCCCCCC------chhHHH
Confidence 366778888775 66666653 221 1233333 22333343343 233333444 4444 458888
Q ss_pred HHHHhcC-----CCCcEEEEccc--------CCChhHHHHHHHcCceEEEcccc
Q 028588 71 ARIMEGG-----YARRLLQVGIR--------SITKEGREQGKRFGVEQYEMRTF 111 (207)
Q Consensus 71 ~~~~~~~-----~~~~vv~iG~r--------~~~~~~~~~~~~~~~~~~~~~~~ 111 (207)
..+-... +.++.+.||=+ +++..+++++...|+++++++++
T Consensus 105 ~~~~~~~~~~~id~~~Sf~VGDaagr~~~~~d~s~~D~~fA~N~gi~f~tpe~~ 158 (159)
T PF08645_consen 105 FALKDYNDGVEIDLANSFYVGDAAGRSKKKKDFSDSDRKFALNCGIKFYTPEEF 158 (159)
T ss_dssp HHCCCTSTT--S-CCC-EEEESSCHCTB-S--S--HHHHHHHHHT--EE-HHHH
T ss_pred HHHHhccccccccccceEEEeccCCCCCcccccChhHHHHHHHcCCcccChhhc
Confidence 7655443 35789999953 23467889999999999998753
No 30
>PRK03094 hypothetical protein; Provisional
Probab=48.02 E-value=87 Score=21.35 Aligned_cols=71 Identities=15% Similarity=0.233 Sum_probs=44.3
Q ss_pred EcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcce-EEEEEeccCCCCCCCCCCCCC--CCCCCCHHHHH
Q 028588 85 VGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKG-VYISVDVDCLDPAFAPGVSHI--EPGGLSFRDVL 161 (207)
Q Consensus 85 iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-vylsiDiDvldp~~~pg~~~p--~pgGl~~~e~~ 161 (207)
||+..--..-.+.+++.|..+.++..-.. ..+++. ||=-.|.+++--+.. .+..| +..|+|++|++
T Consensus 4 IaVE~~Ls~i~~~L~~~GYeVv~l~~~~~----------~~~~Da~VitG~d~n~mgi~d~-~t~~pVI~A~G~TaeEI~ 72 (80)
T PRK03094 4 IGVEQSLTDVQQALKQKGYEVVQLRSEQD----------AQGCDCCVVTGQDSNVMGIADT-STKGSVITASGLTADEIC 72 (80)
T ss_pred EEeecCcHHHHHHHHHCCCEEEecCcccc----------cCCcCEEEEeCCCcceeccccc-ccCCcEEEcCCCCHHHHH
Confidence 34444334456788999999998753221 012344 444477777764433 23344 67899999999
Q ss_pred HHHHh
Q 028588 162 NILHN 166 (207)
Q Consensus 162 ~~l~~ 166 (207)
..++.
T Consensus 73 ~~ve~ 77 (80)
T PRK03094 73 QQVES 77 (80)
T ss_pred HHHHH
Confidence 98863
No 31
>TIGR03099 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosortase system type 1 associated. The sequences in this family contain the pyridoxal binding domain (pfam02784) and C-terminal sheet domain (pfam00278) of a family of Pyridoxal-dependent decarboxylases. Characterized enzymes in this family decarboxylate substrates such as ornithine, diaminopimelate and arginine. The genes of the family modeled here, with the exception of those observed in certain Burkholderia species, are all found in the context of exopolysaccharide biosynthesis loci containing the exosortase/PEP-CTERM protein sorting system. More specifically, these are characteristic of the type 1 exosortase system represented by the Genome Property GenProp0652. The substrate of these enzymes may be a precursor of the carrier or linker which is hypothesized to release the PEP-CTERM protein from the exosortase enzyme. These enzymes are apparently most closely related to the diaminopimelate decarboxylase modeled by TIGR01048
Probab=47.46 E-value=1.9e+02 Score=25.23 Aligned_cols=92 Identities=14% Similarity=0.050 Sum_probs=53.5
Q ss_pred CcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCCCCCC---CCCCCCCCC
Q 028588 80 RRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAPGV---SHIEPGGLS 156 (207)
Q Consensus 80 ~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~---~~p~pgGl~ 156 (207)
.+++..|.- ..+++.+.+-++|+ .+..+.+...+.+.+..+......+++|-+|.+.-.. ..+. +.....|++
T Consensus 94 ~~I~~~gp~-k~~~~l~~a~~~gv-~i~vDs~~el~~l~~~a~~~~~~~~v~LRin~~~~~~--~~~~~~~~~~srFGi~ 169 (398)
T TIGR03099 94 GCISFAGPG-KTDAELRRALAAGV-LINVESLRELNRLAALSEALGLRARVAVRVNPDFELK--GSGMKMGGGAKQFGID 169 (398)
T ss_pred hHEEEeCCC-CCHHHHHHHHhCCC-EEEECCHHHHHHHHHHHHhcCCCCcEEEEECCCCCCC--CcccccCCCCCcCCCC
Confidence 467777653 34677777778898 6666655433222222111111245777777653111 1121 235778999
Q ss_pred HHHHHHHHHhhcC---CeeEEE
Q 028588 157 FRDVLNILHNLQA---DVVAAD 175 (207)
Q Consensus 157 ~~e~~~~l~~i~~---~vvg~d 175 (207)
.+|+.++++.+.. ++.|+.
T Consensus 170 ~~e~~~~~~~~~~~~l~l~Glh 191 (398)
T TIGR03099 170 AEQVPAALAFIKAADLDFQGFH 191 (398)
T ss_pred HHHHHHHHHHHHhCCCeEEEEE
Confidence 9998888887742 677765
No 32
>PF01867 Cas_Cas1: CRISPR associated protein Cas1; InterPro: IPR002729 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents Cas1, which is a metal-dependent DNA-specific endonuclease []. Cas1 may play a role in the recognition, cleavage, and/or integration of foreign nucleic acids into CRISPRs.; PDB: 2YZS_A 3LFX_D 3PV9_E 3NKE_C 3NKD_A 3GOD_D.
Probab=46.49 E-value=26 Score=29.36 Aligned_cols=34 Identities=32% Similarity=0.385 Sum_probs=26.5
Q ss_pred eEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCC
Q 028588 19 PLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDI 55 (207)
Q Consensus 19 pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~ 55 (207)
-|++.|.+++|-.+++.+.++ .+.|+++|.+...
T Consensus 37 ~Ivi~g~~~iSt~ai~~l~~~---gI~v~~~~~~G~~ 70 (282)
T PF01867_consen 37 SIVIFGGVSISTAAIRLLSKN---GIPVVFLDRRGRP 70 (282)
T ss_dssp EEEE-STEEEEHHHHHHHHHT---T-EEEEESTTSEE
T ss_pred EEEEcCCCCCCHHHHHHHHHC---CCcEEEeCCCCCE
Confidence 466777799999999999864 6999999988743
No 33
>TIGR03638 cas1_ECOLI CRISPR-associated endonuclease Cas1, ECOLI subtype. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the ECOLI subtype of CRISPR/Cas system.
Probab=46.34 E-value=28 Score=29.18 Aligned_cols=32 Identities=16% Similarity=0.260 Sum_probs=28.0
Q ss_pred eEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCC
Q 028588 19 PLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHP 53 (207)
Q Consensus 19 pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~ 53 (207)
-|+++|..++|.++++.+.++ ++.|+|+|...
T Consensus 47 ~Ivl~g~~siT~~al~~l~~~---gI~v~~~~~~G 78 (269)
T TIGR03638 47 CLLLGPGTSVTHAAVKLLARH---GCLVVWVGEGG 78 (269)
T ss_pred EEEEeCCCccCHHHHHHHHHC---CCEEEEECCCC
Confidence 578889999999999999874 69999999666
No 34
>PRK14334 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=44.69 E-value=1.9e+02 Score=25.98 Aligned_cols=87 Identities=15% Similarity=0.190 Sum_probs=45.0
Q ss_pred hcCCCCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCCCCCCC
Q 028588 75 EGGYARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHIEPGG 154 (207)
Q Consensus 75 ~~~~~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~pgG 154 (207)
+.+..-+.+++|+++.+++-.+.+++ + ++.+++ .+.++.++. .+ ..+.++.|+ + +|.| |
T Consensus 242 ~~~~g~~~l~igvQSgs~~vLk~m~R-~---~~~~~~---~~~v~~lr~-~~-~~i~i~~d~--I-------vG~P---g 300 (440)
T PRK14334 242 ETPAVCEYIHLPVQSGSDRVLRRMAR-E---YRREKY---LERIAEIRE-AL-PDVVLSTDI--I-------VGFP---G 300 (440)
T ss_pred hcCcCCCeEEeccccCCHHHHHHhCC-C---CCHHHH---HHHHHHHHH-hC-CCcEEEEeE--E-------EECC---C
Confidence 33334578999999998887665532 1 222222 234444441 11 235555554 2 2445 4
Q ss_pred CCHHHHHHHHHhhcC-CeeEEEEeeecCC
Q 028588 155 LSFRDVLNILHNLQA-DVVAADVVEFNPQ 182 (207)
Q Consensus 155 l~~~e~~~~l~~i~~-~vvg~di~E~~P~ 182 (207)
-|.+++.+.++.+.. ++-.+.+.-|+|.
T Consensus 301 Et~ed~~~tl~~i~~l~~~~i~~f~ysp~ 329 (440)
T PRK14334 301 ETEEDFQETLSLYDEVGYDSAYMFIYSPR 329 (440)
T ss_pred CCHHHHHHHHHHHHhcCCCEeeeeEeeCC
Confidence 466666666665531 3334444455554
No 35
>PF01715 IPPT: IPP transferase; InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) [].; GO: 0005524 ATP binding, 0008033 tRNA processing; PDB: 2ZXU_A 3FOZ_A 2ZM5_B 3D3Q_A 3EXA_B 2QGN_A 3A8T_A 3EPK_B 3EPH_A 3EPJ_A ....
Probab=44.36 E-value=20 Score=29.78 Aligned_cols=32 Identities=13% Similarity=0.270 Sum_probs=21.5
Q ss_pred hHHHHHHHHHhcCCcceEEEcCCccchHHHHHH
Q 028588 3 VITESVKLVMEEDPLHPLVLGGDHSISFPVIRA 35 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~ 35 (207)
....++..+.++ |..||++||-+----+.+.+
T Consensus 44 ~a~~~i~~i~~r-gk~PIlvGGTglYi~all~g 75 (253)
T PF01715_consen 44 DAREAIEDILAR-GKIPILVGGTGLYIQALLNG 75 (253)
T ss_dssp HHHHHHHHHHHT-T-EEEEEES-HHHHHHHHCT
T ss_pred HHHHHHHHHHhc-CCeEEEECChHHHHHHHHhC
Confidence 456778888886 78999999976554444444
No 36
>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=41.99 E-value=82 Score=25.22 Aligned_cols=18 Identities=17% Similarity=0.244 Sum_probs=7.4
Q ss_pred EEEcCCccchHHHHHHHH
Q 028588 20 LVLGGDHSISFPVIRAVS 37 (207)
Q Consensus 20 i~iGGdhs~s~~~~~~~~ 37 (207)
.++..+-.++.++++++.
T Consensus 180 ai~~~~d~~a~g~~~~l~ 197 (268)
T cd06270 180 AVFCANDEMAAGAISALR 197 (268)
T ss_pred EEEEcCcHHHHHHHHHHH
Confidence 333333334444444443
No 37
>cd06840 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase. Bifunctional aspartate kinase/diaminopimelate decarboxylase (AspK/DapDC, EC 4.1.1.20/EC 2.7.2.4) typically exists in bacteria. These proteins contain an N-terminal AspK region and a C-terminal DapDC region, which contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, characteristic of fold type III PLP-dependent enzymes. Members of this subfamily have not been fully characterized. Based on their sequence, these proteins may catalyze both reactions catalyzed by AspK and DapDC. AspK catalyzes the phosphorylation of L-aspartate to produce 4-phospho-L-aspartate while DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine.
Probab=41.92 E-value=2.4e+02 Score=24.60 Aligned_cols=109 Identities=12% Similarity=0.025 Sum_probs=67.1
Q ss_pred CccHHHHHHhc--C-CCCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCC
Q 028588 66 HASSFARIMEG--G-YARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPA 142 (207)
Q Consensus 66 ~g~~~~~~~~~--~-~~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~ 142 (207)
+..-++.++.. | .+++++.-|. ..++++.+++-++|+.+ ..+.+.. ++.+.......++.+-+..+.-..+
T Consensus 65 S~~El~~al~~~~G~~~~~Iif~gp-~K~~~~l~~a~~~gv~i-~~Ds~~E----l~~i~~~~~~~~v~lRi~~~~~~~~ 138 (368)
T cd06840 65 SIGELDLVLKLFPDLDPRRVLFTPN-FAARSEYEQALELGVNV-TVDNLHP----LREWPELFRGREVILRIDPGQGEGH 138 (368)
T ss_pred CHHHHHHHHHcccCCCcceEEEcCC-CCCHHHHHHHHHCCCEE-EECCHHH----HHHHHHhcccCCEEEEECCCCCCCC
Confidence 34456666553 2 4677877775 34667888888899954 5554443 2222211123578888887654332
Q ss_pred CC--CCCCCCCCCCCCHHHHHHHHHhhc---CCeeEEEEeeec
Q 028588 143 FA--PGVSHIEPGGLSFRDVLNILHNLQ---ADVVAADVVEFN 180 (207)
Q Consensus 143 ~~--pg~~~p~pgGl~~~e~~~~l~~i~---~~vvg~di~E~~ 180 (207)
.. ...+.+...|++..|+.++++.+. -+++|+.+-=-+
T Consensus 139 ~~~~~~~~~~skFG~~~~~~~~~l~~~~~~~l~l~GlhfH~GS 181 (368)
T cd06840 139 HKHVRTGGPESKFGLDVDELDEARDLAKKAGIIVIGLHAHSGS 181 (368)
T ss_pred CCceecCCCCCCCCCCHHHHHHHHHHHHhCCCcEEEEEEECCC
Confidence 21 111246889999999999887763 288888885433
No 38
>TIGR03641 cas1_HMARI CRISPR-associated endonuclease Cas1, HMARI/TNEAP subtype. It describes Cas1 subgroup that includes Cas1 proteins of the related HMARI and TNEAP subtypes of CRISPR/Cas system.
Probab=40.73 E-value=35 Score=29.38 Aligned_cols=34 Identities=12% Similarity=0.129 Sum_probs=28.4
Q ss_pred eEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCC
Q 028588 19 PLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDI 55 (207)
Q Consensus 19 pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~ 55 (207)
-|+++|.+++|-.+++.+.++ ++.|+++|.+...
T Consensus 36 ~ivi~g~~~ist~al~~l~~~---gI~v~f~~~~G~~ 69 (322)
T TIGR03641 36 EIYVFGEVSLNSKALSFLSKK---GIPIHFFNYYGYY 69 (322)
T ss_pred eEEEEcCCccCHHHHHHHHHC---CCeEEEECCCCcE
Confidence 467788899999999999864 6899999977743
No 39
>PRK13586 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=40.73 E-value=2e+02 Score=23.45 Aligned_cols=120 Identities=18% Similarity=0.275 Sum_probs=67.0
Q ss_pred CeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCCCCcEEEE--cccCCChhHHHHHHHcCceEEEccccc-chHHHHH
Q 028588 43 PVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGYARRLLQV--GIRSITKEGREQGKRFGVEQYEMRTFS-RDRQFLE 119 (207)
Q Consensus 43 ~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~~~~vv~i--G~r~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~ 119 (207)
.+-++-+|+-. +.. .+-..++++.+... . =+++ |+|+ .++.+.+-+.|+..+-..... ++.++++
T Consensus 46 ~lhivDLd~a~-------~~~-~n~~~i~~i~~~~~-~-~v~vGGGIrs--~e~~~~~l~~Ga~kvvigt~a~~~p~~~~ 113 (232)
T PRK13586 46 RIHVVDLDAAE-------GVG-NNEMYIKEISKIGF-D-WIQVGGGIRD--IEKAKRLLSLDVNALVFSTIVFTNFNLFH 113 (232)
T ss_pred EEEEEECCCcC-------CCc-chHHHHHHHHhhCC-C-CEEEeCCcCC--HHHHHHHHHCCCCEEEECchhhCCHHHHH
Confidence 46666666542 111 12256666665321 1 3677 5555 455555556777655544322 2345565
Q ss_pred HhhccCCcceEEEEEeccCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhc-CCeeEEEEe
Q 028588 120 NLKLGEGVKGVYISVDVDCLDPAFAPGVSHIEPGGLSFRDVLNILHNLQ-ADVVAADVV 177 (207)
Q Consensus 120 ~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~pgGl~~~e~~~~l~~i~-~~vvg~di~ 177 (207)
++...-+.+.+.+|+|..- +-..+ +..|...++++.|+...++..+ ..++-.||.
T Consensus 114 ~~~~~~g~~~ivvslD~~~-~~~v~--~~gw~~~~~~~~e~~~~l~~~g~~~ii~tdI~ 169 (232)
T PRK13586 114 DIVREIGSNRVLVSIDYDN-TKRVL--IRGWKEKSMEVIDGIKKVNELELLGIIFTYIS 169 (232)
T ss_pred HHHHHhCCCCEEEEEEcCC-CCEEE--ccCCeeCCCCHHHHHHHHHhcCCCEEEEeccc
Confidence 5432334568999999821 22222 2334557889999988888775 467766663
No 40
>COG3623 SgaU Putative L-xylulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=40.51 E-value=23 Score=29.37 Aligned_cols=26 Identities=31% Similarity=0.521 Sum_probs=21.6
Q ss_pred CCCCCCCHHHHHHHHHhhcCCeeEEEEeeec
Q 028588 150 IEPGGLSFRDVLNILHNLQADVVAADVVEFN 180 (207)
Q Consensus 150 p~pgGl~~~e~~~~l~~i~~~vvg~di~E~~ 180 (207)
.-|++++|.|=+.+.+.+ |+|++|.+
T Consensus 13 Alp~~~sW~erl~~AK~~-----GFDFvEmS 38 (287)
T COG3623 13 ALPNGFSWLERLALAKEL-----GFDFVEMS 38 (287)
T ss_pred hccCCCCHHHHHHHHHHc-----CCCeEEEe
Confidence 468899999988887765 88888887
No 41
>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=40.00 E-value=85 Score=24.90 Aligned_cols=12 Identities=8% Similarity=0.282 Sum_probs=8.4
Q ss_pred CCcEEEEcccCC
Q 028588 79 ARRLLQVGIRSI 90 (207)
Q Consensus 79 ~~~vv~iG~r~~ 90 (207)
++++..+|.-..
T Consensus 204 p~di~vig~d~~ 215 (268)
T cd01575 204 PEDIAIAGFGDL 215 (268)
T ss_pred CcceEEEecCCc
Confidence 567777777654
No 42
>COG3319 Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=38.91 E-value=78 Score=26.42 Aligned_cols=53 Identities=23% Similarity=0.253 Sum_probs=39.9
Q ss_pred hhHHHHHHHHHhcCCcceEEEcC---CccchHHHHHHHHHhcCCCeEEEEEccCCC
Q 028588 2 NVITESVKLVMEEDPLHPLVLGG---DHSISFPVIRAVSEKLGGPVDVLHLDAHPD 54 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGG---dhs~s~~~~~~~~~~~~~~~~vI~~DAH~D 54 (207)
+.++.-+..+.+.++.-|+.++| .+.+++.+.+.+.+.-..=-.++.+|+=..
T Consensus 49 ~~a~~yv~~Ir~~QP~GPy~L~G~S~GG~vA~evA~qL~~~G~~Va~L~llD~~~~ 104 (257)
T COG3319 49 DMAAAYVAAIRRVQPEGPYVLLGWSLGGAVAFEVAAQLEAQGEEVAFLGLLDAVPP 104 (257)
T ss_pred HHHHHHHHHHHHhCCCCCEEEEeeccccHHHHHHHHHHHhCCCeEEEEEEeccCCC
Confidence 35677788888888889999999 477788888888765212245789998777
No 43
>TIGR03640 cas1_DVULG CRISPR-associated endonuclease Cas1, DVULG subtype. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the DVULG subtype of CRISPR/Cas system.
Probab=38.27 E-value=41 Score=29.13 Aligned_cols=32 Identities=16% Similarity=0.218 Sum_probs=26.9
Q ss_pred EEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCC
Q 028588 20 LVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPD 54 (207)
Q Consensus 20 i~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D 54 (207)
|+|.|.+++|..+++.+.++ ++.|+++|.+.-
T Consensus 42 Ivi~g~~~ist~al~~l~~~---~I~v~f~~~~G~ 73 (340)
T TIGR03640 42 IVCFGNVGLSPFLMGRCAED---GISLVFLTENGR 73 (340)
T ss_pred EEEEcCCCcCHHHHHHHHHC---CCEEEEECCCCe
Confidence 56667899999999999864 699999997764
No 44
>COG0065 LeuC 3-isopropylmalate dehydratase large subunit [Amino acid transport and metabolism]
Probab=38.08 E-value=17 Score=32.24 Aligned_cols=18 Identities=28% Similarity=0.582 Sum_probs=15.5
Q ss_pred EEEcCC-ccchHHHHHHHH
Q 028588 20 LVLGGD-HSISFPVIRAVS 37 (207)
Q Consensus 20 i~iGGd-hs~s~~~~~~~~ 37 (207)
+++||| |++|+|++.|++
T Consensus 117 ~Iv~gDSHT~T~GAfGAfA 135 (423)
T COG0065 117 TIVGGDSHTCTHGAFGAFA 135 (423)
T ss_pred EEEecccCcccchhhhhhh
Confidence 567777 999999999987
No 45
>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=37.65 E-value=1.1e+02 Score=24.41 Aligned_cols=50 Identities=14% Similarity=0.078 Sum_probs=31.1
Q ss_pred HHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhc---CCCeEEEEEccCCC
Q 028588 5 TESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL---GGPVDVLHLDAHPD 54 (207)
Q Consensus 5 ~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~---~~~~~vI~~DAH~D 54 (207)
++.++.++++++..-.++..+-.++.+.++++.++. ++++.+|-||....
T Consensus 159 ~~~~~~~l~~~~~~~ai~~~~d~~a~g~~~~l~~~g~~vp~di~vigfd~~~~ 211 (265)
T cd01543 159 QEELAQWLQSLPKPVGIFACTDARARQLLEACRRAGIAVPEEVAVLGVDNDEL 211 (265)
T ss_pred HHHHHHHHhcCCCCcEEEecChHHHHHHHHHHHHhCCCCCCceEEEeeCCchh
Confidence 445666665433334556666667777777776642 35778888886643
No 46
>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=35.87 E-value=1e+02 Score=24.68 Aligned_cols=10 Identities=30% Similarity=0.388 Sum_probs=5.7
Q ss_pred CCcEEEEccc
Q 028588 79 ARRLLQVGIR 88 (207)
Q Consensus 79 ~~~vv~iG~r 88 (207)
|+++..+|.-
T Consensus 203 p~dv~iig~d 212 (269)
T cd06281 203 PRDLSVISIG 212 (269)
T ss_pred CcceeEEEec
Confidence 3566666664
No 47
>PLN02748 tRNA dimethylallyltransferase
Probab=35.64 E-value=31 Score=31.45 Aligned_cols=33 Identities=9% Similarity=0.229 Sum_probs=25.4
Q ss_pred hHHHHHHHHHhcCCcceEEEcCCccchHHHHHHH
Q 028588 3 VITESVKLVMEEDPLHPLVLGGDHSISFPVIRAV 36 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~ 36 (207)
....+++.+.++ |..||++||-|..--+.+.++
T Consensus 99 ~A~~~I~~I~~r-gk~PIlVGGTglYi~aLl~g~ 131 (468)
T PLN02748 99 HAVPLIEEILSR-NGLPVIVGGTNYYIQALVSPF 131 (468)
T ss_pred HHHHHHHHHHhc-CCCeEEEcChHHHHHHHHcCc
Confidence 455677888886 689999999888777766554
No 48
>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=34.84 E-value=1.1e+02 Score=24.52 Aligned_cols=11 Identities=18% Similarity=0.329 Sum_probs=5.8
Q ss_pred CCcEEEEcccC
Q 028588 79 ARRLLQVGIRS 89 (207)
Q Consensus 79 ~~~vv~iG~r~ 89 (207)
++++..+|..+
T Consensus 210 p~dv~vvg~d~ 220 (273)
T cd01541 210 PEDISVVGFDD 220 (273)
T ss_pred CCcEEEEEcCC
Confidence 35555556543
No 49
>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.
Probab=34.52 E-value=49 Score=23.87 Aligned_cols=9 Identities=22% Similarity=0.254 Sum_probs=3.9
Q ss_pred HHHHHHHHh
Q 028588 5 TESVKLVME 13 (207)
Q Consensus 5 ~~~v~~~~~ 13 (207)
++.++.+.+
T Consensus 28 ~~~~~~~~~ 36 (127)
T cd02068 28 DDIVEDIKE 36 (127)
T ss_pred HHHHHHHHH
Confidence 344444443
No 50
>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=34.23 E-value=29 Score=29.87 Aligned_cols=33 Identities=9% Similarity=0.220 Sum_probs=24.0
Q ss_pred hHHHHHHHHHhcCCcceEEEcCCccchHHHHHHH
Q 028588 3 VITESVKLVMEEDPLHPLVLGGDHSISFPVIRAV 36 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~ 36 (207)
....++..+.++ |+.||+.||-...--+.+.++
T Consensus 80 ~a~~~i~~i~~r-gk~pIlVGGTglY~~aL~~g~ 112 (308)
T COG0324 80 DALAAIDDILAR-GKLPILVGGTGLYLKALLEGL 112 (308)
T ss_pred HHHHHHHHHHhC-CCCcEEEccHHHHHHHHHcCC
Confidence 456788889986 789999999665544444444
No 51
>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=33.76 E-value=1.3e+02 Score=24.28 Aligned_cols=12 Identities=17% Similarity=0.216 Sum_probs=7.1
Q ss_pred CCcEEEEcccCC
Q 028588 79 ARRLLQVGIRSI 90 (207)
Q Consensus 79 ~~~vv~iG~r~~ 90 (207)
|+++..+|.-+.
T Consensus 207 P~di~vvg~d~~ 218 (269)
T cd06297 207 GEDVRVVGFDDH 218 (269)
T ss_pred CCceEEEEECCc
Confidence 456666666544
No 52
>PF09936 Methyltrn_RNA_4: SAM-dependent RNA methyltransferase; InterPro: IPR019230 This entry contains proteins that have no known function. They are found as separate proteins and as a C-terminal domain to tRNA (guanine-N(1)-)-methyltransferases to which they are structurally related. ; PDB: 3DCM_X.
Probab=33.03 E-value=98 Score=24.57 Aligned_cols=48 Identities=21% Similarity=0.342 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHhcCCcceEEEc-----CCccchHHHHHHHHHhcCCCeEEEEEc
Q 028588 2 NVITESVKLVMEEDPLHPLVLG-----GDHSISFPVIRAVSEKLGGPVDVLHLD 50 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iG-----Gdhs~s~~~~~~~~~~~~~~~~vI~~D 50 (207)
..++++++.+.++.|..|.+++ +..+++|..++.....- ++.-+|.|=
T Consensus 88 ~sle~a~~~I~~~~G~~P~~v~TsAr~~~~~is~~~lr~~l~~~-~~P~LllFG 140 (185)
T PF09936_consen 88 DSLEEAIEDIEEEEGKRPLLVATSARKYPNTISYAELRRMLEEE-DRPVLLLFG 140 (185)
T ss_dssp SSHHHHHHHHHHHHSS--EEEE--SS--SS-B-HHHHHHHHHH---S-EEEEE-
T ss_pred hhHHHHHHHHHHHhCCCCEEEEecCcCCCCCcCHHHHHHHHhcc-CCeEEEEec
Confidence 3578999999998889999998 67889999998876433 334466665
No 53
>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=32.87 E-value=1.2e+02 Score=24.03 Aligned_cols=11 Identities=9% Similarity=0.217 Sum_probs=6.3
Q ss_pred CCcEEEEcccC
Q 028588 79 ARRLLQVGIRS 89 (207)
Q Consensus 79 ~~~vv~iG~r~ 89 (207)
+.++..+|.-.
T Consensus 205 p~di~v~g~d~ 215 (267)
T cd06283 205 PEDVGLIGFDD 215 (267)
T ss_pred ccceEEEEeCC
Confidence 45666666644
No 54
>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=32.57 E-value=1.5e+02 Score=23.51 Aligned_cols=21 Identities=14% Similarity=0.336 Sum_probs=12.9
Q ss_pred HHHHHHhcCCCCcEEEEcccCC
Q 028588 69 SFARIMEGGYARRLLQVGIRSI 90 (207)
Q Consensus 69 ~~~~~~~~~~~~~vv~iG~r~~ 90 (207)
.++.+.+.+. +++..+|....
T Consensus 194 ~~~al~~~g~-~di~vvg~d~~ 214 (267)
T cd06322 194 AVSAIKAAGR-DNVKVIGFDGM 214 (267)
T ss_pred HHHHHHHCCC-CCeEEEEecCC
Confidence 3344445554 78888888553
No 55
>PF01202 SKI: Shikimate kinase; InterPro: IPR000623 Shikimate kinase (2.7.1.71 from EC) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) []. The enzyme catalyses the following reaction: ATP + shikimate = ADP + shikimate-3-phosphate The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship []. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [].; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 3VAA_C 1KO8_B 1KO4_B 1KO1_A 1KOF_A 1KNQ_A 1KO5_A 1KAG_A 2PT5_D 1SHK_A ....
Probab=31.98 E-value=75 Score=23.88 Aligned_cols=45 Identities=22% Similarity=0.265 Sum_probs=28.3
Q ss_pred HHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCC
Q 028588 6 ESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDI 55 (207)
Q Consensus 6 ~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~ 55 (207)
++++.++.. +...|..||.....-.....+.+. --+||+|+.++.
T Consensus 53 ~~l~~l~~~-~~~VIa~GGG~~~~~~~~~~L~~~----g~vI~L~~~~~~ 97 (158)
T PF01202_consen 53 EALRELLKE-NNCVIACGGGIVLKEENRELLKEN----GLVIYLDADPEE 97 (158)
T ss_dssp HHHHHHHCS-SSEEEEE-TTGGGSHHHHHHHHHH----SEEEEEE--HHH
T ss_pred HHHHHHhcc-CcEEEeCCCCCcCcHHHHHHHHhC----CEEEEEeCCHHH
Confidence 456666664 356888899877777766666633 238999876653
No 56
>PRK01222 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=31.67 E-value=87 Score=25.11 Aligned_cols=32 Identities=28% Similarity=0.384 Sum_probs=24.3
Q ss_pred CCCCCCCCHHHHHHHHHhhcCCeeEEEEe---eecCC
Q 028588 149 HIEPGGLSFRDVLNILHNLQADVVAADVV---EFNPQ 182 (207)
Q Consensus 149 ~p~pgGl~~~e~~~~l~~i~~~vvg~di~---E~~P~ 182 (207)
..-.||++++.+..+++.+ +..|+|+. |..|.
T Consensus 157 ~~LAGGi~peNv~~ai~~~--~p~gvDvsSgvE~~~G 191 (210)
T PRK01222 157 WILAGGLNPDNVAEAIRQV--RPYGVDVSSGVESAPG 191 (210)
T ss_pred EEEECCCCHHHHHHHHHhc--CCCEEEecCceECCCC
Confidence 3467999999999998754 56789986 65554
No 57
>PRK13337 putative lipid kinase; Reviewed
Probab=31.50 E-value=1.1e+02 Score=25.87 Aligned_cols=42 Identities=19% Similarity=0.233 Sum_probs=23.9
Q ss_pred HHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHh-cCCCeEEE
Q 028588 5 TESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEK-LGGPVDVL 47 (207)
Q Consensus 5 ~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~-~~~~~~vI 47 (207)
++.++++.+++....+++|||-++.-.+ .++... .+.++++|
T Consensus 47 ~~~a~~~~~~~~d~vvv~GGDGTl~~vv-~gl~~~~~~~~lgii 89 (304)
T PRK13337 47 TLAAERAVERKFDLVIAAGGDGTLNEVV-NGIAEKENRPKLGII 89 (304)
T ss_pred HHHHHHHHhcCCCEEEEEcCCCHHHHHH-HHHhhCCCCCcEEEE
Confidence 4445555554446789999998875443 444322 11246654
No 58
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=31.43 E-value=64 Score=22.70 Aligned_cols=28 Identities=29% Similarity=0.576 Sum_probs=15.9
Q ss_pred HHHHHHHHHhcCCcceEEEcCCccchHH
Q 028588 4 ITESVKLVMEEDPLHPLVLGGDHSISFP 31 (207)
Q Consensus 4 i~~~v~~~~~~~~~~pi~iGGdhs~s~~ 31 (207)
..+.++.+.+..+..++++||-|....+
T Consensus 68 ~~~l~~~~k~~~p~~~iv~GG~~~t~~~ 95 (121)
T PF02310_consen 68 AKRLARAIKERNPNIPIVVGGPHATADP 95 (121)
T ss_dssp HHHHHHHHHTTCTTSEEEEEESSSGHHH
T ss_pred HHHHHHHHHhcCCCCEEEEECCchhcCh
Confidence 3444445444445567888887754444
No 59
>PF04951 Peptidase_M55: D-aminopeptidase; InterPro: IPR007035 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M55 (DppA aminopeptidase family, clan MN). The type example is Bacillus subtilis DppA, which is a binuclear zinc-dependent, D-specific aminopeptidase. The structure reveals that DppA is a new example of a self-compartmentalising protease, a family of proteolytic complexes. Proteasomes are the most extensively studied representatives of this family. The DppA enzyme is composed of identical 30 kDa subunits organised in a decamer with 52 point-group symmetry. A 20 A wide channel runs through the complex, giving access to a central chamber holding the active sites. The structure shows DppA to be a prototype of a new family of metalloaminopeptidases characterised by the SXDXEG key sequence []. The only known substrates are D-ala-D-ala and D-ala-gly-gly.; PDB: 1HI9_A.
Probab=31.38 E-value=58 Score=27.40 Aligned_cols=35 Identities=20% Similarity=0.409 Sum_probs=20.7
Q ss_pred eEEEEEeccCCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q 028588 129 GVYISVDVDCLDPAFAPGVSHIEPGGLSFRDVLNILH 165 (207)
Q Consensus 129 ~vylsiDiDvldp~~~pg~~~p~pgGl~~~e~~~~l~ 165 (207)
+||||.|+..+.--..+ ..-.||+..+++..+++.
T Consensus 2 KvyISaDmEGiaGv~~~--~q~~~~~~~Y~~~R~~mt 36 (265)
T PF04951_consen 2 KVYISADMEGIAGVVSW--EQTSPGNPEYERARRLMT 36 (265)
T ss_dssp EEEEEE-STTSTT--SG--GGT-TTSTTHHHHHHHHH
T ss_pred eEEEEECCCCCCCCCCH--HHcCCCchHHHHHHHHHH
Confidence 69999999997532222 123457887777666653
No 60
>PRK11914 diacylglycerol kinase; Reviewed
Probab=31.33 E-value=89 Score=26.31 Aligned_cols=42 Identities=19% Similarity=0.315 Sum_probs=24.7
Q ss_pred HHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCCCeEEEE
Q 028588 5 TESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLH 48 (207)
Q Consensus 5 ~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~ 48 (207)
++.++++.+++....|++|||-++.-. +.++... +-++++|=
T Consensus 54 ~~~a~~~~~~~~d~vvv~GGDGTi~ev-v~~l~~~-~~~lgiiP 95 (306)
T PRK11914 54 RHLVAAALAKGTDALVVVGGDGVISNA-LQVLAGT-DIPLGIIP 95 (306)
T ss_pred HHHHHHHHhcCCCEEEEECCchHHHHH-hHHhccC-CCcEEEEe
Confidence 344445555444678999999888743 4455432 23566653
No 61
>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=31.25 E-value=1.5e+02 Score=23.98 Aligned_cols=12 Identities=25% Similarity=0.434 Sum_probs=6.8
Q ss_pred CcEEEEcccCCC
Q 028588 80 RRLLQVGIRSIT 91 (207)
Q Consensus 80 ~~vv~iG~r~~~ 91 (207)
+++..+|.-+..
T Consensus 221 ~di~vig~d~~~ 232 (289)
T cd01540 221 ADVIGVGINGSD 232 (289)
T ss_pred cceEEEecCCch
Confidence 456666665543
No 62
>PLN02840 tRNA dimethylallyltransferase
Probab=31.24 E-value=45 Score=29.99 Aligned_cols=33 Identities=15% Similarity=0.080 Sum_probs=24.4
Q ss_pred hHHHHHHHHHhcCCcceEEEcCCccchHHHHHHH
Q 028588 3 VITESVKLVMEEDPLHPLVLGGDHSISFPVIRAV 36 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~ 36 (207)
....+++.+.++ |..||++||-+.---+.+.++
T Consensus 98 ~A~~~I~~i~~r-gkiPIvVGGTGlYl~aLl~G~ 130 (421)
T PLN02840 98 DARRATQDILNR-GRVPIVAGGTGLYLRWYIYGK 130 (421)
T ss_pred HHHHHHHHHHhc-CCCEEEEcCccHHHHHHhcCC
Confidence 456778888886 789999999776655555543
No 63
>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=30.59 E-value=1.7e+02 Score=23.26 Aligned_cols=19 Identities=21% Similarity=0.431 Sum_probs=8.0
Q ss_pred EEEcCCccchHHHHHHHHH
Q 028588 20 LVLGGDHSISFPVIRAVSE 38 (207)
Q Consensus 20 i~iGGdhs~s~~~~~~~~~ 38 (207)
.+++++=..+.++++++.+
T Consensus 181 ai~~~~d~~a~~~~~~l~~ 199 (270)
T cd06296 181 AIFAGNDLMALGVYEAARE 199 (270)
T ss_pred EEEEcCcHHHHHHHHHHHH
Confidence 3333333334444444443
No 64
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=30.50 E-value=61 Score=23.66 Aligned_cols=38 Identities=11% Similarity=0.155 Sum_probs=22.1
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCcc-chHHHHHHHHHhc
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHS-ISFPVIRAVSEKL 40 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs-~s~~~~~~~~~~~ 40 (207)
+|+..+++.+ .++....++||+||- ++...+....+..
T Consensus 47 ~Rm~~a~~~~-~~g~~~vvliGsD~P~l~~~~l~~A~~~L 85 (122)
T PF09837_consen 47 ERMANAFQQA-ARGYEPVVLIGSDCPDLTPDDLEQAFEAL 85 (122)
T ss_dssp HHHHHHHHHH-HTT-SEEEEE-SS-TT--HHHHHHHHHHT
T ss_pred HHHHHHHHHH-HcCCCcEEEEcCCCCCCCHHHHHHHHHHh
Confidence 4677788888 444567888999964 4666665554443
No 65
>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=30.20 E-value=1.7e+02 Score=23.03 Aligned_cols=9 Identities=11% Similarity=0.324 Sum_probs=4.7
Q ss_pred CcEEEEccc
Q 028588 80 RRLLQVGIR 88 (207)
Q Consensus 80 ~~vv~iG~r 88 (207)
+++..+|..
T Consensus 203 ~di~i~~~d 211 (266)
T cd06278 203 EDVSVIGFD 211 (266)
T ss_pred cceEEEEeC
Confidence 455555553
No 66
>cd06828 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase. Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=30.08 E-value=3.6e+02 Score=23.16 Aligned_cols=107 Identities=14% Similarity=0.173 Sum_probs=60.5
Q ss_pred HHHHHHhcCC-CCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCC---C
Q 028588 69 SFARIMEGGY-ARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAF---A 144 (207)
Q Consensus 69 ~~~~~~~~~~-~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~---~ 144 (207)
-+..+.+.|. +.+++..|. ...+++.+.+-++|+..+..+....-..+.+..+.....-++.+-+..+.-.... .
T Consensus 61 E~~~~~~~G~~~~~I~~~~p-~k~~~~l~~a~~~g~~~~~ids~~el~~l~~~a~~~~~~~~v~lRv~~~~~~~~~~~~~ 139 (373)
T cd06828 61 ELYRALKAGFPPERIVFTGN-GKSDEELELALELGILRINVDSLSELERLGEIAPELGKGAPVALRVNPGVDAGTHPYIS 139 (373)
T ss_pred HHHHHHHcCCCcccEEEeCC-CCCHHHHHHHHHcCCeEEEECCHHHHHHHHHHHHhcCCCCeEEEEECCCCCCCCCCCee
Confidence 3445555443 357776665 3456778888888866666655443322222221111124577777665432211 1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhc--C--CeeEEEEe
Q 028588 145 PGVSHIEPGGLSFRDVLNILHNLQ--A--DVVAADVV 177 (207)
Q Consensus 145 pg~~~p~pgGl~~~e~~~~l~~i~--~--~vvg~di~ 177 (207)
.| ..+...|+++.|+.++++.+. . +++|+..-
T Consensus 140 ~g-~~~srfGi~~~e~~~~~~~~~~~~~l~l~Gi~~H 175 (373)
T cd06828 140 TG-GKDSKFGIPLEQALEAYRRAKELPGLKLVGLHCH 175 (373)
T ss_pred cC-CCCCCCCCCHHHHHHHHHHHHhCCCCcEEEEEEe
Confidence 11 234678999999999888773 2 67777764
No 67
>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=30.00 E-value=1.6e+02 Score=23.33 Aligned_cols=12 Identities=25% Similarity=0.537 Sum_probs=6.7
Q ss_pred CCcEEEEcccCC
Q 028588 79 ARRLLQVGIRSI 90 (207)
Q Consensus 79 ~~~vv~iG~r~~ 90 (207)
++++..+|....
T Consensus 205 p~di~iig~d~~ 216 (268)
T cd06289 205 GRDIAVVGFDDV 216 (268)
T ss_pred CcceEEEeecCc
Confidence 356666666543
No 68
>COG3365 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.73 E-value=97 Score=22.39 Aligned_cols=33 Identities=15% Similarity=0.434 Sum_probs=26.1
Q ss_pred CCCCCHHHHHHHHHhh----c-CCeeEEEEeeecCCCC
Q 028588 152 PGGLSFRDVLNILHNL----Q-ADVVAADVVEFNPQRD 184 (207)
Q Consensus 152 pgGl~~~e~~~~l~~i----~-~~vvg~di~E~~P~~d 184 (207)
.+||+|.|..++++.- . .+..|+||.-|-|.-+
T Consensus 39 E~gL~P~eeaklIe~TM~eId~e~F~GIei~s~p~~~~ 76 (118)
T COG3365 39 EGGLTPEEEAKLIEMTMSEIDPENFSGIEIYSYPPKED 76 (118)
T ss_pred eCCCChHHHHHHHHHHHHhcCcccccceEEEEeCCccc
Confidence 4799999999998753 2 4899999988877633
No 69
>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional
Probab=29.63 E-value=48 Score=28.35 Aligned_cols=33 Identities=12% Similarity=0.125 Sum_probs=23.6
Q ss_pred hHHHHHHHHHhcCCcceEEEcCCccchHHHHHHH
Q 028588 3 VITESVKLVMEEDPLHPLVLGGDHSISFPVIRAV 36 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~ 36 (207)
...+.++.+.++ |..||+.||-+----+.+.++
T Consensus 80 ~a~~~i~~i~~~-gk~PilvGGTglYi~all~gl 112 (300)
T PRK14729 80 EALKIIKELRQQ-KKIPIFVGGSAFYFKHLKYGL 112 (300)
T ss_pred HHHHHHHHHHHC-CCCEEEEeCchHHHHHHHcCC
Confidence 345667777775 689999999776655555443
No 70
>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=29.31 E-value=1.5e+02 Score=23.97 Aligned_cols=8 Identities=38% Similarity=0.480 Sum_probs=3.8
Q ss_pred CcEEEEcc
Q 028588 80 RRLLQVGI 87 (207)
Q Consensus 80 ~~vv~iG~ 87 (207)
+++..+|.
T Consensus 223 ~di~vig~ 230 (283)
T cd06279 223 EDLSVVGF 230 (283)
T ss_pred CceEEeee
Confidence 44444444
No 71
>PRK14340 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=29.30 E-value=4.3e+02 Score=23.81 Aligned_cols=149 Identities=14% Similarity=0.174 Sum_probs=72.2
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHH----------HHHHHHHhcCCCeEEEEEccCCCCCCCCCCCccCCccHHH
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFP----------VIRAVSEKLGGPVDVLHLDAHPDIYDAFEGNKYSHASSFA 71 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~----------~~~~~~~~~~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~ 71 (207)
+.+-+.++.+.++ |..=|++-|.+..+|+ .++.+.+. .+...+-|.-+|++.-+ .-.+.
T Consensus 181 e~Vv~Ei~~l~~~-G~~ei~l~~~~~~~y~d~~~~~~l~~Ll~~l~~~-~~~~rir~~~~~p~~l~---------~ell~ 249 (445)
T PRK14340 181 ASVLDEVRALAEA-GYREITLLGQNVNSYSDPEAGADFAGLLDAVSRA-APEMRIRFTTSHPKDIS---------ESLVR 249 (445)
T ss_pred HHHHHHHHHHHHC-CCeEEEEeecccchhhccCCCchHHHHHHHHhhc-CCCcEEEEccCChhhcC---------HHHHH
Confidence 3455566666664 5666766665555554 22333221 12333333334544321 11233
Q ss_pred HHHhcCCCCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCCCC
Q 028588 72 RIMEGGYARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHIE 151 (207)
Q Consensus 72 ~~~~~~~~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~ 151 (207)
.+.+.+..-+.+++|+++.++...+.+++. ++.+++ .+.++.++.. ...+.++.|+ + +|.|.
T Consensus 250 ~~~~~~~g~~~l~iglQSgsd~vLk~m~R~----~t~~~~---~~~v~~lr~~--~pgi~i~td~--I-------vGfPg 311 (445)
T PRK14340 250 TIAARPNICNHIHLPVQSGSSRMLRRMNRG----HTIEEY---LEKIALIRSA--IPGVTLSTDL--I-------AGFCG 311 (445)
T ss_pred HHHhCCCCCCeEEECCCcCCHHHHHhcCCC----CCHHHH---HHHHHHHHHh--CCCCEEeccE--E-------EECCC
Confidence 333333345789999999998877765432 233322 2345555411 1235555554 2 24453
Q ss_pred CCCCCHHHHHHHHHhhcC-CeeEEEEeeecCC
Q 028588 152 PGGLSFRDVLNILHNLQA-DVVAADVVEFNPQ 182 (207)
Q Consensus 152 pgGl~~~e~~~~l~~i~~-~vvg~di~E~~P~ 182 (207)
. |.+++.+.++.+.. ++-.+.+.-|+|.
T Consensus 312 E---T~edf~~tl~~~~~~~~~~~~~f~~sp~ 340 (445)
T PRK14340 312 E---TEEDHRATLSLMEEVRFDSAFMFYYSVR 340 (445)
T ss_pred C---CHHHHHHHHHHHHhcCCCEEeeEEecCC
Confidence 3 55555555544421 3334455556664
No 72
>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=29.22 E-value=2e+02 Score=23.03 Aligned_cols=16 Identities=19% Similarity=0.219 Sum_probs=10.3
Q ss_pred hcCCCCcEEEEcccCC
Q 028588 75 EGGYARRLLQVGIRSI 90 (207)
Q Consensus 75 ~~~~~~~vv~iG~r~~ 90 (207)
+.+..+++..+|.-..
T Consensus 200 ~~g~~~di~vig~d~~ 215 (271)
T cd06314 200 AAGKLGKVKIVGFDED 215 (271)
T ss_pred HcCCCCceEEEEeCCC
Confidence 3343367888898664
No 73
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=29.02 E-value=1.5e+02 Score=24.98 Aligned_cols=12 Identities=8% Similarity=0.357 Sum_probs=7.0
Q ss_pred CCcEEEEcccCC
Q 028588 79 ARRLLQVGIRSI 90 (207)
Q Consensus 79 ~~~vv~iG~r~~ 90 (207)
|+++..+|.-+.
T Consensus 264 P~disVigfD~~ 275 (343)
T PRK10727 264 PGEISLIGFDDV 275 (343)
T ss_pred CcceeEEeecCc
Confidence 456666666543
No 74
>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=29.01 E-value=1.6e+02 Score=23.44 Aligned_cols=12 Identities=8% Similarity=0.340 Sum_probs=6.6
Q ss_pred CCcEEEEcccCC
Q 028588 79 ARRLLQVGIRSI 90 (207)
Q Consensus 79 ~~~vv~iG~r~~ 90 (207)
|.++..+|.-..
T Consensus 203 p~di~vi~~d~~ 214 (265)
T cd06290 203 PEDVSLIGFDDL 214 (265)
T ss_pred CcceEEeeecCc
Confidence 456666666543
No 75
>PLN02363 phosphoribosylanthranilate isomerase
Probab=28.80 E-value=93 Score=25.93 Aligned_cols=31 Identities=23% Similarity=0.191 Sum_probs=23.9
Q ss_pred CCCCCCCHHHHHHHHHhhcCCeeEEEEe---eecCC
Q 028588 150 IEPGGLSFRDVLNILHNLQADVVAADVV---EFNPQ 182 (207)
Q Consensus 150 p~pgGl~~~e~~~~l~~i~~~vvg~di~---E~~P~ 182 (207)
.-.|||+++.+..+++.+ +..|+|+. |-.|.
T Consensus 203 iLAGGL~peNV~~ai~~~--~P~GVDVsSGVE~~pG 236 (256)
T PLN02363 203 LLAGGLTPENVHEAVSLL--KPTGVDVSSGICGPDG 236 (256)
T ss_pred EEECCCCHHHHHHHHHhc--CCcEEEeCCcccCCCC
Confidence 467999999999998754 56799986 55555
No 76
>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=28.52 E-value=1.7e+02 Score=24.12 Aligned_cols=28 Identities=18% Similarity=0.026 Sum_probs=16.0
Q ss_pred CCcEEEEcccCCChhHHHHHHHcCceEEE
Q 028588 79 ARRLLQVGIRSITKEGREQGKRFGVEQYE 107 (207)
Q Consensus 79 ~~~vv~iG~r~~~~~~~~~~~~~~~~~~~ 107 (207)
++++..+|.-.. +.....+..-.++.+.
T Consensus 229 p~di~vig~D~~-~~~~~~~~~~~lttv~ 256 (305)
T cd06324 229 GRDVLFGGVNWS-PEALRAIKDGRLSVSA 256 (305)
T ss_pred CCCEEEEecCCC-HHHHHHHHcCceEEEe
Confidence 578888888654 4434444444455444
No 77
>TIGR00174 miaA tRNA isopentenyltransferase (miaA). Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.
Probab=28.40 E-value=50 Score=28.05 Aligned_cols=33 Identities=12% Similarity=0.242 Sum_probs=24.0
Q ss_pred hHHHHHHHHHhcCCcceEEEcCCccchHHHHHHH
Q 028588 3 VITESVKLVMEEDPLHPLVLGGDHSISFPVIRAV 36 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~ 36 (207)
...+.++.+.++ |..||+.||-+..--+.+.++
T Consensus 76 ~a~~~i~~~~~~-g~~pi~vGGTg~Yi~all~g~ 108 (287)
T TIGR00174 76 LALNAIADITAR-GKIPLLVGGTGLYLKALLEGL 108 (287)
T ss_pred HHHHHHHHHHhC-CCCEEEEcCcHHHHHHHHcCC
Confidence 355677888886 689999999776665555544
No 78
>cd08663 DAP_dppA_1 Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacteriz
Probab=28.37 E-value=80 Score=26.56 Aligned_cols=31 Identities=29% Similarity=0.638 Sum_probs=20.7
Q ss_pred eEEEEEeccCCCCCCCCCCCCC---CCCCCCHHHHHHHH
Q 028588 129 GVYISVDVDCLDPAFAPGVSHI---EPGGLSFRDVLNIL 164 (207)
Q Consensus 129 ~vylsiDiDvldp~~~pg~~~p---~pgGl~~~e~~~~l 164 (207)
++|||.||..+. |+..| .|++..++...+++
T Consensus 2 KiyISaDmEGia-----Gv~~~~~~~~~~~~Y~r~r~~m 35 (266)
T cd08663 2 KIYISADMEGVT-----GVVSPEQVRPGGREYERARRLM 35 (266)
T ss_pred eEEEEecCCCCC-----CCCCHHHhCCCchHHHHHHHHH
Confidence 699999999875 44444 46766665544433
No 79
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=28.12 E-value=1.6e+02 Score=24.39 Aligned_cols=12 Identities=17% Similarity=0.412 Sum_probs=7.5
Q ss_pred CCcEEEEcccCC
Q 028588 79 ARRLLQVGIRSI 90 (207)
Q Consensus 79 ~~~vv~iG~r~~ 90 (207)
|+++..+|....
T Consensus 262 P~dvsvigfd~~ 273 (327)
T PRK10423 262 PQDIAVIGYDDI 273 (327)
T ss_pred CCceEEEEeCCh
Confidence 566767776553
No 80
>PF14529 Exo_endo_phos_2: Endonuclease-reverse transcriptase ; PDB: 2EI9_A 1WDU_B.
Probab=28.07 E-value=53 Score=22.79 Aligned_cols=23 Identities=22% Similarity=0.639 Sum_probs=16.5
Q ss_pred hHHHHHHHHHhcCCcceEEEcCC
Q 028588 3 VITESVKLVMEEDPLHPLVLGGD 25 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGd 25 (207)
...+.++.+++..+..+++||||
T Consensus 16 ~~~~~l~~~~~~~~~~~~Ii~GD 38 (119)
T PF14529_consen 16 EFFDQLRQLLKNLPPAPIIIGGD 38 (119)
T ss_dssp HHHHHHHHHHHCCTTSSEEEEEE
T ss_pred HHHHHHHHHHHhCCCCCEEEEeE
Confidence 45677788887543338999998
No 81
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=28.07 E-value=1.8e+02 Score=24.28 Aligned_cols=11 Identities=9% Similarity=0.314 Sum_probs=5.8
Q ss_pred CCcEEEEcccC
Q 028588 79 ARRLLQVGIRS 89 (207)
Q Consensus 79 ~~~vv~iG~r~ 89 (207)
|+++..+|.-.
T Consensus 266 p~dv~vvgfD~ 276 (341)
T PRK10703 266 PQDISVIGYDN 276 (341)
T ss_pred CCceEEEEECC
Confidence 45555555543
No 82
>PRK06849 hypothetical protein; Provisional
Probab=27.98 E-value=88 Score=27.28 Aligned_cols=36 Identities=14% Similarity=0.133 Sum_probs=29.7
Q ss_pred CcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCC
Q 028588 16 PLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPD 54 (207)
Q Consensus 16 ~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D 54 (207)
+...+++||++..+++.++++.+. ...++-+|.+.+
T Consensus 4 ~~~VLI~G~~~~~~l~iar~l~~~---G~~Vi~~d~~~~ 39 (389)
T PRK06849 4 KKTVLITGARAPAALELARLFHNA---GHTVILADSLKY 39 (389)
T ss_pred CCEEEEeCCCcHHHHHHHHHHHHC---CCEEEEEeCCch
Confidence 467899999999999999999875 356788888754
No 83
>cd08770 DAP_dppA_3 Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacteriz
Probab=27.89 E-value=93 Score=26.13 Aligned_cols=29 Identities=31% Similarity=0.613 Sum_probs=19.2
Q ss_pred eEEEEEeccCCCCCCCCCCCCC---CCCCCCHHHHHH
Q 028588 129 GVYISVDVDCLDPAFAPGVSHI---EPGGLSFRDVLN 162 (207)
Q Consensus 129 ~vylsiDiDvldp~~~pg~~~p---~pgGl~~~e~~~ 162 (207)
++|||.|+..+. |+..| .|++..++...+
T Consensus 2 KiyISaDiEGia-----GV~~~~~~~~~~~~Y~r~r~ 33 (263)
T cd08770 2 KVYISADIEGIA-----GISSWDETTLGGPDYEEFRE 33 (263)
T ss_pred eEEEEeCCCCCC-----CCCChHHcCCCCchHHHHHH
Confidence 699999999875 44444 456666644444
No 84
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=27.40 E-value=1.7e+02 Score=24.62 Aligned_cols=11 Identities=18% Similarity=0.292 Sum_probs=5.2
Q ss_pred CCcEEEEcccC
Q 028588 79 ARRLLQVGIRS 89 (207)
Q Consensus 79 ~~~vv~iG~r~ 89 (207)
|+++..+|.-+
T Consensus 264 P~disvigfD~ 274 (346)
T PRK10401 264 PLHLSIIGFDD 274 (346)
T ss_pred CCceEEEEeCC
Confidence 34555555543
No 85
>cd03377 TPP_PFOR_PNO Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This subfamily also includes proteins characterized as pyruvate NADP+ oxidoreductase (PNO). These enzymes are dependent on TPP and a divalent metal cation as cofactors. PFOR and PNO catalyze the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The PFOR from cyanobacterium Anabaena (NifJ) is required for the transfer of electrons from pyruvate to flavodoxin, which reduces nitrogenase. The facultative anaerobic mitochondrion of the photosynthetic protist Euglena gra
Probab=27.29 E-value=4.4e+02 Score=23.32 Aligned_cols=84 Identities=20% Similarity=0.254 Sum_probs=45.9
Q ss_pred ceEEEcCCc---cchHHHHHHHHHhcCCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCCCCcEEEEcccCCChhH
Q 028588 18 HPLVLGGDH---SISFPVIRAVSEKLGGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGYARRLLQVGIRSITKEG 94 (207)
Q Consensus 18 ~pi~iGGdh---s~s~~~~~~~~~~~~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~~~~vv~iG~r~~~~~~ 94 (207)
..+++|||- +|-++-+..+.++ +.++.+|.+|.-.=.++ |...+..+|....... ...|-.....+-
T Consensus 153 ~v~v~gGDG~~ydIG~~~l~ha~~r-~~ni~~iv~DNe~Y~nT---GgQ~S~tTp~Ga~t~t------sp~Gk~~~kkd~ 222 (365)
T cd03377 153 SVWIIGGDGWAYDIGYGGLDHVLAS-GENVNILVLDTEVYSNT---GGQASKATPLGAVAKF------AAAGKRTGKKDL 222 (365)
T ss_pred ceEEEecchhhhccchhhHHHHHHc-CCCeEEEEECCcccccC---CCcCCCCCCCcCcCcc------CCCCCCCCCcCH
Confidence 589999995 5666666655555 35899999997665444 2223344444333221 112333322233
Q ss_pred HHHHHHcCceEEEcccc
Q 028588 95 REQGKRFGVEQYEMRTF 111 (207)
Q Consensus 95 ~~~~~~~~~~~~~~~~~ 111 (207)
...+..+|..++-...+
T Consensus 223 ~~ia~a~g~~YVA~~s~ 239 (365)
T cd03377 223 GMIAMSYGNVYVAQIAL 239 (365)
T ss_pred HHHHHHcCCCEEEEEec
Confidence 34455667766543333
No 86
>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=27.23 E-value=2e+02 Score=22.76 Aligned_cols=12 Identities=8% Similarity=0.166 Sum_probs=7.3
Q ss_pred CCcEEEEcccCC
Q 028588 79 ARRLLQVGIRSI 90 (207)
Q Consensus 79 ~~~vv~iG~r~~ 90 (207)
++++..+|.-..
T Consensus 199 p~dv~vvg~d~~ 210 (261)
T cd06272 199 PEDIEIISYDNI 210 (261)
T ss_pred CCceEEEeeCCh
Confidence 566666666553
No 87
>PLN02537 diaminopimelate decarboxylase
Probab=26.98 E-value=4.4e+02 Score=23.19 Aligned_cols=106 Identities=15% Similarity=0.176 Sum_probs=59.4
Q ss_pred HHHHHHhcCC-CCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCCCCC-
Q 028588 69 SFARIMEGGY-ARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAPG- 146 (207)
Q Consensus 69 ~~~~~~~~~~-~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg- 146 (207)
-++.++..|. +.+++.-|. ..++++.+.+.++|+. +..+++...+.+.+..+.....-+|+|-+|.++ ++...+.
T Consensus 76 E~~~al~~G~~~~~ii~~g~-~k~~~~l~~a~~~gv~-i~ids~~el~~l~~~a~~~~~~~~v~lRvnp~~-~~~~~~~i 152 (410)
T PLN02537 76 ELRLALRAGFDPTRCIFNGN-GKLLEDLVLAAQEGVF-VNVDSEFDLENIVEAARIAGKKVNVLLRINPDV-DPQVHPYV 152 (410)
T ss_pred HHHHHHHcCCCcceEEEECC-CCCHHHHHHHHHCCCE-EEECCHHHHHHHHHHHHhcCCCceEEEEECCCC-CCCCCCcc
Confidence 3444445443 355655543 3467788888899985 666655433222221111112246888888664 3332221
Q ss_pred -CC-CCCCCCCCHHHHHHHHHhhc----C-CeeEEEEe
Q 028588 147 -VS-HIEPGGLSFRDVLNILHNLQ----A-DVVAADVV 177 (207)
Q Consensus 147 -~~-~p~pgGl~~~e~~~~l~~i~----~-~vvg~di~ 177 (207)
|+ .....|+++.++.++++.+. . +++|+..-
T Consensus 153 ~tG~~~sRfGi~~~~~~~~~~~~~~~~~~l~l~Glh~H 190 (410)
T PLN02537 153 ATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCH 190 (410)
T ss_pred ccCCCCCCCCCCHHHHHHHHHHHHhCCCCCcEEEEEec
Confidence 22 23678999999888887762 2 46666553
No 88
>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=26.95 E-value=1.9e+02 Score=22.99 Aligned_cols=9 Identities=22% Similarity=0.390 Sum_probs=4.6
Q ss_pred CCcEEEEcc
Q 028588 79 ARRLLQVGI 87 (207)
Q Consensus 79 ~~~vv~iG~ 87 (207)
|+++..+|.
T Consensus 205 p~di~vvg~ 213 (269)
T cd06275 205 PQDLSIIGY 213 (269)
T ss_pred CcceEEEEe
Confidence 345555555
No 89
>PF08013 Tagatose_6_P_K: Tagatose 6 phosphate kinase; InterPro: IPR012062 Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also called agaY, agaZ). The catalytic subunits GatY/KbaY alone are sufficient to show aldolase activity and contain most or all of the residues that have been identified as essential in substrate/product recognition and catalysis for class II aldolases [, ]. However, these aldolases differ from other Class II aldolases (which are homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits alone do not show any aldolase activity []. It should be noted that the previous suggestion of a tagatose 6P-kinase function for AgaZ [] and other members of this family turned out to be erroneous [, ].; GO: 0019402 galactitol metabolic process; PDB: 2FIQ_A 3TXV_A.
Probab=26.69 E-value=1.4e+02 Score=26.91 Aligned_cols=87 Identities=17% Similarity=0.219 Sum_probs=38.3
Q ss_pred HHHHHHHHHhcCCcc--eEEEcCCccc-----hHHHHHHHHH------hc-CCCeEEEEEccCCCCCCCCCCCccCCccH
Q 028588 4 ITESVKLVMEEDPLH--PLVLGGDHSI-----SFPVIRAVSE------KL-GGPVDVLHLDAHPDIYDAFEGNKYSHASS 69 (207)
Q Consensus 4 i~~~v~~~~~~~~~~--pi~iGGdhs~-----s~~~~~~~~~------~~-~~~~~vI~~DAH~D~~~~~~g~~~~~g~~ 69 (207)
..+-|..+.++-|.- .+++||||-= ..+.=.||.. .| ...+..||+|+-.++..+. ..+.-...
T Consensus 67 F~~~V~~iA~~~g~~~~~iiLGGDHLGP~~w~~lpaeeAM~~A~~li~ayv~AGF~KIHLD~Sm~ca~d~--~~L~d~~v 144 (424)
T PF08013_consen 67 FRDFVREIADEVGFPRDRIILGGDHLGPNPWQHLPAEEAMAKAKELIRAYVEAGFTKIHLDCSMDCAGDP--KPLPDETV 144 (424)
T ss_dssp HHHHHHHHHHHCT--GGGEEEEEEEESSCCCTTSBHHHHHHHHHHHHHHHHCTT--EEEE---C--CTS---SC--HHHH
T ss_pred HHHHHHHHHHHcCCchhhEEecCCCCCcccccCCCHHHHHHHHHHHHHHHHHcCCceEeecCCCCCCCCC--CCCChHHH
Confidence 455677777755432 4899999952 1222233322 11 3468899999999886543 33344455
Q ss_pred HHHHHhc------C-----CCCcEEEEcccCCCh
Q 028588 70 FARIMEG------G-----YARRLLQVGIRSITK 92 (207)
Q Consensus 70 ~~~~~~~------~-----~~~~vv~iG~r~~~~ 92 (207)
..|..++ . ...-+..||.--..|
T Consensus 145 A~Raa~L~~~aE~~~~~~~~~~pvYvIGTEVPvP 178 (424)
T PF08013_consen 145 AERAARLCEVAEEAAKRRGGPPPVYVIGTEVPVP 178 (424)
T ss_dssp HHHHHHHHHHHHCCS-HHHHHH-EEEEE-SS---
T ss_pred HHHHHHHHHHHHHHHHhcCCCCceEEeCCccCCC
Confidence 5554432 1 123467777654433
No 90
>PRK14338 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=26.59 E-value=4.8e+02 Score=23.53 Aligned_cols=150 Identities=15% Similarity=0.232 Sum_probs=73.4
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHH-------HHHHHHHhcCCCeEE--E-EEccCCCCCCCCCCCccCCccHHH
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFP-------VIRAVSEKLGGPVDV--L-HLDAHPDIYDAFEGNKYSHASSFA 71 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~-------~~~~~~~~~~~~~~v--I-~~DAH~D~~~~~~g~~~~~g~~~~ 71 (207)
+.+-+.++.+.++ |..-|++.|++..+|+ .+..+.+......++ | |.-.|++.-+ ...+.
T Consensus 187 e~Il~ei~~l~~~-G~keI~l~g~~~~~yG~d~~~~~~l~~Ll~~l~~~~gi~~ir~~~~~p~~i~---------~ell~ 256 (459)
T PRK14338 187 AEIVEEVRRIAAR-GAKEITLLGQIVDSYGHDLPGRPDLADLLEAVHEIPGLERLRFLTSHPAWMT---------DRLIH 256 (459)
T ss_pred HHHHHHHHHHHHC-CCeEEEEeeecCCCcccccCChHHHHHHHHHHHhcCCcceEEEEecChhhcC---------HHHHH
Confidence 3455566677765 6677788776665553 133333322111122 1 2223443222 11233
Q ss_pred HHHhcCCCCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCCCC
Q 028588 72 RIMEGGYARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHIE 151 (207)
Q Consensus 72 ~~~~~~~~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~ 151 (207)
.+.+.+..-+.+++|+++.+++-.+.+++. ++.+++ .+.++.++.. ...+.++.|+ + +|.|
T Consensus 257 ~l~~~~~~~~~v~lglQSgsd~vLk~m~R~----~t~e~~---~~~i~~lr~~--~pgi~i~~d~--I-------vG~P- 317 (459)
T PRK14338 257 AVARLPKCCPHINLPVQAGDDEVLKRMRRG----YTVARY---RELIARIREA--IPDVSLTTDI--I-------VGHP- 317 (459)
T ss_pred HHhcccccccceecCcccCCHHHHHhccCC----CCHHHH---HHHHHHHHHh--CCCCEEEEEE--E-------EECC-
Confidence 333332234688999999998887766532 122222 2344444311 1234444443 3 2344
Q ss_pred CCCCCHHHHHHHHHhhcC-CeeEEEEeeecCC
Q 028588 152 PGGLSFRDVLNILHNLQA-DVVAADVVEFNPQ 182 (207)
Q Consensus 152 pgGl~~~e~~~~l~~i~~-~vvg~di~E~~P~ 182 (207)
|-|.+++.+.++.+.. ++-.+.+.-|.|.
T Consensus 318 --gET~ed~~~ti~~l~~l~~~~v~i~~ysp~ 347 (459)
T PRK14338 318 --GETEEQFQRTYDLLEEIRFDKVHIAAYSPR 347 (459)
T ss_pred --CCCHHHHHHHHHHHHHcCCCEeEEEecCCC
Confidence 4577777777666632 4444455556654
No 91
>cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand-binding domain of DNA transcription repressor GalR 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. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. 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 structurally homologous to the periplasmic sugar bindi
Probab=26.49 E-value=2e+02 Score=23.03 Aligned_cols=11 Identities=0% Similarity=0.120 Sum_probs=5.7
Q ss_pred CCcEEEEcccC
Q 028588 79 ARRLLQVGIRS 89 (207)
Q Consensus 79 ~~~vv~iG~r~ 89 (207)
|+++..+|...
T Consensus 206 p~di~v~g~d~ 216 (270)
T cd01544 206 PEDVSVISFND 216 (270)
T ss_pred CCceEEEEECC
Confidence 34555555544
No 92
>cd06841 PLPDE_III_MccE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE. This subfamily is composed of uncharacterized proteins with similarity to Escherichia coli MccE, a hypothetical protein that is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Most members of this subfamily share the same domain architecture as ODC and DapDC. A few members, including Escherichia coli MccE, contain an additional acetyltransferase domain at the C-terminus.
Probab=26.47 E-value=4.3e+02 Score=22.90 Aligned_cols=90 Identities=19% Similarity=0.171 Sum_probs=49.2
Q ss_pred HHHHHHhcCC-CCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCCCCCC
Q 028588 69 SFARIMEGGY-ARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAPGV 147 (207)
Q Consensus 69 ~~~~~~~~~~-~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~ 147 (207)
-+..+...|. +.+++.-|.- .++++.+.+-++|+ .+..+++..-+.+.+........-+++|-++.|.- .
T Consensus 67 E~~~~~~~G~~~~~Ii~~g~~-k~~~~l~~a~~~g~-~i~ids~~el~~l~~~~~~~~~~~~v~lRv~~~~g-------~ 137 (379)
T cd06841 67 EYELALKLGVPGKRIIFNGPY-KSKEELEKALEEGA-LINIDSFDELERILEIAKELGRVAKVGIRLNMNYG-------N 137 (379)
T ss_pred HHHHHHHcCCChHHEEEECCC-CCHHHHHHHHHCCC-EEEECCHHHHHHHHHHHHhcCCcceEEEEECCCCC-------C
Confidence 3444444443 3567766642 34577777888887 56565554332222211111112467888776531 1
Q ss_pred CCCCCCCCCHHHHHHHHHhh
Q 028588 148 SHIEPGGLSFRDVLNILHNL 167 (207)
Q Consensus 148 ~~p~pgGl~~~e~~~~l~~i 167 (207)
+.....|++..|+..+++.+
T Consensus 138 ~~~~rfGi~~~e~~~~~~~~ 157 (379)
T cd06841 138 NVWSRFGFDIEENGEALAAL 157 (379)
T ss_pred CCCCCCCCchhhhHHHHHHH
Confidence 14577899998875555443
No 93
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=26.30 E-value=2.4e+02 Score=19.89 Aligned_cols=43 Identities=12% Similarity=0.313 Sum_probs=26.8
Q ss_pred HHHHHHhcCCcceEEEcCCcc-chHHHHHHHHHhcCCCeEEEEE
Q 028588 7 SVKLVMEEDPLHPLVLGGDHS-ISFPVIRAVSEKLGGPVDVLHL 49 (207)
Q Consensus 7 ~v~~~~~~~~~~pi~iGGdhs-~s~~~~~~~~~~~~~~~~vI~~ 49 (207)
.++.+++.-+...+++=||-+ -..-++..+++++++++..|+|
T Consensus 54 ~i~~i~~~fP~~kfiLIGDsgq~DpeiY~~ia~~~P~~i~ai~I 97 (100)
T PF09949_consen 54 NIERILRDFPERKFILIGDSGQHDPEIYAEIARRFPGRILAIYI 97 (100)
T ss_pred HHHHHHHHCCCCcEEEEeeCCCcCHHHHHHHHHHCCCCEEEEEE
Confidence 445555544544445444422 2467777888888888887776
No 94
>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=26.30 E-value=2.2e+02 Score=22.50 Aligned_cols=13 Identities=23% Similarity=0.325 Sum_probs=8.5
Q ss_pred CCcEEEEcccCCC
Q 028588 79 ARRLLQVGIRSIT 91 (207)
Q Consensus 79 ~~~vv~iG~r~~~ 91 (207)
++++..+|.....
T Consensus 208 p~~i~iig~d~~~ 220 (268)
T cd06271 208 GRDVSVVGFDDSP 220 (268)
T ss_pred CcceeEEEecCch
Confidence 4677777776653
No 95
>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase. Note that the EC number for the kinase function is: 2.7.1.78
Probab=26.22 E-value=4.6e+02 Score=24.41 Aligned_cols=102 Identities=17% Similarity=0.116 Sum_probs=58.0
Q ss_pred hHHHHHHHHHhcCCcceEEEcCCcc-----chHHH----HHHHHHhcCCCeEEEEEccCCC-CCCCCCCCccCCccHHHH
Q 028588 3 VITESVKLVMEEDPLHPLVLGGDHS-----ISFPV----IRAVSEKLGGPVDVLHLDAHPD-IYDAFEGNKYSHASSFAR 72 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGdhs-----~s~~~----~~~~~~~~~~~~~vI~~DAH~D-~~~~~~g~~~~~g~~~~~ 72 (207)
.+.+.++.+.++ |...+++-.=-. .+... +..+.+..+-++.++. -.|.+ .+.| .-|||...
T Consensus 201 gV~e~L~~L~~~-Gy~IvIvTNQ~gI~~G~~~~~~~~~ki~~iL~~lgipfdvii-a~~~~~~RKP------~pGm~~~a 272 (526)
T TIGR01663 201 EIPEKLKELEAD-GFKICIFTNQGGIARGKINADDFKAKIEAIVAKLGVPFQVFI-AIGAGFYRKP------LTGMWDHL 272 (526)
T ss_pred CHHHHHHHHHHC-CCEEEEEECCcccccCcccHHHHHHHHHHHHHHcCCceEEEE-eCCCCCCCCC------CHHHHHHH
Confidence 456778888775 554444432111 22222 3333344444565443 33433 2333 35777765
Q ss_pred HHhcC-----CCCcEEEEcccC---------------CChhHHHHHHHcCceEEEccccc
Q 028588 73 IMEGG-----YARRLLQVGIRS---------------ITKEGREQGKRFGVEQYEMRTFS 112 (207)
Q Consensus 73 ~~~~~-----~~~~vv~iG~r~---------------~~~~~~~~~~~~~~~~~~~~~~~ 112 (207)
+-..+ ++++.+.||=+. ++..++.++...|+++++++++-
T Consensus 273 ~~~~~~~~~Id~~~S~~VGDaagr~~~g~~ag~~~~D~s~~D~~FA~n~gi~F~tPee~F 332 (526)
T TIGR01663 273 KEEANDGTEIQEDDCFFVGDAAGRPANGKAAGKKKKDFSCADRLFAANLGIPFATPEEFF 332 (526)
T ss_pred HHhcCcccCCCHHHeEEeCCcccchHHHHhcCCCcCCCChhhHHHHHHcCCcccChHHHh
Confidence 54432 356788888544 23457889999999999998764
No 96
>cd02065 B12-binding_like B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif.
Probab=26.07 E-value=79 Score=22.26 Aligned_cols=12 Identities=42% Similarity=0.894 Sum_probs=5.1
Q ss_pred ceEEEcCCccch
Q 028588 18 HPLVLGGDHSIS 29 (207)
Q Consensus 18 ~pi~iGGdhs~s 29 (207)
.++++||-|...
T Consensus 81 ~~ivvGG~~~t~ 92 (125)
T cd02065 81 IPVVVGGAHPTA 92 (125)
T ss_pred CeEEEeCCcCCc
Confidence 444444444333
No 97
>cd08769 DAP_dppA_2 Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacteriz
Probab=25.77 E-value=1e+02 Score=26.03 Aligned_cols=31 Identities=32% Similarity=0.653 Sum_probs=21.6
Q ss_pred eEEEEEeccCCCCCCCCCCCCC---CCCCCCHHHHHHHH
Q 028588 129 GVYISVDVDCLDPAFAPGVSHI---EPGGLSFRDVLNIL 164 (207)
Q Consensus 129 ~vylsiDiDvldp~~~pg~~~p---~pgGl~~~e~~~~l 164 (207)
++|||.|+..+. |+..| .|++..+++..+++
T Consensus 2 KiyISaDmEGi~-----Gv~~~~~~~~~~~~y~~~r~~m 35 (270)
T cd08769 2 KIYISVDIEGLP-----GVVSWEMVAPGKELYKEARRLM 35 (270)
T ss_pred eEEEEeCCCCCC-----CCCCHHHcCCCChhHHHHHHHH
Confidence 699999999875 44444 45677776665555
No 98
>PRK11865 pyruvate ferredoxin oxidoreductase subunit beta; Provisional
Probab=25.47 E-value=4.3e+02 Score=22.60 Aligned_cols=135 Identities=19% Similarity=0.224 Sum_probs=64.7
Q ss_pred cceEEEcCCccc---hHHHHHHHHHhcCCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCCCCcEEEEcccCCChh
Q 028588 17 LHPLVLGGDHSI---SFPVIRAVSEKLGGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGYARRLLQVGIRSITKE 93 (207)
Q Consensus 17 ~~pi~iGGdhs~---s~~~~~~~~~~~~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~~~~vv~iG~r~~~~~ 93 (207)
...++++||-.. -++.+....++ +.++.+|.+|...=.++ |...+.++|...........+. ..|-.....+
T Consensus 92 ~~Vv~~~GDG~~~dIG~~~L~~a~~r-~~ni~~ivlDNe~Y~nT---GgQ~S~~Tp~Ga~t~tsp~Gk~-~~G~~~~kkd 166 (299)
T PRK11865 92 VNVVAIGGDGGTADIGFQSLSGAMER-GHNILYLMYDNEAYMNT---GIQRSGSTPFGASTTTSPAGKY-SRGEDRPKKN 166 (299)
T ss_pred CeEEEEeCCchHhhccHHHHHHHHHc-CCCeEEEEECCccccCC---CCCCCCCCCCCcccccCCCCcc-cCCCCCCCCC
Confidence 468999999654 23333333333 45899999996654443 2223444444332221100111 1133332223
Q ss_pred HHHHHHHcCceEEEcccccchHHHHHHhh-ccCCcceEEEEEeccCCCCCCCCCCCCCCCCCCCHHHHHHHHHhh
Q 028588 94 GREQGKRFGVEQYEMRTFSRDRQFLENLK-LGEGVKGVYISVDVDCLDPAFAPGVSHIEPGGLSFRDVLNILHNL 167 (207)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~vylsiDiDvldp~~~pg~~~p~pgGl~~~e~~~~l~~i 167 (207)
-.+.+..+|+.++-.-......+..+.++ ......+-||.+ .. | +|.--|..+.+..++.+..
T Consensus 167 ~~~Ia~a~g~~YVA~~~~~~~~~l~~~i~~A~~~~Gps~I~v----~s----P---C~~~~~~~~~~~~~~~klA 230 (299)
T PRK11865 167 MPLIMAAHGIPYVATASIGYPEDFMEKVKKAKEVEGPAYIQV----LQ----P---CPTGWGFPPEKTIEIGRLA 230 (299)
T ss_pred HHHHHHHcCCCEEEEEeCCCHHHHHHHHHHHHhCCCCEEEEE----EC----C---CCCCCCCCHHHHHHHHHHH
Confidence 33455667877764333333233333332 112234566654 22 2 2222366777777777654
No 99
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=24.92 E-value=2.2e+02 Score=23.27 Aligned_cols=20 Identities=15% Similarity=0.345 Sum_probs=11.9
Q ss_pred HHHHHhcCCCCcEEEEcccCC
Q 028588 70 FARIMEGGYARRLLQVGIRSI 90 (207)
Q Consensus 70 ~~~~~~~~~~~~vv~iG~r~~ 90 (207)
++.+-+.|. +++..+|..+.
T Consensus 223 l~al~~~G~-~dv~vig~d~~ 242 (295)
T PRK10653 223 LRALQTAGK-SDVMVVGFDGT 242 (295)
T ss_pred HHHHHHcCC-CceEEEEeCCC
Confidence 333444443 57888888765
No 100
>TIGR00147 lipid kinase, YegS/Rv2252/BmrU family. The E. coli member of this family, YegS has been purified and shown to have phosphatidylglycerol kinase activity. The member from M. tuberculosis, Rv2252, has diacylglycerol kinase activity. BmrU from B. subtilis is in an operon with multidrug efflux transporter Bmr, but is uncharacterized.
Probab=24.87 E-value=1.5e+02 Score=24.55 Aligned_cols=41 Identities=22% Similarity=0.110 Sum_probs=23.4
Q ss_pred HHHHHhcCCcceEEEcCCccchHHHHHHHHHhc-CCCeEEEEE
Q 028588 8 VKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL-GGPVDVLHL 49 (207)
Q Consensus 8 v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~-~~~~~vI~~ 49 (207)
++...+.+....+++|||-++.-.+ .++.... ..++++|-.
T Consensus 50 ~~~~~~~~~d~ivv~GGDGTl~~v~-~~l~~~~~~~~lgiiP~ 91 (293)
T TIGR00147 50 VEEARKFGVDTVIAGGGDGTINEVV-NALIQLDDIPALGILPL 91 (293)
T ss_pred HHHHHhcCCCEEEEECCCChHHHHH-HHHhcCCCCCcEEEEcC
Confidence 4444443346789999998886543 3443221 125776643
No 101
>PRK11024 colicin uptake protein TolR; Provisional
Probab=24.68 E-value=1.5e+02 Score=22.04 Aligned_cols=36 Identities=14% Similarity=0.330 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHh
Q 028588 4 ITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEK 39 (207)
Q Consensus 4 i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~ 39 (207)
+...++...++++..+++|-+|..+.|+.+-.+-..
T Consensus 90 L~~~l~~~~~~~~~~~V~i~aD~~~~~~~vv~vmd~ 125 (141)
T PRK11024 90 VVAEAKSRFKANPKTVFLIGGAKDVPYDEIIKALNL 125 (141)
T ss_pred HHHHHHHHHhhCCCceEEEEcCCCCCHHHHHHHHHH
Confidence 444556655545566778888888888777665544
No 102
>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=24.64 E-value=2e+02 Score=22.75 Aligned_cols=12 Identities=33% Similarity=0.434 Sum_probs=7.3
Q ss_pred CCcEEEEcccCC
Q 028588 79 ARRLLQVGIRSI 90 (207)
Q Consensus 79 ~~~vv~iG~r~~ 90 (207)
++++..+|.-..
T Consensus 205 p~~i~vig~d~~ 216 (268)
T cd06273 205 PEDLSIVGFDDI 216 (268)
T ss_pred CCceEEEecCCh
Confidence 466666776543
No 103
>COG2040 MHT1 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]
Probab=24.30 E-value=4.1e+02 Score=22.76 Aligned_cols=75 Identities=17% Similarity=0.213 Sum_probs=49.1
Q ss_pred HHHHHcCceEEEcccccch---HHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCee
Q 028588 96 EQGKRFGVEQYEMRTFSRD---RQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHIEPGGLSFRDVLNILHNLQADVV 172 (207)
Q Consensus 96 ~~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~pgGl~~~e~~~~l~~i~~~vv 172 (207)
+.+.+.|++++-.+.+-.. +.+++.+. .. ..|+|||+-+.= ++-.+.|-+..|+..++... +++.
T Consensus 141 e~l~~ag~Dlla~ETip~i~Ea~Aiv~l~~-~~-s~p~wISfT~~d---------~~~lr~Gt~l~eaa~~~~~~-~~ia 208 (300)
T COG2040 141 EALNEAGADLLACETLPNITEAEAIVQLVQ-EF-SKPAWISFTLND---------DTRLRDGTPLSEAAAILAGL-PNIA 208 (300)
T ss_pred HHHHhCCCcEEeecccCChHHHHHHHHHHH-Hh-CCceEEEEEeCC---------CCccCCCccHHHHHHHHhcC-cchh
Confidence 4556788888877766443 33344333 22 479999998763 34566677788887777764 5677
Q ss_pred EEEEeeecCC
Q 028588 173 AADVVEFNPQ 182 (207)
Q Consensus 173 g~di~E~~P~ 182 (207)
++-|-...|.
T Consensus 209 a~gvNC~~p~ 218 (300)
T COG2040 209 ALGVNCCHPD 218 (300)
T ss_pred heeeccCChh
Confidence 7777666664
No 104
>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=23.99 E-value=2.3e+02 Score=22.55 Aligned_cols=11 Identities=18% Similarity=0.283 Sum_probs=5.5
Q ss_pred CCcEEEEcccC
Q 028588 79 ARRLLQVGIRS 89 (207)
Q Consensus 79 ~~~vv~iG~r~ 89 (207)
|+++..+|.-.
T Consensus 204 p~di~i~g~d~ 214 (269)
T cd06293 204 PGDMSLVGFDD 214 (269)
T ss_pred ccceEEEeecC
Confidence 34555555533
No 105
>PRK14325 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=23.86 E-value=5.2e+02 Score=23.06 Aligned_cols=89 Identities=10% Similarity=0.141 Sum_probs=45.8
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHH---------HHHHHHHhcC--CCeEEEEEc-cCCCCCCCCCCCccCCccH
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFP---------VIRAVSEKLG--GPVDVLHLD-AHPDIYDAFEGNKYSHASS 69 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~---------~~~~~~~~~~--~~~~vI~~D-AH~D~~~~~~g~~~~~g~~ 69 (207)
++|-+.++.+.++ |..-|.+.|++...|. .+..+.+... ..+.-|.+- .|++..+ .-.
T Consensus 179 e~Iv~Ei~~l~~~-g~~ei~l~d~~~~~y~~~~~~~~~~~l~~Ll~~l~~~~~~~~ir~~~~~p~~~~---------~el 248 (444)
T PRK14325 179 DDVLAEVAQLAEQ-GVREITLLGQNVNAYRGEGPDGEIADFAELLRLVAAIDGIERIRYTTSHPRDFT---------DDL 248 (444)
T ss_pred HHHHHHHHHHHHC-CCcEEEEEeeccccccCCCCCCCcchHHHHHHHHHhcCCccEEEEccCCcccCC---------HHH
Confidence 3455556666664 6777888888766652 2333322211 112113332 2333211 112
Q ss_pred HHHHHhcCCCCcEEEEcccCCChhHHHHHHH
Q 028588 70 FARIMEGGYARRLLQVGIRSITKEGREQGKR 100 (207)
Q Consensus 70 ~~~~~~~~~~~~vv~iG~r~~~~~~~~~~~~ 100 (207)
+..+.+.+..-+.+++|+++.++.-.+.+++
T Consensus 249 l~~l~~~~~~~~~l~igiqSgs~~vLk~m~R 279 (444)
T PRK14325 249 IEAYADLPKLVPFLHLPVQSGSDRILKAMNR 279 (444)
T ss_pred HHHHHcCCcccCceeccCCcCCHHHHHhCCC
Confidence 3333333323578899999999887766543
No 106
>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=23.86 E-value=2.4e+02 Score=22.37 Aligned_cols=11 Identities=18% Similarity=0.335 Sum_probs=7.1
Q ss_pred CCcEEEEcccC
Q 028588 79 ARRLLQVGIRS 89 (207)
Q Consensus 79 ~~~vv~iG~r~ 89 (207)
++++..+|...
T Consensus 199 p~di~iig~d~ 209 (263)
T cd06280 199 PQDLALAGFDN 209 (263)
T ss_pred CCcEEEEEeCC
Confidence 56666667655
No 107
>PRK13054 lipid kinase; Reviewed
Probab=23.85 E-value=1.9e+02 Score=24.20 Aligned_cols=43 Identities=16% Similarity=0.132 Sum_probs=25.5
Q ss_pred HHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHh-c--CCCeEEEE
Q 028588 5 TESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEK-L--GGPVDVLH 48 (207)
Q Consensus 5 ~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~-~--~~~~~vI~ 48 (207)
.+.++++.+.+-...+++|||-++.-. +.++.+. . +.++++|=
T Consensus 46 ~~~a~~~~~~~~d~vvv~GGDGTl~ev-v~~l~~~~~~~~~~lgiiP 91 (300)
T PRK13054 46 ARYVEEALALGVATVIAGGGDGTINEV-ATALAQLEGDARPALGILP 91 (300)
T ss_pred HHHHHHHHHcCCCEEEEECCccHHHHH-HHHHHhhccCCCCcEEEEe
Confidence 344555554444678899999988765 4555432 1 12566653
No 108
>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=23.67 E-value=2.7e+02 Score=21.61 Aligned_cols=10 Identities=20% Similarity=0.318 Sum_probs=5.5
Q ss_pred CcEEEEcccC
Q 028588 80 RRLLQVGIRS 89 (207)
Q Consensus 80 ~~vv~iG~r~ 89 (207)
.++..+|...
T Consensus 205 ~~i~i~~~d~ 214 (264)
T cd06267 205 EDVSVVGFDD 214 (264)
T ss_pred CceEEEeeCC
Confidence 4555666544
No 109
>PRK14333 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=23.59 E-value=3.9e+02 Score=23.98 Aligned_cols=82 Identities=15% Similarity=0.206 Sum_probs=42.7
Q ss_pred CcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCCCCCCCCCHHH
Q 028588 80 RRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHIEPGGLSFRD 159 (207)
Q Consensus 80 ~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~pgGl~~~e 159 (207)
-+.+++|+++.++.-.+.+++. ++.+++. +.++.++. . ...+.++.|+ + +|.| |-|.++
T Consensus 265 ~~~l~igiQSgsd~vLk~m~R~----~t~e~~~---~~i~~lr~-~-~p~i~i~~d~--I-------vGfP---gET~ed 323 (448)
T PRK14333 265 CEHFHIPFQSGDNEILKAMARG----YTHEKYR---RIIDKIRE-Y-MPDASISADA--I-------VGFP---GETEAQ 323 (448)
T ss_pred cccccCCCccCCHHHHHhcCCC----CCHHHHH---HHHHHHHH-h-CCCcEEEeeE--E-------EECC---CCCHHH
Confidence 4678899999888776665432 2333222 34444431 1 1124444443 2 2445 446666
Q ss_pred HHHHHHhhc-CCeeEEEEeeecCC
Q 028588 160 VLNILHNLQ-ADVVAADVVEFNPQ 182 (207)
Q Consensus 160 ~~~~l~~i~-~~vvg~di~E~~P~ 182 (207)
+.+.++.+. -++-.+.+.-|+|.
T Consensus 324 f~~tl~~l~~~~~~~~~~~~~sp~ 347 (448)
T PRK14333 324 FENTLKLVEEIGFDQLNTAAYSPR 347 (448)
T ss_pred HHHHHHHHHHcCCCEEeeeeeecC
Confidence 666666553 24444455555654
No 110
>PF00781 DAGK_cat: Diacylglycerol kinase catalytic domain; InterPro: IPR001206 The DAG-kinase catalytic domain or DAGKc domain is present in mammalian lipid kinases, such as diacylglycerol (DAG), ceramide and sphingosine kinases, as well as in related bacterial proteins [, ]. Eukaryotic DAG-kinase (2.7.1.107 from EC) catalyses the phosphorylation of DAG to phosphatidic acid, thus modulating the balance between the two signaling lipids. At least ten different isoforms have been identified in mammals, which form 5 groups characterised by different functional domains, such as the calcium-binding EF hand (see PDOC00018 from PROSITEDOC), PH (see PDOC50003 from PROSITEDOC), SAM (see PDOC50105 from PROSITEDOC) , DAG/PE-binding C1 domain (see PDOC00379 from PROSITEDOC) and ankyrin repeats (see PDOC50088 from PROSITEDOC) []. In bacteria, an integral membrane DAG kinase forms a homotrimeric protein that lacks the DAGKc domain (see PDOC00820 from PROSITEDOC). In contrast, the bacterial yegS protein is a soluble cytosolic protein that contains the DAGKc domain in the N-terminal part. YegS is a lipid kinase with two structural domains, wherein the active site is located in the interdomain cleft, C-terminal to the DAGKc domain which forms an alpha/beta fold []. The tertiary structure resembles that of NAD kinases and contains a metal-binding site in the C-terminal region [, ]. This domain is usually associated with an accessory domain (see IPR000756 from INTERPRO).; GO: 0004143 diacylglycerol kinase activity, 0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway; PDB: 2JGR_A 2BON_A 3T5P_D 3S40_A 2P1R_A 2QV7_A 2QVL_A.
Probab=23.41 E-value=97 Score=22.34 Aligned_cols=22 Identities=18% Similarity=0.274 Sum_probs=16.5
Q ss_pred cceEEEcCCccchHHHHHHHHHh
Q 028588 17 LHPLVLGGDHSISFPVIRAVSEK 39 (207)
Q Consensus 17 ~~pi~iGGdhs~s~~~~~~~~~~ 39 (207)
...+++|||-++... +.++.+.
T Consensus 56 ~~ivv~GGDGTl~~v-v~~l~~~ 77 (130)
T PF00781_consen 56 DVIVVVGGDGTLNEV-VNGLMGS 77 (130)
T ss_dssp SEEEEEESHHHHHHH-HHHHCTS
T ss_pred cEEEEEcCccHHHHH-HHHHhhc
Confidence 589999999888766 5555544
No 111
>cd06842 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA. This subfamily is composed of the hypothetical Rhizobium sp. protein Y4yA and similar uncharacterized bacterial proteins. These proteins are homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarboxylases.
Probab=23.36 E-value=5.3e+02 Score=22.90 Aligned_cols=99 Identities=16% Similarity=0.141 Sum_probs=55.6
Q ss_pred HHHHHHhcCC-CCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhc-cCCcceEEEEEeccCCCCCCCCC
Q 028588 69 SFARIMEGGY-ARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKL-GEGVKGVYISVDVDCLDPAFAPG 146 (207)
Q Consensus 69 ~~~~~~~~~~-~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~vylsiDiDvldp~~~pg 146 (207)
-+..+...|. +.+++..|... ..++.+.+.+.|+. +..+....-..+.+..+. ....-++++-+|.+.-
T Consensus 70 E~~~~~~~G~~~~~I~~~g~~k-~~~~i~~a~~~gi~-i~vDs~~el~~l~~~a~~~~~~~~~v~lRIn~~~~------- 140 (423)
T cd06842 70 ELRQALAAGVRGDRIVATGPAK-TDEFLWLAVRHGAT-IAVDSLDELDRLLALARGYTTGPARVLLRLSPFPA------- 140 (423)
T ss_pred HHHHHHHCCCCCCeEEEECCCC-CHHHHHHHHhCCCE-EEECCHHHHHHHHHHHHhcCCCCCEEEEEEeCCCC-------
Confidence 3444555543 35687776632 44667777788884 555544332222221111 1122356666665431
Q ss_pred CCCCCCCCCCHHHHHHHHHhhc----C-CeeEEEEe
Q 028588 147 VSHIEPGGLSFRDVLNILHNLQ----A-DVVAADVV 177 (207)
Q Consensus 147 ~~~p~pgGl~~~e~~~~l~~i~----~-~vvg~di~ 177 (207)
+.....|++.+++.++++.+. . ++.|+..-
T Consensus 141 -~~~sRfGi~~~e~~~~~~~i~~~~~~l~l~Glh~H 175 (423)
T cd06842 141 -SLPSRFGMPAAEVRTALERLAQLRERVRLVGFHFH 175 (423)
T ss_pred -CCCCCCCCCHHHHHHHHHHHHhcCCCCeEEEEEEE
Confidence 245778999999888887662 2 66777653
No 112
>cd06313 PBP1_ABC_sugar_binding_like_5 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=22.99 E-value=2.9e+02 Score=22.23 Aligned_cols=20 Identities=10% Similarity=0.199 Sum_probs=12.7
Q ss_pred HHHHhcCCCCcEEEEcccCCC
Q 028588 71 ARIMEGGYARRLLQVGIRSIT 91 (207)
Q Consensus 71 ~~~~~~~~~~~vv~iG~r~~~ 91 (207)
+.+-+.+. .++..+|.-...
T Consensus 200 ~al~~~g~-~di~vvgfd~~~ 219 (272)
T cd06313 200 QIMKAAGR-TKIVIGGVDGDP 219 (272)
T ss_pred HHHHHcCC-CceEEEeecCCH
Confidence 33334454 788899986654
No 113
>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=22.91 E-value=2.4e+02 Score=23.38 Aligned_cols=11 Identities=9% Similarity=0.033 Sum_probs=5.7
Q ss_pred CCcEEEEcccC
Q 028588 79 ARRLLQVGIRS 89 (207)
Q Consensus 79 ~~~vv~iG~r~ 89 (207)
|+++..+|.-+
T Consensus 264 P~dvsvigfd~ 274 (327)
T TIGR02417 264 DSQLHLATFGD 274 (327)
T ss_pred CCcceEEEECC
Confidence 45555555543
No 114
>TIGR03639 cas1_NMENI CRISPR-associated endonuclease Cas1, NMENI subtype. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is a prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 variant of the NMENI subtype of CRISPR/Cas system.
Probab=22.83 E-value=1.1e+02 Score=25.78 Aligned_cols=33 Identities=15% Similarity=0.287 Sum_probs=27.4
Q ss_pred eEEEcC-CccchHHHHHHHHHhcCCCeEEEEEccCCC
Q 028588 19 PLVLGG-DHSISFPVIRAVSEKLGGPVDVLHLDAHPD 54 (207)
Q Consensus 19 pi~iGG-dhs~s~~~~~~~~~~~~~~~~vI~~DAH~D 54 (207)
-|++.| .+++|-.+++.+.++ ++.|+++|.+.-
T Consensus 37 ~Ivi~g~~~~lst~~l~~l~~~---~I~v~f~~~~G~ 70 (278)
T TIGR03639 37 VILIENPQITISSALLSALAEN---NIALIFCDEKHL 70 (278)
T ss_pred EEEEeCCCEEEcHHHHHHHHHC---CCeEEEECCCCC
Confidence 466777 899999999999864 689999997754
No 115
>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=22.75 E-value=2.8e+02 Score=22.54 Aligned_cols=30 Identities=10% Similarity=0.038 Sum_probs=16.2
Q ss_pred HHHHHHhcCCCCcEEEEcccCCChhHHHHHH
Q 028588 69 SFARIMEGGYARRLLQVGIRSITKEGREQGK 99 (207)
Q Consensus 69 ~~~~~~~~~~~~~vv~iG~r~~~~~~~~~~~ 99 (207)
.++.+-+.+. +++..+|.-...+.+...++
T Consensus 201 ~~~~l~~~g~-~di~vvg~d~~~~~~~~~~~ 230 (294)
T cd06316 201 VIAALRAAGR-DDIKVTTVDLGLNVALDMAK 230 (294)
T ss_pred HHHHHHHcCC-CCceEEEeCCCcHHHHHHHH
Confidence 3344444443 57888888765554444333
No 116
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=22.60 E-value=2.2e+02 Score=22.98 Aligned_cols=34 Identities=12% Similarity=-0.012 Sum_probs=19.3
Q ss_pred HHHHHHhcCCCCcEEEEcccCCChhHHHHHHHcCc
Q 028588 69 SFARIMEGGYARRLLQVGIRSITKEGREQGKRFGV 103 (207)
Q Consensus 69 ~~~~~~~~~~~~~vv~iG~r~~~~~~~~~~~~~~~ 103 (207)
.++.+-+.|..+++..+|.... ++....+.+-.+
T Consensus 205 ~l~al~~~G~~~dv~vvg~d~~-~~~~~~~~~g~~ 238 (280)
T cd06303 205 ASDALKELGREDDILINGWGGG-SAELDAIQQGEL 238 (280)
T ss_pred HHHHHHHcCCCCCcEEEecCCC-HHHHHHHHcCCc
Confidence 4444444555578889998664 444444543333
No 117
>PRK06806 fructose-bisphosphate aldolase; Provisional
Probab=22.50 E-value=2e+02 Score=24.29 Aligned_cols=44 Identities=16% Similarity=0.206 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccC
Q 028588 5 TESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAH 52 (207)
Q Consensus 5 ~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH 52 (207)
...+....++ -.+|+.+--||.-++..+....+ ..+..|+||+.
T Consensus 63 ~~~~~~~a~~-~~vpv~lHlDH~~~~e~i~~Al~---~G~tsVm~d~s 106 (281)
T PRK06806 63 GPLMVAAAKQ-AKVPVAVHFDHGMTFEKIKEALE---IGFTSVMFDGS 106 (281)
T ss_pred HHHHHHHHHH-CCCCEEEECCCCCCHHHHHHHHH---cCCCEEEEcCC
Confidence 3444555554 46788888888888877755443 35778888843
No 118
>cd00458 SugarP_isomerase SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium, the last step of the metabolic pathway of N-acetyl-D-glucosamine-6-phosphate. 6PGL converts 6-phosphoglucono-1,5-lactone to 6-phosphogluconate, the second step of the oxidative phase of the pentose phosphate pathway.
Probab=22.22 E-value=3e+02 Score=20.94 Aligned_cols=49 Identities=20% Similarity=0.210 Sum_probs=30.3
Q ss_pred hHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcC----CCeEEEEEccC
Q 028588 3 VITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLG----GPVDVLHLDAH 52 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~----~~~~vI~~DAH 52 (207)
.+.+.++..+++++.+.|.++|. +...+.++.+.+... .++-++|.|=-
T Consensus 7 ~i~~~i~~~~~~~~~~~i~lsgG-sTp~~~y~~L~~~~~~~~w~~v~~f~~DEr 59 (169)
T cd00458 7 FIEDKXEKLLEEKDDMVIGLGTG-STPAYFYKLLGEKLKRGEISDIVGFPTDER 59 (169)
T ss_pred HHHHHHHHHHHhCCCEEEEECCC-ccHHHHHHHHHhhhhhCCccceEEEECccc
Confidence 45566666666566778888885 444555666654321 36778887743
No 119
>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=22.19 E-value=2.8e+02 Score=22.06 Aligned_cols=18 Identities=6% Similarity=0.145 Sum_probs=11.2
Q ss_pred HHhcCCCCcEEEEcccCCC
Q 028588 73 IMEGGYARRLLQVGIRSIT 91 (207)
Q Consensus 73 ~~~~~~~~~vv~iG~r~~~ 91 (207)
+-+.+ .+++..+|.-...
T Consensus 200 l~~~g-~~di~v~g~d~~~ 217 (271)
T cd06321 200 AKQAG-RNDIKITSVDGAP 217 (271)
T ss_pred HHHcC-CCCcEEEEecCCH
Confidence 33334 3688888886544
No 120
>PRK13055 putative lipid kinase; Reviewed
Probab=22.15 E-value=1.8e+02 Score=24.95 Aligned_cols=41 Identities=15% Similarity=0.153 Sum_probs=23.3
Q ss_pred HHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhc-CCCeEEE
Q 028588 6 ESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL-GGPVDVL 47 (207)
Q Consensus 6 ~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~-~~~~~vI 47 (207)
+.++++...+....+++|||-++.-. +.++.... ..++++|
T Consensus 50 ~~~~~~~~~~~d~vvv~GGDGTl~ev-vngl~~~~~~~~Lgii 91 (334)
T PRK13055 50 NEAKRAAEAGFDLIIAAGGDGTINEV-VNGIAPLEKRPKMAII 91 (334)
T ss_pred HHHHHHhhcCCCEEEEECCCCHHHHH-HHHHhhcCCCCcEEEE
Confidence 34555554434678899999887643 35554321 1246655
No 121
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=22.08 E-value=2.5e+02 Score=23.27 Aligned_cols=20 Identities=10% Similarity=0.111 Sum_probs=11.6
Q ss_pred HHHHHhcC--CCCcEEEEcccC
Q 028588 70 FARIMEGG--YARRLLQVGIRS 89 (207)
Q Consensus 70 ~~~~~~~~--~~~~vv~iG~r~ 89 (207)
+..+.+.+ -|+++..+|..+
T Consensus 254 ~~al~~~g~~vP~disv~gfd~ 275 (328)
T PRK11303 254 LDVLLERPGELPSDLAIATFGD 275 (328)
T ss_pred HHHHHHcCCCCCCceEEEEeCC
Confidence 33334444 367787788754
No 122
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=22.08 E-value=3e+02 Score=23.56 Aligned_cols=24 Identities=25% Similarity=0.171 Sum_probs=14.2
Q ss_pred CcEEEEcccCCChhHHHHHHHcCce
Q 028588 80 RRLLQVGIRSITKEGREQGKRFGVE 104 (207)
Q Consensus 80 ~~vv~iG~r~~~~~~~~~~~~~~~~ 104 (207)
.++..+|.- ..++..+++++--+.
T Consensus 234 ~~v~VvG~D-~~~~~~~~i~~G~i~ 257 (336)
T PRK15408 234 DKVAIVGFS-TPNVMRPYVKRGTVK 257 (336)
T ss_pred CCEEEEEeC-CcHHHHHHHhcCCcc
Confidence 378888885 344555666543333
No 123
>cd00281 DAP_dppA Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacterized
Probab=22.07 E-value=1.4e+02 Score=25.15 Aligned_cols=29 Identities=31% Similarity=0.558 Sum_probs=18.7
Q ss_pred eEEEEEeccCCCCCCCCCCCCC---CCCCCCHHHHHH
Q 028588 129 GVYISVDVDCLDPAFAPGVSHI---EPGGLSFRDVLN 162 (207)
Q Consensus 129 ~vylsiDiDvldp~~~pg~~~p---~pgGl~~~e~~~ 162 (207)
++|||.|+..+. |+..| .|++..++...+
T Consensus 2 KiyISaDmEGia-----Gv~~~~~~~~~~~~Y~r~r~ 33 (265)
T cd00281 2 KVYISADIEGIA-----GISHWDEATIGQPGYEAFRE 33 (265)
T ss_pred eEEEEeCCCCCC-----CCCChHhcCCCChhHHHHHH
Confidence 699999999875 44433 356555544433
No 124
>PRK11267 biopolymer transport protein ExbD; Provisional
Probab=21.91 E-value=1.8e+02 Score=21.65 Aligned_cols=37 Identities=8% Similarity=0.259 Sum_probs=22.6
Q ss_pred hHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHh
Q 028588 3 VITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEK 39 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~ 39 (207)
.+...++...+..+..+++|-+|..++|+.+..+-+.
T Consensus 85 ~L~~~L~~~~~~~~~~~V~I~aD~~~~~~~vv~vmd~ 121 (141)
T PRK11267 85 TMITALDALTEGKKDTTIFFRADKTVDYETLMKVMDT 121 (141)
T ss_pred HHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHH
Confidence 3445555555544556777777777777777655443
No 125
>PRK11864 2-ketoisovalerate ferredoxin oxidoreductase subunit beta; Provisional
Probab=21.90 E-value=5.1e+02 Score=22.18 Aligned_cols=81 Identities=12% Similarity=0.023 Sum_probs=43.5
Q ss_pred ceEEEcCCccchHHHHHHHHHh--cCCCeEEEEEccCCCCCCCCCCCccCCccHHHHHHhcCCCCcEEEEcccCCChhHH
Q 028588 18 HPLVLGGDHSISFPVIRAVSEK--LGGPVDVLHLDAHPDIYDAFEGNKYSHASSFARIMEGGYARRLLQVGIRSITKEGR 95 (207)
Q Consensus 18 ~pi~iGGdhs~s~~~~~~~~~~--~~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~~~~~~~~~~~vv~iG~r~~~~~~~ 95 (207)
..++++||....-+-+.++.-. .+.++.+|..|...=.++.. ..+.+++...... ....|-+....+-.
T Consensus 94 ~Vva~~GDG~~~~~g~~~l~~A~~~~~~v~~vv~dN~~~~~TGg---Q~S~~Tp~ga~t~------tsp~G~~~~kkdi~ 164 (300)
T PRK11864 94 IVVGWAGDGGTADIGFQALSGAAERNHDILYIMYDNEAYMNTGI---QRSSSTPYGAWTT------TTPGGKREHKKPVP 164 (300)
T ss_pred EEEEEEccCccccccHHHHHHHHHhCcCEEEEEECCeeeecCCC---CCCCCCcCCCccc------cCCCCCcCCCCCHH
Confidence 3444999987755545555432 24589999999877666532 2234444432221 11123333222334
Q ss_pred HHHHHcCceEEE
Q 028588 96 EQGKRFGVEQYE 107 (207)
Q Consensus 96 ~~~~~~~~~~~~ 107 (207)
+.+..+|+.++-
T Consensus 165 ~i~~a~g~~yVA 176 (300)
T PRK11864 165 DIMAAHKVPYVA 176 (300)
T ss_pred HHHHHcCCCEEE
Confidence 455677876654
No 126
>PRK09920 acetyl-CoA:acetoacetyl-CoA transferase subunit alpha; Provisional
Probab=21.74 E-value=4.4e+02 Score=21.37 Aligned_cols=45 Identities=13% Similarity=0.256 Sum_probs=33.9
Q ss_pred HHHHHHHHHhcCCcceEEEcCC--ccchHHHHHHHHHhcCCCeEEEEEcc
Q 028588 4 ITESVKLVMEEDPLHPLVLGGD--HSISFPVIRAVSEKLGGPVDVLHLDA 51 (207)
Q Consensus 4 i~~~v~~~~~~~~~~pi~iGGd--hs~s~~~~~~~~~~~~~~~~vI~~DA 51 (207)
++++++. .+ .|. .|.+||- +......+.++.++.++++.+|+-++
T Consensus 8 ~~eAv~~-I~-DG~-ti~~gGf~~~~~P~ali~al~r~~~~dLtli~~~~ 54 (219)
T PRK09920 8 LQDATGF-FR-DGM-TIMVGGFMGIGTPSRLVEALLESGVRDLTLIANDT 54 (219)
T ss_pred HHHHHhc-CC-CCC-EEEECcccCcCCHHHHHHHHHhcCCCceEEEEeCC
Confidence 5677775 44 344 6788885 67889999999887667899998664
No 127
>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=21.74 E-value=2.8e+02 Score=22.11 Aligned_cols=28 Identities=11% Similarity=0.025 Sum_probs=15.7
Q ss_pred CCcEEEEcccCCChhHHHHHHHcCceEEE
Q 028588 79 ARRLLQVGIRSITKEGREQGKRFGVEQYE 107 (207)
Q Consensus 79 ~~~vv~iG~r~~~~~~~~~~~~~~~~~~~ 107 (207)
|+++..+|.... +...+.+.+-.++.+.
T Consensus 212 p~di~iig~d~~-~~~~~~~~~~~lt~~~ 239 (273)
T cd06309 212 GKDIKIVSIDGT-KDAFQAMADGKLNATV 239 (273)
T ss_pred CCCeEEEecCCC-HHHHHHHHcCceEEEE
Confidence 578889998543 4443344444454433
No 128
>TIGR02803 ExbD_1 TonB system transport protein ExbD, group 1. Members of this family are Gram-negative bacterial inner membrane proteins, generally designated ExbD, related to the TolR family modeled by TIGRFAMs TIGR02801. Members always are encoded next to a protein designated ExbB (TIGR02797), related to the TolQ family modeled by TIGRFAMs TIGR02796. ExbD and ExbB together form a proton channel through which they can harness the proton-motive force to energize TonB, which in turn energizes TonB-dependent receptors in the outer membrane. TonB-dependent receptors with known specificity tend to import siderophores or vitamin B12. A TonB system and Tol-Pal system often will co-exist in a single bacterial genome.
Probab=21.48 E-value=2.3e+02 Score=20.31 Aligned_cols=36 Identities=11% Similarity=0.230 Sum_probs=20.1
Q ss_pred HHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHh
Q 028588 4 ITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEK 39 (207)
Q Consensus 4 i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~ 39 (207)
+...++...++.+..+++|-+|..++|+.+..+-+.
T Consensus 72 L~~~l~~~~~~~~~~~v~I~aD~~~~~~~vv~v~d~ 107 (122)
T TIGR02803 72 LGTALDALTEGDKDTTIFFRADKTVDYGDLMKVMNL 107 (122)
T ss_pred HHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHH
Confidence 334444444444455666667766666666555443
No 129
>PLN03028 pyrophosphate--fructose-6-phosphate 1-phosphotransferase; Provisional
Probab=21.44 E-value=4.9e+02 Score=24.76 Aligned_cols=46 Identities=11% Similarity=0.024 Sum_probs=27.7
Q ss_pred HHHHHHHHHhcCCcceEEEcCCccchHHHHHH-HHHhcCCCeEEEEE
Q 028588 4 ITESVKLVMEEDPLHPLVLGGDHSISFPVIRA-VSEKLGGPVDVLHL 49 (207)
Q Consensus 4 i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~-~~~~~~~~~~vI~~ 49 (207)
.+.+++.+.+.+=...++||||-|.+.+..-+ ..+..+.++.||-+
T Consensus 162 ~~~i~e~l~~l~Id~LvvIGGddS~~~A~~Lae~~~~~~~~i~VIGI 208 (610)
T PLN03028 162 VNAALAACEALKLDGLVIIGGVTSNTDAAQLAETFAEAKCKTKVVGV 208 (610)
T ss_pred HHHHHHHHHHcCCCEEEEeCCchHHHHHHHHHHHHHHcCCCceEEEe
Confidence 34455555554335589999999987775433 22223346778754
No 130
>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=21.35 E-value=3e+02 Score=21.90 Aligned_cols=9 Identities=22% Similarity=0.368 Sum_probs=4.3
Q ss_pred CcEEEEccc
Q 028588 80 RRLLQVGIR 88 (207)
Q Consensus 80 ~~vv~iG~r 88 (207)
+++..+|.-
T Consensus 214 ~~i~ii~~d 222 (275)
T cd06295 214 EDVAVVGFD 222 (275)
T ss_pred cceEEEeeC
Confidence 444445543
No 131
>cd01400 6PGL 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard against the accumulation of the delta form of the lactone, which may be toxic through its reaction with endogenous cellular nucleophiles.
Probab=21.32 E-value=2.5e+02 Score=22.44 Aligned_cols=50 Identities=18% Similarity=0.205 Sum_probs=33.7
Q ss_pred hHHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhc---CCCeEEEEEccCC
Q 028588 3 VITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL---GGPVDVLHLDAHP 53 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~---~~~~~vI~~DAH~ 53 (207)
.+.+.++..+++++.+.+.+.|..+-. +.++.+.+.. -.++.+.|.|=-.
T Consensus 10 ~i~~~i~~~i~~~~~~~l~lsGGstp~-~~y~~L~~~~~i~w~~v~~f~~DEr~ 62 (219)
T cd01400 10 RIAEALAAAIAKRGRFSLALSGGSTPK-PLYELLAAAPALDWSKVHVFLGDERC 62 (219)
T ss_pred HHHHHHHHHHHhcCeEEEEECCCccHH-HHHHHhccccCCCCceEEEEEeeccc
Confidence 455666666665667778887765544 8888887543 2578888888543
No 132
>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]
Probab=21.32 E-value=2.1e+02 Score=22.38 Aligned_cols=45 Identities=24% Similarity=0.205 Sum_probs=33.0
Q ss_pred HHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCCCC
Q 028588 6 ESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHPDI 55 (207)
Q Consensus 6 ~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~D~ 55 (207)
++++.++.. +...|..||.=-.+-...+.+.++. -+||+++-++.
T Consensus 63 ~vl~~l~~~-~~~ViaTGGG~v~~~enr~~l~~~g----~vv~L~~~~e~ 107 (172)
T COG0703 63 EVLKELLEE-DNAVIATGGGAVLSEENRNLLKKRG----IVVYLDAPFET 107 (172)
T ss_pred HHHHHHhhc-CCeEEECCCccccCHHHHHHHHhCC----eEEEEeCCHHH
Confidence 456667765 3578889998888888888887542 58999987654
No 133
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=20.81 E-value=2.8e+02 Score=23.06 Aligned_cols=10 Identities=0% Similarity=0.185 Sum_probs=6.7
Q ss_pred cEEEEcccCC
Q 028588 81 RLLQVGIRSI 90 (207)
Q Consensus 81 ~vv~iG~r~~ 90 (207)
++..+|.-+.
T Consensus 281 di~vigfd~~ 290 (342)
T PRK10014 281 QVALAAFTDV 290 (342)
T ss_pred ceEEEEecCc
Confidence 6777777664
No 134
>PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=20.67 E-value=6e+02 Score=22.56 Aligned_cols=89 Identities=16% Similarity=0.123 Sum_probs=47.5
Q ss_pred hhHHHHHHHHHhcCCcceEEEcCCccchHHH-------HHHHHHhc---CCCeEEEEEccCCCCCCCCCCCccCCccHHH
Q 028588 2 NVITESVKLVMEEDPLHPLVLGGDHSISFPV-------IRAVSEKL---GGPVDVLHLDAHPDIYDAFEGNKYSHASSFA 71 (207)
Q Consensus 2 ~~i~~~v~~~~~~~~~~pi~iGGdhs~s~~~-------~~~~~~~~---~~~~~vI~~DAH~D~~~~~~g~~~~~g~~~~ 71 (207)
++|-+.++.+.++ |..-|++.|++..+|+. +..+.+.. ++...+=|.-.|++.-+ --.+.
T Consensus 156 e~Iv~Ei~~l~~~-G~~ei~l~~~~~~~yg~d~~~~~~l~~Ll~~l~~~~~~~~ir~~~~~p~~i~---------~ell~ 225 (418)
T PRK14336 156 AEIGCEVAELVRR-GSREVVLLGQNVDSYGHDLPEKPCLADLLSALHDIPGLLRIRFLTSHPKDIS---------QKLID 225 (418)
T ss_pred HHHHHHHHHHHHC-CCeEEEEEecCccccccCCCCcccHHHHHHHHHhcCCccEEEEeccChhhcC---------HHHHH
Confidence 4555667777775 67788888888766542 32332221 11112212223433211 11223
Q ss_pred HHHhcCCCCcEEEEcccCCChhHHHHHHH
Q 028588 72 RIMEGGYARRLLQVGIRSITKEGREQGKR 100 (207)
Q Consensus 72 ~~~~~~~~~~vv~iG~r~~~~~~~~~~~~ 100 (207)
.+.+.+..-+.+++|+++.++...+.+++
T Consensus 226 ~l~~~~~~~~~l~lglQSgsd~vLk~M~R 254 (418)
T PRK14336 226 AMAHLPKVCRSLSLPVQAGDDTILAAMRR 254 (418)
T ss_pred HHHhcCccCCceecCCCcCCHHHHHHhCC
Confidence 23333333578999999999888776653
No 135
>PRK07534 methionine synthase I; Validated
Probab=20.62 E-value=5.6e+02 Score=22.16 Aligned_cols=59 Identities=20% Similarity=0.110 Sum_probs=34.4
Q ss_pred HHHHcCceEEEcccccch---HHHHHHhhccCCcceEEEEEeccCCCCCCCCCCCCCCCCCCCHHHHHHHHHh
Q 028588 97 QGKRFGVEQYEMRTFSRD---RQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHIEPGGLSFRDVLNILHN 166 (207)
Q Consensus 97 ~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~vylsiDiDvldp~~~pg~~~p~pgGl~~~e~~~~l~~ 166 (207)
.+.+.|++++-.+.+... ..+++.++. ...|+|+||-++- ..-...|-+..++...+..
T Consensus 139 ~l~~~gvD~l~~ET~p~l~E~~a~~~~~~~--~~~Pv~vSft~~~---------~g~l~~G~~~~~~~~~~~~ 200 (336)
T PRK07534 139 GLKAGGADVLWVETISAPEEIRAAAEAAKL--AGMPWCGTMSFDT---------AGRTMMGLTPADLADLVEK 200 (336)
T ss_pred HHHhCCCCEEEEeccCCHHHHHHHHHHHHH--cCCeEEEEEEECC---------CCeeCCCCcHHHHHHHHHh
Confidence 334667888877766554 233444432 2479999997641 1123446666666666654
No 136
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=20.59 E-value=81 Score=23.08 Aligned_cols=24 Identities=13% Similarity=0.428 Sum_probs=16.8
Q ss_pred CCCCCHH---HHHHHHHhhcCCeeEEE
Q 028588 152 PGGLSFR---DVLNILHNLQADVVAAD 175 (207)
Q Consensus 152 pgGl~~~---e~~~~l~~i~~~vvg~d 175 (207)
|||++++ ++.++++.++-++.-+|
T Consensus 3 pg~~nPr~~~~mkkmMk~MGi~~~eid 29 (116)
T TIGR00264 3 PGKMNPKMLKQMQKMMKQMGMEMEDLD 29 (116)
T ss_pred CCCCCcccHHHHHHHHHHcCCCccccc
Confidence 4579999 99999998753333333
No 137
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=20.48 E-value=3.1e+02 Score=21.78 Aligned_cols=21 Identities=14% Similarity=0.392 Sum_probs=11.5
Q ss_pred HHHHHhcCCCCcEEEEcccCC
Q 028588 70 FARIMEGGYARRLLQVGIRSI 90 (207)
Q Consensus 70 ~~~~~~~~~~~~vv~iG~r~~ 90 (207)
+..+-+.+..+++..+|.-..
T Consensus 198 ~~al~~~g~~~dv~vvg~d~~ 218 (270)
T cd06308 198 YLAAKRAGREKEIKFIGIDGL 218 (270)
T ss_pred HHHHHHcCCCCCcEEEEecCC
Confidence 333334443366777777664
No 138
>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=20.46 E-value=54 Score=27.21 Aligned_cols=49 Identities=18% Similarity=0.260 Sum_probs=37.1
Q ss_pred HHHHHHHHHhcCCcceEEEcCCccchHHHHHHHHHhc----CCCe-----EEEEEccC
Q 028588 4 ITESVKLVMEEDPLHPLVLGGDHSISFPVIRAVSEKL----GGPV-----DVLHLDAH 52 (207)
Q Consensus 4 i~~~v~~~~~~~~~~pi~iGGdhs~s~~~~~~~~~~~----~~~~-----~vI~~DAH 52 (207)
-.+++++++++++.+.-++.++..++.|+++++.++. +..+ +++-||..
T Consensus 167 g~~~~~~ll~~~p~idai~~~nd~~A~ga~~~l~~~gr~~ip~di~~~~~~v~g~d~~ 224 (279)
T PF00532_consen 167 GYEAARELLESHPDIDAIFCANDMMAIGAIRALRERGRLKIPEDIVSGFDSVVGFDNL 224 (279)
T ss_dssp HHHHHHHHHHTSTT-SEEEESSHHHHHHHHHHHHHTT-TCTTTEEEECSCCCGGHHHC
T ss_pred HHHHHHHHHhhCCCCEEEEEeCHHHHHHHHHHHHHcCCcccChhheeeeccchhhccc
Confidence 3567888888766667899999999999999998763 3356 67777765
No 139
>TIGR02429 pcaI_scoA_fam 3-oxoacid CoA-transferase, A subunit. Various members of this family are characterized as the A subunits of succinyl-CoA:3-ketoacid-CoA transferase (EC 2.8.3.5), beta-ketoadipate:succinyl-CoA transferase (EC 2.8.3.6), acetyl-CoA:acetoacetate CoA transferase (EC 2.8.3.8), and butyrate-acetoacetate CoA-transferase (EC 2.8.3.9). This represents a very distinct clade with strong sequence conservation within the larger family defined by Pfam model pfam01144. The B subunit represents a different clade in pfam01144, described by TIGR02428. The two are found in general as tandem genes and occasionally as a fusion.
Probab=20.30 E-value=2e+02 Score=23.46 Aligned_cols=48 Identities=19% Similarity=0.308 Sum_probs=35.4
Q ss_pred hHHHHHHHHHhcCCcceEEEcCC--ccchHHHHHHHHHhcCCCeEEEEEccCC
Q 028588 3 VITESVKLVMEEDPLHPLVLGGD--HSISFPVIRAVSEKLGGPVDVLHLDAHP 53 (207)
Q Consensus 3 ~i~~~v~~~~~~~~~~pi~iGGd--hs~s~~~~~~~~~~~~~~~~vI~~DAH~ 53 (207)
.++++++. .+ .|. .|.+||- |......++++.+..++++.+++-++..
T Consensus 8 s~~eAv~~-I~-DG~-ti~~gGf~~~~~P~ali~~l~r~~~~~Ltlv~~~~g~ 57 (222)
T TIGR02429 8 SAAEAVSV-IP-DGA-TIMIGGFGTAGQPFELIDALIDTGAKDLTIVSNNAGN 57 (222)
T ss_pred CHHHHHhh-CC-CCC-EEEECCcCCccCcHHHHHHHHhcCCCCcEEEecCCCC
Confidence 46778875 44 354 6788984 6788888999887666789999877653
No 140
>COG1518 CRISPR-associated protein Cas1 [Defense mechanisms]
Probab=20.26 E-value=1.4e+02 Score=25.87 Aligned_cols=32 Identities=25% Similarity=0.389 Sum_probs=26.4
Q ss_pred eEEEcCCccchHHHHHHHHHhcCCCeEEEEEccCC
Q 028588 19 PLVLGGDHSISFPVIRAVSEKLGGPVDVLHLDAHP 53 (207)
Q Consensus 19 pi~iGGdhs~s~~~~~~~~~~~~~~~~vI~~DAH~ 53 (207)
-|++.|..++|-++++.+++. .+-|++||...
T Consensus 41 ~I~i~~~~siSs~av~~la~~---gI~i~f~~~~G 72 (327)
T COG1518 41 GIVLFGGTSISSAALRLLAKR---GIPIVFFDQYG 72 (327)
T ss_pred EEEEeCCCcccHHHHHHHHHc---CCEEEEECCCC
Confidence 577888999999999999864 57788888554
No 141
>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=20.24 E-value=3.1e+02 Score=21.61 Aligned_cols=11 Identities=27% Similarity=0.344 Sum_probs=6.1
Q ss_pred CCcEEEEcccC
Q 028588 79 ARRLLQVGIRS 89 (207)
Q Consensus 79 ~~~vv~iG~r~ 89 (207)
+.++..+|...
T Consensus 206 p~~i~vig~d~ 216 (270)
T cd01545 206 PDDLSVVGFDD 216 (270)
T ss_pred CCceEEEEECC
Confidence 34565666554
No 142
>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=20.12 E-value=2.8e+02 Score=22.87 Aligned_cols=30 Identities=10% Similarity=0.117 Sum_probs=18.4
Q ss_pred HHHHHHhcCCCCcEEEEcccCCChhHHHHHH
Q 028588 69 SFARIMEGGYARRLLQVGIRSITKEGREQGK 99 (207)
Q Consensus 69 ~~~~~~~~~~~~~vv~iG~r~~~~~~~~~~~ 99 (207)
.++.+.+.+.+.++..+|.-. ....+..+.
T Consensus 199 ~~~al~~~g~~~di~Vvg~d~-~~~~~~~l~ 228 (302)
T TIGR02634 199 AIQALTAQGLAGKVPISGQDA-DLAAIKRVA 228 (302)
T ss_pred HHHHHHHCCCCCCeEEEcCCC-CHHHHHHHH
Confidence 445555556567888899874 555555444
No 143
>cd06810 PLPDE_III_ODC_DapDC_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate Decarboxylases, and Related Enzymes. This family includes eukaryotic ornithine decarboxylase (ODC, EC 4.1.1.17), diaminopimelate decarboxylase (DapDC, EC 4.1.1.20), plant and prokaryotic biosynthetic arginine decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine decarboxylase (CANSDC), and ODC-like enzymes from diverse bacterial species. These proteins are fold type III PLP-dependent enzymes that catalyze essential steps in the biosynthesis of polyamine and lysine. ODC and ADC participate in alternative pathways of the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. ODC catalyzes the direct synthesis of putrescine from L-ornithine, while ADC converts L-arginine to agmatine, which is hydrolysed to putrescine by agmatinase in a pathway that exists only in plants and bacteria. DapDC converts meso-2,6-diaminoheptanedioate to
Probab=20.00 E-value=5.6e+02 Score=21.88 Aligned_cols=105 Identities=16% Similarity=0.171 Sum_probs=56.7
Q ss_pred HHHHHhcCC-CCcEEEEcccCCChhHHHHHHHcCceEEEcccccchHHHHHHhhccCCcceEEEEEeccCCCCCC--CCC
Q 028588 70 FARIMEGGY-ARRLLQVGIRSITKEGREQGKRFGVEQYEMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAF--APG 146 (207)
Q Consensus 70 ~~~~~~~~~-~~~vv~iG~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~vylsiDiDvldp~~--~pg 146 (207)
+..+.+.+. +.+++.-|. ..++++.+.+-++++..+..+++...+.+.+..+......+++|-+|......+. .++
T Consensus 59 ~~~~~~~G~~~~~iv~~gp-~~~~~~l~~~~~~~~~~~~vds~~el~~l~~~~~~~~~~~~v~lrin~g~~~~~~~~~~~ 137 (368)
T cd06810 59 LALALAAGVPPERIIFTGP-AKSVSEIEAALASGVDHIVVDSLDELERLNELAKKLGPKARILLRVNPDVSAGTHKISTG 137 (368)
T ss_pred HHHHHHcCCCHHHEEEcCC-CCCHHHHHHHHHCCCCEEEeCCHHHHHHHHHHHHHhCCCCeEEEEECCCCCCCcccCccC
Confidence 344444443 245555553 2345777777788854555554433222221111111234678888765432211 111
Q ss_pred CCCCCCCCCCHHHHHHHHHhhc---CCeeEEEE
Q 028588 147 VSHIEPGGLSFRDVLNILHNLQ---ADVVAADV 176 (207)
Q Consensus 147 ~~~p~pgGl~~~e~~~~l~~i~---~~vvg~di 176 (207)
+.+...|++++|+.++++.+. -+++|+..
T Consensus 138 -~~~srfGi~~~e~~~~~~~~~~~~l~l~Gl~~ 169 (368)
T cd06810 138 -GLKSKFGLSLSEARAALERAKELDLRLVGLHF 169 (368)
T ss_pred -CCCCCcCCCHHHHHHHHHHHHhCCCcEEEEEE
Confidence 345778999999988888773 26667665
Done!