Query 029441
Match_columns 193
No_of_seqs 112 out of 185
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 12:58:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029441.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029441hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04722 Ssu72: Ssu72-like pro 100.0 2E-113 4E-118 723.2 14.8 192 2-193 1-195 (195)
2 KOG2424 Protein involved in tr 100.0 9E-105 2E-109 666.4 18.3 191 1-193 4-195 (195)
3 COG5211 SSU72 RNA polymerase I 100.0 2.6E-90 5.6E-95 573.9 17.2 190 2-193 6-197 (197)
4 COG0394 Wzb Protein-tyrosine-p 97.3 0.0017 3.6E-08 52.2 8.5 109 1-144 1-113 (139)
5 PRK11391 etp phosphotyrosine-p 96.7 0.0056 1.2E-07 48.9 6.4 91 3-123 3-95 (144)
6 smart00226 LMWPc Low molecular 96.2 0.0085 1.8E-07 46.4 4.7 87 5-122 1-90 (140)
7 PRK10126 tyrosine phosphatase; 95.9 0.0092 2E-07 47.5 3.7 92 1-122 1-94 (147)
8 PF01451 LMWPc: Low molecular 95.8 0.0099 2.1E-07 45.8 3.5 107 5-144 1-116 (138)
9 TIGR02689 ars_reduc_gluta arse 91.0 0.15 3.3E-06 39.4 2.0 34 3-36 1-37 (126)
10 PRK13530 arsenate reductase; P 89.9 0.29 6.4E-06 38.5 2.8 35 2-36 3-40 (133)
11 cd00115 LMWPc Substituted upda 88.9 0.35 7.5E-06 37.6 2.5 34 3-36 1-38 (141)
12 cd01523 RHOD_Lact_B Member of 86.6 1 2.2E-05 32.4 3.7 32 4-36 63-94 (100)
13 PLN02160 thiosulfate sulfurtra 83.0 1.3 2.9E-05 34.8 3.1 30 4-34 83-113 (136)
14 TIGR03746 conj_TIGR03746 integ 81.9 1.3 2.8E-05 38.7 2.8 96 36-140 51-179 (202)
15 TIGR02691 arsC_pI258_fam arsen 81.0 1.1 2.3E-05 35.2 1.9 32 5-36 1-35 (129)
16 cd01534 4RHOD_Repeat_3 Member 79.7 2.9 6.3E-05 29.9 3.7 29 4-33 58-86 (95)
17 COG0607 PspE Rhodanese-related 79.6 2.5 5.5E-05 30.1 3.4 28 3-31 62-89 (110)
18 cd01447 Polysulfide_ST Polysul 75.1 3.7 8E-05 29.1 3.1 30 3-33 62-92 (103)
19 cd01518 RHOD_YceA Member of th 73.9 3.9 8.4E-05 29.5 3.0 29 4-33 63-92 (101)
20 cd01533 4RHOD_Repeat_2 Member 73.0 5.6 0.00012 29.2 3.7 32 4-36 68-101 (109)
21 TIGR02981 phageshock_pspE phag 71.7 3.2 7E-05 31.3 2.2 30 4-34 60-90 (101)
22 PRK10287 thiosulfate:cyanide s 71.3 3.5 7.7E-05 31.4 2.4 40 4-46 62-102 (104)
23 PRK10310 PTS system galactitol 71.2 4.8 0.0001 30.1 3.0 31 1-31 1-35 (94)
24 cd01526 RHOD_ThiF Member of th 70.2 6.1 0.00013 29.8 3.4 30 3-33 73-104 (122)
25 KOG2424 Protein involved in tr 69.5 2.8 6.1E-05 36.4 1.6 59 3-61 9-68 (195)
26 TIGR03292 PhnH_redo phosphonat 67.4 3.8 8.3E-05 34.6 2.0 26 28-53 108-133 (174)
27 PRK00162 glpE thiosulfate sulf 67.1 8.7 0.00019 28.1 3.7 31 3-34 59-90 (108)
28 cd01520 RHOD_YbbB Member of th 65.8 10 0.00022 29.0 3.9 33 4-36 88-120 (128)
29 cd01524 RHOD_Pyr_redox Member 64.0 11 0.00024 26.6 3.6 29 4-33 53-81 (90)
30 cd01521 RHOD_PspE2 Member of t 63.9 12 0.00025 27.6 3.8 31 3-33 65-96 (110)
31 cd01449 TST_Repeat_2 Thiosulfa 62.0 7.3 0.00016 28.5 2.4 30 4-34 80-110 (118)
32 cd01528 RHOD_2 Member of the R 60.1 15 0.00032 26.4 3.7 31 3-34 59-90 (101)
33 cd01519 RHOD_HSP67B2 Member of 58.9 11 0.00024 26.9 2.9 29 4-33 68-97 (106)
34 cd01391 Periplasmic_Binding_Pr 58.0 27 0.00058 26.8 5.0 131 6-142 61-220 (269)
35 cd01529 4RHOD_Repeats Member o 57.4 14 0.0003 26.4 3.2 30 4-34 58-88 (96)
36 TIGR00725 conserved hypothetic 57.4 13 0.00027 30.4 3.3 32 3-35 2-38 (159)
37 cd01736 LSm14_N LSm14 (also kn 57.2 7.6 0.00016 29.0 1.8 41 6-54 21-62 (74)
38 PRK10147 phnH carbon-phosphoru 56.4 16 0.00035 31.5 3.9 26 28-53 126-151 (196)
39 smart00450 RHOD Rhodanese Homo 54.3 22 0.00047 24.0 3.6 31 3-34 57-88 (100)
40 cd06331 PBP1_AmiC_like Type I 52.1 37 0.0008 29.0 5.5 43 112-154 20-62 (333)
41 PRK05320 rhodanese superfamily 51.7 16 0.00036 32.0 3.3 28 3-31 176-204 (257)
42 PRK01415 hypothetical protein; 50.4 15 0.00033 32.4 2.9 30 3-33 172-202 (247)
43 cd01444 GlpE_ST GlpE sulfurtra 50.3 25 0.00054 24.5 3.5 27 4-31 58-85 (96)
44 KOG0239 Kinesin (KAR3 subfamil 50.1 14 0.0003 37.2 2.9 118 27-158 391-548 (670)
45 KOG1530 Rhodanese-related sulf 49.5 18 0.00038 30.0 2.9 29 5-34 92-121 (136)
46 cd01527 RHOD_YgaP Member of th 49.4 27 0.00058 24.8 3.6 30 4-34 56-86 (99)
47 COG3625 PhnH Uncharacterized e 47.9 31 0.00068 30.1 4.3 58 28-114 128-185 (196)
48 PF06841 Phage_T4_gp19: T4-lik 45.6 9.5 0.00021 29.1 0.8 60 28-87 27-94 (134)
49 cd01525 RHOD_Kc Member of the 45.5 37 0.00081 24.2 3.8 30 4-34 67-97 (105)
50 PF07927 YcfA: YcfA-like prote 45.1 17 0.00036 24.0 1.8 24 18-42 3-26 (56)
51 PF02302 PTS_IIB: PTS system, 44.8 25 0.00054 24.8 2.8 31 4-34 1-35 (90)
52 cd06007 R3H_DEXH_helicase R3H 43.9 13 0.00028 26.2 1.2 26 12-38 27-52 (59)
53 cd06356 PBP1_Amide_Urea_BP_lik 43.7 62 0.0013 27.9 5.6 42 113-154 21-62 (334)
54 cd06354 PBP1_BmpA_PnrA_like Pe 43.7 29 0.00062 28.9 3.4 42 6-48 186-227 (265)
55 cd01448 TST_Repeat_1 Thiosulfa 42.7 45 0.00098 24.6 4.0 31 3-33 80-111 (122)
56 cd06335 PBP1_ABC_ligand_bindin 42.1 52 0.0011 28.5 4.9 44 113-156 21-64 (347)
57 COG4822 CbiK Cobalamin biosynt 41.9 14 0.00029 33.4 1.3 33 51-83 7-52 (265)
58 PF05845 PhnH: Bacterial phosp 41.6 10 0.00022 32.4 0.4 26 29-54 124-149 (192)
59 cd06355 PBP1_FmdD_like Peripla 41.5 71 0.0015 27.8 5.7 43 113-155 21-63 (348)
60 COG0473 LeuB Isocitrate/isopro 41.5 55 0.0012 30.9 5.2 114 45-177 179-320 (348)
61 COG4747 ACT domain-containing 40.8 18 0.0004 29.9 1.7 20 13-32 49-68 (142)
62 cd06346 PBP1_ABC_ligand_bindin 40.0 68 0.0015 27.3 5.2 43 112-154 20-62 (312)
63 cd00636 TroA-like Helical back 39.4 1.4E+02 0.0029 21.1 7.4 77 103-184 61-137 (148)
64 cd06357 PBP1_AmiC Periplasmic 38.8 80 0.0017 27.7 5.6 45 112-156 20-64 (360)
65 cd01530 Cdc25 Cdc25 phosphatas 37.9 48 0.001 25.3 3.6 24 3-26 69-92 (121)
66 COG2169 Ada Adenosine deaminas 37.3 32 0.00069 29.7 2.8 31 134-164 47-94 (187)
67 KOG0391 SNF2 family DNA-depend 37.2 17 0.00036 40.0 1.2 88 5-98 669-760 (1958)
68 cd02645 R3H_AAA R3H domain of 36.8 31 0.00067 24.4 2.2 23 19-41 34-56 (60)
69 TIGR00137 gid_trmFO tRNA:m(5)U 36.7 44 0.00095 31.9 3.9 52 6-58 128-180 (433)
70 TIGR03407 urea_ABC_UrtA urea A 36.2 97 0.0021 27.2 5.7 43 113-155 22-64 (359)
71 COG2198 ArcB FOG: HPt domain [ 35.6 75 0.0016 23.9 4.3 35 147-181 67-104 (122)
72 PF13458 Peripla_BP_6: Peripla 35.5 71 0.0015 26.8 4.6 40 113-152 23-62 (343)
73 cd02325 R3H R3H domain. The na 35.2 38 0.00082 21.4 2.3 20 18-37 32-51 (59)
74 cd06344 PBP1_ABC_ligand_bindin 35.1 91 0.002 26.7 5.3 42 114-155 21-62 (332)
75 PRK01175 phosphoribosylformylg 35.0 53 0.0011 29.1 3.9 34 1-34 2-35 (261)
76 COG3414 SgaB Phosphotransferas 34.9 47 0.001 25.3 3.1 27 2-28 1-31 (93)
77 cd02640 R3H_NRF R3H domain of 34.0 37 0.0008 24.0 2.2 25 13-38 29-53 (60)
78 cd05563 PTS_IIB_ascorbate PTS_ 33.1 33 0.00072 24.2 1.9 25 4-28 1-29 (86)
79 PRK11784 tRNA 2-selenouridine 32.9 51 0.0011 30.3 3.5 171 3-181 89-315 (345)
80 cd01574 PBP1_LacI Ligand-bindi 32.8 1.5E+02 0.0032 23.8 5.9 38 104-141 175-212 (264)
81 KOG3217 Protein tyrosine phosp 32.7 39 0.00084 28.7 2.5 89 2-124 6-102 (159)
82 TIGR03669 urea_ABC_arch urea A 32.7 1.1E+02 0.0023 27.7 5.5 44 112-155 21-64 (374)
83 PRK00142 putative rhodanese-re 32.6 52 0.0011 29.7 3.5 30 3-33 172-202 (314)
84 PRK08762 molybdopterin biosynt 32.3 54 0.0012 29.9 3.6 29 4-33 59-88 (376)
85 cd06366 PBP1_GABAb_receptor Li 32.2 1.1E+02 0.0023 26.4 5.2 41 112-152 18-59 (350)
86 TIGR03167 tRNA_sel_U_synt tRNA 31.0 53 0.0012 29.8 3.3 65 4-69 76-151 (311)
87 cd06358 PBP1_NHase Type I peri 30.9 1.3E+02 0.0029 25.6 5.6 41 113-153 21-61 (333)
88 cd06329 PBP1_SBP_like_3 Peripl 30.4 1.2E+02 0.0026 26.2 5.2 45 112-159 20-64 (342)
89 PLN00123 isocitrate dehydrogen 29.9 60 0.0013 30.6 3.5 115 45-177 191-334 (360)
90 cd01144 BtuF Cobalamin binding 29.4 3.1E+02 0.0068 22.3 8.0 71 103-183 57-130 (245)
91 PRK01220 malonate decarboxylas 29.1 58 0.0013 25.6 2.8 45 112-164 52-96 (99)
92 cd06268 PBP1_ABC_transporter_L 29.1 1.5E+02 0.0033 23.5 5.3 43 18-63 81-123 (298)
93 KOG3212 Uncharacterized conser 28.2 28 0.00061 30.6 1.0 52 5-56 100-151 (208)
94 cd06296 PBP1_CatR_like Ligand- 28.1 2E+02 0.0043 23.2 5.9 40 103-142 178-217 (270)
95 cd05566 PTS_IIB_galactitol PTS 28.0 51 0.0011 23.4 2.1 27 3-29 1-31 (89)
96 cd06276 PBP1_FucR_like Ligand- 27.8 56 0.0012 27.0 2.7 53 6-64 165-223 (247)
97 PF04831 Popeye: Popeye protei 27.6 36 0.00078 28.6 1.5 36 77-114 65-102 (153)
98 cd04918 ACT_AK1-AT_2 ACT domai 27.4 1.4E+02 0.003 20.2 4.2 33 4-36 3-39 (65)
99 smart00393 R3H Putative single 27.3 56 0.0012 23.3 2.3 21 18-38 51-71 (79)
100 PF01320 Colicin_Pyocin: Colic 27.3 64 0.0014 24.6 2.6 34 153-186 14-48 (85)
101 PF08373 RAP: RAP domain; Int 27.1 44 0.00096 22.0 1.6 18 16-33 20-37 (58)
102 cd06334 PBP1_ABC_ligand_bindin 26.8 1.2E+02 0.0027 26.7 4.8 43 112-154 20-62 (351)
103 cd06326 PBP1_STKc_like Type I 26.7 1.8E+02 0.0039 24.5 5.6 36 113-148 22-57 (336)
104 TIGR00730 conserved hypothetic 26.7 66 0.0014 26.8 2.9 32 3-34 1-39 (178)
105 cd06304 PBP1_BmpA_like Peripla 26.5 1E+02 0.0022 25.3 4.0 56 6-67 182-237 (260)
106 cd06293 PBP1_LacI_like_11 Liga 26.3 1.2E+02 0.0026 24.6 4.3 38 103-140 177-214 (269)
107 PF07934 OGG_N: 8-oxoguanine D 26.3 51 0.0011 24.9 2.0 24 50-73 74-97 (117)
108 TIGR01125 MiaB-like tRNA modif 26.2 1E+02 0.0022 28.5 4.4 95 9-125 9-109 (430)
109 PF13377 Peripla_BP_3: Peripla 25.8 1E+02 0.0022 23.0 3.6 36 104-139 69-104 (160)
110 PF01725 Ham1p_like: Ham1 fami 25.4 31 0.00066 28.9 0.7 47 7-61 2-48 (189)
111 PRK02103 malonate decarboxylas 25.2 71 0.0015 25.3 2.7 45 112-164 56-100 (105)
112 cd00158 RHOD Rhodanese Homolog 24.9 80 0.0017 21.0 2.6 27 4-31 52-79 (89)
113 PF11823 DUF3343: Protein of u 24.7 80 0.0017 22.2 2.7 36 8-43 6-49 (73)
114 cd01544 PBP1_GalR Ligand-bindi 24.4 3E+02 0.0064 22.5 6.3 38 103-140 179-216 (270)
115 COG1598 Predicted nuclease of 24.2 1.3E+02 0.0029 21.4 3.7 48 46-98 21-68 (73)
116 cd06341 PBP1_ABC_ligand_bindin 24.1 2E+02 0.0042 24.5 5.4 41 113-153 21-61 (341)
117 smart00280 KAZAL Kazal type se 24.0 56 0.0012 20.8 1.6 29 5-34 10-44 (46)
118 cd06284 PBP1_LacI_like_6 Ligan 23.9 2.8E+02 0.0062 22.0 6.0 40 103-142 176-215 (267)
119 TIGR03130 malonate_delta malon 23.7 70 0.0015 25.1 2.3 44 112-163 54-97 (98)
120 cd02641 R3H_Smubp-2_like R3H d 23.5 77 0.0017 22.1 2.3 21 18-38 33-53 (60)
121 PHA02576 3 tail completion and 23.5 29 0.00062 29.8 0.2 62 37-98 53-130 (177)
122 PRK12702 mannosyl-3-phosphogly 22.9 1.9E+02 0.0042 26.7 5.4 64 6-71 37-113 (302)
123 smart00267 GGDEF diguanylate c 22.8 2.5E+02 0.0053 20.0 5.0 52 112-163 14-70 (163)
124 cd08555 PI-PLCc_GDPD_SF Cataly 22.8 2.1E+02 0.0045 23.0 5.0 45 115-160 62-106 (179)
125 cd06343 PBP1_ABC_ligand_bindin 22.7 2.1E+02 0.0046 24.6 5.4 43 112-154 27-69 (362)
126 PF13399 LytR_C: LytR cell env 22.1 1.7E+02 0.0036 20.8 4.0 36 2-37 3-39 (90)
127 PRK03379 vitamin B12-transport 22.0 4.9E+02 0.011 22.0 7.4 68 104-181 73-143 (260)
128 PRK11041 DNA-binding transcrip 21.9 3.8E+02 0.0082 22.2 6.6 40 103-142 213-252 (309)
129 cd06268 PBP1_ABC_transporter_L 21.7 2.7E+02 0.0058 22.1 5.5 38 113-150 21-58 (298)
130 cd06576 PASTA_Pbp2x-like_1 PAS 21.6 1E+02 0.0023 19.0 2.5 21 17-37 11-31 (55)
131 cd06300 PBP1_ABC_sugar_binding 21.6 1E+02 0.0023 25.0 3.1 25 5-31 187-211 (272)
132 COG0614 FepB ABC-type Fe3+-hyd 21.4 4.8E+02 0.01 21.8 7.2 69 104-183 116-187 (319)
133 cd01575 PBP1_GntR Ligand-bindi 21.3 3.2E+02 0.0068 21.8 5.8 39 103-141 177-215 (268)
134 cd00515 HAM1 NTPase/HAM1. Thi 21.3 1.3E+02 0.0028 25.1 3.6 29 7-35 2-30 (183)
135 PRK06737 acetolactate synthase 21.3 59 0.0013 24.0 1.5 16 21-36 21-36 (76)
136 PRK08178 acetolactate synthase 21.3 53 0.0011 25.5 1.2 26 21-47 27-52 (96)
137 cd01537 PBP1_Repressors_Sugar_ 21.2 2.4E+02 0.0052 22.0 5.0 129 5-141 57-216 (264)
138 TIGR00762 DegV EDD domain prot 21.1 1.7E+02 0.0038 25.3 4.6 143 5-181 1-151 (275)
139 COG1307 DegV Uncharacterized p 21.1 1.6E+02 0.0035 26.3 4.4 46 136-182 110-155 (282)
140 cd06349 PBP1_ABC_ligand_bindin 20.8 2.2E+02 0.0048 24.3 5.1 42 113-154 21-62 (340)
141 cd06327 PBP1_SBP_like_1 Peripl 20.8 2.1E+02 0.0045 24.4 4.9 61 5-67 68-128 (334)
142 cd06348 PBP1_ABC_ligand_bindin 20.6 2.5E+02 0.0054 24.0 5.4 44 112-158 20-63 (344)
143 cd04922 ACT_AKi-HSDH-ThrA_2 AC 20.6 2.5E+02 0.0053 18.0 4.3 51 4-65 3-57 (66)
144 COG4566 TtrR Response regulato 20.1 53 0.0011 28.9 1.1 25 21-45 22-62 (202)
No 1
>PF04722 Ssu72: Ssu72-like protein; InterPro: IPR006811 The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB []. It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs [].; GO: 0004721 phosphoprotein phosphatase activity, 0006397 mRNA processing, 0005634 nucleus; PDB: 3O2S_B 3O2Q_E 3FMV_H 3OMW_D 3P9Y_B 3FDF_A 3OMX_A.
Probab=100.00 E-value=1.8e-113 Score=723.18 Aligned_cols=192 Identities=58% Similarity=1.006 Sum_probs=168.2
Q ss_pred CceEEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhh
Q 029441 2 KYRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPM 81 (193)
Q Consensus 2 ~l~~avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NGlL~M 81 (193)
++|||||||||||||||||++|+++||+|+||||||+|||||||+|+||||+|||||++||+||.+||++||++||||+|
T Consensus 1 ~l~~avVCasN~NRSMEAH~~L~~~G~~V~SfGTGs~VkLPGps~d~PnvY~FgT~Y~~iy~dL~~kd~~lY~~NGlL~M 80 (195)
T PF04722_consen 1 KLRFAVVCASNQNRSMEAHNVLKKAGFNVRSFGTGSHVKLPGPSIDKPNVYDFGTPYDDIYNDLLRKDKELYTQNGLLHM 80 (195)
T ss_dssp -SEEEEEESSSSSHHHHHHHHHHHTT-EEEEEE-SSSEEEEESSTTCEEEE-TTS-HHHHHHHHHHHHHHHHHHTSHHHH
T ss_pred CceEEEEccCCCCcCHHHHHHHHHCCCceEeecCCCcccCCCCCCCCCcccCCCCcHHHHHHHHHHhCHHHHHHcCcHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccCCCCCcccccccCCCCcccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHHH
Q 029441 82 LKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEI 161 (193)
Q Consensus 82 LdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~l 161 (193)
|+|||+||++|||||++++.+.|||||||||||||+|||||++|++++++||||||||||||||||++||++||+||++|
T Consensus 81 L~RN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pvHVINvDIkDnhEeA~~Ga~~ileLc~~l 160 (195)
T PF04722_consen 81 LDRNRRIKPAPERFQDCKEKGKFDVIITCEERVFDQVVEDLNSREQETNQPVHVINVDIKDNHEEATIGAFLILELCQML 160 (195)
T ss_dssp HHHHHCH-SS--BGGG-------SEEEESSHHHHHHHHHHHHCS--SS-EEEEEEEE---SSHHHHHHHHHHHHHHHHHH
T ss_pred HhcCccccCCccchhcCCCCcceeEEEEechHHHHHHHHHHHhccccCCceEEEEEeeccCCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999986669999999999999999999999999999999999999999999999999999999999
Q ss_pred H--hhhhhHHHHHHHHHHHHHHc-CCCcceeeccC
Q 029441 162 E--AAESWEESIDDIIAAFEKRH-RRKLLYSISFY 193 (193)
Q Consensus 162 ~--~~~d~e~~i~~il~~fe~k~-~~~~Lhtv~fY 193 (193)
+ +++|||++|++||++||+|+ ++++|||||||
T Consensus 161 ~~~~~~d~e~~i~~il~~fe~k~p~~~~Lhtv~fY 195 (195)
T PF04722_consen 161 EEEASEDLEDEIDEILQEFEEKHPGRPLLHTVCFY 195 (195)
T ss_dssp H--TSSSHHHHHHHHHHHHHHHH-T--EEEEEEEE
T ss_pred HhhccccHHHHHHHHHHHHHHHcCCCCceEEEecC
Confidence 9 99999999999999999999 78999999998
No 2
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=100.00 E-value=9.1e-105 Score=666.40 Aligned_cols=191 Identities=57% Similarity=0.975 Sum_probs=188.9
Q ss_pred CCceEEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchh
Q 029441 1 MKYRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILP 80 (193)
Q Consensus 1 ~~l~~avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NGlL~ 80 (193)
+++|+|||||||||||||||.+|+++||+|.|||||++||||||++||||||+|||||++||+||.+||+++||+||||+
T Consensus 4 ~~l~~avvC~sN~NRSMeaH~~L~~~G~~v~S~GTg~~vklPG~~~dkPNvY~Fgt~Y~~iy~dL~~kd~~~Y~~nGiL~ 83 (195)
T KOG2424|consen 4 SNLRVAVVCASNQNRSMEAHNILKKKGLNVRSFGTGSHVKLPGPSPDKPNVYDFGTTYKQIYNDLLRKDRELYTRNGILH 83 (195)
T ss_pred ccceeeeeehhcccchHHHHHHHHHcCCcceeecCCCceeCCCCCCCCCCccccCCcHHHHHHHHHhhhHHHHhhcccch
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcccCCCCCcccccccCCCCcccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHH
Q 029441 81 MLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQE 160 (193)
Q Consensus 81 MLdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~ 160 (193)
||+|||+||++|||||++++ .|||||||||||||+|||||++|++.++|||||||+||+||||||++||++||||||+
T Consensus 84 mldRNrriK~~Per~q~~t~--~FDvV~TcEErvyD~VvEdl~~re~~~~qpVhviN~DI~Dn~EdA~~Gaf~I~elcq~ 161 (195)
T KOG2424|consen 84 MLDRNRRIKPAPERFQECTE--VFDVVFTCEERVFDSVVEDLNSREQSLNQPVHVINVDIKDNHEDATLGAFLILELCQC 161 (195)
T ss_pred hhhcccccccCCcchhhccc--cceEEEEehhHHHHHHHHHHHhcccccCCceEEEEeecccCHHhhhhhHHHHHHHHHH
Confidence 99999999999999999987 8999999999999999999999999999999999999999999999999999999999
Q ss_pred HH-hhhhhHHHHHHHHHHHHHHcCCCcceeeccC
Q 029441 161 IE-AAESWEESIDDIIAAFEKRHRRKLLYSISFY 193 (193)
Q Consensus 161 l~-~~~d~e~~i~~il~~fe~k~~~~~Lhtv~fY 193 (193)
|+ +++|||+.||+||++||+++|+++|||||||
T Consensus 162 l~~~s~d~Ed~ideil~~~ee~~~~~~Lhtv~fy 195 (195)
T KOG2424|consen 162 LQAQSDDLEDNIDEILLEFEEKHGRSLLHTVCFY 195 (195)
T ss_pred HHhccccHHHHHHHHHHHHHHhcCCeeEEeeecC
Confidence 99 8999999999999999999999999999998
No 3
>COG5211 SSU72 RNA polymerase II-interacting protein involved in transcription start site selection [Transcription]
Probab=100.00 E-value=2.6e-90 Score=573.90 Aligned_cols=190 Identities=41% Similarity=0.778 Sum_probs=184.1
Q ss_pred CceEEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhh
Q 029441 2 KYRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPM 81 (193)
Q Consensus 2 ~l~~avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NGlL~M 81 (193)
.|||||+||||||||||+|.+|+++||+|.||||||.|||||+|+||||||.||+||++||+||..|+.+.|+.||||.|
T Consensus 6 nlk~~v~CAsNqNRSMetH~vL~~aGy~V~SfGTgsavrLPG~siDKPNvY~FG~pY~~IY~dL~~q~~d~Y~~nGlL~m 85 (197)
T COG5211 6 NLKLAVTCASNQNRSMETHDVLAKAGYPVKSFGTGSAVRLPGESIDKPNVYNFGVPYQQIYDDLCMQNEDHYRENGLLYM 85 (197)
T ss_pred CceEEeeeccCCCcchHHHHHHHHcCCcccccCCCcceeCCCCCCCCCCeeecCCcHHHHHHHHHhhhhhhhhhccHHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccCCCCCcccccccCCCCcccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHHH
Q 029441 82 LKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEI 161 (193)
Q Consensus 82 LdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~l 161 (193)
||||||||.+|||||+..+ .||+||||||||||+|+|||..|++..+|+||+||+||||+||+|.+||++||||+.+|
T Consensus 86 LdRNrrvK~aPe~wq~~~~--~fd~ViTCEERcfdaicEdly~rg~~ln~~v~~iNvDIkD~~e~A~~G~kaILelvd~L 163 (197)
T COG5211 86 LDRNRRVKEAPENWQQRSE--DFDLVITCEERCFDAICEDLYARGPSLNQCVFMINVDIKDTPEDAIAGAKAILELVDVL 163 (197)
T ss_pred HHhcchhhhCchhhhhccc--cccEEEEehHHHHHHHHHHHHhcCccccccEEEEEeeccCChhhhhhhHHHHHHHHHHH
Confidence 9999999999999999987 89999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhhh-hhHHHHHHHHHHHHHHcC-CCcceeeccC
Q 029441 162 EAAE-SWEESIDDIIAAFEKRHR-RKLLYSISFY 193 (193)
Q Consensus 162 ~~~~-d~e~~i~~il~~fe~k~~-~~~Lhtv~fY 193 (193)
...+ -+|+.++.||.+||+.|+ -|+|||+.||
T Consensus 164 ~~~~e~lE~~~~sil~~~qsnh~~lp~Lyt~~~~ 197 (197)
T COG5211 164 AKEEERLEYAVDSILRRYQSNHKGLPLLYTVVNL 197 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCceEEeeccC
Confidence 7765 499999999999999775 5999999987
No 4
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=97.30 E-value=0.0017 Score=52.23 Aligned_cols=109 Identities=23% Similarity=0.323 Sum_probs=69.8
Q ss_pred CCceEEEEccCCCCcchHHHHhHHhC---CCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcC
Q 029441 1 MKYRYAMVCSSNQNRSMEAHYLLKRH---GFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNG 77 (193)
Q Consensus 1 ~~l~~avVCasN~NRSMEaH~~L~~~---g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NG 77 (193)
+..||.+||..|-=||=-|-.++++. ++.|.|.|||+ .||-.++. +. -+- -.+.|
T Consensus 1 ~~~kVLFVC~gN~cRSpmAE~l~~~~~~~~~~v~SAGt~~---~~g~~~~~---------~a--~~v--------l~e~G 58 (139)
T COG0394 1 MMMKVLFVCTGNICRSPMAEALLRHLAPDNVEVDSAGTGG---HPGEPPDP---------RA--VEV--------LAEHG 58 (139)
T ss_pred CCceEEEEcCCCcccCHHHHHHHHHhccCCeEEECCccCC---CCCCCCCH---------HH--HHH--------HHHcC
Confidence 46799999999999998899999865 79999999999 89988773 11 111 11223
Q ss_pred chhhhhcccCCC-CCcccccccCCCCcccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccCCH
Q 029441 78 ILPMLKRNIGVK-AAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNH 144 (193)
Q Consensus 78 lL~MLdRN~~iK-~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~ 144 (193)
| .+. ..|.-+-+..- ..||+|||-++.-...++.-.-.+. ..+..+.-||.|-.
T Consensus 59 i--------d~~~~~~k~i~~~~~-~~~DlIitmd~~~~~~~~~~~p~~~----~~~~~~~~~v~DP~ 113 (139)
T COG0394 59 I--------DISGHRSKQLTEEDF-DEFDLIITMDESNAADLCPLAPGNT----LLLEYEHWEVPDPY 113 (139)
T ss_pred C--------CcCCccCccCchhhh-hhCCEEEEeChHHHhhHhhcCcccc----ccccccCCCCCCCC
Confidence 2 233 23444433221 1599999999777555554221111 33444447788763
No 5
>PRK11391 etp phosphotyrosine-protein phosphatase; Provisional
Probab=96.67 E-value=0.0056 Score=48.90 Aligned_cols=91 Identities=18% Similarity=0.292 Sum_probs=60.3
Q ss_pred ceEEEEccCCCCcchHHHHhHHhC--CCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchh
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRH--GFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILP 80 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~--g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NGlL~ 80 (193)
.||-+||..|.-||=-|..+|++. ++.|.|-||... ||..++ |+ . .+.=++.|+ +
T Consensus 3 ~~ILfVC~gN~cRSpmAEa~~~~~~~~~~v~SaG~~~~---~g~~~~-~~----------a--------~~~l~~~Gi-d 59 (144)
T PRK11391 3 NSILVVCTGNICRSPIGERLLRKRLPGVKVKSAGVHGL---VKHPAD-AT----------A--------ADVAANHGV-S 59 (144)
T ss_pred CeEEEEcCCcHhHHHHHHHHHHHhcCCeEEEcccccCC---CCCCCC-HH----------H--------HHHHHHcCC-C
Confidence 589999999999998899999974 689999999753 665544 11 1 123344453 1
Q ss_pred hhhcccCCCCCcccccccCCCCcccEEEeccchhHHHHHHHHh
Q 029441 81 MLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLN 123 (193)
Q Consensus 81 MLdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~ 123 (193)
+ .. -.|..+.+..- ..||+|||-++..++.+.+..-
T Consensus 60 ~-~~-----h~s~~lt~~~~-~~~DlIl~M~~~~~~~l~~~~p 95 (144)
T PRK11391 60 L-EG-----HAGRKLTAEMA-RNYDLILAMESEHIAQVTAIAP 95 (144)
T ss_pred c-CC-----CccCcCCHHHH-hhCCEEEECCHHHHHHHHHHCC
Confidence 1 11 12333322111 1499999999999998877653
No 6
>smart00226 LMWPc Low molecular weight phosphatase family.
Probab=96.21 E-value=0.0085 Score=46.37 Aligned_cols=87 Identities=24% Similarity=0.352 Sum_probs=57.1
Q ss_pred EEEEccCCCCcchHHHHhHHhC---CCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhh
Q 029441 5 YAMVCSSNQNRSMEAHYLLKRH---GFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPM 81 (193)
Q Consensus 5 ~avVCasN~NRSMEaH~~L~~~---g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NGlL~M 81 (193)
|-.||..|.-||=-|..+|++. ++.|.|-||... ||..++. ..- +.=++.||=
T Consensus 1 vLFVC~~N~cRSpmAEa~~~~~~~~~~~v~SAG~~~~---~g~~~~~-----------~a~--------~~l~~~Gid-- 56 (140)
T smart00226 1 ILFVCTGNICRSPMAEALFKAIVGDRVKIDSAGTGAW---VGGGADP-----------RAV--------EVLKEHGIA-- 56 (140)
T ss_pred CEEEeCChhhhHHHHHHHHHHhcCCCEEEEcCcccCC---CCCCCCH-----------HHH--------HHHHHcCcC--
Confidence 3579999999998899999864 388999998754 7765441 111 234555662
Q ss_pred hhcccCCCCCcccccccCCCCcccEEEeccchhHHHHHHHH
Q 029441 82 LKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDL 122 (193)
Q Consensus 82 LdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl 122 (193)
+..-++ +..++-+ . .+|+|||-++...+.++..+
T Consensus 57 ~~~~~~-~l~~~~~----~--~~DlIv~m~~~~~~~~~~~~ 90 (140)
T smart00226 57 LSHHAS-QLTSSDF----K--NADLVLAMDHSHLRNICRLK 90 (140)
T ss_pred ccceec-cCCHHHH----H--hCCEEEEeCHHHHHHHHHHc
Confidence 222122 3333322 1 49999999998877776654
No 7
>PRK10126 tyrosine phosphatase; Provisional
Probab=95.91 E-value=0.0092 Score=47.46 Aligned_cols=92 Identities=22% Similarity=0.315 Sum_probs=60.7
Q ss_pred CCceEEEEccCCCCcchHHHHhHHhC--CCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCc
Q 029441 1 MKYRYAMVCSSNQNRSMEAHYLLKRH--GFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGI 78 (193)
Q Consensus 1 ~~l~~avVCasN~NRSMEaH~~L~~~--g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NGl 78 (193)
|..||..||..|.-||=-|..+|++. ++.|.|.||... ||..++. ..-. .-++.||
T Consensus 1 ~~~~iLFVC~gN~cRSpmAEa~~~~~~~~~~v~SAG~~~~---~g~~~~~-----------~a~~--------~l~~~Gi 58 (147)
T PRK10126 1 MFNNILVVCVGNICRSPTAERLLQRYHPELKVESAGLGAL---VGKGADP-----------TAIS--------VAAEHQL 58 (147)
T ss_pred CCCeEEEEcCCcHhHHHHHHHHHHHhcCCeEEEeeeccCC---CCCCCCH-----------HHHH--------HHHHcCC
Confidence 34689999999999998899999974 588999999664 7765552 1111 1222342
Q ss_pred hhhhhcccCCCCCcccccccCCCCcccEEEeccchhHHHHHHHH
Q 029441 79 LPMLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDL 122 (193)
Q Consensus 79 L~MLdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl 122 (193)
= + . .-.|.+|.+..- ..||+|||-++.-.+.++...
T Consensus 59 d-~-~-----~h~sr~lt~~~~-~~~DlIl~Md~~~~~~l~~~~ 94 (147)
T PRK10126 59 S-L-E-----GHCARQISRRLC-RNYDLILTMEKRHIERLCEMA 94 (147)
T ss_pred C-c-C-----CCccccCCHHHh-ccCCEEEECCHHHHHHHHHhc
Confidence 1 1 1 123445543321 149999999988888877654
No 8
>PF01451 LMWPc: Low molecular weight phosphotyrosine protein phosphatase; InterPro: IPR023485 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents the low molecular weight (LMW) protein-tyrosine phosphatases (or acid phosphatase), which act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates [, ]. The structure of a LMW PTPase has been solved by X-ray crystallography [] and is found to form a single structural domain. It belongs to the alpha/beta class, with 6 alpha-helices and 4 beta-strands forming a 3-layer alpha-beta-alpha sandwich architecture.; PDB: 3RH0_B 1JL3_B 2IPA_B 1Z2D_A 1Z2E_A 2CWD_D 2L18_A 2L17_A 2L19_A 1BVH_A ....
Probab=95.82 E-value=0.0099 Score=45.79 Aligned_cols=107 Identities=21% Similarity=0.370 Sum_probs=67.5
Q ss_pred EEEEccCCCCcchHHHHhHHhC-------CCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcC
Q 029441 5 YAMVCSSNQNRSMEAHYLLKRH-------GFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNG 77 (193)
Q Consensus 5 ~avVCasN~NRSMEaH~~L~~~-------g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NG 77 (193)
|..||..|.=||--|+.+|++. ++.|.|.||... ||..++ ...-+-| ++.|
T Consensus 1 ILFvC~~N~cRS~mAEai~~~~~~~~~~~~~~v~SAG~~~~---~~~~~~-----------~~a~~~l--------~~~g 58 (138)
T PF01451_consen 1 ILFVCTGNICRSPMAEAILRHLLKQRLGDRFEVESAGTEAW---PGEPVD-----------PRAIAVL--------KEHG 58 (138)
T ss_dssp EEEEESSSSSHHHHHHHHHHHHHHHTHTTTEEEEEEESSST---TTSSST-----------HHHHHHH--------HHTT
T ss_pred CEEEeCCCcchHHHHHHHHHHhccccccCCcEEEEEeeccc---cccccc-----------chHHHHH--------HHhC
Confidence 5689999999999999999876 889999999865 776644 2222323 2334
Q ss_pred chhhhhcccCCCCCcccccccCCCCcccEEEeccchhHHHHHHHHhcCCCCCCceEEEE--EecccCCH
Q 029441 78 ILPMLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVI--NLEVKDNH 144 (193)
Q Consensus 78 lL~MLdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVi--NvdIkDn~ 144 (193)
+ ++ .. ..|..+-+.. -..||+|||.++.-.+.+.+.+-. .....|+.+ +-||.|-.
T Consensus 59 i-d~-~~-----~~s~~l~~~~-~~~~D~Ii~m~~~~~~~~~~~~~~---~~~~kv~~l~~~~~I~DP~ 116 (138)
T PF01451_consen 59 I-DI-SG-----HRSRQLTEED-LDEADLIITMDDSHREELCPLFPG---DYRAKVFLLGEHWDIPDPY 116 (138)
T ss_dssp S-SC-TT-----SBBCBGGHHH-HHHSSEEEESSHHHHHHHHHHHGT---TGGGCEEEGGGESSS-HHT
T ss_pred C-Cc-cc-----ceeccccccc-cccCCEEEEccHHHhhhhhhhcch---hhhhhheeccccCcCCCCC
Confidence 3 21 11 2233333221 114999999999988887776665 122233333 77887743
No 9
>TIGR02689 ars_reduc_gluta arsenate reductase, glutathione/glutaredoxin type. Members of this protein family represent a novel form of arsenate reductase, using glutathione and glutaredoxin rather than thioredoxin for reducing equivalents as do some homologous arsenate reductases. An example of this type is Synechocystis sp. strain PCC 6803 slr0946, and of latter type (excluded from this model) is Staphylococcus aureus plasmid pI258 ArsC. Both are among the subset of arsenate reductases that belong the the low-molecular-weight protein-tyrosine phosphatase superfamily.
Probab=90.98 E-value=0.15 Score=39.37 Aligned_cols=34 Identities=29% Similarity=0.320 Sum_probs=29.3
Q ss_pred ceEEEEccCCCCcchHHHHhHHhC---CCCeeeecCC
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRH---GFDVSSYGTG 36 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~---g~~V~SfGTG 36 (193)
.||..||..|--||--|..+|++. ++.|.|.||.
T Consensus 1 ~~vlfvC~~N~cRS~mAEa~~~~~~~~~~~v~SAG~~ 37 (126)
T TIGR02689 1 KKVMFVCKRNSCRSQMAEGFAKTLGAGNIAVTSAGLE 37 (126)
T ss_pred CeEEEEcCCcHHHHHHHHHHHHHhcCCCEEEEcCcCC
Confidence 478999999999998899999974 3778888886
No 10
>PRK13530 arsenate reductase; Provisional
Probab=89.92 E-value=0.29 Score=38.53 Aligned_cols=35 Identities=29% Similarity=0.273 Sum_probs=29.6
Q ss_pred CceEEEEccCCCCcchHHHHhHHhC---CCCeeeecCC
Q 029441 2 KYRYAMVCSSNQNRSMEAHYLLKRH---GFDVSSYGTG 36 (193)
Q Consensus 2 ~l~~avVCasN~NRSMEaH~~L~~~---g~~V~SfGTG 36 (193)
+.||-.||..|--||=-|..+|++. ++.|.|-||.
T Consensus 3 ~~~vLFvC~~N~cRS~mAEal~~~~~~~~~~v~SAG~~ 40 (133)
T PRK13530 3 KKTIYFLCTGNSCRSQMAEGWGKQYLGDKWNVYSAGIE 40 (133)
T ss_pred CCEEEEEcCCchhHHHHHHHHHHHhcCCCEEEECCCCC
Confidence 6789999999999998899999863 4777888874
No 11
>cd00115 LMWPc Substituted updates: Aug 22, 2001
Probab=88.90 E-value=0.35 Score=37.60 Aligned_cols=34 Identities=29% Similarity=0.426 Sum_probs=29.3
Q ss_pred ceEEEEccCCCCcchHHHHhHHhC----CCCeeeecCC
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRH----GFDVSSYGTG 36 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~----g~~V~SfGTG 36 (193)
+||-.||..|.-||=-|..+|++. ++.|.|-|+-
T Consensus 1 ~~iLfvc~~N~~RS~mAEai~~~~~~~~~~~v~SaG~~ 38 (141)
T cd00115 1 KKVLFVCTGNICRSPMAEAIFRHLAPKLDIEVDSAGTS 38 (141)
T ss_pred CeEEEEecChhhhhHHHHHHHHHHhhhCCEEEECCCCC
Confidence 378999999999998899999974 6788888884
No 12
>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily. This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.
Probab=86.59 E-value=1 Score=32.40 Aligned_cols=32 Identities=25% Similarity=0.473 Sum_probs=26.5
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCCeeeecCC
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTG 36 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~~V~SfGTG 36 (193)
.+.++|++- +||..|=..|++.||+|..+--|
T Consensus 63 ~ivv~C~~G-~rs~~aa~~L~~~G~~~~~l~GG 94 (100)
T cd01523 63 EVTVICAKE-GSSQFVAELLAERGYDVDYLAGG 94 (100)
T ss_pred eEEEEcCCC-CcHHHHHHHHHHcCceeEEeCCc
Confidence 588999875 69999999999999997766443
No 13
>PLN02160 thiosulfate sulfurtransferase
Probab=83.05 E-value=1.3 Score=34.79 Aligned_cols=30 Identities=30% Similarity=0.447 Sum_probs=25.6
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~-~V~SfG 34 (193)
.+.++|+|. +||..|=..|.+.|| +|..+.
T Consensus 83 ~IivyC~sG-~RS~~Aa~~L~~~G~~~v~~l~ 113 (136)
T PLN02160 83 DILVGCQSG-ARSLKATTELVAAGYKKVRNKG 113 (136)
T ss_pred cEEEECCCc-HHHHHHHHHHHHcCCCCeeecC
Confidence 578899866 999999999999999 577764
No 14
>TIGR03746 conj_TIGR03746 integrating conjugative element protein, PFL_4703 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. The function is unknown.
Probab=81.87 E-value=1.3 Score=38.67 Aligned_cols=96 Identities=24% Similarity=0.271 Sum_probs=69.8
Q ss_pred CCceecCCCCCCCCccccCC-CCHHHHH-------------------------HHHhhcChHHHHhcCchhhhhcccCCC
Q 029441 36 GAHVKLPGPSLREPNVYEFG-TPYKQMF-------------------------DDLRRKDPELYKRNGILPMLKRNIGVK 89 (193)
Q Consensus 36 Gs~VrLPGps~d~PNvY~Fg-T~Y~~iy-------------------------~dL~~kd~~lY~~NGlL~MLdRN~~iK 89 (193)
||..|. -.+..+|||.|+ +-.++|- +.+..||-+++++||=| -+|.|.+=
T Consensus 51 Gstr~~--~eVP~~~VYaFa~yI~QQlNrW~~~Ge~dY~~ni~~l~~YlTP~c~~~L~~d~~~R~~~geL--r~R~R~vy 126 (202)
T TIGR03746 51 GSTRKW--WEVPPENVYAFAFYIFQQLNRWPKDGEQDYGANIFRLSPYLTPSCRAFLQQDYELRRSNGEL--RQRVRGVY 126 (202)
T ss_pred CCccCc--ccCCchhhhhhHHHHHHHHhhccccchHHHHHHHHhcccccCHHHHHHHHHHHHHHhhcchH--hhheeeeE
Confidence 666665 557788999998 5666653 56778888889999955 69999999
Q ss_pred CCcccccccC-------CCCcccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecc
Q 029441 90 AAPQRWQDNA-------LDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEV 140 (193)
Q Consensus 90 ~~PERfQ~~~-------~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdI 140 (193)
.=|-|+-+.. +.=..-+.++-+|+.=..+|.+-.-| -|++|+-+|+
T Consensus 127 EIpgrgy~~~rV~~~s~d~W~V~LDl~~~E~~~~e~VK~~~vR-----YpL~VVR~d~ 179 (202)
T TIGR03746 127 EIPGRGYSENRVIVHSDDSWTVNLDLSVDEYYGGEPVKRALVR-----YPLRVVRWDV 179 (202)
T ss_pred ecCCCCCCccceEEeCCCceEEEEEEEEEeeeCCcchhhhhcc-----cceEEEEecC
Confidence 9999985432 11124566667788777777766554 7899998887
No 15
>TIGR02691 arsC_pI258_fam arsenate reductase (thioredoxin). This family describes the well-studied thioredoxin-dependent arsenate reductase of Staphylococcus aureaus plasmid pI258 and other mechanistically similar arsenate reductases. The mechanism involves an intramolecular disulfide bond cascade, and aligned members of this family have four absolutely conserved Cys residues. This group of arsenate reductases belongs to the low-molecular weight protein-tyrosine phosphatase family (pfam01451), as does a group of glutathione/glutaredoxin type arsenate reductases (TIGR02689). At least two other, non-homologous groups of arsenate reductases involved in arsenical resistance are also known. This enzyme reduces arsenate to arsenite, which may be more toxic but which is more easily exported.
Probab=80.99 E-value=1.1 Score=35.22 Aligned_cols=32 Identities=28% Similarity=0.310 Sum_probs=26.2
Q ss_pred EEEEccCCCCcchHHHHhHHhC---CCCeeeecCC
Q 029441 5 YAMVCSSNQNRSMEAHYLLKRH---GFDVSSYGTG 36 (193)
Q Consensus 5 ~avVCasN~NRSMEaH~~L~~~---g~~V~SfGTG 36 (193)
|-.||..|--||=-|..+|++. ++.|.|-||.
T Consensus 1 iLFvC~~N~~RS~mAea~~~~~~~~~~~v~SaG~~ 35 (129)
T TIGR02691 1 IYFLCTGNSCRSQMAEGWGKKYLGDEWEVYSAGIE 35 (129)
T ss_pred CEEEcCCchHHHHHHHHHHHHhcCCCEEEEcCCCC
Confidence 3579999999998899999873 4777888874
No 16
>cd01534 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue.
Probab=79.70 E-value=2.9 Score=29.94 Aligned_cols=29 Identities=17% Similarity=0.195 Sum_probs=24.5
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCCeeee
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGFDVSSY 33 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~~V~Sf 33 (193)
.+.++|.+ -+||..+-..|++.||+|.++
T Consensus 58 ~iv~~c~~-G~rs~~aa~~L~~~G~~v~~l 86 (95)
T cd01534 58 RIVLADDD-GVRADMTASWLAQMGWEVYVL 86 (95)
T ss_pred eEEEECCC-CChHHHHHHHHHHcCCEEEEe
Confidence 57788877 678999999999999987665
No 17
>COG0607 PspE Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=79.65 E-value=2.5 Score=30.14 Aligned_cols=28 Identities=32% Similarity=0.320 Sum_probs=24.3
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCCee
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGFDVS 31 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~~V~ 31 (193)
..+.|+|+| .+||..|=..|+++||...
T Consensus 62 ~~ivv~C~~-G~rS~~aa~~L~~~G~~~~ 89 (110)
T COG0607 62 DPIVVYCAS-GVRSAAAAAALKLAGFTNV 89 (110)
T ss_pred CeEEEEeCC-CCChHHHHHHHHHcCCccc
Confidence 468899987 5899999999999999766
No 18
>cd01447 Polysulfide_ST Polysulfide-sulfurtransferase - Rhodanese Homology Domain. This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The active site contains the same conserved cysteine that is the catalytic residue in other Rhodanese Homology Domain proteins.
Probab=75.06 E-value=3.7 Score=29.11 Aligned_cols=30 Identities=27% Similarity=0.319 Sum_probs=24.8
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeee
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSY 33 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~~-V~Sf 33 (193)
-.+.+.|++ .+||..+=..|.+.||. |..+
T Consensus 62 ~~ivv~c~~-g~~s~~~~~~l~~~G~~~v~~l 92 (103)
T cd01447 62 KPFVFYCAS-GWRSALAGKTLQDMGLKPVYNI 92 (103)
T ss_pred CeEEEEcCC-CCcHHHHHHHHHHcChHHhEee
Confidence 368899987 68999999999999995 7655
No 19
>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.
Probab=73.93 E-value=3.9 Score=29.52 Aligned_cols=29 Identities=31% Similarity=0.474 Sum_probs=24.0
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCC-eeee
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGFD-VSSY 33 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~~-V~Sf 33 (193)
.+-|+|.+ -+||..|=..|++.||+ |...
T Consensus 63 ~ivvyC~~-G~rs~~a~~~L~~~G~~~v~~l 92 (101)
T cd01518 63 KVLMYCTG-GIRCEKASAYLKERGFKNVYQL 92 (101)
T ss_pred EEEEECCC-chhHHHHHHHHHHhCCcceeee
Confidence 57889976 59999999999999994 7554
No 20
>cd01533 4RHOD_Repeat_2 Member of the Rhodanese Homology Domain superfamily, repeat 2. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic Cys residue.
Probab=73.01 E-value=5.6 Score=29.15 Aligned_cols=32 Identities=22% Similarity=0.399 Sum_probs=25.6
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-C-eeeecCC
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGF-D-VSSYGTG 36 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~-~-V~SfGTG 36 (193)
.+.|+|.+. +||..|-..|++.|| + |.++-.|
T Consensus 68 ~ivv~C~~G-~rs~~a~~~L~~~G~~~~v~~l~gG 101 (109)
T cd01533 68 PIVVNCAGR-TRSIIGAQSLINAGLPNPVAALRNG 101 (109)
T ss_pred eEEEECCCC-chHHHHHHHHHHCCCCcceeEecCC
Confidence 578999875 589889999999999 4 7766444
No 21
>TIGR02981 phageshock_pspE phage shock operon rhodanese PspE. Members of this very narrowly defined protein family are proteins active as rhodanese (EC 2.8.1.1) and found in the extended variants of the phage shock protein (psp operon) in Escherichia coli and a few closely related species. Note that the designation phage shock protein PspE has been applied, incorrectly, in many instances where the genome lacks the phage shock regulon entirely.
Probab=71.67 E-value=3.2 Score=31.29 Aligned_cols=30 Identities=20% Similarity=0.368 Sum_probs=24.6
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCC-eeeec
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGFD-VSSYG 34 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~~-V~SfG 34 (193)
++.++|++. +||..+=..|++.||. |...|
T Consensus 60 ~vvlyC~~G-~rS~~aa~~L~~~G~~~v~~~G 90 (101)
T TIGR02981 60 TVKLYCNAG-RQSGMAKDILLDMGYTHAENAG 90 (101)
T ss_pred eEEEEeCCC-HHHHHHHHHHHHcCCCeEEecC
Confidence 578899885 6999999999999995 66553
No 22
>PRK10287 thiosulfate:cyanide sulfurtransferase; Provisional
Probab=71.30 E-value=3.5 Score=31.35 Aligned_cols=40 Identities=18% Similarity=0.409 Sum_probs=31.1
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCC-eeeecCCCceecCCCCC
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGFD-VSSYGTGAHVKLPGPSL 46 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~~-V~SfGTGs~VrLPGps~ 46 (193)
.+.++|++. +||..|=..|.+.||. |.. .|.....++|.+
T Consensus 62 ~IVlyC~~G-~rS~~aa~~L~~~G~~~v~~--~GG~~~~~~~~~ 102 (104)
T PRK10287 62 TVKLYCNAG-RQSGQAKEILSEMGYTHAEN--AGGLKDIAMPKV 102 (104)
T ss_pred eEEEEeCCC-hHHHHHHHHHHHcCCCeEEe--cCCHHHHhhhhc
Confidence 588999864 8999999999999995 544 577777777654
No 23
>PRK10310 PTS system galactitol-specific transporter subunit IIB; Provisional
Probab=71.17 E-value=4.8 Score=30.10 Aligned_cols=31 Identities=23% Similarity=0.318 Sum_probs=25.3
Q ss_pred CCceEEEEccCCCCcchH----HHHhHHhCCCCee
Q 029441 1 MKYRYAMVCSSNQNRSME----AHYLLKRHGFDVS 31 (193)
Q Consensus 1 ~~l~~avVCasN~NRSME----aH~~L~~~g~~V~ 31 (193)
|+.|+-+||.|-..-|+= ...+|+++|+++.
T Consensus 1 mk~kILvvCgsG~~TS~m~~~ki~~~l~~~gi~~~ 35 (94)
T PRK10310 1 MKRKIIVACGGAVATSTMAAEEIKELCQSHNIPVE 35 (94)
T ss_pred CCCeEEEECCCchhHHHHHHHHHHHHHHHCCCeEE
Confidence 677999999999988843 4678899999654
No 24
>cd01526 RHOD_ThiF Member of the Rhodanese Homology Domain superfamily. This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains.
Probab=70.20 E-value=6.1 Score=29.79 Aligned_cols=30 Identities=30% Similarity=0.276 Sum_probs=25.4
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCC--Ceeee
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGF--DVSSY 33 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~--~V~Sf 33 (193)
..+.++|++. +||..+=..|++.|| +|..+
T Consensus 73 ~~ivv~C~~G-~rs~~aa~~L~~~G~~~~v~~l 104 (122)
T cd01526 73 SPIYVVCRRG-NDSQTAVRKLKELGLERFVRDI 104 (122)
T ss_pred CcEEEECCCC-CcHHHHHHHHHHcCCccceeee
Confidence 3578999886 699999999999999 67776
No 25
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=69.46 E-value=2.8 Score=36.41 Aligned_cols=59 Identities=2% Similarity=-0.192 Sum_probs=51.0
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCcccc-CCCCHHHH
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYE-FGTPYKQM 61 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~-FgT~Y~~i 61 (193)
..+|++|-++.++||++|+...-.+-.+-|+++=...++|++-|+.++.+- +.--|++.
T Consensus 9 avvC~sN~NRSMeaH~~L~~~G~~v~S~GTg~~vklPG~~~dkPNvY~Fgt~Y~~iy~dL 68 (195)
T KOG2424|consen 9 AVVCASNQNRSMEAHNILKKKGLNVRSFGTGSHVKLPGPSPDKPNVYDFGTTYKQIYNDL 68 (195)
T ss_pred eeeehhcccchHHHHHHHHHcCCcceeecCCCceeCCCCCCCCCCccccCCcHHHHHHHH
Confidence 368999999999999999999999999999999999999999999888752 33445544
No 26
>TIGR03292 PhnH_redo phosphonate C-P lyase system protein PhnH. PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on Pfam model pfam05845.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context.
Probab=67.44 E-value=3.8 Score=34.59 Aligned_cols=26 Identities=23% Similarity=0.505 Sum_probs=22.4
Q ss_pred CCeeeecCCCceecCCCCCCCCcccc
Q 029441 28 FDVSSYGTGAHVKLPGPSLREPNVYE 53 (193)
Q Consensus 28 ~~V~SfGTGs~VrLPGps~d~PNvY~ 53 (193)
..|.|++.|..++|=||-|...+...
T Consensus 108 l~v~~l~~g~~l~L~GPGI~~~~~i~ 133 (174)
T TIGR03292 108 IEVPSLASGPPLTLTGPGIATERTIA 133 (174)
T ss_pred EEecccCCCCceEEECCCcCCceeEc
Confidence 36889999999999999999877664
No 27
>PRK00162 glpE thiosulfate sulfurtransferase; Validated
Probab=67.15 E-value=8.7 Score=28.08 Aligned_cols=31 Identities=32% Similarity=0.413 Sum_probs=24.5
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeeec
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSYG 34 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~~-V~SfG 34 (193)
..+.++|.+. +||..|-..|++.||. |..+.
T Consensus 59 ~~ivv~c~~g-~~s~~a~~~L~~~G~~~v~~l~ 90 (108)
T PRK00162 59 TPVMVMCYHG-NSSQGAAQYLLQQGFDVVYSID 90 (108)
T ss_pred CCEEEEeCCC-CCHHHHHHHHHHCCchheEEec
Confidence 3578899865 6999999999999995 65443
No 28
>cd01520 RHOD_YbbB Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB.
Probab=65.79 E-value=10 Score=28.98 Aligned_cols=33 Identities=27% Similarity=0.471 Sum_probs=27.4
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCCeeeecCC
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTG 36 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~~V~SfGTG 36 (193)
.+-|.|.+.-.||.-|=.+|+..||+|...--|
T Consensus 88 ~vvvyC~~~G~rs~~a~~~L~~~G~~v~~L~GG 120 (128)
T cd01520 88 KLLIYCARGGMRSQSLAWLLESLGIDVPLLEGG 120 (128)
T ss_pred eEEEEeCCCCccHHHHHHHHHHcCCceeEeCCc
Confidence 678999877788999999999999998776444
No 29
>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.
Probab=64.01 E-value=11 Score=26.57 Aligned_cols=29 Identities=24% Similarity=0.427 Sum_probs=24.6
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCCeeee
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGFDVSSY 33 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~~V~Sf 33 (193)
++.++|++ -.||..+=..|++.||+|..+
T Consensus 53 ~vvl~c~~-g~~a~~~a~~L~~~G~~v~~l 81 (90)
T cd01524 53 EIIVYCAV-GLRGYIAARILTQNGFKVKNL 81 (90)
T ss_pred cEEEEcCC-ChhHHHHHHHHHHCCCCEEEe
Confidence 57788886 578999999999999988776
No 30
>cd01521 RHOD_PspE2 Member of the Rhodanese Homology Domain superfamily. This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins.
Probab=63.85 E-value=12 Score=27.65 Aligned_cols=31 Identities=23% Similarity=0.371 Sum_probs=26.2
Q ss_pred ceEEEEccCCC-CcchHHHHhHHhCCCCeeee
Q 029441 3 YRYAMVCSSNQ-NRSMEAHYLLKRHGFDVSSY 33 (193)
Q Consensus 3 l~~avVCasN~-NRSMEaH~~L~~~g~~V~Sf 33 (193)
-.+-+.|++.. +||..+=..|++.||+|..+
T Consensus 65 ~~vvvyc~~g~~~~s~~~a~~l~~~G~~v~~l 96 (110)
T cd01521 65 KLFVVYCDGPGCNGATKAALKLAELGFPVKEM 96 (110)
T ss_pred CeEEEEECCCCCchHHHHHHHHHHcCCeEEEe
Confidence 35789998875 79999999999999998765
No 31
>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.
Probab=61.96 E-value=7.3 Score=28.53 Aligned_cols=30 Identities=20% Similarity=0.295 Sum_probs=25.6
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~-~V~SfG 34 (193)
.+.++|.+ -+||..+-..|+..|| +|..|-
T Consensus 80 ~iv~yc~~-g~~s~~~~~~l~~~G~~~v~~l~ 110 (118)
T cd01449 80 PVIVYCGS-GVTACVLLLALELLGYKNVRLYD 110 (118)
T ss_pred CEEEECCc-HHHHHHHHHHHHHcCCCCeeeeC
Confidence 57889987 5799999999999999 577775
No 32
>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains.
Probab=60.05 E-value=15 Score=26.44 Aligned_cols=31 Identities=29% Similarity=0.492 Sum_probs=24.7
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~-~V~SfG 34 (193)
..+-++|.+ -+||-.+=..|.+.|| +|..+-
T Consensus 59 ~~vv~~c~~-g~rs~~~~~~l~~~G~~~v~~l~ 90 (101)
T cd01528 59 KDIVVLCHH-GGRSMQVAQWLLRQGFENVYNLQ 90 (101)
T ss_pred CeEEEEeCC-CchHHHHHHHHHHcCCccEEEec
Confidence 357788987 4899999999999999 476553
No 33
>cd01519 RHOD_HSP67B2 Member of the Rhodanese Homology Domain superfamily. This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.
Probab=58.91 E-value=11 Score=26.94 Aligned_cols=29 Identities=28% Similarity=0.504 Sum_probs=23.9
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeee
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSY 33 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~-~V~Sf 33 (193)
.+.++|.+ .+||..+=..|++.|| +|..+
T Consensus 68 ~ivv~c~~-g~~s~~~~~~l~~~G~~~v~~~ 97 (106)
T cd01519 68 ELIFYCKA-GVRSKAAAELARSLGYENVGNY 97 (106)
T ss_pred eEEEECCC-cHHHHHHHHHHHHcCCccceec
Confidence 57788876 6799999999999999 46655
No 34
>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=58.03 E-value=27 Score=26.82 Aligned_cols=131 Identities=13% Similarity=0.137 Sum_probs=70.9
Q ss_pred EEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHh----hcC----------h-
Q 029441 6 AMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLR----RKD----------P- 70 (193)
Q Consensus 6 avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~----~kd----------~- 70 (193)
|++......-+..+...+.+.|.++.+++++..... ..|+++.+++++.+.-..+. ++. .
T Consensus 61 ~ii~~~~~~~~~~~~~~~~~~~ip~v~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~i~~~~~ 135 (269)
T cd01391 61 GIIGPPSSSSALAVVELAAAAGIPVVSLDATAPDLT-----GYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDDG 135 (269)
T ss_pred EEEecCCCHHHHHHHHHHHHcCCcEEEecCCCCccC-----CCceEEEEcCCcHHHHHHHHHHHHHhCCceEEEEecCCc
Confidence 455555554455588889999999999998764322 56788888877665544332 211 0
Q ss_pred HH--HHhcCchhhhhccc-------CCCCCccc-ccc----cCCCCcccEEEeccchhHHHHHHHHhcCCCCCCceEEEE
Q 029441 71 EL--YKRNGILPMLKRNI-------GVKAAPQR-WQD----NALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVI 136 (193)
Q Consensus 71 ~l--Y~~NGlL~MLdRN~-------~iK~~PER-fQ~----~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVi 136 (193)
.. =+.+|+-.-+.++. .....++. ++. .......|+||++....-..++..+...+-. .+.+.||
T Consensus 136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~~~~a~~~~~~~~~~g~~-~~~~~ii 214 (269)
T cd01391 136 AYGRERLEGFKAALKKAGIEVVAIEYGDLDTEKGFQALLQLLKAAPKPDAIFACNDEMAAGALKAAREAGLT-PGDISII 214 (269)
T ss_pred chhhHHHHHHHHHHHhcCcEEEeccccCCCccccHHHHHHHHhcCCCCCEEEEcCchHHHHHHHHHHHcCCC-CCCCEEE
Confidence 00 01122222222210 11111100 110 1111136888888777777788888777655 5567777
Q ss_pred EecccC
Q 029441 137 NLEVKD 142 (193)
Q Consensus 137 NvdIkD 142 (193)
-.|--.
T Consensus 215 ~~~~~~ 220 (269)
T cd01391 215 GFDGSP 220 (269)
T ss_pred eccccc
Confidence 666543
No 35
>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.
Probab=57.45 E-value=14 Score=26.36 Aligned_cols=30 Identities=23% Similarity=0.202 Sum_probs=24.0
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~-~V~SfG 34 (193)
.+.++|++ .+||-.+=..|++.|| +|..+-
T Consensus 58 ~ivv~c~~-g~~s~~~~~~l~~~G~~~v~~l~ 88 (96)
T cd01529 58 RYVLTCDG-SLLARFAAQELLALGGKPVALLD 88 (96)
T ss_pred CEEEEeCC-hHHHHHHHHHHHHcCCCCEEEeC
Confidence 57889974 6899888889999999 676653
No 36
>TIGR00725 conserved hypothetical protein, DprA/Smf-related, family 1. This model represents one branch of a subfamily of uncharacterized proteins. Both PSI-BLAST and weak hits by this model show a low level of similarity and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting the branches may have distinct functions. This family is one of several families within the scope of PFAM model pfam03641, several members of which are annotated as lysine decarboxylases. That larger family, and the branch described by this model, have a well-conserved motif PGGXGTXXE.
Probab=57.35 E-value=13 Score=30.39 Aligned_cols=32 Identities=19% Similarity=0.270 Sum_probs=23.0
Q ss_pred ceEEEEccCCCCcch-----HHHHhHHhCCCCeeeecC
Q 029441 3 YRYAMVCSSNQNRSM-----EAHYLLKRHGFDVSSYGT 35 (193)
Q Consensus 3 l~~avVCasN~NRSM-----EaH~~L~~~g~~V~SfGT 35 (193)
.+|||+|+|+.+-.. |.=+.|.++|+.|.| |-
T Consensus 2 ~~I~V~gss~~~~~~~~~A~~lg~~La~~g~~lv~-Gg 38 (159)
T TIGR00725 2 VQIGVIGSSNKSEELYEIAYRLGKELAKKGHILIN-GG 38 (159)
T ss_pred eEEEEEeCCCCChHHHHHHHHHHHHHHHCCCEEEc-CC
Confidence 589999999854322 222568899998888 64
No 37
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=57.16 E-value=7.6 Score=29.03 Aligned_cols=41 Identities=29% Similarity=0.500 Sum_probs=23.7
Q ss_pred EEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCC-CCCCCccccC
Q 029441 6 AMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGP-SLREPNVYEF 54 (193)
Q Consensus 6 avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGp-s~d~PNvY~F 54 (193)
++..+-|...|+= .|+ +|+||||-.+ |=++| -+..+.||+|
T Consensus 21 GiL~~In~~~sTi---~L~----nVr~fGTEgR-~~~~~~ipp~~~vyd~ 62 (74)
T cd01736 21 GILYTINTEDSTI---ALK----NVRSFGTEGR-PTDGPEIPPSDEVYDY 62 (74)
T ss_pred EEEEeeccccCEE---Eee----eeEeecccCC-CCCCCccCCCCcceeE
Confidence 3445555555542 233 7999999887 22233 3455667765
No 38
>PRK10147 phnH carbon-phosphorus lyase complex subunit; Validated
Probab=56.39 E-value=16 Score=31.47 Aligned_cols=26 Identities=23% Similarity=0.459 Sum_probs=21.6
Q ss_pred CCeeeecCCCceecCCCCCCCCcccc
Q 029441 28 FDVSSYGTGAHVKLPGPSLREPNVYE 53 (193)
Q Consensus 28 ~~V~SfGTGs~VrLPGps~d~PNvY~ 53 (193)
..|.|++.|..++|=||-|.+.+...
T Consensus 126 l~v~~l~~g~~l~L~GPGI~~~~~i~ 151 (196)
T PRK10147 126 LQVASLEGGRPLRLRGPGIEAEERIA 151 (196)
T ss_pred EEccccCCCCceEEECCCcCCcceec
Confidence 36889999999999999997766554
No 39
>smart00450 RHOD Rhodanese Homology Domain. An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.
Probab=54.26 E-value=22 Score=24.00 Aligned_cols=31 Identities=32% Similarity=0.510 Sum_probs=24.8
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeeec
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSYG 34 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~~-V~SfG 34 (193)
-.+.++| .+..||-.+-..|++.||. |.-+-
T Consensus 57 ~~iv~~c-~~g~~a~~~~~~l~~~G~~~v~~l~ 88 (100)
T smart00450 57 KPVVVYC-RSGNRSAKAAWLLRELGFKNVYLLD 88 (100)
T ss_pred CeEEEEe-CCCcHHHHHHHHHHHcCCCceEEec
Confidence 3578889 5688999999999999996 66553
No 40
>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=52.12 E-value=37 Score=28.99 Aligned_cols=43 Identities=12% Similarity=0.070 Sum_probs=35.2
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHH
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~i 154 (193)
.+.+...+++++.+++-.+++|-++-.|.+.+++.|+..++.+
T Consensus 20 ~~g~~~a~~~iN~~gGi~G~~i~l~~~D~~~~p~~a~~~a~~L 62 (333)
T cd06331 20 RNAALLAIEEINAAGGILGRPLELVVEDPASDPAFAAKAARRL 62 (333)
T ss_pred HHHHHHHHHHHHhcCCCCCeEEEEEEECCCCCHHHHHHHHHHH
Confidence 3667889999999998889999999999998888776555433
No 41
>PRK05320 rhodanese superfamily protein; Provisional
Probab=51.66 E-value=16 Score=32.01 Aligned_cols=28 Identities=21% Similarity=0.310 Sum_probs=24.1
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-ee
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VS 31 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~~-V~ 31 (193)
.++.|+|++- .||-+|-..|++.||+ |.
T Consensus 176 k~IvvyC~~G-~Rs~~Aa~~L~~~Gf~~V~ 204 (257)
T PRK05320 176 KTVVSFCTGG-IRCEKAAIHMQEVGIDNVY 204 (257)
T ss_pred CeEEEECCCC-HHHHHHHHHHHHcCCcceE
Confidence 4689999885 8999999999999995 53
No 42
>PRK01415 hypothetical protein; Validated
Probab=50.43 E-value=15 Score=32.44 Aligned_cols=30 Identities=37% Similarity=0.561 Sum_probs=25.1
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeee
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSY 33 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~~-V~Sf 33 (193)
.+++|.|++- .||..|-..|++.||. |.+.
T Consensus 172 k~Iv~yCtgG-iRs~kAa~~L~~~Gf~~Vy~L 202 (247)
T PRK01415 172 KKIAMVCTGG-IRCEKSTSLLKSIGYDEVYHL 202 (247)
T ss_pred CeEEEECCCC-hHHHHHHHHHHHcCCCcEEEe
Confidence 4699999776 7999999999999995 5554
No 43
>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.
Probab=50.29 E-value=25 Score=24.52 Aligned_cols=27 Identities=30% Similarity=0.471 Sum_probs=22.9
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Cee
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVS 31 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~-~V~ 31 (193)
.+-++|+ +-.||+.|-..|++.|| +|.
T Consensus 58 ~ivv~c~-~g~~s~~a~~~l~~~G~~~v~ 85 (96)
T cd01444 58 PVVVYCY-HGNSSAQLAQALREAGFTDVR 85 (96)
T ss_pred CEEEEeC-CCChHHHHHHHHHHcCCceEE
Confidence 5778888 77899999999999999 454
No 44
>KOG0239 consensus Kinesin (KAR3 subfamily) [Cytoskeleton]
Probab=50.13 E-value=14 Score=37.19 Aligned_cols=118 Identities=18% Similarity=0.269 Sum_probs=67.1
Q ss_pred CCCeeee-----cCCCceecCCCCCCCCc--------------------cccCCCCHHHHHH----HHhhcChHHHHhcC
Q 029441 27 GFDVSSY-----GTGAHVKLPGPSLREPN--------------------VYEFGTPYKQMFD----DLRRKDPELYKRNG 77 (193)
Q Consensus 27 g~~V~Sf-----GTGs~VrLPGps~d~PN--------------------vY~FgT~Y~~iy~----dL~~kd~~lY~~NG 77 (193)
||+||.| |+|-...+=||+++.|- -|++.+++-+||+ ||...+.
T Consensus 391 GYnVCIFAYGQTGSGKTyTM~G~~~~~~Giipral~~lF~~~~~~~~g~~y~~~~s~~EIYNe~i~DlL~~~~------- 463 (670)
T KOG0239|consen 391 GYNVCIFAYGQTGSGKTYTMSGPTPEDPGIIPRALEKLFRTITSLKSGWKYDKTVSMLEIYNEAIRDLLSDES------- 463 (670)
T ss_pred CcceeEEEecccCCCccccccCCCcccCCccHHHHHHHHHHHHhhccCceEEeeeehhHHHHHHHHHhccccc-------
Confidence 9999999 78888899998777765 4788899999997 5555554
Q ss_pred chhhhhcccCCCCCcccccccCCCCcccEEEeccchhHHHHHHH-HhcC---------CCCCCceEEEEEecccCCHHHH
Q 029441 78 ILPMLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVED-LNTR---------EQPFMKTVLVINLEVKDNHEEA 147 (193)
Q Consensus 78 lL~MLdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vved-l~~R---------~~~~~~pVHViNvdIkDn~EeA 147 (193)
-.....|+..++-=..-.+ .-=+-|...|-|. .+++. ..+| .++.-..|..|.|.=.|..-++
T Consensus 464 ----~~~k~~I~~~~~~~~~V~~--~t~~~V~s~~~v~-~ll~~g~~nRsv~~T~~Ne~SSRSH~v~~v~v~g~~~~t~~ 536 (670)
T KOG0239|consen 464 ----YVGKLEIVDDAEGNLMVPL--LTVIKVGSSEEVD-ILLEIGLSNRSVASTASNERSSRSHLVFRVRIRGINELTGI 536 (670)
T ss_pred ----cccceeEEEcCCCceeccc--ceEEecCCHHHHH-HHHHHhhccccccccccchhhhccceEEEEEEeccccCccc
Confidence 1112234444432211111 2223344555553 33332 2222 2345556677777666544433
Q ss_pred -HhhHHHHHHHH
Q 029441 148 -AIGGRLTFDLC 158 (193)
Q Consensus 148 -~~Ga~~il~Lc 158 (193)
+.|-..++|||
T Consensus 537 ~~~g~l~LVDLA 548 (670)
T KOG0239|consen 537 RVTGVLNLVDLA 548 (670)
T ss_pred ccccceeEeecc
Confidence 34444555666
No 45
>KOG1530 consensus Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=49.50 E-value=18 Score=30.01 Aligned_cols=29 Identities=31% Similarity=0.571 Sum_probs=23.6
Q ss_pred EEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029441 5 YAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (193)
Q Consensus 5 ~avVCasN~NRSMEaH~~L~~~g~-~V~SfG 34 (193)
+-+-|+|- +||.+|-.+|..+|| +|.-|+
T Consensus 92 iIf~C~SG-~Rs~~A~~~l~s~Gyknv~ny~ 121 (136)
T KOG1530|consen 92 IIFGCASG-VRSLKATKILVSAGYKNVGNYP 121 (136)
T ss_pred EEEEeccC-cchhHHHHHHHHcCcccccccC
Confidence 45678885 699999999999999 666554
No 46
>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.
Probab=49.44 E-value=27 Score=24.82 Aligned_cols=30 Identities=13% Similarity=0.077 Sum_probs=23.1
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~-~V~SfG 34 (193)
.+.++|.+ .+||-.+=..|.+.|| +|..+.
T Consensus 56 ~iv~~c~~-g~~s~~~~~~L~~~g~~~v~~l~ 86 (99)
T cd01527 56 AIIFHCRS-GMRTQQNAERLAAISAGEAYVLE 86 (99)
T ss_pred cEEEEeCC-CchHHHHHHHHHHcCCccEEEee
Confidence 56778876 5778889889999998 666553
No 47
>COG3625 PhnH Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=47.91 E-value=31 Score=30.11 Aligned_cols=58 Identities=21% Similarity=0.371 Sum_probs=40.3
Q ss_pred CCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhhhhcccCCCCCcccccccCCCCcccEE
Q 029441 28 FDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPMLKRNIGVKAAPQRWQDNALDGSFDIV 107 (193)
Q Consensus 28 ~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NGlL~MLdRN~~iK~~PERfQ~~~~~~~fDvI 107 (193)
..|.||--|..++|-||-|..-++-.=|-|.-=+ +-+. .+|+.|- . -.|||
T Consensus 128 iQV~sl~~G~~l~l~GPGI~~~~~Iap~LP~~f~------------------~~w~------~n~~~fP----r-GiDvi 178 (196)
T COG3625 128 IQVASLEGGRPLRLTGPGIAESRIIAPGLPDHFW------------------HFWA------ENRAIFP----R-GIDVI 178 (196)
T ss_pred EEecccCCCCceEeECCCcccccccCCCCchHHH------------------HHHH------hCccccC----C-cceEE
Confidence 3689999999999999999887776655553322 1111 2344442 1 38999
Q ss_pred Eeccchh
Q 029441 108 FTFEEKV 114 (193)
Q Consensus 108 iTcEERv 114 (193)
+||.|++
T Consensus 179 lt~ge~~ 185 (196)
T COG3625 179 LTAGEAL 185 (196)
T ss_pred EecCcee
Confidence 9999987
No 48
>PF06841 Phage_T4_gp19: T4-like virus tail tube protein gp19; InterPro: IPR010667 This family consists of several tail tube protein gp19 sequences from the T4-like viruses [,]. The contractile tail of bacteriophage T4 consists of a contractile sheath, a tube and a baseplate. Protomers of Gp19 form the tail tube, which penetrates the outer membrane of Escherichia coli upon infection.; GO: 0005198 structural molecule activity
Probab=45.64 E-value=9.5 Score=29.10 Aligned_cols=60 Identities=17% Similarity=0.202 Sum_probs=43.5
Q ss_pred CCeeeecCC----CceecCCCCCCCCccccCC-CCHHHHHHHHhhcChHH-H--HhcCchhhhhcccC
Q 029441 28 FDVSSYGTG----AHVKLPGPSLREPNVYEFG-TPYKQMFDDLRRKDPEL-Y--KRNGILPMLKRNIG 87 (193)
Q Consensus 28 ~~V~SfGTG----s~VrLPGps~d~PNvY~Fg-T~Y~~iy~dL~~kd~~l-Y--~~NGlL~MLdRN~~ 87 (193)
+.+..|..| ...++||..--.+-+-.|| +++.++++=+.+=.... = ++++.+.+||++.+
T Consensus 27 ~e~~~~~~gg~~~~~~~~pg~~~~~~ltL~~g~~~~~~l~~W~~~~~~~~~~~~~~~~~I~lld~~~~ 94 (134)
T PF06841_consen 27 IEVVEYREGGSNGFPHKLPGRVKFGNLTLKRGVDESSDLWDWFNAINNGESNSARKDISIELLDSDGK 94 (134)
T ss_pred eeEEEEeeCCCCceeEECCCCcEEcCEEEEEeccCcHHHHHHHHHHhccccccccceEEEEEECCCCC
Confidence 345556445 4569999998888899999 78888877666321111 1 79999999999983
No 49
>cd01525 RHOD_Kc Member of the Rhodanese Homology Domain superfamily. Included in this CD are the rhodanese-like domains found C-terminal of the serine/threonine protein kinases catalytic (S_TKc) domain and the Tre-2, BUB2p, Cdc16p (TBC) domain. The putative active site Cys residue is not present in this CD.
Probab=45.51 E-value=37 Score=24.19 Aligned_cols=30 Identities=17% Similarity=0.155 Sum_probs=23.1
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~-~V~SfG 34 (193)
.+.++|++. +||..+=..|+..|| +|..+-
T Consensus 67 ~vv~~c~~g-~~s~~~a~~L~~~G~~~v~~l~ 97 (105)
T cd01525 67 IIVIVSHSH-KHAALFAAFLVKCGVPRVCILD 97 (105)
T ss_pred eEEEEeCCC-ccHHHHHHHHHHcCCCCEEEEe
Confidence 577788765 589888889999999 476653
No 50
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=45.11 E-value=17 Score=23.98 Aligned_cols=24 Identities=29% Similarity=0.439 Sum_probs=17.8
Q ss_pred HHHHhHHhCCCCeeeecCCCceecC
Q 029441 18 EAHYLLKRHGFDVSSYGTGAHVKLP 42 (193)
Q Consensus 18 EaH~~L~~~g~~V~SfGTGs~VrLP 42 (193)
|.-++|.+.||.+..= +|||+++=
T Consensus 3 el~k~L~~~G~~~~r~-~GSH~~~~ 26 (56)
T PF07927_consen 3 ELIKLLEKAGFEEVRQ-KGSHHIFR 26 (56)
T ss_dssp HHHHHHHHTT-EEEEE-ETTEEEEE
T ss_pred HHHHHHHHCCCEEecC-CCCEEEEE
Confidence 6678999999988843 68887653
No 51
>PF02302 PTS_IIB: PTS system, Lactose/Cellobiose specific IIB subunit; InterPro: IPR003501 The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This signature is often found downstream of IPR003352 from INTERPRO.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TVM_A 2WY2_D 1IIB_A 2WWV_D 1H9C_A 1E2B_A 2L2Q_A 2KYR_A 3CZC_A 3NBM_A ....
Probab=44.75 E-value=25 Score=24.77 Aligned_cols=31 Identities=26% Similarity=0.390 Sum_probs=23.8
Q ss_pred eEEEEccCCCCcchHH----HHhHHhCCCCeeeec
Q 029441 4 RYAMVCSSNQNRSMEA----HYLLKRHGFDVSSYG 34 (193)
Q Consensus 4 ~~avVCasN~NRSMEa----H~~L~~~g~~V~SfG 34 (193)
|+-+||++-+.-|+-+ -+.+++.|+.+.++-
T Consensus 1 kIlvvC~~Gi~TS~~~~~~i~~~~~~~gi~~~~~~ 35 (90)
T PF02302_consen 1 KILVVCGSGIGTSLMVANKIKKALKELGIEVEVSA 35 (90)
T ss_dssp EEEEEESSSSHHHHHHHHHHHHHHHHTTECEEEEE
T ss_pred CEEEECCChHHHHHHHHHHHHHHHHhccCceEEEE
Confidence 6789999999999877 345567887776654
No 52
>cd06007 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=43.93 E-value=13 Score=26.21 Aligned_cols=26 Identities=31% Similarity=0.553 Sum_probs=21.2
Q ss_pred CCCcchHHHHhHHhCCCCeeeecCCCc
Q 029441 12 NQNRSMEAHYLLKRHGFDVSSYGTGAH 38 (193)
Q Consensus 12 N~NRSMEaH~~L~~~g~~V~SfGTGs~ 38 (193)
+.-|. -.|.+-.+.|+.-.|+|.|..
T Consensus 27 ~~eR~-~vH~~a~~~gL~s~S~G~g~~ 52 (59)
T cd06007 27 NHERA-VIHRLCRKLGLKSKSKGKGSN 52 (59)
T ss_pred HHHHH-HHHHHHHHcCCCceeecCCCC
Confidence 33455 389999999999999999874
No 53
>cd06356 PBP1_Amide_Urea_BP_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the type I periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis.
Probab=43.75 E-value=62 Score=27.94 Aligned_cols=42 Identities=10% Similarity=0.166 Sum_probs=34.9
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHH
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~i 154 (193)
...+..+++++.+++-..+||-+|..|.+-+++.|...++.+
T Consensus 21 ~g~~la~~~iNa~gGi~Gr~v~lv~~D~~~~p~~a~~~~~~L 62 (334)
T cd06356 21 HATQLAVDEINASGGILGREVELVDYDTQSDNERYQQYAQRL 62 (334)
T ss_pred HHHHHHHHHHHhcCCCCCceEEEEEECCCCCHHHHHHHHHHH
Confidence 456888999999999999999999999999988876555433
No 54
>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.
Probab=43.72 E-value=29 Score=28.89 Aligned_cols=42 Identities=12% Similarity=0.090 Sum_probs=34.4
Q ss_pred EEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCC
Q 029441 6 AMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLRE 48 (193)
Q Consensus 6 avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~ 48 (193)
|++|+ |-.-.+-+-+.|+++|+.|.+|+....-.+|+|.+..
T Consensus 186 aI~~~-nd~~A~gv~~al~~~gisIvGfD~~~~~~~~~p~ltt 227 (265)
T cd06354 186 VIFAA-AGGTGNGVFQAAKEAGVYAIGVDSDQYYLAPGVVLTS 227 (265)
T ss_pred EEEEC-CCCCchHHHHHHHhcCCeEEEecCcccccCCCcEEEE
Confidence 55555 6677789999999999999999998888888887543
No 55
>cd01448 TST_Repeat_1 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it is believed to be involved in protein interaction.
Probab=42.68 E-value=45 Score=24.57 Aligned_cols=31 Identities=13% Similarity=0.096 Sum_probs=24.9
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeee
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSY 33 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~~-V~Sf 33 (193)
..|.+.|.+-..||-.+-..|+..||+ |..+
T Consensus 80 ~~vv~~c~~g~~~a~~~~~~l~~~G~~~v~~l 111 (122)
T cd01448 80 DTVVVYDDGGGFFAARAWWTLRYFGHENVRVL 111 (122)
T ss_pred CEEEEECCCCCccHHHHHHHHHHcCCCCEEEe
Confidence 358889988656888899999999995 7665
No 56
>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=42.07 E-value=52 Score=28.50 Aligned_cols=44 Identities=5% Similarity=0.077 Sum_probs=36.1
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHH
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFD 156 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~ 156 (193)
+-+...+++++..++...++|.++-.|.+.+++.|...++.+++
T Consensus 21 ~g~~la~~~iN~~gGi~G~~i~lv~~D~~~~p~~a~~~a~~Li~ 64 (347)
T cd06335 21 RGARLAIDEINAAGGVLGRKLELVERDDRGNPARGLQNAQELAA 64 (347)
T ss_pred HHHHHHHHHHHhcCCcCCeEEEEEeccCCCCcHHHHHHHHHHhc
Confidence 45678899999998888999999999999988888766655543
No 57
>COG4822 CbiK Cobalamin biosynthesis protein CbiK, Co2+ chelatase [Coenzyme metabolism]
Probab=41.93 E-value=14 Score=33.42 Aligned_cols=33 Identities=24% Similarity=0.544 Sum_probs=20.2
Q ss_pred cccCCCCHHH--------HHHHHhhcChHH-----HHhcCchhhhh
Q 029441 51 VYEFGTPYKQ--------MFDDLRRKDPEL-----YKRNGILPMLK 83 (193)
Q Consensus 51 vY~FgT~Y~~--------iy~dL~~kd~~l-----Y~~NGlL~MLd 83 (193)
|-.|||+|.+ |-+++..+=+++ ||.+-|+.-|.
T Consensus 7 iVsFGTty~dtre~tIda~e~~va~efpDydvfrAfTS~kIIkkLK 52 (265)
T COG4822 7 IVSFGTTYNDTRELTIDAIEEKVADEFPDYDVFRAFTSRKIIKKLK 52 (265)
T ss_pred EEEcCCccchhHHhhHHHHHHHHHHhCccHHHHHHHhHHHHHHHHH
Confidence 3467888865 445555543332 78888887663
No 58
>PF05845 PhnH: Bacterial phosphonate metabolism protein (PhnH); InterPro: IPR008772 This family consists of several bacterial PhnH sequences, which is a component of the C-P lyase system (GenProp0232 from GENPROP) for the catabolism of phosphonate compounds []. The specific function of this component is unknown.; GO: 0015716 phosphonate transport; PDB: 2FSU_A.
Probab=41.60 E-value=10 Score=32.42 Aligned_cols=26 Identities=23% Similarity=0.455 Sum_probs=11.3
Q ss_pred CeeeecCCCceecCCCCCCCCccccC
Q 029441 29 DVSSYGTGAHVKLPGPSLREPNVYEF 54 (193)
Q Consensus 29 ~V~SfGTGs~VrLPGps~d~PNvY~F 54 (193)
.|.|++.|..++|=||-|...+...=
T Consensus 124 ~v~~l~~g~~l~LsGPGI~~~~~i~~ 149 (192)
T PF05845_consen 124 QVDSLTGGPPLTLSGPGIKGERTIAV 149 (192)
T ss_dssp E-S-SSSS--EEEE-------EEE--
T ss_pred EccccCCCCceEEEcCccccceEEcc
Confidence 67899999999999999998877654
No 59
>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=41.53 E-value=71 Score=27.81 Aligned_cols=43 Identities=9% Similarity=0.034 Sum_probs=35.3
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHH
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTF 155 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il 155 (193)
+-....+|+++..++-.+++|-+|=.|-+-++++|...++.++
T Consensus 21 ~g~~la~~~iN~~GGi~G~~ielv~~D~~~~p~~a~~~a~~Li 63 (348)
T cd06355 21 DAELLAIEEINAAGGVLGRKIEAVVEDGASDWPTFAEKARKLL 63 (348)
T ss_pred HHHHHHHHHHHhcCCCCCcEEEEEEeCCCCCHHHHHHHHHHHH
Confidence 4457789999999998899999999999999888876665543
No 60
>COG0473 LeuB Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]
Probab=41.50 E-value=55 Score=30.86 Aligned_cols=114 Identities=17% Similarity=0.394 Sum_probs=80.5
Q ss_pred CCCCCccccCC-CCHHHHHHHHhhcC------hHHHHhcCchhhhhcccCCCCCcccccccCCCCcccEEEeccchhHHH
Q 029441 45 SLREPNVYEFG-TPYKQMFDDLRRKD------PELYKRNGILPMLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDT 117 (193)
Q Consensus 45 s~d~PNvY~Fg-T~Y~~iy~dL~~kd------~~lY~~NGlL~MLdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~ 117 (193)
+.+|.||-.|. --+.++.+++. |+ ..+|--|.-.+|. ..|| .||||+| +..|=.
T Consensus 179 sv~KaNVl~~s~~lwrev~~eva-~~yPdv~~~~~~VD~aam~lV-------~~P~---------~FDViVt--~NlFGD 239 (348)
T COG0473 179 SVHKANVLKLSDGLWREVVEEVA-KEYPDVELDHMYVDAAAMQLV-------RNPE---------QFDVIVT--SNLFGD 239 (348)
T ss_pred EEehhhhhhhhhHHHHHHHHHHh-hcCCCcchhHHhHHHHHHHHh-------hCcc---------ccCEEEE--ccchhH
Confidence 46999999986 57889999988 43 2335556555554 3465 5899999 578999
Q ss_pred HHHHHhcC-----------------CCCCCceEEEEEeccc----CCHHHHHhhHHHHHHHHHHHHhhhhhHHHHHHHHH
Q 029441 118 VVEDLNTR-----------------EQPFMKTVLVINLEVK----DNHEEAAIGGRLTFDLCQEIEAAESWEESIDDIIA 176 (193)
Q Consensus 118 Vvedl~~R-----------------~~~~~~pVHViNvdIk----Dn~EeA~~Ga~~il~Lc~~l~~~~d~e~~i~~il~ 176 (193)
++-|+.+- +...+.|||=---||. =|+=-++..+-.+|+---..++++.+|+.|..+|.
T Consensus 240 ILSD~aa~l~GslGl~PSAnig~~~~~~lfEPvHGSAPDIAGkgiANPiA~IlS~aMML~~~g~~~~A~~Ie~Av~~vl~ 319 (348)
T COG0473 240 ILSDEAAALTGSLGLAPSANLGDERGPALFEPVHGSAPDIAGKGIANPIATILSAAMMLRHLGEKEAADAIENAVEKVLA 319 (348)
T ss_pred HHHhHHHHhcCccccCccCccCCCCCCceeecCCCCcccccCCCccChHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHH
Confidence 99997653 2457889998888886 46655555555555554444556778888888887
Q ss_pred H
Q 029441 177 A 177 (193)
Q Consensus 177 ~ 177 (193)
+
T Consensus 320 ~ 320 (348)
T COG0473 320 E 320 (348)
T ss_pred c
Confidence 6
No 61
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=40.77 E-value=18 Score=29.89 Aligned_cols=20 Identities=40% Similarity=0.609 Sum_probs=17.0
Q ss_pred CCcchHHHHhHHhCCCCeee
Q 029441 13 QNRSMEAHYLLKRHGFDVSS 32 (193)
Q Consensus 13 ~NRSMEaH~~L~~~g~~V~S 32 (193)
.-|+=|||++|.++||-|+-
T Consensus 49 V~~~d~A~~~Lee~gF~Vr~ 68 (142)
T COG4747 49 VDRPDEAHSVLEEAGFTVRE 68 (142)
T ss_pred cCChHHHHHHHHHCCcEEEe
Confidence 46788999999999997763
No 62
>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=40.01 E-value=68 Score=27.27 Aligned_cols=43 Identities=7% Similarity=0.139 Sum_probs=34.1
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHH
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~i 154 (193)
.+.+...+++++..++-.+++|-++-.|-+.+++.|...+..+
T Consensus 20 ~~g~~lA~~~iN~~ggi~G~~iel~~~D~~~~p~~a~~~a~~l 62 (312)
T cd06346 20 ADAAELAVKEVNAAGGVLGEPVTLVTADTQTDPAAGVAAATKL 62 (312)
T ss_pred HHHHHHHHHHHHHhCCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence 4678899999999998888999888888888877766555433
No 63
>cd00636 TroA-like Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between two globular domains linked by a single helix. Many of these proteins also possess a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). The TroA-like proteins differ in their fold and ligand-binding mechanism from the PBPI and PBPII proteins, but are structurally similar, however, to the beta-subunit of the nitrogenase molybdenum-iron protein MoFe. Most TroA-like proteins are encoded by ABC-type operons and appear to function as periplasmic components of ABC transporters in metal ion uptake.
Probab=39.39 E-value=1.4e+02 Score=21.12 Aligned_cols=77 Identities=16% Similarity=0.141 Sum_probs=44.8
Q ss_pred cccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHc
Q 029441 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEIEAAESWEESIDDIIAAFEKRH 182 (193)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~l~~~~d~e~~i~~il~~fe~k~ 182 (193)
..||||+... .++...+.+..-+ -|+-+++.....+.++...-...+-++...-+.++.+-+.+++.++..+++.
T Consensus 61 ~pDlvi~~~~-~~~~~~~~l~~~~----i~~~~~~~~~~~~~~~~~~~i~~lg~~~~~~~~a~~~~~~~~~~~~~i~~~~ 135 (148)
T cd00636 61 KPDLIIANGS-GLEAWLDKLSKIA----IPVVVVDEASELSLENIKESIRLIGKALGKEENAEELIAELDARLAELRAKL 135 (148)
T ss_pred CCCEEEEecc-cchhHHHHHHHhC----CCEEEECCCCcCCHHHHHHHHHHHHHHHCChHHHHHHHHHHHHHHHHHHHHH
Confidence 3899999874 3344566665533 3444443321125555544445554444444666778888888888877765
Q ss_pred CC
Q 029441 183 RR 184 (193)
Q Consensus 183 ~~ 184 (193)
..
T Consensus 136 ~~ 137 (148)
T cd00636 136 AK 137 (148)
T ss_pred hc
Confidence 43
No 64
>cd06357 PBP1_AmiC Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. This group includes the periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. AmiC controls expression of the amidase operon by the 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 are induced.
Probab=38.81 E-value=80 Score=27.71 Aligned_cols=45 Identities=4% Similarity=0.002 Sum_probs=37.3
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHH
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFD 156 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~ 156 (193)
.+-+...+++++.+++-.++++-++-.|.+-+++.|...++.+++
T Consensus 20 ~~g~~la~~~iN~~GGi~G~~ielv~~D~~~~p~~a~~~a~~li~ 64 (360)
T cd06357 20 RNGALLAIEEINAAGGVLGRELEPVEYDPGGDPDAYRALAERLLR 64 (360)
T ss_pred HHHHHHHHHHHhhcCCCCCeEEEEEEECCCCCHHHHHHHHHHHHh
Confidence 456788999999999989999999999999888888776665553
No 65
>cd01530 Cdc25 Cdc25 phosphatases are members of the Rhodanese Homology Domain superfamily. They activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. Cdc25A phosphatase functions to regulate S phase entry and Cdc25B is required for G2/M phase transition of the cell cycle. The Cdc25 domain binds oxyanions at the catalytic site and has the signature motif (H/YCxxxxxR).
Probab=37.86 E-value=48 Score=25.29 Aligned_cols=24 Identities=13% Similarity=0.124 Sum_probs=20.2
Q ss_pred ceEEEEccCCCCcchHHHHhHHhC
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRH 26 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~ 26 (193)
..+.+.|....+||..|-..|++.
T Consensus 69 ~~vv~yC~~sg~rs~~aa~~L~~~ 92 (121)
T cd01530 69 RVLIFHCEFSSKRGPRMARHLRNL 92 (121)
T ss_pred CEEEEECCCccccHHHHHHHHHHH
Confidence 357889987779999999999985
No 66
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=37.28 E-value=32 Score=29.72 Aligned_cols=31 Identities=29% Similarity=0.273 Sum_probs=25.7
Q ss_pred EEEEecccCCHHHHHhhHH-----------------HHHHHHHHHHhh
Q 029441 134 LVINLEVKDNHEEAAIGGR-----------------LTFDLCQEIEAA 164 (193)
Q Consensus 134 HViNvdIkDn~EeA~~Ga~-----------------~il~Lc~~l~~~ 164 (193)
..=||.+-++.|+|..+|+ .+..+|.+|+..
T Consensus 47 k~eNv~ff~t~~~A~~aGfRPCkRC~P~~~~~~~~~~V~~a~~~ie~~ 94 (187)
T COG2169 47 KRENVSFFHTAEEALAAGFRPCKRCRPDLAAAGRSGLVATACRLIEQN 94 (187)
T ss_pred chhhhhhhcCHHHHHHcCCCcccccCcccccccccHHHHHHHHHHHcC
Confidence 4569999999999999988 677777888775
No 67
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=37.15 E-value=17 Score=40.01 Aligned_cols=88 Identities=26% Similarity=0.390 Sum_probs=64.5
Q ss_pred EEEEccCCC-CcchHHHHhHHhCCCCeeee-cCCCceecCCCCCCCCccccCC-CCHHHHHHHHhhcChHHHHhcCchhh
Q 029441 5 YAMVCSSNQ-NRSMEAHYLLKRHGFDVSSY-GTGAHVKLPGPSLREPNVYEFG-TPYKQMFDDLRRKDPELYKRNGILPM 81 (193)
Q Consensus 5 ~avVCasN~-NRSMEaH~~L~~~g~~V~Sf-GTGs~VrLPGps~d~PNvY~Fg-T~Y~~iy~dL~~kd~~lY~~NGlL~M 81 (193)
.-||=+|+. |+-||--++-- ||+|.+| |+--.-|.--.--.|||-|.-- |+|+..++|+.+ |=+.+==.=.
T Consensus 669 LIVVpTsviLnWEMElKRwcP--glKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~A----FkrkrWqyLv 742 (1958)
T KOG0391|consen 669 LIVVPTSVILNWEMELKRWCP--GLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLTA----FKRKRWQYLV 742 (1958)
T ss_pred eEEeechhhhhhhHHHhhhCC--cceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHHH----HHhhccceee
Confidence 456666765 99999877754 9999885 8777777777778899998887 999999999975 2222222345
Q ss_pred hhcccCCCC-Cccccccc
Q 029441 82 LKRNIGVKA-APQRWQDN 98 (193)
Q Consensus 82 LdRN~~iK~-~PERfQ~~ 98 (193)
||--.+||- .-+|||.-
T Consensus 743 LDEaqnIKnfksqrWQAl 760 (1958)
T KOG0391|consen 743 LDEAQNIKNFKSQRWQAL 760 (1958)
T ss_pred hhhhhhhcchhHHHHHHH
Confidence 777777885 45679863
No 68
>cd02645 R3H_AAA R3H domain of a group of proteins with unknown function, who also contain a AAA-ATPase (AAA) domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA or ssRNA in a sequence-specific manner.
Probab=36.79 E-value=31 Score=24.38 Aligned_cols=23 Identities=26% Similarity=0.482 Sum_probs=19.8
Q ss_pred HHHhHHhCCCCeeeecCCCceec
Q 029441 19 AHYLLKRHGFDVSSYGTGAHVKL 41 (193)
Q Consensus 19 aH~~L~~~g~~V~SfGTGs~VrL 41 (193)
-|.++++.|+.-.|.|.|.+=||
T Consensus 34 ~H~~v~~~~l~s~S~G~ep~Rrv 56 (60)
T cd02645 34 QHDLVERYQLRSESFGSEPNRRL 56 (60)
T ss_pred HHHHHHHCCCeEEEecCCCCcEE
Confidence 79999999999999999976543
No 69
>TIGR00137 gid_trmFO tRNA:m(5)U-54 methyltransferase. This model represents an orthologous set of proteins present in relatively few bacteria but very tightly conserved where it occurs. It is closely related to gidA (glucose-inhibited division protein A), which appears to be present in all complete eubacterial genomes so far and in Saccharomyces cerevisiae. It was designated gid but is now recognized as a tRNA:m(5)U-54 methyltransferase and is now designated trmFO.
Probab=36.73 E-value=44 Score=31.94 Aligned_cols=52 Identities=21% Similarity=0.265 Sum_probs=40.7
Q ss_pred EEEccCCCCcchHHHHhHHh-CCCCeeeecCCCceecCCCCCCCCccccCCCCH
Q 029441 6 AMVCSSNQNRSMEAHYLLKR-HGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPY 58 (193)
Q Consensus 6 avVCasN~NRSMEaH~~L~~-~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y 58 (193)
+||.|+-.=-|-+--.-|++ .|+.+..||||+.-|+=|.|+|---+| |.+.|
T Consensus 128 ~VViATG~~~s~~La~~L~~~~g~~~~~~~da~~p~i~~~sId~~~~~-~~~r~ 180 (433)
T TIGR00137 128 ITVIATGPLTSPALSEDLKELTGMDYLYFYDAAAPIVEGDSIDKEKAF-FASRY 180 (433)
T ss_pred eEEEeCCCCccHHHHHHHHHhhCCceEEEecCcCcEEecCCCCcceEE-eeccC
Confidence 56777665445566677788 499999999999999999999987776 55544
No 70
>TIGR03407 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane.
Probab=36.18 E-value=97 Score=27.18 Aligned_cols=43 Identities=12% Similarity=0.024 Sum_probs=35.7
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHH
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTF 155 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il 155 (193)
+-.+..+++++.+++-.++||-++-.|-+-+++.|...++.++
T Consensus 22 ~g~~lav~~iN~~GGi~G~~i~l~~~Dd~~~p~~a~~~a~~Lv 64 (359)
T TIGR03407 22 DAELMAIEEINASGGVLGKKIEPVVEDGASDWPTFAEKARKLI 64 (359)
T ss_pred HHHHHHHHHHHhcCCCCCcEEEEEEeCCCCCHHHHHHHHHHHH
Confidence 4668889999999998899999999898888888876666554
No 71
>COG2198 ArcB FOG: HPt domain [Signal transduction mechanisms]
Probab=35.59 E-value=75 Score=23.91 Aligned_cols=35 Identities=29% Similarity=0.492 Sum_probs=26.2
Q ss_pred HHhhHHHHHHHHHHHHhh---hhhHHHHHHHHHHHHHH
Q 029441 147 AAIGGRLTFDLCQEIEAA---ESWEESIDDIIAAFEKR 181 (193)
Q Consensus 147 A~~Ga~~il~Lc~~l~~~---~d~e~~i~~il~~fe~k 181 (193)
+.+|+..+-++|+.||.. ..+.+++.+.|.+.++.
T Consensus 67 ~~lg~~~L~~~~~~lE~~~~~~~~~~~~~~~i~~l~~~ 104 (122)
T COG2198 67 ASLGLPALAQLCQQLEDALRSGASLEELEELIAELKDE 104 (122)
T ss_pred HhccHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence 678999999999999984 24556666666666554
No 72
>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=35.48 E-value=71 Score=26.84 Aligned_cols=40 Identities=10% Similarity=0.141 Sum_probs=30.1
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHH
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGR 152 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~ 152 (193)
+.+..-+++++.+++-.+++|-++-.|.+-+.+.|.-.+.
T Consensus 23 ~g~~~a~~~~N~~ggi~G~~i~l~~~D~~~~~~~a~~~~~ 62 (343)
T PF13458_consen 23 RGAELAVDEINAAGGINGRKIELVVYDDGGDPAQAVQAAR 62 (343)
T ss_dssp HHHHHHHHHHHHTTEETTEEEEEEEEE-TT-HHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCcCCccceeeeccCCCChHHHHHHHH
Confidence 4567889999999888889999998888888777754433
No 73
>cd02325 R3H R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=35.18 E-value=38 Score=21.37 Aligned_cols=20 Identities=30% Similarity=0.348 Sum_probs=18.1
Q ss_pred HHHHhHHhCCCCeeeecCCC
Q 029441 18 EAHYLLKRHGFDVSSYGTGA 37 (193)
Q Consensus 18 EaH~~L~~~g~~V~SfGTGs 37 (193)
-.|.+....|+...|.|+|.
T Consensus 32 ~vH~la~~~~L~s~s~g~~~ 51 (59)
T cd02325 32 LIHDLAEYYGLKSESEGEGP 51 (59)
T ss_pred HHHHHHHHCCCEEEEecCCC
Confidence 48999999999999999984
No 74
>cd06344 PBP1_ABC_ligand_binding_like_9 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. 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=35.08 E-value=91 Score=26.66 Aligned_cols=42 Identities=12% Similarity=-0.065 Sum_probs=33.8
Q ss_pred hHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHH
Q 029441 114 VFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTF 155 (193)
Q Consensus 114 vfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il 155 (193)
-....+++++.+++-.++++-+|-.|-+.+++.|...+..+.
T Consensus 21 g~~lA~~~iNa~ggi~G~~ielv~~D~~~~p~~a~~~a~~li 62 (332)
T cd06344 21 GVAQAQTEINLQGGINGKLLKVVIANDGNDPEIAKKVADELV 62 (332)
T ss_pred HHHHHHHHHHhcCCCCCCeEEEEEECCCCChHHHHHHHHHHh
Confidence 345678999999999999999999999999888866555443
No 75
>PRK01175 phosphoribosylformylglycinamidine synthase I; Provisional
Probab=35.01 E-value=53 Score=29.08 Aligned_cols=34 Identities=18% Similarity=0.124 Sum_probs=29.3
Q ss_pred CCceEEEEccCCCCcchHHHHhHHhCCCCeeeec
Q 029441 1 MKYRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYG 34 (193)
Q Consensus 1 ~~l~~avVCasN~NRSMEaH~~L~~~g~~V~SfG 34 (193)
+++|+||++..-.|.-+|+-..|+++|+.|.-..
T Consensus 2 ~~~kvaVl~~pG~n~d~e~~~Al~~aG~~v~~v~ 35 (261)
T PRK01175 2 ESIRVAVLRMEGTNCEDETVKAFRRLGVEPEYVH 35 (261)
T ss_pred CCCEEEEEeCCCCCCHHHHHHHHHHCCCcEEEEe
Confidence 4689999999999988999999999999886543
No 76
>COG3414 SgaB Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism]
Probab=34.93 E-value=47 Score=25.33 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=23.9
Q ss_pred CceEEEEccCCCCcc----hHHHHhHHhCCC
Q 029441 2 KYRYAMVCSSNQNRS----MEAHYLLKRHGF 28 (193)
Q Consensus 2 ~l~~avVCasN~NRS----MEaH~~L~~~g~ 28 (193)
..||-+||-+-++-| |..-.+|++.|+
T Consensus 1 ~~KIL~aCG~GvgSS~~ik~kve~~l~~~gi 31 (93)
T COG3414 1 MIKILAACGNGVGSSTMIKMKVEEVLKELGI 31 (93)
T ss_pred CcEEEEECCCCccHHHHHHHHHHHHHHHcCC
Confidence 368999999999999 567789999999
No 77
>cd02640 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=33.99 E-value=37 Score=23.95 Aligned_cols=25 Identities=28% Similarity=0.606 Sum_probs=20.7
Q ss_pred CCcchHHHHhHHhCCCCeeeecCCCc
Q 029441 13 QNRSMEAHYLLKRHGFDVSSYGTGAH 38 (193)
Q Consensus 13 ~NRSMEaH~~L~~~g~~V~SfGTGs~ 38 (193)
..|+ -.|.+-.+.|+.-.|+|.|..
T Consensus 29 ~eR~-~vH~~a~~~gL~s~S~G~g~~ 53 (60)
T cd02640 29 EERA-LIHQIAQKYGLKSRSYGSGND 53 (60)
T ss_pred HHHH-HHHHHHHHcCCceeeEeCCCC
Confidence 3454 389999999999999999874
No 78
>cd05563 PTS_IIB_ascorbate PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a transmembrane channel IIC subunit. Subunits IIA, IIB, and IIC are encoded by the sgaA, sgaB, and sgaT genes of the E. coli sgaTBA operon. In some bacteria, the IIB (SgaB) domain is fused C-terminal to the IIA (SgaT) domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include ascorbate, chitobiose/lichenan, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=33.11 E-value=33 Score=24.20 Aligned_cols=25 Identities=28% Similarity=0.389 Sum_probs=18.0
Q ss_pred eEEEEccCCCCcchHHHHh----HHhCCC
Q 029441 4 RYAMVCSSNQNRSMEAHYL----LKRHGF 28 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~----L~~~g~ 28 (193)
|+++||++.++-|.=...- +.+.|.
T Consensus 1 kilvvC~~G~~tS~ll~~kl~~~f~~~~i 29 (86)
T cd05563 1 KILAVCGSGLGSSLMLKMNVEKVLKELGI 29 (86)
T ss_pred CEEEECCCCccHHHHHHHHHHHHHHHCCC
Confidence 5899999999988655544 445565
No 79
>PRK11784 tRNA 2-selenouridine synthase; Provisional
Probab=32.86 E-value=51 Score=30.34 Aligned_cols=171 Identities=18% Similarity=0.166 Sum_probs=90.7
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCCeeeecCCC----c-ee--cCCC-CCCCCccc--cCCCCHHHHHHHHhhcC---
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGA----H-VK--LPGP-SLREPNVY--EFGTPYKQMFDDLRRKD--- 69 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs----~-Vr--LPGp-s~d~PNvY--~FgT~Y~~iy~dL~~kd--- 69 (193)
..+.|.|....+||.-+-.+|+..||+|....-|- . +. +.+. ..-..-+. .=|+...+|...|..++
T Consensus 89 ~~ivvyC~rgG~RS~~aa~~L~~~G~~v~~L~GG~~awr~~~~~~~~~~~~~~~~ivl~G~TGsGKT~iL~~L~~~~~~v 168 (345)
T PRK11784 89 PRGLLYCWRGGLRSGSVQQWLKEAGIDVPRLEGGYKAYRRFVIDTLEEAPAQFPLVVLGGNTGSGKTELLQALANAGAQV 168 (345)
T ss_pred CeEEEEECCCChHHHHHHHHHHHcCCCcEEEcCCHHHHHHhhHHHHhhhcccCceEecCCCCcccHHHHHHHHHhcCCeE
Confidence 36889998888999999999999999988775441 0 00 1110 11111122 22578999999998753
Q ss_pred -----hHHHHhc-----------------CchhhhhcccCCCC--------------CcccccccC-CCCcccEEEeccc
Q 029441 70 -----PELYKRN-----------------GILPMLKRNIGVKA--------------APQRWQDNA-LDGSFDIVFTFEE 112 (193)
Q Consensus 70 -----~~lY~~N-----------------GlL~MLdRN~~iK~--------------~PERfQ~~~-~~~~fDvIiTcEE 112 (193)
..-|+.. +|..-|.+-..-++ -|+.+.+.. .+...-|-...|+
T Consensus 169 lDlE~~aehrGS~fG~~~~~qpsQ~~Fe~~l~~~l~~~~~~~~i~vE~Es~~IG~~~lP~~l~~~m~~~~~v~i~~~~e~ 248 (345)
T PRK11784 169 LDLEGLANHRGSSFGRLGGPQPSQKDFENLLAEALLKLDPARPIVVEDESRRIGRVHLPEALYEAMQQAPIVVVEAPLEE 248 (345)
T ss_pred EECCchhhhccccccCCCCCCcchHHHHHHHHHHHHcCCCCCeEEEEeccccccCccCCHHHHHHHhhCCEEEEECCHHH
Confidence 3334443 33333332221000 012211111 1112333344566
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHH------HhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHH
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEA------AIGGRLTFDLCQEIEAAESWEESIDDIIAAFEKR 181 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA------~~Ga~~il~Lc~~l~~~~d~e~~i~~il~~fe~k 181 (193)
|| +.+++|--......... .-.+...+| .+|+..+-++-++|++ +++++-+..+|.++..+
T Consensus 249 Rv-~~l~~~Y~~~~~~~~~~------~~~~~l~~~l~~i~k~lg~~~~~~~~~~~~~-~~~~~~~~~ll~~yYDp 315 (345)
T PRK11784 249 RV-ERLLEDYVLRMHAAGFQ------AYPEYLAEALQRIRKRLGGERYQELLALLDA-GGHLAWIEELLLEYYDP 315 (345)
T ss_pred HH-HHHHHHhhhhhhhhhhh------ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHc-CCHHHHHHHHHHHhCCh
Confidence 66 66666654332211111 111111122 3566677777777776 78899999999888653
No 80
>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=32.77 E-value=1.5e+02 Score=23.79 Aligned_cols=38 Identities=16% Similarity=0.128 Sum_probs=33.0
Q ss_pred ccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEeccc
Q 029441 104 FDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVK 141 (193)
Q Consensus 104 fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIk 141 (193)
+|.|+|+.......|++-+..++-...+.+.||-+|-.
T Consensus 175 ~~ai~~~~d~~a~g~~~~~~~~g~~ip~~i~ii~~d~~ 212 (264)
T cd01574 175 PTAVFAANDQMALGVLRALHELGLRVPDDVSVVGFDDI 212 (264)
T ss_pred CcEEEEcCcHHHHHHHHHHHHcCCCCccceEEecccCc
Confidence 89999999999999999999887666678999999843
No 81
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=32.74 E-value=39 Score=28.68 Aligned_cols=89 Identities=21% Similarity=0.338 Sum_probs=57.2
Q ss_pred CceEEEEccCCCCcchHHHHhHH----hCCC----CeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHH
Q 029441 2 KYRYAMVCSSNQNRSMEAHYLLK----RHGF----DVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELY 73 (193)
Q Consensus 2 ~l~~avVCasN~NRSMEaH~~L~----~~g~----~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY 73 (193)
+.+|+.||--|.=||=-|-.+++ |+|+ +|-|+||+..= -|.++|. -.. .--
T Consensus 6 ~~svlFvclGNiCRSP~AEaVFr~~v~K~~l~~~~~iDSagt~~yh--~G~~PD~-----------R~~--------s~l 64 (159)
T KOG3217|consen 6 TKSVLFVCLGNICRSPIAEAVFRDLVKKRNLSEEWHIDSAGTSGYH--TGRSPDP-----------RTL--------SIL 64 (159)
T ss_pred ceEEEEEEecccccCHHHHHHHHHHHHHcCcceeeeeccccccccc--cCCCCCh-----------HHH--------HHH
Confidence 45788999999999977776654 6664 77999998743 2444442 111 124
Q ss_pred HhcCchhhhhcccCCCCCcccccccCCCCcccEEEeccchhHHHHHHHHhc
Q 029441 74 KRNGILPMLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNT 124 (193)
Q Consensus 74 ~~NGlL~MLdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~ 124 (193)
+++||= +=-+-|.||+ +=| . .||.|++-+|.. ++||+.
T Consensus 65 K~hGI~-~~H~aRqit~--~DF----~--~FDYI~~MDesN----~~dL~~ 102 (159)
T KOG3217|consen 65 KKHGIK-IDHLARQITT--SDF----R--EFDYILAMDESN----LRDLLR 102 (159)
T ss_pred HHcCCc-chhhcccccH--hHh----h--hcceeEEecHHH----HHHHHH
Confidence 667764 5445555553 223 1 599999999754 666665
No 82
>TIGR03669 urea_ABC_arch urea ABC transporter, substrate-binding protein, archaeal type. Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization.
Probab=32.71 E-value=1.1e+02 Score=27.67 Aligned_cols=44 Identities=11% Similarity=0.115 Sum_probs=36.7
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHH
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTF 155 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il 155 (193)
.+-.+.-+|+++..++-.+++|-+|-.|-+-+++.|...++.++
T Consensus 21 ~~G~~lAv~~iNa~GGi~Gr~ielv~~D~~~~p~~a~~~a~~li 64 (374)
T TIGR03669 21 WHASQLAIEEINKSGGILGRQIELIDPDPQSDNERYQELTRRLL 64 (374)
T ss_pred HHHHHHHHHHHHhcCCCCCceeEEEEeCCCCCHHHHHHHHHHHH
Confidence 45677889999999998899999999999999988877766544
No 83
>PRK00142 putative rhodanese-related sulfurtransferase; Provisional
Probab=32.63 E-value=52 Score=29.73 Aligned_cols=30 Identities=27% Similarity=0.444 Sum_probs=24.5
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeee
Q 029441 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSY 33 (193)
Q Consensus 3 l~~avVCasN~NRSMEaH~~L~~~g~~-V~Sf 33 (193)
.+|.|.|++- .||..|=.+|+++||+ |..+
T Consensus 172 k~IvvyC~~G-~Rs~~aa~~L~~~Gf~~V~~L 202 (314)
T PRK00142 172 KKVVMYCTGG-IRCEKASAWMKHEGFKEVYQL 202 (314)
T ss_pred CeEEEECCCC-cHHHHHHHHHHHcCCCcEEEe
Confidence 4789999864 8999999999999994 6544
No 84
>PRK08762 molybdopterin biosynthesis protein MoeB; Validated
Probab=32.34 E-value=54 Score=29.85 Aligned_cols=29 Identities=31% Similarity=0.540 Sum_probs=24.7
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeee
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSY 33 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~-~V~Sf 33 (193)
.+.++|.+ .+||..|-..|++.|| +|..+
T Consensus 59 ~IvvyC~~-G~rs~~aa~~L~~~G~~~v~~l 88 (376)
T PRK08762 59 EIVLICAS-GTRSAHAAATLRELGYTRVASV 88 (376)
T ss_pred eEEEEcCC-CcHHHHHHHHHHHcCCCceEee
Confidence 57889986 5799999999999999 68766
No 85
>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=32.21 E-value=1.1e+02 Score=26.36 Aligned_cols=41 Identities=15% Similarity=0.053 Sum_probs=29.3
Q ss_pred chhHHHHHHHHhcCC-CCCCceEEEEEecccCCHHHHHhhHH
Q 029441 112 EKVFDTVVEDLNTRE-QPFMKTVLVINLEVKDNHEEAAIGGR 152 (193)
Q Consensus 112 ERvfD~Vvedl~~R~-~~~~~pVHViNvdIkDn~EeA~~Ga~ 152 (193)
++.+...+|+++.++ .-.++++.++-.|.+.++..|..++.
T Consensus 18 ~~~~~lAv~~iN~~gg~~~g~~i~~~~~D~~~~~~~a~~~a~ 59 (350)
T cd06366 18 LPAIEMALEDVNADNSILPGYRLVLHVRDSKCDPVQAASAAL 59 (350)
T ss_pred HHHHHHHHHHHhcCCCcCCCcEEEEEecCCCCCHHHHHHHHH
Confidence 467788999999997 44578888877777666655544443
No 86
>TIGR03167 tRNA_sel_U_synt tRNA 2-selenouridine synthase. The Escherichia coli YbbB protein was shown to encode a selenophosphate-dependent tRNA 2-selenouridine synthase, essential for modification of some tRNAs to replace a sulfur atom with selenium. This enzyme works with SelD, the selenium donor protein, which also acts in selenocysteine incorporation. Although the members of this protein family show a fairly deep split, sequences from both sides of the split are supported by co-occurence with, and often proximity to, the selD gene.
Probab=31.01 E-value=53 Score=29.79 Aligned_cols=65 Identities=22% Similarity=0.241 Sum_probs=43.6
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCCeeeecCCC-------c---eecCCCCCC-CCccccCCCCHHHHHHHHhhcC
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGA-------H---VKLPGPSLR-EPNVYEFGTPYKQMFDDLRRKD 69 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs-------~---VrLPGps~d-~PNvY~FgT~Y~~iy~dL~~kd 69 (193)
++-++|..+-.||--+-.+|++.||+|....-|- . -..|+|..- .|+ =.=|+...++.+-|...+
T Consensus 76 ~vvvyC~~gG~RS~~aa~~L~~~G~~v~~L~GG~~aw~~~~~~~~~~~~~~~~~~vl~-g~tg~gKt~Ll~~L~~~~ 151 (311)
T TIGR03167 76 QPLLYCWRGGMRSGSLAWLLAQIGFRVPRLEGGYKAYRRFVIDQLEELPQPFPLIVLG-GMTGSGKTELLHALANAG 151 (311)
T ss_pred cEEEEECCCChHHHHHHHHHHHcCCCEEEecChHHHHHHhhhhhhhccCCCCceeccC-CCCCcCHHHHHHHHhcCC
Confidence 4889998888999999999999999987765442 1 112222211 111 123578999999987663
No 87
>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=30.94 E-value=1.3e+02 Score=25.64 Aligned_cols=41 Identities=17% Similarity=0.160 Sum_probs=32.3
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHH
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRL 153 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~ 153 (193)
+-.+..+++++..++-.+++|-+|-.|-+-+++.|...+..
T Consensus 21 ~g~~la~~~iN~~gGi~G~~i~l~~~D~~~~p~~a~~~a~~ 61 (333)
T cd06358 21 AAAELAVEEINAAGGILGREVELVIVDDGSPPAEAAAAAAR 61 (333)
T ss_pred HHHHHHHHHHHhcCCcCCcEEEEEEECCCCChHHHHHHHHH
Confidence 34677899999999888999999988888887776554443
No 88
>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=30.37 E-value=1.2e+02 Score=26.17 Aligned_cols=45 Identities=11% Similarity=0.159 Sum_probs=32.6
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHH
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQ 159 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~ 159 (193)
++.+...+++++.+++-.+++|-++=.|.+-+++.|. ..+.+|.+
T Consensus 20 ~~g~~~a~~~iN~~GGi~G~~i~l~~~D~~~~p~~a~---~~a~~lv~ 64 (342)
T cd06329 20 RRGLQLAADEINAKGGVDGRPIELVEEDNKGSPQEAL---RKAQKAID 64 (342)
T ss_pred HHHHHHHHHHHHhcCCcCCeEEEEEeccCCCChHHHH---HHHHHHHH
Confidence 4678899999999988888888877666666665554 44455543
No 89
>PLN00123 isocitrate dehydrogenase (NAD+)
Probab=29.87 E-value=60 Score=30.56 Aligned_cols=115 Identities=13% Similarity=0.275 Sum_probs=65.3
Q ss_pred CCCCCccccCC-CCHHHHHHHHhhcChHH-----HHhcCchhhhhcccCCCCCcccccccCCCCcccEEEeccchhHHHH
Q 029441 45 SLREPNVYEFG-TPYKQMFDDLRRKDPEL-----YKRNGILPMLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTV 118 (193)
Q Consensus 45 s~d~PNvY~Fg-T~Y~~iy~dL~~kd~~l-----Y~~NGlL~MLdRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~V 118 (193)
+.+|.||..+. --+.+++++..++=|+. |--+-..+|.. .|+ .||||+| +..|=.+
T Consensus 191 ~v~KaNvl~~t~glf~~~~~eva~eyPdV~~~~~~VDa~~~~Lv~-------~P~---------~fDViVt--~NlfGDI 252 (360)
T PLN00123 191 AVHKANIMKLADGLFLESCREVAKKYPGIKYNEIIVDNCCMQLVS-------KPE---------QFDVMVT--PNLYGNL 252 (360)
T ss_pred EEECCccccchhhHHHHHHHHHHhhCCCceEeeeeHHHHHHHHhh-------Ccc---------cCcEEEE--cCcccch
Confidence 46899999985 46889998886542221 33333333321 233 5899998 4688899
Q ss_pred HHHHhcC---------------CCCCCceEEEEE----eccc----CCHHHHHhhHHHHHHHHHHHHhhhhhHHHHHHHH
Q 029441 119 VEDLNTR---------------EQPFMKTVLVIN----LEVK----DNHEEAAIGGRLTFDLCQEIEAAESWEESIDDII 175 (193)
Q Consensus 119 vedl~~R---------------~~~~~~pVHViN----vdIk----Dn~EeA~~Ga~~il~Lc~~l~~~~d~e~~i~~il 175 (193)
+-|+.+- +...++|||+== =||. =|+=-++.++-.+|+-...-+.++-+++.|..+|
T Consensus 253 LSDlaa~l~GglGl~pSanig~~~a~FEpvh~hGSA~~PdIAGk~iANP~a~IlS~amML~~lG~~~~A~~I~~AV~~~l 332 (360)
T PLN00123 253 VANTAAGIAGGTGVMPGGNVGADHAVFEQGASAGNVGNEKLVEQKKANPVALLLSSAMMLRHLQFPSFADRLETAVKRVI 332 (360)
T ss_pred hhhHHHHhcCCcCccceEeeCCCceEEEecccCCCcCCccccCCCccChHHHHHHHHHHHHHcCChHHHHHHHHHHHHHH
Confidence 9998754 124566877311 2442 2444444444444444333233445666666666
Q ss_pred HH
Q 029441 176 AA 177 (193)
Q Consensus 176 ~~ 177 (193)
.+
T Consensus 333 ~~ 334 (360)
T PLN00123 333 AE 334 (360)
T ss_pred Hc
Confidence 43
No 90
>cd01144 BtuF Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=29.43 E-value=3.1e+02 Score=22.31 Aligned_cols=71 Identities=20% Similarity=0.192 Sum_probs=40.6
Q ss_pred cccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHHHH---hhhhhHHHHHHHHHHHH
Q 029441 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEIE---AAESWEESIDDIIAAFE 179 (193)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~l~---~~~d~e~~i~~il~~fe 179 (193)
..||||+....--+...+.|.+-+. | |+-++ .++.++.. ..+..|++.+. .++.+-+.+++.+++..
T Consensus 57 ~PDlIi~~~~~~~~~~~~~l~~~gi----~--v~~~~-~~~~~~~~---~~~~~lg~~~g~~~~a~~~~~~~~~~~~~~~ 126 (245)
T cd01144 57 KPDLVIAWDDCNVCAVVDQLRAAGI----P--VLVSE-PQTLDDIL---ADIRRLGTLAGRPARAEELAEALRRRLAALR 126 (245)
T ss_pred CCCEEEEecCCCHHHHHHHHHHcCC----c--EEEeC-CCCHHHHH---HHHHHHHHHhCChhHHHHHHHHHHHHHHHHH
Confidence 3899999765433445777766332 2 33333 23333332 34566666663 34557777777777777
Q ss_pred HHcC
Q 029441 180 KRHR 183 (193)
Q Consensus 180 ~k~~ 183 (193)
++.+
T Consensus 127 ~~~~ 130 (245)
T cd01144 127 KQYA 130 (245)
T ss_pred HHhc
Confidence 6654
No 91
>PRK01220 malonate decarboxylase subunit delta; Provisional
Probab=29.13 E-value=58 Score=25.62 Aligned_cols=45 Identities=22% Similarity=0.350 Sum_probs=33.3
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHHHHhh
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEIEAA 164 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~l~~~ 164 (193)
..+|.+|++++..|... -=.+|+|-|. ...=|-.-|+|.|.++..
T Consensus 52 ~~~Wqavl~rf~~~~~~-----~~~~i~InD~---GATP~VV~LRL~QA~e~~ 96 (99)
T PRK01220 52 AARWKALFERFFTAQTP-----PAANIDIHDF---GATPGVVRLRLEQALEEI 96 (99)
T ss_pred HHHHHHHHHHHHhhCCC-----CccEEEEeCC---CCCcHhhhhHHHHHHHHH
Confidence 46899999999998532 2357788888 444456778899998864
No 92
>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=29.06 E-value=1.5e+02 Score=23.52 Aligned_cols=43 Identities=21% Similarity=0.230 Sum_probs=30.5
Q ss_pred HHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHH
Q 029441 18 EAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFD 63 (193)
Q Consensus 18 EaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~ 63 (193)
.+...+.++|..|.+++++... ++. ...||+|..++++.+.-.
T Consensus 81 ~~~~~~~~~~ip~i~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~ 123 (298)
T cd06268 81 AAAPVAEEAGVPLISPGATSPA-LTG--KGNPYVFRTAPSDAQQAA 123 (298)
T ss_pred hhHHHHHhCCCcEEccCCCCcc-ccc--CCCceEEEcccCcHHHHH
Confidence 5678889999999999887542 111 346899998877754443
No 93
>KOG3212 consensus Uncharacterized conserved protein related to IojAP [Function unknown]
Probab=28.17 E-value=28 Score=30.60 Aligned_cols=52 Identities=19% Similarity=0.268 Sum_probs=41.7
Q ss_pred EEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCC
Q 029441 5 YAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGT 56 (193)
Q Consensus 5 ~avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT 56 (193)
+-||||.-.-|.|-|=...-..=|++.|=|.-.|||+||...++=-+-+||.
T Consensus 100 h~VIcSgrs~rhl~aiAe~lv~m~Kik~~kgd~hvriegk~s~dW~v~D~g~ 151 (208)
T KOG3212|consen 100 HTVICSGRSDRHLRAIAEALVYMAKIKSQKGDKHVRIEGKQSSDWIVIDYGK 151 (208)
T ss_pred eEEEEecCchHHHHHHHHHHHHHHHHhhcCCCcccccccccCCCeEEEEece
Confidence 4589999888888766655555567779999999999999988877888873
No 94
>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=28.15 E-value=2e+02 Score=23.18 Aligned_cols=40 Identities=13% Similarity=0.067 Sum_probs=33.4
Q ss_pred cccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccC
Q 029441 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKD 142 (193)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkD 142 (193)
.+|.|||.....-..++.-|...+-...+.|.|+-+|--+
T Consensus 178 ~~~ai~~~~d~~a~~~~~~l~~~g~~~p~~i~v~~~d~~~ 217 (270)
T cd06296 178 RPTAIFAGNDLMALGVYEAARERGLRIPEDLSVVGFDDLP 217 (270)
T ss_pred CCcEEEEcCcHHHHHHHHHHHHhCCCCCCceEEEEECChh
Confidence 4899999999998899999998887666778999987544
No 95
>cd05566 PTS_IIB_galactitol PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) comprise the gatCBA operon. Galactitol PTS permease takes up exogenous galactitol, releasing the phosphate ester into the cytoplasm in preparation for oxidation and further metabolism via a modified glycolytic pathway called the tagatose-6-phosphate glycolytic pathway. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include galactitol, chitobiose/lichenan, ascorbate, lactose, mannitol, fructose, and
Probab=28.00 E-value=51 Score=23.39 Aligned_cols=27 Identities=26% Similarity=0.460 Sum_probs=19.0
Q ss_pred ceEEEEccCCCCcc-hH---HHHhHHhCCCC
Q 029441 3 YRYAMVCSSNQNRS-ME---AHYLLKRHGFD 29 (193)
Q Consensus 3 l~~avVCasN~NRS-ME---aH~~L~~~g~~ 29 (193)
.|+++||++-++-| |= .-+.+++.|+.
T Consensus 1 ~~ilivC~~G~~tS~~l~~~i~~~~~~~~i~ 31 (89)
T cd05566 1 KKILVACGTGVATSTVVASKVKELLKENGID 31 (89)
T ss_pred CEEEEECCCCccHHHHHHHHHHHHHHHCCCc
Confidence 47999999999988 32 23445566764
No 96
>cd06276 PBP1_FucR_like Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. FcuR acts as an inducer of fucRRIAK and as a corepressor of another locus that regulates production of fucosylated glycans. FcuR and its close homologs in this group are a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes t
Probab=27.79 E-value=56 Score=26.97 Aligned_cols=53 Identities=11% Similarity=0.127 Sum_probs=35.4
Q ss_pred EEEccCCCCcchHHHHhHHhCCCC------eeeecCCCceecCCCCCCCCccccCCCCHHHHHHH
Q 029441 6 AMVCSSNQNRSMEAHYLLKRHGFD------VSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDD 64 (193)
Q Consensus 6 avVCasN~NRSMEaH~~L~~~g~~------V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~d 64 (193)
|++|+|..- .+-+-+.|++.|++ |.+|+-...-++ -.|.+-.+..|+++|=+.
T Consensus 165 ai~~~~d~~-A~g~~~~l~~~g~~iP~disvigfd~~~~~~~-----~~p~lttv~~~~~~~g~~ 223 (247)
T cd06276 165 LYIILSDTD-LVFLIKKARESGLLLGKDIGIISYNDTPLKEI-----LRNGITTISTDFENMGKK 223 (247)
T ss_pred EEEEeCHHH-HHHHHHHHHHcCCcCCceeEEEEecCchhhhc-----cCCCceEEecCHHHHHHH
Confidence 788886543 45666788898884 677775534443 345566688899888543
No 97
>PF04831 Popeye: Popeye protein conserved region; InterPro: IPR006916 The Popeye (POP) family of proteins, is restricted to vertebrates and is preferentially expressed in developing and adult striated muscle. It is represented by a conserved region which includes three potential transmembrane domains []. The strong conservation of POP genes during evolution and their preferential expression in heart and skeletal muscle suggest that these novel proteins may have an important function in these tissues in vertebrates.; GO: 0016020 membrane
Probab=27.58 E-value=36 Score=28.64 Aligned_cols=36 Identities=22% Similarity=0.394 Sum_probs=26.9
Q ss_pred CchhhhhcccCCCCCccccccc--CCCCcccEEEeccchh
Q 029441 77 GILPMLKRNIGVKAAPQRWQDN--ALDGSFDIVFTFEEKV 114 (193)
Q Consensus 77 GlL~MLdRN~~iK~~PERfQ~~--~~~~~fDvIiTcEERv 114 (193)
-.||++..+.=+ ..|| |.+. .+++.|-|=||-+|.|
T Consensus 65 ~fLH~I~p~qFl-DSPE-W~s~~~s~~~~FQVTitA~~~C 102 (153)
T PF04831_consen 65 RFLHYIYPYQFL-DSPE-WESLRPSEDDKFQVTITAEEDC 102 (153)
T ss_pred EeeEeecccccc-cChh-hhccccCCCCeEEEEEEEcCCc
Confidence 356666666544 4688 8887 5566899999999988
No 98
>cd04918 ACT_AK1-AT_2 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the second of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine (SAM). This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. In its inactive state, Arabidopsis AK1 binds the effectors lysine and SAM (two molecules each) at the interface of two ACT1 domain subunits. The second ACT domain (ACT2), this CD, does not interact with an effector. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=27.42 E-value=1.4e+02 Score=20.16 Aligned_cols=33 Identities=15% Similarity=0.238 Sum_probs=21.7
Q ss_pred eEEEEccCCCCcchHHH--HhHHhCCCCe--eeecCC
Q 029441 4 RYAMVCSSNQNRSMEAH--YLLKRHGFDV--SSYGTG 36 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH--~~L~~~g~~V--~SfGTG 36 (193)
.+++|-....+...-+. ..|.++|.+| .|+|+.
T Consensus 3 ~VsvVG~~~~~~~~~~~i~~aL~~~~I~v~~i~~g~s 39 (65)
T cd04918 3 IISLIGNVQRSSLILERAFHVLYTKGVNVQMISQGAS 39 (65)
T ss_pred EEEEECCCCCCccHHHHHHHHHHHCCCCEEEEEecCc
Confidence 57778773333334333 4489999999 888774
No 99
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=27.27 E-value=56 Score=23.33 Aligned_cols=21 Identities=29% Similarity=0.588 Sum_probs=18.8
Q ss_pred HHHHhHHhCCCCeeeecCCCc
Q 029441 18 EAHYLLKRHGFDVSSYGTGAH 38 (193)
Q Consensus 18 EaH~~L~~~g~~V~SfGTGs~ 38 (193)
-.|.+++.-|+.-.|+|.|..
T Consensus 51 ~iH~~a~~~~l~s~S~g~g~~ 71 (79)
T smart00393 51 IVHELAEKYGLESESFGEGPK 71 (79)
T ss_pred HHHHHHHHcCCEEEEEcCCCC
Confidence 489999999999999999864
No 100
>PF01320 Colicin_Pyocin: Colicin immunity protein / pyocin immunity protein; InterPro: IPR023802 Bacterial colicin and pyocin immunity proteins [, ] can bind specifically to the DNase-type colicins and pyocins and inhibit their bactericidal activity. The 1.8-angstrom crystal structure of the ImmE7 protein consists of four antiparallel alpha-helices []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. Pyocin protects a cell that harbours the plasmid ColE2 encoding colicin E2 against colicin E2; it is thus essential both for autonomous replication and colicin E2 immunity []. This entry represents the structural domain of colicin and pyocin immunity proteins.; GO: 0015643 toxin binding, 0030153 bacteriocin immunity; PDB: 1GXH_A 1GXG_A 1MZ8_C 2ERH_A 1ZNV_C 1AYI_A 1UNK_A 2JBG_A 7CEI_A 1CEI_A ....
Probab=27.26 E-value=64 Score=24.58 Aligned_cols=34 Identities=29% Similarity=0.336 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhhh-hhHHHHHHHHHHHHHHcCCCc
Q 029441 153 LTFDLCQEIEAAE-SWEESIDDIIAAFEKRHRRKL 186 (193)
Q Consensus 153 ~il~Lc~~l~~~~-d~e~~i~~il~~fe~k~~~~~ 186 (193)
.+++|...|-..+ .-|+.++++|..|++-+++|-
T Consensus 14 EFl~~v~~i~~~~~~~ee~~d~lv~hF~~iteHP~ 48 (85)
T PF01320_consen 14 EFLEFVKEIFNAELKTEEEHDELVDHFEKITEHPD 48 (85)
T ss_dssp HHHHHHHHHHHTCSSSCHHHHHHHHHHHHHH--TT
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCCCC
Confidence 4567777776655 456678888888887766654
No 101
>PF08373 RAP: RAP domain; InterPro: IPR013584 The ~60-residue RAP (an acronym for RNA-binding domain abundant in Apicomplexans) domain is found in various proteins in eukaryotes. It is particularly abundant in apicomplexans and might mediate a range of cellular functions through its potential interactions with RNA []. The RAP domain consists of multiple blocks of charged and aromatics residues and is predicted to be composed of alpha helical and beta strand structures. Two predicted loop regions that are dominated by glycine and tryptophan residues are found before and after the central beta sheet []. Some proteins known to contain a RAP domain are listed below: Human hypothetical protein MGC5297, Mammalian FAST kinase domain-containing proteins (FASTKDs), Chlamydomonas reinhardtii chloroplastic trans-splicing factor Raa3.
Probab=27.08 E-value=44 Score=22.01 Aligned_cols=18 Identities=33% Similarity=0.357 Sum_probs=14.5
Q ss_pred chHHHHhHHhCCCCeeee
Q 029441 16 SMEAHYLLKRHGFDVSSY 33 (193)
Q Consensus 16 SMEaH~~L~~~g~~V~Sf 33 (193)
+.-=|++|++.||+|.+.
T Consensus 20 t~lk~r~L~~~G~~Vi~I 37 (58)
T PF08373_consen 20 TKLKHRHLKALGYKVISI 37 (58)
T ss_pred HHHHHHHHHHCCCEEEEe
Confidence 445689999999999864
No 102
>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=26.82 E-value=1.2e+02 Score=26.70 Aligned_cols=43 Identities=5% Similarity=-0.202 Sum_probs=34.9
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHH
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~i 154 (193)
.+.+...+++++..++-..++|-+|-.|-+-+++.|...++.+
T Consensus 20 ~~g~~la~~~iNa~GGI~Gr~ielv~~D~~~~p~~a~~~a~~L 62 (351)
T cd06334 20 AAGFADYFKYINEDGGINGVKLEWEECDTGYEVPRGVECYERL 62 (351)
T ss_pred HHHHHHHHHHHHHcCCcCCeEEEEEEecCCCCcHHHHHHHHHH
Confidence 3556778999999999889999999999999988886555443
No 103
>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=26.72 E-value=1.8e+02 Score=24.46 Aligned_cols=36 Identities=8% Similarity=0.051 Sum_probs=29.5
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHH
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAA 148 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~ 148 (193)
+..+..+++++.+++-.+.+|-++..|-+.+++.|.
T Consensus 22 ~~~~~a~~~iN~~ggi~G~~v~l~~~D~~~d~~~~~ 57 (336)
T cd06326 22 AGAQAYFDAVNAAGGVNGRKIELVTLDDGYEPERTV 57 (336)
T ss_pred HHHHHHHHHHHhcCCcCCceEEEEEeCCCCChHHHH
Confidence 456788999999998889999999999776666654
No 104
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=26.70 E-value=66 Score=26.84 Aligned_cols=32 Identities=22% Similarity=0.323 Sum_probs=22.3
Q ss_pred ceEEEEccCCC--Ccch-----HHHHhHHhCCCCeeeec
Q 029441 3 YRYAMVCSSNQ--NRSM-----EAHYLLKRHGFDVSSYG 34 (193)
Q Consensus 3 l~~avVCasN~--NRSM-----EaH~~L~~~g~~V~SfG 34 (193)
.+|||.|+|.. +-+. |.=+.|.++|+.+.+=|
T Consensus 1 ~~i~V~~~s~~~~~~~~~~~A~~lG~~la~~g~~lV~GG 39 (178)
T TIGR00730 1 KTVCVYCGSSPGGNAAYKELAAELGAYLAGQGWGLVYGG 39 (178)
T ss_pred CEEEEECcCCCCCCcHHHHHHHHHHHHHHHCCCEEEECC
Confidence 37999999986 2222 22356889999887544
No 105
>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type I periplasmic sugar-binding protein-like fold.
Probab=26.48 E-value=1e+02 Score=25.31 Aligned_cols=56 Identities=7% Similarity=-0.015 Sum_probs=40.0
Q ss_pred EEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhh
Q 029441 6 AMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRR 67 (193)
Q Consensus 6 avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~ 67 (193)
|++| +|..-.+.+...|+++|..|.+|+....-... .|.+.....++.+|......
T Consensus 182 ai~~-~~d~~A~gv~~al~~~gv~vigfD~~~~~~~~-----~p~lttv~~~~~~~~~~~~~ 237 (260)
T cd06304 182 VIFA-AAGGTGPGVIQAAKEAGVYAIGVDSDQSALAP-----DAVLTSAVKNVDVAVYDAIK 237 (260)
T ss_pred EEEE-cCCCCchHHHHHHHHcCCEEEeecCchhhhcC-----ccEEEEEEeccHHHHHHHHH
Confidence 4555 66666788999999999888888876555444 46666677777777766554
No 106
>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=26.33 E-value=1.2e+02 Score=24.59 Aligned_cols=38 Identities=11% Similarity=0.173 Sum_probs=32.6
Q ss_pred cccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecc
Q 029441 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEV 140 (193)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdI 140 (193)
.+|.|||+.....-.|+.-+..++-.-.+.+.|+.+|-
T Consensus 177 ~~~ai~~~~d~~a~g~~~al~~~g~~vp~di~i~g~d~ 214 (269)
T cd06293 177 PPTAIFAASDEIAIGLLEVLRERGLSIPGDMSLVGFDD 214 (269)
T ss_pred CCCEEEEcCcHHHHHHHHHHHHcCCCCccceEEEeecC
Confidence 48999999999988999999988766667799999974
No 107
>PF07934 OGG_N: 8-oxoguanine DNA glycosylase, N-terminal domain; InterPro: IPR012904 The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (3.2.2.23 from EC) and DNA lyase activity (4.2.99.18 from EC) []. The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket []. ; GO: 0003684 damaged DNA binding, 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006289 nucleotide-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 1N39_A 1LWV_A 1YQM_A 2NOL_A 1YQL_A 1LWY_A ....
Probab=26.30 E-value=51 Score=24.92 Aligned_cols=24 Identities=21% Similarity=0.664 Sum_probs=19.4
Q ss_pred ccccCCCCHHHHHHHHhhcChHHH
Q 029441 50 NVYEFGTPYKQMFDDLRRKDPELY 73 (193)
Q Consensus 50 NvY~FgT~Y~~iy~dL~~kd~~lY 73 (193)
..|+.+++|+.||+++.++|+.+-
T Consensus 74 ~YF~Ld~dl~~l~~~~~~~D~~l~ 97 (117)
T PF07934_consen 74 DYFDLDVDLEKLYEDWSKKDPRLA 97 (117)
T ss_dssp HHTTTTS-HHHHHHHHCCHSHHHH
T ss_pred HHhcCCccHHHHHHHHhhhCHHHH
Confidence 346778999999999999999874
No 108
>TIGR01125 MiaB-like tRNA modifying enzyme YliG, TIGR01125. This clade spans alpha and gamma proteobacteria, cyano bacteria, deinococcus, porphyromonas, aquifex, helicobacter, campylobacter, thermotoga, chlamydia, streptococcus coelicolor and clostridium, but does not include most other gram positive bacteria, archaea or eukaryotes.
Probab=26.23 E-value=1e+02 Score=28.48 Aligned_cols=95 Identities=12% Similarity=0.217 Sum_probs=56.4
Q ss_pred ccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCC------CHHHHHHHHhhcChHHHHhcCchhhh
Q 029441 9 CSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGT------PYKQMFDDLRRKDPELYKRNGILPML 82 (193)
Q Consensus 9 CasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT------~Y~~iy~dL~~kd~~lY~~NGlL~ML 82 (193)
|..||--|----..|.++||.+.+. .+...|+-..| ..++.|+-+.+ |++.|.. ..
T Consensus 9 C~~N~~ds~~~~~~l~~~g~~~~~~------------~~~aD~viinTC~v~~~a~~~~~~~i~~-----~~~~~~~-vv 70 (430)
T TIGR01125 9 CPKNLVDSEVMLGILREAGYEVTPN------------YEDADYVIVNTCGFIEDARQESIDTIGE-----LADAGKK-VI 70 (430)
T ss_pred CCCcHHHHHHHHHHHHHCcCEECCC------------cccCCEEEEeCCCccchHHHHHHHHHHH-----HHhcCCC-EE
Confidence 9999999988888999999987762 23456666664 23445555432 3322220 00
Q ss_pred hcccCCCCCcccccccCCCCcccEEEeccchhHHHHHHHHhcC
Q 029441 83 KRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTR 125 (193)
Q Consensus 83 dRN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R 125 (193)
==.=-....||....... ..|+|+ .|..|.++++++...
T Consensus 71 vgGc~a~~~pee~~~~~~--~vd~v~--g~~~~~~l~~~~~~~ 109 (430)
T TIGR01125 71 VTGCLVQRYKEELKEEIP--EVHAIT--GSGDVENILNAIESR 109 (430)
T ss_pred EECCccccchHHHHhhCC--CCcEEE--CCCCHHHHHHHHHHH
Confidence 000012334665533222 388877 567799999998653
No 109
>PF13377 Peripla_BP_3: Periplasmic binding protein-like domain; PDB: 3K9C_B 3BIL_B 3JVD_B 1ZAY_A 1VPW_A 1DBQ_A 2PUA_A 1QQA_A 1PNR_A 1JHZ_A ....
Probab=25.85 E-value=1e+02 Score=22.99 Aligned_cols=36 Identities=11% Similarity=0.165 Sum_probs=31.4
Q ss_pred ccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEec
Q 029441 104 FDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLE 139 (193)
Q Consensus 104 fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvd 139 (193)
.|.|||..+.+.-.|+..|..++-...+-+.||-+|
T Consensus 69 pdaii~~~~~~a~~~~~~l~~~g~~vP~di~vv~~~ 104 (160)
T PF13377_consen 69 PDAIICSNDRLALGVLRALRELGIRVPQDISVVSFD 104 (160)
T ss_dssp SSEEEESSHHHHHHHHHHHHHTTSCTTTTSEEEEES
T ss_pred CcEEEEcCHHHHHHHHHHHHHcCCcccccccEEEec
Confidence 689999999999999999999987666777777776
No 110
>PF01725 Ham1p_like: Ham1 family; InterPro: IPR002637 This family contains the Saccharomyces cerevisiae (Baker's yeast) HAM1 protein P47119 from SWISSPROT and other hypothetical archaeal, bacterial and Caenorhabditis elegans proteins. S. cerevisiae HAM1 protects against the mutagenic effects of the base analog 6-N-hydroxylaminopurine (HAP) which can be a natural product of monooxygenase activity on adenine. HAM1 protein protects the cell from HAP, either on the level of deoxynucleoside triphosphate or the DNA level by a yet unidentified set of reactions [].; GO: 0016787 hydrolase activity; PDB: 3TQU_A 1VP2_B 3S86_D 1B78_A 2MJP_B 2Q16_A 2PYU_A 1K7K_A 2ZTI_A 2DVP_A ....
Probab=25.41 E-value=31 Score=28.87 Aligned_cols=47 Identities=26% Similarity=0.473 Sum_probs=31.7
Q ss_pred EEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHH
Q 029441 7 MVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQM 61 (193)
Q Consensus 7 vVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~i 61 (193)
+..++|.+.-.|+-.+|...|+.|.|+ ..++.+..+-|-+ +++|.++
T Consensus 2 ~~aT~N~~K~~E~~~~l~~~~i~v~~~-----~~~~~~~~~~~E~---~~t~~en 48 (189)
T PF01725_consen 2 IFATGNKGKIREIQELLKPLGIEVISL-----IDLPEPDPEPEET---GETFEEN 48 (189)
T ss_dssp EEE-S-HHHHHHHHHHCTTTTEEEEEC-----EEECEE------B---SSSHHHH
T ss_pred EEEcCCHHHHHHHHHHHhhcCCcEEeH-----HHcCccCcCCCcC---CCCHHHH
Confidence 567899999999999999999999887 4566554444443 7777765
No 111
>PRK02103 malonate decarboxylase subunit delta; Provisional
Probab=25.17 E-value=71 Score=25.34 Aligned_cols=45 Identities=22% Similarity=0.338 Sum_probs=32.8
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHHHHhh
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEIEAA 164 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~l~~~ 164 (193)
..+|.+|++++..|.+ .-=.+|+|-|. ...=|-.-|+|.|.++..
T Consensus 56 ~~~WqaVl~~f~~r~~-----~~~~~i~InD~---GATP~VV~LRL~QA~e~~ 100 (105)
T PRK02103 56 GAVWQAVVADFVERRS-----PGGLRISINDG---GARPDTVSLRLAQAVRAI 100 (105)
T ss_pred HHHHHHHHHHHHhhCC-----CCccEEEEeCC---CCCchhhhhHHHHHHHHH
Confidence 4689999999999852 22356788888 344456678888888764
No 112
>cd00158 RHOD Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins.
Probab=24.88 E-value=80 Score=21.04 Aligned_cols=27 Identities=37% Similarity=0.484 Sum_probs=21.7
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Cee
Q 029441 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVS 31 (193)
Q Consensus 4 ~~avVCasN~NRSMEaH~~L~~~g~-~V~ 31 (193)
++-++|++ ..||..+=..|++.|| +|.
T Consensus 52 ~vv~~c~~-~~~a~~~~~~l~~~G~~~v~ 79 (89)
T cd00158 52 PIVVYCRS-GNRSARAAKLLRKAGGTNVY 79 (89)
T ss_pred eEEEEeCC-CchHHHHHHHHHHhCcccEE
Confidence 57788888 5788889999999987 444
No 113
>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=24.69 E-value=80 Score=22.16 Aligned_cols=36 Identities=28% Similarity=0.460 Sum_probs=26.0
Q ss_pred EccCCCCcchHHHHhHHhCCCCee--------eecCCCceecCC
Q 029441 8 VCSSNQNRSMEAHYLLKRHGFDVS--------SYGTGAHVKLPG 43 (193)
Q Consensus 8 VCasN~NRSMEaH~~L~~~g~~V~--------SfGTGs~VrLPG 43 (193)
+=-+|.+..|.|+++|+++|+.++ |-|=|-.+|++.
T Consensus 6 i~F~st~~a~~~ek~lk~~gi~~~liP~P~~i~~~CG~al~~~~ 49 (73)
T PF11823_consen 6 ITFPSTHDAMKAEKLLKKNGIPVRLIPTPREISAGCGLALRFEP 49 (73)
T ss_pred EEECCHHHHHHHHHHHHHCCCcEEEeCCChhccCCCCEEEEECh
Confidence 334566788999999999999876 444555666653
No 114
>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=24.37 E-value=3e+02 Score=22.48 Aligned_cols=38 Identities=13% Similarity=0.050 Sum_probs=33.0
Q ss_pred cccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecc
Q 029441 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEV 140 (193)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdI 140 (193)
.+|.|||+...+--.|+.-|..++-...+.+.|+-+|-
T Consensus 179 ~~~ai~~~~d~~a~g~~~~l~~~g~~vp~di~v~g~d~ 216 (270)
T cd01544 179 LPTAFFIASDPMAIGALRALQEAGIKVPEDVSVISFND 216 (270)
T ss_pred CCCEEEEcCcHHHHHHHHHHHHcCCCCCCceEEEEECC
Confidence 48999999999999999999998876677789998864
No 115
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=24.23 E-value=1.3e+02 Score=21.41 Aligned_cols=48 Identities=15% Similarity=0.192 Sum_probs=33.5
Q ss_pred CCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhhhhcccCCCCCccccccc
Q 029441 46 LREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPMLKRNIGVKAAPQRWQDN 98 (193)
Q Consensus 46 ~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NGlL~MLdRN~~iK~~PERfQ~~ 98 (193)
++-|+++..|-|+++-.+.++.-=.- |-. .+++=|+.|+..|+.+|..
T Consensus 21 Pdlpgc~s~G~T~eea~~n~~eai~l-~~e----~~~~~~~~iP~~~~~~~~~ 68 (73)
T COG1598 21 PDLPGCHSQGETLEEALQNAKEAIEL-HLE----ALLEEGEPIPAAPESFQRV 68 (73)
T ss_pred CCCCCccccCCCHHHHHHHHHHHHHH-HHH----HHHhcCCcCCCccccccee
Confidence 58899999999999988877653222 211 1556666677688888754
No 116
>cd06341 PBP1_ABC_ligand_binding_like_7 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=24.13 E-value=2e+02 Score=24.53 Aligned_cols=41 Identities=12% Similarity=-0.044 Sum_probs=32.9
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHH
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRL 153 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~ 153 (193)
+-.+..+++++..++-.++++-++-.|.+.+++++...+..
T Consensus 21 ~g~~~a~~~~N~~Ggi~G~~i~lv~~D~~~~~~~~~~~~~~ 61 (341)
T cd06341 21 AGADAAAGYANAAGGIAGRPIEYVWCDDQGDPASAAACARD 61 (341)
T ss_pred HHHHHHHHHHHhcCCcCCceEEEEEecCCCChhHHHHHHHH
Confidence 45678899999888888899999999999888887655443
No 117
>smart00280 KAZAL Kazal type serine protease inhibitors. Kazal type serine protease inhibitors and follistatin-like domains.
Probab=23.95 E-value=56 Score=20.84 Aligned_cols=29 Identities=21% Similarity=0.320 Sum_probs=17.1
Q ss_pred EEEEccCCCCcc------hHHHHhHHhCCCCeeeec
Q 029441 5 YAMVCSSNQNRS------MEAHYLLKRHGFDVSSYG 34 (193)
Q Consensus 5 ~avVCasN~NRS------MEaH~~L~~~g~~V~SfG 34 (193)
..-||+|+ +++ |++++-.....+.+.++|
T Consensus 10 ~~pVCgsd-g~TY~N~C~l~~~~c~~~~~i~~~~~G 44 (46)
T smart00280 10 YDPVCGSD-GVTYSNECHLCKAACESGKSIEVKHDG 44 (46)
T ss_pred CCccCCCC-CCEeCCHhHHHHHHhcCCCCeEEeecC
Confidence 34689998 456 444444444455666655
No 118
>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=23.90 E-value=2.8e+02 Score=22.05 Aligned_cols=40 Identities=13% Similarity=0.200 Sum_probs=33.0
Q ss_pred cccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccC
Q 029441 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKD 142 (193)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkD 142 (193)
.+|.|||+.......++..|...+....+-+.|+-+|-.+
T Consensus 176 ~~~ai~~~~~~~a~g~~~al~~~g~~~p~~v~v~g~d~~~ 215 (267)
T cd06284 176 RPTAIFCFSDEMAIGAISALKELGLRVPEDISVVGFDDID 215 (267)
T ss_pred CCcEEEEcCcHHHHHHHHHHHHcCCCCccceeEEEeCCHH
Confidence 4899999999999999999998876555678889887544
No 119
>TIGR03130 malonate_delta malonate decarboxylase acyl carrier protein. Members of this protein family are the acyl carrier protein, also called the delta subunit, of malonate decarboxylase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=23.69 E-value=70 Score=25.10 Aligned_cols=44 Identities=23% Similarity=0.351 Sum_probs=31.6
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHHHHh
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEIEA 163 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~l~~ 163 (193)
..+|.+|++++..|.+ .-=.+|+|-|. ...=|-.-|+|.|.++.
T Consensus 54 ~~~Wqavl~rf~~~~~-----~~~~~i~InD~---GATP~VV~LRL~QA~e~ 97 (98)
T TIGR03130 54 GAVWQAVIERFFARYP-----LAGLQIEINDF---GATPAVVSLRLRQALEE 97 (98)
T ss_pred HHHHHHHHHHHHhhCC-----CCccEEEEecC---CCCchhhhhhHHHHHhh
Confidence 4689999999999853 22356788888 34445667888888874
No 120
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=23.52 E-value=77 Score=22.10 Aligned_cols=21 Identities=29% Similarity=0.390 Sum_probs=18.9
Q ss_pred HHHHhHHhCCCCeeeecCCCc
Q 029441 18 EAHYLLKRHGFDVSSYGTGAH 38 (193)
Q Consensus 18 EaH~~L~~~g~~V~SfGTGs~ 38 (193)
-.|.+-.+.|+.-.|+|.|..
T Consensus 33 ~vH~lA~~~gL~s~S~G~g~~ 53 (60)
T cd02641 33 LVHELAEELGLRHESTGEGSD 53 (60)
T ss_pred HHHHHHHHcCCceEeeCCCCc
Confidence 489999999999999999874
No 121
>PHA02576 3 tail completion and sheath stabilizer protein; Provisional
Probab=23.46 E-value=29 Score=29.78 Aligned_cols=62 Identities=16% Similarity=0.247 Sum_probs=42.8
Q ss_pred CceecCCCCC-CCCccccCC-----CCHHHHHHHHhhcC----------hHHHHhcCchhhhhcccCCCCCccccccc
Q 029441 37 AHVKLPGPSL-REPNVYEFG-----TPYKQMFDDLRRKD----------PELYKRNGILPMLKRNIGVKAAPQRWQDN 98 (193)
Q Consensus 37 s~VrLPGps~-d~PNvY~Fg-----T~Y~~iy~dL~~kd----------~~lY~~NGlL~MLdRN~~iK~~PERfQ~~ 98 (193)
..+++||-.. -.|-+-.|- ..|-+||+=+.+-. ..=|.+++.||+|++|.+-=-+-=+|.++
T Consensus 53 ~~~~ipg~~~efDpl~i~FivDed~rny~e~y~Wm~si~d~~~~~~~~~~~~~~~d~~LhiLdn~~~~iv~t~~F~~~ 130 (177)
T PHA02576 53 ARAKIPGSTVEFDPLIVRFLVDEELRSYLEVYKWMLSTNDYNTGNSTAWDKSQPEAITLHILDNSKTKIVATFNFYGA 130 (177)
T ss_pred eeEecCCCCeecCCEEEEEEEcHHHHHHHHHHHHHHHhcccccCCccccCccCCcceEEEeecCCCCceEEEEEEeee
Confidence 4699999987 678777774 58999999877643 22356789999999994311122236654
No 122
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=22.92 E-value=1.9e+02 Score=26.69 Aligned_cols=64 Identities=16% Similarity=0.266 Sum_probs=42.1
Q ss_pred EEEccCCCCcchHHHHhHHhCCCC-eeeecCCCceecCCCCC----------CCCc--cccCCCCHHHHHHHHhhcChH
Q 029441 6 AMVCSSNQNRSMEAHYLLKRHGFD-VSSYGTGAHVKLPGPSL----------REPN--VYEFGTPYKQMFDDLRRKDPE 71 (193)
Q Consensus 6 avVCasN~NRSMEaH~~L~~~g~~-V~SfGTGs~VrLPGps~----------d~PN--vY~FgT~Y~~iy~dL~~kd~~ 71 (193)
-|+|+|..-. |...++++-|+. -.-.--|+.|-.|.--. ..++ +..||.||.+|-.-|..--.+
T Consensus 37 vVlaTGRt~~--ev~~l~~~Lgl~~p~I~eNGA~I~~p~~~~~~~~~~~~~~~~~~~~~~~lg~~y~~ir~~L~~l~~~ 113 (302)
T PRK12702 37 LVLYSLRTRA--QLEHLCRQLRLEHPFICEDGSAIYVPEHYFPAGILDEQWQHRPPYYVCALGLPYPCLRHILQQVRQD 113 (302)
T ss_pred EEEEcCCCHH--HHHHHHHHhCCCCeEEEeCCcEEEEccccccccccccccccCCCceEEecCCCHHHHHHHHHHHHHH
Confidence 3678887765 455577777875 23334677887774222 3344 778999999999888654333
No 123
>smart00267 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria
Probab=22.76 E-value=2.5e+02 Score=19.98 Aligned_cols=52 Identities=15% Similarity=0.303 Sum_probs=32.7
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHH-HH----HhhHHHHHHHHHHHHh
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHE-EA----AIGGRLTFDLCQEIEA 163 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~E-eA----~~Ga~~il~Lc~~l~~ 163 (193)
.+-|...++.+..+......++.++.++|.+-.+ .. ..+...+-++++.|..
T Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~l~~i~i~~~~~~~~~~g~~~~~~~l~~i~~~l~~ 70 (163)
T smart00267 14 RRYFEEELEQELQRAQRQGSPFALLLIDLDNFKDINDTYGHAVGDELLQEVAQRLSS 70 (163)
T ss_pred HHHHHHHHHHHHHHhhccCCeEEEEEEEccccchhhhccCchhHHHHHHHHHHHHHH
Confidence 3456666655555555556678999999965333 11 2356677777777755
No 124
>cd08555 PI-PLCc_GDPD_SF Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily. The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosph
Probab=22.75 E-value=2.1e+02 Score=23.00 Aligned_cols=45 Identities=16% Similarity=0.086 Sum_probs=25.0
Q ss_pred HHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHH
Q 029441 115 FDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQE 160 (193)
Q Consensus 115 fD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~ 160 (193)
|+.|++.+....+....+ ..+|+|||.......-....+++++..
T Consensus 62 l~evl~~~~~~~~~~~~~-~~l~iEiK~~~~~~~~~~~~~~~~~~~ 106 (179)
T cd08555 62 LEEVLELIADYLKNPDYT-IILSLEIKQDSPEYDEFLAKVLKELRV 106 (179)
T ss_pred HHHHHHHHHhhhhcCCCc-eEEEEEeCCCCCcchHHHHHHHHHHHH
Confidence 677777665533322233 479999997754222223344455443
No 125
>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=22.67 E-value=2.1e+02 Score=24.60 Aligned_cols=43 Identities=7% Similarity=-0.184 Sum_probs=33.2
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHH
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~i 154 (193)
.+-++..++.++.+++-.+++|-++-.|-+.+++.|...+..+
T Consensus 27 ~~g~~~a~~~~Na~gGi~G~~i~l~~~D~~~~~~~a~~~a~~l 69 (362)
T cd06343 27 RTGAAYFFMINNDQGGINGRKIELIVEDDGYSPPKTVEQTRKL 69 (362)
T ss_pred HHHHHHHHHHHHhcCCcCCeEEEEEEecCCCChHHHHHHHHHH
Confidence 3567888999999888889999998888888777765544443
No 126
>PF13399 LytR_C: LytR cell envelope-related transcriptional attenuator
Probab=22.12 E-value=1.7e+02 Score=20.84 Aligned_cols=36 Identities=17% Similarity=0.268 Sum_probs=28.3
Q ss_pred CceEEEEccCCCCcc-hHHHHhHHhCCCCeeeecCCC
Q 029441 2 KYRYAMVCSSNQNRS-MEAHYLLKRHGFDVSSYGTGA 37 (193)
Q Consensus 2 ~l~~avVCasN~NRS-MEaH~~L~~~g~~V~SfGTGs 37 (193)
..+|.|.-+|..+.- =.+-..|+++||.|.+.|..+
T Consensus 3 ~v~V~VlNgt~~~GlA~~~a~~L~~~Gf~v~~~~n~~ 39 (90)
T PF13399_consen 3 DVRVEVLNGTGVSGLAARVADALRNRGFTVVEVGNAP 39 (90)
T ss_pred ceEEEEEECcCCcCHHHHHHHHHHHCCCceeecCCCC
Confidence 357788888877543 467788999999999988876
No 127
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=21.97 E-value=4.9e+02 Score=22.04 Aligned_cols=68 Identities=21% Similarity=0.198 Sum_probs=34.8
Q ss_pred ccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHHH---HhhhhhHHHHHHHHHHHHH
Q 029441 104 FDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEI---EAAESWEESIDDIIAAFEK 180 (193)
Q Consensus 104 fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~l---~~~~d~e~~i~~il~~fe~ 180 (193)
.||||+...---...++.|.+ .+-||.+++. ++.++.. ..+-.|.+.+ ++++.+-+.+++-+++.++
T Consensus 73 PDlVi~~~~~~~~~~~~~L~~----~gi~v~~~~~---~~~~~~~---~~i~~lg~~~g~~~~A~~li~~~~~~l~~i~~ 142 (260)
T PRK03379 73 PDLVLAWRGGNAERQVDQLAS----LGIKVMWVDA---TSIEQIA---NALRQLAPWSPQPEKAEQAAQSLLQQYAALKA 142 (260)
T ss_pred CCEEEEecCCCcHHHHHHHHH----CCCCEEEeCC---CCHHHHH---HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence 899999643212456677765 4457777763 3444422 2233444444 2334444444444444444
Q ss_pred H
Q 029441 181 R 181 (193)
Q Consensus 181 k 181 (193)
+
T Consensus 143 ~ 143 (260)
T PRK03379 143 Q 143 (260)
T ss_pred H
Confidence 3
No 128
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=21.89 E-value=3.8e+02 Score=22.21 Aligned_cols=40 Identities=10% Similarity=0.079 Sum_probs=32.4
Q ss_pred cccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccC
Q 029441 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKD 142 (193)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkD 142 (193)
.+|.|||+.+...-.|+.-|...+-...+-+-||-+|-..
T Consensus 213 ~~~ai~~~~d~~a~gv~~al~~~g~~ip~di~vvg~D~~~ 252 (309)
T PRK11041 213 PPTAVFCHSDVMALGALSQAKRMGLRVPQDLSIIGFDDID 252 (309)
T ss_pred CCCEEEEcCcHHHHHHHHHHHHcCCCCCcceEEEEeCCch
Confidence 4899999999999899999988775555678888887543
No 129
>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=21.72 E-value=2.7e+02 Score=22.08 Aligned_cols=38 Identities=16% Similarity=0.209 Sum_probs=28.4
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhh
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIG 150 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~G 150 (193)
+.+...+++++.+++..++++.++-.|.+.+.+.+.-.
T Consensus 21 ~g~~~a~~~~n~~gg~~g~~v~~~~~d~~~~~~~~~~~ 58 (298)
T cd06268 21 NGAELAVEEINAAGGILGRKIELVVEDTQGDPEAAAAA 58 (298)
T ss_pred HHHHHHHHHHHhcCCCCCeEEEEEEecCCCCHHHHHHH
Confidence 45677888999888777888888888887766655433
No 130
>cd06576 PASTA_Pbp2x-like_1 PASTA domain of PBP2x-like proteins, first repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid residues) and the cross-linking (transpeptidation) of short stem peptides, which are connected to glycan chains. Peptidoglycan is essential in cell division and protects bacteria from osmotic shock and lysis. PBP2x is one of the two monofunctional high molecular mass PBPs in Streptococcus pneumoniae and has been seen as the primary PBP target in beta-lactam-resistant strains. The PASTA domain is found at the C-termini of several PBPs and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine
Probab=21.60 E-value=1e+02 Score=19.02 Aligned_cols=21 Identities=33% Similarity=0.395 Sum_probs=18.0
Q ss_pred hHHHHhHHhCCCCeeeecCCC
Q 029441 17 MEAHYLLKRHGFDVSSYGTGA 37 (193)
Q Consensus 17 MEaH~~L~~~g~~V~SfGTGs 37 (193)
-+|...|.++||.+..-|.|.
T Consensus 11 ~~a~~~l~~~g~~~~~~~~g~ 31 (55)
T cd06576 11 EEAKKELKEAGLQPVVIGNGK 31 (55)
T ss_pred HHHHHHHHHCCCEEEEeCCCC
Confidence 368899999999998888876
No 131
>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=21.56 E-value=1e+02 Score=24.96 Aligned_cols=25 Identities=12% Similarity=0.187 Sum_probs=19.7
Q ss_pred EEEEccCCCCcchHHHHhHHhCCCCee
Q 029441 5 YAMVCSSNQNRSMEAHYLLKRHGFDVS 31 (193)
Q Consensus 5 ~avVCasN~NRSMEaH~~L~~~g~~V~ 31 (193)
-|++|++.. .+-+.+.|+++|+++-
T Consensus 187 ~~i~~~~d~--A~g~~~al~~~g~~~p 211 (272)
T cd06300 187 DGIWTQGGD--AVGAVQAFEQAGRDIP 211 (272)
T ss_pred CEEEecCCC--cHHHHHHHHHcCCCCc
Confidence 367777666 8999999999998643
No 132
>COG0614 FepB ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=21.42 E-value=4.8e+02 Score=21.84 Aligned_cols=69 Identities=19% Similarity=0.205 Sum_probs=39.4
Q ss_pred ccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHHHHH---HhhhhhHHHHHHHHHHHHH
Q 029441 104 FDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEI---EAAESWEESIDDIIAAFEK 180 (193)
Q Consensus 104 fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc~~l---~~~~d~e~~i~~il~~fe~ 180 (193)
.|+||+... -.+..+.++.+. .-||-++.-. +.++.. ..+..+++.+ ++++.|-+.+++-+.+..+
T Consensus 116 PDlIi~~~~-~~~~~~~~~~~~----~~pvv~~~~~---~~~~~~---~~i~~lg~~~g~e~~A~~li~~~~~~~~~~~~ 184 (319)
T COG0614 116 PDLIIASSS-SQDDLIYKLLSL----GAPVVVVDYG---SLDDIK---EQIRLLGKALGKEEKAEELIAEYDQRLAALRA 184 (319)
T ss_pred CCEEEEecc-cchhHHHHHHhc----CCCEEEECCc---chhhHH---HHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHH
Confidence 899999988 557777777774 4455555443 222221 2233333333 3445566666666666666
Q ss_pred HcC
Q 029441 181 RHR 183 (193)
Q Consensus 181 k~~ 183 (193)
+.+
T Consensus 185 ~~~ 187 (319)
T COG0614 185 RTA 187 (319)
T ss_pred Hhc
Confidence 654
No 133
>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=21.28 E-value=3.2e+02 Score=21.80 Aligned_cols=39 Identities=10% Similarity=0.120 Sum_probs=32.9
Q ss_pred cccEEEeccchhHHHHHHHHhcCCCCCCceEEEEEeccc
Q 029441 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVK 141 (193)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHViNvdIk 141 (193)
..|.||++.......++..|...+-...+-+-||-+|=.
T Consensus 177 ~~~ai~~~~d~~a~~~~~~l~~~g~~~p~di~vig~d~~ 215 (268)
T cd01575 177 DLDAVFCSNDDLALGALFECQRRGISVPEDIAIAGFGDL 215 (268)
T ss_pred CCCEEEECCcHHHHHHHHHHHHhCCCCCcceEEEecCCc
Confidence 489999999999999999999887666677888888833
No 134
>cd00515 HAM1 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard nucleotides such as XTP to XMP and ITP to IMP, but not the standard nucleotides, in the presence of Mg or Mn ions. The enzyme exists as a homodimer. The HAM1 protein may be acting as an NTPase by hydrolyzing the HAP triphosphate.
Probab=21.28 E-value=1.3e+02 Score=25.13 Aligned_cols=29 Identities=21% Similarity=0.316 Sum_probs=25.0
Q ss_pred EEccCCCCcchHHHHhHHhCCCCeeeecC
Q 029441 7 MVCSSNQNRSMEAHYLLKRHGFDVSSYGT 35 (193)
Q Consensus 7 vVCasN~NRSMEaH~~L~~~g~~V~SfGT 35 (193)
+..++|.+.--|+-.+|...|+.|.++..
T Consensus 2 ~~aT~N~~K~~E~~~il~~~~i~v~~~~~ 30 (183)
T cd00515 2 VFATGNKGKLKEFKEILAPFGIEVVSLKD 30 (183)
T ss_pred EEECCCHHHHHHHHHHHhhcCcEEEEcCc
Confidence 56899999999999999988888877664
No 135
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=21.27 E-value=59 Score=23.96 Aligned_cols=16 Identities=25% Similarity=0.451 Sum_probs=13.9
Q ss_pred HhHHhCCCCeeeecCC
Q 029441 21 YLLKRHGFDVSSYGTG 36 (193)
Q Consensus 21 ~~L~~~g~~V~SfGTG 36 (193)
.+++.+|||+.|.-.|
T Consensus 21 ~lf~rRgfNI~Sl~vg 36 (76)
T PRK06737 21 GIFARRGYYISSLNLN 36 (76)
T ss_pred HHHhccCcceEEEEec
Confidence 5678999999999876
No 136
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=21.27 E-value=53 Score=25.54 Aligned_cols=26 Identities=19% Similarity=0.074 Sum_probs=19.3
Q ss_pred HhHHhCCCCeeeecCCCceecCCCCCC
Q 029441 21 YLLKRHGFDVSSYGTGAHVKLPGPSLR 47 (193)
Q Consensus 21 ~~L~~~g~~V~SfGTGs~VrLPGps~d 47 (193)
.+++++|||+.|.-.| ....||-|.-
T Consensus 27 glFsRRgyNIeSLtvg-~te~~~iSRm 52 (96)
T PRK08178 27 GLFARRAFNVEGILCL-PIQDGDKSRI 52 (96)
T ss_pred HHHhcCCcCeeeEEEe-ecCCCCceEE
Confidence 4678999999999886 4456665543
No 137
>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=21.24 E-value=2.4e+02 Score=21.98 Aligned_cols=129 Identities=12% Similarity=0.094 Sum_probs=70.8
Q ss_pred EEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHH----HhhcC-hH--------
Q 029441 5 YAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDD----LRRKD-PE-------- 71 (193)
Q Consensus 5 ~avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~d----L~~kd-~~-------- 71 (193)
-|+|+++-.+.++.+=..|.++|.+|..++++... .++.+.+++.+.++-.. |.++- ++
T Consensus 57 d~ii~~~~~~~~~~~~~~l~~~~ip~v~~~~~~~~--------~~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~ 128 (264)
T cd01537 57 DGIIIAPSDLTAPTIVKLARKAGIPVVLVDRDIPD--------GDRVPSVGSDNEQAGYLAGEHLAEKGHRRIALLAGPL 128 (264)
T ss_pred CEEEEecCCCcchhHHHHhhhcCCCEEEeccCCCC--------CcccceEecCcHHHHHHHHHHHHHhcCCcEEEEECCC
Confidence 36777776666655446677889999999988643 24445555444333322 22211 00
Q ss_pred -----HHHhcCchhhhhcccCCC---CCcccc---------cccCCC-CcccEEEeccchhHHHHHHHHhcCCCCCCceE
Q 029441 72 -----LYKRNGILPMLKRNIGVK---AAPQRW---------QDNALD-GSFDIVFTFEEKVFDTVVEDLNTREQPFMKTV 133 (193)
Q Consensus 72 -----lY~~NGlL~MLdRN~~iK---~~PERf---------Q~~~~~-~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pV 133 (193)
--+.+|+...+...-.++ ..+..| +..-.. ...|+|||......-.++..+...+-.-.+.+
T Consensus 129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~~~~a~~~~~~~~~~g~~i~~~i 208 (264)
T cd01537 129 GSSTARERVAGFKDALKEAGPIEIVLVQEGDWDAEKGYQAAEELLTAHPDPTAIFAANDDMALGALRALREAGLRVPDDI 208 (264)
T ss_pred CCCcHHHHHHHHHHHHHHcCCcChhhhccCCCCHHHHHHHHHHHHhcCCCCCEEEEcCcHHHHHHHHHHHHhCCCCCCCe
Confidence 012345544443321111 111111 111111 13899999987777778888887766555678
Q ss_pred EEEEeccc
Q 029441 134 LVINLEVK 141 (193)
Q Consensus 134 HViNvdIk 141 (193)
.++-.|-.
T Consensus 209 ~i~~~d~~ 216 (264)
T cd01537 209 SVIGFDGT 216 (264)
T ss_pred EEEeecCc
Confidence 88877743
No 138
>TIGR00762 DegV EDD domain protein, DegV family. This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each than to most homologs from other species. This suggests both recent paralogy and diversity of function. DegV itself is encoded immediately downstream of DegU, a transcriptional regulator of degradation, but is itself uncharacterized. Crystallography suggested a lipid-binding site, while comparison of the crystal structure to dihydroxyacetone kinase and to a mannose transporter EIIA domain suggests a conserved domain, EDD, with phosphotransferase activity.
Probab=21.13 E-value=1.7e+02 Score=25.32 Aligned_cols=143 Identities=18% Similarity=0.270 Sum_probs=73.6
Q ss_pred EEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhhhhc
Q 029441 5 YAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPMLKR 84 (193)
Q Consensus 5 ~avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~kd~~lY~~NGlL~MLdR 84 (193)
||+||-|--+=+-| .+++.|+.|.++- |.+-|..-.. .-.-+.+++|+.|..... .
T Consensus 1 iaiitDS~~dl~~~---~~~~~~I~vvPl~----I~~~~~~y~D----~~~i~~~~~y~~~~~~~~--------~----- 56 (275)
T TIGR00762 1 IAIVTDSTADLPPE---LIEEYGITVVPLT----VIIDGKTYRD----GVDITPEEFYEKLKESKE--------L----- 56 (275)
T ss_pred CEEEEecccCCCHH---HHHHcCCEEEEEE----EEECCEEeec----CCCCCHHHHHHHHHhcCC--------C-----
Confidence 46666665553332 3456788887763 4444432211 012356777776643210 0
Q ss_pred ccCCCCCcccccccC----CCCcccEEEe-ccch---hHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHH
Q 029441 85 NIGVKAAPQRWQDNA----LDGSFDIVFT-FEEK---VFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFD 156 (193)
Q Consensus 85 N~~iK~~PERfQ~~~----~~~~fDvIiT-cEER---vfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~ 156 (193)
=+.-=|.|+-|.+.- .++ -+||+. .-.. .|+....--.. ....+|||| |+.--+..-|..+++
T Consensus 57 p~TS~ps~~~~~~~~~~l~~~~-~~vi~i~iSs~lSgty~~a~~aa~~---~~~~~i~Vi-----DS~~~s~~~g~~v~~ 127 (275)
T TIGR00762 57 PKTSQPSPGEFLELYEKLLEEG-DEVLSIHLSSGLSGTYQSARQAAEM---VDEAKVTVI-----DSKSASMGLGLLVLE 127 (275)
T ss_pred CCcCCCCHHHHHHHHHHHHhCC-CeEEEEEcCCchhHHHHHHHHHHhh---CCCCCEEEE-----CChHHHHHHHHHHHH
Confidence 012235566666532 222 245443 3222 23333221111 112245554 788778888899999
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHH
Q 029441 157 LCQEIEAAESWEESIDDIIAAFEKR 181 (193)
Q Consensus 157 Lc~~l~~~~d~e~~i~~il~~fe~k 181 (193)
.++++++..++|+ |.+.|+++.++
T Consensus 128 a~~~~~~G~s~~e-I~~~l~~~~~~ 151 (275)
T TIGR00762 128 AAKLAEEGKSLEE-ILAKLEELRER 151 (275)
T ss_pred HHHHHHcCCCHHH-HHHHHHHHHhh
Confidence 9999999876653 33455555544
No 139
>COG1307 DegV Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.06 E-value=1.6e+02 Score=26.31 Aligned_cols=46 Identities=17% Similarity=0.166 Sum_probs=34.3
Q ss_pred EEecccCCHHHHHhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHc
Q 029441 136 INLEVKDNHEEAAIGGRLTFDLCQEIEAAESWEESIDDIIAAFEKRH 182 (193)
Q Consensus 136 iNvdIkDn~EeA~~Ga~~il~Lc~~l~~~~d~e~~i~~il~~fe~k~ 182 (193)
++|-+-|++--+..-+.++++.+.++++..+ -++|.+.|+++.+++
T Consensus 110 ~~v~viDS~~~s~~~g~~v~~a~~l~~~G~s-~~ei~~~l~~~~~~t 155 (282)
T COG1307 110 AKVHVIDSKSVSMGLGFLVLEAAELAKAGKS-FEEILKKLEEIREKT 155 (282)
T ss_pred ceEEEEcCcchhhHHHHHHHHHHHHHHcCCC-HHHHHHHHHHHHhhc
Confidence 4455557877788889999999999999888 445556666666654
No 140
>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=20.80 E-value=2.2e+02 Score=24.27 Aligned_cols=42 Identities=12% Similarity=0.164 Sum_probs=33.4
Q ss_pred hhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHH
Q 029441 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (193)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~i 154 (193)
+.....+++++..++-.++++.++-.|-+.+++.|...+..+
T Consensus 21 ~g~~~a~~~iN~~ggi~G~~i~l~~~D~~~~~~~a~~~a~~l 62 (340)
T cd06349 21 RAFDLALDEINAAGGVGGRPLNIVFEDSKSDPRQAVTIAQKF 62 (340)
T ss_pred HHHHHHHHHHHhhCCcCCeEEEEEEeCCCCChHHHHHHHHHH
Confidence 456778899999988888999999999998887776554433
No 141
>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=20.79 E-value=2.1e+02 Score=24.41 Aligned_cols=61 Identities=8% Similarity=0.043 Sum_probs=0.0
Q ss_pred EEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhh
Q 029441 5 YAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRR 67 (193)
Q Consensus 5 ~avVCasN~NRSMEaH~~L~~~g~~V~SfGTGs~VrLPGps~d~PNvY~FgT~Y~~iy~dL~~ 67 (193)
.+|+-...-.-++.+..++.+.|..+.|.++++.---+.. ..|++|.++.++.+.-.-|.+
T Consensus 68 ~aviG~~~s~~~~a~~~~~~~~~vp~i~~~s~~~~~~~~~--~~~~~f~~~~~~~~~~~~~~~ 128 (334)
T cd06327 68 DMIVGGPNSAVALAVQEVAREKKKIYIVTGAGSDDLTGKD--CSPYTFHWAYDTYMLANGTAP 128 (334)
T ss_pred eEEECCccHHHHHHHHHHHHHhCceEEecCCCccccccCC--CCCceEEccCChHHHHHHHHH
No 142
>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=20.62 E-value=2.5e+02 Score=23.98 Aligned_cols=44 Identities=9% Similarity=-0.032 Sum_probs=30.3
Q ss_pred chhHHHHHHHHhcCCCCCCceEEEEEecccCCHHHHHhhHHHHHHHH
Q 029441 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLC 158 (193)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHViNvdIkDn~EeA~~Ga~~il~Lc 158 (193)
.+.....+++++.+++-.+++|-++=.|-+-+++.| ...+.+|.
T Consensus 20 ~~g~~~a~~~iNa~ggi~G~~v~lv~~D~~~~p~~a---~~~~~~li 63 (344)
T cd06348 20 LAGLKLAEDRFNQAGGVNGRPIKLVIEDSGGDEAEA---INAFQTLI 63 (344)
T ss_pred HHHHHHHHHHHhhcCCcCCcEEEEEEecCCCChHHH---HHHHHHHh
Confidence 456778899999999888888777766655555544 44444444
No 143
>cd04922 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathwa
Probab=20.62 E-value=2.5e+02 Score=18.03 Aligned_cols=51 Identities=10% Similarity=0.053 Sum_probs=30.6
Q ss_pred eEEEEccCCCCcc---hHHHHhHHhCCCCeeeecCC-CceecCCCCCCCCccccCCCCHHHHHHHH
Q 029441 4 RYAMVCSSNQNRS---MEAHYLLKRHGFDVSSYGTG-AHVKLPGPSLREPNVYEFGTPYKQMFDDL 65 (193)
Q Consensus 4 ~~avVCasN~NRS---MEaH~~L~~~g~~V~SfGTG-s~VrLPGps~d~PNvY~FgT~Y~~iy~dL 65 (193)
.+++|+.-..++. -..-..|+++|.+|....+| +. +-+.|..+.++.-+-+
T Consensus 3 ~isvvg~~~~~~~~~~~~i~~~l~~~~I~v~~i~~~~s~-----------~~is~~v~~~~~~~~~ 57 (66)
T cd04922 3 ILALVGDGMAGTPGVAATFFSALAKANVNIRAIAQGSSE-----------RNISAVIDEDDATKAL 57 (66)
T ss_pred EEEEECCCCCCCccHHHHHHHHHHHCCCCEEEEEecCcc-----------cEEEEEEeHHHHHHHH
Confidence 4778887665543 23445578999999544332 22 3466777776654443
No 144
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=20.06 E-value=53 Score=28.86 Aligned_cols=25 Identities=36% Similarity=0.830 Sum_probs=19.3
Q ss_pred HhHHhCCCCeeeecCCCc----------------eecCCCC
Q 029441 21 YLLKRHGFDVSSYGTGAH----------------VKLPGPS 45 (193)
Q Consensus 21 ~~L~~~g~~V~SfGTGs~----------------VrLPGps 45 (193)
.+|...||+|.+|-+|.. ||+||-|
T Consensus 22 ~Ll~s~G~~v~~~~s~~~fL~~~~~~~pGclllDvrMPg~s 62 (202)
T COG4566 22 FLLESAGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMS 62 (202)
T ss_pred HHHHhCCceeeeecCHHHHHhhccCCCCCeEEEecCCCCCc
Confidence 357788999999987642 7888876
Done!