Query 037201
Match_columns 177
No_of_seqs 31 out of 33
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 09:44:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037201.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037201hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06167 LabA_like LabA_like pr 98.2 4.1E-06 8.9E-11 63.4 6.5 46 122-167 99-146 (149)
2 PF01936 NYN: NYN domain; Int 98.2 4.7E-06 1E-10 61.8 5.9 48 122-169 95-144 (146)
3 TIGR00288 conserved hypothetic 97.7 6.9E-05 1.5E-09 61.5 6.2 64 106-169 70-154 (160)
4 COG1432 Uncharacterized conser 97.3 0.00022 4.9E-09 58.1 4.0 64 106-169 83-159 (181)
5 cd05013 SIS_RpiR RpiR-like pro 96.4 0.01 2.2E-07 42.8 5.7 62 108-169 32-110 (139)
6 PF13894 zf-C2H2_4: C2H2-type 96.3 0.0024 5.3E-08 34.5 1.4 23 48-70 2-24 (24)
7 PF00096 zf-C2H2: Zinc finger, 96.2 0.0023 4.9E-08 35.5 1.2 22 48-70 2-23 (23)
8 cd05014 SIS_Kpsf KpsF-like pro 96.2 0.014 3E-07 42.8 5.5 50 122-171 47-99 (128)
9 cd05005 SIS_PHI Hexulose-6-pho 95.3 0.05 1.1E-06 43.0 5.9 62 109-170 53-126 (179)
10 PF13913 zf-C2HC_2: zinc-finge 94.8 0.016 3.5E-07 34.1 1.3 19 49-68 5-23 (25)
11 PF01380 SIS: SIS domain SIS d 94.7 0.064 1.4E-06 38.8 4.6 47 122-168 53-102 (131)
12 cd05008 SIS_GlmS_GlmD_1 SIS (S 94.5 0.077 1.7E-06 38.8 4.6 48 122-169 46-96 (126)
13 smart00355 ZnF_C2H2 zinc finge 93.9 0.039 8.4E-07 29.6 1.6 22 49-71 3-24 (26)
14 PRK11557 putative DNA-binding 93.7 0.16 3.4E-06 42.6 5.5 83 87-169 114-225 (278)
15 TIGR03127 RuMP_HxlB 6-phospho 93.7 0.23 5E-06 39.0 6.2 59 110-168 51-121 (179)
16 cd05710 SIS_1 A subgroup of th 93.4 0.16 3.5E-06 38.0 4.6 48 122-169 47-97 (120)
17 PRK15482 transcriptional regul 93.3 0.23 5E-06 42.0 5.9 82 88-169 122-232 (285)
18 TIGR00441 gmhA phosphoheptose 93.2 0.14 3E-06 40.1 4.2 47 123-169 80-129 (154)
19 PRK11337 DNA-binding transcrip 93.2 0.24 5.2E-06 41.8 5.9 82 88-169 127-237 (292)
20 cd05006 SIS_GmhA Phosphoheptos 92.0 0.28 6.1E-06 38.6 4.5 48 123-170 102-152 (177)
21 PRK13937 phosphoheptose isomer 91.7 0.31 6.6E-06 39.5 4.5 48 123-170 107-157 (188)
22 PRK13936 phosphoheptose isomer 90.5 0.46 1E-05 38.9 4.5 48 122-169 111-164 (197)
23 TIGR00393 kpsF KpsF/GutQ famil 90.3 0.67 1.4E-05 38.2 5.4 49 122-170 47-98 (268)
24 PRK00414 gmhA phosphoheptose i 89.7 0.61 1.3E-05 38.2 4.6 45 124-168 113-160 (192)
25 PHA00616 hypothetical protein 89.6 0.15 3.2E-06 34.3 0.8 26 47-72 2-27 (44)
26 PF12171 zf-C2H2_jaz: Zinc-fin 89.1 0.12 2.5E-06 30.0 -0.0 22 47-68 2-23 (27)
27 PRK10892 D-arabinose 5-phospha 88.9 1 2.2E-05 38.7 5.5 60 109-168 67-143 (326)
28 PF12874 zf-met: Zinc-finger o 88.2 0.21 4.6E-06 27.9 0.7 21 48-68 2-22 (25)
29 smart00451 ZnF_U1 U1-like zinc 87.4 0.45 9.7E-06 28.3 1.8 31 47-77 4-34 (35)
30 PF07279 DUF1442: Protein of u 87.4 0.84 1.8E-05 39.7 4.1 51 122-176 115-166 (218)
31 PHA02768 hypothetical protein; 87.1 0.37 8.1E-06 33.7 1.5 23 48-71 7-29 (55)
32 PRK13938 phosphoheptose isomer 87.0 0.8 1.7E-05 38.1 3.7 50 122-171 113-165 (196)
33 PRK11543 gutQ D-arabinose 5-ph 87.0 1.5 3.3E-05 37.3 5.5 79 90-168 30-138 (321)
34 PRK14101 bifunctional glucokin 86.2 2.9 6.2E-05 39.9 7.4 82 87-169 454-564 (638)
35 PRK11302 DNA-binding transcrip 86.1 1.2 2.6E-05 37.1 4.3 81 88-169 115-224 (284)
36 PRK02947 hypothetical protein; 86.0 1.2 2.6E-05 37.8 4.4 48 122-169 106-167 (246)
37 PF09237 GAGA: GAGA factor; I 85.9 0.49 1.1E-05 33.4 1.6 24 48-71 26-49 (54)
38 PF13912 zf-C2H2_6: C2H2-type 85.8 0.3 6.6E-06 27.7 0.4 22 47-68 2-23 (27)
39 PF05605 zf-Di19: Drought indu 85.2 0.48 1E-05 31.6 1.3 28 47-75 3-30 (54)
40 cd01545 PBP1_SalR Ligand-bindi 85.1 1.7 3.7E-05 34.3 4.5 51 105-155 19-89 (270)
41 cd06305 PBP1_methylthioribose_ 84.5 2.3 4.9E-05 33.7 5.0 50 106-155 20-89 (273)
42 cd06282 PBP1_GntR_like_2 Ligan 83.4 3 6.5E-05 32.7 5.2 34 122-155 55-88 (266)
43 PF12756 zf-C2H2_2: C2H2 type 83.3 0.65 1.4E-05 32.1 1.3 24 47-70 51-74 (100)
44 cd01542 PBP1_TreR_like Ligand- 82.1 3.4 7.4E-05 32.5 5.1 50 105-155 19-87 (259)
45 COG1737 RpiR Transcriptional r 81.9 3.5 7.5E-05 35.5 5.5 83 88-170 117-228 (281)
46 PRK05441 murQ N-acetylmuramic 81.7 2.4 5.1E-05 37.3 4.5 49 122-170 131-182 (299)
47 cd06295 PBP1_CelR Ligand bindi 81.2 3.9 8.4E-05 32.7 5.2 32 122-154 64-95 (275)
48 cd05007 SIS_Etherase N-acetylm 80.9 2.8 6.1E-05 35.9 4.6 48 122-169 118-168 (257)
49 PF14258 DUF4350: Domain of un 80.8 3.8 8.1E-05 27.9 4.3 48 105-153 8-69 (70)
50 cd06281 PBP1_LacI_like_5 Ligan 80.7 4.2 9.1E-05 32.4 5.2 51 106-156 20-89 (269)
51 TIGR00274 N-acetylmuramic acid 80.6 2.8 6E-05 36.9 4.5 49 122-170 126-177 (291)
52 cd01540 PBP1_arabinose_binding 80.1 3.6 7.8E-05 33.1 4.7 34 122-155 54-88 (289)
53 PF13407 Peripla_BP_4: Peripla 80.1 3.2 7E-05 32.9 4.4 50 106-155 19-89 (257)
54 cd06318 PBP1_ABC_sugar_binding 79.8 4.6 0.0001 32.2 5.2 51 105-155 19-89 (282)
55 KOG1074 Transcriptional repres 79.0 0.29 6.3E-06 49.8 -2.3 35 44-78 379-413 (958)
56 cd05017 SIS_PGI_PMI_1 The memb 78.8 4.3 9.3E-05 30.1 4.4 42 122-165 43-87 (119)
57 cd06299 PBP1_LacI_like_13 Liga 78.3 5.5 0.00012 31.4 5.2 33 122-155 55-87 (265)
58 PRK11382 frlB fructoselysine-6 78.2 3.5 7.6E-05 36.3 4.4 49 123-171 93-144 (340)
59 cd06312 PBP1_ABC_sugar_binding 77.0 6.3 0.00014 31.6 5.2 34 122-155 57-91 (271)
60 PHA00732 hypothetical protein 76.9 1.3 2.9E-05 32.3 1.2 25 47-71 2-26 (79)
61 PF12756 zf-C2H2_2: C2H2 type 76.8 0.79 1.7E-05 31.7 0.0 25 49-73 2-26 (100)
62 cd01541 PBP1_AraR Ligand-bindi 76.6 6.4 0.00014 31.3 5.2 50 106-155 20-92 (273)
63 PF11823 DUF3343: Protein of u 75.7 5.8 0.00013 27.7 4.2 42 108-149 18-66 (73)
64 PRK10886 DnaA initiator-associ 75.0 5.2 0.00011 33.4 4.4 47 122-168 109-161 (196)
65 KOG1074 Transcriptional repres 74.8 0.93 2E-05 46.3 -0.1 26 44-70 631-656 (958)
66 cd06294 PBP1_ycjW_transcriptio 74.6 7 0.00015 30.8 4.8 32 122-154 60-91 (270)
67 cd01538 PBP1_ABC_xylose_bindin 73.8 8 0.00017 31.6 5.2 51 105-155 19-89 (288)
68 PHA00733 hypothetical protein 73.7 2.2 4.8E-05 33.4 1.8 25 46-70 99-123 (128)
69 TIGR02634 xylF D-xylose ABC tr 73.6 7.8 0.00017 32.4 5.1 34 122-155 54-88 (302)
70 PF13909 zf-H2C2_5: C2H2-type 73.5 2.4 5.2E-05 23.6 1.4 22 48-70 2-23 (24)
71 PRK12570 N-acetylmuramic acid- 73.5 6 0.00013 34.9 4.6 49 122-170 127-178 (296)
72 cd06324 PBP1_ABC_sugar_binding 73.2 7.7 0.00017 32.2 5.0 50 106-155 21-91 (305)
73 cd06313 PBP1_ABC_sugar_binding 72.8 7.6 0.00016 31.5 4.8 51 105-155 19-89 (272)
74 cd06322 PBP1_ABC_sugar_binding 72.7 8.4 0.00018 30.5 4.9 51 105-155 19-89 (267)
75 TIGR03590 PseG pseudaminic aci 72.7 10 0.00022 32.3 5.7 42 127-170 83-125 (279)
76 PRK10653 D-ribose transporter 72.6 7.7 0.00017 31.9 4.8 51 105-155 46-116 (295)
77 PF13380 CoA_binding_2: CoA bi 72.2 3.4 7.4E-05 31.3 2.4 53 103-155 15-88 (116)
78 cd06319 PBP1_ABC_sugar_binding 72.1 8.6 0.00019 30.5 4.8 34 122-155 55-89 (277)
79 cd06316 PBP1_ABC_sugar_binding 72.1 8.5 0.00018 31.4 4.9 34 122-155 56-90 (294)
80 cd06308 PBP1_sensor_kinase_lik 71.9 9.7 0.00021 30.4 5.1 34 122-155 56-90 (270)
81 cd06289 PBP1_MalI_like Ligand- 71.6 11 0.00023 29.6 5.2 34 122-155 55-88 (268)
82 PF12013 DUF3505: Protein of u 71.6 2.2 4.8E-05 31.7 1.3 22 50-71 88-109 (109)
83 PF04959 ARS2: Arsenite-resist 71.5 1.8 3.8E-05 37.3 0.8 28 45-72 76-103 (214)
84 PF13465 zf-H2C2_2: Zinc-finge 71.3 0.8 1.7E-05 26.6 -0.9 15 44-58 12-26 (26)
85 PF13580 SIS_2: SIS domain; PD 71.2 5.9 0.00013 30.4 3.6 31 122-152 103-136 (138)
86 cd04795 SIS SIS domain. SIS (S 71.0 8 0.00017 26.0 3.9 32 122-153 47-81 (87)
87 cd06270 PBP1_GalS_like Ligand 70.7 11 0.00024 29.9 5.2 49 106-155 20-87 (268)
88 PF09538 FYDLN_acid: Protein o 70.7 1.4 3E-05 34.2 -0.0 14 46-59 9-22 (108)
89 cd06342 PBP1_ABC_LIVBP_like Ty 70.7 8.5 0.00018 31.6 4.6 34 122-155 190-223 (334)
90 cd06320 PBP1_allose_binding Pe 70.4 8.8 0.00019 30.6 4.6 33 122-154 57-90 (275)
91 TIGR01512 ATPase-IB2_Cd heavy 69.9 5.1 0.00011 37.5 3.5 63 109-171 372-451 (536)
92 cd06296 PBP1_CatR_like Ligand- 69.7 11 0.00024 29.7 5.0 48 106-154 20-86 (270)
93 cd06315 PBP1_ABC_sugar_binding 69.5 9.8 0.00021 31.0 4.7 50 106-155 21-90 (280)
94 cd01575 PBP1_GntR Ligand-bindi 69.3 14 0.0003 28.9 5.4 33 122-155 55-87 (268)
95 cd06323 PBP1_ribose_binding Pe 69.2 10 0.00022 29.7 4.7 51 106-156 20-90 (268)
96 cd06314 PBP1_tmGBP Periplasmic 69.0 10 0.00023 30.3 4.7 50 105-155 18-88 (271)
97 cd06306 PBP1_TorT-like TorT-li 69.0 11 0.00024 30.4 4.9 34 122-155 57-90 (268)
98 PRK00331 glucosamine--fructose 69.0 7.6 0.00017 36.6 4.5 47 123-169 337-386 (604)
99 cd06311 PBP1_ABC_sugar_binding 68.6 14 0.0003 29.5 5.4 34 122-155 60-94 (274)
100 cd06309 PBP1_YtfQ_like Peripla 68.5 12 0.00026 29.9 5.0 50 106-155 20-89 (273)
101 cd06317 PBP1_ABC_sugar_binding 68.4 13 0.00028 29.4 5.1 34 122-155 56-90 (275)
102 PRK10014 DNA-binding transcrip 67.9 13 0.00028 31.0 5.2 33 122-154 120-152 (342)
103 PF02310 B12-binding: B12 bind 66.8 18 0.0004 26.0 5.3 49 107-155 20-89 (121)
104 cd01473 vWA_CTRP CTRP for CS 66.8 12 0.00027 30.3 4.8 41 125-165 111-160 (192)
105 cd06361 PBP1_GPC6A_like Ligand 66.7 14 0.0003 33.0 5.5 34 122-155 234-267 (403)
106 cd01539 PBP1_GGBP Periplasmic 66.5 15 0.00032 30.6 5.3 34 122-155 57-91 (303)
107 PRK15408 autoinducer 2-binding 66.3 11 0.00024 32.9 4.7 50 106-155 44-114 (336)
108 PRK04148 hypothetical protein; 66.2 15 0.00032 29.5 5.1 55 103-169 25-83 (134)
109 cd06302 PBP1_LsrB_Quorum_Sensi 66.1 13 0.00029 30.7 4.9 50 106-155 20-90 (298)
110 cd01477 vWA_F09G8-8_type VWA F 65.8 13 0.00028 30.5 4.8 32 125-156 134-171 (193)
111 cd06301 PBP1_rhizopine_binding 65.6 17 0.00036 28.9 5.2 35 122-156 56-91 (272)
112 cd06277 PBP1_LacI_like_1 Ligan 65.5 15 0.00033 29.1 5.0 32 122-155 58-89 (268)
113 cd06273 PBP1_GntR_like_1 This 65.1 18 0.00039 28.5 5.3 32 122-154 55-86 (268)
114 TIGR01135 glmS glucosamine--fr 65.0 11 0.00023 35.6 4.7 47 123-169 339-388 (607)
115 cd06298 PBP1_CcpA_like Ligand- 64.7 17 0.00037 28.6 5.1 33 122-155 55-87 (268)
116 cd06292 PBP1_LacI_like_10 Liga 64.3 16 0.00035 29.0 4.9 51 105-155 19-92 (273)
117 cd06303 PBP1_LuxPQ_Quorum_Sens 64.2 15 0.00032 29.9 4.8 34 122-155 60-93 (280)
118 KOG3408 U1-like Zn-finger-cont 63.9 4.1 8.8E-05 33.1 1.4 30 49-78 60-89 (129)
119 cd04509 PBP1_ABC_transporter_G 63.6 13 0.00027 29.0 4.1 33 122-154 191-225 (299)
120 cd06297 PBP1_LacI_like_12 Liga 63.2 18 0.00039 29.1 5.1 33 122-155 55-87 (269)
121 cd06271 PBP1_AglR_RafR_like Li 62.9 17 0.00036 28.5 4.7 33 122-155 59-91 (268)
122 TIGR02417 fruct_sucro_rep D-fr 62.5 19 0.0004 29.9 5.2 33 122-154 116-148 (327)
123 PF00702 Hydrolase: haloacid d 62.2 15 0.00033 28.1 4.3 48 109-156 137-205 (215)
124 PF05368 NmrA: NmrA-like famil 61.4 19 0.00041 28.7 4.9 49 107-155 36-103 (233)
125 cd00861 ProRS_anticodon_short 61.0 14 0.00031 25.4 3.7 43 105-155 21-64 (94)
126 cd06293 PBP1_LacI_like_11 Liga 60.8 23 0.0005 28.1 5.3 49 106-155 20-87 (269)
127 cd01544 PBP1_GalR Ligand-bindi 60.5 17 0.00037 29.1 4.5 32 122-155 52-83 (270)
128 cd01987 USP_OKCHK USP domain i 60.4 20 0.00043 25.6 4.4 33 130-162 69-101 (124)
129 cd06310 PBP1_ABC_sugar_binding 60.2 21 0.00045 28.4 4.9 34 122-155 57-91 (273)
130 PRK08674 bifunctional phosphog 60.1 14 0.0003 32.4 4.2 43 122-166 78-123 (337)
131 cd02755 MopB_Thiosulfate-R-lik 59.9 16 0.00034 33.1 4.6 47 122-169 156-208 (454)
132 cd06321 PBP1_ABC_sugar_binding 59.6 23 0.0005 28.1 5.1 34 122-155 57-91 (271)
133 TIGR02300 FYDLN_acid conserved 59.5 3.2 7E-05 33.7 0.2 14 46-59 9-22 (129)
134 PF04780 DUF629: Protein of un 59.2 6.2 0.00013 37.8 2.0 31 48-78 59-89 (466)
135 smart00734 ZnF_Rad18 Rad18-lik 59.1 6.4 0.00014 23.3 1.4 18 49-67 4-21 (26)
136 TIGR02637 RhaS rhamnose ABC tr 58.6 20 0.00043 29.5 4.6 34 122-155 56-90 (302)
137 PF05605 zf-Di19: Drought indu 58.6 5 0.00011 26.6 0.9 22 47-70 32-53 (54)
138 PRK10355 xylF D-xylose transpo 58.4 22 0.00048 30.6 5.1 33 122-154 81-114 (330)
139 cd02750 MopB_Nitrate-R-NarG-li 58.3 17 0.00038 33.0 4.6 47 122-169 170-221 (461)
140 cd06348 PBP1_ABC_ligand_bindin 58.2 15 0.00033 30.8 3.9 33 122-154 192-224 (344)
141 PRK11303 DNA-binding transcrip 58.1 23 0.00049 29.3 4.9 33 122-154 117-149 (328)
142 cd06347 PBP1_ABC_ligand_bindin 57.7 16 0.00035 29.9 4.0 32 122-153 191-222 (334)
143 cd06278 PBP1_LacI_like_2 Ligan 57.5 28 0.0006 27.3 5.1 33 122-155 54-86 (266)
144 COG4229 Predicted enolase-phos 57.5 27 0.00059 30.7 5.4 122 22-153 25-204 (229)
145 cd05009 SIS_GlmS_GlmD_2 SIS (S 57.2 22 0.00049 26.3 4.3 42 123-166 62-107 (153)
146 cd02751 MopB_DMSOR-like The Mo 57.2 14 0.00031 34.8 4.0 46 123-169 170-229 (609)
147 PRK14987 gluconate operon tran 56.8 28 0.0006 29.0 5.3 33 122-155 119-151 (331)
148 cd06272 PBP1_hexuronate_repres 56.7 31 0.00067 27.3 5.3 33 122-155 51-83 (261)
149 TIGR01525 ATPase-IB_hvy heavy 56.6 16 0.00035 34.3 4.2 63 109-171 394-473 (556)
150 cd06285 PBP1_LacI_like_7 Ligan 56.3 27 0.00058 27.7 4.9 50 105-155 19-87 (265)
151 cd06360 PBP1_alkylbenzenes_lik 56.0 28 0.0006 28.7 5.1 33 122-154 189-223 (336)
152 TIGR01511 ATPase-IB1_Cu copper 55.8 20 0.00043 34.0 4.7 62 109-171 415-492 (562)
153 cd06350 PBP1_GPCR_family_C_lik 55.7 30 0.00065 28.8 5.3 35 122-156 217-253 (348)
154 cd01536 PBP1_ABC_sugar_binding 55.6 32 0.00069 26.7 5.1 34 122-155 55-89 (267)
155 PRK03094 hypothetical protein; 55.4 10 0.00022 28.4 2.2 32 107-138 13-51 (80)
156 PRK10936 TMAO reductase system 55.3 23 0.00051 30.4 4.7 33 122-155 104-137 (343)
157 PLN02981 glucosamine:fructose- 54.9 19 0.00041 35.2 4.5 47 123-169 411-460 (680)
158 cd06267 PBP1_LacI_sugar_bindin 54.7 34 0.00074 26.3 5.1 31 122-153 55-85 (264)
159 cd06274 PBP1_FruR Ligand bindi 54.3 30 0.00065 27.4 4.9 32 122-154 55-86 (264)
160 cd06337 PBP1_ABC_ligand_bindin 54.0 20 0.00043 30.7 4.1 32 122-153 203-234 (357)
161 PF04423 Rad50_zn_hook: Rad50 54.0 9.6 0.00021 25.3 1.7 21 48-68 22-44 (54)
162 KOG3576 Ovo and related transc 53.8 7.2 0.00016 34.7 1.4 24 45-68 144-167 (267)
163 KOG1842 FYVE finger-containing 53.4 9.2 0.0002 37.0 2.1 53 45-97 14-69 (505)
164 cd06268 PBP1_ABC_transporter_L 53.1 27 0.00058 27.2 4.3 33 122-154 190-222 (298)
165 cd06346 PBP1_ABC_ligand_bindin 52.4 31 0.00066 28.8 4.8 32 122-153 192-223 (312)
166 cd06330 PBP1_Arsenic_SBP_like 52.2 22 0.00049 29.7 4.0 26 122-147 195-220 (346)
167 PHA00733 hypothetical protein 52.0 7.8 0.00017 30.4 1.2 23 45-67 72-94 (128)
168 cd06300 PBP1_ABC_sugar_binding 51.9 49 0.0011 26.3 5.7 34 122-155 60-94 (272)
169 cd06343 PBP1_ABC_ligand_bindin 51.8 27 0.00059 29.4 4.5 34 122-155 199-233 (362)
170 PF00532 Peripla_BP_1: Peripla 51.8 33 0.00071 28.9 5.0 51 105-156 21-89 (279)
171 PRK15404 leucine ABC transport 51.8 24 0.00052 30.7 4.3 33 122-154 216-248 (369)
172 cd06375 PBP1_mGluR_groupII Lig 51.4 34 0.00074 31.1 5.3 33 122-154 232-264 (458)
173 cd01537 PBP1_Repressors_Sugar_ 50.8 41 0.00089 25.7 5.0 34 122-155 55-88 (264)
174 cd06279 PBP1_LacI_like_3 Ligan 50.8 39 0.00085 27.4 5.1 33 122-155 56-88 (283)
175 TIGR02955 TMAO_TorT TMAO reduc 50.8 33 0.00072 28.3 4.8 33 122-155 57-90 (295)
176 PF02892 zf-BED: BED zinc fing 50.7 8.2 0.00018 24.2 0.9 25 46-70 16-44 (45)
177 cd06336 PBP1_ABC_ligand_bindin 50.6 25 0.00054 29.8 4.1 31 122-152 193-224 (347)
178 PRK11199 tyrA bifunctional cho 50.4 33 0.00071 30.9 5.0 132 9-153 20-173 (374)
179 cd06338 PBP1_ABC_ligand_bindin 50.4 25 0.00055 29.3 4.0 31 122-152 196-226 (345)
180 cd06335 PBP1_ABC_ligand_bindin 50.3 26 0.00057 29.7 4.2 32 122-153 193-224 (347)
181 cd06291 PBP1_Qymf_like Ligand 50.3 31 0.00067 27.2 4.4 29 122-154 55-83 (265)
182 PTZ00295 glucosamine-fructose- 50.2 29 0.00064 33.3 4.9 48 123-170 370-420 (640)
183 PF15608 PELOTA_1: PELOTA RNA 50.0 29 0.00064 26.9 4.1 35 122-156 54-90 (100)
184 cd01989 STK_N The N-terminal d 49.8 48 0.001 24.3 5.1 29 133-161 90-118 (146)
185 cd06287 PBP1_LacI_like_8 Ligan 48.9 39 0.00085 27.6 4.9 50 105-155 27-88 (269)
186 cd02753 MopB_Formate-Dh-H Form 48.9 27 0.00058 31.8 4.3 47 122-169 156-207 (512)
187 cd06283 PBP1_RegR_EndR_KdgR_li 48.6 46 0.00099 26.0 5.0 15 139-153 71-85 (267)
188 PTZ00394 glucosamine-fructose- 48.5 33 0.00073 33.6 5.1 47 123-169 402-451 (670)
189 KOG2462 C2H2-type Zn-finger pr 48.2 9.1 0.0002 34.6 1.2 25 44-68 213-237 (279)
190 cd02766 MopB_3 The MopB_3 CD i 48.0 28 0.00061 32.1 4.3 48 122-170 157-209 (501)
191 TIGR00522 dph5 diphthine synth 48.0 29 0.00063 29.7 4.1 51 106-156 94-168 (257)
192 PF03698 UPF0180: Uncharacteri 47.6 16 0.00035 27.2 2.2 32 107-138 13-51 (80)
193 cd06334 PBP1_ABC_ligand_bindin 47.6 37 0.0008 29.4 4.8 33 122-154 195-227 (351)
194 PF00564 PB1: PB1 domain; Int 47.3 17 0.00037 24.9 2.2 35 114-148 40-75 (84)
195 cd01574 PBP1_LacI Ligand-bindi 47.3 52 0.0011 25.9 5.2 33 122-155 56-88 (264)
196 cd01391 Periplasmic_Binding_Pr 47.2 48 0.001 24.8 4.7 35 122-156 58-92 (269)
197 cd06345 PBP1_ABC_ligand_bindin 46.8 39 0.00085 28.4 4.7 31 122-152 199-229 (344)
198 TIGR01522 ATPase-IIA2_Ca golgi 46.8 38 0.00082 34.0 5.3 37 135-171 606-643 (884)
199 TIGR03479 DMSO_red_II_alp DMSO 46.7 27 0.00058 35.1 4.2 47 122-169 224-275 (912)
200 cd02759 MopB_Acetylene-hydrata 46.3 36 0.00077 31.0 4.6 47 122-169 160-212 (477)
201 cd01461 vWA_interalpha_trypsin 46.3 23 0.0005 26.4 2.9 44 123-166 100-151 (171)
202 cd00858 GlyRS_anticodon GlyRS 46.1 48 0.001 24.7 4.6 42 105-155 45-87 (121)
203 cd06363 PBP1_Taste_receptor Li 46.0 45 0.00099 29.3 5.1 33 122-154 234-267 (410)
204 cd06284 PBP1_LacI_like_6 Ligan 45.9 53 0.0011 25.7 5.0 32 122-155 55-86 (267)
205 cd06362 PBP1_mGluR Ligand bind 45.9 50 0.0011 29.2 5.4 32 122-153 230-263 (452)
206 TIGR00250 RNAse_H_YqgF RNAse H 45.7 37 0.00079 26.5 4.1 41 123-163 25-70 (130)
207 PRK09701 D-allose transporter 44.4 50 0.0011 27.7 5.0 34 122-155 82-116 (311)
208 cd06286 PBP1_CcpB_like Ligand- 44.2 58 0.0013 25.6 5.1 32 122-155 55-86 (260)
209 cd01475 vWA_Matrilin VWA_Matri 44.0 37 0.0008 27.7 4.0 40 125-164 111-155 (224)
210 cd01476 VWA_integrin_invertebr 43.8 57 0.0012 24.5 4.8 34 124-157 105-142 (163)
211 COG1609 PurR Transcriptional r 43.7 54 0.0012 28.7 5.2 50 106-156 79-147 (333)
212 COG0560 SerB Phosphoserine pho 43.7 76 0.0016 26.5 5.9 89 79-167 55-182 (212)
213 cd06327 PBP1_SBP_like_1 Peripl 43.5 33 0.0007 28.7 3.7 33 122-154 190-224 (334)
214 PF06153 DUF970: Protein of un 43.4 36 0.00078 26.7 3.7 43 105-147 14-65 (109)
215 cd01988 Na_H_Antiporter_C The 43.0 47 0.001 23.4 4.0 36 123-159 72-107 (132)
216 cd00293 USP_Like Usp: Universa 42.9 64 0.0014 21.9 4.5 28 132-159 79-106 (130)
217 PF12076 Wax2_C: WAX2 C-termin 42.8 21 0.00045 30.1 2.4 51 101-164 8-73 (164)
218 cd06269 PBP1_glutamate_recepto 42.7 77 0.0017 24.7 5.5 35 122-156 195-232 (298)
219 cd06326 PBP1_STKc_like Type I 42.5 38 0.00082 27.9 3.9 32 122-153 191-222 (336)
220 PF03720 UDPG_MGDP_dh_C: UDP-g 42.4 23 0.0005 26.0 2.4 16 122-137 66-81 (106)
221 PF09338 Gly_reductase: Glycin 42.4 12 0.00027 35.4 1.1 35 121-155 302-341 (428)
222 KOG2231 Predicted E3 ubiquitin 42.1 13 0.00029 37.1 1.4 23 49-71 102-139 (669)
223 cd06331 PBP1_AmiC_like Type I 41.9 67 0.0015 26.8 5.3 27 122-148 187-213 (333)
224 PF10727 Rossmann-like: Rossma 41.6 54 0.0012 25.7 4.4 20 102-121 20-39 (127)
225 cd01480 vWA_collagen_alpha_1-V 41.3 55 0.0012 25.8 4.5 43 123-165 110-161 (186)
226 cd02765 MopB_4 The MopB_4 CD i 41.2 42 0.00092 31.6 4.4 47 122-169 159-210 (567)
227 cd06340 PBP1_ABC_ligand_bindin 41.1 42 0.0009 28.5 4.0 28 122-149 199-226 (347)
228 cd06333 PBP1_ABC-type_HAAT_lik 41.1 51 0.0011 27.1 4.4 32 122-153 188-219 (312)
229 PRK14649 UDP-N-acetylenolpyruv 41.1 25 0.00055 30.9 2.8 35 122-156 20-54 (295)
230 cd05992 PB1 The PB1 domain is 41.1 28 0.0006 23.7 2.5 26 125-150 51-76 (81)
231 PRK13602 putative ribosomal pr 40.9 73 0.0016 23.1 4.7 58 109-168 4-73 (82)
232 PF02844 GARS_N: Phosphoribosy 40.8 30 0.00064 26.6 2.8 25 131-155 47-71 (100)
233 cd00859 HisRS_anticodon HisRS 40.8 56 0.0012 21.4 3.9 42 105-154 18-60 (91)
234 PRK00109 Holliday junction res 40.5 46 0.001 26.2 3.9 28 133-160 41-73 (138)
235 cd06409 PB1_MUG70 The MUG70 pr 40.3 44 0.00096 25.1 3.6 39 113-152 41-81 (86)
236 PRK05752 uroporphyrinogen-III 40.3 12 0.00026 31.3 0.6 59 104-162 15-99 (255)
237 PRK15395 methyl-galactoside AB 40.1 68 0.0015 27.4 5.2 34 122-155 81-115 (330)
238 cd02760 MopB_Phenylacetyl-CoA- 40.1 43 0.00092 33.4 4.5 48 122-170 173-226 (760)
239 PF10622 Ehbp: Energy-converti 40.0 27 0.00058 26.3 2.4 19 126-144 55-73 (78)
240 TIGR01591 Fdh-alpha formate de 39.9 48 0.001 31.3 4.6 47 122-169 155-206 (671)
241 PRK10671 copA copper exporting 39.8 37 0.0008 33.6 4.0 63 109-171 660-738 (834)
242 TIGR02717 AcCoA-syn-alpha acet 39.8 35 0.00075 31.5 3.6 50 103-152 22-94 (447)
243 cd01450 vWFA_subfamily_ECM Von 39.8 73 0.0016 23.0 4.7 43 124-166 105-154 (161)
244 cd02762 MopB_1 The MopB_1 CD i 39.7 38 0.00083 31.4 3.9 47 122-169 156-213 (539)
245 PTZ00175 diphthine synthase; P 39.4 77 0.0017 27.8 5.5 50 106-155 95-167 (270)
246 PRK00046 murB UDP-N-acetylenol 39.3 28 0.0006 31.7 2.8 34 123-156 21-54 (334)
247 KOG3993 Transcription factor ( 39.2 12 0.00026 36.1 0.5 30 48-77 358-387 (500)
248 TIGR01481 ccpA catabolite cont 39.1 79 0.0017 26.1 5.3 14 8-21 3-16 (329)
249 cd01453 vWA_transcription_fact 39.0 56 0.0012 26.3 4.3 41 125-165 110-156 (183)
250 PRK10339 DNA-binding transcrip 38.7 67 0.0015 26.8 4.9 32 122-155 114-145 (327)
251 smart00614 ZnF_BED BED zinc fi 38.7 14 0.00031 24.1 0.7 25 47-71 19-48 (50)
252 PF01565 FAD_binding_4: FAD bi 38.5 41 0.00089 24.9 3.2 33 124-156 2-34 (139)
253 cd02757 MopB_Arsenate-R This C 37.3 54 0.0012 30.6 4.4 47 122-169 162-215 (523)
254 TIGR00179 murB UDP-N-acetyleno 37.2 35 0.00076 29.7 3.1 33 124-156 14-46 (284)
255 PRK15400 lysine decarboxylase 37.1 48 0.001 33.3 4.3 49 106-155 21-85 (714)
256 TIGR00244 transcriptional regu 37.1 9.4 0.0002 31.5 -0.5 18 45-62 27-44 (147)
257 PRK15399 lysine decarboxylase 36.9 51 0.0011 33.1 4.5 48 107-155 22-85 (713)
258 COG5236 Uncharacterized conser 36.9 21 0.00046 34.0 1.8 28 48-75 222-249 (493)
259 TIGR00073 hypB hydrogenase acc 36.7 37 0.0008 27.3 2.9 43 109-152 66-108 (207)
260 COG0566 SpoU rRNA methylases [ 36.5 40 0.00086 29.2 3.3 28 129-156 117-144 (260)
261 PF02254 TrkA_N: TrkA-N domain 36.5 49 0.0011 23.5 3.3 45 104-160 10-54 (116)
262 PRK15488 thiosulfate reductase 36.1 51 0.0011 32.0 4.2 48 122-170 196-250 (759)
263 PF02638 DUF187: Glycosyl hydr 36.1 26 0.00057 30.9 2.1 39 110-154 1-40 (311)
264 PRK14652 UDP-N-acetylenolpyruv 35.9 37 0.00079 30.1 3.0 35 122-156 35-69 (302)
265 cd06355 PBP1_FmdD_like Peripla 35.7 79 0.0017 27.0 4.9 33 122-154 188-223 (348)
266 cd01482 vWA_collagen_alphaI-XI 35.6 64 0.0014 24.7 4.0 31 125-155 106-139 (164)
267 cd00860 ThrRS_anticodon ThrRS 35.0 1.1E+02 0.0024 20.6 4.7 43 105-155 18-61 (91)
268 PRK13903 murB UDP-N-acetylenol 34.8 40 0.00086 31.0 3.1 35 122-156 32-66 (363)
269 TIGR02128 G6PI_arch bifunction 34.4 62 0.0014 28.7 4.2 41 122-164 66-109 (308)
270 PF13528 Glyco_trans_1_3: Glyc 34.3 49 0.0011 27.4 3.4 43 122-171 94-136 (318)
271 cd01454 vWA_norD_type norD typ 34.0 84 0.0018 24.2 4.4 35 123-157 104-153 (174)
272 cd02770 MopB_DmsA-EC This CD ( 33.7 52 0.0011 31.2 3.8 47 122-169 166-221 (617)
273 cd00368 Molybdopterin-Binding 33.1 77 0.0017 27.0 4.4 47 122-169 156-207 (374)
274 cd00198 vWFA Von Willebrand fa 32.8 94 0.002 21.7 4.2 35 122-156 101-141 (161)
275 TIGR00868 hCaCC calcium-activa 32.7 65 0.0014 33.2 4.5 44 123-166 405-452 (863)
276 PRK04213 GTP-binding protein; 32.7 84 0.0018 24.3 4.3 37 122-158 90-142 (201)
277 PF01363 FYVE: FYVE zinc finge 32.6 15 0.00034 24.8 0.1 19 35-56 1-19 (69)
278 cd01493 APPBP1_RUB Ubiquitin a 32.5 1.2E+02 0.0027 28.3 6.0 117 8-143 181-297 (425)
279 TIGR03649 ergot_EASG ergot alk 32.3 64 0.0014 26.5 3.7 33 123-155 68-105 (285)
280 PRK10703 DNA-binding transcrip 32.3 1.1E+02 0.0025 25.4 5.2 32 122-154 115-147 (341)
281 cd01457 vWA_ORF176_type VWA OR 32.1 81 0.0018 25.1 4.2 42 124-166 109-165 (199)
282 PF10740 DUF2529: Protein of u 32.0 97 0.0021 26.3 4.7 48 122-169 81-133 (172)
283 PRK13054 lipid kinase; Reviewe 32.0 1.3E+02 0.0028 25.7 5.7 52 108-166 24-75 (300)
284 PF03411 Peptidase_M74: Penici 31.8 38 0.00082 30.0 2.4 33 137-169 46-90 (240)
285 cd00738 HGTP_anticodon HGTP an 31.6 1E+02 0.0023 20.7 4.2 41 107-155 23-64 (94)
286 cd02121 PA_GCPII_like PA_GCPII 31.4 91 0.002 26.9 4.6 45 104-152 53-101 (220)
287 KOG2893 Zn finger protein [Gen 31.3 20 0.00043 32.7 0.6 25 49-73 13-37 (341)
288 TIGR02815 agaS_fam putative su 31.2 71 0.0015 28.7 4.1 42 124-165 94-140 (372)
289 cd01467 vWA_BatA_type VWA BatA 31.1 1.1E+02 0.0024 23.2 4.6 31 124-154 104-142 (180)
290 PRK13906 murB UDP-N-acetylenol 31.1 45 0.00098 29.6 2.8 34 123-156 37-70 (307)
291 cd01474 vWA_ATR ATR (Anthrax T 31.1 70 0.0015 25.1 3.6 41 124-164 105-154 (185)
292 cd02126 PA_EDEM3_like PA_EDEM3 31.0 1E+02 0.0022 23.6 4.4 47 124-171 41-88 (126)
293 TIGR01553 formate-DH-alph form 31.0 70 0.0015 33.1 4.4 47 122-169 221-272 (1009)
294 TIGR00509 bisC_fam molybdopter 30.9 68 0.0015 31.3 4.2 47 122-169 167-227 (770)
295 PF03652 UPF0081: Uncharacteri 30.9 1E+02 0.0022 24.2 4.5 32 123-154 28-59 (135)
296 PRK11587 putative phosphatase; 30.6 66 0.0014 25.7 3.5 25 130-156 161-185 (218)
297 PF13519 VWA_2: von Willebrand 30.5 91 0.002 22.7 3.9 35 122-156 99-136 (172)
298 PF00582 Usp: Universal stress 30.5 1.3E+02 0.0028 20.4 4.5 37 126-162 82-118 (140)
299 PRK14653 UDP-N-acetylenolpyruv 30.2 44 0.00095 29.7 2.5 34 122-156 33-66 (297)
300 PRK13337 putative lipid kinase 30.1 1.5E+02 0.0031 25.5 5.6 49 110-165 27-75 (304)
301 PF12745 HGTP_anticodon2: Anti 30.1 30 0.00064 30.5 1.5 29 103-131 21-66 (273)
302 PF00571 CBS: CBS domain CBS d 29.8 1.1E+02 0.0023 18.9 3.7 31 126-156 9-39 (57)
303 PRK01122 potassium-transportin 29.7 82 0.0018 31.4 4.5 62 109-170 455-532 (679)
304 cd02763 MopB_2 The MopB_2 CD i 29.6 89 0.0019 30.9 4.7 47 122-169 155-206 (679)
305 cd01451 vWA_Magnesium_chelatas 29.4 1.1E+02 0.0025 23.8 4.5 43 124-166 100-156 (178)
306 TIGR03830 CxxCG_CxxCG_HTH puta 29.4 66 0.0014 23.6 3.0 38 49-86 34-78 (127)
307 PF02225 PA: PA domain; Inter 29.4 1.1E+02 0.0023 21.2 4.0 30 125-154 35-65 (101)
308 TIGR02137 HSK-PSP phosphoserin 29.3 47 0.001 27.3 2.4 37 134-170 132-169 (203)
309 smart00481 POLIIIAc DNA polyme 29.3 72 0.0016 21.2 3.0 24 133-156 15-38 (67)
310 KOG1531 F0F1-type ATP synthase 29.1 1.5E+02 0.0033 27.3 5.8 83 79-162 36-149 (304)
311 cd02754 MopB_Nitrate-R-NapA-li 28.8 88 0.0019 29.0 4.4 47 122-169 157-210 (565)
312 PRK14650 UDP-N-acetylenolpyruv 28.7 50 0.0011 29.7 2.7 34 123-156 33-66 (302)
313 cd04623 CBS_pair_10 The CBS do 28.6 1E+02 0.0022 20.7 3.7 30 127-156 4-33 (113)
314 cd06280 PBP1_LacI_like_4 Ligan 28.5 1.3E+02 0.0029 23.8 4.8 10 144-153 75-84 (263)
315 COG1231 Monoamine oxidase [Ami 28.3 77 0.0017 30.5 3.9 70 108-177 23-123 (450)
316 cd01891 TypA_BipA TypA (tyrosi 28.3 1.2E+02 0.0027 23.6 4.5 37 122-158 88-129 (194)
317 cd00338 Ser_Recombinase Serine 28.2 61 0.0013 23.6 2.6 34 129-164 48-81 (137)
318 cd06275 PBP1_PurR Ligand-bindi 28.2 1.5E+02 0.0033 23.3 5.1 7 115-121 79-85 (269)
319 PRK06975 bifunctional uroporph 28.2 27 0.00058 34.1 0.9 59 104-162 15-97 (656)
320 PF14336 DUF4392: Domain of un 28.0 54 0.0012 29.0 2.7 24 132-155 161-184 (291)
321 PRK11133 serB phosphoserine ph 28.0 1.6E+02 0.0035 26.2 5.7 35 136-170 250-289 (322)
322 cd01464 vWA_subfamily VWA subf 27.9 1.1E+02 0.0023 23.7 4.1 42 124-165 109-159 (176)
323 PRK12436 UDP-N-acetylenolpyruv 27.8 55 0.0012 29.0 2.7 34 123-156 37-70 (305)
324 KOG3608 Zn finger proteins [Ge 27.7 23 0.00051 33.7 0.4 20 49-68 210-229 (467)
325 cd02769 MopB_DMSOR-BSOR-TMAOR 27.7 1E+02 0.0022 29.4 4.6 47 122-169 170-231 (609)
326 TIGR01973 NuoG NADH-quinone ox 27.6 89 0.0019 29.7 4.2 48 122-170 362-415 (603)
327 PRK07239 bifunctional uroporph 27.5 84 0.0018 27.8 3.8 58 104-162 22-114 (381)
328 KOG0717 Molecular chaperone (D 27.3 46 0.001 32.5 2.3 32 47-81 293-324 (508)
329 cd01465 vWA_subgroup VWA subgr 27.2 1.4E+02 0.0031 22.2 4.6 42 124-165 98-151 (170)
330 cd04630 CBS_pair_17 The CBS do 26.7 1.1E+02 0.0024 21.0 3.6 31 126-156 3-33 (114)
331 PRK09484 3-deoxy-D-manno-octul 26.6 1.2E+02 0.0026 24.2 4.2 38 126-168 115-152 (183)
332 KOG2071 mRNA cleavage and poly 26.5 44 0.00095 33.1 2.0 33 48-81 420-452 (579)
333 cd01472 vWA_collagen von Wille 26.5 1.1E+02 0.0025 23.1 4.0 41 125-165 106-151 (164)
334 PF13242 Hydrolase_like: HAD-h 26.5 75 0.0016 21.5 2.7 29 126-156 24-52 (75)
335 cd01481 vWA_collagen_alpha3-VI 26.3 1.2E+02 0.0026 23.9 4.2 31 125-155 109-142 (165)
336 COG0794 GutQ Predicted sugar p 26.3 1.3E+02 0.0028 25.9 4.6 63 107-169 57-136 (202)
337 PRK00464 nrdR transcriptional 26.3 18 0.00038 29.7 -0.6 18 47-64 29-46 (154)
338 PF11814 DUF3335: Peptidase_C3 26.2 46 0.001 28.8 1.9 34 88-121 36-73 (207)
339 COG0569 TrkA K+ transport syst 26.1 80 0.0017 26.4 3.3 53 102-155 10-75 (225)
340 COG4049 Uncharacterized protei 26.1 27 0.00057 25.4 0.4 24 49-72 20-43 (65)
341 cd06379 PBP1_iGluR_NMDA_NR1 N- 26.0 92 0.002 26.8 3.7 27 122-148 213-239 (377)
342 TIGR01501 MthylAspMutase methy 26.0 1E+02 0.0022 24.6 3.8 47 108-155 22-91 (134)
343 COG2103 Predicted sugar phosph 26.0 71 0.0015 29.3 3.1 49 122-170 129-180 (298)
344 COG1327 Predicted transcriptio 26.0 25 0.00053 29.5 0.2 18 45-62 27-44 (156)
345 cd06358 PBP1_NHase Type I peri 25.9 1.2E+02 0.0026 25.4 4.3 28 122-149 187-214 (333)
346 cd06364 PBP1_CaSR Ligand-bindi 25.8 1.6E+02 0.0035 27.3 5.5 27 122-148 244-270 (510)
347 PF09986 DUF2225: Uncharacteri 25.6 22 0.00048 29.9 -0.1 13 47-59 6-18 (214)
348 cd06410 PB1_UP2 Uncharacterize 25.6 47 0.001 25.1 1.7 22 122-143 62-83 (97)
349 TIGR03470 HpnH hopanoid biosyn 25.0 1.4E+02 0.0029 26.3 4.6 43 109-154 156-199 (318)
350 PF10013 DUF2256: Uncharacteri 24.9 36 0.00079 22.9 0.8 21 48-68 10-30 (42)
351 smart00327 VWA von Willebrand 24.9 1.4E+02 0.0031 21.7 4.1 33 124-156 107-144 (177)
352 cd06290 PBP1_LacI_like_9 Ligan 24.8 1.7E+02 0.0037 23.0 4.8 31 122-154 55-85 (265)
353 cd06371 PBP1_sensory_GC_DEF_li 24.7 1.4E+02 0.0031 26.1 4.8 26 123-148 189-219 (382)
354 TIGR01116 ATPase-IIA1_Ca sarco 24.7 1.4E+02 0.003 30.2 5.2 36 136-171 620-656 (917)
355 PRK13905 murB UDP-N-acetylenol 24.7 70 0.0015 27.9 2.8 34 123-156 31-64 (298)
356 cd00287 ribokinase_pfkB_like r 24.5 1.2E+02 0.0025 23.0 3.7 48 104-151 39-89 (196)
357 cd06328 PBP1_SBP_like_2 Peripl 24.5 1.6E+02 0.0035 24.8 4.9 32 122-153 191-224 (333)
358 PF01661 Macro: Macro domain; 24.5 1.4E+02 0.0031 21.1 3.9 34 135-174 82-115 (118)
359 cd01425 RPS2 Ribosomal protein 24.4 1.4E+02 0.0029 24.6 4.3 35 122-156 126-160 (193)
360 TIGR01490 HAD-SF-IB-hyp1 HAD-s 24.4 3.4E+02 0.0073 21.0 7.1 50 72-121 52-109 (202)
361 PRK09189 uroporphyrinogen-III 24.2 1.4E+02 0.003 24.5 4.3 56 105-161 131-215 (240)
362 PF13419 HAD_2: Haloacid dehal 24.2 1E+02 0.0022 22.2 3.2 14 108-121 86-99 (176)
363 TIGR00542 hxl6Piso_put hexulos 24.2 67 0.0015 26.8 2.5 49 107-155 57-116 (279)
364 cd06307 PBP1_uncharacterized_s 24.2 1.2E+02 0.0026 24.2 3.8 33 122-154 58-91 (275)
365 TIGR01489 DKMTPPase-SF 2,3-dik 24.0 89 0.0019 23.5 3.0 32 137-168 152-185 (188)
366 cd06367 PBP1_iGluR_NMDA N-term 24.0 1.4E+02 0.0031 25.3 4.5 35 122-156 194-232 (362)
367 TIGR00640 acid_CoA_mut_C methy 23.7 2E+02 0.0044 22.4 5.0 47 108-154 23-91 (132)
368 PRK10530 pyridoxal phosphate ( 23.5 1E+02 0.0023 25.0 3.4 38 133-170 199-240 (272)
369 PF03129 HGTP_anticodon: Antic 23.4 1.9E+02 0.0042 19.9 4.4 41 107-155 21-62 (94)
370 cd06366 PBP1_GABAb_receptor Li 23.3 1.7E+02 0.0037 24.5 4.8 27 122-148 192-218 (350)
371 PF02811 PHP: PHP domain; Int 23.2 92 0.002 23.2 2.9 22 134-155 17-38 (175)
372 cd06352 PBP1_NPR_GC_like Ligan 23.2 1.6E+02 0.0035 25.1 4.7 31 124-154 196-229 (389)
373 KOG1256 Long-chain acyl-CoA sy 23.2 79 0.0017 31.9 3.1 50 126-175 183-239 (691)
374 PF05443 ROS_MUCR: ROS/MUCR tr 23.2 39 0.00084 27.2 0.9 20 48-70 74-93 (132)
375 PRK04322 peptidyl-tRNA hydrola 23.1 89 0.0019 24.2 2.8 40 109-155 40-80 (113)
376 PF03749 SfsA: Sugar fermentat 23.1 1.5E+02 0.0032 25.4 4.4 22 132-153 180-201 (215)
377 PF09151 DUF1936: Domain of un 23.1 30 0.00065 22.4 0.2 8 47-54 2-9 (36)
378 PF13893 RRM_5: RNA recognitio 23.0 55 0.0012 20.7 1.4 26 9-34 1-26 (56)
379 cd03109 DTBS Dethiobiotin synt 22.9 1.5E+02 0.0032 22.6 4.0 50 106-158 18-80 (134)
380 PF01866 Diphthamide_syn: Puta 22.7 1.8E+02 0.0039 25.5 5.0 53 69-130 191-268 (307)
381 cd01466 vWA_C3HC4_type VWA C3H 22.6 94 0.002 23.8 2.9 42 124-166 100-146 (155)
382 TIGR03677 rpl7ae 50S ribosomal 22.6 1.2E+02 0.0027 23.2 3.5 40 124-165 43-86 (117)
383 cd06329 PBP1_SBP_like_3 Peripl 22.5 1.6E+02 0.0035 24.8 4.5 33 122-154 201-233 (342)
384 PRK12305 thrS threonyl-tRNA sy 22.5 1.6E+02 0.0034 27.8 4.8 43 105-155 493-536 (575)
385 cd04104 p47_IIGP_like p47 (47- 22.5 1.5E+02 0.0032 23.6 4.1 36 122-158 80-119 (197)
386 PF13458 Peripla_BP_6: Peripla 22.4 1.7E+02 0.0037 24.0 4.5 27 122-148 190-216 (343)
387 PF07918 CAP160: CAP160 repeat 22.4 34 0.00073 21.2 0.3 14 93-106 13-26 (27)
388 cd02170 cytidylyltransferase c 22.4 1.2E+02 0.0025 22.9 3.3 31 122-156 64-94 (136)
389 PF10571 UPF0547: Uncharacteri 22.4 38 0.00082 20.2 0.5 10 48-57 16-25 (26)
390 PRK13226 phosphoglycolate phos 22.3 1.8E+02 0.0038 23.7 4.6 46 126-174 171-221 (229)
391 COG4567 Response regulator con 22.3 89 0.0019 26.8 2.9 32 125-156 11-43 (182)
392 PF00384 Molybdopterin: Molybd 22.2 1.2E+02 0.0026 26.4 3.7 46 123-169 112-163 (432)
393 smart00666 PB1 PB1 domain. Pho 22.2 96 0.0021 21.2 2.6 32 115-146 40-72 (81)
394 TIGR01580 narG respiratory nit 22.1 1.3E+02 0.0028 32.5 4.5 47 122-169 245-296 (1235)
395 PF13821 DUF4187: Domain of un 22.1 52 0.0011 22.7 1.2 17 49-65 30-46 (55)
396 cd04171 SelB SelB subfamily. 22.1 2E+02 0.0044 20.7 4.5 37 122-158 74-116 (164)
397 PRK08811 uroporphyrinogen-III 22.0 26 0.00057 30.0 -0.3 41 122-162 69-111 (266)
398 TIGR01524 ATPase-IIIB_Mg magne 21.9 1.9E+02 0.0041 29.2 5.5 32 138-169 594-626 (867)
399 COG0279 GmhA Phosphoheptose is 21.9 94 0.002 26.6 2.9 46 124-169 111-159 (176)
400 cd04643 CBS_pair_30 The CBS do 21.9 1.5E+02 0.0032 20.1 3.5 31 126-156 3-33 (116)
401 TIGR01487 SPP-like sucrose-pho 21.8 2.5E+02 0.0054 22.3 5.2 57 108-165 122-183 (215)
402 PF05198 IF3_N: Translation in 21.8 1.5E+02 0.0033 21.4 3.7 37 123-159 12-54 (76)
403 KOG1994 Predicted RNA binding 21.8 38 0.00082 30.5 0.6 23 49-71 242-264 (268)
404 PRK13582 thrH phosphoserine ph 21.7 87 0.0019 24.4 2.6 37 134-170 132-169 (205)
405 PRK14799 thrS threonyl-tRNA sy 21.7 1.6E+02 0.0034 28.5 4.7 42 106-155 456-498 (545)
406 PF03033 Glyco_transf_28: Glyc 21.7 1.5E+02 0.0032 21.5 3.6 38 106-155 17-54 (139)
407 KOG2882 p-Nitrophenyl phosphat 21.6 61 0.0013 29.8 1.9 136 9-153 18-160 (306)
408 smart00391 MBD Methyl-CpG bind 21.6 59 0.0013 23.6 1.5 17 52-68 36-52 (77)
409 cd06349 PBP1_ABC_ligand_bindin 21.6 1.8E+02 0.0038 24.3 4.5 32 122-153 190-221 (340)
410 TIGR01497 kdpB K+-transporting 21.5 1.5E+02 0.0033 29.6 4.7 63 109-171 456-534 (675)
411 cd00291 SirA_YedF_YeeD SirA, Y 21.5 2.4E+02 0.0053 18.5 4.4 32 124-155 27-59 (69)
412 PRK10423 transcriptional repre 21.4 2.1E+02 0.0045 23.5 4.9 7 144-150 171-177 (327)
413 PLN02908 threonyl-tRNA synthet 21.3 1.6E+02 0.0035 28.9 4.8 42 106-155 607-649 (686)
414 PF13788 DUF4180: Domain of un 21.1 98 0.0021 24.4 2.7 37 122-158 35-81 (113)
415 PRK09248 putative hydrolase; V 20.9 1.1E+02 0.0025 25.3 3.2 27 130-156 14-42 (246)
416 TIGR01488 HAD-SF-IB Haloacid D 20.8 1.4E+02 0.0031 22.3 3.5 24 133-156 76-99 (177)
417 PRK11914 diacylglycerol kinase 20.7 1.8E+02 0.0038 24.9 4.4 50 110-166 34-83 (306)
418 cd06380 PBP1_iGluR_AMPA N-term 20.6 1.2E+02 0.0025 26.1 3.3 28 122-149 183-210 (382)
419 cd03174 DRE_TIM_metallolyase D 20.5 1.2E+02 0.0027 24.6 3.3 45 109-156 122-169 (265)
420 KOG3623 Homeobox transcription 20.5 36 0.00079 35.2 0.2 30 44-74 279-308 (1007)
421 PF00462 Glutaredoxin: Glutare 20.5 1.4E+02 0.0029 19.2 2.9 39 110-154 18-57 (60)
422 TIGR00854 pts-sorbose PTS syst 20.4 95 0.0021 25.0 2.6 40 116-155 19-62 (151)
423 cd06388 PBP1_iGluR_AMPA_GluR4 20.3 1.5E+02 0.0032 26.3 4.0 33 122-154 178-214 (371)
424 PF08790 zf-LYAR: LYAR-type C2 20.2 16 0.00035 22.6 -1.4 25 48-73 2-26 (28)
425 COG2896 MoaA Molybdenum cofact 20.1 1.1E+02 0.0024 28.0 3.2 71 96-170 89-179 (322)
426 PF06506 PrpR_N: Propionate ca 20.1 56 0.0012 26.0 1.2 30 126-156 105-134 (176)
427 COG0300 DltE Short-chain dehyd 20.1 1.2E+02 0.0026 26.9 3.3 70 103-174 18-109 (265)
428 PF08032 SpoU_sub_bind: RNA 2' 20.0 1.7E+02 0.0037 19.4 3.5 31 132-165 29-59 (76)
429 PTZ00295 glucosamine-fructose- 20.0 1.6E+02 0.0034 28.5 4.4 78 88-166 483-593 (640)
No 1
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=98.21 E-value=4.1e-06 Score=63.39 Aligned_cols=46 Identities=28% Similarity=0.469 Sum_probs=41.1
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC--Cchhhhhhhccc
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM--SDGALKRIANAF 167 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~--~~~~L~r~Ad~~ 167 (177)
++|++||||-|+||+++++.+++.|.+.+|+|-. ....|...||-.
T Consensus 99 ~~d~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~~~~s~~L~~~~d~f 146 (149)
T cd06167 99 RIDTIVLVSGDSDFVPLVERLRELGKRVIVVGFEAKTSRELRKAADRF 146 (149)
T ss_pred CCCEEEEEECCccHHHHHHHHHHcCCEEEEEccCccChHHHHHhCCcc
Confidence 5899999999999999999999999999999984 346899999843
No 2
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=98.17 E-value=4.7e-06 Score=61.83 Aligned_cols=48 Identities=31% Similarity=0.496 Sum_probs=36.3
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEe--cCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVG--DMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG--d~~~~~L~r~Ad~~~s 169 (177)
..|.+||||-|+||.++++.++++|.+++|+| +.....|.+.||-+++
T Consensus 95 ~~d~ivLvSgD~Df~~~v~~l~~~g~~V~v~~~~~~~s~~L~~~ad~f~~ 144 (146)
T PF01936_consen 95 PPDTIVLVSGDSDFAPLVRKLRERGKRVIVVGAEDSASEALRSAADEFIS 144 (146)
T ss_dssp G-SEEEEE---GGGHHHHHHHHHH--EEEEEE-GGGS-HHHHHHSSEEEE
T ss_pred CCCEEEEEECcHHHHHHHHHHHHcCCEEEEEEeCCCCCHHHHHhcCEEEe
Confidence 45999999999999999999999999999999 3555799999997654
No 3
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=97.75 E-value=6.9e-05 Score=61.53 Aligned_cols=64 Identities=19% Similarity=0.239 Sum_probs=53.1
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC--Cchhhhhhh
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM--SDGALKRIA 164 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~--~~~~L~r~A 164 (177)
+|...|++.||.+..+ .+|++||||-|+||+.+++.+|++|.+.+|||-. ...+|.+.|
T Consensus 70 ~l~~~l~~~Gf~pv~~kG~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~~ts~~L~~ac 149 (160)
T TIGR00288 70 KLIEAVVNQGFEPIIVAGDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVINKAKENGKETIVIGAEPGFSTALQNSA 149 (160)
T ss_pred HHHHHHHHCCceEEEecCcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHHHHHHCCCEEEEEeCCCCChHHHHHhc
Confidence 3566777888876654 8899999999999999999999999999999943 335899999
Q ss_pred ccccc
Q 037201 165 NAFFS 169 (177)
Q Consensus 165 d~~~s 169 (177)
|-++.
T Consensus 150 d~FI~ 154 (160)
T TIGR00288 150 DIAII 154 (160)
T ss_pred CeEEe
Confidence 87664
No 4
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=97.34 E-value=0.00022 Score=58.15 Aligned_cols=64 Identities=19% Similarity=0.349 Sum_probs=54.0
Q ss_pred CchH-HhhhhcEEEEEe----------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC--chhhhhhhccccc
Q 037201 106 GFAD-ELKRAWFCVRNV----------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS--DGALKRIANAFFS 169 (177)
Q Consensus 106 gLa~-eLrRAGv~Vr~V----------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~--~~~L~r~Ad~~~s 169 (177)
|+.+ .+....+-|+.. .+|+++|+|=|.||..+++.|+++|.+|+|+|-+. -.+|...||-+..
T Consensus 83 ~~~~~~~~k~~vDv~la~D~~~l~~~~~~D~ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~~~s~~L~~~aD~~i~ 159 (181)
T COG1432 83 GFTDLRITKGDVDVELAVDAMELADKKNVDTIVLFSGDGDFIPLVEAARDKGKRVEVAGIEPMTSSDLRNAADYYID 159 (181)
T ss_pred ccCcccccccCcchhhHHHHHHhhcccCCCEEEEEcCCccHHHHHHHHHHcCCEEEEEecCCcCHHHHHHhhcceEE
Confidence 5556 777777777777 89999999999999999999999999999999864 2389999986544
No 5
>cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
Probab=96.40 E-value=0.01 Score=42.83 Aligned_cols=62 Identities=21% Similarity=0.162 Sum_probs=48.3
Q ss_pred hHHhhhhcEEEEEe--------------ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 108 ADELKRAWFCVRNV--------------RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 108 a~eLrRAGv~Vr~V--------------~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
+.-|++.|..+..+ .-||++++|-. .+..++++.|+++|.++|+|.+..+..|.+.+|..|.
T Consensus 32 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iS~~g~~~~~~~~~~~a~~~g~~iv~iT~~~~~~l~~~~d~~i~ 110 (139)
T cd05013 32 AYKLLRLGKPVVLLSDPHLQLMSAANLTPGDVVIAISFSGETKETVEAAEIAKERGAKVIAITDSANSPLAKLADIVLL 110 (139)
T ss_pred HHHHHHcCCceEEecCHHHHHHHHHcCCCCCEEEEEeCCCCCHHHHHHHHHHHHcCCeEEEEcCCCCChhHHhcCEEEE
Confidence 34455666666665 45788888854 4477788999999999999999888899999998764
No 6
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.26 E-value=0.0024 Score=34.45 Aligned_cols=23 Identities=22% Similarity=0.222 Sum_probs=19.3
Q ss_pred hhhhcCCCcCChhHHHHHHHhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIH 70 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlH 70 (177)
-|..||..|++...|..|.++-|
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCcCCCCcCCcHHHHHHHHHhhC
Confidence 38999999999999999999876
No 7
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.23 E-value=0.0023 Score=35.46 Aligned_cols=22 Identities=23% Similarity=0.271 Sum_probs=20.2
Q ss_pred hhhhcCCCcCChhHHHHHHHhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIH 70 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlH 70 (177)
.|..||+.|++...|.+|-+. |
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~-H 23 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMRR-H 23 (23)
T ss_dssp EETTTTEEESSHHHHHHHHHH-H
T ss_pred CCCCCCCccCCHHHHHHHHhH-C
Confidence 389999999999999999887 6
No 8
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=96.18 E-value=0.014 Score=42.83 Aligned_cols=50 Identities=6% Similarity=0.256 Sum_probs=43.5
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccchh
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSWS 171 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW~ 171 (177)
.-|+++++|-. .+..++++.|+++|.++|+|-+..+..|.+.||..|...
T Consensus 47 ~~d~vi~iS~sG~t~~~~~~~~~a~~~g~~vi~iT~~~~s~la~~ad~~l~~~ 99 (128)
T cd05014 47 PGDVVIAISNSGETDELLNLLPHLKRRGAPIIAITGNPNSTLAKLSDVVLDLP 99 (128)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCCCchhhhCCEEEECC
Confidence 45788888854 788899999999999999999998899999999988663
No 9
>cd05005 SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.
Probab=95.33 E-value=0.05 Score=42.98 Aligned_cols=62 Identities=21% Similarity=0.193 Sum_probs=50.7
Q ss_pred HHhhhhcEEEEEe---------ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 109 DELKRAWFCVRNV---------RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 109 ~eLrRAGv~Vr~V---------~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
..|.+.|..|..+ .-|+++.+|-. .+..++++.|+++|.++|.|-|..+..|.+.||..|..
T Consensus 53 ~~l~~~g~~~~~~~~~~~~~~~~~D~vI~iS~sG~t~~~i~~~~~ak~~g~~iI~IT~~~~s~la~~ad~~l~~ 126 (179)
T cd05005 53 MRLMHLGLNVYVVGETTTPAIGPGDLLIAISGSGETSSVVNAAEKAKKAGAKVVLITSNPDSPLAKLADVVVVI 126 (179)
T ss_pred HHHHhCCCeEEEeCCCCCCCCCCCCEEEEEcCCCCcHHHHHHHHHHHHCCCeEEEEECCCCCchHHhCCEEEEe
Confidence 3466677777665 56788889855 67778889999999999999998888999999998754
No 10
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.79 E-value=0.016 Score=34.07 Aligned_cols=19 Identities=26% Similarity=0.273 Sum_probs=16.9
Q ss_pred hhhcCCCcCChhHHHHHHHh
Q 037201 49 LIRNQGRFYNNDKLVNHFRQ 68 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kHFkq 68 (177)
|+.|||+| ..+.|.+|.+.
T Consensus 5 C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 5 CPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CCCCCCEE-CHHHHHHHHHh
Confidence 99999999 88999999763
No 11
>PF01380 SIS: SIS domain SIS domain web page.; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A ....
Probab=94.69 E-value=0.064 Score=38.84 Aligned_cols=47 Identities=17% Similarity=0.316 Sum_probs=39.5
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhcccc
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFF 168 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~ 168 (177)
.-|+++++|-+ .+..+.++.|+++|.++|+|-+..+..+.+.||.-|
T Consensus 53 ~~d~vi~is~sg~~~~~~~~~~~ak~~g~~vi~iT~~~~~~l~~~ad~~l 102 (131)
T PF01380_consen 53 PDDLVIIISYSGETRELIELLRFAKERGAPVILITSNSESPLARLADIVL 102 (131)
T ss_dssp TTEEEEEEESSSTTHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEE
T ss_pred ccceeEeeeccccchhhhhhhHHHHhcCCeEEEEeCCCCCchhhhCCEEE
Confidence 56889999943 456677888999999999999988899999998765
No 12
>cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=94.50 E-value=0.077 Score=38.77 Aligned_cols=48 Identities=15% Similarity=0.193 Sum_probs=39.9
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
.-|.++.+|-. .+-.++++.|+++|.++|.|-+..+..|.+.||..|.
T Consensus 46 ~~d~~I~iS~sG~t~e~~~~~~~a~~~g~~vi~iT~~~~s~la~~ad~~l~ 96 (126)
T cd05008 46 EDTLVIAISQSGETADTLAALRLAKEKGAKTVAITNVVGSTLAREADYVLY 96 (126)
T ss_pred CCcEEEEEeCCcCCHHHHHHHHHHHHcCCeEEEEECCCCChHHHhCCEEEE
Confidence 45778888854 4566778889999999999999888899999998763
No 13
>smart00355 ZnF_C2H2 zinc finger.
Probab=93.93 E-value=0.039 Score=29.61 Aligned_cols=22 Identities=23% Similarity=0.282 Sum_probs=19.9
Q ss_pred hhhcCCCcCChhHHHHHHHhhhh
Q 037201 49 LIRNQGRFYNNDKLVNHFRQIHE 71 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kHFkqlHe 71 (177)
|..|+..|.+...|..|.+ +|.
T Consensus 3 C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 3 CPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCcchhCCHHHHHHHHH-Hhc
Confidence 8899999999999999987 664
No 14
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=93.71 E-value=0.16 Score=42.56 Aligned_cols=83 Identities=18% Similarity=0.130 Sum_probs=64.1
Q ss_pred chHHHHHHHHhhcCCCC----CCCc--------hHHhhhhcEEEEEe--------------ecceEEEEeC---CCchHH
Q 037201 87 KMEKYKMAVSAILTPKV----GYGF--------ADELKRAWFCVRNV--------------RFGCLMVVSD---DSNFVE 137 (177)
Q Consensus 87 K~~KY~~Aar~vl~pkv----gygL--------a~eLrRAGv~Vr~V--------------~v~clvLVSD---dsdf~~ 137 (177)
..++.++++..+...+. |.|. +..|.+.|..+... .-|+++.+|= ..+..+
T Consensus 114 ~~~~l~~~~~~i~~a~~I~i~G~G~s~~~A~~~~~~l~~~g~~~~~~~d~~~~~~~~~~~~~~Dv~I~iS~sg~~~~~~~ 193 (278)
T PRK11557 114 SEEKLHECVTMLRSARRIILTGIGASGLVAQNFAWKLMKIGINAVAERDMHALLATVQALSPDDLLLAISYSGERRELNL 193 (278)
T ss_pred CHHHHHHHHHHHhcCCeEEEEecChhHHHHHHHHHHHhhCCCeEEEcCChHHHHHHHHhCCCCCEEEEEcCCCCCHHHHH
Confidence 35778888887766664 6663 34567889888765 4577888884 355667
Q ss_pred HHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 138 VFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 138 ~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
+++.|+++|.++|+|-|..+..+.+.||.-|.
T Consensus 194 ~~~~ak~~ga~iI~IT~~~~s~la~~ad~~l~ 225 (278)
T PRK11557 194 AADEALRVGAKVLAITGFTPNALQQRASHCLY 225 (278)
T ss_pred HHHHHHHcCCCEEEEcCCCCCchHHhCCEEEE
Confidence 88999999999999999988999999998773
No 15
>TIGR03127 RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin.
Probab=93.69 E-value=0.23 Score=39.00 Aligned_cols=59 Identities=19% Similarity=0.219 Sum_probs=47.3
Q ss_pred HhhhhcEEEEEe---------ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhcccc
Q 037201 110 ELKRAWFCVRNV---------RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFF 168 (177)
Q Consensus 110 eLrRAGv~Vr~V---------~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~ 168 (177)
-|.+.|..+..+ .-|+++++|-. .+..++++.|+++|.++|+|-|..+..|.+.||.-|
T Consensus 51 ~l~~~g~~~~~~~~~~~~~~~~~Dv~I~iS~sG~t~~~i~~~~~ak~~g~~ii~IT~~~~s~la~~ad~~l 121 (179)
T TIGR03127 51 RLMHLGFNVYVVGETTTPSIKKGDLLIAISGSGETESLVTVAKKAKEIGATVAAITTNPESTLGKLADVVV 121 (179)
T ss_pred HHHhCCCeEEEeCCcccCCCCCCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCCCCchHHhCCEEE
Confidence 356667766555 45778888854 567788888999999999999988899999999866
No 16
>cd05710 SIS_1 A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=93.38 E-value=0.16 Score=37.96 Aligned_cols=48 Identities=15% Similarity=0.173 Sum_probs=40.3
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
.-|+++.+|-. .+-.++++.|+++|.++|.|-+..+..|.+.||..|.
T Consensus 47 ~~dl~I~iS~SG~t~~~~~~~~~a~~~g~~vi~iT~~~~s~la~~ad~~l~ 97 (120)
T cd05710 47 EKSVVILASHSGNTKETVAAAKFAKEKGATVIGLTDDEDSPLAKLADYVIV 97 (120)
T ss_pred CCcEEEEEeCCCCChHHHHHHHHHHHcCCeEEEEECCCCCcHHHhCCEEEE
Confidence 34788888855 6777888889999999999999888899999998663
No 17
>PRK15482 transcriptional regulator MurR; Provisional
Probab=93.28 E-value=0.23 Score=41.96 Aligned_cols=82 Identities=15% Similarity=0.204 Sum_probs=63.2
Q ss_pred hHHHHHHHHhhcCCCC----CCCc--------hHHhhhhcEEEEEe--------------ecceEEEEeCC---CchHHH
Q 037201 88 MEKYKMAVSAILTPKV----GYGF--------ADELKRAWFCVRNV--------------RFGCLMVVSDD---SNFVEV 138 (177)
Q Consensus 88 ~~KY~~Aar~vl~pkv----gygL--------a~eLrRAGv~Vr~V--------------~v~clvLVSDd---sdf~~~ 138 (177)
.+.+++++..+...+. |.|. .--|.+.|..|... .-|+++.+|-. .+..++
T Consensus 122 ~~~l~~~~~~i~~A~~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~d~~~~~~~~~~~~~~Dv~i~iS~sg~t~~~~~~ 201 (285)
T PRK15482 122 YARLQKIIEVISKAPFIQITGLGGSALVGRDLSFKLMKIGYRVACEADTHVQATVSQALKKGDVQIAISYSGSKKEIVLC 201 (285)
T ss_pred HHHHHHHHHHHHhCCeeEEEEeChhHHHHHHHHHHHHhCCCeeEEeccHhHHHHHHhcCCCCCEEEEEeCCCCCHHHHHH
Confidence 4577788877766553 5553 33456788888765 34889999954 667788
Q ss_pred HHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 139 FQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 139 lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
++.|+++|.++|.|-|..+..|.+.||.-|.
T Consensus 202 ~~~a~~~g~~iI~IT~~~~s~la~~ad~~l~ 232 (285)
T PRK15482 202 AEAARKQGATVIAITSLADSPLRRLAHFTLD 232 (285)
T ss_pred HHHHHHCCCEEEEEeCCCCCchHHhCCEEEE
Confidence 8889999999999999988899999998764
No 18
>TIGR00441 gmhA phosphoheptose isomerase. Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi.
Probab=93.24 E-value=0.14 Score=40.10 Aligned_cols=47 Identities=15% Similarity=0.253 Sum_probs=39.7
Q ss_pred cceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 123 FGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 123 v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
-|.++++|-. .+-.++++.|+++|+++|.|-+..+..|.+.||.-|.
T Consensus 80 ~D~~i~iS~sG~t~~~~~~~~~a~~~g~~ii~iT~~~~s~l~~~ad~~l~ 129 (154)
T TIGR00441 80 GDVLLGISTSGNSKNVLKAIEAAKDKGMKTITLAGKDGGKMAGLADIELR 129 (154)
T ss_pred CCEEEEEcCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCCchhhhCCEEEE
Confidence 3788999955 5666788889999999999999888899999998764
No 19
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=93.22 E-value=0.24 Score=41.82 Aligned_cols=82 Identities=15% Similarity=0.255 Sum_probs=62.8
Q ss_pred hHHHHHHHHhhcCCCC----CCC--------chHHhhhhcEEEEEe--------------ecceEEEEeCC---CchHHH
Q 037201 88 MEKYKMAVSAILTPKV----GYG--------FADELKRAWFCVRNV--------------RFGCLMVVSDD---SNFVEV 138 (177)
Q Consensus 88 ~~KY~~Aar~vl~pkv----gyg--------La~eLrRAGv~Vr~V--------------~v~clvLVSDd---sdf~~~ 138 (177)
.+..++++..+...+. |.| ++..|.|.|+.+..+ .-|++|++|-. .+..++
T Consensus 127 ~~~l~~~~~~i~~A~~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~d~~~~~~~~~~~~~~Dl~I~iS~sG~t~~~~~~ 206 (292)
T PRK11337 127 VDEFHRAARFFYQARQRDLYGAGGSAAIARDVQHKFLRIGVRCQAYDDAHIMLMSAALLQEGDVVLVVSHSGRTSDVIEA 206 (292)
T ss_pred HHHHHHHHHHHHcCCeEEEEEecHHHHHHHHHHHHHhhCCCeEEEcCCHHHHHHHHhcCCCCCEEEEEeCCCCCHHHHHH
Confidence 4667777776665543 655 234567888888755 34778888864 568888
Q ss_pred HHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 139 FQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 139 lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
++.|+++|.++|+|-|..+..|.+.||.-|.
T Consensus 207 ~~~ak~~g~~ii~IT~~~~s~la~~ad~~l~ 237 (292)
T PRK11337 207 VELAKKNGAKIICITNSYHSPIAKLADYVIC 237 (292)
T ss_pred HHHHHHCCCeEEEEeCCCCChhHHhCCEEEE
Confidence 9999999999999999988999999998774
No 20
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=91.96 E-value=0.28 Score=38.63 Aligned_cols=48 Identities=19% Similarity=0.245 Sum_probs=39.8
Q ss_pred cceEEEEeC---CCchHHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 123 FGCLMVVSD---DSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 123 v~clvLVSD---dsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
-|++|++|- ..+-.++++.|+++|+++|.|-+..+..|.+.||.-|.-
T Consensus 102 ~Dv~I~iS~SG~t~~~i~~~~~ak~~Ga~vI~IT~~~~s~La~~aD~~l~~ 152 (177)
T cd05006 102 GDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDGGKLLELADIEIHV 152 (177)
T ss_pred CCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCCchhhhCCEEEEe
Confidence 467778874 456778888999999999999998888999999987753
No 21
>PRK13937 phosphoheptose isomerase; Provisional
Probab=91.72 E-value=0.31 Score=39.45 Aligned_cols=48 Identities=15% Similarity=0.239 Sum_probs=40.7
Q ss_pred cceEEEEe---CCCchHHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 123 FGCLMVVS---DDSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 123 v~clvLVS---Ddsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
-|+++.+| ...+-.++++.|+++|.+||.|-+..+..|.+.||..+..
T Consensus 107 ~Dl~i~iS~sG~t~~~~~~~~~ak~~g~~~I~iT~~~~s~L~~~ad~~l~~ 157 (188)
T PRK13937 107 GDVLIGISTSGNSPNVLAALEKARELGMKTIGLTGRDGGKMKELCDHLLIV 157 (188)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEeCCCCChhHHhCCEEEEe
Confidence 37888888 4577788899999999999999887778999999987753
No 22
>PRK13936 phosphoheptose isomerase; Provisional
Probab=90.49 E-value=0.46 Score=38.85 Aligned_cols=48 Identities=17% Similarity=0.279 Sum_probs=39.8
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhh---hccccc
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRI---ANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~---Ad~~~s 169 (177)
.=|+++++|-. .+..++++.|+++|+++|.|.+..++.|.+. ||..+.
T Consensus 111 ~~Dv~i~iS~sG~t~~~~~~~~~ak~~g~~iI~IT~~~~s~l~~l~~~ad~~l~ 164 (197)
T PRK13936 111 PGDVLLAISTSGNSANVIQAIQAAHEREMHVVALTGRDGGKMASLLLPEDVEIR 164 (197)
T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCCCChhhhhhccCCEEEE
Confidence 35889999955 6778889999999999999999877888885 887663
No 23
>TIGR00393 kpsF KpsF/GutQ family protein. This model describes a number of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. One is GutQ, a protein of the glucitol operon. Another is KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of E. coli.
Probab=90.34 E-value=0.67 Score=38.18 Aligned_cols=49 Identities=10% Similarity=0.178 Sum_probs=42.6
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
.-|+++.+|-. .+-.++++.|+++|.++|.|-+.....|...||..|..
T Consensus 47 ~~d~~i~iS~sG~t~~~~~~~~~a~~~g~~ii~iT~~~~s~l~~~~d~~l~~ 98 (268)
T TIGR00393 47 PNDVVLMISYSGESLELLNLIPHLKRLSHKIIAFTGSPNSSLARAADYVLDI 98 (268)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHcCCcEEEEECCCCCcccccCCEEEEc
Confidence 44788899865 66778889999999999999998888999999999876
No 24
>PRK00414 gmhA phosphoheptose isomerase; Reviewed
Probab=89.67 E-value=0.61 Score=38.16 Aligned_cols=45 Identities=16% Similarity=0.338 Sum_probs=39.3
Q ss_pred ceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhcccc
Q 037201 124 GCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFF 168 (177)
Q Consensus 124 ~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~ 168 (177)
|+++.+|-. .+-.++++.|+++|++||.|-...+..|.+.||.-+
T Consensus 113 Dv~I~iS~SG~t~~~i~~~~~ak~~g~~iI~iT~~~~s~l~~~ad~~l 160 (192)
T PRK00414 113 DVLLGISTSGNSGNIIKAIEAARAKGMKVITLTGKDGGKMAGLADIEI 160 (192)
T ss_pred CEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCCChhHHhCCEEE
Confidence 788889955 677788899999999999999887889999999865
No 25
>PHA00616 hypothetical protein
Probab=89.57 E-value=0.15 Score=34.34 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=22.7
Q ss_pred hhhhhcCCCcCChhHHHHHHHhhhhh
Q 037201 47 CLLIRNQGRFYNNDKLVNHFRQIHEG 72 (177)
Q Consensus 47 ~Lc~~CGrrf~t~~~L~kHFkqlHer 72 (177)
..|+.||..|.....|.+|-++-|-.
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 34999999999999999999887754
No 26
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=89.08 E-value=0.12 Score=30.04 Aligned_cols=22 Identities=14% Similarity=0.208 Sum_probs=19.8
Q ss_pred hhhhhcCCCcCChhHHHHHHHh
Q 037201 47 CLLIRNQGRFYNNDKLVNHFRQ 68 (177)
Q Consensus 47 ~Lc~~CGrrf~t~~~L~kHFkq 68 (177)
+.|..|++.|.+...|..|.+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5699999999999999999875
No 27
>PRK10892 D-arabinose 5-phosphate isomerase; Provisional
Probab=88.86 E-value=1 Score=38.69 Aligned_cols=60 Identities=8% Similarity=0.120 Sum_probs=49.6
Q ss_pred HHhhhhcEEEEEe--------------ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhcccc
Q 037201 109 DELKRAWFCVRNV--------------RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFF 168 (177)
Q Consensus 109 ~eLrRAGv~Vr~V--------------~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~ 168 (177)
..|-+.|..+..+ .-|+++.+|-. .+..++++.|+++|.++|.|-+..+..|.+.||..|
T Consensus 67 ~~l~~~g~~~~~~~~~~~~~~~~~~~~~~d~~I~iS~sG~t~~~~~~~~~ak~~g~~vi~iT~~~~s~la~~ad~~l 143 (326)
T PRK10892 67 ATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEILALIPVLKRLHVPLICITGRPESSMARAADIHL 143 (326)
T ss_pred HHHhcCCceeEEeChHHhhccccccCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCcEEEEECCCCCcccccCCEEE
Confidence 3455677766654 34788999964 778889999999999999999998899999999987
No 28
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=88.20 E-value=0.21 Score=27.92 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=18.8
Q ss_pred hhhhcCCCcCChhHHHHHHHh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQ 68 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkq 68 (177)
.|.+|+..|.+...|..|++-
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCcCCHHHHHHHHCc
Confidence 389999999999999999863
No 29
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=87.45 E-value=0.45 Score=28.27 Aligned_cols=31 Identities=10% Similarity=0.072 Sum_probs=25.8
Q ss_pred hhhhhcCCCcCChhHHHHHHHhhhhhhhhhh
Q 037201 47 CLLIRNQGRFYNNDKLVNHFRQIHEGEQKKR 77 (177)
Q Consensus 47 ~Lc~~CGrrf~t~~~L~kHFkqlHerEr~Kr 77 (177)
+.|..|+..|.+...+..|.+.-.-+++.++
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred eEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 5699999999999999999988766665544
No 30
>PF07279 DUF1442: Protein of unknown function (DUF1442); InterPro: IPR009902 This family consists of several hypothetical Arabidopsis thaliana proteins of around 225 residues in length. The function of this family is unknown.
Probab=87.40 E-value=0.84 Score=39.68 Aligned_cols=51 Identities=27% Similarity=0.382 Sum_probs=42.8
Q ss_pred ecceEEEEeCCCchH-HHHHHHHHcCccEEEEecCCchhhhhhhccccchhhhhcC
Q 037201 122 RFGCLMVVSDDSNFV-EVFQEATLRCLKMVVVGDMSDGALKRIANAFFSWSDLLMG 176 (177)
Q Consensus 122 ~v~clvLVSDdsdf~-~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW~ev~~G 176 (177)
++|-+++=|+..||. .+|+.|+.-.-+.||||... +.|. .-.|+|..+..|
T Consensus 115 ~iDF~vVDc~~~d~~~~vl~~~~~~~~GaVVV~~Na---~~r~-~~~~~w~~~~~~ 166 (218)
T PF07279_consen 115 GIDFVVVDCKREDFAARVLRAAKLSPRGAVVVCYNA---FSRS-TNGFSWRSVLRG 166 (218)
T ss_pred CCCEEEEeCCchhHHHHHHHHhccCCCceEEEEecc---ccCC-cCCccHHHhcCC
Confidence 899999999999999 99999997667899999983 4443 467899988765
No 31
>PHA02768 hypothetical protein; Provisional
Probab=87.08 E-value=0.37 Score=33.74 Aligned_cols=23 Identities=13% Similarity=0.267 Sum_probs=20.3
Q ss_pred hhhhcCCCcCChhHHHHHHHhhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIHE 71 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlHe 71 (177)
-|..||++|.....|..|-+. |.
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~-H~ 29 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRK-HN 29 (55)
T ss_pred CcchhCCeeccHHHHHHHHHh-cC
Confidence 399999999999999999877 55
No 32
>PRK13938 phosphoheptose isomerase; Provisional
Probab=87.03 E-value=0.8 Score=38.09 Aligned_cols=50 Identities=16% Similarity=0.165 Sum_probs=40.3
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccchh
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSWS 171 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW~ 171 (177)
.-|.++.+|-. .+-.++++.|+++|+++|.+.+..++.|.+.||.-+...
T Consensus 113 ~~DllI~iS~SG~t~~vi~a~~~Ak~~G~~vI~iT~~~~s~La~~aD~~l~v~ 165 (196)
T PRK13938 113 PGDTLFAISTSGNSMSVLRAAKTARELGVTVVAMTGESGGQLAEFADFLINVP 165 (196)
T ss_pred CCCEEEEEcCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCChhhhhCCEEEEeC
Confidence 44778888875 345577788899999999999988899999999877543
No 33
>PRK11543 gutQ D-arabinose 5-phosphate isomerase; Provisional
Probab=86.96 E-value=1.5 Score=37.30 Aligned_cols=79 Identities=16% Similarity=0.156 Sum_probs=58.5
Q ss_pred HHHHHHHhhcCCC--C---CCCc--------hHHhhhhcEEEEEe--------------ecceEEEEeCC---CchHHHH
Q 037201 90 KYKMAVSAILTPK--V---GYGF--------ADELKRAWFCVRNV--------------RFGCLMVVSDD---SNFVEVF 139 (177)
Q Consensus 90 KY~~Aar~vl~pk--v---gygL--------a~eLrRAGv~Vr~V--------------~v~clvLVSDd---sdf~~~l 139 (177)
...+++..++..+ + |.|- +.-|-+.|..+..+ .-|+++.+|-. .+-.+++
T Consensus 30 ~~~~~~~~l~~~~~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~d~~i~iS~sG~t~~~~~~~ 109 (321)
T PRK11543 30 DFVRAANIILHCEGKVVVSGIGKSGHIGKKIAATLASTGTPAFFVHPAEALHGDLGMIESRDVMLFISYSGGAKELDLII 109 (321)
T ss_pred HHHHHHHHHHhcCCcEEEEecChhHHHHHHHHHHHHcCCCceeecChHHHhhCCcCccCCCCEEEEEeCCCCcHHHHHHH
Confidence 4666666666643 3 5552 34456678876655 44788888876 5566778
Q ss_pred HHHHHcCccEEEEecCCchhhhhhhcccc
Q 037201 140 QEATLRCLKMVVVGDMSDGALKRIANAFF 168 (177)
Q Consensus 140 r~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~ 168 (177)
+.|+++|.++|.|-+..+..|.+.||.-|
T Consensus 110 ~~ak~~g~~vI~iT~~~~s~la~~ad~~l 138 (321)
T PRK11543 110 PRLEDKSIALLAMTGKPTSPLGLAAKAVL 138 (321)
T ss_pred HHHHHcCCeEEEEECCCCChhHHhCCEEE
Confidence 88889999999999988899999999877
No 34
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=86.17 E-value=2.9 Score=39.87 Aligned_cols=82 Identities=15% Similarity=0.178 Sum_probs=63.0
Q ss_pred chHHHHHHHHhhcCCCC----CCCc--------hHHhhhhcEEEEEe--------------ecceEEEEeCCC---chHH
Q 037201 87 KMEKYKMAVSAILTPKV----GYGF--------ADELKRAWFCVRNV--------------RFGCLMVVSDDS---NFVE 137 (177)
Q Consensus 87 K~~KY~~Aar~vl~pkv----gygL--------a~eLrRAGv~Vr~V--------------~v~clvLVSDds---df~~ 137 (177)
..+.+++++..+...+. |+|- ...|.|.|+.+... .-|++|++|-.- +..+
T Consensus 454 d~~~l~~aa~~L~~a~rI~i~G~G~S~~~A~~~~~~l~~lg~~~~~~~d~~~~~~~~~~l~~~DvvI~iS~sG~t~e~i~ 533 (638)
T PRK14101 454 NFEHVEQAIDILNNARRIEFYGLGNSNIVAQDAHYKFFRFGIPTIAYGDLYMQAASAALLGKGDVIVAVSKSGRAPELLR 533 (638)
T ss_pred CHHHHHHHHHHHhcCCEEEEEEccHHHHHHHHHHHHHhcCCceEEEcCCHHHHHHHHhcCCCCCEEEEEeCCCCCHHHHH
Confidence 45778888888776665 6664 33567788887755 348899999754 4567
Q ss_pred HHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 138 VFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 138 ~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
+++.|+++|.++|.|-|. +..|.+.||.-|+
T Consensus 534 ~~~~Ak~~Ga~vIaIT~~-~spLa~~aD~~L~ 564 (638)
T PRK14101 534 VLDVAMQAGAKVIAITSS-NTPLAKRATVALE 564 (638)
T ss_pred HHHHHHHCCCeEEEEcCC-CChhHhhCCEEEE
Confidence 778888999999999996 6899999998764
No 35
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=86.13 E-value=1.2 Score=37.09 Aligned_cols=81 Identities=19% Similarity=0.165 Sum_probs=57.9
Q ss_pred hHHHHHHHHhhcCCCC----CCCchHH--------hhhhcEEEEEe--------------ecceEEEEeCC---CchHHH
Q 037201 88 MEKYKMAVSAILTPKV----GYGFADE--------LKRAWFCVRNV--------------RFGCLMVVSDD---SNFVEV 138 (177)
Q Consensus 88 ~~KY~~Aar~vl~pkv----gygLa~e--------LrRAGv~Vr~V--------------~v~clvLVSDd---sdf~~~ 138 (177)
.+..++++..+...+- |.|-..- |-|-|+.+... .-|+++++|-. .+..++
T Consensus 115 ~~~i~~~~~~i~~a~~I~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~D~vI~iS~sG~t~~~~~~ 194 (284)
T PRK11302 115 PSAINRAVDLLTQAKKISFFGLGASAAVAHDAQNKFFRFNVPVVYFDDIVMQRMSCMNSSDGDVVVLISHTGRTKSLVEL 194 (284)
T ss_pred HHHHHHHHHHHHcCCeEEEEEcchHHHHHHHHHHHHHhcCCceEecCCHHHHHHHHHhCCCCCEEEEEeCCCCCHHHHHH
Confidence 4567777777665554 6554222 55677766654 34677888754 356667
Q ss_pred HHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 139 FQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 139 lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
++.|+++|.++|+|.+ .+..|.+.||.-|.
T Consensus 195 ~~~ak~~g~~vI~IT~-~~s~l~~~ad~~l~ 224 (284)
T PRK11302 195 AQLARENGATVIAITS-AGSPLAREATLALT 224 (284)
T ss_pred HHHHHHcCCeEEEECC-CCChhHHhCCEEEe
Confidence 8888999999999998 56899999998774
No 36
>PRK02947 hypothetical protein; Provisional
Probab=86.01 E-value=1.2 Score=37.76 Aligned_cols=48 Identities=25% Similarity=0.302 Sum_probs=39.5
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCC-----------chhhhhhhccccc
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMS-----------DGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~-----------~~~L~r~Ad~~~s 169 (177)
.-|+++++|-. .+-.++++.|+++|.++|.|-+.. +..|.+.||+-+.
T Consensus 106 ~~Dv~i~iS~sG~t~~~i~~~~~a~~~g~~vI~iT~~~~s~~~~~~h~~gs~l~~~ad~~l~ 167 (246)
T PRK02947 106 PGDVLIVVSNSGRNPVPIEMALEAKERGAKVIAVTSLAYSASVASRHSSGKRLAEVADVVLD 167 (246)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEcCCcccccccccCCCcCchhHhCCEEEE
Confidence 45889999954 667778889999999999999975 3699999998763
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=85.91 E-value=0.49 Score=33.37 Aligned_cols=24 Identities=13% Similarity=-0.029 Sum_probs=19.2
Q ss_pred hhhhcCCCcCChhHHHHHHHhhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIHE 71 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlHe 71 (177)
-|+.||+-++...+|.+|.+--|.
T Consensus 26 tCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 26 TCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp E-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCcchhhccchhhHHHHHHHHhc
Confidence 499999999999999999988875
No 38
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=85.76 E-value=0.3 Score=27.72 Aligned_cols=22 Identities=18% Similarity=0.018 Sum_probs=19.2
Q ss_pred hhhhhcCCCcCChhHHHHHHHh
Q 037201 47 CLLIRNQGRFYNNDKLVNHFRQ 68 (177)
Q Consensus 47 ~Lc~~CGrrf~t~~~L~kHFkq 68 (177)
+.|..|+..|.+...|..|-+.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCccCCccCChhHHHHHhHH
Confidence 3499999999999999999754
No 39
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=85.25 E-value=0.48 Score=31.56 Aligned_cols=28 Identities=21% Similarity=0.196 Sum_probs=24.1
Q ss_pred hhhhhcCCCcCChhHHHHHHHhhhhhhhh
Q 037201 47 CLLIRNQGRFYNNDKLVNHFRQIHEGEQK 75 (177)
Q Consensus 47 ~Lc~~CGrrf~t~~~L~kHFkqlHerEr~ 75 (177)
+.|+.||. --+...|..|..+-|..+..
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~ 30 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESK 30 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCC
Confidence 56999999 57789999999999998754
No 40
>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=85.06 E-value=1.7 Score=34.26 Aligned_cols=51 Identities=12% Similarity=0.055 Sum_probs=34.9
Q ss_pred CCchHHhhhhcEEEEEe--------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV--------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V--------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..+++..|+.+... ++|.|++++.+.+..++++.+.+.++..|+|+-.
T Consensus 19 ~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~~ipvv~i~~~ 89 (270)
T cd01545 19 LGALDACRDTGYQLVIEPCDSGSPDLAERVRALLQRSRVDGVILTPPLSDNPELLDLLDEAGVPYVRIAPG 89 (270)
T ss_pred HHHHHHHHhCCCeEEEEeCCCCchHHHHHHHHHHHHCCCCEEEEeCCCCCccHHHHHHHhcCCCEEEEecC
Confidence 35556666666665544 6788888765544567788888888888888643
No 41
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=84.53 E-value=2.3 Score=33.73 Aligned_cols=50 Identities=10% Similarity=0.026 Sum_probs=37.8
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|+..+++..|+.+... ++|.||+.+.+++ ..++++.+.++|+..|.++..
T Consensus 20 gi~~~~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~vdgii~~~~~~~~~~~~i~~~~~~~ipvV~~~~~ 89 (273)
T cd06305 20 GTKAEAEALGGDLRVYDAGGDDAKQADQIDQAIAQKVDAIIIQHGRAEVLKPWVKRALDAGIPVVAFDVD 89 (273)
T ss_pred HHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEecCChhhhHHHHHHHHHcCCCEEEecCC
Confidence 4456666666666554 8999999875544 578899999999999999764
No 42
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=83.44 E-value=3 Score=32.68 Aligned_cols=34 Identities=12% Similarity=0.092 Sum_probs=26.0
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++.+.+.+..++++.++++|+..|+++..
T Consensus 55 ~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~~~~ 88 (266)
T cd06282 55 RVDGLILTVADAATSPALDLLDAERVPYVLAYND 88 (266)
T ss_pred CCCEEEEecCCCCchHHHHHHhhCCCCEEEEecc
Confidence 6888888776655556788888889998888654
No 43
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=83.35 E-value=0.65 Score=32.11 Aligned_cols=24 Identities=21% Similarity=0.241 Sum_probs=20.5
Q ss_pred hhhhhcCCCcCChhHHHHHHHhhh
Q 037201 47 CLLIRNQGRFYNNDKLVNHFRQIH 70 (177)
Q Consensus 47 ~Lc~~CGrrf~t~~~L~kHFkqlH 70 (177)
+.|..|+..|++...|..|.+.-|
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCccCCCCcCHHHHHHHHcCcc
Confidence 559999999999999999999753
No 44
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=82.07 E-value=3.4 Score=32.45 Aligned_cols=50 Identities=14% Similarity=0.137 Sum_probs=36.2
Q ss_pred CCchHHhhhhcEEEEEe-------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV-------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..++++.|+.+... ++|.+|+.+.+.+ .++++.+++.+...|++|..
T Consensus 19 ~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~~dgii~~~~~~~-~~~~~~~~~~~ipvv~~~~~ 87 (259)
T cd01542 19 KGILAALYENGYQMLLMNTNFSIEKEIEALELLARQKVDGIILLATTIT-DEHREAIKKLNVPVVVVGQD 87 (259)
T ss_pred HHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHHHHHHhcCCCCEEEEecc
Confidence 45566677777766554 7888888876543 46778888888999999764
No 45
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=81.87 E-value=3.5 Score=35.46 Aligned_cols=83 Identities=23% Similarity=0.248 Sum_probs=63.0
Q ss_pred hHHHHHHHHhhcCCCC----CCCc--------hHHhhhhcEEEEEe--------------ecceEEEEeCC---CchHHH
Q 037201 88 MEKYKMAVSAILTPKV----GYGF--------ADELKRAWFCVRNV--------------RFGCLMVVSDD---SNFVEV 138 (177)
Q Consensus 88 ~~KY~~Aar~vl~pkv----gygL--------a~eLrRAGv~Vr~V--------------~v~clvLVSDd---sdf~~~ 138 (177)
.+..++|+..+...+. |.|. +--|-|-|+.|..+ .-|++|.+|-. .+-.++
T Consensus 117 ~~~l~~av~~L~~A~rI~~~G~g~S~~vA~~~~~~l~~ig~~~~~~~d~~~~~~~~~~~~~~Dv~i~iS~sG~t~e~i~~ 196 (281)
T COG1737 117 EEALERAVELLAKARRIYFFGLGSSGLVASDLAYKLMRIGLNVVALSDTHGQLMQLALLTPGDVVIAISFSGYTREIVEA 196 (281)
T ss_pred HHHHHHHHHHHHcCCeEEEEEechhHHHHHHHHHHHHHcCCceeEecchHHHHHHHHhCCCCCEEEEEeCCCCcHHHHHH
Confidence 5778888888887773 5553 33467788888887 44556666654 345667
Q ss_pred HHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 139 FQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 139 lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
++.|+++|.++|.|=|..+..|.+.||..+.=
T Consensus 197 a~~ak~~ga~vIaiT~~~~spla~~Ad~~L~~ 228 (281)
T COG1737 197 AELAKERGAKVIAITDSADSPLAKLADIVLLV 228 (281)
T ss_pred HHHHHHCCCcEEEEcCCCCCchhhhhceEEec
Confidence 78889999999999999889999999998753
No 46
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=81.72 E-value=2.4 Score=37.29 Aligned_cols=49 Identities=8% Similarity=0.034 Sum_probs=42.2
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
.-|++|.+|-. .+..++++.|+++|.+||.|-+..+..|.+.||+-+.-
T Consensus 131 ~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~tI~IT~~~~s~La~~aD~~I~~ 182 (299)
T PRK05441 131 AKDVVVGIAASGRTPYVIGALEYARERGALTIGISCNPGSPLSKEADIAIEV 182 (299)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEECCCCChhhHhCCEEEEc
Confidence 45888888865 67888999999999999999998888999999987753
No 47
>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=81.18 E-value=3.9 Score=32.66 Aligned_cols=32 Identities=16% Similarity=0.202 Sum_probs=20.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
++|.|++++.+.+ ...++.+.+.|+.+|++|-
T Consensus 64 ~~dgiii~~~~~~-~~~~~~~~~~~ipvV~~~~ 95 (275)
T cd06295 64 RADGVILIGQHDQ-DPLPERLAETGLPFVVWGR 95 (275)
T ss_pred CCCEEEEeCCCCC-hHHHHHHHhCCCCEEEECC
Confidence 6777777665433 4556777777777777753
No 48
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=80.90 E-value=2.8 Score=35.91 Aligned_cols=48 Identities=8% Similarity=0.089 Sum_probs=40.9
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
.-|++|.+|-. ++..++++.|+++|..||.|....+..|.+.||.-+.
T Consensus 118 ~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~~I~It~~~~s~L~~~aD~~I~ 168 (257)
T cd05007 118 ERDVVIGIAASGRTPYVLGALRYARARGALTIGIACNPGSPLLQLADIAIA 168 (257)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEECCCCChhHHhCCEEEE
Confidence 56888888854 6778889999999999999998888899999998663
No 49
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=80.76 E-value=3.8 Score=27.86 Aligned_cols=48 Identities=21% Similarity=0.217 Sum_probs=33.5
Q ss_pred CCchHHhhhhcEEEEEe---------ecceEEEEeCCCchHH-----HHHHHHHcCccEEEEe
Q 037201 105 YGFADELKRAWFCVRNV---------RFGCLMVVSDDSNFVE-----VFQEATLRCLKMVVVG 153 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V---------~v~clvLVSDdsdf~~-----~lr~Ar~r~l~TVVVG 153 (177)
|.++..|++.|+.|+.+ .-..|++++.+..+.+ -|...-++| .|+||-
T Consensus 8 ~a~~~~L~~~g~~v~~~~~~~~~l~~~~~tll~i~~~~~~~~~~~~~~l~~~v~~G-~~lvl~ 69 (70)
T PF14258_consen 8 YALYQLLEEQGVKVERWRKPYEALEADDGTLLVIGPDLRLSEPEEAEALLEWVEAG-NTLVLA 69 (70)
T ss_pred HHHHHHHHHCCCeeEEecccHHHhCCCCCEEEEEeCCCCCCchHHHHHHHHHHHcC-CEEEEe
Confidence 44678899999999977 4556888888866653 444444577 666654
No 50
>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=80.71 E-value=4.2 Score=32.44 Aligned_cols=51 Identities=18% Similarity=0.230 Sum_probs=36.2
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
|+..+++..|+.+-.. ++|.+++++.+.+-.++++.++++++..|+++...
T Consensus 20 ~i~~~a~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~~ipvV~i~~~~ 89 (269)
T cd06281 20 GAEDRLRAAGYSLLIANSLNDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALASLDLPIVLLDRDM 89 (269)
T ss_pred HHHHHHHHcCCEEEEEeCCCChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHhCCCCEEEEeccc
Confidence 4556666667666543 78888888765555667888888888888887543
No 51
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=80.61 E-value=2.8 Score=36.91 Aligned_cols=49 Identities=10% Similarity=0.027 Sum_probs=41.7
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
.-|++|.+|-. .+..++++.|+++|.+||.|....+..|.+.||+.+.-
T Consensus 126 ~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~tIaIT~~~~s~La~~aD~~I~~ 177 (291)
T TIGR00274 126 KNDVVVGIAASGRTPYVIAGLQYARSLGALTISIACNPKSAASEIADIAIET 177 (291)
T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCCCChhHHhCCEEEec
Confidence 45889999865 56778899999999999999988778999999998764
No 52
>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=80.07 E-value=3.6 Score=33.08 Aligned_cols=34 Identities=18% Similarity=0.225 Sum_probs=28.3
Q ss_pred ecceEEEEeCCCch-HHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNF-VEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf-~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-||+.+.|++. .++++.+.+.|+..|++++.
T Consensus 54 ~~dgiii~~~~~~~~~~~~~~~~~~~iPvV~~~~~ 88 (289)
T cd01540 54 GAKGFVICVPDVKLGPAIVAKAKAYNMKVVAVDDR 88 (289)
T ss_pred CCCEEEEccCchhhhHHHHHHHHhCCCeEEEecCC
Confidence 78999998877654 55789999999999999854
No 53
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=80.07 E-value=3.2 Score=32.87 Aligned_cols=50 Identities=18% Similarity=0.203 Sum_probs=40.3
Q ss_pred CchHHhhhhcEEEEEe--------------------ecceEEEE-eCCCchHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV--------------------RFGCLMVV-SDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V--------------------~v~clvLV-SDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|+..+++.-|+.+..+ ++|.|++. .|.+...+.|+.|.+.|+..|.+...
T Consensus 19 g~~~~a~~~g~~~~~~~~~~~d~~~q~~~i~~~i~~~~d~Iiv~~~~~~~~~~~l~~~~~~gIpvv~~d~~ 89 (257)
T PF13407_consen 19 GAKAAAKELGYEVEIVFDAQNDPEEQIEQIEQAISQGVDGIIVSPVDPDSLAPFLEKAKAAGIPVVTVDSD 89 (257)
T ss_dssp HHHHHHHHHTCEEEEEEESTTTHHHHHHHHHHHHHTTESEEEEESSSTTTTHHHHHHHHHTTSEEEEESST
T ss_pred HHHHHHHHcCCEEEEeCCCCCCHHHHHHHHHHHHHhcCCEEEecCCCHHHHHHHHHHHhhcCceEEEEecc
Confidence 5566777778888884 99999988 45557889999999999988887655
No 54
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=79.77 E-value=4.6 Score=32.23 Aligned_cols=51 Identities=16% Similarity=0.133 Sum_probs=37.8
Q ss_pred CCchHHhhhhcEEEEEe-------------------ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV-------------------RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..++++-|+.|... ++|.|++.+-+++ +.+.++.+.++|+..|+++..
T Consensus 19 ~~i~~~~~~~g~~v~~~~~~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~ 89 (282)
T cd06318 19 EAAKAHAKALGYELISTDAQGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKAAGVPVVVVDSS 89 (282)
T ss_pred HHHHHHHHHcCCEEEEEcCCCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHHCCCCEEEecCC
Confidence 35566666666666554 7899998765544 457889999999999999864
No 55
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=78.98 E-value=0.29 Score=49.77 Aligned_cols=35 Identities=17% Similarity=0.142 Sum_probs=28.6
Q ss_pred hhhhhhhhcCCCcCChhHHHHHHHhhhhhhhhhhh
Q 037201 44 KENCLLIRNQGRFYNNDKLVNHFRQIHEGEQKKRS 78 (177)
Q Consensus 44 er~~Lc~~CGrrf~t~~~L~kHFkqlHerEr~Krl 78 (177)
||.|-|-+||++|.|.-+|+-||-.=||-+=-+.|
T Consensus 379 ERPfqCnvCG~~FSTkGNLKvH~~rH~e~~p~~~m 413 (958)
T KOG1074|consen 379 ERPFQCNVCGNRFSTKGNLKVHFQRHREKYPHVQM 413 (958)
T ss_pred CCCeeecccccccccccceeeeeeeccccCCcccc
Confidence 67788999999999999999999877776643333
No 56
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=78.76 E-value=4.3 Score=30.09 Aligned_cols=42 Identities=24% Similarity=0.272 Sum_probs=33.2
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhc
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIAN 165 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad 165 (177)
.-|+++.+|-. .+-.++++.|+++|.++|+|-+. +.|...||
T Consensus 43 ~~dl~I~iS~SG~t~e~i~~~~~a~~~g~~iI~IT~~--~~l~~~~~ 87 (119)
T cd05017 43 RKTLVIAVSYSGNTEETLSAVEQAKERGAKIVAITSG--GKLLEMAR 87 (119)
T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEeCC--chHHHHHH
Confidence 45788888854 56777888999999999999864 35888887
No 57
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=78.30 E-value=5.5 Score=31.39 Aligned_cols=33 Identities=21% Similarity=0.353 Sum_probs=20.2
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-|++.+.+.+ ...++.++++|+..|++|..
T Consensus 55 ~vdgiIi~~~~~~-~~~~~~l~~~~ipvV~~~~~ 87 (265)
T cd06299 55 RVDGIIVVPHEQS-AEQLEDLLKRGIPVVFVDRE 87 (265)
T ss_pred CCCEEEEcCCCCC-hHHHHHHHhCCCCEEEEecc
Confidence 5666666655443 24566666677777777653
No 58
>PRK11382 frlB fructoselysine-6-P-deglycase; Provisional
Probab=78.18 E-value=3.5 Score=36.32 Aligned_cols=49 Identities=10% Similarity=0.101 Sum_probs=40.7
Q ss_pred cceEEEEeC---CCchHHHHHHHHHcCccEEEEecCCchhhhhhhccccchh
Q 037201 123 FGCLMVVSD---DSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSWS 171 (177)
Q Consensus 123 v~clvLVSD---dsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW~ 171 (177)
-+++|.+|= ..|-..+++.|+++|.+||.|-+..+..|.+.||.-+...
T Consensus 93 ~~lvI~iS~SGeT~e~i~al~~ak~~Ga~~I~IT~~~~S~L~~~ad~~l~~~ 144 (340)
T PRK11382 93 RCAVIGVSDYGKTEEVIKALELGRACGALTAAFTKRADSPITSAAEFSIDYQ 144 (340)
T ss_pred CCEEEEEcCCCCCHHHHHHHHHHHHcCCeEEEEECCCCChHHHhCCEEEEeC
Confidence 356777874 4678899999999999999998877789999999877554
No 59
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=76.98 E-value=6.3 Score=31.58 Aligned_cols=34 Identities=9% Similarity=0.124 Sum_probs=28.5
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-+|+.+.+.+ +.++++.++++|+..|+++..
T Consensus 57 ~vdgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~ 91 (271)
T cd06312 57 KPDGIVVTIPDPDALDPAIKRAVAAGIPVISFNAG 91 (271)
T ss_pred CCCEEEEeCCChHHhHHHHHHHHHCCCeEEEeCCC
Confidence 7899999886654 678899999999999999754
No 60
>PHA00732 hypothetical protein
Probab=76.88 E-value=1.3 Score=32.31 Aligned_cols=25 Identities=16% Similarity=-0.161 Sum_probs=21.5
Q ss_pred hhhhhcCCCcCChhHHHHHHHhhhh
Q 037201 47 CLLIRNQGRFYNNDKLVNHFRQIHE 71 (177)
Q Consensus 47 ~Lc~~CGrrf~t~~~L~kHFkqlHe 71 (177)
+-|..||+.|.+...|.+|-+..|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~ 26 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT 26 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC
Confidence 3499999999999999999876665
No 61
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=76.82 E-value=0.79 Score=31.68 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=0.0
Q ss_pred hhhcCCCcCChhHHHHHHHhhhhhh
Q 037201 49 LIRNQGRFYNNDKLVNHFRQIHEGE 73 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kHFkqlHerE 73 (177)
|..|+..|.+..+|+.|.+..|.-.
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~ 26 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFD 26 (100)
T ss_dssp -------------------------
T ss_pred ccccccccccccccccccccccccc
Confidence 8899999999999999999999754
No 62
>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=76.64 E-value=6.4 Score=31.35 Aligned_cols=50 Identities=10% Similarity=0.173 Sum_probs=31.8
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCc----hHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSN----FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsd----f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|+..+++..|+.+.+. ++|.+++.+-+++ ..++++.+.+.++..|+++..
T Consensus 20 gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~~~~~~ipvV~~~~~ 92 (273)
T cd01541 20 GIESVLSEKGYSLLLASTNNDPERERKCLENMLSQGIDGLIIEPTKSALPNPNIDLYLKLEKLGIPYVFINAS 92 (273)
T ss_pred HHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEeccccccccccHHHHHHHHHCCCCEEEEecC
Confidence 4556666666666443 7788777654332 346677777778888877643
No 63
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=75.72 E-value=5.8 Score=27.65 Aligned_cols=42 Identities=17% Similarity=0.222 Sum_probs=36.2
Q ss_pred hHHhhhhcEEEEEe------ecce-EEEEeCCCchHHHHHHHHHcCccE
Q 037201 108 ADELKRAWFCVRNV------RFGC-LMVVSDDSNFVEVFQEATLRCLKM 149 (177)
Q Consensus 108 a~eLrRAGv~Vr~V------~v~c-lvLVSDdsdf~~~lr~Ar~r~l~T 149 (177)
-..|+.+|+.++.+ +.+| ++|-.++.|...+.+..++.|+..
T Consensus 18 ek~lk~~gi~~~liP~P~~i~~~CG~al~~~~~d~~~i~~~l~~~~i~~ 66 (73)
T PF11823_consen 18 EKLLKKNGIPVRLIPTPREISAGCGLALRFEPEDLEKIKEILEENGIEY 66 (73)
T ss_pred HHHHHHCCCcEEEeCCChhccCCCCEEEEEChhhHHHHHHHHHHCCCCe
Confidence 35699999999999 6777 889999999999999999988753
No 64
>PRK10886 DnaA initiator-associating protein DiaA; Provisional
Probab=75.02 E-value=5.2 Score=33.36 Aligned_cols=47 Identities=17% Similarity=0.287 Sum_probs=37.5
Q ss_pred ecceEEEEeCCC---chHHHHHHHHHcCccEEEEecCCchhhhhh---hcccc
Q 037201 122 RFGCLMVVSDDS---NFVEVFQEATLRCLKMVVVGDMSDGALKRI---ANAFF 168 (177)
Q Consensus 122 ~v~clvLVSDds---df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~---Ad~~~ 168 (177)
.-|+++.+|-.- +...+++.|+++|.++|+|-...++.|.+. +|+-+
T Consensus 109 ~gDvli~iS~SG~s~~v~~a~~~Ak~~G~~vI~IT~~~~s~l~~l~~~~D~~i 161 (196)
T PRK10886 109 AGDVLLAISTRGNSRDIVKAVEAAVTRDMTIVALTGYDGGELAGLLGPQDVEI 161 (196)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCChhhhccccCCEEE
Confidence 348888898754 466778889999999999998877889986 57654
No 65
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=74.77 E-value=0.93 Score=46.33 Aligned_cols=26 Identities=15% Similarity=0.171 Sum_probs=23.1
Q ss_pred hhhhhhhhcCCCcCChhHHHHHHHhhh
Q 037201 44 KENCLLIRNQGRFYNNDKLVNHFRQIH 70 (177)
Q Consensus 44 er~~Lc~~CGrrf~t~~~L~kHFkqlH 70 (177)
||.|-|-+|||-|.|.-+|+-||- +|
T Consensus 631 ERPFkCKiCgRAFtTkGNLkaH~~-vH 656 (958)
T KOG1074|consen 631 ERPFKCKICGRAFTTKGNLKAHMS-VH 656 (958)
T ss_pred cCccccccccchhccccchhhccc-cc
Confidence 678889999999999999999994 44
No 66
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=74.65 E-value=7 Score=30.81 Aligned_cols=32 Identities=13% Similarity=0.255 Sum_probs=19.0
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
++|.|++++-+.+ .++++.+.++|...|.++.
T Consensus 60 ~~dgiii~~~~~~-~~~~~~~~~~~ipvV~~~~ 91 (270)
T cd06294 60 RVDGFILLYSRED-DPIIDYLKEEKFPFVVIGK 91 (270)
T ss_pred CcCEEEEecCcCC-cHHHHHHHhcCCCEEEECC
Confidence 3666666653322 4556666666777777654
No 67
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=73.81 E-value=8 Score=31.63 Aligned_cols=51 Identities=14% Similarity=0.134 Sum_probs=40.4
Q ss_pred CCchHHhhhhcEEEEEe-------------------ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV-------------------RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..+++..|+.+... ++|-|++++.+++ ..+.++.+++.|...|+++..
T Consensus 19 ~gi~~~a~~~g~~~~~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l~~~~ipvV~~~~~ 89 (288)
T cd01538 19 PNFEAALKELGAEVIVQNANGDPAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAADAGIPVIAYDRL 89 (288)
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHHHHCCCCEEEECCC
Confidence 36677777778777766 8999999876544 678999999999999988754
No 68
>PHA00733 hypothetical protein
Probab=73.68 E-value=2.2 Score=33.41 Aligned_cols=25 Identities=20% Similarity=0.223 Sum_probs=18.8
Q ss_pred hhhhhhcCCCcCChhHHHHHHHhhh
Q 037201 46 NCLLIRNQGRFYNNDKLVNHFRQIH 70 (177)
Q Consensus 46 ~~Lc~~CGrrf~t~~~L~kHFkqlH 70 (177)
.+-|.+||+.|.....|.+|..+-|
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhc
Confidence 3457888888888888888877766
No 69
>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=73.62 E-value=7.8 Score=32.38 Aligned_cols=34 Identities=18% Similarity=0.330 Sum_probs=28.4
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.|++++.+++ ..+.++.+++.++..|+++..
T Consensus 54 ~vDgIIi~~~~~~~~~~~l~~~~~~~iPvV~~d~~ 88 (302)
T TIGR02634 54 GVDVLVIIPQNGQVLSNAVQEAKDEGIKVVAYDRL 88 (302)
T ss_pred CCCEEEEeCCChhHHHHHHHHHHHCCCeEEEecCc
Confidence 7999999987765 578899999999988888654
No 70
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=73.51 E-value=2.4 Score=23.56 Aligned_cols=22 Identities=14% Similarity=0.081 Sum_probs=17.4
Q ss_pred hhhhcCCCcCChhHHHHHHHhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIH 70 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlH 70 (177)
.|..|..... ..+|.+|.+.-|
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHHhhC
Confidence 3889999998 889999998877
No 71
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=73.48 E-value=6 Score=34.88 Aligned_cols=49 Identities=10% Similarity=0.080 Sum_probs=40.9
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
.-|++|.+|-. ++-.++++.|+++|..||.|....+..|.+.||.-+..
T Consensus 127 ~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~~IaIT~~~~s~La~~aD~~I~~ 178 (296)
T PRK12570 127 ADDVVVGIAASGRTPYVIGALEYAKQIGATTIALSCNPDSPIAKIADIAISP 178 (296)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEECCCCChhHHhCCEEEee
Confidence 34888888854 56778899999999999999988778999999987653
No 72
>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=73.25 E-value=7.7 Score=32.20 Aligned_cols=50 Identities=12% Similarity=0.052 Sum_probs=38.3
Q ss_pred CchHHhhhhcEEEEEe---------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV---------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V---------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|+..+++..|+.+..+ ++|.|++.+.++...++++.+.++|+..|+++..
T Consensus 21 gi~~~~~~~g~~v~~~~~~~~~~~~~~~i~~~~~~~~~vdgiIi~~~~~~~~~~~~~~~~~giPvV~~~~~ 91 (305)
T cd06324 21 FMQAAADDLGIELEVLYAERDRFLMLQQARTILQRPDKPDALIFTNEKSVAPELLRLAEGAGVKLFLVNSG 91 (305)
T ss_pred HHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHHHhccCCCEEEEcCCccchHHHHHHHHhCCCeEEEEecC
Confidence 5566666677766554 5889999876655678899999999999999754
No 73
>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=72.85 E-value=7.6 Score=31.51 Aligned_cols=51 Identities=16% Similarity=0.089 Sum_probs=39.8
Q ss_pred CCchHHhhhhcEEEEEe-------------------ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV-------------------RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..+++..|+.+... ++|-|++.+-|++ ..+.++.+.++++..|+++..
T Consensus 19 ~gi~~~~~~~G~~~~~~~~~~d~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~ 89 (272)
T cd06313 19 QAADEAGKLLGVDVTWYGGALDAVKQVAAIENMASQGWDFIAVDPLGIGTLTEAVQKAIARGIPVIDMGTL 89 (272)
T ss_pred HHHHHHHHHcCCEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHhHHHHHHHHHCCCcEEEeCCC
Confidence 35566777778777766 7899999876655 577889999999999999754
No 74
>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=72.73 E-value=8.4 Score=30.50 Aligned_cols=51 Identities=12% Similarity=0.135 Sum_probs=36.1
Q ss_pred CCchHHhhhhcEEEEEe-------------------ecceEEEEeCCC-chHHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV-------------------RFGCLMVVSDDS-NFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V-------------------~v~clvLVSDds-df~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..+++..|+.+... ++|.+++.+-++ .+.++++.+++.|+..|.++..
T Consensus 19 ~~i~~~~~~~g~~~~i~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~~~~ 89 (267)
T cd06322 19 NAMKEEAKKQKVNLIVSIANQDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKKAGIPVITVDIA 89 (267)
T ss_pred HHHHHHHHhcCCEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHHHHCCCCEEEEccc
Confidence 34555666666666443 789888876544 3678889998899999998753
No 75
>TIGR03590 PseG pseudaminic acid biosynthesis-associated protein PseG. This protein is found in association with enzymes involved in the biosynthesis of pseudaminic acid, a component of polysaccharide in certain Pseudomonas strains as well as a modification of flagellin in Campylobacter and Hellicobacter. The role of this protein is unclear, although it may participate in N-acetylation in conjunction with, or in the absence of PseH (TIGR03585) as it often scores above the trusted cutoff to pfam00583 representing a family of acetyltransferases.
Probab=72.72 E-value=10 Score=32.30 Aligned_cols=42 Identities=12% Similarity=0.116 Sum_probs=28.9
Q ss_pred EEEeCCCchHHH-HHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 127 MVVSDDSNFVEV-FQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 127 vLVSDdsdf~~~-lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
++|.|.-+|..- .+..++.+.++++|-|..++.. .||+.+..
T Consensus 83 ~vV~D~y~~~~~~~~~~k~~~~~l~~iDD~~~~~~--~~D~vin~ 125 (279)
T TIGR03590 83 ILIVDHYGLDADWEKLIKEFGRKILVIDDLADRPH--DCDLLLDQ 125 (279)
T ss_pred EEEEcCCCCCHHHHHHHHHhCCeEEEEecCCCCCc--CCCEEEeC
Confidence 567787666543 3444567889999999865544 88887743
No 76
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=72.62 E-value=7.7 Score=31.85 Aligned_cols=51 Identities=12% Similarity=0.104 Sum_probs=36.1
Q ss_pred CCchHHhhhhcEEEEEe-------------------ecceEEEEeCCCch-HHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV-------------------RFGCLMVVSDDSNF-VEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsdf-~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..++++.|+.+... ++|.+++.+.+++. .+.++.+++.|+..|+++..
T Consensus 46 ~~i~~~~~~~G~~~~~~~~~~d~~~~~~~~~~l~~~~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~ 116 (295)
T PRK10653 46 DGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRG 116 (295)
T ss_pred HHHHHHHHHcCCeEEEecCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHHCCCCEEEEccC
Confidence 35566666666665543 67878888766544 57888888889998988754
No 77
>PF13380 CoA_binding_2: CoA binding domain; PDB: 3FF4_A 2D5A_A 2D59_A 2E6U_X 1IUL_A 1IUK_A 1Y81_A 2DUW_A.
Probab=72.18 E-value=3.4 Score=31.27 Aligned_cols=53 Identities=25% Similarity=0.219 Sum_probs=38.8
Q ss_pred CCCCchHHhhhhcEEEEEe---------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 103 VGYGFADELKRAWFCVRNV---------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 103 vgygLa~eLrRAGv~Vr~V---------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.||-+...|++.|+-|-.| .+|.++++.....-.++++++.+.|++.|++=-+
T Consensus 15 ~g~~v~~~l~~~G~~v~~Vnp~~~~i~G~~~y~sl~e~p~~iDlavv~~~~~~~~~~v~~~~~~g~~~v~~~~g 88 (116)
T PF13380_consen 15 FGYRVLRNLKAAGYEVYPVNPKGGEILGIKCYPSLAEIPEPIDLAVVCVPPDKVPEIVDEAAALGVKAVWLQPG 88 (116)
T ss_dssp HHHHHHHHHHHTT-EEEEESTTCSEETTEE-BSSGGGCSST-SEEEE-S-HHHHHHHHHHHHHHT-SEEEE-TT
T ss_pred hHHHHHHHHHhCCCEEEEECCCceEECcEEeeccccCCCCCCCEEEEEcCHHHHHHHHHHHHHcCCCEEEEEcc
Confidence 3666778888899888887 6788888888888899999999999999887544
No 78
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=72.08 E-value=8.6 Score=30.51 Aligned_cols=34 Identities=12% Similarity=0.152 Sum_probs=28.1
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-+++.+.+++ ..++++.+.+.++..|+++..
T Consensus 55 ~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~ 89 (277)
T cd06319 55 GVSGIIISPTNSSAAVTLLKLAAQAKIPVVIADIG 89 (277)
T ss_pred CCCEEEEcCCchhhhHHHHHHHHHCCCCEEEEecC
Confidence 7888888887766 457899999999999999754
No 79
>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=72.05 E-value=8.5 Score=31.40 Aligned_cols=34 Identities=9% Similarity=0.243 Sum_probs=27.9
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-||+.+.|.+ ..++++.++++|+..|.++..
T Consensus 56 ~~dgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~ 90 (294)
T cd06316 56 KPDIIISIPVDPVSTAAAYKKVAEAGIKLVFMDNV 90 (294)
T ss_pred CCCEEEEcCCCchhhhHHHHHHHHcCCcEEEecCC
Confidence 7898888776554 578899999999999998774
No 80
>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=71.86 E-value=9.7 Score=30.37 Aligned_cols=34 Identities=12% Similarity=0.269 Sum_probs=28.1
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-|++++.+.+ +.+.++.+.+.++..|+++..
T Consensus 56 ~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~~~~ 90 (270)
T cd06308 56 GVDLLIISPNEAAPLTPVVEEAYRAGIPVILLDRK 90 (270)
T ss_pred CCCEEEEecCchhhchHHHHHHHHCCCCEEEeCCC
Confidence 7898988886654 578889999999999999864
No 81
>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=71.62 E-value=11 Score=29.61 Aligned_cols=34 Identities=6% Similarity=0.141 Sum_probs=25.1
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-+++++-+++-.++++.+.+.|+..|.++..
T Consensus 55 ~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~~~~ 88 (268)
T cd06289 55 GVAGIILCPAAGTSPDLLKRLAESGIPVVLVARE 88 (268)
T ss_pred CCCEEEEeCCCCccHHHHHHHHhcCCCEEEEecc
Confidence 6788888775544345788888889988888754
No 82
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=71.56 E-value=2.2 Score=31.73 Aligned_cols=22 Identities=14% Similarity=0.108 Sum_probs=20.7
Q ss_pred hhcCCCcCChhHHHHHHHhhhh
Q 037201 50 IRNQGRFYNNDKLVNHFRQIHE 71 (177)
Q Consensus 50 ~~CGrrf~t~~~L~kHFkqlHe 71 (177)
..|+..+++..++.+||++.|.
T Consensus 88 ~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCcEeccHHHHHHHHHHhcC
Confidence 8999999999999999999883
No 83
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=71.45 E-value=1.8 Score=37.32 Aligned_cols=28 Identities=11% Similarity=-0.005 Sum_probs=22.4
Q ss_pred hhhhhhhcCCCcCChhHHHHHHHhhhhh
Q 037201 45 ENCLLIRNQGRFYNNDKLVNHFRQIHEG 72 (177)
Q Consensus 45 r~~Lc~~CGrrf~t~~~L~kHFkqlHer 72 (177)
-+++|+.||..|+..+=..||.+.-|.-
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 4567999999999999999999999984
No 84
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=71.29 E-value=0.8 Score=26.63 Aligned_cols=15 Identities=13% Similarity=-0.046 Sum_probs=12.4
Q ss_pred hhhhhhhhcCCCcCC
Q 037201 44 KENCLLIRNQGRFYN 58 (177)
Q Consensus 44 er~~Lc~~CGrrf~t 58 (177)
|+.+.|..||++|.+
T Consensus 12 ~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 12 EKPYKCPYCGKSFSN 26 (26)
T ss_dssp SSSEEESSSSEEESS
T ss_pred CCCCCCCCCcCeeCc
Confidence 566779999999975
No 85
>PF13580 SIS_2: SIS domain; PDB: 1TK9_C 2I22_B 2I2W_A 1X92_A 3BJZ_D 2XBL_B 2X3Y_F 2YVA_B 3CVJ_D 3TRJ_D ....
Probab=71.21 E-value=5.9 Score=30.41 Aligned_cols=31 Identities=29% Similarity=0.442 Sum_probs=24.3
Q ss_pred ecceEEEEeC---CCchHHHHHHHHHcCccEEEE
Q 037201 122 RFGCLMVVSD---DSNFVEVFQEATLRCLKMVVV 152 (177)
Q Consensus 122 ~v~clvLVSD---dsdf~~~lr~Ar~r~l~TVVV 152 (177)
.=|+||.+|. .+.-.++++.|+++|.+||.|
T Consensus 103 ~gDvli~iS~SG~s~~vi~a~~~Ak~~G~~vIal 136 (138)
T PF13580_consen 103 PGDVLIVISNSGNSPNVIEAAEEAKERGMKVIAL 136 (138)
T ss_dssp TT-EEEEEESSS-SHHHHHHHHHHHHTT-EEEEE
T ss_pred CCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEE
Confidence 4589999987 456778899999999999987
No 86
>cd04795 SIS SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=71.04 E-value=8 Score=25.97 Aligned_cols=32 Identities=6% Similarity=0.150 Sum_probs=25.7
Q ss_pred ecceEEEEeCC---CchHHHHHHHHHcCccEEEEe
Q 037201 122 RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVG 153 (177)
.-|+++++|-. .+-.++++.|+++|.++|+|-
T Consensus 47 ~~d~~i~iS~sg~t~~~~~~~~~a~~~g~~ii~it 81 (87)
T cd04795 47 KGDVVIALSYSGRTEELLAALEIAKELGIPVIAIT 81 (87)
T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHcCCeEEEEe
Confidence 45788888865 567778889999999999875
No 87
>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=70.72 E-value=11 Score=29.92 Aligned_cols=49 Identities=14% Similarity=0.129 Sum_probs=34.3
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|+..++++.|+.+..+ ++|.+++++.+.+- ..++.+.+.|...|+++..
T Consensus 20 g~~~~a~~~g~~~~~~~~~~~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~~~~~~~~~~ipvV~~~~~ 87 (268)
T cd06270 20 GVESVARKAGKHLIITAGHHSAEKEREAIEFLLERRCDALILHSKALSD-DELIELAAQVPPLVLINRH 87 (268)
T ss_pred HHHHHHHHCCCEEEEEeCCCchHHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhCCCCEEEEecc
Confidence 5566667777776655 88888887643222 2378888889999999764
No 88
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=70.69 E-value=1.4 Score=34.23 Aligned_cols=14 Identities=14% Similarity=0.178 Sum_probs=11.2
Q ss_pred hhhhhhcCCCcCCh
Q 037201 46 NCLLIRNQGRFYNN 59 (177)
Q Consensus 46 ~~Lc~~CGrrf~t~ 59 (177)
|+.|+.||.|||..
T Consensus 9 KR~Cp~CG~kFYDL 22 (108)
T PF09538_consen 9 KRTCPSCGAKFYDL 22 (108)
T ss_pred cccCCCCcchhccC
Confidence 56799999999863
No 89
>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.
Probab=70.67 E-value=8.5 Score=31.62 Aligned_cols=34 Identities=9% Similarity=-0.038 Sum_probs=29.8
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
+.|.+++.+...+...+++.+++.|+...++|..
T Consensus 190 ~~~~vi~~~~~~~~~~~~~~~~~~g~~~~~~~~~ 223 (334)
T cd06342 190 NPDAVFFGGYYPEAGPLVRQMRQLGLKAPFMGGD 223 (334)
T ss_pred CCCEEEEcCcchhHHHHHHHHHHcCCCCcEEecC
Confidence 6788999999999999999999999988888753
No 90
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=70.38 E-value=8.8 Score=30.60 Aligned_cols=33 Identities=18% Similarity=0.245 Sum_probs=20.5
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd 154 (177)
++|.||+.+.+++ ..+.++.++++++..|.+|.
T Consensus 57 ~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~ 90 (275)
T cd06320 57 GYKGLLFSPISDVNLVPAVERAKKKGIPVVNVND 90 (275)
T ss_pred CCCEEEECCCChHHhHHHHHHHHHCCCeEEEECC
Confidence 5677766654432 34566777777777776654
No 91
>TIGR01512 ATPase-IB2_Cd heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase. .
Probab=69.88 E-value=5.1 Score=37.47 Aligned_cols=63 Identities=17% Similarity=0.086 Sum_probs=43.1
Q ss_pred HHhhhhcE-EEEEe---------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC-Cchhhhhhhccccchh
Q 037201 109 DELKRAWF-CVRNV---------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM-SDGALKRIANAFFSWS 171 (177)
Q Consensus 109 ~eLrRAGv-~Vr~V---------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~-~~~~L~r~Ad~~~sW~ 171 (177)
.+|+++|+ .+-.+ |++-..--....+=..+++.....+-.++.|||+ +|-...+.||+.++|.
T Consensus 372 ~~L~~~Gi~~v~vvTgd~~~~a~~i~~~lgi~~~f~~~~p~~K~~~i~~l~~~~~~v~~vGDg~nD~~al~~A~vgia~g 451 (536)
T TIGR01512 372 AELKALGIEKVVMLTGDRRAVAERVARELGIDEVHAELLPEDKLEIVKELREKYGPVAMVGDGINDAPALAAADVGIAMG 451 (536)
T ss_pred HHHHHcCCCcEEEEcCCCHHHHHHHHHHcCChhhhhccCcHHHHHHHHHHHhcCCEEEEEeCCHHHHHHHHhCCEEEEeC
Confidence 56777787 66666 5543222111223355777777778889999997 5667789999999996
No 92
>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=69.67 E-value=11 Score=29.72 Aligned_cols=48 Identities=17% Similarity=0.131 Sum_probs=30.7
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
|+.++++..|+.+... ++|-|++++.+.+ ...++.+.++++..|.|+.
T Consensus 20 gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~-~~~~~~~~~~~ipvV~i~~ 86 (270)
T cd06296 20 GVEEAAAAAGYDVVLSESGRRTSPERQWVERLSARRTDGVILVTPELT-SAQRAALRRTGIPFVVVDP 86 (270)
T ss_pred HHHHHHHHcCCeEEEecCCCchHHHHHHHHHHHHcCCCEEEEecCCCC-hHHHHHHhcCCCCEEEEec
Confidence 5555666666665544 6777777655433 3557777777777777764
No 93
>cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=69.45 E-value=9.8 Score=30.99 Aligned_cols=50 Identities=12% Similarity=0.062 Sum_probs=36.9
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|+..+++..|+.+-.. ++|.|++++-+.+ ..+.++.+++.++..|+++..
T Consensus 21 gi~~~a~~~gy~~~~~~~~~~~~~~~~~i~~l~~~~vdgiil~~~~~~~~~~~~~~~~~~~iPvV~~d~~ 90 (280)
T cd06315 21 GVREAAKAIGWNLRILDGRGSEAGQAAALNQAIALKPDGIVLGGVDAAELQAELELAQKAGIPVVGWHAG 90 (280)
T ss_pred HHHHHHHHcCcEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHHHHHHHHHCCCCEEEecCC
Confidence 4556666667666554 8899999986654 356778888899999999753
No 94
>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=69.33 E-value=14 Score=28.95 Aligned_cols=33 Identities=15% Similarity=0.098 Sum_probs=21.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-+++++-+.+ .+.+..+.+.++.-|++++.
T Consensus 55 ~vdgiii~~~~~~-~~~~~~~~~~~ipvv~~~~~ 87 (268)
T cd01575 55 RPAGLILTGLEHT-ERTRQLLRAAGIPVVEIMDL 87 (268)
T ss_pred CCCEEEEeCCCCC-HHHHHHHHhcCCCEEEEecC
Confidence 6777777664443 45666677777777777764
No 95
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=69.22 E-value=10 Score=29.69 Aligned_cols=51 Identities=14% Similarity=0.197 Sum_probs=37.0
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCch-HHHHHHHHHcCccEEEEecCC
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSNF-VEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsdf-~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
|+..+++..|+.+... ++|-+++++.+++. .++++.+++.++..|.++...
T Consensus 20 ~i~~~~~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~~dgii~~~~~~~~~~~~l~~l~~~~ipvv~~~~~~ 90 (268)
T cd06323 20 GAQKEAKELGYELTVLDAQNDAAKQLNDIEDLITRGVDAIIINPTDSDAVVPAVKAANEAGIPVFTIDREA 90 (268)
T ss_pred HHHHHHHHcCceEEecCCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHHCCCcEEEEccCC
Confidence 5556666666666544 78888888876654 367888888999999997753
No 96
>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=69.04 E-value=10 Score=30.32 Aligned_cols=50 Identities=14% Similarity=0.127 Sum_probs=37.3
Q ss_pred CCchHHhhhhcEEEEEe--------------------ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV--------------------RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V--------------------~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..++++.|+.+..+ ++|-+++.+-+.+ ..++++.+.+ +...|++|..
T Consensus 18 ~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~~l~~~~~-~ipvV~~~~~ 88 (271)
T cd06314 18 AGVKAAGKELGVDVEFVVPQQGTVNAQLRMLEDLIAEGVDGIAISPIDPKAVIPALNKAAA-GIKLITTDSD 88 (271)
T ss_pred HHHHHHHHHcCCeEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEecCChhHhHHHHHHHhc-CCCEEEecCC
Confidence 45666777777766543 7899998875543 5688999888 9999999864
No 97
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=69.02 E-value=11 Score=30.37 Aligned_cols=34 Identities=0% Similarity=0.024 Sum_probs=26.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-|++++-+.+....+..++.+|+..|++++.
T Consensus 57 ~vdgiI~~~~~~~~~~~~~~~~~~giPvV~~~~~ 90 (268)
T cd06306 57 GADAILLGAVSPDGLNEILQQVAASIPVIALVND 90 (268)
T ss_pred CCCEEEEcCCChhhHHHHHHHHHCCCCEEEeccC
Confidence 7888999876655433678889999999999754
No 98
>PRK00331 glucosamine--fructose-6-phosphate aminotransferase; Reviewed
Probab=69.00 E-value=7.6 Score=36.61 Aligned_cols=47 Identities=11% Similarity=0.171 Sum_probs=38.3
Q ss_pred cceEEEEeC---CCchHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 123 FGCLMVVSD---DSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 123 v~clvLVSD---dsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
-|.+|.+|= ..+-.++++.|+++|..||.|-+..+..|.+.||.-+.
T Consensus 337 ~dlvI~iS~SG~T~e~i~a~~~ak~~ga~~IaIT~~~~S~La~~aD~~l~ 386 (604)
T PRK00331 337 KTLVIAISQSGETADTLAALRLAKELGAKTLAICNVPGSTIARESDAVLY 386 (604)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHHCCCCEEEEECCCCChhHHhcCcEEE
Confidence 356677764 44677788899999999999999888999999997664
No 99
>cd06311 PBP1_ABC_sugar_binding_like_3 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=68.59 E-value=14 Score=29.53 Aligned_cols=34 Identities=15% Similarity=0.217 Sum_probs=27.9
Q ss_pred ecceEEEEeCC-CchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDD-SNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDd-sdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-|++.+-| +.+.+.++.|.++|+..|.++..
T Consensus 60 ~vDgiii~~~~~~~~~~~i~~~~~~gIpvV~~d~~ 94 (274)
T cd06311 60 KIDALVILPFESAPLTQPVAKAKKAGIFVVVVDRG 94 (274)
T ss_pred CCCEEEEeCCCchhhHHHHHHHHHCCCeEEEEcCC
Confidence 78988888754 45678899999999999999754
No 100
>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=68.54 E-value=12 Score=29.91 Aligned_cols=50 Identities=12% Similarity=0.193 Sum_probs=37.6
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|+..+++..|+.+... ++|-|++.+.+++ +.+.++.+.+.++..|+++..
T Consensus 20 ~~~~~a~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~i~~~~~~~iPvV~~~~~ 89 (273)
T cd06309 20 SIKDAAEKRGFDLKFADAQQKQENQISAIRSFIAQGVDVIILAPVVETGWDPVLKEAKAAGIPVILVDRG 89 (273)
T ss_pred HHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHHHcCCCEEEEcCCccccchHHHHHHHHCCCCEEEEecC
Confidence 4455566666666554 7899998887655 568899999999999999854
No 101
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=68.38 E-value=13 Score=29.37 Aligned_cols=34 Identities=9% Similarity=0.276 Sum_probs=27.7
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++.+.+++ ..+.++.++++++..|.++..
T Consensus 56 ~vdgiii~~~~~~~~~~~l~~~~~~~iPvV~~~~~ 90 (275)
T cd06317 56 KVDGIILWPTDGQAYIPGLRKAKQAGIPVVITNSN 90 (275)
T ss_pred CCCEEEEecCCccccHHHHHHHHHCCCcEEEeCCC
Confidence 8898988876655 468889999999999988754
No 102
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=67.87 E-value=13 Score=30.96 Aligned_cols=33 Identities=6% Similarity=0.082 Sum_probs=22.2
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
++|.+++.+.+....+.++.+++.++..|.++.
T Consensus 120 ~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~~ 152 (342)
T PRK10014 120 GVDGVVIAGAAGSSDDLREMAEEKGIPVVFASR 152 (342)
T ss_pred CCCEEEEeCCCCCcHHHHHHHhhcCCCEEEEec
Confidence 567777766544445667777777777777764
No 103
>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=66.82 E-value=18 Score=25.97 Aligned_cols=49 Identities=24% Similarity=0.160 Sum_probs=32.2
Q ss_pred chHHhhhhcEEEEEe----------------ecceEEEEe-CCCchHHHHHHHHH---cCcc-EEEEecC
Q 037201 107 FADELKRAWFCVRNV----------------RFGCLMVVS-DDSNFVEVFQEATL---RCLK-MVVVGDM 155 (177)
Q Consensus 107 La~eLrRAGv~Vr~V----------------~v~clvLVS-Ddsdf~~~lr~Ar~---r~l~-TVVVGd~ 155 (177)
+++.|+++|+.|..+ +.|.+.+-+ -.+.+..+.+.++. .+-+ .||+|..
T Consensus 20 la~~l~~~G~~v~~~d~~~~~~~l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~~p~~~iv~GG~ 89 (121)
T PF02310_consen 20 LAAYLRKAGHEVDILDANVPPEELVEALRAERPDVVGISVSMTPNLPEAKRLARAIKERNPNIPIVVGGP 89 (121)
T ss_dssp HHHHHHHTTBEEEEEESSB-HHHHHHHHHHTTCSEEEEEESSSTHHHHHHHHHHHHHTTCTTSEEEEEES
T ss_pred HHHHHHHCCCeEEEECCCCCHHHHHHHHhcCCCcEEEEEccCcCcHHHHHHHHHHHHhcCCCCEEEEECC
Confidence 578999999999988 556555544 56666666666653 4333 5556654
No 104
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=66.81 E-value=12 Score=30.26 Aligned_cols=41 Identities=24% Similarity=0.320 Sum_probs=28.5
Q ss_pred eEEEEeCCCc-------hHHHHHHHHHcCccEEEEecC--Cchhhhhhhc
Q 037201 125 CLMVVSDDSN-------FVEVFQEATLRCLKMVVVGDM--SDGALKRIAN 165 (177)
Q Consensus 125 clvLVSDdsd-------f~~~lr~Ar~r~l~TVVVGd~--~~~~L~r~Ad 165 (177)
.+||++|-.+ ..++.+.+++.|++..+||-+ ....|.-.|.
T Consensus 111 v~IllTDG~s~~~~~~~~~~~a~~lk~~gV~i~~vGiG~~~~~el~~ia~ 160 (192)
T cd01473 111 VTMLFTDGNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLKLLAG 160 (192)
T ss_pred EEEEEecCCCCCcchhhHHHHHHHHHHCCCEEEEEEeccccHHHHHHhcC
Confidence 4788888643 456677889999997666654 4446777764
No 105
>cd06361 PBP1_GPC6A_like Ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor. This family includes the ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor, and its fish homolog, the 5.24 chemoreceptor. GPRC6A is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses.
Probab=66.73 E-value=14 Score=33.05 Aligned_cols=34 Identities=15% Similarity=0.250 Sum_probs=30.7
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
+.+.+|+.++..+-..+++.|++.|++.+.||-.
T Consensus 234 ~a~vVvv~~~~~~~~~l~~~a~~~g~~~~wigs~ 267 (403)
T cd06361 234 KVNVIVVFARQFHVFLLFNKAIERNINKVWIASD 267 (403)
T ss_pred CCeEEEEEeChHHHHHHHHHHHHhCCCeEEEEEC
Confidence 7888999999999999999999999998888754
No 106
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=66.55 E-value=15 Score=30.62 Aligned_cols=34 Identities=15% Similarity=0.122 Sum_probs=28.0
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-+++.+.|++ +.++++.|++.|+..|.++..
T Consensus 57 ~vdgiii~~~~~~~~~~~~~~~~~~giPvV~~~~~ 91 (303)
T cd01539 57 GVDLLAVNLVDPTAAQTVINKAKQKNIPVIFFNRE 91 (303)
T ss_pred CCCEEEEecCchhhHHHHHHHHHHCCCCEEEeCCC
Confidence 8898988876655 678999999999998888753
No 107
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=66.34 E-value=11 Score=32.95 Aligned_cols=50 Identities=14% Similarity=0.153 Sum_probs=37.6
Q ss_pred CchHHhhhhcEEEEEe--------------------ecceEEEEe-CCCchHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV--------------------RFGCLMVVS-DDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V--------------------~v~clvLVS-Ddsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|+..+.++.|+.|... ++|.|++++ |...+.+.|+.|+++|+..|++...
T Consensus 44 Gi~~aa~~~G~~v~~~~~~~~d~~~q~~~i~~li~~~vdgIiv~~~d~~al~~~l~~a~~~gIpVV~~d~~ 114 (336)
T PRK15408 44 GAKEAGKELGVDVTYDGPTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALKRAMQRGVKVLTWDSD 114 (336)
T ss_pred HHHHHHHHhCCEEEEECCCCCCHHHHHHHHHHHHHcCCCEEEEecCCHHHHHHHHHHHHHCCCeEEEeCCC
Confidence 4455566667666552 899999987 4455789999999999999998654
No 108
>PRK04148 hypothetical protein; Provisional
Probab=66.21 E-value=15 Score=29.46 Aligned_cols=55 Identities=24% Similarity=0.262 Sum_probs=37.5
Q ss_pred CCCC--chHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCccEEEEecCCc--hhhhhhhccccc
Q 037201 103 VGYG--FADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMSD--GALKRIANAFFS 169 (177)
Q Consensus 103 vgyg--La~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~--~~L~r~Ad~~~s 169 (177)
.|+| +|..|.+.|+.|.-+ |-+.- .++.|++.++ .++++|..+ .++-+.||+=.|
T Consensus 25 ~GfG~~vA~~L~~~G~~ViaI---------Di~~~--aV~~a~~~~~-~~v~dDlf~p~~~~y~~a~liys 83 (134)
T PRK04148 25 IGFYFKVAKKLKESGFDVIVI---------DINEK--AVEKAKKLGL-NAFVDDLFNPNLEIYKNAKLIYS 83 (134)
T ss_pred ecCCHHHHHHHHHCCCEEEEE---------ECCHH--HHHHHHHhCC-eEEECcCCCCCHHHHhcCCEEEE
Confidence 4777 688999999866433 33322 5888888877 788999643 456677776443
No 109
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=66.11 E-value=13 Score=30.71 Aligned_cols=50 Identities=20% Similarity=0.202 Sum_probs=38.1
Q ss_pred CchHHhhhhcEEEEEe--------------------ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV--------------------RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V--------------------~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|+..++++.|+.|..+ ++|.|++++-+++ +.+.++.+++.++..|.++..
T Consensus 20 gi~~~a~~~g~~v~~~~~~~~d~~~~~~~i~~~~~~~~DgiIi~~~~~~~~~~~~~~~~~~~iPvV~v~~~ 90 (298)
T cd06302 20 GAKEAAKELGVDAIYVGPTTADAAGQVQIIEDLIAQGVDAIAVVPNDPDALEPVLKKAREAGIKVVTHDSD 90 (298)
T ss_pred HHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHHhcCCCEEEEecCCHHHHHHHHHHHHHCCCeEEEEcCC
Confidence 5566667777776653 7899999875543 678899999999999999754
No 110
>cd01477 vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of mo
Probab=65.79 E-value=13 Score=30.49 Aligned_cols=32 Identities=9% Similarity=0.143 Sum_probs=23.8
Q ss_pred eEEEEeCC------CchHHHHHHHHHcCccEEEEecCC
Q 037201 125 CLMVVSDD------SNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 125 clvLVSDd------sdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.+||++|| .+...+.+.+++.|+...+||-++
T Consensus 134 vvIllTDg~~~~~~~~~~~~a~~l~~~GI~i~tVGiG~ 171 (193)
T cd01477 134 VVIVFASDYNDEGSNDPRPIAARLKSTGIAIITVAFTQ 171 (193)
T ss_pred EEEEEecCccCCCCCCHHHHHHHHHHCCCEEEEEEeCC
Confidence 38888874 256788888999999966665554
No 111
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=65.57 E-value=17 Score=28.87 Aligned_cols=35 Identities=17% Similarity=0.248 Sum_probs=28.8
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
++|-+++.+.+++ ..++++.+.+.++..|.++...
T Consensus 56 ~vdgiii~~~~~~~~~~~~~~l~~~~iPvv~~~~~~ 91 (272)
T cd06301 56 GVDAIIVVPVDTAATAPIVKAANAAGIPLVYVNRRP 91 (272)
T ss_pred CCCEEEEecCchhhhHHHHHHHHHCCCeEEEecCCC
Confidence 8899998887665 4578899999999999998753
No 112
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=65.55 E-value=15 Score=29.12 Aligned_cols=32 Identities=16% Similarity=0.239 Sum_probs=19.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-||+.+.+++ ++++.++++++..|+++..
T Consensus 58 ~vdgiii~~~~~~--~~~~~l~~~~ipvV~~~~~ 89 (268)
T cd06277 58 KVDGIILLGGIST--EYIKEIKELGIPFVLVDHY 89 (268)
T ss_pred CCCEEEEeCCCCh--HHHHHHhhcCCCEEEEccC
Confidence 5666666664432 3466666677777776643
No 113
>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=65.14 E-value=18 Score=28.53 Aligned_cols=32 Identities=13% Similarity=0.067 Sum_probs=20.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
++|.+++++.++ -.++++.+.++++..|.++.
T Consensus 55 ~vdgiii~~~~~-~~~~~~~l~~~~iPvv~~~~ 86 (268)
T cd06273 55 GVDGLALIGLDH-SPALLDLLARRGVPYVATWN 86 (268)
T ss_pred CCCEEEEeCCCC-CHHHHHHHHhCCCCEEEEcC
Confidence 577777765543 24666777777777777764
No 114
>TIGR01135 glmS glucosamine--fructose-6-phosphate aminotransferase (isomerizing). The member from Methanococcus jannaschii contains an intein.
Probab=65.02 E-value=11 Score=35.65 Aligned_cols=47 Identities=11% Similarity=0.099 Sum_probs=38.2
Q ss_pred cceEEEEeC---CCchHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 123 FGCLMVVSD---DSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 123 v~clvLVSD---dsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
-+.+|.+|- ..+-.+.++.|+++|..||.|-+..+..|.+.||..+.
T Consensus 339 ~dlvI~iS~SG~T~e~v~a~~~ak~~ga~~IaIT~~~~S~La~~ad~~l~ 388 (607)
T TIGR01135 339 DTLVIAISQSGETADTLAALRLAKELGAKTLGICNVPGSTLVRESDHTLY 388 (607)
T ss_pred CCEEEEEeCCCCCHHHHHHHHHHHHcCCcEEEEECCCCChHHhhcCceEE
Confidence 456677764 34677788899999999999999888999999997664
No 115
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=64.67 E-value=17 Score=28.56 Aligned_cols=33 Identities=12% Similarity=0.149 Sum_probs=22.3
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++.+.+.+ .++++.+.+.++..|+++..
T Consensus 55 ~vdgiii~~~~~~-~~~~~~l~~~~ipvV~~~~~ 87 (268)
T cd06298 55 QVDGIIFMGGKIS-EEHREEFKRSPTPVVLAGSV 87 (268)
T ss_pred cCCEEEEeCCCCc-HHHHHHHhcCCCCEEEEccc
Confidence 7777777654322 35777777778888888754
No 116
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=64.31 E-value=16 Score=29.00 Aligned_cols=51 Identities=16% Similarity=0.141 Sum_probs=36.8
Q ss_pred CCchHHhhhhcEEEEEe-------------------ecceEEEEe---CCC-chHHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV-------------------RFGCLMVVS---DDS-NFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V-------------------~v~clvLVS---Dds-df~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..++++.|+.+... ++|.|++.+ |+. ...+.++.+.++|+..|+||-.
T Consensus 19 ~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~i~~~~~~~ipvV~i~~~ 92 (273)
T cd06292 19 EAIEAALAQYGYTVLLCNTYRGGVSEADYVEDLLARGVRGVVFISSLHADTHADHSHYERLAERGLPVVLVNGR 92 (273)
T ss_pred HHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHHcCCCEEEEeCCCCCcccchhHHHHHHHhCCCCEEEEcCC
Confidence 46677778888777544 789988875 222 2456678888899999999854
No 117
>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=64.23 E-value=15 Score=29.86 Aligned_cols=34 Identities=6% Similarity=0.140 Sum_probs=27.0
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.||+.+++....+.++.+.+.+.-.|++.|.
T Consensus 60 ~vDgiIv~~~~~~~~~~~~~l~~~~~p~V~i~~~ 93 (280)
T cd06303 60 KPDYLIFTLDSLRHRKLIERVLASGKTKIILQNI 93 (280)
T ss_pred CCCEEEEcCCchhhHHHHHHHHhCCCCeEEEeCC
Confidence 7899999876655678888888888888888664
No 118
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=63.87 E-value=4.1 Score=33.15 Aligned_cols=30 Identities=20% Similarity=0.244 Sum_probs=24.8
Q ss_pred hhhcCCCcCChhHHHHHHHhhhhhhhhhhh
Q 037201 49 LIRNQGRFYNNDKLVNHFRQIHEGEQKKRS 78 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kHFkqlHerEr~Krl 78 (177)
|+.|-|=|-+...|.-|||+-=-+-|.|.|
T Consensus 60 Ci~CaRyFi~~~~l~~H~ktK~HKrRvK~l 89 (129)
T KOG3408|consen 60 CIECARYFIDAKALKTHFKTKVHKRRVKEL 89 (129)
T ss_pred hhhhhhhhcchHHHHHHHhccHHHHHHHhc
Confidence 999999999999999999986544454444
No 119
>cd04509 PBP1_ABC_transporter_GCPR_C_like Family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. This CD includes members of the family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. The family C GPCR includes glutamate/glycine-gated ion channels such as the NMDA receptor, G-protein-coupled receptors, metabotropic glutamate, GABA-B, calcium sensing, phermone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. The glutamate receptors that form cation-selective ion channels, iGluR, can be classified into three different subgroups according to their binding-affinity for the agonists NMDA (N-methyl-D-asparate), AMPA (alpha-amino-3-dihydro-5-methyl-3-oxo-4-isoxazolepropionic acid), and kainate. L-glutamate is a major neurotransmitter in the brain of vertebrates and acts th
Probab=63.65 E-value=13 Score=29.03 Aligned_cols=33 Identities=9% Similarity=0.212 Sum_probs=27.3
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCc--cEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCL--KMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l--~TVVVGd 154 (177)
+.+.+++.+|.++...+++.+++.|+ +..+||-
T Consensus 191 ~~~~v~~~~~~~~~~~~~~~~~~~g~~~~~~~i~~ 225 (299)
T cd04509 191 KPDVIVLCGSGEDAATILKQAAEAGLTGGYPILGI 225 (299)
T ss_pred CCCEEEEcccchHHHHHHHHHHHcCCCCCCcEEec
Confidence 46788888888999999999999998 6677763
No 120
>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=63.18 E-value=18 Score=29.08 Aligned_cols=33 Identities=15% Similarity=0.031 Sum_probs=22.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++.+.+.+ .++++.+++.|+..|+++..
T Consensus 55 ~vdgvi~~~~~~~-~~~~~~l~~~~iPvv~~~~~ 87 (269)
T cd06297 55 LTDGLLLASYDLT-ERLAERRLPTERPVVLVDAE 87 (269)
T ss_pred CCCEEEEecCccC-hHHHHHHhhcCCCEEEEccC
Confidence 5777777775544 45667777778777777653
No 121
>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=62.88 E-value=17 Score=28.52 Aligned_cols=33 Identities=9% Similarity=0.040 Sum_probs=22.1
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|++++.+.+.+ ...++.+.+.++..|+++..
T Consensus 59 ~vdgiii~~~~~~-~~~~~~~~~~~ipvV~~~~~ 91 (268)
T cd06271 59 LVDGVIISRTRPD-DPRVALLLERGFPFVTHGRT 91 (268)
T ss_pred CCCEEEEecCCCC-ChHHHHHHhcCCCEEEECCc
Confidence 5788887764433 34566777788888888643
No 122
>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=62.50 E-value=19 Score=29.89 Aligned_cols=33 Identities=18% Similarity=0.134 Sum_probs=19.8
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
++|.||+.+.+.+..+.++...+.++..|+++-
T Consensus 116 ~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~~ 148 (327)
T TIGR02417 116 QVDALIVASCMPPEDAYYQKLQNEGLPVVALDR 148 (327)
T ss_pred CCCEEEEeCCCCCChHHHHHHHhcCCCEEEEcc
Confidence 567777665443234555666666777777664
No 123
>PF00702 Hydrolase: haloacid dehalogenase-like hydrolase; InterPro: IPR005834 This group of hydrolase enzymes is structurally different from the alpha/beta hydrolase family (abhydrolase). This group includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of HAD1_PSESP. The rest of the fold is composed of the core alpha/beta domain.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1TE2_A 3NAL_A 3NAM_A 3NAN_A 3A1D_B 3J09_A 3J08_A 2B8E_C 3A1E_A 2VOY_J ....
Probab=62.24 E-value=15 Score=28.11 Aligned_cols=48 Identities=23% Similarity=0.211 Sum_probs=31.3
Q ss_pred HHhhhhcEEEEEe---------------ecceEEEEeCC--C----chHHHHHHHHHcCccEEEEecCC
Q 037201 109 DELKRAWFCVRNV---------------RFGCLMVVSDD--S----NFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 109 ~eLrRAGv~Vr~V---------------~v~clvLVSDd--s----df~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.+|+.+|+.+..+ |++-.+..++. + -|..+++.-...+=.++.|||+.
T Consensus 137 ~~L~~~Gi~~~i~TGD~~~~a~~~~~~lgi~~~~v~a~~~~kP~~k~~~~~i~~l~~~~~~v~~vGDg~ 205 (215)
T PF00702_consen 137 QELKEAGIKVAILTGDNESTASAIAKQLGIFDSIVFARVIGKPEPKIFLRIIKELQVKPGEVAMVGDGV 205 (215)
T ss_dssp HHHHHTTEEEEEEESSEHHHHHHHHHHTTSCSEEEEESHETTTHHHHHHHHHHHHTCTGGGEEEEESSG
T ss_pred hhhhccCcceeeeeccccccccccccccccccccccccccccccchhHHHHHHHHhcCCCEEEEEccCH
Confidence 5788899977777 77554444444 2 34555555553333899999974
No 124
>PF05368 NmrA: NmrA-like family; InterPro: IPR008030 NmrA is a negative transcriptional regulator involved in the post-translational modification of the transcription factor AreA. NmrA is part of a system controlling nitrogen metabolite repression in fungi []. This family only contains a few sequences as iteration results in significant matches to other Rossmann fold families.; PDB: 2ZCV_A 2ZCU_A 2R6J_B 3C3X_A 2QZZ_B 2QYS_A 2QX7_A 2QW8_A 2R2G_B 3E5M_B ....
Probab=61.39 E-value=19 Score=28.72 Aligned_cols=49 Identities=16% Similarity=0.099 Sum_probs=36.9
Q ss_pred chHHhhhhcEEEEEe-------------ecceEEEEeC---CCc---hHHHHHHHHHcCccEEEEecC
Q 037201 107 FADELKRAWFCVRNV-------------RFGCLMVVSD---DSN---FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 107 La~eLrRAGv~Vr~V-------------~v~clvLVSD---dsd---f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.+.+|+..|+.|-.+ |+|+++++.. +.. ...+++.|.+.||+.+|.++.
T Consensus 36 ~~~~l~~~g~~vv~~d~~~~~~l~~al~g~d~v~~~~~~~~~~~~~~~~~li~Aa~~agVk~~v~ss~ 103 (233)
T PF05368_consen 36 RAQQLQALGAEVVEADYDDPESLVAALKGVDAVFSVTPPSHPSELEQQKNLIDAAKAAGVKHFVPSSF 103 (233)
T ss_dssp HHHHHHHTTTEEEES-TT-HHHHHHHHTTCSEEEEESSCSCCCHHHHHHHHHHHHHHHT-SEEEESEE
T ss_pred hhhhhhcccceEeecccCCHHHHHHHHcCCceEEeecCcchhhhhhhhhhHHHhhhccccceEEEEEe
Confidence 356677777766555 9999999988 433 456888899999999998775
No 125
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=60.99 E-value=14 Score=25.42 Aligned_cols=43 Identities=23% Similarity=0.113 Sum_probs=31.9
Q ss_pred CCchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCcc-EEEEecC
Q 037201 105 YGFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLK-MVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~-TVVVGd~ 155 (177)
+.++.+|+.+|+.|.. | .+ +..+..-++.|...|.. .++||+.
T Consensus 21 ~~la~~Lr~~g~~v~~---d----~~-~~~l~k~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 21 EKLYAELQAAGVDVLL---D----DR-NERPGVKFADADLIGIPYRIVVGKK 64 (94)
T ss_pred HHHHHHHHHCCCEEEE---E----CC-CCCcccchhHHHhcCCCEEEEECCc
Confidence 4568999999876642 1 12 34889999999999998 6677865
No 126
>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=60.85 E-value=23 Score=28.11 Aligned_cols=49 Identities=10% Similarity=0.099 Sum_probs=32.2
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|+..++++.|+.|... ++|.+++.+.+.+. +.++.+...+...|+++..
T Consensus 20 gi~~~~~~~gy~v~~~~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~-~~~~~~~~~~~pvV~i~~~ 87 (269)
T cd06293 20 AVEEEADARGLSLVLCATRNRPERELTYLRWLDTNHVDGLIFVTNRPDD-GALAKLINSYGNIVLVDED 87 (269)
T ss_pred HHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHHCCCCEEEEeCCCCCH-HHHHHHHhcCCCEEEECCC
Confidence 5566777777666444 78888888755443 3345555667888888753
No 127
>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=60.47 E-value=17 Score=29.15 Aligned_cols=32 Identities=13% Similarity=0.114 Sum_probs=23.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++++..++ +.++.+.++++..|+++..
T Consensus 52 ~vdgii~~~~~~~--~~~~~~~~~~~pvV~~~~~ 83 (270)
T cd01544 52 DVDGIIAIGKFSQ--EQLAKLAKLNPNLVFVDSN 83 (270)
T ss_pred CcCEEEEecCCCH--HHHHHHHhhCCCEEEECCC
Confidence 6788888765544 6777788888888888643
No 128
>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.
Probab=60.37 E-value=20 Score=25.56 Aligned_cols=33 Identities=15% Similarity=0.171 Sum_probs=25.6
Q ss_pred eCCCchHHHHHHHHHcCccEEEEecCCchhhhh
Q 037201 130 SDDSNFVEVFQEATLRCLKMVVVGDMSDGALKR 162 (177)
Q Consensus 130 SDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r 162 (177)
.+++-...+++.|.+.+...||+|-...+.+++
T Consensus 69 ~~~~~~~~I~~~~~~~~~dllviG~~~~~~~~~ 101 (124)
T cd01987 69 PGDDVAEAIVEFAREHNVTQIVVGKSRRSRWRE 101 (124)
T ss_pred eCCcHHHHHHHHHHHcCCCEEEeCCCCCchHHH
Confidence 344456778999999999999999986555554
No 129
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=60.20 E-value=21 Score=28.37 Aligned_cols=34 Identities=15% Similarity=0.242 Sum_probs=26.4
Q ss_pred ecceEEEEeCCC-chHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDS-NFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDds-df~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+|+.+-+. ...++++.+++.++..|+++..
T Consensus 57 ~vdgvii~~~~~~~~~~~l~~~~~~~ipvV~~~~~ 91 (273)
T cd06310 57 GPDAILLAPTDAKALVPPLKEAKDAGIPVVLIDSG 91 (273)
T ss_pred CCCEEEEcCCChhhhHHHHHHHHHCCCCEEEecCC
Confidence 788888876443 3457889999999999999764
No 130
>PRK08674 bifunctional phosphoglucose/phosphomannose isomerase; Validated
Probab=60.08 E-value=14 Score=32.43 Aligned_cols=43 Identities=21% Similarity=0.271 Sum_probs=32.4
Q ss_pred ecceEEEEeCCC---chHHHHHHHHHcCccEEEEecCCchhhhhhhcc
Q 037201 122 RFGCLMVVSDDS---NFVEVFQEATLRCLKMVVVGDMSDGALKRIANA 166 (177)
Q Consensus 122 ~v~clvLVSDds---df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~ 166 (177)
.-|++|.+|..- +-..+++.|+++|.++|+|.+. +.|.+.||.
T Consensus 78 ~~dlvI~iS~SG~T~e~~~a~~~a~~~ga~vIaIT~~--~~L~~~a~~ 123 (337)
T PRK08674 78 EKTLVIAVSYSGNTEETLSAVEQALKRGAKIIAITSG--GKLKEMAKE 123 (337)
T ss_pred CCcEEEEEcCCCCCHHHHHHHHHHHHCCCeEEEECCC--chHHHHHHh
Confidence 345677777553 4556688889999999999975 469998885
No 131
>cd02755 MopB_Thiosulfate-R-like The MopB_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Members of the MopB_Thiosulfate-R-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=59.90 E-value=16 Score=33.11 Aligned_cols=47 Identities=15% Similarity=0.105 Sum_probs=35.8
Q ss_pred ecceEEEEeCCC------chHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDS------NFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDds------df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|+||++.-|. .+..-++.|+++|.+.|||+-.- ....+.||.|++
T Consensus 156 ~ad~il~~G~n~~~~~~~~~~~~~~~a~~~g~kiivIdPr~-t~ta~~AD~~i~ 208 (454)
T cd02755 156 NARYIILFGRNLAEAIIVVDARRLMKALENGAKVVVVDPRF-SELASKADEWIP 208 (454)
T ss_pred cCCEEEEECcCcccccccHHHHHHHHHHHCCCeEEEECCCC-ChhhHhhCEecC
Confidence 668888885542 13555678889999999998864 677889999975
No 132
>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=59.62 E-value=23 Score=28.13 Aligned_cols=34 Identities=15% Similarity=0.197 Sum_probs=22.8
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-||+.+-|.+ ..++++.+.+.++..|+++..
T Consensus 57 ~~dgiIi~~~~~~~~~~~i~~~~~~~ipvv~~~~~ 91 (271)
T cd06321 57 KVDLILLNAVDSKGIAPAVKRAQAAGIVVVAVDVA 91 (271)
T ss_pred CCCEEEEeCCChhHhHHHHHHHHHCCCeEEEecCC
Confidence 6677777664432 456777777777777777654
No 133
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=59.52 E-value=3.2 Score=33.67 Aligned_cols=14 Identities=14% Similarity=0.339 Sum_probs=11.2
Q ss_pred hhhhhhcCCCcCCh
Q 037201 46 NCLLIRNQGRFYNN 59 (177)
Q Consensus 46 ~~Lc~~CGrrf~t~ 59 (177)
|++|+.||.|||..
T Consensus 9 Kr~Cp~cg~kFYDL 22 (129)
T TIGR02300 9 KRICPNTGSKFYDL 22 (129)
T ss_pred cccCCCcCcccccc
Confidence 56799999999863
No 134
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=59.22 E-value=6.2 Score=37.76 Aligned_cols=31 Identities=19% Similarity=0.315 Sum_probs=27.5
Q ss_pred hhhhcCCCcCChhHHHHHHHhhhhhhhhhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIHEGEQKKRS 78 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlHerEr~Krl 78 (177)
+|+.|..+|.+-+.++.|+.|-|...-..++
T Consensus 59 iCp~CskkF~d~~~~~~H~~~eH~~~l~P~l 89 (466)
T PF04780_consen 59 ICPRCSKKFSDAESCLSHMEQEHPAGLKPKL 89 (466)
T ss_pred eCCcccceeCCHHHHHHHHHHhhhhhcChhh
Confidence 4999999999999999999999998765544
No 135
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=59.13 E-value=6.4 Score=23.32 Aligned_cols=18 Identities=6% Similarity=-0.029 Sum_probs=15.9
Q ss_pred hhhcCCCcCChhHHHHHHH
Q 037201 49 LIRNQGRFYNNDKLVNHFR 67 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kHFk 67 (177)
|++|+..+ +...+..|.+
T Consensus 4 CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 4 CPVCFREV-PENLINSHLD 21 (26)
T ss_pred CCCCcCcc-cHHHHHHHHH
Confidence 99999999 6788889987
No 136
>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein. This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of this gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source.
Probab=58.57 E-value=20 Score=29.49 Aligned_cols=34 Identities=18% Similarity=0.328 Sum_probs=27.4
Q ss_pred ecceEEEEeCCC-chHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDS-NFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDds-df~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.||+++-|+ .+.+.++.++++|+..|+++..
T Consensus 56 ~vdgiIi~~~~~~~~~~~l~~~~~~giPvV~~~~~ 90 (302)
T TIGR02637 56 KVDAIAISANDPDALVPALKKAMKRGIKVVTWDSG 90 (302)
T ss_pred CCCEEEEeCCChHHHHHHHHHHHHCCCEEEEeCCC
Confidence 789998887554 4567899999999999999754
No 137
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=58.56 E-value=5 Score=26.61 Aligned_cols=22 Identities=18% Similarity=0.304 Sum_probs=18.6
Q ss_pred hhhhhcCCCcCChhHHHHHHHhhh
Q 037201 47 CLLIRNQGRFYNNDKLVNHFRQIH 70 (177)
Q Consensus 47 ~Lc~~CGrrf~t~~~L~kHFkqlH 70 (177)
..|++|..++.+ +|..|+...|
T Consensus 32 v~CPiC~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 32 VVCPICSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred ccCCCchhhhhh--HHHHHHHHhc
Confidence 459999997664 9999999888
No 138
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=58.37 E-value=22 Score=30.58 Aligned_cols=33 Identities=15% Similarity=0.313 Sum_probs=22.2
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd 154 (177)
++|-|++++.+++ +.+.++.+.++++..|+++.
T Consensus 81 ~vDGiIi~~~~~~~~~~~l~~~~~~~iPvV~id~ 114 (330)
T PRK10355 81 GVDVLVIIPYNGQVLSNVIKEAKQEGIKVLAYDR 114 (330)
T ss_pred CCCEEEEeCCChhhHHHHHHHHHHCCCeEEEECC
Confidence 6777777665443 56677777777777777754
No 139
>cd02750 MopB_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. Members of the MopB_Nitrate-R-NarG-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=58.31 E-value=17 Score=33.00 Aligned_cols=47 Identities=15% Similarity=0.138 Sum_probs=35.8
Q ss_pred ecceEEEEeCCCc-----hHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDSN-----FVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsd-----f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|+|+++.-|.. +...|+.||++|.+.|||.-. .......||.|++
T Consensus 170 ~ad~il~~G~N~~~~~~~~~~~l~~ar~~GaklividPr-~s~ta~~Ad~~l~ 221 (461)
T cd02750 170 NADYIIMWGSNVPVTRTPDAHFLTEARYNGAKVVVVSPD-YSPSAKHADLWVP 221 (461)
T ss_pred cCcEEEEECCChHHccCchHHHHHHHHHCCCEEEEEcCC-CCcchhhcCEEec
Confidence 5788999876642 234567799999999999554 4678889999885
No 140
>cd06348 PBP1_ABC_ligand_binding_like_13 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=58.18 E-value=15 Score=30.75 Aligned_cols=33 Identities=6% Similarity=0.058 Sum_probs=27.5
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
+.|.+++.....+...+++.|++.|+...++|-
T Consensus 192 ~~d~vi~~~~~~~~~~~~~~~~~~g~~~~~~~~ 224 (344)
T cd06348 192 KPDLIVISALAADGGNLVRQLRELGYNGLIVGG 224 (344)
T ss_pred CCCEEEECCcchhHHHHHHHHHHcCCCCceecc
Confidence 678888888888888999999998888777764
No 141
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=58.05 E-value=23 Score=29.33 Aligned_cols=33 Identities=12% Similarity=0.150 Sum_probs=17.5
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
++|.|++.+.+.+-.+.++.+.+.++..|+|+.
T Consensus 117 ~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~v~~ 149 (328)
T PRK11303 117 QVDALIVSTSLPPEHPFYQRLQNDGLPIIALDR 149 (328)
T ss_pred CCCEEEEcCCCCCChHHHHHHHhcCCCEEEECC
Confidence 556666554433223445555556666666654
No 142
>cd06347 PBP1_ABC_ligand_binding_like_12 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=57.70 E-value=16 Score=29.88 Aligned_cols=32 Identities=9% Similarity=0.093 Sum_probs=25.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEe
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG 153 (177)
+.|.+++.+...+...+++.+++.|++..++|
T Consensus 191 ~~d~i~~~~~~~~~~~~~~~~~~~g~~~~i~~ 222 (334)
T cd06347 191 NPDVIFLPGYYTEVGLIAKQARELGIKVPILG 222 (334)
T ss_pred CCCEEEEcCchhhHHHHHHHHHHcCCCCcEEe
Confidence 67788888888888888888888888766665
No 143
>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=57.50 E-value=28 Score=27.25 Aligned_cols=33 Identities=18% Similarity=0.279 Sum_probs=22.0
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-+++.+.+.+ ..+++.+.+.|+..|.++..
T Consensus 54 ~vdgiii~~~~~~-~~~~~~~~~~~ipvV~~~~~ 86 (266)
T cd06278 54 RVDGVIVTSGTLS-SELAEECRRNGIPVVLINRY 86 (266)
T ss_pred CCCEEEEecCCCC-HHHHHHHhhcCCCEEEECCc
Confidence 6777777655433 24577777788888888653
No 144
>COG4229 Predicted enolase-phosphatase [Energy production and conversion]
Probab=57.46 E-value=27 Score=30.72 Aligned_cols=122 Identities=20% Similarity=0.238 Sum_probs=75.7
Q ss_pred ehhhccCCccccCChhhHhhhhhhhh---h---hhhcCCCcCChhHHHHHHHhhhhhhhhhhhhhhhhhcc---------
Q 037201 22 MVANANSHAFGYVPQVVREQRKKENC---L---LIRNQGRFYNNDKLVNHFRQIHEGEQKKRSNQIESARG--------- 86 (177)
Q Consensus 22 ~~AyAnrhaf~~lP~~v~e~r~er~~---L---c~~CGrrf~t~~~L~kHFkqlHerEr~Krl~ri~s~kG--------- 86 (177)
+-.||-+| ||+.|++-+.+-.- + ...-|..+. .+.|+.||-++|...+.-+ -++.+.|
T Consensus 25 lFPYa~~~----lp~fv~e~~e~~~v~~~v~~v~~e~g~~~s-~E~lva~~~~wiaed~K~t--~lK~lQG~iWa~Gy~s 97 (229)
T COG4229 25 LFPYAARK----LPDFVRENTEDSEVKKIVDEVLSEFGIANS-EEALVALLLEWIAEDSKDT--PLKALQGMIWAHGYES 97 (229)
T ss_pred hhHHHHHH----hHHHHHhhccCChhhHHHHHHHHHhCccch-HHHHHHHHHHHHhcccccc--hHHHHHhHHHHhcccc
Confidence 35788887 99999988764322 2 334676665 8999999999988765432 2444555
Q ss_pred ---chHHHHHHHHhh---c-------------CC--CC--CCCchHHhhh--hcEEEEEe----------------ecc-
Q 037201 87 ---KMEKYKMAVSAI---L-------------TP--KV--GYGFADELKR--AWFCVRNV----------------RFG- 124 (177)
Q Consensus 87 ---K~~KY~~Aar~v---l-------------~p--kv--gygLa~eLrR--AGv~Vr~V----------------~v~- 124 (177)
|-.-|..|.-.+ . .| |. ||.-+..|.. -|++=.|. |+.
T Consensus 98 gelkahlypDav~~ik~wk~~g~~vyiYSSGSV~AQkL~Fghs~agdL~~lfsGyfDttiG~KrE~~SY~kIa~~iGl~p 177 (229)
T COG4229 98 GELKAHLYPDAVQAIKRWKALGMRVYIYSSGSVKAQKLFFGHSDAGDLNSLFSGYFDTTIGKKRESQSYAKIAGDIGLPP 177 (229)
T ss_pred CccccccCHhHHHHHHHHHHcCCcEEEEcCCCchhHHHhhcccccccHHhhhcceeeccccccccchhHHHHHHhcCCCc
Confidence 434444443322 1 01 11 5666666654 35555555 222
Q ss_pred -eEEEEeCCCchHHHHHHHHHcCccEEEEe
Q 037201 125 -CLMVVSDDSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 125 -clvLVSDdsdf~~~lr~Ar~r~l~TVVVG 153 (177)
-++..||.. .=|+.|+..|++|+.+-
T Consensus 178 ~eilFLSDn~---~EL~AA~~vGl~t~l~~ 204 (229)
T COG4229 178 AEILFLSDNP---EELKAAAGVGLATGLAV 204 (229)
T ss_pred hheEEecCCH---HHHHHHHhcchheeeee
Confidence 255567765 56889999999998863
No 145
>cd05009 SIS_GlmS_GlmD_2 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=57.23 E-value=22 Score=26.26 Aligned_cols=42 Identities=21% Similarity=0.333 Sum_probs=29.3
Q ss_pred cceEEEEe-CCCc---hHHHHHHHHHcCccEEEEecCCchhhhhhhcc
Q 037201 123 FGCLMVVS-DDSN---FVEVFQEATLRCLKMVVVGDMSDGALKRIANA 166 (177)
Q Consensus 123 v~clvLVS-Ddsd---f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~ 166 (177)
-++++++| ++.. ..++++.+++.|.++++|.+..+. .+.+|.
T Consensus 62 ~~~vi~is~~g~t~~~~~~~~~~~~~~~~~vi~it~~~~s--~~~~d~ 107 (153)
T cd05009 62 GTPVIFLAPEDRLEEKLESLIKEVKARGAKVIVITDDGDA--KDLADV 107 (153)
T ss_pred CCcEEEEecCChhHHHHHHHHHHHHHcCCEEEEEecCCcc--cccCCe
Confidence 45677777 4432 557888889999999999887532 455554
No 146
>cd02751 MopB_DMSOR-like The MopB_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. Members of the MopB_DMSOR-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=57.16 E-value=14 Score=34.78 Aligned_cols=46 Identities=4% Similarity=0.057 Sum_probs=34.3
Q ss_pred cceEEEEeCCCc-------------hHHHHHHHHHcCccEEEEecCCchhhhh-hhccccc
Q 037201 123 FGCLMVVSDDSN-------------FVEVFQEATLRCLKMVVVGDMSDGALKR-IANAFFS 169 (177)
Q Consensus 123 v~clvLVSDdsd-------------f~~~lr~Ar~r~l~TVVVGd~~~~~L~r-~Ad~~~s 169 (177)
.|||+++.-|.. +...++.|+++|.+-|||.=. ...... .||.|++
T Consensus 170 ad~il~wG~N~~~~~~~~~~~~~~~~~~~~~~a~~~GakiivIDPr-~s~ta~~~AD~~l~ 229 (609)
T cd02751 170 SDLVVLFGANPLKTRQGGGGGPDHGSYYYLKQAKDAGVRFICIDPR-YTDTAAVLAAEWIP 229 (609)
T ss_pred CCEEEEECCCHHHhcCCCCCccCcchHHHHHHHHHCCCeEEEECCC-CCccccccCCEEEC
Confidence 788888865532 336788899999999999544 345665 7999986
No 147
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=56.85 E-value=28 Score=29.00 Aligned_cols=33 Identities=9% Similarity=0.108 Sum_probs=21.6
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-+++++.+. -.+.++.+.+.++..|+++|.
T Consensus 119 ~vdgiI~~~~~~-~~~~~~~l~~~~iPvV~~~~~ 151 (331)
T PRK14987 119 NIDGLILTERTH-TPRTLKMIEVAGIPVVELMDS 151 (331)
T ss_pred CCCEEEEcCCCC-CHHHHHHHHhCCCCEEEEecC
Confidence 677777765332 246677777778887777654
No 148
>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=56.75 E-value=31 Score=27.25 Aligned_cols=33 Identities=12% Similarity=0.184 Sum_probs=22.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++++.+.+ ...++.+.+.+...|++|..
T Consensus 51 ~vdgii~~~~~~~-~~~~~~~~~~~ipvV~~~~~ 83 (261)
T cd06272 51 RFDGVIIFGESAS-DVEYLYKIKLAIPVVSYGVD 83 (261)
T ss_pred CcCEEEEeCCCCC-hHHHHHHHHcCCCEEEEccc
Confidence 7888888765433 23467777888888888764
No 149
>TIGR01525 ATPase-IB_hvy heavy metal translocating P-type ATPase. This alignment encompasses two equivalog models for the copper and cadmium-type heavy metal transporting P-type ATPases (TIGR01511 and TIGR01512) as well as those species which score ambiguously between both models. For more comments and references, see the files on TIGR01511 and 01512.
Probab=56.58 E-value=16 Score=34.26 Aligned_cols=63 Identities=16% Similarity=0.048 Sum_probs=42.5
Q ss_pred HHhhhhc-EEEEEe---------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC-chhhhhhhccccchh
Q 037201 109 DELKRAW-FCVRNV---------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS-DGALKRIANAFFSWS 171 (177)
Q Consensus 109 ~eLrRAG-v~Vr~V---------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~-~~~L~r~Ad~~~sW~ 171 (177)
.+|+..| +.+-.+ |++...--....+=..+++.....+-.++.|||+. |-.-.+.||+.++|.
T Consensus 394 ~~L~~~g~i~v~ivTgd~~~~a~~i~~~lgi~~~f~~~~p~~K~~~v~~l~~~~~~v~~vGDg~nD~~al~~A~vgia~g 473 (556)
T TIGR01525 394 AALKRAGGIKLVMLTGDNRSAAEAVAAELGIDEVHAELLPEDKLAIVKELQEEGGVVAMVGDGINDAPALAAADVGIAMG 473 (556)
T ss_pred HHHHHcCCCeEEEEeCCCHHHHHHHHHHhCCCeeeccCCHHHHHHHHHHHHHcCCEEEEEECChhHHHHHhhCCEeEEeC
Confidence 5678888 777776 66543322222233456777776777999999953 445668899999986
No 150
>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=56.32 E-value=27 Score=27.68 Aligned_cols=50 Identities=18% Similarity=0.170 Sum_probs=34.7
Q ss_pred CCchHHhhhhcEEEEEe-------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV-------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..+++..|+.+... ++|-+++.+-+.+ .+.++.+.+.++..|+++..
T Consensus 19 ~gi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~-~~~~~~~~~~~iPvv~~~~~ 87 (265)
T cd06285 19 EGIEEAAAERGYSTFVANTGDNPDAQRRAIEMLLDRRVDGLILGDARSD-DHFLDELTRRGVPFVLVLRH 87 (265)
T ss_pred HHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEecCCCC-hHHHHHHHHcCCCEEEEccC
Confidence 46677777777776543 7787777653333 35678888888888888764
No 151
>cd06360 PBP1_alkylbenzenes_like Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene. This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.
Probab=55.96 E-value=28 Score=28.74 Aligned_cols=33 Identities=12% Similarity=0.210 Sum_probs=27.2
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCc--cEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCL--KMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l--~TVVVGd 154 (177)
+.|.|++.+-.++...+++.+++.|+ +..++|.
T Consensus 189 ~pd~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 223 (336)
T cd06360 189 VPDAVFVFFAGGDAIKFVKQYDAAGLKAKIPLIGS 223 (336)
T ss_pred CCCEEEEecccccHHHHHHHHHHcCCccCCeEEec
Confidence 67888888888899999999999999 5566664
No 152
>TIGR01511 ATPase-IB1_Cu copper-(or silver)-translocating P-type ATPase. One member from Halobacterium is annotated as "molybdenum-binding protein" although no evidence can be found for this classification.
Probab=55.79 E-value=20 Score=33.95 Aligned_cols=62 Identities=15% Similarity=0.042 Sum_probs=42.3
Q ss_pred HHhhhhcEEEEEe---------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC-Cchhhhhhhccccchh
Q 037201 109 DELKRAWFCVRNV---------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM-SDGALKRIANAFFSWS 171 (177)
Q Consensus 109 ~eLrRAGv~Vr~V---------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~-~~~~L~r~Ad~~~sW~ 171 (177)
.+|++.|+.+-.+ |++..- -....+=.++++...+.+=+++.|||+ +|-...+.||+.+.|.
T Consensus 415 ~~Lk~~Gi~v~ilSgd~~~~a~~ia~~lgi~~~~-~~~p~~K~~~v~~l~~~~~~v~~VGDg~nD~~al~~A~vgia~g 492 (562)
T TIGR01511 415 QALKRRGIEPVMLTGDNRKTAKAVAKELGINVRA-EVLPDDKAALIKELQEKGRVVAMVGDGINDAPALAQADVGIAIG 492 (562)
T ss_pred HHHHHcCCeEEEEcCCCHHHHHHHHHHcCCcEEc-cCChHHHHHHHHHHHHcCCEEEEEeCCCccHHHHhhCCEEEEeC
Confidence 4677788776655 666211 111134466777777778789999996 5667778899998886
No 153
>cd06350 PBP1_GPCR_family_C_like Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). The metabotropic glutamate receptors (mGluR) are key receptors in the modulation of excitatory synaptic transmission in the central nervous system. The mGluRs are coupled to G proteins and are thus distinct from the iGluRs which internally contain ligand-gated ion channels. The mGluR structure is divided into three regions: the extracellular region, the seven-spanning transmembrane region and the cytoplasmic region. The extr
Probab=55.74 E-value=30 Score=28.79 Aligned_cols=35 Identities=17% Similarity=0.216 Sum_probs=28.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCc--cEEEEecCC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCL--KMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l--~TVVVGd~~ 156 (177)
+.|.+++.++..+...+++.|++.|+ +.+++++.+
T Consensus 217 ~~~vvv~~~~~~~~~~~~~~a~~~g~~~~~~i~~~~~ 253 (348)
T cd06350 217 TARVIVVFGDEDDALRLFCEAYKLGMTGKYWIISTDW 253 (348)
T ss_pred CCcEEEEEeCcHHHHHHHHHHHHhCCCCeEEEEEccc
Confidence 66899999999999999999999998 344555543
No 154
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=55.62 E-value=32 Score=26.66 Aligned_cols=34 Identities=15% Similarity=0.178 Sum_probs=25.1
Q ss_pred ecceEEEEeCCCch-HHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNF-VEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf-~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++++-+++. .++++.+++.++..|.++..
T Consensus 55 ~vdgvi~~~~~~~~~~~~~~~l~~~~ip~V~~~~~ 89 (267)
T cd01536 55 GVDGIIISPVDSAALTPALKKANAAGIPVVTVDSD 89 (267)
T ss_pred CCCEEEEeCCCchhHHHHHHHHHHCCCcEEEecCC
Confidence 67888888765544 35788888888888888764
No 155
>PRK03094 hypothetical protein; Provisional
Probab=55.41 E-value=10 Score=28.39 Aligned_cols=32 Identities=25% Similarity=0.422 Sum_probs=28.5
Q ss_pred chHHhhhhcEEEEEe-------ecceEEEEeCCCchHHH
Q 037201 107 FADELKRAWFCVRNV-------RFGCLMVVSDDSNFVEV 138 (177)
Q Consensus 107 La~eLrRAGv~Vr~V-------~v~clvLVSDdsdf~~~ 138 (177)
+..+|+..|+.|-.. ++||+|.-..|+||.++
T Consensus 13 i~~~L~~~GYeVv~l~~~~~~~~~Da~VitG~d~n~mgi 51 (80)
T PRK03094 13 VQQALKQKGYEVVQLRSEQDAQGCDCCVVTGQDSNVMGI 51 (80)
T ss_pred HHHHHHHCCCEEEecCcccccCCcCEEEEeCCCcceecc
Confidence 678999999999766 69999999999999884
No 156
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=55.27 E-value=23 Score=30.36 Aligned_cols=33 Identities=3% Similarity=0.039 Sum_probs=25.1
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-|++++.+++ +.+.+ .+++.|+..|.+++.
T Consensus 104 ~vdgIIl~~~~~~~~~~~l-~~~~~giPvV~~~~~ 137 (343)
T PRK10936 104 GADAILLGAVTPDGLNPDL-ELQAANIPVIALVNG 137 (343)
T ss_pred CCCEEEEeCCChHHhHHHH-HHHHCCCCEEEecCC
Confidence 7888999886544 45677 888999998878654
No 157
>PLN02981 glucosamine:fructose-6-phosphate aminotransferase
Probab=54.89 E-value=19 Score=35.22 Aligned_cols=47 Identities=13% Similarity=0.049 Sum_probs=39.1
Q ss_pred cceEEEEeC---CCchHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 123 FGCLMVVSD---DSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 123 v~clvLVSD---dsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
-+++|+||- ..|-.+.++.|+++|.+||.|-+..+..|.+.||.-+.
T Consensus 411 ~~lvI~ISqSGeT~eti~Al~~Ak~~Ga~~IaITn~~~S~La~~ad~~i~ 460 (680)
T PLN02981 411 EDTAVFVSQSGETADTLRALEYAKENGALCVGITNTVGSAISRGTHCGVH 460 (680)
T ss_pred CCeEEEEeCCcCCHHHHHHHHHHHHCCCcEEEEECCCCChhHhccCeeEE
Confidence 367888985 44778889999999999999988878899999997443
No 158
>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=54.71 E-value=34 Score=26.26 Aligned_cols=31 Identities=13% Similarity=0.168 Sum_probs=13.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEe
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG 153 (177)
++|.+++...++.-.. ++.+.+.++.-|.++
T Consensus 55 ~~d~iii~~~~~~~~~-~~~~~~~~ipvv~~~ 85 (264)
T cd06267 55 RVDGIILAPSRLDDEL-LEELAALGIPVVLVD 85 (264)
T ss_pred CcCEEEEecCCcchHH-HHHHHHcCCCEEEec
Confidence 4444444444333222 444444454444444
No 159
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=54.26 E-value=30 Score=27.38 Aligned_cols=32 Identities=13% Similarity=0.122 Sum_probs=18.0
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
++|.+++++.+.+- ..++.+++.|+..|+++-
T Consensus 55 ~vdgiii~~~~~~~-~~~~~~~~~~ipvV~~~~ 86 (264)
T cd06274 55 QVDALIVAGSLPPD-DPYYLCQKAGLPVVALDR 86 (264)
T ss_pred CCCEEEEcCCCCch-HHHHHHHhcCCCEEEecC
Confidence 56666666554322 225556666666666644
No 160
>cd06337 PBP1_ABC_ligand_binding_like_4 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=54.01 E-value=20 Score=30.71 Aligned_cols=32 Identities=13% Similarity=0.153 Sum_probs=27.6
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEe
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG 153 (177)
+.|.|++.+..++...+++.+++.|+..-+++
T Consensus 203 ~pD~v~~~~~~~~~~~~~~~~~~~G~~~~~~~ 234 (357)
T cd06337 203 GVDIVTGFAIPPDFATFWRQAAQAGFKPKIVT 234 (357)
T ss_pred CCCEEEeCCCccHHHHHHHHHHHCCCCCCeEE
Confidence 78999999999999999999999999754443
No 161
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=53.98 E-value=9.6 Score=25.31 Aligned_cols=21 Identities=5% Similarity=0.107 Sum_probs=11.1
Q ss_pred hhhhcCCCcCChh--HHHHHHHh
Q 037201 48 LLIRNQGRFYNND--KLVNHFRQ 68 (177)
Q Consensus 48 Lc~~CGrrf~t~~--~L~kHFkq 68 (177)
-||+|||.|.... +|++++++
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~~~ 44 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKYKS 44 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHHHH
Confidence 4999999997654 45555544
No 162
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=53.77 E-value=7.2 Score=34.69 Aligned_cols=24 Identities=21% Similarity=0.133 Sum_probs=20.1
Q ss_pred hhhhhhhcCCCcCChhHHHHHHHh
Q 037201 45 ENCLLIRNQGRFYNNDKLVNHFRQ 68 (177)
Q Consensus 45 r~~Lc~~CGrrf~t~~~L~kHFkq 68 (177)
+.+||.-||.-|..-.+|++|-++
T Consensus 144 kr~lct~cgkgfndtfdlkrh~rt 167 (267)
T KOG3576|consen 144 KRHLCTFCGKGFNDTFDLKRHTRT 167 (267)
T ss_pred HHHHHhhccCcccchhhhhhhhcc
Confidence 457799999999999999998764
No 163
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=53.44 E-value=9.2 Score=36.98 Aligned_cols=53 Identities=25% Similarity=0.175 Sum_probs=38.2
Q ss_pred hhhhhhhcCCCcCChhHHHHHHHhhhhhhhhh-hhhhhhhh--ccchHHHHHHHHh
Q 037201 45 ENCLLIRNQGRFYNNDKLVNHFRQIHEGEQKK-RSNQIESA--RGKMEKYKMAVSA 97 (177)
Q Consensus 45 r~~Lc~~CGrrf~t~~~L~kHFkqlHerEr~K-rl~ri~s~--kGK~~KY~~Aar~ 97 (177)
.-++||.|+..|.+..-|.-||.-=|--|-.| -++...|. +||..|-+.++++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~ed~~D~lgs~~s~~~~~kkk~~r~~~~~ 69 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEEDEKDSLGSFKSRVLNGKKKKQRKAAQE 69 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhccccchhhHhhhHHHHHHhHHHHHhhhHHHH
Confidence 45789999999999999999999999888764 33334433 4454444444444
No 164
>cd06268 PBP1_ABC_transporter_LIVBP_like Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity. Members of this group include ABC
Probab=53.07 E-value=27 Score=27.17 Aligned_cols=33 Identities=15% Similarity=0.191 Sum_probs=27.7
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
+.+.+++.+|..+...+++.+++.|+.-.++|-
T Consensus 190 ~~~~vi~~~~~~~~~~~~~~~~~~g~~~~~~~~ 222 (298)
T cd06268 190 GPDAVFLAGYGGDAALFLKQAREAGLKVPIVGG 222 (298)
T ss_pred CCCEEEEccccchHHHHHHHHHHcCCCCcEEec
Confidence 467888999989999999999999987666663
No 165
>cd06346 PBP1_ABC_ligand_binding_like_11 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=52.43 E-value=31 Score=28.76 Aligned_cols=32 Identities=13% Similarity=-0.039 Sum_probs=25.7
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEe
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG 153 (177)
+.|.|++.+...+-..+++.+++.|+..-++|
T Consensus 192 ~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~~~ 223 (312)
T cd06346 192 GPDALVVIGYPETGSGILRSAYEQGLFDKFLL 223 (312)
T ss_pred CCCEEEEecccchHHHHHHHHHHcCCCCceEe
Confidence 77888888888888899999999888654444
No 166
>cd06330 PBP1_Arsenic_SBP_like Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds. Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa.
Probab=52.16 E-value=22 Score=29.67 Aligned_cols=26 Identities=15% Similarity=0.187 Sum_probs=23.2
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCc
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCL 147 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l 147 (177)
+.|.+++++...+...+++.|++.|+
T Consensus 195 ~~d~ii~~~~~~~~~~~~~~~~~~g~ 220 (346)
T cd06330 195 KPDAIFSSLWGGDLVTFVRQANARGL 220 (346)
T ss_pred CCCEEEEecccccHHHHHHHHHhcCc
Confidence 67888888888899999999999998
No 167
>PHA00733 hypothetical protein
Probab=52.05 E-value=7.8 Score=30.38 Aligned_cols=23 Identities=17% Similarity=0.079 Sum_probs=20.3
Q ss_pred hhhhhhhcCCCcCChhHHHHHHH
Q 037201 45 ENCLLIRNQGRFYNNDKLVNHFR 67 (177)
Q Consensus 45 r~~Lc~~CGrrf~t~~~L~kHFk 67 (177)
+.+.|..||..|.+...|..|-+
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHh
Confidence 45679999999999999999976
No 168
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=51.94 E-value=49 Score=26.32 Aligned_cols=34 Identities=12% Similarity=0.189 Sum_probs=26.3
Q ss_pred ecceEEEEeCC-CchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDD-SNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDd-sdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-+++.+-| ..+.+++..+.++|+..|+++..
T Consensus 60 ~vdgiIi~~~~~~~~~~~l~~~~~~~iPvv~~~~~ 94 (272)
T cd06300 60 GVDAIIINPASPTALNPVIEEACEAGIPVVSFDGT 94 (272)
T ss_pred CCCEEEEeCCChhhhHHHHHHHHHCCCeEEEEecC
Confidence 78888887644 44677889999999988888654
No 169
>cd06343 PBP1_ABC_ligand_binding_like_8 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=51.84 E-value=27 Score=29.45 Aligned_cols=34 Identities=6% Similarity=0.056 Sum_probs=27.8
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccE-EEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKM-VVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~T-VVVGd~ 155 (177)
+.|.|++..+..+...+++.+++.|+.. +++++.
T Consensus 199 ~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 233 (362)
T cd06343 199 GADVVVLATTPKFAAQAIRKAAELGWKPTFLLSSV 233 (362)
T ss_pred CCCEEEEEcCcHHHHHHHHHHHHcCCCceEEEEec
Confidence 7889999999999999999999999863 444443
No 170
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=51.81 E-value=33 Score=28.94 Aligned_cols=51 Identities=12% Similarity=0.165 Sum_probs=41.8
Q ss_pred CCchHHhhhhcEEEEEe------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 105 YGFADELKRAWFCVRNV------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.|+..++++.|+.+-.. +||-||+.|-..+...+.+..+. +.-.|+++...
T Consensus 21 ~gIe~~a~~~Gy~l~l~~t~~~~~~e~~i~~l~~~~vDGiI~~s~~~~~~~l~~~~~~-~iPvV~~~~~~ 89 (279)
T PF00532_consen 21 RGIEQEAREHGYQLLLCNTGDDEEKEEYIELLLQRRVDGIILASSENDDEELRRLIKS-GIPVVLIDRYI 89 (279)
T ss_dssp HHHHHHHHHTTCEEEEEEETTTHHHHHHHHHHHHTTSSEEEEESSSCTCHHHHHHHHT-TSEEEEESS-S
T ss_pred HHHHHHHHHcCCEEEEecCCCchHHHHHHHHHHhcCCCEEEEecccCChHHHHHHHHc-CCCEEEEEecc
Confidence 46788899999988765 89999999998887787777777 99988888764
No 171
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=51.78 E-value=24 Score=30.74 Aligned_cols=33 Identities=12% Similarity=0.144 Sum_probs=27.7
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
+.|.|++.+...++..+++.+++.|+..-++|-
T Consensus 216 ~~d~v~~~~~~~~~~~~~k~~~~~G~~~~~i~~ 248 (369)
T PRK15404 216 NVDFVYYGGYHPEMGQILRQAREAGLKTQFMGP 248 (369)
T ss_pred CCCEEEECCCchHHHHHHHHHHHCCCCCeEEec
Confidence 778888888888999999999999998766655
No 172
>cd06375 PBP1_mGluR_groupII Ligand binding domain of the group II metabotropic glutamate receptor. Ligand binding domain of the group II metabotropic glutamate receptor, a family that contains mGlu2R and mGlu3R, all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes
Probab=51.38 E-value=34 Score=31.09 Aligned_cols=33 Identities=9% Similarity=0.082 Sum_probs=26.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
+.+.+|+.++..+...+++.|++.|+..+.||-
T Consensus 232 ~a~vVvl~~~~~~~~~ll~~a~~~g~~~~wigs 264 (458)
T cd06375 232 NARVVVLFTRSEDARELLAAAKRLNASFTWVAS 264 (458)
T ss_pred CCEEEEEecChHHHHHHHHHHHHcCCcEEEEEe
Confidence 567788888888999999999999998666653
No 173
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=50.83 E-value=41 Score=25.71 Aligned_cols=34 Identities=12% Similarity=0.140 Sum_probs=15.6
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+|+.+.+.....+++.+.+.++..|.++..
T Consensus 55 ~~d~ii~~~~~~~~~~~~~~l~~~~ip~v~~~~~ 88 (264)
T cd01537 55 GVDGIIIAPSDLTAPTIVKLARKAGIPVVLVDRD 88 (264)
T ss_pred CCCEEEEecCCCcchhHHHHhhhcCCCEEEeccC
Confidence 4454444444333322345555555555555443
No 174
>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=50.81 E-value=39 Score=27.36 Aligned_cols=33 Identities=18% Similarity=0.120 Sum_probs=22.6
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++.+.+.. .+.++.+++.|+..|.++..
T Consensus 56 ~~dgiii~~~~~~-~~~~~~~~~~~ipvV~~~~~ 88 (283)
T cd06279 56 LVDGFIVYGVPRD-DPLVAALLRRGLPVVVVDQP 88 (283)
T ss_pred CCCEEEEeCCCCC-hHHHHHHHHcCCCEEEEecC
Confidence 7777777764432 25677788888887777654
No 175
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT. Members of this family are the periplasmic protein TorT which, together with the the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase, and shows homology to a periplasmic D-ribose binding protein.
Probab=50.80 E-value=33 Score=28.29 Aligned_cols=33 Identities=0% Similarity=0.043 Sum_probs=23.0
Q ss_pred ecceEEEEeC-CCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSD-DSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSD-dsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.|++++- +..+.+.++.+ +.++..|++++.
T Consensus 57 ~vDgiIi~~~~~~~~~~~l~~~-~~~iPvV~~~~~ 90 (295)
T TIGR02955 57 GADAILLGTVSPEALNHDLAQL-TKSIPVFALVNQ 90 (295)
T ss_pred CCCEEEEecCChhhhhHHHHHH-hcCCCEEEEecC
Confidence 8899988863 34456777766 458888877543
No 176
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=50.69 E-value=8.2 Score=24.16 Aligned_cols=25 Identities=12% Similarity=0.086 Sum_probs=16.9
Q ss_pred hhhhhhcCCCcCCh----hHHHHHHHhhh
Q 037201 46 NCLLIRNQGRFYNN----DKLVNHFRQIH 70 (177)
Q Consensus 46 ~~Lc~~CGrrf~t~----~~L~kHFkqlH 70 (177)
..-|..|+..++.. ..|.+|.+..|
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 34599999977764 78999998777
No 177
>cd06336 PBP1_ABC_ligand_binding_like_3 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=50.60 E-value=25 Score=29.83 Aligned_cols=31 Identities=10% Similarity=-0.001 Sum_probs=25.6
Q ss_pred ecceEEEEeCCC-chHHHHHHHHHcCccEEEE
Q 037201 122 RFGCLMVVSDDS-NFVEVFQEATLRCLKMVVV 152 (177)
Q Consensus 122 ~v~clvLVSDds-df~~~lr~Ar~r~l~TVVV 152 (177)
+.|.|++.+... +...+++.+++.|+..-++
T Consensus 193 ~~d~v~~~~~~~~~~~~~~~~~~~~g~~~~~~ 224 (347)
T cd06336 193 KPDVIFLGGPSPAPAALVIKQARELGFKGGFL 224 (347)
T ss_pred CCCEEEEcCCCchHHHHHHHHHHHcCCCccEE
Confidence 778888888888 8999999999998875443
No 178
>PRK11199 tyrA bifunctional chorismate mutase/prephenate dehydrogenase; Provisional
Probab=50.40 E-value=33 Score=30.88 Aligned_cols=132 Identities=17% Similarity=0.172 Sum_probs=76.3
Q ss_pred HHHHHhcccceeeehhhccCCccccCChhhHhhhhhhhhh--hhh-cCCCcCChhHHHHHHHhhh----hhhhhhhhhhh
Q 037201 9 LKKLISSFEVVKYMVANANSHAFGYVPQVVREQRKKENCL--LIR-NQGRFYNNDKLVNHFRQIH----EGEQKKRSNQI 81 (177)
Q Consensus 9 Lr~~A~~FG~Vv~~~AyAnrhaf~~lP~~v~e~r~er~~L--c~~-CGrrf~t~~~L~kHFkqlH----erEr~Krl~ri 81 (177)
+..+++++..+.++.+|=..+. +| +.+.-+|...+ ... ....--..+-..+-|+.|+ .+|+++.++.+
T Consensus 20 v~Ll~~R~~~~~~ia~~K~~~~---~~--v~d~~Re~~vl~~~~~~~~~~~l~~~~~~~i~~~i~~~s~~~q~~~~~~~~ 94 (374)
T PRK11199 20 LELLAKRLELVAQVGEVKSRHG---LP--IYVPEREAAMLASRRAEAEALGVPPDLIEDVLRRVMRESYSSENDKGFKTL 94 (374)
T ss_pred HHHHHHHHHHHHHHHHHHHhCC---CC--CCChHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHhHHhccccc
Confidence 5678889999999988876652 34 44444443333 122 2222234555778899998 56677776665
Q ss_pred hhhccchHHHHHHHHhhc--CCCCCCCchHHhhhhcEEEEEe-------------ecceEEEEeCCCchHHHHHHHHHcC
Q 037201 82 ESARGKMEKYKMAVSAIL--TPKVGYGFADELKRAWFCVRNV-------------RFGCLMVVSDDSNFVEVFQEATLRC 146 (177)
Q Consensus 82 ~s~kGK~~KY~~Aar~vl--~pkvgygLa~eLrRAGv~Vr~V-------------~v~clvLVSDdsdf~~~lr~Ar~r~ 146 (177)
+....+. .++ +-..|-++|..|+++|+.|..+ +.|.+|+.-=++...++++......
T Consensus 95 ~~~~~~I--------~IiGG~GlmG~slA~~l~~~G~~V~~~d~~~~~~~~~~~~~aDlVilavP~~~~~~~~~~l~~l~ 166 (374)
T PRK11199 95 NPDLRPV--------VIVGGKGQLGRLFAKMLTLSGYQVRILEQDDWDRAEDILADAGMVIVSVPIHLTEEVIARLPPLP 166 (374)
T ss_pred CcccceE--------EEEcCCChhhHHHHHHHHHCCCeEEEeCCCcchhHHHHHhcCCEEEEeCcHHHHHHHHHHHhCCC
Confidence 5422111 122 2333567899999999887766 4555555544555566666543323
Q ss_pred ccEEEEe
Q 037201 147 LKMVVVG 153 (177)
Q Consensus 147 l~TVVVG 153 (177)
-+++|+-
T Consensus 167 ~~~iv~D 173 (374)
T PRK11199 167 EDCILVD 173 (374)
T ss_pred CCcEEEE
Confidence 3344443
No 179
>cd06338 PBP1_ABC_ligand_binding_like_5 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT); however their ligand specificity has not been determined experimentally.
Probab=50.37 E-value=25 Score=29.27 Aligned_cols=31 Identities=6% Similarity=-0.040 Sum_probs=26.3
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEE
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVV 152 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVV 152 (177)
+.|.|++..+..++..+++.+++.|+..-++
T Consensus 196 ~~d~i~~~~~~~~~~~~~~~~~~~g~~~~~~ 226 (345)
T cd06338 196 GPDAVVVAGHFPDAVLLVRQMKELGYNPKAL 226 (345)
T ss_pred CCCEEEECCcchhHHHHHHHHHHcCCCCCEE
Confidence 6889999999999999999999999864333
No 180
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=50.29 E-value=26 Score=29.69 Aligned_cols=32 Identities=6% Similarity=0.137 Sum_probs=27.5
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEe
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG 153 (177)
+.|.|++.+...++..+++.+++.|++.-++|
T Consensus 193 ~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~ 224 (347)
T cd06335 193 GADAIIIVGNGPEGAQIANGMAKLGWKVPIIS 224 (347)
T ss_pred CCCEEEEEecChHHHHHHHHHHHcCCCCcEec
Confidence 67889999999999999999999999866665
No 181
>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription
Probab=50.28 E-value=31 Score=27.22 Aligned_cols=29 Identities=10% Similarity=0.092 Sum_probs=12.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
++|.+++.+.|++ ++.+++.|...|+++.
T Consensus 55 ~~dgiii~~~~~~----~~~~~~~gipvv~~~~ 83 (265)
T cd06291 55 QVDGIIAGTHNLG----IEEYENIDLPIVSFDR 83 (265)
T ss_pred CCCEEEEecCCcC----HHHHhcCCCCEEEEeC
Confidence 4555555444333 1233444555555443
No 182
>PTZ00295 glucosamine-fructose-6-phosphate aminotransferase; Provisional
Probab=50.16 E-value=29 Score=33.32 Aligned_cols=48 Identities=13% Similarity=0.070 Sum_probs=40.3
Q ss_pred cceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 123 FGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 123 v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
-+.++.+|-. .|-.++++.|+++|..||.|-+..+..|.+.||.-+..
T Consensus 370 ~~lvI~ISqSGeT~d~i~al~~ak~~Ga~~IaITn~~~S~La~~ad~~l~~ 420 (640)
T PTZ00295 370 DAGVIFISQSGETLDVVRALNLADELNLPKISVVNTVGSLIARSTDCGVYL 420 (640)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHHCCCCEEEEECCCCChhHHhcCEEEEe
Confidence 4678888754 46777888999999999999888888999999998765
No 183
>PF15608 PELOTA_1: PELOTA RNA binding domain
Probab=50.01 E-value=29 Score=26.93 Aligned_cols=35 Identities=20% Similarity=0.290 Sum_probs=31.4
Q ss_pred ecceEEEEe--CCCchHHHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVS--DDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVS--Ddsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
++.|-|||- ||+|..-++.+|.++|+.-.+++|..
T Consensus 54 RvP~~vLVr~~~~pd~~Hl~~LA~ekgVpVe~~~d~~ 90 (100)
T PF15608_consen 54 RVPWKVLVRDPDDPDLAHLLLLAEEKGVPVEVYPDLP 90 (100)
T ss_pred cCCCEEEECCCCCccHHHHHHHHHHcCCcEEEeCCCC
Confidence 789999996 67889999999999999999999974
No 184
>cd01989 STK_N The N-terminal domain of Eukaryotic Serine Threonine kinases. The Serine Threonine kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The N-terminal domain is homologous to the USP family which has a ATP binding fold. The N-terminal domain is predicted to be involved in ATP binding.
Probab=49.82 E-value=48 Score=24.29 Aligned_cols=29 Identities=14% Similarity=0.158 Sum_probs=23.3
Q ss_pred CchHHHHHHHHHcCccEEEEecCCchhhh
Q 037201 133 SNFVEVFQEATLRCLKMVVVGDMSDGALK 161 (177)
Q Consensus 133 sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~ 161 (177)
+--..+++.|.+.+...||+|-...+.|+
T Consensus 90 ~~~~~I~~~a~~~~~dlIV~Gs~g~~~l~ 118 (146)
T cd01989 90 DVAKAIVEYVADHGITKLVMGASSDNHFS 118 (146)
T ss_pred cHHHHHHHHHHHcCCCEEEEeccCCCcee
Confidence 44678999999999999999987544443
No 185
>cd06287 PBP1_LacI_like_8 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=48.90 E-value=39 Score=27.65 Aligned_cols=50 Identities=12% Similarity=0.067 Sum_probs=34.1
Q ss_pred CCchHHhhhhcEEEEEe------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+..+++..|+.+-.. ++|-+|+++.+.+ .+.++...+.++..|++|..
T Consensus 27 ~~i~~~~~~~gy~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~-~~~~~~l~~~~iPvV~i~~~ 88 (269)
T cd06287 27 AAAAESALERGLALCLVPPHEADSPLDALDIDGAILVEPMAD-DPQVARLRQRGIPVVSIGRP 88 (269)
T ss_pred HHHHHHHHHCCCEEEEEeCCCchhhhhccCcCeEEEecCCCC-CHHHHHHHHcCCCEEEeCCC
Confidence 35566666666665443 7888888875433 25667777789999999764
No 186
>cd02753 MopB_Formate-Dh-H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. Members of the MopB_Formate-Dh-H CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=48.88 E-value=27 Score=31.79 Aligned_cols=47 Identities=15% Similarity=0.259 Sum_probs=35.5
Q ss_pred ecceEEEEeCCC-----chHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDS-----NFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDds-----df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|+||++..|. .+..-++.|+++|.+.|||+=.. ......||.|++
T Consensus 156 ~ad~il~~G~n~~~~~~~~~~~i~~a~~~G~k~i~Idp~~-s~ta~~Ad~~l~ 207 (512)
T cd02753 156 EADVILVIGSNTTEAHPVIARRIKRAKRNGAKLIVADPRR-TELARFADLHLQ 207 (512)
T ss_pred hCCEEEEECCChhhhhHHHHHHHHHHHHCCCeEEEEcCCC-ccchHhhCeeeC
Confidence 678888887664 33345678889999999998653 566778999986
No 187
>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=48.59 E-value=46 Score=26.03 Aligned_cols=15 Identities=20% Similarity=0.255 Sum_probs=6.6
Q ss_pred HHHHHHcCccEEEEe
Q 037201 139 FQEATLRCLKMVVVG 153 (177)
Q Consensus 139 lr~Ar~r~l~TVVVG 153 (177)
++.+.+.++.-|+++
T Consensus 71 l~~~~~~~ipvV~~~ 85 (267)
T cd06283 71 YQRLAKNGKPVVLVD 85 (267)
T ss_pred HHHHhcCCCCEEEEc
Confidence 344444444444443
No 188
>PTZ00394 glucosamine-fructose-6-phosphate aminotransferase; Provisional
Probab=48.51 E-value=33 Score=33.57 Aligned_cols=47 Identities=11% Similarity=0.090 Sum_probs=38.8
Q ss_pred cceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 123 FGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 123 v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
-+++|.+|-. .|-..+++.|+++|.+||.|-+..+..|.|.||.-+.
T Consensus 402 ~dlvI~ISqSGeT~dtl~Al~~Ak~~Ga~tIaITn~~~S~La~~AD~~l~ 451 (670)
T PTZ00394 402 DDVCFFVSQSGETADTLMALQLCKEAGAMCVGITNVVGSSISRLTHYAIH 451 (670)
T ss_pred CCEEEEEECCcCcHHHHHHHHHHHHCCCcEEEEECCCCCHHHHhcCeEEE
Confidence 4678888744 4566778899999999999988878899999998665
No 189
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=48.24 E-value=9.1 Score=34.59 Aligned_cols=25 Identities=12% Similarity=0.135 Sum_probs=21.6
Q ss_pred hhhhhhhhcCCCcCChhHHHHHHHh
Q 037201 44 KENCLLIRNQGRFYNNDKLVNHFRQ 68 (177)
Q Consensus 44 er~~Lc~~CGrrf~t~~~L~kHFkq 68 (177)
|..|.|+.||+.|-.+.+|.-|..+
T Consensus 213 EKPF~C~hC~kAFADRSNLRAHmQT 237 (279)
T KOG2462|consen 213 EKPFSCPHCGKAFADRSNLRAHMQT 237 (279)
T ss_pred CCCccCCcccchhcchHHHHHHHHh
Confidence 6677799999999999999998754
No 190
>cd02766 MopB_3 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins
Probab=48.03 E-value=28 Score=32.14 Aligned_cols=48 Identities=19% Similarity=0.216 Sum_probs=36.5
Q ss_pred ecceEEEEeCCC-----chHHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 122 RFGCLMVVSDDS-----NFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 122 ~v~clvLVSDds-----df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
..|||+++--|. .+...++.|+++|.+-|||.=. .....+.||.|++-
T Consensus 157 ~ad~il~~G~Np~~s~p~~~~~~~~a~~~GaklivvDPr-~t~ta~~Ad~~l~i 209 (501)
T cd02766 157 NADLIVIWGINPAATNIHLMRIIQEARKRGAKVVVIDPY-RTATAARADLHIQI 209 (501)
T ss_pred cCCEEEEECCChhhhchhHHHHHHHHHHCCCEEEEECCC-CCccHHHhCeeecc
Confidence 678888885443 3446677899999999999654 46788999999863
No 191
>TIGR00522 dph5 diphthine synthase. This protein participates in the modification of a specific His of elongation factor 2 of eukarotes and Archaea to diphthamide. The protein was characterized in Saccharomyces cerevisiae and designated DPH5.
Probab=48.03 E-value=29 Score=29.71 Aligned_cols=51 Identities=20% Similarity=0.172 Sum_probs=38.8
Q ss_pred CchHHhhhhcEEEEEe--------------------ec-ceEEEEeCCC---chHHHHHHHHHcCccEEEEecCC
Q 037201 106 GFADELKRAWFCVRNV--------------------RF-GCLMVVSDDS---NFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V--------------------~v-~clvLVSDds---df~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.|..+|+++|+.|+.| |. .++.++|+.- .+.+.+.....++.+|+|+=|..
T Consensus 94 ~l~~~l~~~~i~vevIPGiSs~~aaaa~~g~~lt~~g~~~~v~~~s~~~~~~~~~~~~~~~l~~~~~Tlvll~~~ 168 (257)
T TIGR00522 94 DLKLEAKRKGIETRIIHGASISSAVCGLTGLQLYKFGKTATIVFFTDNYRPQTPYNVIKENRKIGLHTLVLLDIH 168 (257)
T ss_pred HHHHHHHHCCCeEEEECcHhHHHHHHHHcCCCcccCCCcEEEEEecCCcCCCCHHHHHHHHHhcCCCcEEEEecc
Confidence 4566779999999999 33 6688888764 45567777778899999996543
No 192
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=47.58 E-value=16 Score=27.18 Aligned_cols=32 Identities=16% Similarity=0.399 Sum_probs=27.2
Q ss_pred chHHhhhhcEEEEEe-------ecceEEEEeCCCchHHH
Q 037201 107 FADELKRAWFCVRNV-------RFGCLMVVSDDSNFVEV 138 (177)
Q Consensus 107 La~eLrRAGv~Vr~V-------~v~clvLVSDdsdf~~~ 138 (177)
+..+|+..||.|-.. ++||+|.--.|+||.++
T Consensus 13 v~~~L~~~GyeVv~l~~~~~~~~~daiVvtG~~~n~mg~ 51 (80)
T PF03698_consen 13 VKEALREKGYEVVDLENEQDLQNVDAIVVTGQDTNMMGI 51 (80)
T ss_pred HHHHHHHCCCEEEecCCccccCCcCEEEEECCCcccccc
Confidence 578999999999988 79999988888887665
No 193
>cd06334 PBP1_ABC_ligand_binding_like_1 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=47.56 E-value=37 Score=29.39 Aligned_cols=33 Identities=12% Similarity=-0.018 Sum_probs=27.8
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
+.|.|++.....+-..+++.+++.|+..-++|.
T Consensus 195 ~pd~V~~~~~~~~~~~~~~~~~~~G~~~~~~~~ 227 (351)
T cd06334 195 GPDYVILWGWGVMNPVAIKEAKRVGLDDKFIGN 227 (351)
T ss_pred CCCEEEEecccchHHHHHHHHHHcCCCceEEEe
Confidence 788888888888999999999999997666654
No 194
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=47.31 E-value=17 Score=24.92 Aligned_cols=35 Identities=20% Similarity=0.196 Sum_probs=24.7
Q ss_pred hcEEEEEeecce-EEEEeCCCchHHHHHHHHHcCcc
Q 037201 114 AWFCVRNVRFGC-LMVVSDDSNFVEVFQEATLRCLK 148 (177)
Q Consensus 114 AGv~Vr~V~v~c-lvLVSDdsdf~~~lr~Ar~r~l~ 148 (177)
..+.++-..-|- +|.+++|+||..+++.+++.+-+
T Consensus 40 ~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~~~~~~ 75 (84)
T PF00564_consen 40 EDFQLKYKDEDGDLVTISSDEDLQEAIEQAKESGSK 75 (84)
T ss_dssp SSEEEEEEETTSSEEEESSHHHHHHHHHHHHHCTTS
T ss_pred ccEEEEeeCCCCCEEEeCCHHHHHHHHHHHHhcCCC
Confidence 345555553332 78889999999999999986433
No 195
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=47.29 E-value=52 Score=25.87 Aligned_cols=33 Identities=15% Similarity=0.041 Sum_probs=20.6
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++.+.+.+-.. +..+.++|+..|+++..
T Consensus 56 ~vdgiii~~~~~~~~~-~~~~~~~~ipvv~~~~~ 88 (264)
T cd01574 56 RVDGVIVNAPLDDADA-ALAAAPADVPVVFVDGS 88 (264)
T ss_pred CCCEEEEeCCCCChHH-HHHHHhcCCCEEEEecc
Confidence 6777777654332223 44456788888888754
No 196
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=47.20 E-value=48 Score=24.77 Aligned_cols=35 Identities=11% Similarity=0.110 Sum_probs=28.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
++|.+++.+.+..-..++..+.+.++.+|.++-..
T Consensus 58 ~~d~ii~~~~~~~~~~~~~~~~~~~ip~v~~~~~~ 92 (269)
T cd01391 58 GVDGIIGPPSSSSALAVVELAAAAGIPVVSLDATA 92 (269)
T ss_pred CCCEEEecCCCHHHHHHHHHHHHcCCcEEEecCCC
Confidence 78888888877666668899999999999998664
No 197
>cd06345 PBP1_ABC_ligand_binding_like_10 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=46.81 E-value=39 Score=28.37 Aligned_cols=31 Identities=6% Similarity=-0.103 Sum_probs=24.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEE
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVV 152 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVV 152 (177)
+.|.|++.+...+...+++.+++.|+..-.+
T Consensus 199 ~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~ 229 (344)
T cd06345 199 DPDVIIAGFSGNVGVLFTQQWAEQKVPIPTI 229 (344)
T ss_pred CCCEEEEeecCchHHHHHHHHHHcCCCCceE
Confidence 6788888888888899999999998754333
No 198
>TIGR01522 ATPase-IIA2_Ca golgi membrane calcium-translocating P-type ATPase. The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1 the former of which is modelled by TIGR01116.
Probab=46.78 E-value=38 Score=33.96 Aligned_cols=37 Identities=14% Similarity=0.153 Sum_probs=28.8
Q ss_pred hHHHHHHHHHcCccEEEEecC-Cchhhhhhhccccchh
Q 037201 135 FVEVFQEATLRCLKMVVVGDM-SDGALKRIANAFFSWS 171 (177)
Q Consensus 135 f~~~lr~Ar~r~l~TVVVGd~-~~~~L~r~Ad~~~sW~ 171 (177)
=..+++..++.|-.+..|||+ +|-.--+.||+.++|.
T Consensus 606 K~~iv~~lq~~g~~v~mvGDGvND~pAl~~AdVGia~g 643 (884)
T TIGR01522 606 KMKIVKALQKRGDVVAMTGDGVNDAPALKLADIGVAMG 643 (884)
T ss_pred HHHHHHHHHHCCCEEEEECCCcccHHHHHhCCeeEecC
Confidence 455777778888888899994 4555568999999994
No 199
>TIGR03479 DMSO_red_II_alp DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane.
Probab=46.66 E-value=27 Score=35.14 Aligned_cols=47 Identities=9% Similarity=0.094 Sum_probs=35.0
Q ss_pred ecceEEEEeCCC-----chHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDS-----NFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDds-----df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..+||+++--|. -....|++|+++|.+-|||.=. -......||.|++
T Consensus 224 na~~Il~~G~Np~~t~~~~~~~l~~a~~~GaklVvIdPr-~t~tA~~AD~wlp 275 (912)
T TIGR03479 224 NADYIIMWGSNPSVTRIPDAHFLSEARYNGARVVSIAPD-YNPSTIHADLWLP 275 (912)
T ss_pred cCcEEEEecCChHHcCCchHHHHHHHHhcCCeEEEECCC-CChhhhhCCeecC
Confidence 678888885442 2345677899999999999543 3577889999986
No 200
>cd02759 MopB_Acetylene-hydratase The MopB_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=46.27 E-value=36 Score=31.01 Aligned_cols=47 Identities=17% Similarity=0.143 Sum_probs=35.8
Q ss_pred ecceEEEEeCCC------chHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDS------NFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDds------df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|+||++.-|. .+...++.|+++|.+-|||.-. .......||.|++
T Consensus 160 ~ad~Il~~G~n~~~~~~~~~~~~~~~ar~~g~klividpr-~s~ta~~Ad~~l~ 212 (477)
T cd02759 160 NPECIVLWGKNPLNSNLDLQGHWLVAAMKRGAKLIVVDPR-LTWLAARADLWLP 212 (477)
T ss_pred cCCEEEEEccChhhhCcHHHHHHHHHHHHCCCEEEEECCC-CChhhHhhCeeec
Confidence 678888887664 3445667888899888888554 4678899999985
No 201
>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix.
Probab=46.26 E-value=23 Score=26.42 Aligned_cols=44 Identities=20% Similarity=0.257 Sum_probs=25.0
Q ss_pred cceEEEEeC-----CCchHHHHHHHHH--cCccEEEEecCCc-hhhhhhhcc
Q 037201 123 FGCLMVVSD-----DSNFVEVFQEATL--RCLKMVVVGDMSD-GALKRIANA 166 (177)
Q Consensus 123 v~clvLVSD-----dsdf~~~lr~Ar~--r~l~TVVVGd~~~-~~L~r~Ad~ 166 (177)
...|+++|| +.++...++.+.+ -.+.+|.+|+..+ ..|.+.|+.
T Consensus 100 ~~~iillTDG~~~~~~~~~~~~~~~~~~~i~i~~i~~g~~~~~~~l~~ia~~ 151 (171)
T cd01461 100 VPQIILLTDGEVTNESQILKNVREALSGRIRLFTFGIGSDVNTYLLERLARE 151 (171)
T ss_pred ccEEEEEeCCCCCCHHHHHHHHHHhcCCCceEEEEEeCCccCHHHHHHHHHc
Confidence 467888888 2334455555543 3456777775432 346665553
No 202
>cd00858 GlyRS_anticodon GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=46.06 E-value=48 Score=24.71 Aligned_cols=42 Identities=17% Similarity=0.062 Sum_probs=31.3
Q ss_pred CCchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCcc-EEEEecC
Q 037201 105 YGFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLK-MVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~-TVVVGd~ 155 (177)
+.++.+||.+|+.|.. -.+ ..+..-++.|.+.|.. .++||+.
T Consensus 45 ~~la~~LR~~gi~v~~-------d~~--~sl~kqlk~A~k~g~~~~iiiG~~ 87 (121)
T cd00858 45 KEISEELRELGFSVKY-------DDS--GSIGRRYARQDEIGTPFCVTVDFD 87 (121)
T ss_pred HHHHHHHHHCCCEEEE-------eCC--CCHHHHHHHhHhcCCCEEEEECcC
Confidence 3568889998876542 123 6899999999999998 6666865
No 203
>cd06363 PBP1_Taste_receptor Ligand-binding domain of the T1R taste receptor. Ligand-binding domain of the T1R taste receptor. The T1R is a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptors, GABAb receptors, the calcium-sensing receptor (CaSR), the V2R pheromone receptors, and a small group of uncharacterized orphan receptors.
Probab=46.00 E-value=45 Score=29.27 Aligned_cols=33 Identities=12% Similarity=0.199 Sum_probs=27.1
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCc-cEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCL-KMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l-~TVVVGd 154 (177)
+.|.|++.++.++...+++.|++.|+ ..+.||.
T Consensus 234 ~~dvIil~~~~~~~~~il~qa~~~g~~~~~~i~~ 267 (410)
T cd06363 234 KVNVIVVFASRQPAEAFFNSVIQQNLTGKVWIAS 267 (410)
T ss_pred CCeEEEEEcChHHHHHHHHHHHhcCCCCCEEEEe
Confidence 78889999999999999999999888 4454553
No 204
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=45.89 E-value=53 Score=25.69 Aligned_cols=32 Identities=6% Similarity=0.062 Sum_probs=15.6
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.|++.+.+.+-. ++ .+.+.|+..|++++.
T Consensus 55 ~vdgiii~~~~~~~~-~~-~~~~~~ipvv~~~~~ 86 (267)
T cd06284 55 QADGIILLDGSLPPT-AL-TALAKLPPIVQACEY 86 (267)
T ss_pred CCCEEEEecCCCCHH-HH-HHHhcCCCEEEEecc
Confidence 566666655433322 22 233446666666543
No 205
>cd06362 PBP1_mGluR Ligand binding domain of the metabotropic glutamate receptors (mGluR). Ligand binding domain of the metabotropic glutamate receptors (mGluR), which are members of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses. mGluRs bind to glutamate and function as an excitatory neurotransmitter; they are involved in learning, memory, anxiety, and the perception of pain. Eight subtypes of mGluRs have been cloned so far, and are classified into three groups according to their sequence similarities, transduction mechanisms, and pharmacological profiles. Group I is composed of mGlu1R and mGlu5R that both stimulate PLC hydrolysis. Group II includes mGlu2R and mGlu3R, which inhibit adenylyl cyclase, as do mGlu4R, mGlu6R, mGlu7R, and mGlu8R, which form group III.
Probab=45.88 E-value=50 Score=29.19 Aligned_cols=32 Identities=3% Similarity=0.066 Sum_probs=26.2
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCc--cEEEEe
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCL--KMVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l--~TVVVG 153 (177)
+.+.+||.+...+...+++.|++.|+ +.+.||
T Consensus 230 ~a~viil~~~~~~~~~~~~~a~~~g~~~~~~~i~ 263 (452)
T cd06362 230 NARVVVLFCREDDIRGLLAAAKRLNAEGHFQWIA 263 (452)
T ss_pred CCeEEEEEcChHHHHHHHHHHHHcCCcCceEEEE
Confidence 46778899999999999999999999 445554
No 206
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=45.74 E-value=37 Score=26.51 Aligned_cols=41 Identities=15% Similarity=0.226 Sum_probs=28.9
Q ss_pred cceEEEEeCCCchHHHHHHHHHcCccEEEEe-----cCCchhhhhh
Q 037201 123 FGCLMVVSDDSNFVEVFQEATLRCLKMVVVG-----DMSDGALKRI 163 (177)
Q Consensus 123 v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG-----d~~~~~L~r~ 163 (177)
+.++..-....++..+.+..++.++..+||| |++.+...+.
T Consensus 25 l~~i~~~~~~~~~~~l~~~i~~~~~~~iVvGlP~~~dG~~~~~a~~ 70 (130)
T TIGR00250 25 IPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTER 70 (130)
T ss_pred eEEEEecCCcHHHHHHHHHHHHcCCCEEEEeccCCCCcCcCHHHHH
Confidence 3444333345678889999999999999999 8765554333
No 207
>PRK09701 D-allose transporter subunit; Provisional
Probab=44.41 E-value=50 Score=27.69 Aligned_cols=34 Identities=12% Similarity=0.089 Sum_probs=25.8
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|-||+.+-+++ -.+.+..+.+.|+..|+++..
T Consensus 82 ~vDgiIi~~~~~~~~~~~l~~~~~~giPvV~~~~~ 116 (311)
T PRK09701 82 NYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEK 116 (311)
T ss_pred CCCEEEEeCCChHHHHHHHHHHHHCCCcEEEeCCC
Confidence 7888888865543 335678888899999999865
No 208
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=44.24 E-value=58 Score=25.59 Aligned_cols=32 Identities=19% Similarity=0.267 Sum_probs=18.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++.+.+.+ .+.++.+.+.+ ..|+++..
T Consensus 55 ~vdgiii~~~~~~-~~~~~~~~~~~-pvv~~~~~ 86 (260)
T cd06286 55 QVDGLILCSREND-WEVIEPYTKYG-PIVLCEEY 86 (260)
T ss_pred CCCEEEEeCCCCC-HHHHHHHhcCC-CEEEEecc
Confidence 5777777654433 34556666655 66666543
No 209
>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=43.98 E-value=37 Score=27.68 Aligned_cols=40 Identities=30% Similarity=0.409 Sum_probs=24.0
Q ss_pred eEEEEeCC---CchHHHHHHHHHcCccEEEEe--cCCchhhhhhh
Q 037201 125 CLMVVSDD---SNFVEVFQEATLRCLKMVVVG--DMSDGALKRIA 164 (177)
Q Consensus 125 clvLVSDd---sdf~~~lr~Ar~r~l~TVVVG--d~~~~~L~r~A 164 (177)
.|||++|- .+..++.+.+++.|+...+|| +.+...|.+.|
T Consensus 111 vvillTDG~s~~~~~~~a~~lk~~gv~i~~VgvG~~~~~~L~~ia 155 (224)
T cd01475 111 VGIVVTDGRPQDDVSEVAAKARALGIEMFAVGVGRADEEELREIA 155 (224)
T ss_pred EEEEEcCCCCcccHHHHHHHHHHCCcEEEEEeCCcCCHHHHHHHh
Confidence 45677775 235566777778888855555 33333555555
No 210
>cd01476 VWA_integrin_invertebrates VWA_integrin (invertebrates): Integrins are a family of cell surface receptors that have diverse functions in cell-cell and cell-extracellular matrix interactions. Because of their involvement in many biologically important adhesion processes, integrins are conserved across a wide range of multicellular animals. Integrins from invertebrates have been identified from six phyla. There are no data to date to suggest any immunological functions for the invertebrate integrins. The members of this sub-group have the conserved MIDAS motif that is charateristic of this domain suggesting the involvement of the integrins in the recognition and binding of multi-ligands.
Probab=43.78 E-value=57 Score=24.51 Aligned_cols=34 Identities=12% Similarity=0.109 Sum_probs=23.6
Q ss_pred ceEEEEeCCC---chHHHHHHHHH-cCccEEEEecCCc
Q 037201 124 GCLMVVSDDS---NFVEVFQEATL-RCLKMVVVGDMSD 157 (177)
Q Consensus 124 ~clvLVSDds---df~~~lr~Ar~-r~l~TVVVGd~~~ 157 (177)
.-+||+||-. +-..+.+..+. .++.++.||-+++
T Consensus 105 ~~villTDG~~~~~~~~~~~~l~~~~~v~v~~vg~g~~ 142 (163)
T cd01476 105 KVVVVLTDGRSHDDPEKQARILRAVPNIETFAVGTGDP 142 (163)
T ss_pred eEEEEECCCCCCCchHHHHHHHhhcCCCEEEEEECCCc
Confidence 3578889842 24456677777 8888888887653
No 211
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=43.67 E-value=54 Score=28.66 Aligned_cols=50 Identities=12% Similarity=0.218 Sum_probs=38.1
Q ss_pred CchHHhhhhcEEEEEe-------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 106 GFADELKRAWFCVRNV-------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V-------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
|+.+++...|+.+-.. ++|-||+.+ -..=...++...+.++..|+|+...
T Consensus 79 gi~~~~~~~gy~~~l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~-~~~~~~~~~~l~~~~~P~V~i~~~~ 147 (333)
T COG1609 79 GIEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRVDGLILLG-ERPNDSLLELLAAAGIPVVVIDRSP 147 (333)
T ss_pred HHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEec-CCCCHHHHHHHHhcCCCEEEEeCCC
Confidence 6788999999998877 899999998 2222334555566699999999864
No 212
>COG0560 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]
Probab=43.65 E-value=76 Score=26.46 Aligned_cols=89 Identities=16% Similarity=0.075 Sum_probs=53.6
Q ss_pred hhhhhhcc-chHHHHHHHHhh-cCCCCCCCchHHhhhhcEEEEEe---------------ecce---EEEEeCCCchH--
Q 037201 79 NQIESARG-KMEKYKMAVSAI-LTPKVGYGFADELKRAWFCVRNV---------------RFGC---LMVVSDDSNFV-- 136 (177)
Q Consensus 79 ~ri~s~kG-K~~KY~~Aar~v-l~pkvgygLa~eLrRAGv~Vr~V---------------~v~c---lvLVSDdsdf~-- 136 (177)
.++..++| ..+.=++..++. ......--|...|+.+|..|=.| |+|- ..|..||--|+
T Consensus 55 ~~v~~l~g~~~~~v~~~~~~~~~l~~ga~elv~~lk~~G~~v~iiSgg~~~lv~~ia~~lg~d~~~an~l~~~dG~ltG~ 134 (212)
T COG0560 55 LRVALLKGLPVEVLEEVREEFLRLTPGAEELVAALKAAGAKVVIISGGFTFLVEPIAERLGIDYVVANELEIDDGKLTGR 134 (212)
T ss_pred HHHHHhCCCCHHHHHHHHHhcCcCCccHHHHHHHHHHCCCEEEEEcCChHHHHHHHHHHhCCchheeeEEEEeCCEEece
Confidence 45666777 455556666663 22222345778899999999888 3332 34555541133
Q ss_pred ------------HHH-HHHHHcCcc---EEEEecCC-chhhhhhhccc
Q 037201 137 ------------EVF-QEATLRCLK---MVVVGDMS-DGALKRIANAF 167 (177)
Q Consensus 137 ------------~~l-r~Ar~r~l~---TVVVGd~~-~~~L~r~Ad~~ 167 (177)
..| +.+++.|+. |+-+||+. |-.+-+.|+..
T Consensus 135 v~g~~~~~~~K~~~l~~~~~~~g~~~~~~~a~gDs~nDlpml~~ag~~ 182 (212)
T COG0560 135 VVGPICDGEGKAKALRELAAELGIPLEETVAYGDSANDLPMLEAAGLP 182 (212)
T ss_pred eeeeecCcchHHHHHHHHHHHcCCCHHHeEEEcCchhhHHHHHhCCCC
Confidence 344 677788997 99999974 22334444433
No 213
>cd06327 PBP1_SBP_like_1 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Solute binding proteins are the primary specific receptors that initiate uptake of a broad range of solutes, including amino acids, peptides and inorganic ions. The members are predicted to have a similar function to an active transport system for short chain amides and urea by sequence comparison and phylogenetic analysis. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus may also be involved in transport of amino acids.
Probab=43.48 E-value=33 Score=28.73 Aligned_cols=33 Identities=15% Similarity=0.148 Sum_probs=26.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCc--cEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCL--KMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l--~TVVVGd 154 (177)
+.|.|++.+...+...+++.+++.|+ +..++|-
T Consensus 190 ~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 224 (334)
T cd06327 190 GADVLVLANAGADTVNAIKQAAEFGLTKGQKLAGL 224 (334)
T ss_pred CCCEEEEeccchhHHHHHHHHHHhCCccCCcEEEe
Confidence 67889999999999999999999998 4555543
No 214
>PF06153 DUF970: Protein of unknown function (DUF970); InterPro: IPR010375 This is a family of uncharacterised bacterial proteins.; PDB: 3M05_A.
Probab=43.39 E-value=36 Score=26.68 Aligned_cols=43 Identities=21% Similarity=0.283 Sum_probs=35.5
Q ss_pred CCchHHhhhhcEEEEEe---------ecceEEEEeCCCchHHHHHHHHHcCc
Q 037201 105 YGFADELKRAWFCVRNV---------RFGCLMVVSDDSNFVEVFQEATLRCL 147 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V---------~v~clvLVSDdsdf~~~lr~Ar~r~l 147 (177)
..|.++|.+.||.+... |.-+|++-.||....++|..-++.|-
T Consensus 14 ~~l~~~L~~~g~~~TkLsstGGFLr~GNtTlliGvede~v~~vl~iIk~~c~ 65 (109)
T PF06153_consen 14 DDLSDALNENGFRVTKLSSTGGFLREGNTTLLIGVEDEKVDEVLEIIKENCK 65 (109)
T ss_dssp HHHHHHHHHTT--EEEEEEEETTTTEEEEEEEEEEEGGGHHHHHHHHHHHH-
T ss_pred HHHHHHHHHCCceEEEEecccceeccCCEEEEEEecHHHHHHHHHHHHHhhc
Confidence 45789999999999988 88899999999999999999887554
No 215
>cd01988 Na_H_Antiporter_C The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea . Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this activity is carried out by a family of Na+ /H+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity wit h other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the regio
Probab=43.03 E-value=47 Score=23.40 Aligned_cols=36 Identities=8% Similarity=0.173 Sum_probs=27.0
Q ss_pred cceEEEEeCCCchHHHHHHHHHcCccEEEEecCCchh
Q 037201 123 FGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMSDGA 159 (177)
Q Consensus 123 v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~ 159 (177)
+++++.++. +...++++.|.+.+...||+|....+.
T Consensus 72 ~~~~~~~~~-~~~~~I~~~a~~~~~dlIV~G~~~~~~ 107 (132)
T cd01988 72 VHTIIRIDH-DIASGILRTAKERQADLIIMGWHGSTS 107 (132)
T ss_pred eEEEEEecC-CHHHHHHHHHHhcCCCEEEEecCCCCC
Confidence 455555554 366789999999999999999985443
No 216
>cd00293 USP_Like Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, athough Usp lacks ATP-binding activity.
Probab=42.86 E-value=64 Score=21.86 Aligned_cols=28 Identities=11% Similarity=0.171 Sum_probs=22.7
Q ss_pred CCchHHHHHHHHHcCccEEEEecCCchh
Q 037201 132 DSNFVEVFQEATLRCLKMVVVGDMSDGA 159 (177)
Q Consensus 132 dsdf~~~lr~Ar~r~l~TVVVGd~~~~~ 159 (177)
.+...++++.+.+.+...||+|-...+.
T Consensus 79 ~~~~~~i~~~~~~~~~dlvvig~~~~~~ 106 (130)
T cd00293 79 GDPAEAILEAAEELGADLIVMGSRGRSG 106 (130)
T ss_pred CCCHHHHHHHHHHcCCCEEEEcCCCCCc
Confidence 3348899999999999999999865443
No 217
>PF12076 Wax2_C: WAX2 C-terminal domain; InterPro: IPR021940 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 170 amino acids in length. This domain is found associated with PF04116 from PFAM. This domain has a conserved LEGW sequence motif. This region has similarity to short chain dehydrogenases [].
Probab=42.80 E-value=21 Score=30.14 Aligned_cols=51 Identities=24% Similarity=0.100 Sum_probs=36.1
Q ss_pred CCCCCCchHHhhhhcEEEEEe------------e---cceEEEEeCCCchHHHHHHHHHcCccEEEEecCCchhhhhhh
Q 037201 101 PKVGYGFADELKRAWFCVRNV------------R---FGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMSDGALKRIA 164 (177)
Q Consensus 101 pkvgygLa~eLrRAGv~Vr~V------------~---v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~A 164 (177)
-|||+.+|..|=+-||.|-+. . -+-|++++..+. ++-+|||+.+..=-++|
T Consensus 8 sKvaraiA~~LC~rgv~V~m~~~~~y~~lk~~~~~~~~~~Lv~~~~~~~-------------K~WlVGd~l~~~EQ~~A 73 (164)
T PF12076_consen 8 SKVARAIALALCRRGVQVVMLSKERYESLKSEAPEECQSNLVQSTSYQA-------------KTWLVGDGLTEEEQKWA 73 (164)
T ss_pred cHHHHHHHHHHHhcCCEEEEecHHHHHHHHHHcCHHhhccEEeecCCCc-------------eeEEeCCCCCHHHHhcC
Confidence 578899999999999999887 1 223666655433 88999998765433333
No 218
>cd06269 PBP1_glutamate_receptors_like Family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domain of the ionotropic glutamate receptors. This CD represents the ligand-binding domain of the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domain of the ionotropic glutamate receptors, all of which are structurally similar and related to the periplasmic-binding fold type I family. The family C GPCRs consist of metabotropic glutamate receptor (mGluR) receptors, a calcium-sensing receptor (CaSR), gamma-aminobutyric receptors (GABAb), the promiscuous L-alpha-amino acid receptor GPR6A, families of taste and pheromone receptors, and orphan receptors. Truncated splicing va
Probab=42.70 E-value=77 Score=24.71 Aligned_cols=35 Identities=14% Similarity=0.218 Sum_probs=25.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCc---cEEEEecCC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCL---KMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l---~TVVVGd~~ 156 (177)
+.+.+|+.+...+...+++.|++.|+ ...++.+.+
T Consensus 195 ~~~viv~~~~~~~~~~~l~~a~~~g~~~~~~~i~~~~~ 232 (298)
T cd06269 195 TARVIVVFSSEEDALRLLEEAVELGMMTGYHWIITDLW 232 (298)
T ss_pred CCcEEEEEechHHHHHHHHHHHHcCCCCCeEEEEEChh
Confidence 33667777777889999999999987 555555543
No 219
>cd06326 PBP1_STKc_like Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins. The type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins, some of which contain a conserved catalytic serine/threonine protein kinase (STKc) domain in the N-terminal region. Members of this group are sequence-similar to the branched-chain amino acid ABC transporter leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=42.47 E-value=38 Score=27.94 Aligned_cols=32 Identities=6% Similarity=-0.072 Sum_probs=26.7
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEe
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG 153 (177)
+.|.|++.+|+.+...+++.+++.|++.=++|
T Consensus 191 ~~dav~~~~~~~~a~~~i~~~~~~G~~~~~~~ 222 (336)
T cd06326 191 RPQAVIMVGAYKAAAAFIRALRKAGGGAQFYN 222 (336)
T ss_pred CCCEEEEEcCcHHHHHHHHHHHhcCCCCcEEE
Confidence 46888888888899999999999999775554
No 220
>PF03720 UDPG_MGDP_dh_C: UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; InterPro: IPR014027 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the C-terminal substrate-binding domain of these enzymes. Structural studies indicate that this domain forms an incomplete dinucleotide binding fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3GG2_D 1DLI_A 1DLJ_A 2Y0E_D 2Y0D_B 2Y0C_D 1MV8_B 1MUU_A 1MFZ_C 3TDK_B ....
Probab=42.45 E-value=23 Score=26.04 Aligned_cols=16 Identities=19% Similarity=0.401 Sum_probs=13.0
Q ss_pred ecceEEEEeCCCchHH
Q 037201 122 RFGCLMVVSDDSNFVE 137 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~ 137 (177)
+.||+|+.++...|..
T Consensus 66 ~~D~vvl~t~h~~f~~ 81 (106)
T PF03720_consen 66 GADAVVLATDHDEFRE 81 (106)
T ss_dssp TESEEEESS--GGGGC
T ss_pred CCCEEEEEecCHHHhc
Confidence 8999999999999987
No 221
>PF09338 Gly_reductase: Glycine/sarcosine/betaine reductase component B subunits; InterPro: IPR015417 This is a family of glycine reductase, sarcosine reductase and betaine reductases. These enzymes catalyse the following reactions: sarcosine reductase: Acetyl phosphate + methylamine + thioredoxin disulphide = N-methylglycine + phosphate + thioredoxin. glycine reductase: Acetyl phosphate + NH3 + thioredoxin disulphide = glycine + phosphate + thioredoxin. betaine reductase: Acetyl phosphate + trimethylamine + thioredoxin disulphide = N,N,N-trimethylglycine + phosphate + thioredoxin. ; GO: 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process
Probab=42.38 E-value=12 Score=35.44 Aligned_cols=35 Identities=23% Similarity=0.270 Sum_probs=28.0
Q ss_pred eecceEEEEeC-----CCchHHHHHHHHHcCccEEEEecC
Q 037201 121 VRFGCLMVVSD-----DSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 121 V~v~clvLVSD-----dsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|.|++|+..+ |.||.-.++.+-++|++||.|-|.
T Consensus 302 LgaDGaIvs~eG~GN~d~D~~~~~~~~e~~GIktV~it~e 341 (428)
T PF09338_consen 302 LGADGAIVSEEGFGNPDVDFAMNIEEIEKRGIKTVGITDE 341 (428)
T ss_pred hCCCEEEEEecCCCchhHHHHHHHHHHHHCCCCEEEecce
Confidence 34555554443 889999999999999999999975
No 222
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.14 E-value=13 Score=37.07 Aligned_cols=23 Identities=30% Similarity=0.417 Sum_probs=20.4
Q ss_pred hhhcCCCcC---------------ChhHHHHHHHhhhh
Q 037201 49 LIRNQGRFY---------------NNDKLVNHFRQIHE 71 (177)
Q Consensus 49 c~~CGrrf~---------------t~~~L~kHFkqlHe 71 (177)
|.+|+++|. +-+.|++|+.++|+
T Consensus 102 C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~ 139 (669)
T KOG2231|consen 102 CHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHK 139 (669)
T ss_pred cCccccchhhhcccCCCccccchhHHHHHHHHHHHhhh
Confidence 889999884 77899999999996
No 223
>cd06331 PBP1_AmiC_like Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two t
Probab=41.87 E-value=67 Score=26.83 Aligned_cols=27 Identities=7% Similarity=0.041 Sum_probs=24.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCcc
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLK 148 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~ 148 (177)
+.|.|++..+-.+...+++.+++.|+.
T Consensus 187 ~~d~v~~~~~~~~~~~~~~~~~~~g~~ 213 (333)
T cd06331 187 GPDVVLSTLVGDSNVAFYRQFAAAGLD 213 (333)
T ss_pred CCCEEEEecCCCChHHHHHHHHHcCCC
Confidence 788899999999999999999999996
No 224
>PF10727 Rossmann-like: Rossmann-like domain; InterPro: IPR019665 This entry represents an NAD/NADP-binding domain with a core Rossmann-type fold, found in an uncharacterised protein family thought to be putative NADP oxidoreductase coenzyme F420-dependent proteins and/or NAD-dependent glycerol-3-phosphate dehydrogenase-like proteins. This Rossmann-fold domain consists of 3-layers alpha/beta/alpha, where the six beta strands are parallel in the order 321456.; PDB: 3DFU_A 3C24_A.
Probab=41.56 E-value=54 Score=25.70 Aligned_cols=20 Identities=40% Similarity=0.404 Sum_probs=18.6
Q ss_pred CCCCCchHHhhhhcEEEEEe
Q 037201 102 KVGYGFADELKRAWFCVRNV 121 (177)
Q Consensus 102 kvgygLa~eLrRAGv~Vr~V 121 (177)
|||+-|+..|.++|+.|..|
T Consensus 20 rVG~~La~aL~~ag~~v~~v 39 (127)
T PF10727_consen 20 RVGTALARALARAGHEVVGV 39 (127)
T ss_dssp CCCCHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHHCCCeEEEE
Confidence 78999999999999999888
No 225
>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=41.28 E-value=55 Score=25.83 Aligned_cols=43 Identities=28% Similarity=0.393 Sum_probs=27.7
Q ss_pred cceEEEEeCCC-------chHHHHHHHHHcCccEEEE--ecCCchhhhhhhc
Q 037201 123 FGCLMVVSDDS-------NFVEVFQEATLRCLKMVVV--GDMSDGALKRIAN 165 (177)
Q Consensus 123 v~clvLVSDds-------df~~~lr~Ar~r~l~TVVV--Gd~~~~~L~r~Ad 165 (177)
...+||+||=. +.....+.+++.|+...+| |+.+...|.+.|.
T Consensus 110 ~~~iillTDG~~~~~~~~~~~~~~~~~~~~gi~i~~vgig~~~~~~L~~IA~ 161 (186)
T cd01480 110 NKFLLVITDGHSDGSPDGGIEKAVNEADHLGIKIFFVAVGSQNEEPLSRIAC 161 (186)
T ss_pred ceEEEEEeCCCcCCCcchhHHHHHHHHHHCCCEEEEEecCccchHHHHHHHc
Confidence 35688888863 3456678888888885554 4434346666664
No 226
>cd02765 MopB_4 The MopB_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins
Probab=41.24 E-value=42 Score=31.58 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=35.9
Q ss_pred ecceEEEEeCCC-----chHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDS-----NFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDds-----df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|+||++.-|. .+...+..|+++|.+.|||.=. .......||.|++
T Consensus 159 ~ad~il~~G~Np~~s~~~~~~~~~~a~~~GakliviDPr-~s~ta~~Ad~~l~ 210 (567)
T cd02765 159 NAKTIIIWGSNILETQFQDAEFFLDARENGAKIVVIDPV-YSTTAAKADQWVP 210 (567)
T ss_pred cCcEEEEECCChHHccchhHHHHHHHHHcCCeEEEECCC-CCcchhhcCEEec
Confidence 578888887663 2445667889999999999554 4678889999985
No 227
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=41.14 E-value=42 Score=28.50 Aligned_cols=28 Identities=4% Similarity=0.018 Sum_probs=23.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccE
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKM 149 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~T 149 (177)
+.|.|++.....+...+++.+++.|+..
T Consensus 199 ~~d~v~~~~~~~~~~~~~~~~~~~G~~~ 226 (347)
T cd06340 199 NPDAILPASYTNDAILLVRTMKEQRVEP 226 (347)
T ss_pred CCCEEEEcccchhHHHHHHHHHHcCCCC
Confidence 6788888888888888889888888854
No 228
>cd06333 PBP1_ABC-type_HAAT_like Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. This subgroup includes the type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. Members of this subgroup are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=41.10 E-value=51 Score=27.12 Aligned_cols=32 Identities=9% Similarity=-0.009 Sum_probs=26.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEe
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG 153 (177)
+.|.|++.+|+.+-..+++.+++.|++.=++|
T Consensus 188 ~pdaIi~~~~~~~~~~~~~~l~~~g~~~p~~~ 219 (312)
T cd06333 188 RPDAVLIWGSGTPAALPAKNLRERGYKGPIYQ 219 (312)
T ss_pred CCCEEEEecCCcHHHHHHHHHHHcCCCCCEEe
Confidence 67899999988888889999999999865553
No 229
>PRK14649 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=41.07 E-value=25 Score=30.91 Aligned_cols=35 Identities=14% Similarity=0.054 Sum_probs=30.6
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
..++++.+.+-.|+.++++.|++.++...|+|.++
T Consensus 20 ~a~~~v~p~~~~dl~~~l~~~~~~~ip~~vlG~GS 54 (295)
T PRK14649 20 PARYFVEPTTPDEAIAAAAWAEQRQLPLFWLGGGS 54 (295)
T ss_pred eeeEEEEcCCHHHHHHHHHHHHHCCCCEEEEecce
Confidence 45678889999999999999999999999999875
No 230
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=41.05 E-value=28 Score=23.68 Aligned_cols=26 Identities=27% Similarity=0.318 Sum_probs=19.6
Q ss_pred eEEEEeCCCchHHHHHHHHHcCccEE
Q 037201 125 CLMVVSDDSNFVEVFQEATLRCLKMV 150 (177)
Q Consensus 125 clvLVSDdsdf~~~lr~Ar~r~l~TV 150 (177)
-+|.+++|.||..+++.++..+-+++
T Consensus 51 d~v~l~sd~Dl~~a~~~~~~~~~~~l 76 (81)
T cd05992 51 DLVTISSDEDLEEAIEEARRSGSKKL 76 (81)
T ss_pred CEEEeCCHHHHHHHHHHHhhcCCccE
Confidence 46777788999999999987444443
No 231
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=40.86 E-value=73 Score=23.08 Aligned_cols=58 Identities=16% Similarity=0.093 Sum_probs=35.5
Q ss_pred HHhhhhcEEEEEe----------ecceEEEEeCCCchH--HHHHHHHHcCccEEEEecCCchhhhhhhcccc
Q 037201 109 DELKRAWFCVRNV----------RFGCLMVVSDDSNFV--EVFQEATLRCLKMVVVGDMSDGALKRIANAFF 168 (177)
Q Consensus 109 ~eLrRAGv~Vr~V----------~v~clvLVSDdsdf~--~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~ 168 (177)
.+|+|||=.+.=. .+..++|.+|=|+-. .+...+.+.++.-+.+++. ..|++..-..+
T Consensus 4 ~~~~ragkl~~G~~~v~kai~~gkaklViiA~D~~~~~~~~i~~~c~~~~Vp~~~~~s~--~eLG~a~G~~~ 73 (82)
T PRK13602 4 EKVSQAKSIVIGTKQTVKALKRGSVKEVVVAEDADPRLTEKVEALANEKGVPVSKVDSM--KKLGKACGIEV 73 (82)
T ss_pred HHHHhcCCEEEcHHHHHHHHHcCCeeEEEEECCCCHHHHHHHHHHHHHcCCCEEEECCH--HHHHHHHCCCc
Confidence 3567887322221 334455555544432 3667788999999999965 57887665443
No 232
>PF02844 GARS_N: Phosphoribosylglycinamide synthetase, N domain; InterPro: IPR020562 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the N-domain, which is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (IPR005481 from INTERPRO).; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process; PDB: 3MJF_A 2XD4_A 2XCL_A 2IP4_A 2YW2_B 2YYA_A 3LP8_A 1VKZ_A 2YS6_A 2YRX_A ....
Probab=40.84 E-value=30 Score=26.57 Aligned_cols=25 Identities=28% Similarity=0.221 Sum_probs=22.0
Q ss_pred CCCchHHHHHHHHHcCccEEEEecC
Q 037201 131 DDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 131 Ddsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
|..|+.++++.|++.++.-||||=.
T Consensus 47 ~~~d~~~l~~~a~~~~idlvvvGPE 71 (100)
T PF02844_consen 47 DITDPEELADFAKENKIDLVVVGPE 71 (100)
T ss_dssp -TT-HHHHHHHHHHTTESEEEESSH
T ss_pred CCCCHHHHHHHHHHcCCCEEEECCh
Confidence 8999999999999999999999975
No 233
>cd00859 HisRS_anticodon HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=40.80 E-value=56 Score=21.38 Aligned_cols=42 Identities=17% Similarity=0.168 Sum_probs=30.7
Q ss_pred CCchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCc-cEEEEec
Q 037201 105 YGFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCL-KMVVVGD 154 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l-~TVVVGd 154 (177)
+.++.+||.+|+.|.. ...+..+...++.|...|. ..+++|+
T Consensus 18 ~~i~~~Lr~~g~~v~~--------~~~~~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 18 LELAEQLRDAGIKAEI--------DYGGRKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred HHHHHHHHHCCCEEEE--------ecCCCCHHHHHHHHHHcCCCEEEEEcH
Confidence 5678999999985532 1223468999999999886 4688884
No 234
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=40.51 E-value=46 Score=26.20 Aligned_cols=28 Identities=18% Similarity=0.154 Sum_probs=23.3
Q ss_pred CchHHHHHHHHHcCccEEEEe-----cCCchhh
Q 037201 133 SNFVEVFQEATLRCLKMVVVG-----DMSDGAL 160 (177)
Q Consensus 133 sdf~~~lr~Ar~r~l~TVVVG-----d~~~~~L 160 (177)
.++..+.+..++.++..|||| |++.+..
T Consensus 41 ~~~~~l~~~i~~~~i~~iVvGlP~~~~G~~~~~ 73 (138)
T PRK00109 41 PDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPR 73 (138)
T ss_pred hHHHHHHHHHHHhCCCEEEEeccCCCCCCcCHH
Confidence 468889999999999999999 7765443
No 235
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=40.33 E-value=44 Score=25.08 Aligned_cols=39 Identities=21% Similarity=0.231 Sum_probs=29.6
Q ss_pred hhcEEEEEe--ecceEEEEeCCCchHHHHHHHHHcCccEEEE
Q 037201 113 RAWFCVRNV--RFGCLMVVSDDSNFVEVFQEATLRCLKMVVV 152 (177)
Q Consensus 113 RAGv~Vr~V--~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVV 152 (177)
..++..+-+ .-||+.|.| |+|+.+.+..||..|.++|.+
T Consensus 41 ~~~~~L~YlDDEgD~VllT~-D~DL~e~v~iar~~g~~~v~L 81 (86)
T cd06409 41 THLYALSYVDDEGDIVLITS-DSDLVAAVLVARSAGLKKLDL 81 (86)
T ss_pred CCcccEEEEcCCCCEEEEec-cchHHHHHHHHHHcCCCEEEE
Confidence 345555555 556766666 579999999999999999865
No 236
>PRK05752 uroporphyrinogen-III synthase; Validated
Probab=40.31 E-value=12 Score=31.26 Aligned_cols=59 Identities=19% Similarity=0.182 Sum_probs=38.6
Q ss_pred CCCchHHhhhhcEEEEEe----------------------ecceEEEEeCCCc--hHHHHHHHH--HcCccEEEEecCCc
Q 037201 104 GYGFADELKRAWFCVRNV----------------------RFGCLMVVSDDSN--FVEVFQEAT--LRCLKMVVVGDMSD 157 (177)
Q Consensus 104 gygLa~eLrRAGv~Vr~V----------------------~v~clvLVSDdsd--f~~~lr~Ar--~r~l~TVVVGd~~~ 157 (177)
+..++..|+..|..|-.+ ..||||.+|-+.- |.+.|+.+. .++++...||+.+.
T Consensus 15 ~~~l~~~l~~~G~~~~~~P~i~i~p~~~~~~~~~~l~~l~~~d~iifTS~naV~~~~~~l~~~~~~~~~~~~~aVG~~Ta 94 (255)
T PRK05752 15 CAALAASLAEAGIFSSSLPLLAIEPLPETPEQRALLLELDRYCAVIVVSKPAARLGLELLDRYWPQPPQQPWFSVGAATA 94 (255)
T ss_pred HHHHHHHHHHcCCCEEEcCcEEEeeCCCCHHHHHHHhcCCCCCEEEEECHHHHHHHHHHHHhhCCCCcCCEEEEECHHHH
Confidence 355667777777766554 6689999997762 334444332 13578889999886
Q ss_pred hhhhh
Q 037201 158 GALKR 162 (177)
Q Consensus 158 ~~L~r 162 (177)
.+|..
T Consensus 95 ~al~~ 99 (255)
T PRK05752 95 AILQD 99 (255)
T ss_pred HHHHH
Confidence 66654
No 237
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=40.14 E-value=68 Score=27.36 Aligned_cols=34 Identities=15% Similarity=0.071 Sum_probs=26.8
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.+++..-|++ ..+.++.+++.++..|+|+..
T Consensus 81 ~vdgiIi~~~~~~~~~~~l~~l~~~giPvV~vd~~ 115 (330)
T PRK15395 81 GVKALAINLVDPAAAPTVIEKARGQDVPVVFFNKE 115 (330)
T ss_pred CCCEEEEeccCHHHHHHHHHHHHHCCCcEEEEcCC
Confidence 7899998764444 455789999999999999864
No 238
>cd02760 MopB_Phenylacetyl-CoA-OR The MopB_Phenylacetyl-CoA-OR CD contains the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), and other related proteins. The phenylacetyl-CoA:acceptor oxidoreductase has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=40.11 E-value=43 Score=33.36 Aligned_cols=48 Identities=13% Similarity=0.088 Sum_probs=35.5
Q ss_pred ecceEEEEeCCCc------hHHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 122 RFGCLMVVSDDSN------FVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 122 ~v~clvLVSDdsd------f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
..++|+++--+.. +...+..|+++|.+-||| |--.......||.|++-
T Consensus 173 ~ad~Il~~G~Np~~s~~~~~~~~~~~ar~~GaKlIvV-DPr~t~ta~~AD~wlpi 226 (760)
T cd02760 173 LANYVISFGSNVEASGGPCAVTRHADARVRGYKRVQV-EPHLSVTGACSAEWVPI 226 (760)
T ss_pred cCCEEEEECCCchHhcCcHHHHHHHHHHHcCCeEEEE-cCCCCcchhhcCeEeCc
Confidence 6788888865542 334567788899999999 54346788899999864
No 239
>PF10622 Ehbp: Energy-converting hydrogenase B subunit P (EhbP); InterPro: IPR019597 Ehb (energy-converting hydrogenase B) is an methanogenic archaeal enzyme that functions in one of the metabolic pathways involved in methanol reduction to methane. This entry contains subunit P of Ehb.
Probab=40.01 E-value=27 Score=26.30 Aligned_cols=19 Identities=32% Similarity=0.569 Sum_probs=16.9
Q ss_pred EEEEeCCCchHHHHHHHHH
Q 037201 126 LMVVSDDSNFVEVFQEATL 144 (177)
Q Consensus 126 lvLVSDdsdf~~~lr~Ar~ 144 (177)
++=||+|.||.+|.++|.+
T Consensus 55 vvPv~~~ddfv~~fk~~~~ 73 (78)
T PF10622_consen 55 VVPVSEDDDFVGMFKMVKE 73 (78)
T ss_pred EEeccccccHHHHHHHHHH
Confidence 5678999999999999986
No 240
>TIGR01591 Fdh-alpha formate dehydrogenase, alpha subunit, archaeal-type. This model is well-defined, with only a single fragmentary sequence falling between trusted and noise. The alpha subunit of a version of nitrate reductase is closely related.
Probab=39.89 E-value=48 Score=31.29 Aligned_cols=47 Identities=11% Similarity=0.214 Sum_probs=35.6
Q ss_pred ecceEEEEeCCC-----chHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDS-----NFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDds-----df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|+++++..|. .....|+.|+++|.+.|||.-. ...+...||.|++
T Consensus 155 ~ad~il~~G~n~~~~~~~~~~~i~~a~~~G~klvvidp~-~s~ta~~ad~~i~ 206 (671)
T TIGR01591 155 NADLIVIIGYNPAESHPVVAQYLKNAKRNGAKIIVIDPR-KTETAKIADLHIP 206 (671)
T ss_pred hCCEEEEECCChhhccCHHHHHHHHHHHCCCeEEEECCC-CChhhHhhCcccC
Confidence 567777775553 3556778899999999999654 3577788999986
No 241
>PRK10671 copA copper exporting ATPase; Provisional
Probab=39.85 E-value=37 Score=33.60 Aligned_cols=63 Identities=13% Similarity=0.096 Sum_probs=41.5
Q ss_pred HHhhhhcEEEEEe---------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC-Cchhhhhhhccccchh
Q 037201 109 DELKRAWFCVRNV---------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM-SDGALKRIANAFFSWS 171 (177)
Q Consensus 109 ~eLrRAGv~Vr~V---------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~-~~~~L~r~Ad~~~sW~ 171 (177)
.+|+..|+.+-.+ |++-++--....+=..+++.....+-.++.|||+ +|....+.||+.+.|.
T Consensus 660 ~~L~~~gi~v~~~Tgd~~~~a~~ia~~lgi~~~~~~~~p~~K~~~i~~l~~~~~~v~~vGDg~nD~~al~~Agvgia~g 738 (834)
T PRK10671 660 QRLHKAGYRLVMLTGDNPTTANAIAKEAGIDEVIAGVLPDGKAEAIKRLQSQGRQVAMVGDGINDAPALAQADVGIAMG 738 (834)
T ss_pred HHHHHCCCeEEEEcCCCHHHHHHHHHHcCCCEEEeCCCHHHHHHHHHHHhhcCCEEEEEeCCHHHHHHHHhCCeeEEec
Confidence 5678888876665 5543222111223445666666677789999995 5567778999998885
No 242
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=39.83 E-value=35 Score=31.51 Aligned_cols=50 Identities=22% Similarity=0.274 Sum_probs=37.2
Q ss_pred CCCCchHHhhhhcE--EEEEe---------------------ecceEEEEeCCCchHHHHHHHHHcCccEEEE
Q 037201 103 VGYGFADELKRAWF--CVRNV---------------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVV 152 (177)
Q Consensus 103 vgygLa~eLrRAGv--~Vr~V---------------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVV 152 (177)
.|+-+...|++.|| .|-.| .+|+.++.-....-.++++++-++|++.+||
T Consensus 22 ~g~~~~~~l~~~gf~g~v~~Vnp~~~~i~G~~~~~sl~~lp~~~Dlavi~vp~~~~~~~l~e~~~~gv~~~vi 94 (447)
T TIGR02717 22 VGYAIMKNLIEGGYKGKIYPVNPKAGEILGVKAYPSVLEIPDPVDLAVIVVPAKYVPQVVEECGEKGVKGAVV 94 (447)
T ss_pred hHHHHHHHHHhCCCCCcEEEECCCCCccCCccccCCHHHCCCCCCEEEEecCHHHHHHHHHHHHhcCCCEEEE
Confidence 35556666777776 34344 6788887777777889999999999999987
No 243
>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=39.76 E-value=73 Score=23.04 Aligned_cols=43 Identities=23% Similarity=0.311 Sum_probs=30.2
Q ss_pred ceEEEEeCCC-----chHHHHHHHHHcCccEEEEecC--Cchhhhhhhcc
Q 037201 124 GCLMVVSDDS-----NFVEVFQEATLRCLKMVVVGDM--SDGALKRIANA 166 (177)
Q Consensus 124 ~clvLVSDds-----df~~~lr~Ar~r~l~TVVVGd~--~~~~L~r~Ad~ 166 (177)
..+||+||-. +..++++..++.++..++||-+ ....|...|+.
T Consensus 105 ~~iiliTDG~~~~~~~~~~~~~~~~~~~v~v~~i~~g~~~~~~l~~la~~ 154 (161)
T cd01450 105 KVIIVLTDGRSDDGGDPKEAAAKLKDEGIKVFVVGVGPADEEELREIASC 154 (161)
T ss_pred eEEEEECCCCCCCCcchHHHHHHHHHCCCEEEEEeccccCHHHHHHHhCC
Confidence 4578888832 2788999999999996666654 34466666654
No 244
>cd02762 MopB_1 The MopB_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=39.71 E-value=38 Score=31.41 Aligned_cols=47 Identities=17% Similarity=0.185 Sum_probs=35.5
Q ss_pred ecceEEEEeCCCc-----------hHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDSN-----------FVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsd-----------f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|+|+++--|.- +...++.|+++|.+-|||.=. .......||.|++
T Consensus 156 ~ad~il~~G~N~~~s~~~~~~~~~~~~~~~~a~~~G~kliviDPr-~t~ta~~AD~~l~ 213 (539)
T cd02762 156 RTDYLLILGANPLQSNGSLRTAPDRVLRLKAAKDRGGSLVVIDPR-RTETAKLADEHLF 213 (539)
T ss_pred hCCEEEEEecChHhhCCccccccCHHHHHHHHHhCCCEEEEECCC-CchhhHhcCEeeC
Confidence 6788888865543 334677899999999999554 4677889999986
No 245
>PTZ00175 diphthine synthase; Provisional
Probab=39.40 E-value=77 Score=27.79 Aligned_cols=50 Identities=10% Similarity=0.096 Sum_probs=37.7
Q ss_pred CchHHhhhhcEEEEEe--------------------ecceEEEEeCC---CchHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV--------------------RFGCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V--------------------~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|..+++.+|+.|+.+ ..-.+..++++ .-|-+.++...++|++|.|.=|.
T Consensus 95 ~l~~~~~~~gi~vevIPGvSi~sA~~~~Gl~~~~fg~~~sv~~~t~~~~~~s~~~~i~~n~~~glhTl~lldi 167 (270)
T PTZ00175 95 DLYLRAKKKGIEVEVIHNASIMNAIGCTGLQLYRFGETVSIPFFTETWKPDSFYDKIKANRDNGLHTLCLLDI 167 (270)
T ss_pred HHHHHHHHCCCcEEEECCcCHHHHHhhcCCCcCCCCceEEEEEEeCCCCCCChhHHHHHHHHcCCceEEEEee
Confidence 3556777888888888 33447777764 45777799999999999999665
No 246
>PRK00046 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=39.33 E-value=28 Score=31.67 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=23.0
Q ss_pred cceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 123 FGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 123 v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.++++..+|-.++.++++.|++.++...|+|.+|
T Consensus 21 A~~~~~p~~~~el~~~~~~~~~~~~p~~vlG~GS 54 (334)
T PRK00046 21 ARHLVEAESEEQLLEALADARAAGLPVLVLGGGS 54 (334)
T ss_pred EeEEEeeCCHHHHHHHHHHHHHcCCCEEEEeceE
Confidence 4566667777777777777777777766666654
No 247
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=39.19 E-value=12 Score=36.10 Aligned_cols=30 Identities=13% Similarity=0.020 Sum_probs=25.8
Q ss_pred hhhhcCCCcCChhHHHHHHHhhhhhhhhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIHEGEQKKR 77 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlHerEr~Kr 77 (177)
-|..||.+|+...-|+||--.-|+-+.+|-
T Consensus 358 ~C~~C~KkFrRqAYLrKHqlthq~~~~~k~ 387 (500)
T KOG3993|consen 358 SCHTCGKKFRRQAYLRKHQLTHQRAPLAKE 387 (500)
T ss_pred ecHHhhhhhHHHHHHHHhHHhhhccccchh
Confidence 399999999999999999888777776663
No 248
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=39.14 E-value=79 Score=26.12 Aligned_cols=14 Identities=7% Similarity=-0.050 Sum_probs=8.0
Q ss_pred HHHHHHhcccceee
Q 037201 8 ELKKLISSFEVVKY 21 (177)
Q Consensus 8 ~Lr~~A~~FG~Vv~ 21 (177)
.++++|..=|.=+.
T Consensus 3 ti~dIA~~agvS~~ 16 (329)
T TIGR01481 3 TIYDVAREAGVSMA 16 (329)
T ss_pred cHHHHHHHhCCCHH
Confidence 45666666665433
No 249
>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.
Probab=39.04 E-value=56 Score=26.27 Aligned_cols=41 Identities=22% Similarity=0.320 Sum_probs=26.4
Q ss_pred eEEEEeCCC-----chHHHHHHHHHcCccEEEEecCCc-hhhhhhhc
Q 037201 125 CLMVVSDDS-----NFVEVFQEATLRCLKMVVVGDMSD-GALKRIAN 165 (177)
Q Consensus 125 clvLVSDds-----df~~~lr~Ar~r~l~TVVVGd~~~-~~L~r~Ad 165 (177)
.|+|.||.+ +..++.+.+++.|++-.+||=+.+ ..|+..|+
T Consensus 110 iiil~sd~~~~~~~~~~~~~~~l~~~~I~v~~IgiG~~~~~L~~ia~ 156 (183)
T cd01453 110 VLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICK 156 (183)
T ss_pred EEEEEcCCCcCChhhHHHHHHHHHHcCcEEEEEEechHHHHHHHHHH
Confidence 566777633 355788889888888777765532 23555554
No 250
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=38.71 E-value=67 Score=26.76 Aligned_cols=32 Identities=6% Similarity=0.049 Sum_probs=21.5
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
++|.|++++.++ .++++.+.+.+...|+++..
T Consensus 114 ~vDgiI~~~~~~--~~~~~~l~~~~~pvV~~~~~ 145 (327)
T PRK10339 114 NVTGILIVGKPT--PALRAAASALTDNICFIDFH 145 (327)
T ss_pred cCCEEEEeCCCC--HHHHHHHHhcCCCEEEEeCC
Confidence 678888777433 25667777777777777643
No 251
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=38.70 E-value=14 Score=24.11 Aligned_cols=25 Identities=16% Similarity=0.192 Sum_probs=20.3
Q ss_pred hhhhhcCCCcCCh-----hHHHHHHHhhhh
Q 037201 47 CLLIRNQGRFYNN-----DKLVNHFRQIHE 71 (177)
Q Consensus 47 ~Lc~~CGrrf~t~-----~~L~kHFkqlHe 71 (177)
-.|..||..+... ..|.+|.+..|.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 4599999988766 599999998775
No 252
>PF01565 FAD_binding_4: FAD binding domain This is only a subset of the Pfam family; InterPro: IPR006094 Various enzymes use FAD as a co-factor, most of these enzymes are oxygen-dependent oxidoreductases, containing a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. One of the enzymes Vanillyl-alcohol oxidase (VAO, 1.1.3.38 from EC) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 []. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging from aromatic amines to 4-alkylphenols. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZR6_A 3HSU_A 2AXR_A 3D2J_A 3D2H_A 3FW9_A 3FW8_A 3FW7_A 3GSY_A 3FWA_A ....
Probab=38.55 E-value=41 Score=24.91 Aligned_cols=33 Identities=9% Similarity=0.027 Sum_probs=29.6
Q ss_pred ceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 124 GCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 124 ~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
++++..++-.|+..+++.|++.+++-.+.|.++
T Consensus 2 ~~vv~P~s~~ev~~~v~~a~~~~~~v~~~g~G~ 34 (139)
T PF01565_consen 2 AAVVRPKSVEEVQAIVKFANENGVPVRVRGGGH 34 (139)
T ss_dssp SEEEEESSHHHHHHHHHHHHHTTSEEEEESSST
T ss_pred cEEEEeCCHHHHHHHHHHHHHcCCcEEEEcCCC
Confidence 467888889999999999999999999999865
No 253
>cd02757 MopB_Arsenate-R This CD includes the respiratory arsenate reductase, As(V), catalytic subunit (ArrA) and other related proteins. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=37.27 E-value=54 Score=30.64 Aligned_cols=47 Identities=13% Similarity=0.116 Sum_probs=33.8
Q ss_pred ecceEEEEeCCCc-------hHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDSN-------FVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsd-------f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|+||+++-|.. +..-+..|+++|.+.|||.-. .......||.|++
T Consensus 162 ~a~~Il~~G~n~~~t~~~~~~~~~~~~a~~~gakliviDPr-~s~ta~~AD~~l~ 215 (523)
T cd02757 162 NAKYILFFGADPLESNRQNPHAQRIWGGKMDQAKVVVVDPR-LSNTAAKADEWLP 215 (523)
T ss_pred cCcEEEEECCChHHhCCCcHHHHHHHHHHHCCCEEEEECCC-CChhhHhcCEeeC
Confidence 6788999985532 123355678899999999554 3567788999985
No 254
>TIGR00179 murB UDP-N-acetylenolpyruvoylglucosamine reductase. This model describes MurB, UDP-N-acetylenolpyruvoylglucosamine reductase, which is also called UDP-N-acetylmuramate dehydrogenase. It is part of the pathway for the biosynthesis of the UDP-N-acetylmuramoyl-pentapeptide that is a precursor of bacterial peptidoglycan.
Probab=37.18 E-value=35 Score=29.74 Aligned_cols=33 Identities=15% Similarity=0.242 Sum_probs=29.5
Q ss_pred ceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 124 GCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 124 ~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
+.++.+.+-.|+.++++.|++.++..+|+|.++
T Consensus 14 ~~~v~p~s~edl~~~l~~a~~~~~p~~vlGgGS 46 (284)
T TIGR00179 14 RHIVCPESIEQLVNVLDNAKEEDQPLLILGEGS 46 (284)
T ss_pred eEEEEeCCHHHHHHHHHHHHHcCCCEEEEecce
Confidence 457788899999999999999999999999876
No 255
>PRK15400 lysine decarboxylase CadA; Provisional
Probab=37.08 E-value=48 Score=33.34 Aligned_cols=49 Identities=18% Similarity=0.205 Sum_probs=39.0
Q ss_pred CchHHhhhhcEEEEEe--------------ecceEEEEeCCCchHHHHHHHHHcC--ccEEEEecC
Q 037201 106 GFADELKRAWFCVRNV--------------RFGCLMVVSDDSNFVEVFQEATLRC--LKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V--------------~v~clvLVSDdsdf~~~lr~Ar~r~--l~TVVVGd~ 155 (177)
.|+.+|.+-||.|..+ .+.|+|+-.||.+ .+++.+.|++| +--.+++|.
T Consensus 21 ~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~Pv~~~~~~ 85 (714)
T PRK15400 21 ELHRALERLNFQIVYPNDRDDLLKLIENNARLCGVIFDWDKYN-LELCEEISKMNENLPLYAFANT 85 (714)
T ss_pred HHHHHHHHCCcEEEEeCCHHHHHHHHhcccceeEEEEecchhh-HHHHHHHHHhCCCCCEEEEccc
Confidence 3689999999999998 8999999988877 56888888765 445666664
No 256
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=37.07 E-value=9.4 Score=31.53 Aligned_cols=18 Identities=11% Similarity=0.139 Sum_probs=14.7
Q ss_pred hhhhhhhcCCCcCChhHH
Q 037201 45 ENCLLIRNQGRFYNNDKL 62 (177)
Q Consensus 45 r~~Lc~~CGrrf~t~~~L 62 (177)
|..-|..||+||.|.+..
T Consensus 27 RRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 27 RRRECLECHERFTTFERA 44 (147)
T ss_pred ecccCCccCCccceeeec
Confidence 344599999999998875
No 257
>PRK15399 lysine decarboxylase LdcC; Provisional
Probab=36.90 E-value=51 Score=33.12 Aligned_cols=48 Identities=8% Similarity=0.023 Sum_probs=38.8
Q ss_pred chHHhhhhcEEEEEe--------------ecceEEEEeCCCchHHHHHHHHHcCcc--EEEEecC
Q 037201 107 FADELKRAWFCVRNV--------------RFGCLMVVSDDSNFVEVFQEATLRCLK--MVVVGDM 155 (177)
Q Consensus 107 La~eLrRAGv~Vr~V--------------~v~clvLVSDdsdf~~~lr~Ar~r~l~--TVVVGd~ 155 (177)
|+++|..-||.|..+ .+.|+|+-.||.+ .+++.+.+++|.. -.+++|.
T Consensus 22 l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~Pv~~~~~~ 85 (713)
T PRK15399 22 LESALQAQGFQTIWPQNSVDLLKFIEHNPRICGVIFDWDEYS-LDLCSDINQLNEYLPLYAFINT 85 (713)
T ss_pred HHHHHHHCCcEEEEecCHHHHHHHHhcccceeEEEEecccch-HHHHHHHHHhCCCCCEEEEcCc
Confidence 689999999999988 8999999988887 6688888876554 4566664
No 258
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=36.88 E-value=21 Score=34.01 Aligned_cols=28 Identities=36% Similarity=0.432 Sum_probs=25.6
Q ss_pred hhhhcCCCcCChhHHHHHHHhhhhhhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIHEGEQK 75 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlHerEr~ 75 (177)
+|.-|.-.|++-+.|.+|-+.-||+=+-
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE~ChI 249 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHEACHI 249 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhhhhhh
Confidence 3999999999999999999999998663
No 259
>TIGR00073 hypB hydrogenase accessory protein HypB. HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.
Probab=36.66 E-value=37 Score=27.33 Aligned_cols=43 Identities=9% Similarity=0.127 Sum_probs=34.7
Q ss_pred HHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCccEEEE
Q 037201 109 DELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLKMVVV 152 (177)
Q Consensus 109 ~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVV 152 (177)
..++.+|..|..+.-.|+|. .+..++.++|+.....+...|+|
T Consensus 66 ~~~~~~~~~~~~l~~gcic~-~~~~~~~~~l~~~~~~~~d~IiI 108 (207)
T TIGR00073 66 ERLRKYGAPAIQINTGKECH-LDAHMVAHALEDLPLDDIDLLFI 108 (207)
T ss_pred HHHHHcCCcEEEEcCCCccc-CChHHHHHHHHHhccCCCCEEEE
Confidence 35778898888888888884 66678888888887778899999
No 260
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=36.51 E-value=40 Score=29.16 Aligned_cols=28 Identities=18% Similarity=0.202 Sum_probs=25.8
Q ss_pred EeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 129 VSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 129 VSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
|+|..+++.+||-|-..|++.|++.+..
T Consensus 117 V~DP~NlGaIiRtA~a~Gv~~Vi~~~~~ 144 (260)
T COG0566 117 VTDPHNLGAIIRTADAFGVDGVILPKRR 144 (260)
T ss_pred CcCCcchhhHHhhHHHhCCCEEEECCCc
Confidence 7899999999999999999999998753
No 261
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....
Probab=36.48 E-value=49 Score=23.53 Aligned_cols=45 Identities=27% Similarity=0.369 Sum_probs=23.2
Q ss_pred CCCchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCccEEEEecCCchhh
Q 037201 104 GYGFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMSDGAL 160 (177)
Q Consensus 104 gygLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~L 160 (177)
|+.++..|++.|..|. +|..|.+- .+.+++.++. ++.||..+...
T Consensus 10 ~~~i~~~L~~~~~~vv--------vid~d~~~---~~~~~~~~~~-~i~gd~~~~~~ 54 (116)
T PF02254_consen 10 GREIAEQLKEGGIDVV--------VIDRDPER---VEELREEGVE-VIYGDATDPEV 54 (116)
T ss_dssp HHHHHHHHHHTTSEEE--------EEESSHHH---HHHHHHTTSE-EEES-TTSHHH
T ss_pred HHHHHHHHHhCCCEEE--------EEECCcHH---HHHHHhcccc-cccccchhhhH
Confidence 4457888888663333 44444333 4455555533 55566554433
No 262
>PRK15488 thiosulfate reductase PhsA; Provisional
Probab=36.15 E-value=51 Score=31.97 Aligned_cols=48 Identities=13% Similarity=0.062 Sum_probs=34.2
Q ss_pred ecceEEEEeCCC----c--hHHHHHHHH-HcCccEEEEecCCchhhhhhhccccch
Q 037201 122 RFGCLMVVSDDS----N--FVEVFQEAT-LRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 122 ~v~clvLVSDds----d--f~~~lr~Ar-~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
..|+||++.-|. - +...+..|+ ++|.+-|||.=. .......||.|++-
T Consensus 196 ~ad~Il~~G~N~~~~~~~~~~~~~~~a~~~~G~kiivIDPr-~s~ta~~Ad~~l~i 250 (759)
T PRK15488 196 NSKYIINFGHNLYEGINMSDTRGLMTAQMEKGAKLVVFEPR-FSVVASKADEWHAI 250 (759)
T ss_pred hCcEEEEeccChHhcCCcHHHHHHHHHHHhCCCEEEEECCC-CCcchhhCCeeecc
Confidence 578899997553 1 233355666 899999999443 46788899999864
No 263
>PF02638 DUF187: Glycosyl hydrolase like GH101; InterPro: IPR003790 This entry describes proteins of unknown function.
Probab=36.08 E-value=26 Score=30.92 Aligned_cols=39 Identities=13% Similarity=0.159 Sum_probs=31.8
Q ss_pred HhhhhcEEEEEe-ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 110 ELKRAWFCVRNV-RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 110 eLrRAGv~Vr~V-~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
|+| |||+.++ ++++- +...+..+|+..++.|+-||++-=
T Consensus 1 E~R--gvWi~~~~~~~~~----~~~~~~~~l~~l~~~~~N~V~~qV 40 (311)
T PF02638_consen 1 EFR--GVWISTVANIDWP----SKEQIDEMLDDLKSAGFNAVFVQV 40 (311)
T ss_pred CeE--EEEEeecCCCCCC----CHHHHHHHHHHHHHcCCCEEEEEE
Confidence 566 9999999 45544 667799999999999999998743
No 264
>PRK14652 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=35.90 E-value=37 Score=30.08 Aligned_cols=35 Identities=9% Similarity=0.134 Sum_probs=31.6
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
..++++...|-.|+..+++.|++.++..+|+|.++
T Consensus 35 ~a~~~v~p~~~edl~~~v~~a~~~~ip~~vlGgGS 69 (302)
T PRK14652 35 PADLLVRPADPDALSALLRAVRELGVPLSILGGGA 69 (302)
T ss_pred cceEEEEcCCHHHHHHHHHHHHHCCCcEEEEcCCc
Confidence 45678889999999999999999999999999976
No 265
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=35.74 E-value=79 Score=26.98 Aligned_cols=33 Identities=9% Similarity=0.139 Sum_probs=26.3
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCcc---EEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLK---MVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~---TVVVGd 154 (177)
+.|.|++.+.-.+...+++.+++.|+. ..++|.
T Consensus 188 ~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~ 223 (348)
T cd06355 188 KPDVVVSTVNGDSNVAFFKQLKAAGITASKVPVLSF 223 (348)
T ss_pred CCCEEEEeccCCchHHHHHHHHHcCCCccCCeeEEc
Confidence 778888888888889999999999986 344554
No 266
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=35.59 E-value=64 Score=24.71 Aligned_cols=31 Identities=10% Similarity=0.116 Sum_probs=23.3
Q ss_pred eEEEEeCC---CchHHHHHHHHHcCccEEEEecC
Q 037201 125 CLMVVSDD---SNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 125 clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+|+||- .+..++.+.+++.|+...+||-+
T Consensus 106 ~iillTDG~~~~~~~~~a~~lk~~gi~i~~ig~g 139 (164)
T cd01482 106 VVILITDGKSQDDVELPARVLRNLGVNVFAVGVK 139 (164)
T ss_pred EEEEEcCCCCCchHHHHHHHHHHCCCEEEEEecC
Confidence 46777772 34567778888999999999865
No 267
>cd00860 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=35.04 E-value=1.1e+02 Score=20.56 Aligned_cols=43 Identities=26% Similarity=0.299 Sum_probs=31.2
Q ss_pred CCchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCcc-EEEEecC
Q 037201 105 YGFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLK-MVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~-TVVVGd~ 155 (177)
+.++.+||+.|+.|.+ -.+ +..+...++.|.+.|.. .++||+.
T Consensus 18 ~~~~~~Lr~~g~~v~~-------d~~-~~~~~~~~~~a~~~g~~~~iiig~~ 61 (91)
T cd00860 18 KEVAKKLSDAGIRVEV-------DLR-NEKLGKKIREAQLQKIPYILVVGDK 61 (91)
T ss_pred HHHHHHHHHCCCEEEE-------ECC-CCCHHHHHHHHHHcCCCEEEEECcc
Confidence 4568899998875532 234 46889999999999987 5667753
No 268
>PRK13903 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=34.79 E-value=40 Score=30.95 Aligned_cols=35 Identities=17% Similarity=0.190 Sum_probs=31.7
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
..++++.+.|..|+..+++.|++.++...|+|.++
T Consensus 32 ~A~~~~~p~s~edl~~~l~~a~~~~~p~~vlGgGS 66 (363)
T PRK13903 32 PARRLVTCTSTEELVAAVRELDAAGEPLLVLGGGS 66 (363)
T ss_pred cceEEEEeCCHHHHHHHHHHHHHCCCCEEEEeCCe
Confidence 45678899999999999999999999999999876
No 269
>TIGR02128 G6PI_arch bifunctional phosphoglucose/phosphomannose isomerase. This bifunctional isomerase is a member of the larger PGI superfamily and only distantly related to other glucose-6-phosphate isomerases. The family is limited to the archaea.
Probab=34.38 E-value=62 Score=28.66 Aligned_cols=41 Identities=22% Similarity=0.270 Sum_probs=31.4
Q ss_pred ecceEEEEeCCC---chHHHHHHHHHcCccEEEEecCCchhhhhhh
Q 037201 122 RFGCLMVVSDDS---NFVEVFQEATLRCLKMVVVGDMSDGALKRIA 164 (177)
Q Consensus 122 ~v~clvLVSDds---df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~A 164 (177)
.-|.++.+|.+- +-...++.|+++|.++|+|.+. +.|.+.|
T Consensus 66 ~~dlvI~iS~SG~t~e~~~a~~~A~~~g~~ii~iT~~--g~L~~~a 109 (308)
T TIGR02128 66 GKTLLIAVSYSGNTEETLSAVEEAKKKGAKVIAITSG--GRLEEMA 109 (308)
T ss_pred CCeEEEEEcCCCCCHHHHHHHHHHHHcCCEEEEECCC--cHHHHHH
Confidence 345788888664 5556688889999999999974 5788877
No 270
>PF13528 Glyco_trans_1_3: Glycosyl transferase family 1
Probab=34.27 E-value=49 Score=27.36 Aligned_cols=43 Identities=19% Similarity=0.255 Sum_probs=29.7
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCCchhhhhhhccccchh
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSWS 171 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW~ 171 (177)
..| ++|||-.-+ .+..|+..|+..|+|++.. .-..++.+++|.
T Consensus 94 ~pD--lVIsD~~~~--~~~aa~~~giP~i~i~~~~---~~~~~~~~~~~~ 136 (318)
T PF13528_consen 94 RPD--LVISDFYPL--AALAARRAGIPVIVISNQY---WFLHPNFWLPWD 136 (318)
T ss_pred CCC--EEEEcChHH--HHHHHHhcCCCEEEEEehH---HcccccCCcchh
Confidence 456 467885555 3688899999999999975 223345666654
No 271
>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------ NO2- ------ NO ------- N2O --------- N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif.
Probab=33.96 E-value=84 Score=24.21 Aligned_cols=35 Identities=20% Similarity=0.123 Sum_probs=25.4
Q ss_pred cceEEEEeCCCc------------hHHH---HHHHHHcCccEEEEecCCc
Q 037201 123 FGCLMVVSDDSN------------FVEV---FQEATLRCLKMVVVGDMSD 157 (177)
Q Consensus 123 v~clvLVSDdsd------------f~~~---lr~Ar~r~l~TVVVGd~~~ 157 (177)
-..|||+||=.+ +.+. .++|++.|+...+||-+++
T Consensus 104 ~~~iiliTDG~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~v~~igig~~ 153 (174)
T cd01454 104 RKILLVISDGEPNDLDYYEGNVFATEDALRAVIEARKLGIEVFGITIDRD 153 (174)
T ss_pred CcEEEEEeCCCcCcccccCcchhHHHHHHHHHHHHHhCCcEEEEEEecCc
Confidence 346888888543 3455 6778888999988888763
No 272
>cd02770 MopB_DmsA-EC This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=33.75 E-value=52 Score=31.19 Aligned_cols=47 Identities=9% Similarity=0.111 Sum_probs=35.0
Q ss_pred ecceEEEEeCCCc--------hHHHHHHHHHcCccEEEEecCCchhhhh-hhccccc
Q 037201 122 RFGCLMVVSDDSN--------FVEVFQEATLRCLKMVVVGDMSDGALKR-IANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsd--------f~~~lr~Ar~r~l~TVVVGd~~~~~L~r-~Ad~~~s 169 (177)
..||||++.-|.- ....++.|+++|.+-|||.=.. ....+ .||.|++
T Consensus 166 ~a~~ii~wG~N~~~~~~~~~~~~~~~~~a~~~G~klivIDPr~-t~tA~~~AD~~i~ 221 (617)
T cd02770 166 DSKLVVLFGHNPAETRMGGGGSTYYYLQAKKAGAKFIVIDPRY-TDTAVTLADEWIP 221 (617)
T ss_pred cCCEEEEECCCHHHhcCCCCchHHHHHHHHHcCCeEEEECCCC-CccccccCCEEEC
Confidence 5788999877642 3456788999999999995543 45665 7999885
No 273
>cd00368 Molybdopterin-Binding Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=33.11 E-value=77 Score=26.97 Aligned_cols=47 Identities=11% Similarity=0.192 Sum_probs=35.3
Q ss_pred ecceEEEEeCCC-----chHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDS-----NFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDds-----df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|+|+++--|. .+..-++.|+++|.+.|||+-.. ..+...||.|++
T Consensus 156 ~ad~il~~G~n~~~~~~~~~~~~~~a~~~g~kvv~idp~~-s~t~~~ad~~i~ 207 (374)
T cd00368 156 NADLILLWGSNPAETHPVLAARLRRAKKRGAKLIVIDPRR-TETAAKADEWLP 207 (374)
T ss_pred hCCEEEEEcCChHHhChHHHHHHHHHHHCCCeEEEEcCCC-CcchHhhCEeeC
Confidence 678888876554 34456678888999999998763 566888999874
No 274
>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.
Probab=32.80 E-value=94 Score=21.71 Aligned_cols=35 Identities=11% Similarity=0.163 Sum_probs=26.1
Q ss_pred ecceEEEEeCCCc------hHHHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVSDDSN------FVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsd------f~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
....||++||-.. ...+++.+++.+++..+||-++
T Consensus 101 ~~~~lvvitDg~~~~~~~~~~~~~~~~~~~~v~v~~v~~g~ 141 (161)
T cd00198 101 ARRVIILLTDGEPNDGPELLAEAARELRKLGITVYTIGIGD 141 (161)
T ss_pred CceEEEEEeCCCCCCCcchhHHHHHHHHHcCCEEEEEEcCC
Confidence 3455788888654 6678999999888887777664
No 275
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=32.69 E-value=65 Score=33.17 Aligned_cols=44 Identities=11% Similarity=0.229 Sum_probs=33.8
Q ss_pred cceEEEEeCCCch--HHHHHHHHHcCcc--EEEEecCCchhhhhhhcc
Q 037201 123 FGCLMVVSDDSNF--VEVFQEATLRCLK--MVVVGDMSDGALKRIANA 166 (177)
Q Consensus 123 v~clvLVSDdsdf--~~~lr~Ar~r~l~--TVVVGd~~~~~L~r~Ad~ 166 (177)
...|||+||-.+- .++++.++++|+. ||-+|...+..|...|+.
T Consensus 405 ~~~IILLTDGedn~~~~~l~~lk~~gVtI~TIg~G~dad~~L~~IA~~ 452 (863)
T TIGR00868 405 GSEIVLLTDGEDNTISSCFEEVKQSGAIIHTIALGPSAAKELEELSDM 452 (863)
T ss_pred CCEEEEEeCCCCCCHHHHHHHHHHcCCEEEEEEeCCChHHHHHHHHHh
Confidence 3579999997654 6778888888876 888888777778777764
No 276
>PRK04213 GTP-binding protein; Provisional
Probab=32.65 E-value=84 Score=24.34 Aligned_cols=37 Identities=22% Similarity=0.265 Sum_probs=27.5
Q ss_pred ecceEEEEeCCCchH----------------HHHHHHHHcCccEEEEecCCch
Q 037201 122 RFGCLMVVSDDSNFV----------------EVFQEATLRCLKMVVVGDMSDG 158 (177)
Q Consensus 122 ~v~clvLVSDdsdf~----------------~~lr~Ar~r~l~TVVVGd~~~~ 158 (177)
+++.+++|.|.++|. .+++.+...++..++|++-.|.
T Consensus 90 ~~~~vi~v~d~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~p~iiv~NK~Dl 142 (201)
T PRK04213 90 RILAAVLVVDGKSFIEIIERWEGRGEIPIDVEMFDFLRELGIPPIVAVNKMDK 142 (201)
T ss_pred hheEEEEEEeCccccccccccccCCCcHHHHHHHHHHHHcCCCeEEEEECccc
Confidence 466788888887663 2466777789999999997653
No 277
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=32.57 E-value=15 Score=24.80 Aligned_cols=19 Identities=16% Similarity=0.231 Sum_probs=7.1
Q ss_pred ChhhHhhhhhhhhhhhhcCCCc
Q 037201 35 PQVVREQRKKENCLLIRNQGRF 56 (177)
Q Consensus 35 P~~v~e~r~er~~Lc~~CGrrf 56 (177)
|.|+++... .-|..|+.+|
T Consensus 1 ~~W~~d~~~---~~C~~C~~~F 19 (69)
T PF01363_consen 1 PHWVPDSEA---SNCMICGKKF 19 (69)
T ss_dssp --SSSGGG----SB-TTT--B-
T ss_pred CCcCCCCCC---CcCcCcCCcC
Confidence 778877554 3355555555
No 278
>cd01493 APPBP1_RUB Ubiquitin activating enzyme (E1) subunit APPBP1. APPBP1 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. ABPP1 contains part of the adenylation domain.
Probab=32.47 E-value=1.2e+02 Score=28.33 Aligned_cols=117 Identities=16% Similarity=0.183 Sum_probs=72.7
Q ss_pred HHHHHHhcccceeeehhhccCCccccCChhhHhhhhhhhhhhhhcCCCcCChhHHHHHHHhhhhhhhhhhhhhhhhhccc
Q 037201 8 ELKKLISSFEVVKYMVANANSHAFGYVPQVVREQRKKENCLLIRNQGRFYNNDKLVNHFRQIHEGEQKKRSNQIESARGK 87 (177)
Q Consensus 8 ~Lr~~A~~FG~Vv~~~AyAnrhaf~~lP~~v~e~r~er~~Lc~~CGrrf~t~~~L~kHFkqlHerEr~Krl~ri~s~kGK 87 (177)
.|++++.++ .+-.| +.+..+|+|-.+-=..--.+.- ...+..++++.+-++=||++..-.... .+-
T Consensus 181 eL~~~~~~~-dl~~l----d~~~h~hvPy~viL~~~l~~w~-~~~~g~~p~~~~ek~~f~~~i~~~~~~--------~~~ 246 (425)
T cd01493 181 ELREHADSI-DLDDM----DPAEHSHTPYIVILIKYLEKWR-SAHNGQLPSTYKEKKEFRDLVRSLMRS--------NED 246 (425)
T ss_pred HHHHHHHhc-CCccC----ChhhcCCCCHHHHHHHHHHHHH-HhcCCCCCCCHHHHHHHHHHHHHhccc--------CCC
Confidence 366777777 56555 4556677996654332211111 123456888889999999997432211 245
Q ss_pred hHHHHHHHHhhcCCCCCCCchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHH
Q 037201 88 MEKYKMAVSAILTPKVGYGFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEAT 143 (177)
Q Consensus 88 ~~KY~~Aar~vl~pkvgygLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar 143 (177)
++-|++|.+.+...=.++.+.++++.. + =...|--+-+..++|--|++--+
T Consensus 247 eeNf~EA~~~~~~~~~~~~i~~~v~~~-~----~~~~~~~~~~~~~~fwi~~~alk 297 (425)
T cd01493 247 EENFEEAIKAVNKALNRTKIPSSVEEI-F----NDDRCENLTSQSSSFWIMARALK 297 (425)
T ss_pred ccchHHHHHHHHHhhCCCCCcHHHHHH-H----hchhcccCCCCCchHHHHHHHHH
Confidence 789999999888777777888888854 1 02333335566677766655443
No 279
>TIGR03649 ergot_EASG ergot alkaloid biosynthesis protein, AFUA_2G17970 family. This family consists of fungal proteins of unknown function associated with secondary metabolite biosynthesis, such as of the ergot alkaloids such as ergovaline. Nomenclature differs because gene order differs - this is EasG in Neotyphodium lolii but is designated ergot alkaloid biosynthetic protein A in several other fungi.
Probab=32.31 E-value=64 Score=26.46 Aligned_cols=33 Identities=9% Similarity=0.143 Sum_probs=23.4
Q ss_pred cceEEEEeCCC-----chHHHHHHHHHcCccEEEEecC
Q 037201 123 FGCLMVVSDDS-----NFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 123 v~clvLVSDds-----df~~~lr~Ar~r~l~TVVVGd~ 155 (177)
+|.+++++.+. ....+++.|++.|++.+|.-.+
T Consensus 68 ~d~v~~~~~~~~~~~~~~~~~i~aa~~~gv~~~V~~Ss 105 (285)
T TIGR03649 68 ISAVYLVAPPIPDLAPPMIKFIDFARSKGVRRFVLLSA 105 (285)
T ss_pred eeEEEEeCCCCCChhHHHHHHHHHHHHcCCCEEEEeec
Confidence 78888776532 2346778899999998887543
No 280
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=32.27 E-value=1.1e+02 Score=25.39 Aligned_cols=32 Identities=22% Similarity=0.216 Sum_probs=18.8
Q ss_pred ecceEEEEeCCCchHHHHHHHHH-cCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATL-RCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~-r~l~TVVVGd 154 (177)
++|.|++.+.+. ..+.++...+ .++..|+++.
T Consensus 115 ~vdgiii~~~~~-~~~~~~~l~~~~~iPvV~~d~ 147 (341)
T PRK10703 115 RVDGLLVMCSEY-PEPLLAMLEEYRHIPMVVMDW 147 (341)
T ss_pred CCCEEEEecCCC-CHHHHHHHHhcCCCCEEEEec
Confidence 567766655332 2355666666 6777777753
No 281
>cd01457 vWA_ORF176_type VWA ORF176 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most
Probab=32.07 E-value=81 Score=25.13 Aligned_cols=42 Identities=19% Similarity=0.340 Sum_probs=26.0
Q ss_pred ceEEEEeCCCc-----hHHHHHHHHH-------cCccEEEEecCCchh---hhhhhcc
Q 037201 124 GCLMVVSDDSN-----FVEVFQEATL-------RCLKMVVVGDMSDGA---LKRIANA 166 (177)
Q Consensus 124 ~clvLVSDdsd-----f~~~lr~Ar~-------r~l~TVVVGd~~~~~---L~r~Ad~ 166 (177)
..||++||=.. ..++|..|.. -++.+|-||+.. ++ |...+|.
T Consensus 109 ~~vIiiTDG~~~d~~~~~~~i~~a~~~l~~~~~i~i~~v~vG~~~-~~~~~L~~ld~~ 165 (199)
T cd01457 109 ETFLVITDGAPDDKDAVERVIIKASDELDADNELAISFLQIGRDP-AATAFLKALDDQ 165 (199)
T ss_pred eEEEEEcCCCCCcHHHHHHHHHHHHHhhccccCceEEEEEeCCcH-HHHHHHHHHhHH
Confidence 45677777543 2345555542 589999999862 33 6666664
No 282
>PF10740 DUF2529: Protein of unknown function (DUF2529); InterPro: IPR019676 This entry represents a protein family conserved in the Bacillales. Their function is not known. ; PDB: 3JX9_A.
Probab=32.04 E-value=97 Score=26.26 Aligned_cols=48 Identities=17% Similarity=0.142 Sum_probs=29.1
Q ss_pred ecceEEEEeCCCchHHHHHHHH---HcCccEEEEe-cCC-chhhhhhhccccc
Q 037201 122 RFGCLMVVSDDSNFVEVFQEAT---LRCLKMVVVG-DMS-DGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar---~r~l~TVVVG-d~~-~~~L~r~Ad~~~s 169 (177)
..|-++|.|..++=.++.+.|. ++|+..|+|. ... +..|..+||+.++
T Consensus 81 ~~DRVllfs~~~~~~e~~~~a~~L~~~gi~~v~Vs~~~~~~~~l~~~~~~~Id 133 (172)
T PF10740_consen 81 ETDRVLLFSPFSTDEEAVALAKQLIEQGIPFVGVSPNKPDEEDLEDLADVHID 133 (172)
T ss_dssp TT-EEEEEES-S--HHHHHHHHHHHHHT--EEEEE-SS---TTGGG-SSS-EE
T ss_pred ccceEEEEeCCCCCHHHHHHHHHHHHCCCCEEEEEecCCCCCchhhhhhheee
Confidence 6788999998888766666555 6999999999 322 2378888888775
No 283
>PRK13054 lipid kinase; Reviewed
Probab=32.02 E-value=1.3e+02 Score=25.74 Aligned_cols=52 Identities=19% Similarity=0.241 Sum_probs=34.4
Q ss_pred hHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCccEEEEecCCchhhhhhhcc
Q 037201 108 ADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANA 166 (177)
Q Consensus 108 a~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~ 166 (177)
...|+++|+.+.. .......+..++.+.|.+.+...|||..+ ||.+...++.
T Consensus 24 ~~~l~~~g~~~~v------~~t~~~~~a~~~a~~~~~~~~d~vvv~GG-DGTl~evv~~ 75 (300)
T PRK13054 24 VGLLREEGHTLHV------RVTWEKGDAARYVEEALALGVATVIAGGG-DGTINEVATA 75 (300)
T ss_pred HHHHHHcCCEEEE------EEecCCCcHHHHHHHHHHcCCCEEEEECC-ccHHHHHHHH
Confidence 3456667664332 23344567778888887778888888888 5877777654
No 284
>PF03411 Peptidase_M74: Penicillin-insensitive murein endopeptidase; InterPro: IPR005073 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 peptidases belong to MEROPS peptidase family M74 (murein endopeptidase family, clan MD). The type example is murein endopeptidase from Escherichia coli (MepA). The entry represents a family of penicillin-insensitive murein endopeptidases involved in the removal of murein from the sacculus by cleaving the peptide bonds between neighbouring strands in mature murein. The crystal structure of MepA has been determined revealing similarities to the D-Ala-D-Ala carboxypeptidases in MEROPS peptidase family M15 []. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis, 0030288 outer membrane-bounded periplasmic space; PDB: 1U10_F 1TZP_A.
Probab=31.83 E-value=38 Score=30.00 Aligned_cols=33 Identities=15% Similarity=0.189 Sum_probs=17.6
Q ss_pred HHHHHHHHcCccEEEEecCCch------------hhhhhhccccc
Q 037201 137 EVFQEATLRCLKMVVVGDMSDG------------ALKRIANAFFS 169 (177)
Q Consensus 137 ~~lr~Ar~r~l~TVVVGd~~~~------------~L~r~Ad~~~s 169 (177)
.+-+.++..++.+++|||++-- -.++-+|+||.
T Consensus 46 ~l~~~~~~~g~~~llIGDiS~prGG~m~sgH~SHQ~GLDvDIwl~ 90 (240)
T PF03411_consen 46 RLAREAAQAGWPGLLIGDISQPRGGPMSSGHASHQSGLDVDIWLR 90 (240)
T ss_dssp HHHHHHHHTTS--EEE---B-TT----SSS-S--TTS-EEEEES-
T ss_pred HHHHHHHHcCCCceEEeecCCcCCCCCCCCccccccCccceeeee
Confidence 3445667799999999998621 23566899986
No 285
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=31.58 E-value=1e+02 Score=20.74 Aligned_cols=41 Identities=27% Similarity=0.283 Sum_probs=29.0
Q ss_pred chHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCcc-EEEEecC
Q 037201 107 FADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLK-MVVVGDM 155 (177)
Q Consensus 107 La~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~-TVVVGd~ 155 (177)
++.+||.+|+.|.. -.....+..-++.|...|.. .++||+.
T Consensus 23 ~~~~Lr~~g~~v~~--------~~~~~~~~k~~~~a~~~g~~~~iiig~~ 64 (94)
T cd00738 23 LLNALLANGIRVLY--------DDRERKIGKKFREADLRGVPFAVVVGED 64 (94)
T ss_pred HHHHHHHCCCEEEe--------cCCCcCHhHHHHHHHhCCCCEEEEECCC
Confidence 47889999975442 12246788999999988876 5666754
No 286
>cd02121 PA_GCPII_like PA_GCPII_like: Protease-associated domain containing protein, glutamate carboxypeptidase II (GCPII)-like. This group contains various PA domain-containing proteins similar to GCPII including, GCPIII (NAALADase2) and NAALADase L. These proteins belong to the peptidase M28 family. GCPII is also known N-acetylated-alpha-linked acidic dipeptidase (NAALDase1), folate hydrolase or prostate-specific membrane antigen (PSMA). GCPII is found in various human tissues including prostate, small intestine, and the central nervous system. In the brain, GCPII is known as NAALDase1, it functions as a NAALDase hydrolyzing the neuropeptide N-acetyl-L-aspartyl-L-glutamate (alpha-NAAG), to release free glutamate. In the small intestine, GCPII releases the terminal glutamate from poly-gamma-glutamated folates. GCPII (PSMA) is a useful cancer marker; its expression is markedly increased in prostate cancer and in tumor-associated neovasculature. GCPIII hydrolyzes alpha-NAAG with a lower
Probab=31.37 E-value=91 Score=26.85 Aligned_cols=45 Identities=18% Similarity=0.175 Sum_probs=31.2
Q ss_pred CCCchHH---hhhhcEEEEEeecceEEEEeCC-CchHHHHHHHHHcCccEEEE
Q 037201 104 GYGFADE---LKRAWFCVRNVRFGCLMVVSDD-SNFVEVFQEATLRCLKMVVV 152 (177)
Q Consensus 104 gygLa~e---LrRAGv~Vr~V~v~clvLVSDd-sdf~~~lr~Ar~r~l~TVVV 152 (177)
|||..+. |+.+|+.|+ +.|+|+-.. .-+.+-++.|.++|..-|+|
T Consensus 53 nyG~~~D~~~L~~~gvdv~----GKIvLvr~G~~~~~~Kv~~A~~~GA~gVIi 101 (220)
T cd02121 53 NYGSPEDFEYLEDLGIDVK----GKIVIARYGGIFRGLKVKNAQLAGAVGVII 101 (220)
T ss_pred CCCcHHHHHHHhhcCCCCC----CeEEEEECCCccHHHHHHHHHHcCCEEEEE
Confidence 7777664 445565554 568888544 44478899999999887765
No 287
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=31.29 E-value=20 Score=32.74 Aligned_cols=25 Identities=16% Similarity=0.115 Sum_probs=18.2
Q ss_pred hhhcCCCcCChhHHHHHHHhhhhhh
Q 037201 49 LIRNQGRFYNNDKLVNHFRQIHEGE 73 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kHFkqlHerE 73 (177)
|=.|+|.|....-|+.|-|..|-.=
T Consensus 13 cwycnrefddekiliqhqkakhfkc 37 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKHFKC 37 (341)
T ss_pred eeecccccchhhhhhhhhhhcccee
Confidence 7778888887777777777666543
No 288
>TIGR02815 agaS_fam putative sugar isomerase, AgaS family. Some members of this protein family are found in regions associated with N-acetyl-galactosamine and galactosamine untilization and are suggested to be isomerases.
Probab=31.25 E-value=71 Score=28.72 Aligned_cols=42 Identities=21% Similarity=0.089 Sum_probs=33.3
Q ss_pred ceEEEEeCC---CchHHHHHHHHHc--CccEEEEecCCchhhhhhhc
Q 037201 124 GCLMVVSDD---SNFVEVFQEATLR--CLKMVVVGDMSDGALKRIAN 165 (177)
Q Consensus 124 ~clvLVSDd---sdf~~~lr~Ar~r--~l~TVVVGd~~~~~L~r~Ad 165 (177)
+.+|.+|=. .|-...++.|++. |.+|+.|-+..++.|.+.||
T Consensus 94 ~lvi~iSqSGeT~etv~a~~~ak~~~~g~~~i~it~~~~s~la~~ad 140 (372)
T TIGR02815 94 TLLVSFARSGNSPESVAAVELADQLLPECYHLVLTCNEEGALYRNAI 140 (372)
T ss_pred eEEEEEeCCcCcHHHHHHHHHHHHhCCCCcEEEEEcCCCCHHHHhhc
Confidence 346666653 4666777999988 89999998877789999999
No 289
>cd01467 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=31.13 E-value=1.1e+02 Score=23.23 Aligned_cols=31 Identities=13% Similarity=0.249 Sum_probs=19.7
Q ss_pred ceEEEEeCCC------chHHHHHHHHHcCcc--EEEEec
Q 037201 124 GCLMVVSDDS------NFVEVFQEATLRCLK--MVVVGD 154 (177)
Q Consensus 124 ~clvLVSDds------df~~~lr~Ar~r~l~--TVVVGd 154 (177)
..|||+||-. +...+.+.++++|+. +|.||+
T Consensus 104 ~~iiliTDG~~~~g~~~~~~~~~~~~~~gi~i~~i~ig~ 142 (180)
T cd01467 104 RVIVLLTDGENNAGEIDPATAAELAKNKGVRIYTIGVGK 142 (180)
T ss_pred CEEEEEeCCCCCCCCCCHHHHHHHHHHCCCEEEEEEecC
Confidence 5688898842 234566777777654 555665
No 290
>PRK13906 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=31.10 E-value=45 Score=29.56 Aligned_cols=34 Identities=12% Similarity=0.121 Sum_probs=31.3
Q ss_pred cceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 123 FGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 123 v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.++++...+-.|+..+++.|++.++..+++|.++
T Consensus 37 A~~~v~p~~~edv~~~v~~a~~~~ip~~vlGgGS 70 (307)
T PRK13906 37 ADFYITPTKNEEVQAVVKYAYQNEIPVTYLGNGS 70 (307)
T ss_pred eEEEEEcCCHHHHHHHHHHHHHcCCCEEEEcCce
Confidence 6778899999999999999999999999999886
No 291
>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax. ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.
Probab=31.09 E-value=70 Score=25.05 Aligned_cols=41 Identities=17% Similarity=0.123 Sum_probs=25.6
Q ss_pred ceEEEEeCCCch-------HHHHHHHHHcCccE--EEEecCCchhhhhhh
Q 037201 124 GCLMVVSDDSNF-------VEVFQEATLRCLKM--VVVGDMSDGALKRIA 164 (177)
Q Consensus 124 ~clvLVSDdsdf-------~~~lr~Ar~r~l~T--VVVGd~~~~~L~r~A 164 (177)
..+||+||=.+. ....+.+++.|+.. |-|||.+...|...|
T Consensus 105 ~~villTDG~~~~~~~~~~~~~a~~l~~~gv~i~~vgv~~~~~~~L~~iA 154 (185)
T cd01474 105 SVIIALTDGQLLLNGHKYPEHEAKLSRKLGAIVYCVGVTDFLKSQLINIA 154 (185)
T ss_pred eEEEEEcCCCcCCCCCcchHHHHHHHHHcCCEEEEEeechhhHHHHHHHh
Confidence 568888886552 13456677788874 444455445677776
No 292
>cd02126 PA_EDEM3_like PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I alpha-mannosidases (gylcosyl hydrolase family 47), N-terminal to the PA domain. EDEM3 accelerates glycoprotein ERAD (ER-associated degradation). In transfected mammalian cells, overexpression of EDEM3 enhances the mannose trimming from the N-glycans, of a model misfolded protein [alpha1-antitrypsin null (Hong Kong)] as well as, from total glycoproteins. Mannose trimming appears to be involved in the selection of ERAD substrates. EDEM3 has a different specificity of trimming than ER alpha-mannosidase 1. The significance of the PA domain to EDEM3 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or pr
Probab=31.04 E-value=1e+02 Score=23.62 Aligned_cols=47 Identities=21% Similarity=0.227 Sum_probs=32.2
Q ss_pred ceEEEEeC-CCchHHHHHHHHHcCccEEEEecCCchhhhhhhccccchh
Q 037201 124 GCLMVVSD-DSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSWS 171 (177)
Q Consensus 124 ~clvLVSD-dsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW~ 171 (177)
+.++||.. .+.|.+-.+.|.++|-.-|+|-|..++... +-+-+++|.
T Consensus 41 gkIaLv~RG~C~f~~K~~~Aq~aGA~avII~n~~~~~~~-~~~~~~~m~ 88 (126)
T cd02126 41 GKIAIMERGDCMFVEKARRVQKAGAIGGIVIDNNEGSSS-DTAPMFAMS 88 (126)
T ss_pred ceEEEEECCCCcHHHHHHHHHHCCCcEEEEEECCCCccc-cccceeEee
Confidence 45666654 478999999999999999999876544321 122355553
No 293
>TIGR01553 formate-DH-alph formate dehydrogenase, alpha subunit, proteobacterial-type. This model is well-defined, with a large, unpopulated trusted/noise gap.
Probab=31.01 E-value=70 Score=33.13 Aligned_cols=47 Identities=9% Similarity=0.072 Sum_probs=35.1
Q ss_pred ecceEEEEeCCCc-----hHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDSN-----FVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsd-----f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|||+++--|.. ....+..|+++|.+-|||--. .......||.|++
T Consensus 221 ~Ad~Ilv~G~Np~es~p~~~~~i~~Ak~~GakiIvIDPR-~t~tA~~AD~~l~ 272 (1009)
T TIGR01553 221 NSDLILVMGGNPAENHPIGFKWAIRAKKKGAKIIHIDPR-FNRTATVADLYAP 272 (1009)
T ss_pred hCCEEEEECCChhhhChHHHHHHHHHHHcCCEEEEEcCC-CCchhHhhccEeC
Confidence 5789998876532 234566789999999999544 4677889999985
No 294
>TIGR00509 bisC_fam molybdopterin guanine dinucleotide-containing S/N-oxide reductases. This enzyme family shares sequence similarity and a requirement for a molydenum cofactor as the only prosthetic group. The form of the cofactor is a single molybdenum atom coordinated by two molybdopterin guanine dinucleotide molecules. Members of the family include biotin sulfoxide reductase, dimethylsulfoxide reductase, and trimethylamine-N-oxide reductase, although a single member may show all those activities and related activities; it may not be possible to resolve the primary function for members of this family by sequence comparison alone. A number of similar molybdoproteins in which the N-terminal region contains a CXXXC motif and may bind an iron-sulfur cluster are excluded from this set, including formate dehydrogenases and nitrate reductases. Also excluded is the A chain of a heteromeric, anaerobic DMSO reductase, which also contains the CXXXC motif.
Probab=30.89 E-value=68 Score=31.32 Aligned_cols=47 Identities=6% Similarity=0.102 Sum_probs=32.9
Q ss_pred ecceEEEEeCCCc-------------hHHHHHHHHHcCccEEEEecCCchhhhhh-hccccc
Q 037201 122 RFGCLMVVSDDSN-------------FVEVFQEATLRCLKMVVVGDMSDGALKRI-ANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsd-------------f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~-Ad~~~s 169 (177)
..||||+..-+.- ....|+.|+++|.+-|||-=.- ...... ||.|++
T Consensus 167 ~a~~il~~G~Np~~t~~~~~~~~~~~~~~~~~~a~~~G~klIvIDPr~-t~tA~~aaD~~l~ 227 (770)
T TIGR00509 167 NSKVLVLWGADPLKTSQIAWGIPDHGGYEYLERLKAKGKRVISIDPVR-TETAEFFGAEWIP 227 (770)
T ss_pred cCCEEEEeCCCHHHhCccccccCCcchHHHHHHHHHcCCEEEEEcCCC-CcchhhccCeEeC
Confidence 5677887765532 3367888999999988886553 455565 589885
No 295
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=30.88 E-value=1e+02 Score=24.16 Aligned_cols=32 Identities=13% Similarity=0.075 Sum_probs=25.9
Q ss_pred cceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 123 FGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 123 v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
...|.--++..++..+.+..++.++.++|||-
T Consensus 28 l~~i~~~~~~~~~~~l~~li~~~~i~~iVvGl 59 (135)
T PF03652_consen 28 LETIPRRNREKDIEELKKLIEEYQIDGIVVGL 59 (135)
T ss_dssp EEEEEECCCCCCHHHHHHHHHHCCECEEEEEE
T ss_pred eEEEECCCCchHHHHHHHHHHHhCCCEEEEeC
Confidence 34444444579999999999999999999996
No 296
>PRK11587 putative phosphatase; Provisional
Probab=30.59 E-value=66 Score=25.73 Aligned_cols=25 Identities=8% Similarity=0.084 Sum_probs=17.6
Q ss_pred eCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 130 SDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 130 SDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
=+||. .+ ++-|+.+|+.||.|.+..
T Consensus 161 igDs~-~d-i~aA~~aG~~~i~v~~~~ 185 (218)
T PRK11587 161 VEDAP-AG-VLSGLAAGCHVIAVNAPA 185 (218)
T ss_pred Eecch-hh-hHHHHHCCCEEEEECCCC
Confidence 35553 34 678888999998887654
No 297
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=30.54 E-value=91 Score=22.66 Aligned_cols=35 Identities=17% Similarity=0.228 Sum_probs=22.9
Q ss_pred ecceEEEEeCCCchH---HHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVSDDSNFV---EVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~---~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.-..||++||-.+-. ++++.++..++...+||-+.
T Consensus 99 ~~~~iv~iTDG~~~~~~~~~~~~~~~~~i~i~~v~~~~ 136 (172)
T PF13519_consen 99 RRRAIVLITDGEDNSSDIEAAKALKQQGITIYTVGIGS 136 (172)
T ss_dssp EEEEEEEEES-TTHCHHHHHHHHHHCTTEEEEEEEES-
T ss_pred CceEEEEecCCCCCcchhHHHHHHHHcCCeEEEEEECC
Confidence 345689999966444 57777777887766666544
No 298
>PF00582 Usp: Universal stress protein family; InterPro: IPR006016 The universal stress protein UspA P28242 from SWISSPROT [] is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [] reveals an alpha/beta fold similar to that of the Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0577 protein, which binds ATP [], though UspA lacks ATP-binding activity.; GO: 0006950 response to stress; PDB: 3DLO_C 3QTB_A 2PFS_A 3TNJ_A 1JMV_D 3FH0_B 3FDX_B 3AB7_A 3AB8_A 2GM3_F ....
Probab=30.51 E-value=1.3e+02 Score=20.44 Aligned_cols=37 Identities=16% Similarity=0.235 Sum_probs=29.2
Q ss_pred EEEEeCCCchHHHHHHHHHcCccEEEEecCCchhhhh
Q 037201 126 LMVVSDDSNFVEVFQEATLRCLKMVVVGDMSDGALKR 162 (177)
Q Consensus 126 lvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r 162 (177)
-+.+...+-...+++.+.+.+...||+|-...+.+.+
T Consensus 82 ~~~~~~~~~~~~i~~~~~~~~~dliv~G~~~~~~~~~ 118 (140)
T PF00582_consen 82 EVVIESGDVADAIIEFAEEHNADLIVMGSRGRSGLER 118 (140)
T ss_dssp EEEEEESSHHHHHHHHHHHTTCSEEEEESSSTTSTTT
T ss_pred EEEEEeeccchhhhhccccccceeEEEeccCCCCccC
Confidence 3456667788999999999999999999986444443
No 299
>PRK14653 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=30.19 E-value=44 Score=29.73 Aligned_cols=34 Identities=9% Similarity=0.234 Sum_probs=29.8
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
..++++...|-.++..+++.+++ ++..+|+|.++
T Consensus 33 ~A~~~v~p~s~eel~~~~~~~~~-~~p~~vlG~GS 66 (297)
T PRK14653 33 PVPLFAIPNSTNGFIETINLLKE-GIEVKILGNGT 66 (297)
T ss_pred EEEEEEecCCHHHHHHHHHHHhc-CCCEEEEcCCe
Confidence 45778889999999999999999 99999999876
No 300
>PRK13337 putative lipid kinase; Reviewed
Probab=30.11 E-value=1.5e+02 Score=25.51 Aligned_cols=49 Identities=18% Similarity=0.271 Sum_probs=31.6
Q ss_pred HhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCccEEEEecCCchhhhhhhc
Q 037201 110 ELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMSDGALKRIAN 165 (177)
Q Consensus 110 eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad 165 (177)
.|..+|+.+.. +......+...+.+.+.+.+..+|||..+ ||.+...++
T Consensus 27 ~l~~~~~~~~~------~~t~~~~~a~~~a~~~~~~~~d~vvv~GG-DGTl~~vv~ 75 (304)
T PRK13337 27 KLEQAGYETSA------HATTGPGDATLAAERAVERKFDLVIAAGG-DGTLNEVVN 75 (304)
T ss_pred HHHHcCCEEEE------EEecCCCCHHHHHHHHHhcCCCEEEEEcC-CCHHHHHHH
Confidence 46666655433 24445566777777777777778877777 477766665
No 301
>PF12745 HGTP_anticodon2: Anticodon binding domain of tRNAs; InterPro: IPR024435 This is an anticodon binding domain, found largely on Gcn2 proteins which bind tRNA to down regulate translation in certain stress situations [].; GO: 0000049 tRNA binding
Probab=30.05 E-value=30 Score=30.52 Aligned_cols=29 Identities=14% Similarity=0.204 Sum_probs=25.5
Q ss_pred CCCCchHHhhhhcEEEEEe-----------------ecceEEEEeC
Q 037201 103 VGYGFADELKRAWFCVRNV-----------------RFGCLMVVSD 131 (177)
Q Consensus 103 vgygLa~eLrRAGv~Vr~V-----------------~v~clvLVSD 131 (177)
.|+.+..+|-.+|+...++ |+.|||+|.+
T Consensus 21 ~~~~iv~~LW~~gIsAd~~~~~~~S~Eel~~~~~~~gi~wiViikq 66 (273)
T PF12745_consen 21 EGIEIVQELWAAGISADLMYDASPSQEELQSYCREDGISWIVIIKQ 66 (273)
T ss_pred HHHHHHHHHHHCCCceEeccccCCCHHHHHHHHHHCCCCEEEEEec
Confidence 4778899999999999986 8999999988
No 302
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=29.76 E-value=1.1e+02 Score=18.92 Aligned_cols=31 Identities=19% Similarity=0.172 Sum_probs=27.6
Q ss_pred EEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 126 LMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 126 lvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
++.|+.+....++++..++.++..+.|=|..
T Consensus 9 ~~~v~~~~~l~~~~~~~~~~~~~~~~V~d~~ 39 (57)
T PF00571_consen 9 PITVSPDDSLEEALEIMRKNGISRLPVVDED 39 (57)
T ss_dssp SEEEETTSBHHHHHHHHHHHTSSEEEEESTT
T ss_pred CEEEcCcCcHHHHHHHHHHcCCcEEEEEecC
Confidence 4578899999999999999999999998875
No 303
>PRK01122 potassium-transporting ATPase subunit B; Provisional
Probab=29.67 E-value=82 Score=31.35 Aligned_cols=62 Identities=10% Similarity=0.090 Sum_probs=41.2
Q ss_pred HHhhhhcEEEEEe---------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC-chhhhhhhccccch
Q 037201 109 DELKRAWFCVRNV---------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS-DGALKRIANAFFSW 170 (177)
Q Consensus 109 ~eLrRAGv~Vr~V---------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~-~~~L~r~Ad~~~sW 170 (177)
.+||++|+.|.++ |+|-+.==+-..|=..+++.-++.|-...++||+. |-.-=+.||+.+.-
T Consensus 455 ~~Lr~~GI~vvMiTGDn~~TA~aIA~elGId~v~A~~~PedK~~iV~~lQ~~G~~VaMtGDGvNDAPALa~ADVGIAM 532 (679)
T PRK01122 455 AELRKMGIKTVMITGDNPLTAAAIAAEAGVDDFLAEATPEDKLALIRQEQAEGRLVAMTGDGTNDAPALAQADVGVAM 532 (679)
T ss_pred HHHHHCCCeEEEECCCCHHHHHHHHHHcCCcEEEccCCHHHHHHHHHHHHHcCCeEEEECCCcchHHHHHhCCEeEEe
Confidence 4799999988887 77643222233344566777777887778999953 43233568887754
No 304
>cd02763 MopB_2 The MopB_2 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins
Probab=29.57 E-value=89 Score=30.94 Aligned_cols=47 Identities=19% Similarity=0.217 Sum_probs=33.8
Q ss_pred ecceEEEEeCCCc-----hHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDSN-----FVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsd-----f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|++|++.-+.+ +.--++.|+++|.+-|||.=. .......||.|++
T Consensus 155 ~Ad~Ivl~G~n~~~~~~p~~~~i~~ak~~GaKlIvIDPr-~t~ta~~AD~wl~ 206 (679)
T cd02763 155 HTKYFMMIGVAEDHHSNPFKIGIQKLKRRGGKFVAVNPV-RTGYAAIADEWVP 206 (679)
T ss_pred hCCEEEEECCCCcccCchHHHHHHHHHhCCCcEEEEcCc-CCcchHhhCeecC
Confidence 5678888753322 334567888999999999544 3577899999885
No 305
>cd01451 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto). In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is a three sub-unit (BchI, BchD and BchH) enzyme with a novel arrangement of domains: the C-terminal helical domain is located behind the nucleotide binding site. The BchD domain contains a AAA domain at its N-terminus and a VWA domain at its C-terminus. The VWA domain has been speculated to be involved in mediating protein-protein interactions.
Probab=29.42 E-value=1.1e+02 Score=23.77 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=28.7
Q ss_pred ceEEEEeCCCch----------HHHHHHHHHcCccEEEEecCCc----hhhhhhhcc
Q 037201 124 GCLMVVSDDSNF----------VEVFQEATLRCLKMVVVGDMSD----GALKRIANA 166 (177)
Q Consensus 124 ~clvLVSDdsdf----------~~~lr~Ar~r~l~TVVVGd~~~----~~L~r~Ad~ 166 (177)
..+||+||=.+- .++.+.+++.++..++||-..+ ..|.+.|+.
T Consensus 100 ~~ivliTDG~~~~g~~~~~~~~~~~~~~l~~~gi~v~~I~~~~~~~~~~~l~~iA~~ 156 (178)
T cd01451 100 PLIVVITDGRANVGPDPTADRALAAARKLRARGISALVIDTEGRPVRRGLAKDLARA 156 (178)
T ss_pred eEEEEECCCCCCCCCCchhHHHHHHHHHHHhcCCcEEEEeCCCCccCccHHHHHHHH
Confidence 467888875432 3456777889999999886532 346666664
No 306
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=29.41 E-value=66 Score=23.62 Aligned_cols=38 Identities=8% Similarity=0.021 Sum_probs=26.0
Q ss_pred hhhcCCCcCChhHHHHHHHhhhhhhhhh-------hhhhhhhhcc
Q 037201 49 LIRNQGRFYNNDKLVNHFRQIHEGEQKK-------RSNQIESARG 86 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kHFkqlHerEr~K-------rl~ri~s~kG 86 (177)
|..||..+.+.+......+.+=+--+.+ +|..+....|
T Consensus 34 C~~CGe~~~~~e~~~~~~~~i~~~~~~~~~~~~~~~i~~~r~~~g 78 (127)
T TIGR03830 34 CPACGEELLDPEESKRNSAALADFYRKVDGLLTPPEIRRIRKKLG 78 (127)
T ss_pred CCCCCCEEEcHHHHHHHHHHHHHHHHHccCCcCHHHHHHHHHHcC
Confidence 9999999999988877776665544433 4444444444
No 307
>PF02225 PA: PA domain; InterPro: IPR003137 The PA (Protease associated) domain is found as an insert domain in diverse proteases, which include the MEROPS peptidase families A22B, M28, and S8A []. The PA domain is also found in a plant vacuolar sorting receptor O22925 from SWISSPROT and members of the RZF family, e.g. O43567 from SWISSPROT.; PDB: 3EIF_A 1XF1_B 3BXM_A 2C6P_A 1Z8L_C 3SJF_A 3BHX_A 2C6G_A 3D7F_A 2XEG_A ....
Probab=29.39 E-value=1.1e+02 Score=21.21 Aligned_cols=30 Identities=17% Similarity=0.222 Sum_probs=24.5
Q ss_pred eEEEE-eCCCchHHHHHHHHHcCccEEEEec
Q 037201 125 CLMVV-SDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 125 clvLV-SDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
.+||| ..++.|.+-++.|.+.|..-|+|.+
T Consensus 35 kIvlv~rg~~~~~~k~~~a~~~GA~gvIi~~ 65 (101)
T PF02225_consen 35 KIVLVERGSCSFDDKVRNAQKAGAKGVIIYN 65 (101)
T ss_dssp SEEEEESTSSCHHHHHHHHHHTTESEEEEE-
T ss_pred eEEEEecCCCCHHHHHHHHHHcCCEEEEEEe
Confidence 35666 4556899999999999999999999
No 308
>TIGR02137 HSK-PSP phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein. This enzyme is a member of the haloacid dehalogenase (HAD) superfamily, specifically part of subfamily IB by virtue of the presence of an alpha helical domain in between motifs I and II of the HAD domain . The closest homologs to this family are monofunctional phosphoserine phosphatases (TIGR00338).
Probab=29.35 E-value=47 Score=27.32 Aligned_cols=37 Identities=14% Similarity=0.062 Sum_probs=25.2
Q ss_pred chHHHHHHHHHcCccEEEEecCC-chhhhhhhccccch
Q 037201 134 NFVEVFQEATLRCLKMVVVGDMS-DGALKRIANAFFSW 170 (177)
Q Consensus 134 df~~~lr~Ar~r~l~TVVVGd~~-~~~L~r~Ad~~~sW 170 (177)
+=..+++...+.|.+++.|||+. |-.+.+.||..+-|
T Consensus 132 ~K~~~l~~l~~~~~~~v~vGDs~nDl~ml~~Ag~~ia~ 169 (203)
T TIGR02137 132 PKRQSVIAFKSLYYRVIAAGDSYNDTTMLSEAHAGILF 169 (203)
T ss_pred hHHHHHHHHHhhCCCEEEEeCCHHHHHHHHhCCCCEEe
Confidence 33445666677888999999963 44666777765543
No 309
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=29.32 E-value=72 Score=21.16 Aligned_cols=24 Identities=21% Similarity=0.162 Sum_probs=21.5
Q ss_pred CchHHHHHHHHHcCccEEEEecCC
Q 037201 133 SNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 133 sdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
....++++.|++.|+..|.|-|-+
T Consensus 15 ~~~~~~~~~a~~~g~~~v~iTDh~ 38 (67)
T smart00481 15 LSPEELVKRAKELGLKAIAITDHG 38 (67)
T ss_pred CCHHHHHHHHHHcCCCEEEEeeCC
Confidence 457899999999999999999974
No 310
>KOG1531 consensus F0F1-type ATP synthase, gamma subunit [Energy production and conversion]
Probab=29.15 E-value=1.5e+02 Score=27.30 Aligned_cols=83 Identities=23% Similarity=0.282 Sum_probs=49.6
Q ss_pred hhhhhhcc--------c---hHHHHHHHHhhcCCCCCCC--chHHhhhhcEEEEEee-----cceEEEEeCCCch-----
Q 037201 79 NQIESARG--------K---MEKYKMAVSAILTPKVGYG--FADELKRAWFCVRNVR-----FGCLMVVSDDSNF----- 135 (177)
Q Consensus 79 ~ri~s~kG--------K---~~KY~~Aar~vl~pkvgyg--La~eLrRAGv~Vr~V~-----v~clvLVSDdsdf----- 135 (177)
.||+|.|- | -.||.+|=+++.. ..+|| +-.-+..+-..|-.+. =.-||+||-|-..
T Consensus 36 ~RlkSVKNiQKITksMKmVAaaK~~rAer~~~~-ar~~~~~~~~~~~~~d~~~p~~e~~~~kK~~lV~vtsDrGLCGgih 114 (304)
T KOG1531|consen 36 IRLKSVKNIQKITKSMKMVAAAKYARAERALKA-ARPYGEGAVEFFKNIDIDVPLTEEGEVKKVLLVAVTSDRGLCGGIH 114 (304)
T ss_pred HHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHhc-cCccchHHHHHHhhccCCCCccccccccceEEEEEecCCccccchh
Confidence 35666666 3 2699988887654 44554 4445565655444332 2257888777654
Q ss_pred HHHHHHHHH--------cCccEEEEecCCchhhhh
Q 037201 136 VEVFQEATL--------RCLKMVVVGDMSDGALKR 162 (177)
Q Consensus 136 ~~~lr~Ar~--------r~l~TVVVGd~~~~~L~r 162 (177)
+.+.+.+|. .++.-|.|||-...-|-|
T Consensus 115 ssi~K~~r~~l~~~~~~~e~~vv~iGdK~ra~l~R 149 (304)
T KOG1531|consen 115 SSIAKKARRELNDLKGGKEVRVVIIGDKIRAILLR 149 (304)
T ss_pred HHHHHHHHHHHHhccCCCceEEEEEchhhhhheee
Confidence 456677663 345567788865555544
No 311
>cd02754 MopB_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. Members of the MopB_Nitrate-R-NapA CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=28.79 E-value=88 Score=28.97 Aligned_cols=47 Identities=13% Similarity=0.257 Sum_probs=34.2
Q ss_pred ecceEEEEeCCCc-----hHHHHHHHHHc--CccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDSN-----FVEVFQEATLR--CLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsd-----f~~~lr~Ar~r--~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
..|+|+++--|.. ...-++.|+++ |.+.|||.-. .......||.|++
T Consensus 157 ~ad~Il~~G~n~~~s~~~~~~~~~~a~~~~~G~klividP~-~t~ta~~Ad~~l~ 210 (565)
T cd02754 157 HADCFFLIGSNMAECHPILFRRLLDRKKANPGAKIIVVDPR-RTRTADIADLHLP 210 (565)
T ss_pred hCCEEEEECCChhhhhhHHHHHHHHHHhcCCCCEEEEEcCC-CCcchHHhCeeeC
Confidence 5678887766642 33456778887 9999999654 3677889999885
No 312
>PRK14650 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=28.71 E-value=50 Score=29.68 Aligned_cols=34 Identities=15% Similarity=0.193 Sum_probs=20.2
Q ss_pred cceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 123 FGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 123 v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.++++.+.|..++..+++.+++.++...|+|.+|
T Consensus 33 A~~~~~p~~~~eL~~~l~~~~~~~~p~~vlG~GS 66 (302)
T PRK14650 33 SKLFLTPKTIKDAEHIFKAAIEEKIKIFILGGGS 66 (302)
T ss_pred EEEEEecCCHHHHHHHHHHHHHcCCCEEEEecee
Confidence 3455556666666666666666666666666543
No 313
>cd04623 CBS_pair_10 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=28.59 E-value=1e+02 Score=20.70 Aligned_cols=30 Identities=23% Similarity=0.220 Sum_probs=24.5
Q ss_pred EEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 127 MVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 127 vLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
+-++.+..+.++++...+.+...+.|.|.+
T Consensus 4 ~~i~~~~~~~~~~~~~~~~~~~~~~V~~~~ 33 (113)
T cd04623 4 ITVRPDATVAEAAKLMAEKNIGAVVVVDDG 33 (113)
T ss_pred EEECCCCcHHHHHHHHHHcCCCeEEEECCC
Confidence 346788889999998888888888888764
No 314
>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=28.53 E-value=1.3e+02 Score=23.76 Aligned_cols=10 Identities=10% Similarity=0.238 Sum_probs=4.6
Q ss_pred HcCccEEEEe
Q 037201 144 LRCLKMVVVG 153 (177)
Q Consensus 144 ~r~l~TVVVG 153 (177)
..++..|+|+
T Consensus 75 ~~~iPvV~~~ 84 (263)
T cd06280 75 RLSFPVVLID 84 (263)
T ss_pred hcCCCEEEEC
Confidence 3344444444
No 315
>COG1231 Monoamine oxidase [Amino acid transport and metabolism]
Probab=28.27 E-value=77 Score=30.49 Aligned_cols=70 Identities=20% Similarity=0.104 Sum_probs=46.0
Q ss_pred hHHhhhhcEEEEEe------ecceEEEEe--CCCchH---------HHHHHHHHcCcc---EEEEecCCch---------
Q 037201 108 ADELKRAWFCVRNV------RFGCLMVVS--DDSNFV---------EVFQEATLRCLK---MVVVGDMSDG--------- 158 (177)
Q Consensus 108 a~eLrRAGv~Vr~V------~v~clvLVS--Ddsdf~---------~~lr~Ar~r~l~---TVVVGd~~~~--------- 158 (177)
|.||++||+.|... |=.|.-+-+ +..|+. ..|-.+++.|+. +|+.||..-+
T Consensus 23 A~eL~kaG~~v~ilEar~r~GGR~~t~r~~~~~~d~gG~~i~p~~~~~l~~~k~~gv~~~~fi~~g~~~~~~~~~~~~~p 102 (450)
T COG1231 23 AYELKKAGYQVQILEARDRVGGRSLTARAGGEYTDLGGQYINPTHDALLAYAKEFGVPLEPFIRDGDNVIGYVGSSKSTP 102 (450)
T ss_pred HHHHhhcCcEEEEEeccCCcCceeEEEeccceeeccCCcccCccchhhhhhHHhcCCCCCceeccCcccccccccccccc
Confidence 57999999999877 444433333 333443 678899999986 4565664211
Q ss_pred --hhhhhhccccchhhhhcCC
Q 037201 159 --ALKRIANAFFSWSDLLMGK 177 (177)
Q Consensus 159 --~L~r~Ad~~~sW~ev~~Gk 177 (177)
...-.||+.+.|.+.+.++
T Consensus 103 ~~~~~~~~d~~~~~~~~~~~a 123 (450)
T COG1231 103 KRSLTAAADVRGLVAELEAKA 123 (450)
T ss_pred hhccchhhhhcchhhhhhhhh
Confidence 2233578888888887653
No 316
>cd01891 TypA_BipA TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella typhimurium after exposure to bactericidal/permeability-inducing protein (a cationic antimicrobial protein produced by neutrophils), and has since been identified in E. coli as well. The properties thus far described for BipA are related to its role in the process of pathogenesis by enteropathogenic E. coli. It appears to be involved in the regulation of several processes important for infection, including rearrangements of the cytoskeleton of the host, bacterial resistance to host defense peptides, flagellum-mediated cell motility, and expression of K5 capsular genes. It has been proposed that BipA may utilize a novel mechanism to regulate the expression of target genes. In addition, BipA from enteropathogenic E. co
Probab=28.26 E-value=1.2e+02 Score=23.59 Aligned_cols=37 Identities=24% Similarity=0.166 Sum_probs=27.9
Q ss_pred ecceEEEEeCCCc-----hHHHHHHHHHcCccEEEEecCCch
Q 037201 122 RFGCLMVVSDDSN-----FVEVFQEATLRCLKMVVVGDMSDG 158 (177)
Q Consensus 122 ~v~clvLVSDdsd-----f~~~lr~Ar~r~l~TVVVGd~~~~ 158 (177)
+.|++++|-|-++ ...+++.+...+...++|++-.|.
T Consensus 88 ~~d~~ilV~d~~~~~~~~~~~~~~~~~~~~~p~iiv~NK~Dl 129 (194)
T cd01891 88 MVDGVLLLVDASEGPMPQTRFVLKKALELGLKPIVVINKIDR 129 (194)
T ss_pred hcCEEEEEEECCCCccHHHHHHHHHHHHcCCCEEEEEECCCC
Confidence 7789888887554 234567777789999999987764
No 317
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=28.21 E-value=61 Score=23.62 Aligned_cols=34 Identities=15% Similarity=0.287 Sum_probs=27.2
Q ss_pred EeCCCchHHHHHHHHHcCccEEEEecCCchhhhhhh
Q 037201 129 VSDDSNFVEVFQEATLRCLKMVVVGDMSDGALKRIA 164 (177)
Q Consensus 129 VSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~A 164 (177)
..+.+.|..||+.++.....+|||-+.+ -|+|..
T Consensus 48 ~~~R~~~~~ll~~~~~~~~d~ivv~~~~--Rl~R~~ 81 (137)
T cd00338 48 LVDRPGLQRLLADVKAGKIDVVLVEKLD--RLSRNL 81 (137)
T ss_pred ccCCHHHHHHHHHHHcCCCCEEEEEecc--hhhCCH
Confidence 3467889999999998888999999885 566654
No 318
>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=28.17 E-value=1.5e+02 Score=23.25 Aligned_cols=7 Identities=0% Similarity=-0.183 Sum_probs=3.2
Q ss_pred cEEEEEe
Q 037201 115 WFCVRNV 121 (177)
Q Consensus 115 Gv~Vr~V 121 (177)
|+-|-++
T Consensus 79 ~ipvV~i 85 (269)
T cd06275 79 HIPMVVM 85 (269)
T ss_pred CCCEEEE
Confidence 4444444
No 319
>PRK06975 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed
Probab=28.16 E-value=27 Score=34.14 Aligned_cols=59 Identities=24% Similarity=0.234 Sum_probs=41.4
Q ss_pred CCCchHHhhhhcEEEEEe----------------------ecceEEEEeCCCc--hHHHHHHHHHcCccEEEEecCCchh
Q 037201 104 GYGFADELKRAWFCVRNV----------------------RFGCLMVVSDDSN--FVEVFQEATLRCLKMVVVGDMSDGA 159 (177)
Q Consensus 104 gygLa~eLrRAGv~Vr~V----------------------~v~clvLVSDdsd--f~~~lr~Ar~r~l~TVVVGd~~~~~ 159 (177)
+..|+..|+..|..|-.. ..||||.+|-+.- |-+.|+..+..+++..+||..+..+
T Consensus 15 a~~la~~L~~~G~~vi~~Pli~i~p~~~~~~l~~~l~~L~~yd~iIFTS~nAV~~~~~~l~~~~~~~~~i~AVG~~Ta~a 94 (656)
T PRK06975 15 SAALAAQLAAAGLDVLDFPLLDIAPVADDAPLRAALARLSDYALVVFVSPNAVDRALARLDAIWPHALPVAVVGPGSVAA 94 (656)
T ss_pred HHHHHHHHHHcCCCEEEcccEEeeCCCChHHHHHHHHhCCCCCEEEEECHHHHHHHHHHHHhhCccCCeEEEECHHHHHH
Confidence 455677777777766554 6789999997763 3444444444678999999988666
Q ss_pred hhh
Q 037201 160 LKR 162 (177)
Q Consensus 160 L~r 162 (177)
|..
T Consensus 95 L~~ 97 (656)
T PRK06975 95 LAR 97 (656)
T ss_pred HHH
Confidence 654
No 320
>PF14336 DUF4392: Domain of unknown function (DUF4392)
Probab=28.03 E-value=54 Score=28.99 Aligned_cols=24 Identities=17% Similarity=0.216 Sum_probs=22.4
Q ss_pred CCchHHHHHHHHHcCccEEEEecC
Q 037201 132 DSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 132 dsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
-..|-.++..|++.|+.|+.|||+
T Consensus 161 ~a~~D~lf~~a~~~gi~tigIGDG 184 (291)
T PF14336_consen 161 VAPLDDLFLAAKEPGIPTIGIGDG 184 (291)
T ss_pred cccHHHHHHHhhcCCCCEEEECCC
Confidence 678999999999999999999997
No 321
>PRK11133 serB phosphoserine phosphatase; Provisional
Probab=28.01 E-value=1.6e+02 Score=26.25 Aligned_cols=35 Identities=14% Similarity=0.211 Sum_probs=21.6
Q ss_pred HHHHHHHH-HcCc---cEEEEecCC-chhhhhhhccccch
Q 037201 136 VEVFQEAT-LRCL---KMVVVGDMS-DGALKRIANAFFSW 170 (177)
Q Consensus 136 ~~~lr~Ar-~r~l---~TVVVGd~~-~~~L~r~Ad~~~sW 170 (177)
.++|+.+. +-|+ +||+|||+. |-...+.|++.+-|
T Consensus 250 ~~~L~~la~~lgi~~~qtIaVGDg~NDl~m~~~AGlgiA~ 289 (322)
T PRK11133 250 ADTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAY 289 (322)
T ss_pred HHHHHHHHHHcCCChhhEEEEECCHHHHHHHHHCCCeEEe
Confidence 44555554 5665 699999974 23445566666554
No 322
>cd01464 vWA_subfamily VWA subfamily: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=27.92 E-value=1.1e+02 Score=23.71 Aligned_cols=42 Identities=21% Similarity=0.287 Sum_probs=23.7
Q ss_pred ceEEEEeCCCc---hH---HHHHHHHHc--CccEEEEec-CCchhhhhhhc
Q 037201 124 GCLMVVSDDSN---FV---EVFQEATLR--CLKMVVVGD-MSDGALKRIAN 165 (177)
Q Consensus 124 ~clvLVSDdsd---f~---~~lr~Ar~r--~l~TVVVGd-~~~~~L~r~Ad 165 (177)
..+||+||=.+ .. +.++.+.+. .+-+|.||+ .+...|.+.|+
T Consensus 109 ~~iillTDG~~~~~~~~~~~~~~~~~~~~~~i~~igiG~~~~~~~L~~ia~ 159 (176)
T cd01464 109 PWVFLLTDGEPTDDLTAAIERIKEARDSKGRIVACAVGPKADLDTLKQITE 159 (176)
T ss_pred cEEEEEcCCCCCchHHHHHHHHHhhcccCCcEEEEEeccccCHHHHHHHHC
Confidence 46899998433 33 335555543 445666774 33335666665
No 323
>PRK12436 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=27.78 E-value=55 Score=28.97 Aligned_cols=34 Identities=15% Similarity=0.185 Sum_probs=31.4
Q ss_pred cceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 123 FGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 123 v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.+.++...+-.|...+++.|++.++..+++|.++
T Consensus 37 a~~vv~p~~~edv~~~l~~a~~~~ip~~v~GgGS 70 (305)
T PRK12436 37 ADVFVAPTNYDEIQEVIKYANKYNIPVTFLGNGS 70 (305)
T ss_pred EEEEEecCCHHHHHHHHHHHHHcCCCEEEEcCCe
Confidence 6778899999999999999999999999999886
No 324
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=27.68 E-value=23 Score=33.75 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=18.5
Q ss_pred hhhcCCCcCChhHHHHHHHh
Q 037201 49 LIRNQGRFYNNDKLVNHFRQ 68 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kHFkq 68 (177)
|+.||+=|+++++|.-|.+.
T Consensus 210 Cp~Cg~~F~~~tkl~DH~rR 229 (467)
T KOG3608|consen 210 CPHCGELFRTKTKLFDHLRR 229 (467)
T ss_pred cchHHHHhccccHHHHHHHh
Confidence 99999999999999999764
No 325
>cd02769 MopB_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=27.67 E-value=1e+02 Score=29.42 Aligned_cols=47 Identities=4% Similarity=0.094 Sum_probs=34.1
Q ss_pred ecceEEEEeCCCc--------------hHHHHHHHHHcCccEEEEecCCchhhhhhhc-cccc
Q 037201 122 RFGCLMVVSDDSN--------------FVEVFQEATLRCLKMVVVGDMSDGALKRIAN-AFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsd--------------f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad-~~~s 169 (177)
..||||++.-+.- ....|..||++|.+-|||.=.- ......|| .|++
T Consensus 170 ~a~~il~wG~Np~~t~~~~~~~~~~~~~~~~~~~ar~~GaklIvIDPr~-t~tA~~add~~l~ 231 (609)
T cd02769 170 HTELVVAFGADPLKNAQIAWGGIPDHQAYSYLKALKDRGIRFISISPLR-DDTAAELGAEWIA 231 (609)
T ss_pred hCCeEEEECCChHHhCcccccccCCcchHHHHHHHHhCCCEEEEEcCCC-CcchhhhcCcEec
Confidence 5688888876632 2355778999999999997653 56677776 7875
No 326
>TIGR01973 NuoG NADH-quinone oxidoreductase, chain G. This model represents the G subunit (one of 14: A-N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes related subunits from formate dehydrogenase complexes.
Probab=27.59 E-value=89 Score=29.71 Aligned_cols=48 Identities=17% Similarity=0.165 Sum_probs=34.3
Q ss_pred ecceEEEEeCCCc-----hHHHHHHHHHcC-ccEEEEecCCchhhhhhhccccch
Q 037201 122 RFGCLMVVSDDSN-----FVEVFQEATLRC-LKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 122 ~v~clvLVSDdsd-----f~~~lr~Ar~r~-l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
..|+++++..|.. +..-++.|.++| .+.|||+-.. ..+...||.|++-
T Consensus 362 ~ad~il~~G~N~~~s~p~~~~~i~~a~~~ggaklividpr~-s~ta~~Ad~~l~i 415 (603)
T TIGR01973 362 EADLVLLVGADLRQEAPLLNLRLRKAVKKGGAKVALIGIEK-WNLTYPANTNLVF 415 (603)
T ss_pred hCCEEEEEccCchhhhHHHHHHHHHHHhcCCcEEEEECCcc-ccchhhhccceee
Confidence 5788888876642 333456677666 8889998653 6788999998863
No 327
>PRK07239 bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated
Probab=27.46 E-value=84 Score=27.80 Aligned_cols=58 Identities=17% Similarity=0.181 Sum_probs=39.1
Q ss_pred CCCchHHhhhhcEEEEEe------------------------ecceEEEEeCCCchHHHHHHHH-----------HcCcc
Q 037201 104 GYGFADELKRAWFCVRNV------------------------RFGCLMVVSDDSNFVEVFQEAT-----------LRCLK 148 (177)
Q Consensus 104 gygLa~eLrRAGv~Vr~V------------------------~v~clvLVSDdsdf~~~lr~Ar-----------~r~l~ 148 (177)
+..|+..|+..|..|-.+ ..||||+.|-+. ..-+++..+ ..+++
T Consensus 22 a~~la~~L~~~G~~~~~~P~i~i~~~~~~~~~~~~~~~l~~~~~d~vvfTS~ng-v~~~~~~l~~~~~~~~~~~~l~~~~ 100 (381)
T PRK07239 22 AEELAALLERRGARVVHAPALRIVPLADDDELRAATRALIAAPPDIVVATTGIG-FRGWVEAADGWGLADELLEALSSAR 100 (381)
T ss_pred HHHHHHHHHHcCCeEEEecCEEEecCCCcHHHHHHHHHHHcCCCCEEEEeChHH-HHHHHHHHHHcCChHHHHHHHcCCe
Confidence 455677788888777665 358999999766 222222221 36788
Q ss_pred EEEEecCCchhhhh
Q 037201 149 MVVVGDMSDGALKR 162 (177)
Q Consensus 149 TVVVGd~~~~~L~r 162 (177)
.++||..+..+|..
T Consensus 101 i~aVG~~Ta~aL~~ 114 (381)
T PRK07239 101 LLARGPKATGAIRA 114 (381)
T ss_pred EEEECccHHHHHHH
Confidence 99999998776664
No 328
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=27.34 E-value=46 Score=32.46 Aligned_cols=32 Identities=16% Similarity=0.224 Sum_probs=23.9
Q ss_pred hhhhhcCCCcCChhHHHHHHHhhhhhhhhhhhhhh
Q 037201 47 CLLIRNQGRFYNNDKLVNHFRQIHEGEQKKRSNQI 81 (177)
Q Consensus 47 ~Lc~~CGrrf~t~~~L~kHFkqlHerEr~Krl~ri 81 (177)
..|++|...|+|.--|+||=..- .|.+.|+.|
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSK---KHkenv~eL 324 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSK---KHKENVAEL 324 (508)
T ss_pred eEEeeccccccchHHHHhhHHHH---HHHHHHHHH
Confidence 34999999999999999997654 344444444
No 329
>cd01465 vWA_subgroup VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if n
Probab=27.20 E-value=1.4e+02 Score=22.19 Aligned_cols=42 Identities=12% Similarity=0.183 Sum_probs=23.3
Q ss_pred ceEEEEeCCCc------hHHH---HHHHHHcCccEEEEecCC--c-hhhhhhhc
Q 037201 124 GCLMVVSDDSN------FVEV---FQEATLRCLKMVVVGDMS--D-GALKRIAN 165 (177)
Q Consensus 124 ~clvLVSDdsd------f~~~---lr~Ar~r~l~TVVVGd~~--~-~~L~r~Ad 165 (177)
..|||+||=.+ +.++ ++.++..++...+||-+. + ..|++.|+
T Consensus 98 ~~ivl~TDG~~~~~~~~~~~~~~~~~~~~~~~v~i~~i~~g~~~~~~~l~~ia~ 151 (170)
T cd01465 98 NRILLATDGDFNVGETDPDELARLVAQKRESGITLSTLGFGDNYNEDLMEAIAD 151 (170)
T ss_pred eEEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCeEEEEEEeCCCcCHHHHHHHHh
Confidence 45889988642 3433 444455666665555542 1 34655554
No 330
>cd04630 CBS_pair_17 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=26.75 E-value=1.1e+02 Score=21.03 Aligned_cols=31 Identities=13% Similarity=0.138 Sum_probs=23.8
Q ss_pred EEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 126 LMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 126 lvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
++.++.+..+.++++..++.+.+.++|.|.+
T Consensus 3 ~~~v~~~~~~~~~~~~~~~~~~~~~~V~~~~ 33 (114)
T cd04630 3 VVTIDGLATVAEALQLMKEHGVSSLVVEKRR 33 (114)
T ss_pred cEEECCCCcHHHHHHHHHHcCCCEEEEEECC
Confidence 3467777788888888888888888887754
No 331
>PRK09484 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase; Provisional
Probab=26.56 E-value=1.2e+02 Score=24.19 Aligned_cols=38 Identities=21% Similarity=0.149 Sum_probs=17.6
Q ss_pred EEEEeCCCchHHHHHHHHHcCccEEEEecCCchhhhhhhcccc
Q 037201 126 LMVVSDDSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFF 168 (177)
Q Consensus 126 lvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~ 168 (177)
++.|-|+.. | +..|+..|+. ++|+|.. ..++..||.-+
T Consensus 115 v~~VGDs~~--D-~~~a~~aG~~-~~v~~~~-~~~~~~a~~v~ 152 (183)
T PRK09484 115 VAYIGDDLI--D-WPVMEKVGLS-VAVADAH-PLLLPRADYVT 152 (183)
T ss_pred EEEECCCHH--H-HHHHHHCCCe-EecCChh-HHHHHhCCEEe
Confidence 455555531 1 2344445555 3455542 33445555555
No 332
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=26.54 E-value=44 Score=33.10 Aligned_cols=33 Identities=18% Similarity=0.331 Sum_probs=27.6
Q ss_pred hhhhcCCCcCChhHHHHHHHhhhhhhhhhhhhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIHEGEQKKRSNQI 81 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlHerEr~Krl~ri 81 (177)
.|-.||.||...+...+|. ++|-..|-+.=-++
T Consensus 420 qC~~CG~R~~~~ee~sk~m-d~H~dwh~r~n~~~ 452 (579)
T KOG2071|consen 420 QCKSCGLRFDDSEERSKHM-DIHDDWHRRKNTTI 452 (579)
T ss_pred hhcccccccccchhhhhHh-hhhhhhhhhhhhhc
Confidence 4999999999999999997 58998887655444
No 333
>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.
Probab=26.50 E-value=1.1e+02 Score=23.10 Aligned_cols=41 Identities=24% Similarity=0.320 Sum_probs=25.8
Q ss_pred eEEEEeCCCchHH---HHHHHHHcCccEEEEecC--Cchhhhhhhc
Q 037201 125 CLMVVSDDSNFVE---VFQEATLRCLKMVVVGDM--SDGALKRIAN 165 (177)
Q Consensus 125 clvLVSDdsdf~~---~lr~Ar~r~l~TVVVGd~--~~~~L~r~Ad 165 (177)
-+||+||-..-.+ .....++.|+...+||-+ ....|.+.|+
T Consensus 106 ~iiliTDG~~~~~~~~~~~~l~~~gv~i~~ig~g~~~~~~L~~ia~ 151 (164)
T cd01472 106 VLVVITDGKSQDDVEEPAVELKQAGIEVFAVGVKNADEEELKQIAS 151 (164)
T ss_pred EEEEEcCCCCCchHHHHHHHHHHCCCEEEEEECCcCCHHHHHHHHC
Confidence 4788888755433 344566788888877654 3345666554
No 334
>PF13242 Hydrolase_like: HAD-hyrolase-like; PDB: 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A 2HX1_D 2X4D_A 3HLT_C 3L1U_B ....
Probab=26.50 E-value=75 Score=21.55 Aligned_cols=29 Identities=14% Similarity=0.117 Sum_probs=19.3
Q ss_pred EEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 126 LMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 126 lvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.+.|.|+ -.+| ++.|++.|+.||.|..+.
T Consensus 24 ~~~VGD~-~~~D-i~~a~~~G~~~ilV~tG~ 52 (75)
T PF13242_consen 24 CVMVGDS-LETD-IEAAKAAGIDTILVLTGV 52 (75)
T ss_dssp EEEEESS-TTTH-HHHHHHTTSEEEEESSSS
T ss_pred EEEEcCC-cHhH-HHHHHHcCCcEEEECCCC
Confidence 5566665 1222 467888899999887754
No 335
>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=26.32 E-value=1.2e+02 Score=23.87 Aligned_cols=31 Identities=6% Similarity=0.068 Sum_probs=22.5
Q ss_pred eEEEEeCCCc---hHHHHHHHHHcCccEEEEecC
Q 037201 125 CLMVVSDDSN---FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 125 clvLVSDdsd---f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|||++|-.. .....+.+|..|+..++||.+
T Consensus 109 v~vviTdG~s~d~~~~~a~~lr~~gv~i~~vG~~ 142 (165)
T cd01481 109 FLVLITGGKSQDDVERPAVALKRAGIVPFAIGAR 142 (165)
T ss_pred EEEEEeCCCCcchHHHHHHHHHHCCcEEEEEeCC
Confidence 4677777544 444556667899999999987
No 336
>COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]
Probab=26.32 E-value=1.3e+02 Score=25.93 Aligned_cols=63 Identities=16% Similarity=0.184 Sum_probs=47.3
Q ss_pred chHHhhhhcEEEEEe--------------ecceEEEEeCCC---chHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 107 FADELKRAWFCVRNV--------------RFGCLMVVSDDS---NFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 107 La~eLrRAGv~Vr~V--------------~v~clvLVSDds---df~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
+|.-|-.-|..+=-| .-|.||+.|-.= ....++..|++.|.+-|-|=-.-+..|++.||+-+.
T Consensus 57 ~Aa~L~s~G~~a~fv~p~ea~hgdlg~i~~~DvviaiS~SGeT~el~~~~~~aK~~g~~liaiT~~~~SsLak~aDvvl~ 136 (202)
T COG0794 57 FAARLASTGTPAFFVGPAEALHGDLGMITPGDVVIAISGSGETKELLNLAPKAKRLGAKLIAITSNPDSSLAKAADVVLV 136 (202)
T ss_pred HHHHHHccCCceEEecCchhccCCccCCCCCCEEEEEeCCCcHHHHHHHHHHHHHcCCcEEEEeCCCCChHHHhcCeEEE
Confidence 455555566555555 578999999764 455667778889999888877778899999998764
No 337
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=26.27 E-value=18 Score=29.69 Aligned_cols=18 Identities=11% Similarity=0.027 Sum_probs=15.2
Q ss_pred hhhhhcCCCcCChhHHHH
Q 037201 47 CLLIRNQGRFYNNDKLVN 64 (177)
Q Consensus 47 ~Lc~~CGrrf~t~~~L~k 64 (177)
.-|+.||++|.|.+++.+
T Consensus 29 ~~c~~c~~~f~~~e~~~~ 46 (154)
T PRK00464 29 RECLACGKRFTTFERVEL 46 (154)
T ss_pred eeccccCCcceEeEeccC
Confidence 459999999999988754
No 338
>PF11814 DUF3335: Peptidase_C39 like family; InterPro: IPR021770 This family of proteins are functionally uncharacterised. This family is only found in bacteria. This presumed domain is typically between 226 to 230 amino acids in length.
Probab=26.19 E-value=46 Score=28.83 Aligned_cols=34 Identities=21% Similarity=0.232 Sum_probs=23.4
Q ss_pred hHHHHHHHHhhcCC---C-CCCCchHHhhhhcEEEEEe
Q 037201 88 MEKYKMAVSAILTP---K-VGYGFADELKRAWFCVRNV 121 (177)
Q Consensus 88 ~~KY~~Aar~vl~p---k-vgygLa~eLrRAGv~Vr~V 121 (177)
++-+++|..=..|- - -+||||-...|.|+.|+..
T Consensus 36 L~lWREATTifmtsGhGGC~P~GLAlAA~rrG~~vev~ 73 (207)
T PF11814_consen 36 LRLWREATTIFMTSGHGGCGPFGLALAAARRGFKVEVW 73 (207)
T ss_pred HHHHHHhceecccCCCCCcChHHHHHHHHHcCCceEEE
Confidence 34555554433331 1 3799999999999999877
No 339
>COG0569 TrkA K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]
Probab=26.12 E-value=80 Score=26.44 Aligned_cols=53 Identities=25% Similarity=0.300 Sum_probs=33.7
Q ss_pred CCCCCchHHhhhhcEEEEEe-----------e--cceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 102 KVGYGFADELKRAWFCVRNV-----------R--FGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 102 kvgygLa~eLrRAGv~Vr~V-----------~--v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.+|+.+|..|-+.|..|-.+ . .++.+.+.|.+| .++|++|=-.+..+||+-=+
T Consensus 10 ~vG~~va~~L~~~g~~Vv~Id~d~~~~~~~~~~~~~~~~v~gd~t~-~~~L~~agi~~aD~vva~t~ 75 (225)
T COG0569 10 RVGRSVARELSEEGHNVVLIDRDEERVEEFLADELDTHVVIGDATD-EDVLEEAGIDDADAVVAATG 75 (225)
T ss_pred HHHHHHHHHHHhCCCceEEEEcCHHHHHHHhhhhcceEEEEecCCC-HHHHHhcCCCcCCEEEEeeC
Confidence 35888888888888888777 2 555665555555 34555555555555554433
No 340
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=26.11 E-value=27 Score=25.39 Aligned_cols=24 Identities=17% Similarity=0.152 Sum_probs=21.8
Q ss_pred hhhcCCCcCChhHHHHHHHhhhhh
Q 037201 49 LIRNQGRFYNNDKLVNHFRQIHEG 72 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kHFkqlHer 72 (177)
|+.||--|+...+..+|--.-|-.
T Consensus 20 CPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 20 CPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred CCchhHHHHHhHHHHHHhhHHhhh
Confidence 999999999999999998877754
No 341
>cd06379 PBP1_iGluR_NMDA_NR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore
Probab=25.99 E-value=92 Score=26.83 Aligned_cols=27 Identities=4% Similarity=0.235 Sum_probs=18.2
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCcc
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLK 148 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~ 148 (177)
+.+.+++.+...+...+++.|++.|+.
T Consensus 213 ~~~vIvl~~~~~~~~~l~~qa~~~g~~ 239 (377)
T cd06379 213 TSRVILLSASEDDAAVIYRNAGMLNMT 239 (377)
T ss_pred CCeEEEEEcCHHHHHHHHHHHHHcCCC
Confidence 566666667777777777777766663
No 342
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=25.98 E-value=1e+02 Score=24.56 Aligned_cols=47 Identities=21% Similarity=0.249 Sum_probs=31.6
Q ss_pred hHHhhhhcEEEEEe----------------ecceEEEEe-----CCCchHHHHHHHHHcCc--cEEEEecC
Q 037201 108 ADELKRAWFCVRNV----------------RFGCLMVVS-----DDSNFVEVFQEATLRCL--KMVVVGDM 155 (177)
Q Consensus 108 a~eLrRAGv~Vr~V----------------~v~clvLVS-----Ddsdf~~~lr~Ar~r~l--~TVVVGd~ 155 (177)
+..|+.+||.|-.. ++|. |.+| -...|.++++..+++|+ ..|+||..
T Consensus 22 ~~~l~~~GfeVi~LG~~v~~e~~v~aa~~~~adi-VglS~l~~~~~~~~~~~~~~l~~~gl~~~~vivGG~ 91 (134)
T TIGR01501 22 DHAFTNAGFNVVNLGVLSPQEEFIKAAIETKADA-ILVSSLYGHGEIDCKGLRQKCDEAGLEGILLYVGGN 91 (134)
T ss_pred HHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCE-EEEecccccCHHHHHHHHHHHHHCCCCCCEEEecCC
Confidence 66789999999877 3332 2333 34458888888888887 33556763
No 343
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=25.98 E-value=71 Score=29.31 Aligned_cols=49 Identities=12% Similarity=0.152 Sum_probs=39.0
Q ss_pred ecceEEEEeCC--Cch-HHHHHHHHHcCccEEEEecCCchhhhhhhccccch
Q 037201 122 RFGCLMVVSDD--SNF-VEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSW 170 (177)
Q Consensus 122 ~v~clvLVSDd--sdf-~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW 170 (177)
.-||||=++.. .-| -+-|+.||++|..||-|....+..+.+.||+.++=
T Consensus 129 ~~DvvvgIaASGrTPYvigal~yAr~~Ga~Ti~iacNp~s~i~~~Ad~~I~~ 180 (298)
T COG2103 129 AKDVVVGIAASGRTPYVIGALEYARQRGATTIGIACNPGSAISRIADIAIEP 180 (298)
T ss_pred cCCEEEEEecCCCCchhhHHHHHHHhcCCeEEEeecCCCchhhhhcCcceee
Confidence 34666665543 333 47899999999999999999889999999998753
No 344
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=25.95 E-value=25 Score=29.52 Aligned_cols=18 Identities=11% Similarity=0.099 Sum_probs=14.0
Q ss_pred hhhhhhhcCCCcCChhHH
Q 037201 45 ENCLLIRNQGRFYNNDKL 62 (177)
Q Consensus 45 r~~Lc~~CGrrf~t~~~L 62 (177)
|..-|..||.||.|.+..
T Consensus 27 RRReC~~C~~RFTTfE~~ 44 (156)
T COG1327 27 RRRECLECGERFTTFERA 44 (156)
T ss_pred hhhcccccccccchhhee
Confidence 444599999999997653
No 345
>cd06358 PBP1_NHase Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides. This group includes the type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and characterized. In Rhodococcus sp., the nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit, and NHase activator. The operon produces a constitutive hydratase that has a broad substrate spectrum: aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles, and a constitutive amidase of equally low substrate specificity. NHases are metalloenzymes containing either cobalt or iron, and therefore can be classified int
Probab=25.85 E-value=1.2e+02 Score=25.44 Aligned_cols=28 Identities=7% Similarity=-0.022 Sum_probs=24.2
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccE
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKM 149 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~T 149 (177)
+.|.|++.....+.+.+++.+++.|+..
T Consensus 187 ~pd~v~~~~~~~~~~~~~~~~~~~G~~~ 214 (333)
T cd06358 187 GADAVLSTLVGQDAVAFNRQFAAAGLRD 214 (333)
T ss_pred CCCEEEEeCCCCchHHHHHHHHHcCCCc
Confidence 6788888888889999999999998874
No 346
>cd06364 PBP1_CaSR Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. CaSR provides feedback control of extracellular calcium homeostasis by responding sensitively to acute fluctuations in extracellular ionized Ca2+ concentration. This ligand-binding domain has homology to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). CaSR is widely expressed in mammalian tissues and is active in tissues that are not directly involved in extracellular calcium homeostasis. Moreover, CaSR responds to aromatic, aliphatic, and polar amino acids, but not to positively charged or branched chain amino acids, which suggests that changes in plasma amino acid levels are likely to modulate whole body calci
Probab=25.79 E-value=1.6e+02 Score=27.34 Aligned_cols=27 Identities=15% Similarity=0.249 Sum_probs=20.3
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCcc
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLK 148 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~ 148 (177)
+.+.||+.+...+...+++.|++.|+.
T Consensus 244 ~a~vVvl~~~~~~~~~ll~qa~~~g~~ 270 (510)
T cd06364 244 TAKVIVVFSSGPDLEPLIKEIVRRNIT 270 (510)
T ss_pred CCeEEEEEeCcHHHHHHHHHHHHhCCC
Confidence 567777777777777888887777774
No 347
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=25.64 E-value=22 Score=29.89 Aligned_cols=13 Identities=8% Similarity=-0.146 Sum_probs=10.1
Q ss_pred hhhhhcCCCcCCh
Q 037201 47 CLLIRNQGRFYNN 59 (177)
Q Consensus 47 ~Lc~~CGrrf~t~ 59 (177)
.-||+||..|+|.
T Consensus 6 ~~CPvC~~~F~~~ 18 (214)
T PF09986_consen 6 ITCPVCGKEFKTK 18 (214)
T ss_pred eECCCCCCeeeee
Confidence 4499999988765
No 348
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=25.61 E-value=47 Score=25.14 Aligned_cols=22 Identities=23% Similarity=0.459 Sum_probs=18.7
Q ss_pred ecceEEEEeCCCchHHHHHHHH
Q 037201 122 RFGCLMVVSDDSNFVEVFQEAT 143 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar 143 (177)
..|.|+-|+||.|+..|+.+--
T Consensus 62 dld~Lisv~~DeDl~~M~~e~~ 83 (97)
T cd06410 62 DLDALISVSNDEDLKNMMEEYD 83 (97)
T ss_pred CcceeEEecCcHHHHHHHHhhc
Confidence 5578999999999999998743
No 349
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=25.00 E-value=1.4e+02 Score=26.30 Aligned_cols=43 Identities=19% Similarity=0.156 Sum_probs=29.5
Q ss_pred HHhhhhcEEEEEeecceEEEE-eCCCchHHHHHHHHHcCccEEEEec
Q 037201 109 DELKRAWFCVRNVRFGCLMVV-SDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 109 ~eLrRAGv~Vr~V~v~clvLV-SDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
..|+++|+.|.+ .+.+.- .+..++.++++.+.+.|+..+.|.-
T Consensus 156 ~~l~~~G~~v~v---~~tv~~~~n~~ei~~~~~~~~~lGv~~i~i~p 199 (318)
T TIGR03470 156 REAKARGFRVTT---NTTLFNDTDPEEVAEFFDYLTDLGVDGMTISP 199 (318)
T ss_pred HHHHHCCCcEEE---EEEEeCCCCHHHHHHHHHHHHHcCCCEEEEec
Confidence 567778876543 332221 2346788899999999999998853
No 350
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.88 E-value=36 Score=22.90 Aligned_cols=21 Identities=10% Similarity=0.017 Sum_probs=15.9
Q ss_pred hhhhcCCCcCChhHHHHHHHh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQ 68 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkq 68 (177)
.|++|||-|.-+.+..+-..+
T Consensus 10 ~C~~C~rpf~WRKKW~~~Wd~ 30 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWARCWDE 30 (42)
T ss_pred cCcccCCcchHHHHHHHhchh
Confidence 499999999888776654443
No 351
>smart00327 VWA von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
Probab=24.86 E-value=1.4e+02 Score=21.74 Aligned_cols=33 Identities=21% Similarity=0.367 Sum_probs=24.3
Q ss_pred ceEEEEeCC-----CchHHHHHHHHHcCccEEEEecCC
Q 037201 124 GCLMVVSDD-----SNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 124 ~clvLVSDd-----sdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
..|+++||- .+..+.++.+++.++.-+.||-+.
T Consensus 107 ~~iviitDg~~~~~~~~~~~~~~~~~~~i~i~~i~~~~ 144 (177)
T smart00327 107 KVLILITDGESNDGGDLLKAAKELKRSGVKVFVVGVGN 144 (177)
T ss_pred eEEEEEcCCCCCCCccHHHHHHHHHHCCCEEEEEEccC
Confidence 468888876 356778888888877777776653
No 352
>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=24.78 E-value=1.7e+02 Score=22.99 Aligned_cols=31 Identities=19% Similarity=0.293 Sum_probs=14.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
++|-+++++.+.+- +.++..+ .++..|++|.
T Consensus 55 ~~dgiii~~~~~~~-~~~~~~~-~~iPvV~i~~ 85 (265)
T cd06290 55 RVDALILLGGDLPE-EEILALA-EEIPVLAVGR 85 (265)
T ss_pred CCCEEEEeCCCCCh-HHHHHHh-cCCCEEEECC
Confidence 56666666543222 2222222 3566666654
No 353
>cd06371 PBP1_sensory_GC_DEF_like Ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. This group includes the ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. They share a similar topology with an N-terminal extracellular ligand-binding domain, a single transmembrane domain, and a C-terminal cytosolic region that contains kinase-like and catalytic domains. GC-D is specifically expressed in a subpopulation of olfactory sensory neurons. GC-E and GC-F are colocalized within the same photoreceptor cells of the retina and have important roles in phototransduction. Unlike the other family members, GC-E and GC-F have no known extracellular ligands. Instead, they are activated under low calcium conditions by guanylyl cyclase activating proteins called GCAPs. GC-D expressing neurons have been implicated in pheromone detection and GC-D is phyloge
Probab=24.70 E-value=1.4e+02 Score=26.08 Aligned_cols=26 Identities=4% Similarity=0.017 Sum_probs=15.9
Q ss_pred cceEEEEeCC-----CchHHHHHHHHHcCcc
Q 037201 123 FGCLMVVSDD-----SNFVEVFQEATLRCLK 148 (177)
Q Consensus 123 v~clvLVSDd-----sdf~~~lr~Ar~r~l~ 148 (177)
.+.|++.++. .+-..+++.|++.|+.
T Consensus 189 ~~viv~~~~~~~~~~~~~~~i~~qa~~~Gm~ 219 (382)
T cd06371 189 VRVVIMCMHSVLIGGEEQRLLLETALEMGMT 219 (382)
T ss_pred cEEEEEEeeccccCcHHHHHHHHHHHHcCCc
Confidence 3555554443 2336777778887777
No 354
>TIGR01116 ATPase-IIA1_Ca sarco/endoplasmic reticulum calcium-translocating P-type ATPase. The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1, the latter of which is modelled by TIGR01522.
Probab=24.69 E-value=1.4e+02 Score=30.24 Aligned_cols=36 Identities=14% Similarity=0.085 Sum_probs=26.0
Q ss_pred HHHHHHHHHcCccEEEEecC-Cchhhhhhhccccchh
Q 037201 136 VEVFQEATLRCLKMVVVGDM-SDGALKRIANAFFSWS 171 (177)
Q Consensus 136 ~~~lr~Ar~r~l~TVVVGd~-~~~~L~r~Ad~~~sW~ 171 (177)
..+++.-++.|-.+..+||+ +|-.--+.||+.++|.
T Consensus 620 ~~iV~~lq~~g~~va~iGDG~ND~~alk~AdVGia~g 656 (917)
T TIGR01116 620 SELVELLQEQGEIVAMTGDGVNDAPALKKADIGIAMG 656 (917)
T ss_pred HHHHHHHHhcCCeEEEecCCcchHHHHHhCCeeEECC
Confidence 34455556677777779994 4556668999999984
No 355
>PRK13905 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=24.67 E-value=70 Score=27.86 Aligned_cols=34 Identities=18% Similarity=0.194 Sum_probs=29.6
Q ss_pred cceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 123 FGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 123 v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
.++++...+-.|+..+++.|++.++..+++|.++
T Consensus 31 a~~vv~P~s~edv~~~v~~a~~~~~p~~v~GgGs 64 (298)
T PRK13905 31 ADYLVEPADIEDLQEFLKLLKENNIPVTVLGNGS 64 (298)
T ss_pred EeEEEeCCCHHHHHHHHHHHHHcCCCEEEEeCCc
Confidence 4567778899999999999999999999999876
No 356
>cd00287 ribokinase_pfkB_like ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase).
Probab=24.50 E-value=1.2e+02 Score=22.99 Aligned_cols=48 Identities=19% Similarity=0.193 Sum_probs=36.0
Q ss_pred CCCchHHhhhhcEEEEEeecceEEEEeCC---CchHHHHHHHHHcCccEEE
Q 037201 104 GYGFADELKRAWFCVRNVRFGCLMVVSDD---SNFVEVFQEATLRCLKMVV 151 (177)
Q Consensus 104 gygLa~eLrRAGv~Vr~V~v~clvLVSDd---sdf~~~lr~Ar~r~l~TVV 151 (177)
|...|--|.+-|..+..++.|++++=..- ..+..+++.|++.|...++
T Consensus 39 ~~n~a~~l~~LG~~~~~~~~~~v~i~~~~~~~~~~~~~~~~~~~~~~~v~~ 89 (196)
T cd00287 39 AANVAVALARLGVSVTLVGADAVVISGLSPAPEAVLDALEEARRRGVPVVL 89 (196)
T ss_pred HHHHHHHHHHCCCcEEEEEccEEEEecccCcHHHHHHHHHHHHHcCCeEEE
Confidence 45567889999999999998876665444 3577889999988776433
No 357
>cd06328 PBP1_SBP_like_2 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=24.48 E-value=1.6e+02 Score=24.85 Aligned_cols=32 Identities=9% Similarity=-0.004 Sum_probs=20.5
Q ss_pred ecceEEEEeCCC-chHHHHHHHHHcCcc-EEEEe
Q 037201 122 RFGCLMVVSDDS-NFVEVFQEATLRCLK-MVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDds-df~~~lr~Ar~r~l~-TVVVG 153 (177)
+.|.|+++.... +|..+++.+++.|+. ++++|
T Consensus 191 ~pd~V~~~~~~~~~~~~~~~~~~~~g~~~~~~~~ 224 (333)
T cd06328 191 LKKVLFVIWAGAGGPWPKLQQMGVLGYGIEITLA 224 (333)
T ss_pred CCCEEEEEecCchhHHHHHHHhhhhcCCCeEEec
Confidence 567666664444 677788888777766 44444
No 358
>PF01661 Macro: Macro domain; InterPro: IPR002589 The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose, an NAD metabolite or related ligands. Binding to ADP-ribose could be either covalent or non-covalent []: in certain cases it is believed to bind non-covalently []; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein []. The domain was described originally in association with ADP-ribose 1''-phosphate (Appr-1''-P) processing activity (A1pp) of the yeast YBR022W protein []. The domain is also called Macro domain as it is the C-terminal domain of mammalian core histone macro-H2A [, ]. Macro domain proteins can be found in eukaryotes, in (mostly pathogenic) bacteria, in archaea and in ssRNA viruses, such as coronaviruses, Rubella and Hepatitis E viruses. In vertebrates the domain occurs e.g. in histone macroH2A, in predicted poly-ADP-ribose polymerases (PARPs) and in B aggressive lymphoma (BAL) protein. The macro domain can be associated with catalytic domains, such as PARP, or sirtuin. The Macro domain can recognise ADP-ribose or in some cases poly-ADP-ribose, which can be involved in ADP-ribosylation reactions that occur in important processes, such as chromatin biology, DNA repair and transcription regulation []. The human macroH2A1.1 Macro domain binds an NAD metabolite O-acetyl-ADP-ribose []. The Macro domain has been suggested to play a regulatory role in ADP-ribosylation, which is involved in inter- and intracellular signaling, transcriptional regulation, DNA repair pathways and maintenance of genomic stability, telomere dynamics, cell differentiation and proliferation, and necrosis and apoptosis. The 3D structure of the Macro domain has a mixed alpha/beta fold of a mixed beta sheet sandwiched between four helices. Several Macro domain only domains are shorter than the structure of AF1521 and lack either the first strand or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [, , , ]. ; PDB: 2DX6_A 2XD7_D 3Q71_A 2FAV_B 1SPV_A 3EKE_A 3EJF_A 1YD9_B 3GPG_B 3GPQ_A ....
Probab=24.48 E-value=1.4e+02 Score=21.07 Aligned_cols=34 Identities=18% Similarity=0.425 Sum_probs=25.0
Q ss_pred hHHHHHHHHHcCccEEEEecCCchhhhhhhccccchhhhh
Q 037201 135 FVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFSWSDLL 174 (177)
Q Consensus 135 f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~sW~ev~ 174 (177)
|..+|+.|.+.++++|.+=-..-|. ..+||++++
T Consensus 82 ~~~~l~~a~~~~~~sIa~P~ig~G~------~g~~~~~~a 115 (118)
T PF01661_consen 82 YRNALQKAEENGIKSIAFPAIGTGI------GGFPWDEVA 115 (118)
T ss_dssp HHHHHHHHHHTTTSEEEEESTTSST------TSBTHHHHH
T ss_pred HHHHHHHHHHcCCcccccCcccCCC------CCCCHHHHH
Confidence 6678899999999999986543221 357888875
No 359
>cd01425 RPS2 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane an
Probab=24.38 E-value=1.4e+02 Score=24.60 Aligned_cols=35 Identities=20% Similarity=0.267 Sum_probs=29.4
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
...-+|+|.|...=..++++|...|+-||-+.|++
T Consensus 126 ~~Pdlviv~~~~~~~~ai~Ea~~l~IP~I~i~Dtn 160 (193)
T cd01425 126 RLPDLVIVLDPRKEHQAIREASKLGIPVIAIVDTN 160 (193)
T ss_pred cCCCEEEEeCCccchHHHHHHHHcCCCEEEEecCC
Confidence 45556677777777999999999999999999985
No 360
>TIGR01490 HAD-SF-IB-hyp1 HAD-superfamily subfamily IB hydrolase, TIGR01490. A subset of these sequences, including the Caulobacter crescentus CicA protein, cluster together and may represent a separate equivalog.
Probab=24.36 E-value=3.4e+02 Score=20.98 Aligned_cols=50 Identities=14% Similarity=-0.027 Sum_probs=24.8
Q ss_pred hhhhhhhhhhhhhcc-chHHHHHH----HHhhcCCCCCCCchH---HhhhhcEEEEEe
Q 037201 72 GEQKKRSNQIESARG-KMEKYKMA----VSAILTPKVGYGFAD---ELKRAWFCVRNV 121 (177)
Q Consensus 72 rEr~Krl~ri~s~kG-K~~KY~~A----ar~vl~pkvgygLa~---eLrRAGv~Vr~V 121 (177)
....++.-....++| +.+.-+.. ..+.+.++.--|... .|++.|+.|-.+
T Consensus 52 ~~~~~~~~~~~~~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~v~iv 109 (202)
T TIGR01490 52 YMAYYRAFALDALAGLLEEDVRAIVEEFVNQKIESILYPEARDLIRWHKAEGHTIVLV 109 (202)
T ss_pred hHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHCCCEEEEE
Confidence 444555444556788 22222222 233344444334333 346778877666
No 361
>PRK09189 uroporphyrinogen-III synthase; Validated
Probab=24.24 E-value=1.4e+02 Score=24.50 Aligned_cols=56 Identities=20% Similarity=0.185 Sum_probs=37.0
Q ss_pred CCchHHhhhhcEEEEEe----------------------ecceEEEEeCCCchHHHHHHHHH-------cCccEEEEecC
Q 037201 105 YGFADELKRAWFCVRNV----------------------RFGCLMVVSDDSNFVEVFQEATL-------RCLKMVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V----------------------~v~clvLVSDdsdf~~~lr~Ar~-------r~l~TVVVGd~ 155 (177)
..|+..|+..|+.|..+ ++|++++-|-.+ ...+++.... .+.+-|+||..
T Consensus 131 ~~l~~~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~l~~~~~d~i~f~S~~~-~~~f~~~~~~~~~~~~l~~~~~v~Ig~~ 209 (240)
T PRK09189 131 PVFEDRLAAAGIPFRVAECYDMLPVMYSPATLSAILGGAPFDAVLLYSRVA-ARRFFALMRLSIAPPADEKTRFLCLSAR 209 (240)
T ss_pred chhHHHHHhCCCeeEEEEEEEeecCCCChHHHHHHHhcCCCCEEEEeCHHH-HHHHHHHHhhhcCcccccccCeEEeCHH
Confidence 35889999999888876 578888888543 4444444321 35567888886
Q ss_pred Cchhhh
Q 037201 156 SDGALK 161 (177)
Q Consensus 156 ~~~~L~ 161 (177)
...++.
T Consensus 210 ta~al~ 215 (240)
T PRK09189 210 VAAALP 215 (240)
T ss_pred HHHHHh
Confidence 544443
No 362
>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A ....
Probab=24.23 E-value=1e+02 Score=22.23 Aligned_cols=14 Identities=21% Similarity=0.059 Sum_probs=9.2
Q ss_pred hHHhhhhcEEEEEe
Q 037201 108 ADELKRAWFCVRNV 121 (177)
Q Consensus 108 a~eLrRAGv~Vr~V 121 (177)
-.+|+..|+.+=.+
T Consensus 86 L~~l~~~~~~~~i~ 99 (176)
T PF13419_consen 86 LERLKAKGIPLVIV 99 (176)
T ss_dssp HHHHHHTTSEEEEE
T ss_pred hhhcccccceeEEe
Confidence 34567677777666
No 363
>TIGR00542 hxl6Piso_put hexulose-6-phosphate isomerase, putative. This family is conserved at better than 40 % identity among the four known examples from three species: Escherichia coli (SgbU and SgaU), Haemophilus influenzae, and Mycoplasma pneumoniae. The rarity of the family, high level of conservation, and proposed catabolic role suggests lateral transfer may be a part of the evolutionary history of this protein.
Probab=24.21 E-value=67 Score=26.79 Aligned_cols=49 Identities=8% Similarity=0.089 Sum_probs=35.2
Q ss_pred chHHhhhhcEEEEEeecce---EEEEeCCC--------chHHHHHHHHHcCccEEEEecC
Q 037201 107 FADELKRAWFCVRNVRFGC---LMVVSDDS--------NFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 107 La~eLrRAGv~Vr~V~v~c---lvLVSDds--------df~~~lr~Ar~r~l~TVVVGd~ 155 (177)
+...|+++|+.|-.+...+ .-+.+.|+ .+...++.|.+-|.++|+++..
T Consensus 57 ~~~~l~~~gl~i~~~~~~~~~~~~l~~~~~~~r~~~~~~~~~~i~~a~~lG~~~v~~~~~ 116 (279)
T TIGR00542 57 LVNAIIETGVRIPSMCLSAHRRFPLGSKDKAVRQQGLEIMEKAIQLARDLGIRTIQLAGY 116 (279)
T ss_pred HHHHHHHcCCCceeeecCCCccCcCCCcCHHHHHHHHHHHHHHHHHHHHhCCCEEEecCc
Confidence 4566888899887664333 23455455 3788999999999999999753
No 364
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=24.16 E-value=1.2e+02 Score=24.22 Aligned_cols=33 Identities=12% Similarity=0.099 Sum_probs=25.3
Q ss_pred ecceEEEEeCCCc-hHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSN-FVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd 154 (177)
++|-|++++.+.+ +.++++.+.+.|+..|+++.
T Consensus 58 ~vdgiii~~~~~~~~~~~i~~~~~~~ipvV~~~~ 91 (275)
T cd06307 58 RSDGVALVAPDHPQVRAAVARLAAAGVPVVTLVS 91 (275)
T ss_pred cCCEEEEeCCCcHHHHHHHHHHHHCCCcEEEEeC
Confidence 6788888876543 46788888888888888864
No 365
>TIGR01489 DKMTPPase-SF 2,3-diketo-5-methylthio-1-phosphopentane phosphatase. Note that SP|P53981 from S. cerevisiae, a member of this family, is annotated as a "probable membrane protein" due to a predicted transmembrane helix. The region in question contains the second of the three conserved HAD superfamily catalytic motifs and thus, considering the fold of the HAD catalytic domain, is unlikely to be a transmembrane region in fact.
Probab=24.04 E-value=89 Score=23.54 Aligned_cols=32 Identities=16% Similarity=0.342 Sum_probs=22.7
Q ss_pred HHHHHHHHc-CccEEEEecCC-chhhhhhhcccc
Q 037201 137 EVFQEATLR-CLKMVVVGDMS-DGALKRIANAFF 168 (177)
Q Consensus 137 ~~lr~Ar~r-~l~TVVVGd~~-~~~L~r~Ad~~~ 168 (177)
.+++...+. .-++|.|||+. |-.-.+.||+-|
T Consensus 152 ~~~~~~~~~~~~~~i~iGD~~~D~~aa~~~d~~~ 185 (188)
T TIGR01489 152 KVIHKLSEPKYQHIIYIGDGVTDVCPAKLSDVVF 185 (188)
T ss_pred HHHHHHHhhcCceEEEECCCcchhchHhcCCccc
Confidence 477777766 78899999964 335566677755
No 366
>cd06367 PBP1_iGluR_NMDA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits
Probab=24.04 E-value=1.4e+02 Score=25.33 Aligned_cols=35 Identities=14% Similarity=0.312 Sum_probs=22.5
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCcc----EEEEecCC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLK----MVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~----TVVVGd~~ 156 (177)
+.+.+|+.++..+-..+++.|++.|+. ..+++|..
T Consensus 194 ~~~vivl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~ 232 (362)
T cd06367 194 ESRVILLYCSKEEAERIFEAAASLGLTGPGYVWIVGELA 232 (362)
T ss_pred CCcEEEEeCCHHHHHHHHHHHHHcCCCCCCcEEEECccc
Confidence 456667777777777777777777663 44555543
No 367
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=23.67 E-value=2e+02 Score=22.40 Aligned_cols=47 Identities=21% Similarity=0.042 Sum_probs=33.3
Q ss_pred hHHhhhhcEEEEEe----------------ecceEEEEeCCCc----hHHHHHHHHHcCc--cEEEEec
Q 037201 108 ADELKRAWFCVRNV----------------RFGCLMVVSDDSN----FVEVFQEATLRCL--KMVVVGD 154 (177)
Q Consensus 108 a~eLrRAGv~Vr~V----------------~v~clvLVSDdsd----f~~~lr~Ar~r~l--~TVVVGd 154 (177)
+.-|+-+||.|-.. +.|.++|-|=+.. +..+++.-++++. -.|++|.
T Consensus 23 ~~~l~~~GfeVi~lg~~~s~e~~v~aa~e~~adii~iSsl~~~~~~~~~~~~~~L~~~g~~~i~vivGG 91 (132)
T TIGR00640 23 ATAYADLGFDVDVGPLFQTPEEIARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILVVVGG 91 (132)
T ss_pred HHHHHhCCcEEEECCCCCCHHHHHHHHHHcCCCEEEEcCchhhhHHHHHHHHHHHHhcCCCCCEEEEeC
Confidence 56789999999877 7788888776653 4455555666765 2577774
No 368
>PRK10530 pyridoxal phosphate (PLP) phosphatase; Provisional
Probab=23.47 E-value=1e+02 Score=24.97 Aligned_cols=38 Identities=18% Similarity=0.052 Sum_probs=24.2
Q ss_pred CchHHHHHHHHHcCcc---EEEEecC-Cchhhhhhhccccch
Q 037201 133 SNFVEVFQEATLRCLK---MVVVGDM-SDGALKRIANAFFSW 170 (177)
Q Consensus 133 sdf~~~lr~Ar~r~l~---TVVVGd~-~~~~L~r~Ad~~~sW 170 (177)
+--..+.+.++..|+. +++|||+ +|-...+.|...+.|
T Consensus 199 ~K~~~l~~l~~~~gi~~~e~i~~GD~~NDi~m~~~ag~~vam 240 (272)
T PRK10530 199 SKGKRLTQWVEAQGWSMKNVVAFGDNFNDISMLEAAGLGVAM 240 (272)
T ss_pred ChHHHHHHHHHHcCCCHHHeEEeCCChhhHHHHHhcCceEEe
Confidence 3344455566667764 8899995 455666777766654
No 369
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=23.41 E-value=1.9e+02 Score=19.88 Aligned_cols=41 Identities=17% Similarity=0.319 Sum_probs=29.8
Q ss_pred chHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCccEE-EEecC
Q 037201 107 FADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLKMV-VVGDM 155 (177)
Q Consensus 107 La~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~TV-VVGd~ 155 (177)
++..|+.+|+.|. +=..+..+..-|+.|...|...+ +||+.
T Consensus 21 l~~~L~~~gi~v~--------~d~~~~~~~k~~~~a~~~g~p~~iiiG~~ 62 (94)
T PF03129_consen 21 LANKLRKAGIRVE--------LDDSDKSLGKQIKYADKLGIPFIIIIGEK 62 (94)
T ss_dssp HHHHHHHTTSEEE--------EESSSSTHHHHHHHHHHTTESEEEEEEHH
T ss_pred HHHHHHHCCCEEE--------EECCCCchhHHHHHHhhcCCeEEEEECch
Confidence 4889999995543 22267788999999998888864 55654
No 370
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=23.30 E-value=1.7e+02 Score=24.54 Aligned_cols=27 Identities=19% Similarity=-0.004 Sum_probs=22.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCcc
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLK 148 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~ 148 (177)
+.|.+++.++..+...+++.|++.|+.
T Consensus 192 ~~dvvi~~~~~~~~~~~~~~a~~~g~~ 218 (350)
T cd06366 192 DSRVIVVHFSPDLARRVFCEAYKLGMM 218 (350)
T ss_pred CCeEEEEECChHHHHHHHHHHHHcCCc
Confidence 677888888888888999999998884
No 371
>PF02811 PHP: PHP domain; InterPro: IPR004013 The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. This family is often associated with an N-terminal region IPR003141 from INTERPRO.; GO: 0003824 catalytic activity; PDB: 2WJE_A 3QY8_A 2WJD_A 2WJF_A 1PB0_B 1M68_A 1M65_A 3E38_B 2W9M_A 3E0F_A ....
Probab=23.25 E-value=92 Score=23.18 Aligned_cols=22 Identities=18% Similarity=0.214 Sum_probs=20.5
Q ss_pred chHHHHHHHHHcCccEEEEecC
Q 037201 134 NFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 134 df~~~lr~Ar~r~l~TVVVGd~ 155 (177)
...++++.|.++|+.++.|-|-
T Consensus 17 ~~~e~v~~A~~~Gl~~i~iTDH 38 (175)
T PF02811_consen 17 SPEEYVEQAKEKGLDAIAITDH 38 (175)
T ss_dssp SHHHHHHHHHHTTESEEEEEEE
T ss_pred CHHHHHHHHHHcCCCEEEEcCC
Confidence 6789999999999999999996
No 372
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=23.25 E-value=1.6e+02 Score=25.06 Aligned_cols=31 Identities=13% Similarity=0.096 Sum_probs=24.4
Q ss_pred ceEEEEeCCCchHHHHHHHHHcCcc---EEEEec
Q 037201 124 GCLMVVSDDSNFVEVFQEATLRCLK---MVVVGD 154 (177)
Q Consensus 124 ~clvLVSDdsdf~~~lr~Ar~r~l~---TVVVGd 154 (177)
+.+++.+...+...+++.+++.|+. .++||.
T Consensus 196 ~vii~~~~~~~~~~~l~q~~~~g~~~~~~~~i~~ 229 (389)
T cd06352 196 RIIIMCGSSEDVRELLLAAHDLGLTSGDYVFILI 229 (389)
T ss_pred eEEEEECCHHHHHHHHHHHHHcCCCCCcEEEEEE
Confidence 6677777778888999999999984 677764
No 373
>KOG1256 consensus Long-chain acyl-CoA synthetases (AMP-forming) [Lipid transport and metabolism]
Probab=23.23 E-value=79 Score=31.94 Aligned_cols=50 Identities=20% Similarity=0.366 Sum_probs=36.0
Q ss_pred EEEEeCCCchHHHHHHHH---HcCccEEEEecCCchhhhhhhcc----ccchhhhhc
Q 037201 126 LMVVSDDSNFVEVFQEAT---LRCLKMVVVGDMSDGALKRIANA----FFSWSDLLM 175 (177)
Q Consensus 126 lvLVSDdsdf~~~lr~Ar---~r~l~TVVVGd~~~~~L~r~Ad~----~~sW~ev~~ 175 (177)
+|.|.|+.-+..+|+-.. ...++++|+=|.....++..|.- -+||+|+++
T Consensus 183 iv~vd~~~k~~~ll~~~~~~~~~~LK~iI~~~~~~~~~~~~~~~~gv~v~S~~e~~~ 239 (691)
T KOG1256|consen 183 IVFVDNAKKAEKLLEIKENDSLPSLKAIIQLDEPSDELKEKAENNGVEVYSWDEFEE 239 (691)
T ss_pred EEEEeCHHHHHHHHhhcccccCccceeEEEecCCchhhhhhhhcCCeEEEEHHHHHh
Confidence 444444555555555444 34699999999887888888877 899999864
No 374
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=23.22 E-value=39 Score=27.22 Aligned_cols=20 Identities=20% Similarity=0.348 Sum_probs=13.8
Q ss_pred hhhhcCCCcCChhHHHHHHHhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIH 70 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlH 70 (177)
.|=.||++|++- ++|..+-|
T Consensus 74 ~clecGk~~k~L---krHL~~~~ 93 (132)
T PF05443_consen 74 ICLECGKKFKTL---KRHLRTHH 93 (132)
T ss_dssp E-TBT--EESBH---HHHHHHTT
T ss_pred EEccCCcccchH---HHHHHHcc
Confidence 388899999984 89988765
No 375
>PRK04322 peptidyl-tRNA hydrolase; Provisional
Probab=23.12 E-value=89 Score=24.18 Aligned_cols=40 Identities=15% Similarity=0.176 Sum_probs=29.6
Q ss_pred HHhhhhcEEEEEeecceEEE-EeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 109 DELKRAWFCVRNVRFGCLMV-VSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 109 ~eLrRAGv~Vr~V~v~clvL-VSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
..+.+.|.. .+|| |.|..++.++.+.|++.|+.+++|=|.
T Consensus 40 ~~W~~~G~~-------Kvvlkv~~~~el~~l~~~a~~~~l~~~~v~DA 80 (113)
T PRK04322 40 EEWLNEGQK-------KVVLKVNSEEELLELKEKAERLGLPTALIRDA 80 (113)
T ss_pred HHHHHCCCc-------EEEEeCCCHHHHHHHHHHHHHcCCCEEEEEeC
Confidence 344556544 3445 456778999999999999999999774
No 376
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [].
Probab=23.11 E-value=1.5e+02 Score=25.42 Aligned_cols=22 Identities=23% Similarity=0.394 Sum_probs=19.2
Q ss_pred CCchHHHHHHHHHcCccEEEEe
Q 037201 132 DSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 132 dsdf~~~lr~Ar~r~l~TVVVG 153 (177)
|++|++.|+.|.++||....+.
T Consensus 180 Dp~fa~~l~~A~~~GV~v~a~~ 201 (215)
T PF03749_consen 180 DPEFAEALREAAEAGVEVLAYR 201 (215)
T ss_pred CHHHHHHHHHHHHCCCEEEEEE
Confidence 6799999999999999877654
No 377
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=23.11 E-value=30 Score=22.45 Aligned_cols=8 Identities=13% Similarity=-0.197 Sum_probs=4.4
Q ss_pred hhhhhcCC
Q 037201 47 CLLIRNQG 54 (177)
Q Consensus 47 ~Lc~~CGr 54 (177)
+||+.||-
T Consensus 2 hlcpkcgv 9 (36)
T PF09151_consen 2 HLCPKCGV 9 (36)
T ss_dssp -B-TTTSS
T ss_pred ccCCccCc
Confidence 57888874
No 378
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=23.04 E-value=55 Score=20.72 Aligned_cols=26 Identities=35% Similarity=0.459 Sum_probs=17.6
Q ss_pred HHHHHhcccceeeehhhccCCccccC
Q 037201 9 LKKLISSFEVVKYMVANANSHAFGYV 34 (177)
Q Consensus 9 Lr~~A~~FG~Vv~~~AyAnrhaf~~l 34 (177)
|+++.+.||.|..+.-.-+.-.+.||
T Consensus 1 L~~~f~~fG~V~~i~~~~~~~~~a~V 26 (56)
T PF13893_consen 1 LYKLFSKFGEVKKIKIFKKKRGFAFV 26 (56)
T ss_dssp HHHHHTTTS-EEEEEEETTSTTEEEE
T ss_pred ChHHhCCcccEEEEEEEeCCCCEEEE
Confidence 67889999999988776554234443
No 379
>cd03109 DTBS Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms. The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors.
Probab=22.95 E-value=1.5e+02 Score=22.57 Aligned_cols=50 Identities=20% Similarity=0.131 Sum_probs=29.2
Q ss_pred CchHHhhhhcEEEEEe------------ec-ceEEEEeCCCchHHHHHHHHHcCccEEEEecCCch
Q 037201 106 GFADELKRAWFCVRNV------------RF-GCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMSDG 158 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V------------~v-~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~ 158 (177)
||...|++.|..|... |. .+.+-.+++-+ ++..|++-++..++|.+...+
T Consensus 18 ~l~~~l~~~~~~v~~~kp~~~~d~vliEGaGg~~~p~~~~~~---~~d~~~~~~~~vllV~~~~~g 80 (134)
T cd03109 18 ILARALKEKGYRVAPLKPVQTYDFVLVEGAGGLCVPLKEDFT---NADVAKELNLPAILVTSAGLG 80 (134)
T ss_pred HHHHHHHHCCCeEEEEecCCCCCEEEEECCCccccCCCCCCC---HHHHHHHhCCCEEEEEcCCCC
Confidence 5667777777776665 22 12233344443 445566667888888776533
No 380
>PF01866 Diphthamide_syn: Putative diphthamide synthesis protein; InterPro: IPR002728 Members of this family include Q16439 from SWISSPROT, a candidate tumour suppressor gene [], and DPH2 from yeast P32461 from SWISSPROT [], which confers resistance to diphtheria toxin and has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a posttranslationally modified histidine residue present in EF2. The exact function of the members of this family is unknown.; GO: 0017183 peptidyl-diphthamide biosynthetic process from peptidyl-histidine, 0005737 cytoplasm; PDB: 3LZD_B 3LZC_A.
Probab=22.72 E-value=1.8e+02 Score=25.49 Aligned_cols=53 Identities=17% Similarity=0.144 Sum_probs=36.4
Q ss_pred hhhhhhhhhhhhhhhhcc-----------chHHHHHHHHhhcCCCCCCCchHHhhhhcEEEEEe--------------ec
Q 037201 69 IHEGEQKKRSNQIESARG-----------KMEKYKMAVSAILTPKVGYGFADELKRAWFCVRNV--------------RF 123 (177)
Q Consensus 69 lHerEr~Krl~ri~s~kG-----------K~~KY~~Aar~vl~pkvgygLa~eLrRAGv~Vr~V--------------~v 123 (177)
-++|-..+|.+.|..++- ..|.|.+.+..+ ...|+++|-.+-++ ++
T Consensus 191 ~~~~~l~~R~~~i~ka~~a~~~GIiv~tl~~q~~~~~~~~l---------~~~l~~~gkk~y~~~~~~i~~~kL~nf~ei 261 (307)
T PF01866_consen 191 DIERLLRRRYALIEKAKDAKTFGIIVGTLGGQGYLELIKRL---------KKLLKKAGKKSYTLSVGEINPAKLANFPEI 261 (307)
T ss_dssp -THHHHHHHHHHHHHHTT--EEEEEEE-STTT--HHHHHHH---------HHHHHHTT-EEEEEEESS--GGGGTTS---
T ss_pred cHHHHHHHHHHHHHHHhcCCEEEEEEecCCCCCCHHHHHHH---------HHHHHHcCCEEEEEEECCCCHHHHhcCccc
Confidence 366777788888888876 357888888776 67889999888887 58
Q ss_pred ceEEEEe
Q 037201 124 GCLMVVS 130 (177)
Q Consensus 124 ~clvLVS 130 (177)
|+.|++|
T Consensus 262 d~fV~~a 268 (307)
T PF01866_consen 262 DAFVQIA 268 (307)
T ss_dssp SEEEE-S
T ss_pred CEEEEec
Confidence 8888887
No 381
>cd01466 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most,
Probab=22.64 E-value=94 Score=23.76 Aligned_cols=42 Identities=26% Similarity=0.286 Sum_probs=23.3
Q ss_pred ceEEEEeC--CCchHHHHHHHHH--cCccEEEEecCCc-hhhhhhhcc
Q 037201 124 GCLMVVSD--DSNFVEVFQEATL--RCLKMVVVGDMSD-GALKRIANA 166 (177)
Q Consensus 124 ~clvLVSD--dsdf~~~lr~Ar~--r~l~TVVVGd~~~-~~L~r~Ad~ 166 (177)
..++|+|| +++-..+++ +++ -.+.||-+|...+ ..|.+.|++
T Consensus 100 ~~iillTDG~~~~~~~~~~-~~~~~v~v~~igig~~~~~~~l~~iA~~ 146 (155)
T cd01466 100 ASIMLLSDGQDNHGAVVLR-ADNAPIPIHTFGLGASHDPALLAFIAEI 146 (155)
T ss_pred eEEEEEcCCCCCcchhhhc-ccCCCceEEEEecCCCCCHHHHHHHHhc
Confidence 56999998 333333433 444 4455566663233 457777764
No 382
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=22.59 E-value=1.2e+02 Score=23.24 Aligned_cols=40 Identities=18% Similarity=0.169 Sum_probs=28.5
Q ss_pred ceEEEEeCCC-c--h-HHHHHHHHHcCccEEEEecCCchhhhhhhc
Q 037201 124 GCLMVVSDDS-N--F-VEVFQEATLRCLKMVVVGDMSDGALKRIAN 165 (177)
Q Consensus 124 ~clvLVSDds-d--f-~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad 165 (177)
-.||+++.|. . . ..+...|++.++..+.+|+. ..|++..-
T Consensus 43 a~LVilA~D~s~~~~~~~i~~lc~~~~Ip~~~~~sk--~eLG~a~G 86 (117)
T TIGR03677 43 AKLVVIAEDVEPPEIVAHLPALCEEKGIPYVYVKKK--EDLGAAAG 86 (117)
T ss_pred ccEEEEeCCCCcHHHHHHHHHHHHHcCCCEEEeCCH--HHHHHHhC
Confidence 3466666666 3 2 67788899999999999876 46766543
No 383
>cd06329 PBP1_SBP_like_3 Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=22.52 E-value=1.6e+02 Score=24.80 Aligned_cols=33 Identities=9% Similarity=0.044 Sum_probs=27.2
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd 154 (177)
+.|.|++.....+...+++.+++.|+..-++|.
T Consensus 201 ~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~ 233 (342)
T cd06329 201 GADTVITGNWGNDLLLLVKQAADAGLKLPFYTP 233 (342)
T ss_pred CCCEEEEcccCchHHHHHHHHHHcCCCceEEec
Confidence 578888888888899999999999998666664
No 384
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=22.48 E-value=1.6e+02 Score=27.77 Aligned_cols=43 Identities=26% Similarity=0.267 Sum_probs=30.5
Q ss_pred CCchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCcc-EEEEecC
Q 037201 105 YGFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLK-MVVVGDM 155 (177)
Q Consensus 105 ygLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~-TVVVGd~ 155 (177)
..++.+|+++|+.|.+ -.+ +..+..-++.|...|.. .|+||+.
T Consensus 493 ~~i~~~Lr~~gi~v~~-------d~~-~~~l~kk~~~A~~~g~p~~iivG~~ 536 (575)
T PRK12305 493 EEVAKKLRAAGIRVEV-------DTS-NERLNKKIRNAQKQKIPYMLVVGDK 536 (575)
T ss_pred HHHHHHHHHCCCEEEE-------ECC-CCCHHHHHHHHHhcCCCEEEEEech
Confidence 3467888888876542 122 33589999999998887 6777875
No 385
>cd04104 p47_IIGP_like p47 (47-kDa) family. The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protei
Probab=22.45 E-value=1.5e+02 Score=23.58 Aligned_cols=36 Identities=14% Similarity=0.239 Sum_probs=27.5
Q ss_pred ecceEEEEeCCCchH----HHHHHHHHcCccEEEEecCCch
Q 037201 122 RFGCLMVVSDDSNFV----EVFQEATLRCLKMVVVGDMSDG 158 (177)
Q Consensus 122 ~v~clvLVSDdsdf~----~~lr~Ar~r~l~TVVVGd~~~~ 158 (177)
+.|.+++|+|++ |+ .+++..++.+.+.++|++-+|.
T Consensus 80 ~~d~~l~v~~~~-~~~~d~~~~~~l~~~~~~~ilV~nK~D~ 119 (197)
T cd04104 80 EYDFFIIISSTR-FSSNDVKLAKAIQCMGKKFYFVRTKVDR 119 (197)
T ss_pred CcCEEEEEeCCC-CCHHHHHHHHHHHHhCCCEEEEEecccc
Confidence 678888887764 55 3567777788899999998765
No 386
>PF13458 Peripla_BP_6: Periplasmic binding protein; PDB: 4EVS_A 4EY3_A 4EYG_B 4EYK_A 3H5L_B 3TD9_A 3EAF_A 1Z18_A 1Z17_A 2LIV_A ....
Probab=22.43 E-value=1.7e+02 Score=24.01 Aligned_cols=27 Identities=11% Similarity=0.143 Sum_probs=22.9
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCcc
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLK 148 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~ 148 (177)
+.|.|++.++.++-..+++.+++.++.
T Consensus 190 ~~d~v~~~~~~~~~~~~~~~~~~~~~~ 216 (343)
T PF13458_consen 190 GPDVVVLAGDPADAAAFLRQLRQLGLK 216 (343)
T ss_dssp TTSEEEEESTHHHHHHHHHHHHHTTGC
T ss_pred CCCEEEEeccchhHHHHHHHHHhhccc
Confidence 678888888888888888888888877
No 387
>PF07918 CAP160: CAP160 repeat; InterPro: IPR012418 This region featured in this family is repeated in spinach cold acclimation protein CAP160 (O50054 from SWISSPROT) CAP160 is induced during periods of drought stress; its precise function is unknown but it has been implicated in the stabilisation of membranes, cytoskeletal elements, and ribosomes. By acting as a compatible solute, it may reduce the toxic effects of cellular solutes that accumulate at high concentration []. Other members of this family are also induced by water stress, abscisic acid, and/or low temperature, such as desiccation-responsive protein 29B (Q04980 from SWISSPROT) and CDet11-24 protein (O23764 from SWISSPROT).
Probab=22.43 E-value=34 Score=21.20 Aligned_cols=14 Identities=29% Similarity=0.843 Sum_probs=11.8
Q ss_pred HHHHhhcCCCCCCC
Q 037201 93 MAVSAILTPKVGYG 106 (177)
Q Consensus 93 ~Aar~vl~pkvgyg 106 (177)
.+|.++++-|.|||
T Consensus 13 ~~AknvvaSKLGyg 26 (27)
T PF07918_consen 13 ISAKNVVASKLGYG 26 (27)
T ss_pred HHHHHHHHHhccCC
Confidence 46778999999998
No 388
>cd02170 cytidylyltransferase cytidylyltransferase. The cytidylyltransferase family includes cholinephosphate cytidylyltransferase (CCT), glycerol-3-phosphate cytidylyltransferase, RafE and phosphoethanolamine cytidylyltransferase (ECT). All enzymes catalyze the transfer of a cytidylyl group from CTP to various substrates.
Probab=22.42 E-value=1.2e+02 Score=22.86 Aligned_cols=31 Identities=10% Similarity=0.131 Sum_probs=20.2
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
++|.++..+ ..+|...|. +....+||+|+..
T Consensus 64 ~vd~v~~~~-~~~~~~~l~---~~~~~~vv~G~d~ 94 (136)
T cd02170 64 YVDEVILGH-PWSYFKPLE---ELKPDVIVLGDDQ 94 (136)
T ss_pred CcCEEEECC-CCCHhHHHH---HHCCCEEEECCCC
Confidence 556655544 557877663 3455899999765
No 389
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=22.40 E-value=38 Score=20.20 Aligned_cols=10 Identities=10% Similarity=-0.140 Sum_probs=8.4
Q ss_pred hhhhcCCCcC
Q 037201 48 LLIRNQGRFY 57 (177)
Q Consensus 48 Lc~~CGrrf~ 57 (177)
.|+.||+.|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4999999885
No 390
>PRK13226 phosphoglycolate phosphatase; Provisional
Probab=22.35 E-value=1.8e+02 Score=23.68 Aligned_cols=46 Identities=15% Similarity=-0.062 Sum_probs=25.9
Q ss_pred EEEEeCCCchHHHHHHHHHcCccEEEEecCCc---hhh-hhhhccccc-hhhhh
Q 037201 126 LMVVSDDSNFVEVFQEATLRCLKMVVVGDMSD---GAL-KRIANAFFS-WSDLL 174 (177)
Q Consensus 126 lvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~---~~L-~r~Ad~~~s-W~ev~ 174 (177)
.+.|-|. ..| +..|+..|++||.|.-+.. ..+ ...||..+. |+++.
T Consensus 171 ~l~IGDs--~~D-i~aA~~aG~~~i~v~~g~~~~~~~~~~~~~~~~i~~~~el~ 221 (229)
T PRK13226 171 CVYVGDD--ERD-ILAARAAGMPSVAALWGYRLHDDDPLAWQADVLVEQPQLLW 221 (229)
T ss_pred EEEeCCC--HHH-HHHHHHCCCcEEEEeecCCCCCcChhhcCCCeeeCCHHHHH
Confidence 4444444 345 6788888888888754321 122 234666664 55553
No 391
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=22.33 E-value=89 Score=26.81 Aligned_cols=32 Identities=25% Similarity=0.458 Sum_probs=28.1
Q ss_pred eEEEEeCCCchHHHHHHHHH-cCccEEEEecCC
Q 037201 125 CLMVVSDDSNFVEVFQEATL-RCLKMVVVGDMS 156 (177)
Q Consensus 125 clvLVSDdsdf~~~lr~Ar~-r~l~TVVVGd~~ 156 (177)
.|.||-||.-|...|..|=+ ||...++.++..
T Consensus 11 ~lllvdDD~~f~~~LaRa~e~RGf~v~~a~~~~ 43 (182)
T COG4567 11 SLLLVDDDTPFLRTLARAMERRGFAVVTAESVE 43 (182)
T ss_pred eeEEecCChHHHHHHHHHHhccCceeEeeccHH
Confidence 48999999999999988885 999999988864
No 392
>PF00384 Molybdopterin: Molybdopterin oxidoreductase; InterPro: IPR006656 This domain is found in a number of molybdopterin-containing oxidoreductases, tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where a single domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor []. ; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E 3DMR_A 4DMR_A 1H5N_C 1E5V_A ....
Probab=22.25 E-value=1.2e+02 Score=26.41 Aligned_cols=46 Identities=15% Similarity=0.160 Sum_probs=31.5
Q ss_pred cceEEEEeCCCc------hHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 123 FGCLMVVSDDSN------FVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 123 v~clvLVSDdsd------f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
.|++++..-|.. ...+++.++++|.+.|||+=.. ......||.|++
T Consensus 112 ad~il~~G~n~~~~~~~~~~~~~~~~~~~g~k~v~vdP~~-t~~a~~ad~~i~ 163 (432)
T PF00384_consen 112 ADVILIWGANPAESHPHLNARFRKAARKRGAKLVVVDPRR-TPTAAKADEWIP 163 (432)
T ss_dssp -SEEEEES--HHHHSHHHHHHHHHHHHHCTSEEEEEESSB--HHGGGTSEEEE
T ss_pred cceEEEcccCccccccccccccccccccCCcceEEEEecc-chhhhhcccccc
Confidence 344555553322 3566788999999999998874 568889999986
No 393
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=22.15 E-value=96 Score=21.17 Aligned_cols=32 Identities=19% Similarity=0.222 Sum_probs=22.3
Q ss_pred cEEEEEeec-ceEEEEeCCCchHHHHHHHHHcC
Q 037201 115 WFCVRNVRF-GCLMVVSDDSNFVEVFQEATLRC 146 (177)
Q Consensus 115 Gv~Vr~V~v-~clvLVSDdsdf~~~lr~Ar~r~ 146 (177)
++.++-..- .-+|.+++|+|+..+++.+++.+
T Consensus 40 ~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~~~~ 72 (81)
T smart00666 40 SFTLKYQDEDGDLVSLTSDEDLEEAIEEYDSLG 72 (81)
T ss_pred CeEEEEECCCCCEEEecCHHHHHHHHHHHHHcC
Confidence 444444422 22677788899999999999754
No 394
>TIGR01580 narG respiratory nitrate reductase, alpha subunit. The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the alpha subunit for nitrate reductase I (narG) and nitrate reductase II (narZ) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model The seed members used to make the model include Nitrate reductases from Pseudomonas fluorescens, E.coli and B.subtilis. All seed members are experimentally characterized. Some unpublished nitrate reductases, that are shorter sequences, and probably fragments fall in between the noise and trusted cutoffs. P
Probab=22.14 E-value=1.3e+02 Score=32.47 Aligned_cols=47 Identities=9% Similarity=0.203 Sum_probs=34.6
Q ss_pred ecceEEEEeCCCch-----HHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 122 RFGCLMVVSDDSNF-----VEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 122 ~v~clvLVSDdsdf-----~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
+.++||+..-+... ...|.+|+++|.+.|||.=.- ......||.|++
T Consensus 245 nS~~II~WGsN~~~T~~p~a~~l~eAr~rGaKvVVVDPr~-t~tA~~AD~WLp 296 (1235)
T TIGR01580 245 NSSYIIAWGSNVPQTRTPDAHFFTEVRYKGTKTVAITPDY-AEIAKLCDLWLA 296 (1235)
T ss_pred cCCEEEEECCChhhhcchhHHHHHHHHHcCCeEEEEcCCC-ChhhHhhCEEeC
Confidence 56677777655322 356788999999999997643 566789999986
No 395
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=22.12 E-value=52 Score=22.67 Aligned_cols=17 Identities=6% Similarity=0.177 Sum_probs=15.7
Q ss_pred hhhcCCCcCChhHHHHH
Q 037201 49 LIRNQGRFYNNDKLVNH 65 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kH 65 (177)
|.-||-+|.+.++|..|
T Consensus 30 C~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 30 CFWCGTKYDDEEDLERN 46 (55)
T ss_pred eeeeCCccCCHHHHHhC
Confidence 99999999999999875
No 396
>cd04171 SelB SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryo
Probab=22.11 E-value=2e+02 Score=20.67 Aligned_cols=37 Identities=16% Similarity=0.104 Sum_probs=25.3
Q ss_pred ecceEEEEeCCCc-----hHHHHHHHHHcCc-cEEEEecCCch
Q 037201 122 RFGCLMVVSDDSN-----FVEVFQEATLRCL-KMVVVGDMSDG 158 (177)
Q Consensus 122 ~v~clvLVSDdsd-----f~~~lr~Ar~r~l-~TVVVGd~~~~ 158 (177)
+.|++++|-|-++ ..+.+..++..+. ..++|++-.|-
T Consensus 74 ~ad~ii~V~d~~~~~~~~~~~~~~~~~~~~~~~~ilv~NK~Dl 116 (164)
T cd04171 74 GIDLVLLVVAADEGIMPQTREHLEILELLGIKRGLVVLTKADL 116 (164)
T ss_pred cCCEEEEEEECCCCccHhHHHHHHHHHHhCCCcEEEEEECccc
Confidence 6888888877443 3344555666676 78899987653
No 397
>PRK08811 uroporphyrinogen-III synthase; Validated
Probab=21.98 E-value=26 Score=30.05 Aligned_cols=41 Identities=12% Similarity=0.045 Sum_probs=26.1
Q ss_pred ecceEEEEeCCCc--hHHHHHHHHHcCccEEEEecCCchhhhh
Q 037201 122 RFGCLMVVSDDSN--FVEVFQEATLRCLKMVVVGDMSDGALKR 162 (177)
Q Consensus 122 ~v~clvLVSDdsd--f~~~lr~Ar~r~l~TVVVGd~~~~~L~r 162 (177)
..||||.+|-+.- |...+..-...+++-..||+.+..+|..
T Consensus 69 ~~d~iiftS~NAV~~~~~~~~~~~~~~~~~~AVG~~TA~aL~~ 111 (266)
T PRK08811 69 AAPIVVFTSPAAVRAAHRLLPLQRPARAHWLSVGEGTARALQA 111 (266)
T ss_pred cCCEEEEECHHHHHHHHHHhcccCccCCeEEEECHHHHHHHHH
Confidence 5689999997762 1122211113577888999988777765
No 398
>TIGR01524 ATPase-IIIB_Mg magnesium-translocating P-type ATPase. The magnesium ATPases have been classified as type IIIB by a phylogenetic analysis.
Probab=21.94 E-value=1.9e+02 Score=29.23 Aligned_cols=32 Identities=19% Similarity=0.097 Sum_probs=22.1
Q ss_pred HHHHHHHcCccEEEEecC-Cchhhhhhhccccc
Q 037201 138 VFQEATLRCLKMVVVGDM-SDGALKRIANAFFS 169 (177)
Q Consensus 138 ~lr~Ar~r~l~TVVVGd~-~~~~L~r~Ad~~~s 169 (177)
+++.-+++|-...++||+ +|-.-=+.||+.++
T Consensus 594 iV~~lq~~G~vVam~GDGvNDapALk~AdVGIA 626 (867)
T TIGR01524 594 IIGLLKKAGHTVGFLGDGINDAPALRKADVGIS 626 (867)
T ss_pred HHHHHHhCCCEEEEECCCcccHHHHHhCCEEEE
Confidence 455556778788899995 34434477898876
No 399
>COG0279 GmhA Phosphoheptose isomerase [Carbohydrate transport and metabolism]
Probab=21.92 E-value=94 Score=26.58 Aligned_cols=46 Identities=13% Similarity=0.267 Sum_probs=35.8
Q ss_pred ceEEEEeCC---CchHHHHHHHHHcCccEEEEecCCchhhhhhhccccc
Q 037201 124 GCLMVVSDD---SNFVEVFQEATLRCLKMVVVGDMSDGALKRIANAFFS 169 (177)
Q Consensus 124 ~clvLVSDd---sdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~~~s 169 (177)
|.|+=.|-. .+-...++.|+++|+.||+.-..+.|.++-.+|+.+.
T Consensus 111 DvLigISTSGNS~nVl~Ai~~Ak~~gm~vI~ltG~~GG~~~~~~D~~i~ 159 (176)
T COG0279 111 DVLIGISTSGNSKNVLKAIEAAKEKGMTVIALTGKDGGKLAGLLDVEIR 159 (176)
T ss_pred CEEEEEeCCCCCHHHHHHHHHHHHcCCEEEEEecCCCcccccccceEEe
Confidence 556656543 4556677889999999999988888999999998653
No 400
>cd04643 CBS_pair_30 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=21.90 E-value=1.5e+02 Score=20.13 Aligned_cols=31 Identities=16% Similarity=0.106 Sum_probs=23.6
Q ss_pred EEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 126 LMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 126 lvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
++.|+.+....++++..++.+...+.|-|..
T Consensus 3 ~~~v~~~~~~~~~~~~~~~~~~~~~~V~d~~ 33 (116)
T cd04643 3 VAYVQDTNTLRHALLVLTKHGYSAIPVLDKE 33 (116)
T ss_pred cEEECCCCcHHHHHHHHHHCCCceeeeECCC
Confidence 3456777778888888888888888887754
No 401
>TIGR01487 SPP-like sucrose-phosphate phosphatase-like hydrolase, Archaeal. TIGR01482, in turn, is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases.
Probab=21.82 E-value=2.5e+02 Score=22.31 Aligned_cols=57 Identities=14% Similarity=0.126 Sum_probs=32.0
Q ss_pred hHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHH-HcCcc---EEEEecCC-chhhhhhhc
Q 037201 108 ADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEAT-LRCLK---MVVVGDMS-DGALKRIAN 165 (177)
Q Consensus 108 a~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar-~r~l~---TVVVGd~~-~~~L~r~Ad 165 (177)
...|+..|+.+.. +-.++-+.....+=+..|+... ..|+. +++|||+. |-...+.|+
T Consensus 122 ~~~l~~~~~~~~~-~~~~~ei~~~~~~K~~~i~~l~~~~~i~~~~~i~iGDs~ND~~ml~~ag 183 (215)
T TIGR01487 122 REIIKERGLNLVD-SGFAIHIMKKGVDKGVGVEKLKELLGIKPEEVAAIGDSENDIDLFRVVG 183 (215)
T ss_pred HHHHHhCCeEEEe-cCceEEEecCCCChHHHHHHHHHHhCCCHHHEEEECCCHHHHHHHHhCC
Confidence 3445555655532 2234555566666666666655 45665 89999963 334444444
No 402
>PF05198 IF3_N: Translation initiation factor IF-3, N-terminal domain; InterPro: IPR019814 Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit []. The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 []. ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1TIF_A.
Probab=21.82 E-value=1.5e+02 Score=21.42 Aligned_cols=37 Identities=19% Similarity=0.239 Sum_probs=25.0
Q ss_pred cceEEEEeCCCc------hHHHHHHHHHcCccEEEEecCCchh
Q 037201 123 FGCLMVVSDDSN------FVEVFQEATLRCLKMVVVGDMSDGA 159 (177)
Q Consensus 123 v~clvLVSDdsd------f~~~lr~Ar~r~l~TVVVGd~~~~~ 159 (177)
...+-||.+|-. ..+.|+.|++.|+.=|.|....+-.
T Consensus 12 ~~~VrlI~~~g~~lGv~~~~eAl~~A~~~~lDLV~v~~~~~PP 54 (76)
T PF05198_consen 12 APEVRLIDEDGEQLGVMSLREALRLAKEKGLDLVEVSPNADPP 54 (76)
T ss_dssp -SEEEEE-TTS-EEEEEEHHHHHHHHHHTT-EEEEEETTSSS-
T ss_pred CCEEEEECCCCcEeceEEHHHHHHHHHHcCCcEEEEcCCCCCC
Confidence 345566766644 4799999999999999999765433
No 403
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=21.77 E-value=38 Score=30.49 Aligned_cols=23 Identities=13% Similarity=0.234 Sum_probs=19.3
Q ss_pred hhhcCCCcCChhHHHHHHHhhhh
Q 037201 49 LIRNQGRFYNNDKLVNHFRQIHE 71 (177)
Q Consensus 49 c~~CGrrf~t~~~L~kHFkqlHe 71 (177)
|.-||-+|.+.++|+-|---.-|
T Consensus 242 C~fCG~~y~~~edl~ehCPGvne 264 (268)
T KOG1994|consen 242 CFFCGIKYKDEEDLYEHCPGVNE 264 (268)
T ss_pred EEEeccccCCHHHHHHhCCCCCc
Confidence 99999999999999998544433
No 404
>PRK13582 thrH phosphoserine phosphatase; Provisional
Probab=21.73 E-value=87 Score=24.35 Aligned_cols=37 Identities=11% Similarity=0.090 Sum_probs=25.3
Q ss_pred chHHHHHHHHHcCccEEEEecCCc-hhhhhhhccccch
Q 037201 134 NFVEVFQEATLRCLKMVVVGDMSD-GALKRIANAFFSW 170 (177)
Q Consensus 134 df~~~lr~Ar~r~l~TVVVGd~~~-~~L~r~Ad~~~sW 170 (177)
.....++.....+-.+|+|||+.- -...+.|++.+.|
T Consensus 132 ~k~~~l~~~~~~~~~~v~iGDs~~D~~~~~aa~~~v~~ 169 (205)
T PRK13582 132 GKRQAVKALKSLGYRVIAAGDSYNDTTMLGEADAGILF 169 (205)
T ss_pred hHHHHHHHHHHhCCeEEEEeCCHHHHHHHHhCCCCEEE
Confidence 455667766777788999999852 2356777766544
No 405
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=21.68 E-value=1.6e+02 Score=28.54 Aligned_cols=42 Identities=7% Similarity=0.170 Sum_probs=30.7
Q ss_pred CchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCcc-EEEEecC
Q 037201 106 GFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLK-MVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~-TVVVGd~ 155 (177)
.++.+||.+|+.|.+ | ..+..+..-++.|...|.. .+|||+.
T Consensus 456 ~Ia~~LR~~GirVel---D-----~~~~~lgkkir~A~k~gip~viIIG~~ 498 (545)
T PRK14799 456 KVLNDMRKRRIRAEI---D-----YAGETLSKRIKNAYDQGVPYILIVGKK 498 (545)
T ss_pred HHHHHHHhCCCEEEE---E-----CCCCCHHHHHHHHHHcCCCEEEEEChh
Confidence 467888888887653 1 2244699999999999988 5667864
No 406
>PF03033 Glyco_transf_28: Glycosyltransferase family 28 N-terminal domain; InterPro: IPR004276 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 28 GT28 from CAZY comprises enzymes with a number of known activities; 1,2-diacylglycerol 3-beta-galactosyltransferase (2.4.1.46 from EC); 1,2-diacylglycerol 3-beta-glucosyltransferase (2.4.1.157 from EC); beta-N-acetylglucosamine transferase (2.4.1 from EC).; GO: 0016758 transferase activity, transferring hexosyl groups, 0005975 carbohydrate metabolic process, 0030259 lipid glycosylation; PDB: 2IYF_B 2YJN_A 2P6P_A 1PNV_A 3H4T_A 3H4I_A 1PN3_B 3IA7_B 1NLM_B 1F0K_B ....
Probab=21.66 E-value=1.5e+02 Score=21.48 Aligned_cols=38 Identities=24% Similarity=0.223 Sum_probs=26.9
Q ss_pred CchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCccEEEEecC
Q 037201 106 GFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~ 155 (177)
.|+.+|+++|..|... -+++|.+.+ .+.|+..+-++..
T Consensus 17 ala~~L~~rGh~V~~~---------~~~~~~~~v---~~~Gl~~~~~~~~ 54 (139)
T PF03033_consen 17 ALARALRRRGHEVRLA---------TPPDFRERV---EAAGLEFVPIPGD 54 (139)
T ss_dssp HHHHHHHHTT-EEEEE---------ETGGGHHHH---HHTT-EEEESSSC
T ss_pred HHHHHHhccCCeEEEe---------ecccceecc---cccCceEEEecCC
Confidence 4789999999988632 235677666 6788888888776
No 407
>KOG2882 consensus p-Nitrophenyl phosphatase [Inorganic ion transport and metabolism]
Probab=21.65 E-value=61 Score=29.77 Aligned_cols=136 Identities=15% Similarity=0.090 Sum_probs=63.4
Q ss_pred HHHHHhcccceeeehhhccCCccccCChhhHhhhhhhhhhhhhcCCCcCChhHHHHHHHhhhhhhhhhhhhhhhhhccch
Q 037201 9 LKKLISSFEVVKYMVANANSHAFGYVPQVVREQRKKENCLLIRNQGRFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKM 88 (177)
Q Consensus 9 Lr~~A~~FG~Vv~~~AyAnrhaf~~lP~~v~e~r~er~~Lc~~CGrrf~t~~~L~kHFkqlHerEr~Krl~ri~s~kGK~ 88 (177)
+..-.+.|.+.-+.+.+--..+.-..|.|.---+..-|....+=+.-++|+..+.+-|+.+=-.- =+-+.|=|.-.-.
T Consensus 18 ~l~~~DtfifDcDGVlW~g~~~ipGs~e~l~~L~~~gK~i~fvTNNStksr~~y~kK~~~lG~~~--v~e~~i~ssa~~~ 95 (306)
T KOG2882|consen 18 LLDSFDTFIFDCDGVLWLGEKPIPGSPEALNLLKSLGKQIIFVTNNSTKSREQYMKKFAKLGFNS--VKEENIFSSAYAI 95 (306)
T ss_pred HHhhcCEEEEcCCcceeecCCCCCChHHHHHHHHHcCCcEEEEeCCCcchHHHHHHHHHHhCccc--cCcccccChHHHH
Confidence 33444445555555555544333333333333333223334445667888888876555432110 0001111111112
Q ss_pred HHHHHHHHhhcCCC---C----CCCchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCccEEEEe
Q 037201 89 EKYKMAVSAILTPK---V----GYGFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 89 ~KY~~Aar~vl~pk---v----gygLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG 153 (177)
..|- ++.. |. | ++|+-.||+.|||..-..+.+-.-- -++.+|.. ..+-+-.|+-||||
T Consensus 96 a~yl---k~~~-~~~k~Vyvig~~gi~~eL~~aG~~~~g~~~~~~~~-~~~~~~~~--~~~~d~~VgAVvvg 160 (306)
T KOG2882|consen 96 ADYL---KKRK-PFGKKVYVIGEEGIREELDEAGFEYFGGGPDGKDT-DGAKSFVL--SIGLDPDVGAVVVG 160 (306)
T ss_pred HHHH---HHhC-cCCCeEEEecchhhhHHHHHcCceeecCCCCcccc-cccccchh--hcCCCCCCCEEEEe
Confidence 2332 1222 32 2 8999999999997655443332211 11222322 22336667777776
No 408
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=21.62 E-value=59 Score=23.56 Aligned_cols=17 Identities=6% Similarity=0.172 Sum_probs=15.3
Q ss_pred cCCCcCChhHHHHHHHh
Q 037201 52 NQGRFYNNDKLVNHFRQ 68 (177)
Q Consensus 52 CGrrf~t~~~L~kHFkq 68 (177)
||++|++..++.++..+
T Consensus 36 ~GkklRs~~ev~~YL~~ 52 (77)
T smart00391 36 CGKKLRSKSELARYLHK 52 (77)
T ss_pred CCCeeeCHHHHHHHHHh
Confidence 99999999999988764
No 409
>cd06349 PBP1_ABC_ligand_binding_like_14 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=21.56 E-value=1.8e+02 Score=24.33 Aligned_cols=32 Identities=16% Similarity=0.157 Sum_probs=23.1
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEEEEe
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVG 153 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVG 153 (177)
+.|.|++.....+...+++.+++.|+..=++|
T Consensus 190 ~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~ 221 (340)
T cd06349 190 NPDAIILISYYNDGAPIARQARAVGLDIPVVA 221 (340)
T ss_pred CCCEEEEccccchHHHHHHHHHHcCCCCcEEc
Confidence 56777777777777788888887777654554
No 410
>TIGR01497 kdpB K+-transporting ATPase, B subunit. One sequence is apparently mis-annotated in the primary literature, but properly annotated by TIGR.
Probab=21.54 E-value=1.5e+02 Score=29.57 Aligned_cols=63 Identities=8% Similarity=0.084 Sum_probs=41.1
Q ss_pred HHhhhhcEEEEEe---------------ecceEEEEeCCCchHHHHHHHHHcCccEEEEecC-Cchhhhhhhccccchh
Q 037201 109 DELKRAWFCVRNV---------------RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDM-SDGALKRIANAFFSWS 171 (177)
Q Consensus 109 ~eLrRAGv~Vr~V---------------~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~-~~~~L~r~Ad~~~sW~ 171 (177)
.+|+++|+.+.++ |++-++-=.-..|=..+++.-++.|-....+||+ +|-..=+.||+.+...
T Consensus 456 ~~l~~~Gi~v~miTGD~~~ta~~iA~~lGI~~v~a~~~PedK~~~v~~lq~~g~~VamvGDG~NDapAL~~AdvGiAm~ 534 (675)
T TIGR01497 456 AQLRKMGIKTIMITGDNRLTAAAIAAEAGVDDFIAEATPEDKIALIRQEQAEGKLVAMTGDGTNDAPALAQADVGVAMN 534 (675)
T ss_pred HHHHHCCCEEEEEcCCCHHHHHHHHHHcCCCEEEcCCCHHHHHHHHHHHHHcCCeEEEECCCcchHHHHHhCCEeEEeC
Confidence 4678889888777 7654332222244455667777778789999995 3444446788887653
No 411
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=21.47 E-value=2.4e+02 Score=18.47 Aligned_cols=32 Identities=19% Similarity=0.125 Sum_probs=23.0
Q ss_pred ceEEEEeCCCc-hHHHHHHHHHcCccEEEEecC
Q 037201 124 GCLMVVSDDSN-FVEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 124 ~clvLVSDdsd-f~~~lr~Ar~r~l~TVVVGd~ 155 (177)
+.|.+.+||.. ..++-+.+++.|.+-+.+=+.
T Consensus 27 ~~l~v~~d~~~~~~~i~~~~~~~g~~~~~~~~~ 59 (69)
T cd00291 27 EVLEVLLDDPGAVEDIPAWAKETGHEVLEVEEE 59 (69)
T ss_pred CEEEEEecCCcHHHHHHHHHHHcCCEEEEEEEe
Confidence 45666677665 677778899999997665544
No 412
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=21.41 E-value=2.1e+02 Score=23.54 Aligned_cols=7 Identities=0% Similarity=-0.083 Sum_probs=3.4
Q ss_pred HcCccEE
Q 037201 144 LRCLKMV 150 (177)
Q Consensus 144 ~r~l~TV 150 (177)
++|-+.|
T Consensus 171 ~~G~~~I 177 (327)
T PRK10423 171 DKGYTRI 177 (327)
T ss_pred HcCCCeE
Confidence 4555544
No 413
>PLN02908 threonyl-tRNA synthetase
Probab=21.25 E-value=1.6e+02 Score=28.88 Aligned_cols=42 Identities=29% Similarity=0.385 Sum_probs=31.4
Q ss_pred CchHHhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCcc-EEEEecC
Q 037201 106 GFADELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLK-MVVVGDM 155 (177)
Q Consensus 106 gLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~-TVVVGd~ 155 (177)
.++.+||++|+.|.. | .+ +..+..-++.|...|.. .+|||+.
T Consensus 607 ~va~~LR~~Gi~vev---d----~~-~~~l~kkir~A~~~g~~~viivG~~ 649 (686)
T PLN02908 607 EVRAQLHAAGFYVDV---D----VT-DRKIQKKVREAQLAQYNYILVVGEA 649 (686)
T ss_pred HHHHHHHHCCCEEEE---E----CC-CCCHHHHHHHHHHcCCCEEEEECch
Confidence 358899999998753 2 23 44699999999999988 4556764
No 414
>PF13788 DUF4180: Domain of unknown function (DUF4180)
Probab=21.09 E-value=98 Score=24.42 Aligned_cols=37 Identities=22% Similarity=0.351 Sum_probs=27.4
Q ss_pred ecceEEEEeC--CCch--------HHHHHHHHHcCccEEEEecCCch
Q 037201 122 RFGCLMVVSD--DSNF--------VEVFQEATLRCLKMVVVGDMSDG 158 (177)
Q Consensus 122 ~v~clvLVSD--dsdf--------~~~lr~Ar~r~l~TVVVGd~~~~ 158 (177)
+.++++|=.+ +.|| +++|++..--+++..||||.+..
T Consensus 35 ~~~~i~l~~~~l~~dFF~L~TglAGeiLQKf~NY~iklAivGD~s~~ 81 (113)
T PF13788_consen 35 GADRIILPKEALSEDFFDLRTGLAGEILQKFVNYRIKLAIVGDFSAY 81 (113)
T ss_pred CCCEEEEEhHHCCHHHHHhhcchHHHHHHHHHhhceeEEEEEccccc
Confidence 5666666444 2344 57899999999999999998633
No 415
>PRK09248 putative hydrolase; Validated
Probab=20.94 E-value=1.1e+02 Score=25.34 Aligned_cols=27 Identities=30% Similarity=0.316 Sum_probs=23.2
Q ss_pred eCC--CchHHHHHHHHHcCccEEEEecCC
Q 037201 130 SDD--SNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 130 SDd--sdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
|+| +...++++.|.+.|+.++.|-|-+
T Consensus 14 s~~~~~~~~e~v~~A~~~G~~~i~iTdH~ 42 (246)
T PRK09248 14 SGHAYSTLHENAAEAKQKGLKLFAITDHG 42 (246)
T ss_pred CCCCCCCHHHHHHHHHHCCCCEEEECCCC
Confidence 544 368999999999999999999975
No 416
>TIGR01488 HAD-SF-IB Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like. Subfamily IA includes the enzyme phosphoserine phosphatase (TIGR00338) as well as three hypothetical equivalogs. Many members of these hypothetical equivalogs have been annotated as PSPase-like or PSPase-family proteins. In particular, the hypothetical equivalog which appears to be most closely related to PSPase contains only Archaea (while TIGR00338 contains only eukaryotes and bacteria) of which some are annotated as PSPases. Although this is a reasonable conjecture, none of these sequences has sufficient evidence for this assignment. If such should be found, this model should be retired while the PSPase model should be broadened to include these sequences.
Probab=20.77 E-value=1.4e+02 Score=22.34 Aligned_cols=24 Identities=17% Similarity=0.064 Sum_probs=12.2
Q ss_pred CchHHHHHHHHHcCccEEEEecCC
Q 037201 133 SNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 133 sdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
+.+.++|+..+++|.+.+||+++.
T Consensus 76 ~g~~~~l~~l~~~g~~~~ivS~~~ 99 (177)
T TIGR01488 76 PGARELISWLKERGIDTVIVSGGF 99 (177)
T ss_pred cCHHHHHHHHHHCCCEEEEECCCc
Confidence 445555555555555555555443
No 417
>PRK11914 diacylglycerol kinase; Reviewed
Probab=20.75 E-value=1.8e+02 Score=24.89 Aligned_cols=50 Identities=18% Similarity=0.159 Sum_probs=28.7
Q ss_pred HhhhhcEEEEEeecceEEEEeCCCchHHHHHHHHHcCccEEEEecCCchhhhhhhcc
Q 037201 110 ELKRAWFCVRNVRFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMSDGALKRIANA 166 (177)
Q Consensus 110 eLrRAGv~Vr~V~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~ 166 (177)
.|+.+|+.+..+ ......+-..+.++|.+.+..+|||..+ ||.+...++.
T Consensus 34 ~l~~~g~~~~~~------~t~~~~~~~~~a~~~~~~~~d~vvv~GG-DGTi~evv~~ 83 (306)
T PRK11914 34 RLHHRGVDVVEI------VGTDAHDARHLVAAALAKGTDALVVVGG-DGVISNALQV 83 (306)
T ss_pred HHHHcCCeEEEE------EeCCHHHHHHHHHHHHhcCCCEEEEECC-chHHHHHhHH
Confidence 456666543321 2223344555666666677777887777 4777766653
No 418
>cd06380 PBP1_iGluR_AMPA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, a member of the glutamate-receptor ion channels (iGluRs). AMPA receptors are the major mediators of excitatory synaptic transmission in the central nervous system. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excita
Probab=20.62 E-value=1.2e+02 Score=26.12 Aligned_cols=28 Identities=0% Similarity=0.006 Sum_probs=18.6
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccE
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKM 149 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~T 149 (177)
+.|.+||.+-..+-..+++.|++.|+.+
T Consensus 183 ~~~~iil~~~~~~~~~i~~qa~~~gm~~ 210 (382)
T cd06380 183 KEKRIVLDCESERLNKILEQIVDVGKNR 210 (382)
T ss_pred cceEEEEECCHHHHHHHHHHHHHhhhcc
Confidence 4566666666666777777777766655
No 419
>cd03174 DRE_TIM_metallolyase DRE-TIM metallolyase superfamily. The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".
Probab=20.54 E-value=1.2e+02 Score=24.65 Aligned_cols=45 Identities=22% Similarity=0.279 Sum_probs=33.0
Q ss_pred HHhhhhcEEEEEe---ecceEEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 109 DELKRAWFCVRNV---RFGCLMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 109 ~eLrRAGv~Vr~V---~v~clvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
..++..|+.|... -..| ..+...+.++++.+.+.|+.+|.+-|..
T Consensus 122 ~~a~~~G~~v~~~~~~~~~~---~~~~~~l~~~~~~~~~~g~~~i~l~Dt~ 169 (265)
T cd03174 122 EAAKEAGLEVEGSLEDAFGC---KTDPEYVLEVAKALEEAGADEISLKDTV 169 (265)
T ss_pred HHHHHCCCeEEEEEEeecCC---CCCHHHHHHHHHHHHHcCCCEEEechhc
Confidence 3456677665543 1222 4667778899999999999999999985
No 420
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=20.46 E-value=36 Score=35.20 Aligned_cols=30 Identities=27% Similarity=0.350 Sum_probs=26.1
Q ss_pred hhhhhhhhcCCCcCChhHHHHHHHhhhhhhh
Q 037201 44 KENCLLIRNQGRFYNNDKLVNHFRQIHEGEQ 74 (177)
Q Consensus 44 er~~Lc~~CGrrf~t~~~L~kHFkqlHerEr 74 (177)
-|||-|..||.-|+-...|+-|.+ ||--|.
T Consensus 279 lRKFKCtECgKAFKfKHHLKEHlR-IHSGEK 308 (1007)
T KOG3623|consen 279 LRKFKCTECGKAFKFKHHLKEHLR-IHSGEK 308 (1007)
T ss_pred hccccccccchhhhhHHHHHhhhe-eecCCC
Confidence 488889999999999999999985 888875
No 421
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=20.45 E-value=1.4e+02 Score=19.15 Aligned_cols=39 Identities=15% Similarity=0.123 Sum_probs=25.6
Q ss_pred HhhhhcEEEEEeecceEEEEeCC-CchHHHHHHHHHcCccEEEEec
Q 037201 110 ELKRAWFCVRNVRFGCLMVVSDD-SNFVEVFQEATLRCLKMVVVGD 154 (177)
Q Consensus 110 eLrRAGv~Vr~V~v~clvLVSDd-sdf~~~lr~Ar~r~l~TVVVGd 154 (177)
.|+..|+....+.++ +| ....++.+......+-+|+||+
T Consensus 18 ~L~~~~i~y~~~dv~------~~~~~~~~l~~~~g~~~~P~v~i~g 57 (60)
T PF00462_consen 18 FLDEKGIPYEEVDVD------EDEEAREELKELSGVRTVPQVFIDG 57 (60)
T ss_dssp HHHHTTBEEEEEEGG------GSHHHHHHHHHHHSSSSSSEEEETT
T ss_pred HHHHcCCeeeEcccc------cchhHHHHHHHHcCCCccCEEEECC
Confidence 467778777666554 44 4444455555668888999976
No 422
>TIGR00854 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters.
Probab=20.43 E-value=95 Score=24.95 Aligned_cols=40 Identities=15% Similarity=0.063 Sum_probs=30.8
Q ss_pred EEEEEeecceEEEEeCCCch----HHHHHHHHHcCccEEEEecC
Q 037201 116 FCVRNVRFGCLMVVSDDSNF----VEVFQEATLRCLKMVVVGDM 155 (177)
Q Consensus 116 v~Vr~V~v~clvLVSDdsdf----~~~lr~Ar~r~l~TVVVGd~ 155 (177)
-|++..+++.|++|+|..-- ..+|++|.=.|+++.+.+-.
T Consensus 19 ~W~~~~~~~~IiVvdD~~A~D~~~k~~lkma~P~gvk~~i~sve 62 (151)
T TIGR00854 19 TWTKVAGANRIIVVNDDVANDEVRQTLMGIVAPTGFKVRFVSLE 62 (151)
T ss_pred hhhcccCCCEEEEEcccccCCHHHHHHHHhhCCCCCEEEEEEHH
Confidence 48888899999999986543 45566777789999888754
No 423
>cd06388 PBP1_iGluR_AMPA_GluR4 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=20.28 E-value=1.5e+02 Score=26.29 Aligned_cols=33 Identities=0% Similarity=0.076 Sum_probs=25.8
Q ss_pred ecceEEEEeCCCchHHHHHHHHHcCccEE----EEec
Q 037201 122 RFGCLMVVSDDSNFVEVFQEATLRCLKMV----VVGD 154 (177)
Q Consensus 122 ~v~clvLVSDdsdf~~~lr~Ar~r~l~TV----VVGd 154 (177)
+.+.+||.+-..+-..+|+.|++.|+.+- ++|+
T Consensus 178 ~~~~iil~~~~~~~~~il~qa~~~gm~~~~y~~il~~ 214 (371)
T cd06388 178 QEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIAN 214 (371)
T ss_pred ccEEEEEECCHHHHHHHHHHHHhcCccccceEEEEcc
Confidence 67788888888888888888888888775 5565
No 424
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=20.24 E-value=16 Score=22.57 Aligned_cols=25 Identities=28% Similarity=0.312 Sum_probs=14.1
Q ss_pred hhhhcCCCcCChhHHHHHHHhhhhhh
Q 037201 48 LLIRNQGRFYNNDKLVNHFRQIHEGE 73 (177)
Q Consensus 48 Lc~~CGrrf~t~~~L~kHFkqlHerE 73 (177)
.|+-||..| +.++.+.|=+=|=|-|
T Consensus 2 sCiDC~~~F-~~~~y~~Ht~CItE~e 26 (28)
T PF08790_consen 2 SCIDCSKDF-DGDSYKSHTSCITEAE 26 (28)
T ss_dssp EETTTTEEE-EGGGTTT-----S---
T ss_pred eeecCCCCc-CcCCcCCCCcccCccc
Confidence 488999999 7788888876665554
No 425
>COG2896 MoaA Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism]
Probab=20.13 E-value=1.1e+02 Score=28.02 Aligned_cols=71 Identities=21% Similarity=0.205 Sum_probs=45.4
Q ss_pred HhhcCCCCCC---CchHHhhhhcEEEEEeecceEEEEeCCCchH---------HH---HHHHHHcCcc-----EEEEecC
Q 037201 96 SAILTPKVGY---GFADELKRAWFCVRNVRFGCLMVVSDDSNFV---------EV---FQEATLRCLK-----MVVVGDM 155 (177)
Q Consensus 96 r~vl~pkvgy---gLa~eLrRAGv~Vr~V~v~clvLVSDdsdf~---------~~---lr~Ar~r~l~-----TVVVGd~ 155 (177)
.++.+=-.|| ..|.+||.||+-=-+|++|.| |+.-|. .+ ++.|.++|+. |||+-+-
T Consensus 89 ~~islTTNG~~L~~~a~~Lk~AGl~rVNVSLDsl----d~e~f~~IT~~~~~~~Vl~GI~~A~~~Gl~pVKlN~Vv~kgv 164 (322)
T COG2896 89 RDLSLTTNGVLLARRAADLKEAGLDRVNVSLDSL----DPEKFRKITGRDRLDRVLEGIDAAVEAGLTPVKLNTVLMKGV 164 (322)
T ss_pred ceEEEecchhhHHHHHHHHHHcCCcEEEeecccC----CHHHHHHHhCCCcHHHHHHHHHHHHHcCCCceEEEEEEecCC
Confidence 4455555788 678999999998878866643 333333 22 3567777665 7888776
Q ss_pred Cchhhhhhhccccch
Q 037201 156 SDGALKRIANAFFSW 170 (177)
Q Consensus 156 ~~~~L~r~Ad~~~sW 170 (177)
++..+-..++..-+|
T Consensus 165 Nd~ei~~l~e~~~~~ 179 (322)
T COG2896 165 NDDEIEDLLEFAKER 179 (322)
T ss_pred CHHHHHHHHHHHhhc
Confidence 666665555544444
No 426
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=20.08 E-value=56 Score=26.03 Aligned_cols=30 Identities=13% Similarity=0.207 Sum_probs=22.5
Q ss_pred EEEEeCCCchHHHHHHHHHcCccEEEEecCC
Q 037201 126 LMVVSDDSNFVEVFQEATLRCLKMVVVGDMS 156 (177)
Q Consensus 126 lvLVSDdsdf~~~lr~Ar~r~l~TVVVGd~~ 156 (177)
...+.+..|....++.+++.|. .|+||+..
T Consensus 105 ~~~~~~~~e~~~~i~~~~~~G~-~viVGg~~ 134 (176)
T PF06506_consen 105 IYPYDSEEEIEAAIKQAKAEGV-DVIVGGGV 134 (176)
T ss_dssp EEEESSHHHHHHHHHHHHHTT---EEEESHH
T ss_pred EEEECCHHHHHHHHHHHHHcCC-cEEECCHH
Confidence 3455678899999999999995 57788863
No 427
>COG0300 DltE Short-chain dehydrogenases of various substrate specificities [General function prediction only]
Probab=20.08 E-value=1.2e+02 Score=26.90 Aligned_cols=70 Identities=17% Similarity=0.114 Sum_probs=47.3
Q ss_pred CCCCchHHhhhhcEEEEEe------------------ecceEEEEeCCCchHHHHHHHHH---c-CccEEEEecCCchhh
Q 037201 103 VGYGFADELKRAWFCVRNV------------------RFGCLMVVSDDSNFVEVFQEATL---R-CLKMVVVGDMSDGAL 160 (177)
Q Consensus 103 vgygLa~eLrRAGv~Vr~V------------------~v~clvLVSDdsdf~~~lr~Ar~---r-~l~TVVVGd~~~~~L 160 (177)
.|+.+|.+|-+-|+.|-.| +++|-|+..|=++..++.+...+ + +-=+|.|=+--=|..
T Consensus 18 IG~~~A~~lA~~g~~liLvaR~~~kL~~la~~l~~~~~v~v~vi~~DLs~~~~~~~l~~~l~~~~~~IdvLVNNAG~g~~ 97 (265)
T COG0300 18 IGAELAKQLARRGYNLILVARREDKLEALAKELEDKTGVEVEVIPADLSDPEALERLEDELKERGGPIDVLVNNAGFGTF 97 (265)
T ss_pred HHHHHHHHHHHCCCEEEEEeCcHHHHHHHHHHHHHhhCceEEEEECcCCChhHHHHHHHHHHhcCCcccEEEECCCcCCc
Confidence 4888999999999999999 88999999888888777776654 3 223445543211333
Q ss_pred hhhhccccchhhhh
Q 037201 161 KRIANAFFSWSDLL 174 (177)
Q Consensus 161 ~r~Ad~~~sW~ev~ 174 (177)
+..+| .||++.+
T Consensus 98 g~f~~--~~~~~~~ 109 (265)
T COG0300 98 GPFLE--LSLDEEE 109 (265)
T ss_pred cchhh--CChHHHH
Confidence 43433 5666643
No 428
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=20.03 E-value=1.7e+02 Score=19.44 Aligned_cols=31 Identities=16% Similarity=0.324 Sum_probs=22.2
Q ss_pred CCchHHHHHHHHHcCccEEEEecCCchhhhhhhc
Q 037201 132 DSNFVEVFQEATLRCLKMVVVGDMSDGALKRIAN 165 (177)
Q Consensus 132 dsdf~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad 165 (177)
|..+.++++.|++.|+....|.+. .|.+.+|
T Consensus 29 ~~~~~~i~~~~~~~~i~v~~v~~~---~l~~ls~ 59 (76)
T PF08032_consen 29 DKRIKEILKLAKKKGIPVYEVSKK---VLDKLSD 59 (76)
T ss_dssp -CCTHHHHHHHHHCT-EEEEE-HH---HHHHCTT
T ss_pred chhHHHHHHHHHHcCCeEEEeCHH---HHHHHcC
Confidence 356899999999999999998765 4555554
No 429
>PTZ00295 glucosamine-fructose-6-phosphate aminotransferase; Provisional
Probab=20.00 E-value=1.6e+02 Score=28.47 Aligned_cols=78 Identities=18% Similarity=0.297 Sum_probs=46.3
Q ss_pred hHHHHHHHHhhcCCCC----CCC----chH----HhhhhcE-EEEEe-------------e----cceEEEEeCCCc---
Q 037201 88 MEKYKMAVSAILTPKV----GYG----FAD----ELKRAWF-CVRNV-------------R----FGCLMVVSDDSN--- 134 (177)
Q Consensus 88 ~~KY~~Aar~vl~pkv----gyg----La~----eLrRAGv-~Vr~V-------------~----v~clvLVSDdsd--- 134 (177)
.++++++|..+...+. |+| .|. -|++.+. .+... . ...+++.+.|..
T Consensus 483 ~~~~~~~a~~l~~a~~i~~lGrG~~~~iA~E~ALKLkEi~~i~ae~~~~~E~~HGp~ali~~~~~~~VI~i~~~~~~~~~ 562 (640)
T PTZ00295 483 EEQCKRIAEKLKNAKSMFILGKGLGYPIALEGALKIKEITYIHAEGFSGGALKHGPFALIDKEKNTPVILIILDDEHKEL 562 (640)
T ss_pred HHHHHHHHHHHhCCCcEEEEECCCCHHHHHHHHHHHHHHhhhhhhhcChHHhhhhHHHHhcCCCCCeEEEEEcCCccHHH
Confidence 4678888877665543 444 333 3556654 33222 2 223555556553
Q ss_pred hHHHHHHHHHcCccEEEEecCCchhhhhhhcc
Q 037201 135 FVEVFQEATLRCLKMVVVGDMSDGALKRIANA 166 (177)
Q Consensus 135 f~~~lr~Ar~r~l~TVVVGd~~~~~L~r~Ad~ 166 (177)
...+++.++++|.+.++|++.. ..+...+|.
T Consensus 563 ~~~~~~~lk~rga~vi~It~~~-~~l~~~ad~ 593 (640)
T PTZ00295 563 MINAAEQVKARGAYIIVITDDE-DLVKDFADE 593 (640)
T ss_pred HHHHHHHHHHcCCEEEEEecCC-ccccccCCe
Confidence 3456677778999999999874 345556664
Done!