Query 029616
Match_columns 190
No_of_seqs 104 out of 176
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 15:46:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029616.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029616hhsearch_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 5E-102 1E-106 652.2 13.4 177 2-178 1-183 (195)
2 KOG2424 Protein involved in tr 100.0 5.5E-93 1.2E-97 595.2 16.5 176 1-178 4-184 (195)
3 COG5211 SSU72 RNA polymerase I 100.0 1E-83 2.3E-88 535.2 15.6 178 2-181 6-188 (197)
4 COG0394 Wzb Protein-tyrosine-p 97.3 0.0014 3E-08 52.4 8.1 109 1-144 1-113 (139)
5 PRK10126 tyrosine phosphatase; 95.8 0.011 2.4E-07 46.7 3.8 92 1-122 1-94 (147)
6 PF01451 LMWPc: Low molecular 95.8 0.011 2.4E-07 45.2 3.4 107 5-144 1-116 (138)
7 PRK11391 etp phosphotyrosine-p 95.3 0.023 5E-07 45.1 4.0 90 3-122 3-94 (144)
8 smart00226 LMWPc Low molecular 93.3 0.069 1.5E-06 41.0 2.6 86 6-122 2-90 (140)
9 TIGR02689 ars_reduc_gluta arse 90.8 0.17 3.7E-06 38.9 2.1 34 3-36 1-37 (126)
10 PRK13530 arsenate reductase; P 89.5 0.34 7.4E-06 38.0 2.9 35 2-36 3-40 (133)
11 cd00115 LMWPc Substituted upda 88.2 0.42 9.1E-06 36.9 2.5 34 3-36 1-38 (141)
12 cd01523 RHOD_Lact_B Member of 86.9 1 2.2E-05 32.2 3.8 32 4-36 63-94 (100)
13 TIGR03746 conj_TIGR03746 integ 83.5 1 2.3E-05 39.2 2.9 96 36-140 51-179 (202)
14 PLN02160 thiosulfate sulfurtra 83.4 1.3 2.8E-05 34.6 3.2 30 4-34 83-113 (136)
15 COG0607 PspE Rhodanese-related 80.4 2.4 5.3E-05 30.0 3.4 28 3-31 62-89 (110)
16 cd01534 4RHOD_Repeat_3 Member 79.9 3 6.5E-05 29.7 3.8 29 4-33 58-86 (95)
17 TIGR02691 arsC_pI258_fam arsen 79.7 1.2 2.7E-05 34.6 1.9 32 5-36 1-35 (129)
18 cd01518 RHOD_YceA Member of th 75.1 3.6 7.9E-05 29.5 3.1 29 4-33 63-92 (101)
19 cd01447 Polysulfide_ST Polysul 74.9 3.9 8.6E-05 28.7 3.2 30 3-33 62-92 (103)
20 cd01533 4RHOD_Repeat_2 Member 73.1 5.8 0.00013 28.8 3.8 32 4-36 68-101 (109)
21 PRK10310 PTS system galactitol 71.0 5.1 0.00011 29.8 3.1 31 1-31 1-35 (94)
22 PRK10287 thiosulfate:cyanide s 70.7 4.1 8.9E-05 30.9 2.6 40 4-46 62-102 (104)
23 TIGR02981 phageshock_pspE phag 70.6 4 8.6E-05 30.7 2.5 30 4-34 60-90 (101)
24 cd01526 RHOD_ThiF Member of th 70.5 6.1 0.00013 29.6 3.5 31 3-34 73-105 (122)
25 PRK00162 glpE thiosulfate sulf 66.5 10 0.00022 27.5 3.9 31 3-34 59-90 (108)
26 cd01520 RHOD_YbbB Member of th 66.1 10 0.00022 28.8 4.0 34 3-36 87-120 (128)
27 cd01521 RHOD_PspE2 Member of t 65.3 11 0.00024 27.6 3.9 31 3-33 65-96 (110)
28 cd01524 RHOD_Pyr_redox Member 63.6 12 0.00026 26.2 3.7 30 3-33 52-81 (90)
29 cd01449 TST_Repeat_2 Thiosulfa 62.6 7.3 0.00016 28.3 2.5 31 3-34 79-110 (118)
30 KOG2424 Protein involved in tr 62.5 4.7 0.0001 35.1 1.6 59 3-61 9-68 (195)
31 cd01391 Periplasmic_Binding_Pr 61.5 23 0.0005 26.8 5.1 132 6-143 61-221 (269)
32 cd01528 RHOD_2 Member of the R 61.1 15 0.00031 26.3 3.8 31 3-34 59-90 (101)
33 cd01519 RHOD_HSP67B2 Member of 59.6 11 0.00024 26.7 2.9 30 3-33 67-97 (106)
34 cd01529 4RHOD_Repeats Member o 59.3 13 0.00028 26.3 3.2 30 4-34 58-88 (96)
35 smart00450 RHOD Rhodanese Homo 56.5 20 0.00044 23.9 3.7 31 3-34 57-88 (100)
36 cd01736 LSm14_N LSm14 (also kn 56.4 8 0.00017 29.0 1.8 25 29-54 37-62 (74)
37 TIGR00725 conserved hypothetic 54.6 16 0.00034 29.7 3.4 32 3-35 2-38 (159)
38 PRK05320 rhodanese superfamily 53.2 16 0.00034 32.0 3.4 28 3-31 176-204 (257)
39 cd06331 PBP1_AmiC_like Type I 52.7 36 0.00079 28.8 5.4 43 112-154 20-62 (333)
40 PRK01415 hypothetical protein; 51.8 15 0.00032 32.4 3.0 30 3-33 172-202 (247)
41 cd01444 GlpE_ST GlpE sulfurtra 51.6 24 0.00052 24.4 3.5 27 4-31 58-85 (96)
42 COG4822 CbiK Cobalamin biosynt 51.1 8.2 0.00018 34.9 1.3 58 51-108 7-79 (265)
43 PRK10147 phnH carbon-phosphoru 50.9 23 0.0005 30.4 4.0 26 28-53 126-151 (196)
44 cd01527 RHOD_YgaP Member of th 50.3 27 0.00058 24.7 3.6 30 4-34 56-86 (99)
45 PF06841 Phage_T4_gp19: T4-lik 48.7 7.5 0.00016 29.5 0.6 60 28-87 27-94 (134)
46 KOG1530 Rhodanese-related sulf 48.6 19 0.00041 29.9 2.9 29 5-34 92-121 (136)
47 KOG0239 Kinesin (KAR3 subfamil 48.0 16 0.00034 36.6 2.9 45 26-70 390-463 (670)
48 COG3625 PhnH Uncharacterized e 47.9 30 0.00064 30.3 4.2 58 28-114 128-185 (196)
49 PF07927 YcfA: YcfA-like prote 46.4 16 0.00035 24.0 1.9 24 18-42 3-26 (56)
50 cd06356 PBP1_Amide_Urea_BP_lik 45.7 56 0.0012 28.0 5.6 42 113-154 21-62 (334)
51 cd01525 RHOD_Kc Member of the 45.6 39 0.00085 23.9 3.9 30 4-34 67-97 (105)
52 PF02302 PTS_IIB: PTS system, 44.2 28 0.0006 24.4 2.9 32 4-35 1-36 (90)
53 cd06355 PBP1_FmdD_like Peripla 43.7 66 0.0014 27.8 5.7 43 113-155 21-63 (348)
54 cd06354 PBP1_BmpA_PnrA_like Pe 42.6 31 0.00068 28.4 3.4 41 6-47 186-226 (265)
55 cd01448 TST_Repeat_1 Thiosulfa 42.2 49 0.0011 24.2 4.1 31 3-33 80-111 (122)
56 cd06346 PBP1_ABC_ligand_bindin 41.2 65 0.0014 27.2 5.2 43 112-154 20-62 (312)
57 cd06335 PBP1_ABC_ligand_bindin 40.8 56 0.0012 28.0 4.8 44 113-156 21-64 (347)
58 cd01530 Cdc25 Cdc25 phosphatas 39.6 45 0.00096 25.3 3.6 24 3-26 69-92 (121)
59 COG4747 ACT domain-containing 39.3 20 0.00043 29.8 1.8 20 13-32 49-68 (142)
60 cd06357 PBP1_AmiC Periplasmic 39.2 81 0.0017 27.5 5.6 45 112-156 20-64 (360)
61 TIGR03407 urea_ABC_UrtA urea A 37.9 92 0.002 27.1 5.7 43 113-155 22-64 (359)
62 TIGR00137 gid_trmFO tRNA:m(5)U 36.7 45 0.00098 31.8 3.9 52 6-58 128-180 (433)
63 PF13458 Peripla_BP_6: Peripla 36.2 73 0.0016 26.5 4.7 41 113-153 23-63 (343)
64 cd06344 PBP1_ABC_ligand_bindin 36.2 83 0.0018 26.7 5.1 42 114-155 21-62 (332)
65 cd02325 R3H R3H domain. The na 36.2 36 0.00078 21.3 2.3 21 17-37 31-51 (59)
66 cd02645 R3H_AAA R3H domain of 36.1 32 0.0007 24.3 2.2 23 19-41 34-56 (60)
67 PRK01175 phosphoribosylformylg 35.6 53 0.0011 29.0 3.9 34 1-34 2-35 (261)
68 PRK00142 putative rhodanese-re 35.1 47 0.001 29.9 3.6 30 3-33 172-202 (314)
69 PF01857 RB_B: Retinoblastoma- 34.4 34 0.00073 27.6 2.3 39 148-188 12-53 (135)
70 PRK08762 molybdopterin biosynt 33.5 53 0.0011 29.7 3.7 30 3-33 58-88 (376)
71 COG3414 SgaB Phosphotransferas 33.2 54 0.0012 25.0 3.2 27 2-28 1-31 (93)
72 TIGR03669 urea_ABC_arch urea A 33.0 1.1E+02 0.0023 27.5 5.5 44 112-155 21-64 (374)
73 PRK01220 malonate decarboxylas 32.8 46 0.001 26.2 2.8 46 112-165 52-97 (99)
74 PRK11784 tRNA 2-selenouridine 32.7 54 0.0012 30.1 3.6 66 3-68 89-164 (345)
75 cd06366 PBP1_GABAb_receptor Li 32.6 1E+02 0.0023 26.2 5.1 41 112-152 18-59 (350)
76 cd06268 PBP1_ABC_transporter_L 32.5 1.3E+02 0.0028 23.7 5.3 43 18-63 81-123 (298)
77 KOG3217 Protein tyrosine phosp 32.4 40 0.00087 28.7 2.5 89 2-124 6-102 (159)
78 TIGR01125 MiaB-like tRNA modif 32.4 75 0.0016 29.2 4.5 94 9-124 9-108 (430)
79 TIGR03167 tRNA_sel_U_synt tRNA 32.4 55 0.0012 29.6 3.6 65 4-69 76-151 (311)
80 cd02640 R3H_NRF R3H domain of 32.0 42 0.0009 23.7 2.2 21 18-38 33-53 (60)
81 cd06358 PBP1_NHase Type I peri 31.8 1.3E+02 0.0029 25.4 5.7 41 113-153 21-61 (333)
82 cd01574 PBP1_LacI Ligand-bindi 31.2 1.7E+02 0.0037 23.2 5.9 38 104-141 175-212 (264)
83 cd06329 PBP1_SBP_like_3 Peripl 31.1 1.1E+02 0.0025 26.0 5.2 45 112-159 20-64 (342)
84 cd06007 R3H_DEXH_helicase R3H 30.3 43 0.00093 23.6 2.0 21 18-38 32-52 (59)
85 PRK02103 malonate decarboxylas 29.9 53 0.0011 26.1 2.7 45 112-164 56-100 (105)
86 PF07934 OGG_N: 8-oxoguanine D 29.7 41 0.00088 25.3 2.0 24 50-73 74-97 (117)
87 TIGR03130 malonate_delta malon 29.6 48 0.001 26.0 2.4 44 112-163 54-97 (98)
88 cd05563 PTS_IIB_ascorbate PTS_ 29.5 49 0.0011 23.2 2.3 26 4-29 1-30 (86)
89 PF02084 Bindin: Bindin; Inte 29.2 20 0.00044 32.1 0.3 37 145-181 97-143 (238)
90 cd01531 Acr2p Eukaryotic arsen 29.0 93 0.002 22.7 3.7 33 4-36 64-105 (113)
91 cd06296 PBP1_CatR_like Ligand- 28.4 2E+02 0.0043 22.9 5.8 40 103-142 178-217 (270)
92 cd06304 PBP1_BmpA_like Peripla 28.1 96 0.0021 25.2 4.0 56 6-67 182-237 (260)
93 PF03698 UPF0180: Uncharacteri 27.9 1.5E+02 0.0032 22.3 4.7 51 18-68 12-78 (80)
94 cd04918 ACT_AK1-AT_2 ACT domai 27.9 1.4E+02 0.0031 20.1 4.3 33 4-36 3-39 (65)
95 cd06326 PBP1_STKc_like Type I 27.8 1.7E+02 0.0038 24.3 5.6 37 113-149 22-58 (336)
96 PF01725 Ham1p_like: Ham1 fami 27.4 28 0.0006 29.0 0.8 47 7-61 2-48 (189)
97 PF04831 Popeye: Popeye protei 27.3 37 0.0008 28.6 1.5 36 77-114 65-102 (153)
98 cd06334 PBP1_ABC_ligand_bindin 27.2 1.2E+02 0.0026 26.5 4.8 43 112-154 20-62 (351)
99 smart00393 R3H Putative single 27.2 57 0.0012 23.2 2.3 22 17-38 50-71 (79)
100 cd06276 PBP1_FucR_like Ligand- 27.0 62 0.0013 26.5 2.7 53 6-64 165-223 (247)
101 PF08373 RAP: RAP domain; Int 26.4 47 0.001 21.8 1.6 18 16-33 20-37 (58)
102 smart00267 GGDEF diguanylate c 26.3 2.2E+02 0.0048 20.0 5.2 51 113-163 15-70 (163)
103 cd05566 PTS_IIB_galactitol PTS 26.3 58 0.0013 23.0 2.2 28 3-30 1-32 (89)
104 cd00158 RHOD Rhodanese Homolog 25.2 82 0.0018 20.8 2.7 29 3-32 51-80 (89)
105 PF11823 DUF3343: Protein of u 24.8 84 0.0018 22.0 2.7 36 8-43 6-49 (73)
106 cd08555 PI-PLCc_GDPD_SF Cataly 24.8 2E+02 0.0044 22.9 5.3 45 115-160 62-106 (179)
107 COG1598 Predicted nuclease of 24.6 1.3E+02 0.0028 21.4 3.8 48 46-98 21-68 (73)
108 PF06288 DUF1040: Protein of u 24.5 80 0.0017 24.5 2.7 11 168-178 47-57 (86)
109 cd06293 PBP1_LacI_like_11 Liga 24.3 1.4E+02 0.003 24.0 4.3 38 103-140 177-214 (269)
110 cd06284 PBP1_LacI_like_6 Ligan 24.1 2.9E+02 0.0063 21.8 6.0 40 103-142 176-215 (267)
111 cd01537 PBP1_Repressors_Sugar_ 24.1 2E+02 0.0044 22.2 5.0 129 5-141 57-216 (264)
112 cd06341 PBP1_ABC_ligand_bindin 23.8 2E+02 0.0044 24.2 5.4 41 113-153 21-61 (341)
113 PF13377 Peripla_BP_3: Peripla 23.7 1.2E+02 0.0026 22.4 3.5 36 104-139 69-104 (160)
114 smart00280 KAZAL Kazal type se 23.7 58 0.0013 20.7 1.6 29 5-34 10-44 (46)
115 cd01544 PBP1_GalR Ligand-bindi 23.5 3.3E+02 0.0071 22.1 6.3 38 103-140 179-216 (270)
116 PHA02576 3 tail completion and 23.5 29 0.00063 29.7 0.2 62 37-98 53-130 (177)
117 cd06327 PBP1_SBP_like_1 Peripl 23.5 1.8E+02 0.0039 24.6 5.0 57 5-63 68-124 (334)
118 PF13399 LytR_C: LytR cell env 23.5 1.4E+02 0.0031 21.1 3.8 36 2-37 3-39 (90)
119 PRK08178 acetolactate synthase 23.4 51 0.0011 25.7 1.5 26 21-47 27-52 (96)
120 TIGR00730 conserved hypothetic 23.4 87 0.0019 26.0 3.0 32 3-34 1-39 (178)
121 cd05567 PTS_IIB_mannitol PTS_I 23.3 1.2E+02 0.0026 21.7 3.3 27 3-29 1-31 (87)
122 cd02641 R3H_Smubp-2_like R3H d 23.1 80 0.0017 22.0 2.3 22 17-38 32-53 (60)
123 cd06343 PBP1_ABC_ligand_bindin 23.0 2E+02 0.0043 24.6 5.2 43 112-154 27-69 (362)
124 COG4800 Predicted transcriptio 22.9 3.5E+02 0.0076 23.2 6.5 84 55-154 40-123 (170)
125 PRK11041 DNA-binding transcrip 22.8 3.6E+02 0.0078 22.2 6.5 40 103-142 213-252 (309)
126 cd06576 PASTA_Pbp2x-like_1 PAS 22.1 1E+02 0.0023 18.9 2.6 21 17-37 11-31 (55)
127 PRK12702 mannosyl-3-phosphogly 22.0 2.2E+02 0.0047 26.4 5.5 64 6-71 37-113 (302)
128 cd06268 PBP1_ABC_transporter_L 21.7 2.8E+02 0.006 21.8 5.4 37 113-149 21-57 (298)
129 cd01575 PBP1_GntR Ligand-bindi 21.7 3.1E+02 0.0067 21.6 5.7 61 103-163 177-249 (268)
130 cd06326 PBP1_STKc_like Type I 21.5 2.6E+02 0.0057 23.3 5.5 47 16-65 81-127 (336)
131 cd00515 HAM1 NTPase/HAM1. Thi 21.3 1.3E+02 0.0029 25.0 3.7 29 7-35 2-30 (183)
132 cd06348 PBP1_ABC_ligand_bindin 21.3 2.4E+02 0.0052 23.9 5.3 44 112-158 20-63 (344)
133 cd04922 ACT_AKi-HSDH-ThrA_2 AC 21.3 2.1E+02 0.0045 18.3 3.9 52 4-66 3-58 (66)
134 KOG0391 SNF2 family DNA-depend 20.9 51 0.0011 36.5 1.4 88 5-98 669-760 (1958)
135 cd06349 PBP1_ABC_ligand_bindin 20.8 2.2E+02 0.0049 24.0 5.0 42 113-154 21-62 (340)
136 TIGR02553 SipD_IpaD_SspD type 20.5 67 0.0015 29.9 1.9 56 17-100 198-257 (308)
137 cd06272 PBP1_hexuronate_repres 20.5 4.3E+02 0.0093 21.0 6.4 40 103-142 172-211 (261)
138 PF13912 zf-C2H2_6: C2H2-type 20.4 57 0.0012 18.3 1.0 13 168-180 14-26 (27)
139 cd06300 PBP1_ABC_sugar_binding 20.4 1.2E+02 0.0026 24.4 3.2 25 5-31 187-211 (272)
140 cd06392 PBP1_iGluR_delta_1 N-t 20.3 1.2E+02 0.0026 28.2 3.5 46 111-158 13-59 (400)
141 cd01443 Cdc25_Acr2p Cdc25 enzy 20.2 1.6E+02 0.0034 21.5 3.5 25 4-28 68-96 (113)
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=5.1e-102 Score=652.20 Aligned_cols=177 Identities=56% Similarity=0.905 Sum_probs=152.7
Q ss_pred CceEEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhh
Q 029616 2 KYRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPM 81 (190)
Q Consensus 2 ~l~~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY~~NGlL~M 81 (190)
++|||||||||||||||||++|+++||+|+|||||++|||||||+|+||||+|||||++||+||.+||++||++||||+|
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 hhcccCCCCCccccccccCCCcccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHHHHHHH
Q 029616 82 LKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEV 161 (190)
Q Consensus 82 LdRNr~IK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ileLc~~l 161 (190)
|+|||+||++|||||++++.+.|||||||||||||+|||||++|++++++||||||||||||||||++||++||+||++|
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--hhhhh----HHHHHhhhhcc
Q 029616 162 C--LLLFF----IVSLVYHLKHH 178 (190)
Q Consensus 162 ~--~~~~~----~~~~~~~~~~~ 178 (190)
+ ++.|+ |.+|..+++.|
T Consensus 161 ~~~~~~d~e~~i~~il~~fe~k~ 183 (195)
T PF04722_consen 161 EEEASEDLEDEIDEILQEFEEKH 183 (195)
T ss_dssp H--TSSSHHHHHHHHHHHHHHHH
T ss_pred HhhccccHHHHHHHHHHHHHHHc
Confidence 9 88887 67788888877
No 2
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=100.00 E-value=5.5e-93 Score=595.22 Aligned_cols=176 Identities=56% Similarity=0.884 Sum_probs=171.3
Q ss_pred CCceEEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchh
Q 029616 1 MKYRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILP 80 (190)
Q Consensus 1 ~~l~~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY~~NGlL~ 80 (190)
+++|+|||||||||||||||.+|+++||+|.|||||++||||||++||||||+|||||++||+||.+||+++||+||||+
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 hhhcccCCCCCccccccccCCCcccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHHHHHH
Q 029616 81 MLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQE 160 (190)
Q Consensus 81 MLdRNr~IK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ileLc~~ 160 (190)
||+|||+||++|||||++++ .|||||||||||||+|||||++|++.++|||||||+|||||||||++||++||||||+
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-hhhhh----HHHHHhhhhcc
Q 029616 161 VC-LLLFF----IVSLVYHLKHH 178 (190)
Q Consensus 161 l~-~~~~~----~~~~~~~~~~~ 178 (190)
|+ +++|+ |.+|.+-++.|
T Consensus 162 l~~~s~d~Ed~ideil~~~ee~~ 184 (195)
T KOG2424|consen 162 LQAQSDDLEDNIDEILLEFEEKH 184 (195)
T ss_pred HHhccccHHHHHHHHHHHHHHhc
Confidence 99 88877 77888888887
No 3
>COG5211 SSU72 RNA polymerase II-interacting protein involved in transcription start site selection [Transcription]
Probab=100.00 E-value=1e-83 Score=535.20 Aligned_cols=178 Identities=40% Similarity=0.710 Sum_probs=170.0
Q ss_pred CceEEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhh
Q 029616 2 KYRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPM 81 (190)
Q Consensus 2 ~l~~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY~~NGlL~M 81 (190)
.+||||+||||||||||+|.+|+++||+|.||||||.|||||+|+||||||.||+||++||+||..|+++.|+.||||.|
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 hhcccCCCCCccccccccCCCcccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHHHHHHH
Q 029616 82 LKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEV 161 (190)
Q Consensus 82 LdRNr~IK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ileLc~~l 161 (190)
||||||||++|||||+..+ .||+||||||||||+|+|||..|++..+|+||+||+||||+||+|.+||++||||+.+|
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 Hhhhh-----hHHHHHhhhhcccce
Q 029616 162 CLLLF-----FIVSLVYHLKHHCTF 181 (190)
Q Consensus 162 ~~~~~-----~~~~~~~~~~~~~~~ 181 (190)
.+.-+ +|.||..-|..|-..
T Consensus 164 ~~~~e~lE~~~~sil~~~qsnh~~l 188 (197)
T COG5211 164 AKEEERLEYAVDSILRRYQSNHKGL 188 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 66543 488998888877543
No 4
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=97.32 E-value=0.0014 Score=52.45 Aligned_cols=109 Identities=23% Similarity=0.326 Sum_probs=70.1
Q ss_pred CCceEEEEccCCCCcchHHHHhHHhC---CCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcC
Q 029616 1 MKYRYAMVCSSNQNRSMEAHYLLKRH---GFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNG 77 (190)
Q Consensus 1 ~~l~~AvVCaSN~NRSMEAH~~L~k~---Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY~~NG 77 (190)
+..||.+||..|-=||=-|-.++++. ++.|.|.|||+ .||..++. +. -+ --.+.|
T Consensus 1 ~~~kVLFVC~gN~cRSpmAE~l~~~~~~~~~~v~SAGt~~---~~g~~~~~---------~a--~~--------vl~e~G 58 (139)
T COG0394 1 MMMKVLFVCTGNICRSPMAEALLRHLAPDNVEVDSAGTGG---HPGEPPDP---------RA--VE--------VLAEHG 58 (139)
T ss_pred CCceEEEEcCCCcccCHHHHHHHHHhccCCeEEECCccCC---CCCCCCCH---------HH--HH--------HHHHcC
Confidence 46799999999999999999999865 79999999999 89988773 11 01 112233
Q ss_pred chhhhhcccCCC-CCccccccccCCCcccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeeccCCH
Q 029616 78 ILPMLKRNIGVK-AAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNH 144 (190)
Q Consensus 78 lL~MLdRNr~IK-~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnh 144 (190)
| .+. ..|.-|-+..- ..||+|||-++.-...++.-. +.....+..+.-||.|-.
T Consensus 59 i--------d~~~~~~k~i~~~~~-~~~DlIitmd~~~~~~~~~~~----p~~~~~~~~~~~~v~DP~ 113 (139)
T COG0394 59 I--------DISGHRSKQLTEEDF-DEFDLIITMDESNAADLCPLA----PGNTLLLEYEHWEVPDPY 113 (139)
T ss_pred C--------CcCCccCccCchhhh-hhCCEEEEeChHHHhhHhhcC----ccccccccccCCCCCCCC
Confidence 2 233 23444433221 259999999876655554422 111133444457888865
No 5
>PRK10126 tyrosine phosphatase; Provisional
Probab=95.82 E-value=0.011 Score=46.66 Aligned_cols=92 Identities=22% Similarity=0.315 Sum_probs=61.1
Q ss_pred CCceEEEEccCCCCcchHHHHhHHhC--CCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCc
Q 029616 1 MKYRYAMVCSSNQNRSMEAHYLLKRH--GFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGI 78 (190)
Q Consensus 1 ~~l~~AvVCaSN~NRSMEAH~~L~k~--Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY~~NGl 78 (190)
|..||-.||..|.-||=-|..+|++. ++.|.|.||... ||..++. ..-. .-++.||
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 34689999999999999999999974 589999999664 7765542 1111 2233343
Q ss_pred hhhhhcccCCCCCccccccccCCCcccEEEecccchHHHHHHHH
Q 029616 79 LPMLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDL 122 (190)
Q Consensus 79 L~MLdRNr~IK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl 122 (190)
= + . .-.|.+|.+..- ..||+|||-++.-.+.++...
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 123445544321 249999999988888877654
No 6
>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=95.76 E-value=0.011 Score=45.17 Aligned_cols=107 Identities=21% Similarity=0.370 Sum_probs=67.6
Q ss_pred EEEEccCCCCcchHHHHhHHhC-------CCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcC
Q 029616 5 YAMVCSSNQNRSMEAHYLLKRH-------GFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNG 77 (190)
Q Consensus 5 ~AvVCaSN~NRSMEAH~~L~k~-------Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY~~NG 77 (190)
|..||..|.=||--|+.+|++. ++.|.|-||... ||..++ ...-+-| ++.|
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 776544 2222222 3344
Q ss_pred chhhhhcccCCCCCccccccccCCCcccEEEecccchHHHHHHHHhcCCCCCCCeEEEE--EeeccCCH
Q 029616 78 ILPMLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVI--NLEVKDNH 144 (190)
Q Consensus 78 lL~MLdRNr~IK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVI--NvDIkDnh 144 (190)
+ ++ .. ..|..+-+.. -..||+|||.++.-++.+.+.+-. .....|+.+ +-||.|-.
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 114999999999988888776665 122223333 77888744
No 7
>PRK11391 etp phosphotyrosine-protein phosphatase; Provisional
Probab=95.31 E-value=0.023 Score=45.09 Aligned_cols=90 Identities=18% Similarity=0.299 Sum_probs=60.4
Q ss_pred ceEEEEccCCCCcchHHHHhHHhC--CCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchh
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRH--GFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILP 80 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~--Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY~~NGlL~ 80 (190)
.||-+||..|.-||=-|..+|++. ++.|.|-||... ||..++ |+ . .+.-++.|| +
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 589999999999999999999974 689999999753 665544 11 1 123344554 1
Q ss_pred hhhcccCCCCCccccccccCCCcccEEEecccchHHHHHHHH
Q 029616 81 MLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDL 122 (190)
Q Consensus 81 MLdRNr~IK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl 122 (190)
+ .. -.|..+.+..- ..||+|||-++..++.+.+..
T Consensus 60 ~-~~-----h~s~~lt~~~~-~~~DlIl~M~~~~~~~l~~~~ 94 (144)
T PRK11391 60 L-EG-----HAGRKLTAEMA-RNYDLILAMESEHIAQVTAIA 94 (144)
T ss_pred c-CC-----CccCcCCHHHH-hhCCEEEECCHHHHHHHHHHC
Confidence 1 11 12333322211 149999999999999887764
No 8
>smart00226 LMWPc Low molecular weight phosphatase family.
Probab=93.32 E-value=0.069 Score=40.97 Aligned_cols=86 Identities=24% Similarity=0.358 Sum_probs=56.8
Q ss_pred EEEccCCCCcchHHHHhHHhC---CCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhhh
Q 029616 6 AMVCSSNQNRSMEAHYLLKRH---GFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPML 82 (190)
Q Consensus 6 AvVCaSN~NRSMEAH~~L~k~---Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY~~NGlL~ML 82 (190)
-.||..|.-||=-|..+|++. ++.|.|-||... ||..++. ..- +.-++.||= +
T Consensus 2 LFVC~~N~cRSpmAEa~~~~~~~~~~~v~SAG~~~~---~g~~~~~-----------~a~--------~~l~~~Gid--~ 57 (140)
T smart00226 2 LFVCTGNICRSPMAEALFKAIVGDRVKIDSAGTGAW---VGGGADP-----------RAV--------EVLKEHGIA--L 57 (140)
T ss_pred EEEeCChhhhHHHHHHHHHHhcCCCEEEEcCcccCC---CCCCCCH-----------HHH--------HHHHHcCcC--c
Confidence 479999999999999999864 388999998754 7765441 111 234556762 2
Q ss_pred hcccCCCCCccccccccCCCcccEEEecccchHHHHHHHH
Q 029616 83 KRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDL 122 (190)
Q Consensus 83 dRNr~IK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl 122 (190)
..-++ +..++-+ + .+|+|||-++...+.++..+
T Consensus 58 ~~~~~-~l~~~~~----~--~~DlIv~m~~~~~~~~~~~~ 90 (140)
T smart00226 58 SHHAS-QLTSSDF----K--NADLVLAMDHSHLRNICRLK 90 (140)
T ss_pred cceec-cCCHHHH----H--hCCEEEEeCHHHHHHHHHHc
Confidence 22222 3333322 1 49999999998877776654
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=90.83 E-value=0.17 Score=38.91 Aligned_cols=34 Identities=29% Similarity=0.320 Sum_probs=29.3
Q ss_pred ceEEEEccCCCCcchHHHHhHHhC---CCCeeeecCC
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRH---GFDVSSYGTG 36 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~---Gf~V~SfGTG 36 (190)
.|+..||..|--||--|..+|++. ++.|.|.||.
T Consensus 1 ~~vlfvC~~N~cRS~mAEa~~~~~~~~~~~v~SAG~~ 37 (126)
T TIGR02689 1 KKVMFVCKRNSCRSQMAEGFAKTLGAGNIAVTSAGLE 37 (126)
T ss_pred CeEEEEcCCcHHHHHHHHHHHHHhcCCCEEEEcCcCC
Confidence 478899999999999999999974 3778888886
No 10
>PRK13530 arsenate reductase; Provisional
Probab=89.54 E-value=0.34 Score=37.97 Aligned_cols=35 Identities=29% Similarity=0.298 Sum_probs=29.6
Q ss_pred CceEEEEccCCCCcchHHHHhHHh---CCCCeeeecCC
Q 029616 2 KYRYAMVCSSNQNRSMEAHYLLKR---HGFDVSSYGTG 36 (190)
Q Consensus 2 ~l~~AvVCaSN~NRSMEAH~~L~k---~Gf~V~SfGTG 36 (190)
+.++-.||..|--||=-|..+|++ .++.|.|-|+.
T Consensus 3 ~~~vLFvC~~N~cRS~mAEal~~~~~~~~~~v~SAG~~ 40 (133)
T PRK13530 3 KKTIYFLCTGNSCRSQMAEGWGKQYLGDKWNVYSAGIE 40 (133)
T ss_pred CCEEEEEcCCchhHHHHHHHHHHHhcCCCEEEECCCCC
Confidence 678999999999999999999986 34777888874
No 11
>cd00115 LMWPc Substituted updates: Aug 22, 2001
Probab=88.21 E-value=0.42 Score=36.86 Aligned_cols=34 Identities=29% Similarity=0.426 Sum_probs=29.3
Q ss_pred ceEEEEccCCCCcchHHHHhHHhC----CCCeeeecCC
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRH----GFDVSSYGTG 36 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~----Gf~V~SfGTG 36 (190)
+||-.||..|.-||=-|..+|++. ++.|.|-|+-
T Consensus 1 ~~iLfvc~~N~~RS~mAEai~~~~~~~~~~~v~SaG~~ 38 (141)
T cd00115 1 KKVLFVCTGNICRSPMAEAIFRHLAPKLDIEVDSAGTS 38 (141)
T ss_pred CeEEEEecChhhhhHHHHHHHHHHhhhCCEEEECCCCC
Confidence 378899999999999999999974 6788888874
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=86.89 E-value=1 Score=32.18 Aligned_cols=32 Identities=25% Similarity=0.473 Sum_probs=26.6
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCCeeeecCC
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTG 36 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTG 36 (190)
.+.++|++- +||..|=..|++.||+|..+--|
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
>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=83.47 E-value=1 Score=39.21 Aligned_cols=96 Identities=24% Similarity=0.271 Sum_probs=68.9
Q ss_pred CCceecCCCCCCCCccccCC-CCHHHHH-------------------------HHHhhcChHHHHhcCchhhhhcccCCC
Q 029616 36 GAHVKLPGPSLREPNVYEFG-TPYKQMF-------------------------DDLRRKDPELYKRNGILPMLKRNIGVK 89 (190)
Q Consensus 36 Gs~VkLPGps~dkPNvY~Fg-T~Y~~Iy-------------------------~dL~~kD~~lY~~NGlL~MLdRNr~IK 89 (190)
||..|. -.+..+|||.|+ +-+++|- +.+..||-+++++||=| -+|.|.+=
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 666555 556788999997 4555553 56778888889999955 69999999
Q ss_pred CCcccccccc-------CCCcccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeec
Q 029616 90 AAPQRWQDNA-------LDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEV 140 (190)
Q Consensus 90 ~~PERfQ~~~-------~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDI 140 (190)
+=|-|+-+.. +.=..-+.++-+|+.=.++|.+-.-| -|++|+-+|+
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 11124455666788777777766654 7999998887
No 14
>PLN02160 thiosulfate sulfurtransferase
Probab=83.40 E-value=1.3 Score=34.65 Aligned_cols=30 Identities=30% Similarity=0.447 Sum_probs=25.7
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~SfG 34 (190)
.+.++|.|. +||..|=..|.+.|| +|..+.
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 588999866 999999999999999 577764
No 15
>COG0607 PspE Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=80.40 E-value=2.4 Score=29.98 Aligned_cols=28 Identities=32% Similarity=0.320 Sum_probs=24.5
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCCee
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFDVS 31 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~V~ 31 (190)
..+.|+|++ .+||..|=..|+++||...
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 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=79.87 E-value=3 Score=29.66 Aligned_cols=29 Identities=17% Similarity=0.195 Sum_probs=24.7
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCCeeee
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGFDVSSY 33 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf~V~Sf 33 (190)
.+.++|.+ -+||..+-..|++.||+|.++
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 57888877 678999999999999997665
No 17
>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=79.70 E-value=1.2 Score=34.63 Aligned_cols=32 Identities=28% Similarity=0.310 Sum_probs=26.1
Q ss_pred EEEEccCCCCcchHHHHhHHhC---CCCeeeecCC
Q 029616 5 YAMVCSSNQNRSMEAHYLLKRH---GFDVSSYGTG 36 (190)
Q Consensus 5 ~AvVCaSN~NRSMEAH~~L~k~---Gf~V~SfGTG 36 (190)
|-.||..|--||=-|..+|++. ++.|.|-|+.
T Consensus 1 iLFvC~~N~~RS~mAea~~~~~~~~~~~v~SaG~~ 35 (129)
T TIGR02691 1 IYFLCTGNSCRSQMAEGWGKKYLGDEWEVYSAGIE 35 (129)
T ss_pred CEEEcCCchHHHHHHHHHHHHhcCCCEEEEcCCCC
Confidence 3579999999999999999873 4677888874
No 18
>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.
Probab=75.12 E-value=3.6 Score=29.45 Aligned_cols=29 Identities=31% Similarity=0.494 Sum_probs=24.2
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeee
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSY 33 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~Sf 33 (190)
.+-|+|.+ -+||..|=..|++.|| +|...
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 57889986 5999999999999999 47554
No 19
>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=74.88 E-value=3.9 Score=28.73 Aligned_cols=30 Identities=27% Similarity=0.319 Sum_probs=24.9
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeee
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSY 33 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~-V~Sf 33 (190)
-.+.+.|.+ .+||..+=..|.+.||. |..+
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 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=73.11 E-value=5.8 Score=28.85 Aligned_cols=32 Identities=22% Similarity=0.399 Sum_probs=25.7
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-C-eeeecCC
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGF-D-VSSYGTG 36 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf-~-V~SfGTG 36 (190)
.+.|+|.+. +||..|-..|++.|| + |.++-.|
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 588999875 589989999999999 4 7766444
No 21
>PRK10310 PTS system galactitol-specific transporter subunit IIB; Provisional
Probab=71.01 E-value=5.1 Score=29.85 Aligned_cols=31 Identities=23% Similarity=0.318 Sum_probs=25.4
Q ss_pred CCceEEEEccCCCCcchH----HHHhHHhCCCCee
Q 029616 1 MKYRYAMVCSSNQNRSME----AHYLLKRHGFDVS 31 (190)
Q Consensus 1 ~~l~~AvVCaSN~NRSME----AH~~L~k~Gf~V~ 31 (190)
|+.|+-+||.|-..-|+- ...+|+++|+++.
T Consensus 1 mk~kILvvCgsG~~TS~m~~~ki~~~l~~~gi~~~ 35 (94)
T PRK10310 1 MKRKIIVACGGAVATSTMAAEEIKELCQSHNIPVE 35 (94)
T ss_pred CCCeEEEECCCchhHHHHHHHHHHHHHHHCCCeEE
Confidence 677999999999998843 5678899999654
No 22
>PRK10287 thiosulfate:cyanide sulfurtransferase; Provisional
Probab=70.72 E-value=4.1 Score=30.88 Aligned_cols=40 Identities=18% Similarity=0.409 Sum_probs=31.0
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCC-eeeecCCCceecCCCCC
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGFD-VSSYGTGAHVKLPGPSL 46 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf~-V~SfGTGs~VkLPGps~ 46 (190)
.+.++|++. +||..|=..|.+.||. |.. .|.....++|.+
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 577777776654
No 23
>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=70.60 E-value=4 Score=30.66 Aligned_cols=30 Identities=20% Similarity=0.368 Sum_probs=24.7
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCC-eeeec
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGFD-VSSYG 34 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf~-V~SfG 34 (190)
++.++|++. +||..|=..|++.||. |...|
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 65553
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=70.48 E-value=6.1 Score=29.56 Aligned_cols=31 Identities=29% Similarity=0.219 Sum_probs=25.9
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCC--Ceeeec
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGF--DVSSYG 34 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf--~V~SfG 34 (190)
..+.++|++. +||..|=..|++.|| +|..+-
T Consensus 73 ~~ivv~C~~G-~rs~~aa~~L~~~G~~~~v~~l~ 105 (122)
T cd01526 73 SPIYVVCRRG-NDSQTAVRKLKELGLERFVRDII 105 (122)
T ss_pred CcEEEECCCC-CcHHHHHHHHHHcCCccceeeec
Confidence 3588999886 699999999999999 677763
No 25
>PRK00162 glpE thiosulfate sulfurtransferase; Validated
Probab=66.46 E-value=10 Score=27.50 Aligned_cols=31 Identities=32% Similarity=0.413 Sum_probs=24.6
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeeec
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSYG 34 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~-V~SfG 34 (190)
..+.++|.+. +||..|-..|++.||. |..+.
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 3578999865 6999999999999994 65443
No 26
>cd01520 RHOD_YbbB Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB.
Probab=66.13 E-value=10 Score=28.75 Aligned_cols=34 Identities=26% Similarity=0.427 Sum_probs=27.9
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCCeeeecCC
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTG 36 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTG 36 (190)
-.+-|.|.+.-.||..|=.+|+..||+|...--|
T Consensus 87 ~~vvvyC~~~G~rs~~a~~~L~~~G~~v~~L~GG 120 (128)
T cd01520 87 PKLLIYCARGGMRSQSLAWLLESLGIDVPLLEGG 120 (128)
T ss_pred CeEEEEeCCCCccHHHHHHHHHHcCCceeEeCCc
Confidence 3688999877788999999999999998876444
No 27
>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=65.31 E-value=11 Score=27.59 Aligned_cols=31 Identities=23% Similarity=0.371 Sum_probs=26.3
Q ss_pred ceEEEEccCCC-CcchHHHHhHHhCCCCeeee
Q 029616 3 YRYAMVCSSNQ-NRSMEAHYLLKRHGFDVSSY 33 (190)
Q Consensus 3 l~~AvVCaSN~-NRSMEAH~~L~k~Gf~V~Sf 33 (190)
-.+.+.|++.. +||..+=..|++.||+|..+
T Consensus 65 ~~vvvyc~~g~~~~s~~~a~~l~~~G~~v~~l 96 (110)
T cd01521 65 KLFVVYCDGPGCNGATKAALKLAELGFPVKEM 96 (110)
T ss_pred CeEEEEECCCCCchHHHHHHHHHHcCCeEEEe
Confidence 35889998875 79999999999999998765
No 28
>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=63.58 E-value=12 Score=26.23 Aligned_cols=30 Identities=23% Similarity=0.390 Sum_probs=25.1
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCCeeee
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFDVSSY 33 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~V~Sf 33 (190)
.++.++|++ -+||..+=..|++.||+|..+
T Consensus 52 ~~vvl~c~~-g~~a~~~a~~L~~~G~~v~~l 81 (90)
T cd01524 52 KEIIVYCAV-GLRGYIAARILTQNGFKVKNL 81 (90)
T ss_pred CcEEEEcCC-ChhHHHHHHHHHHCCCCEEEe
Confidence 357788886 578999999999999988776
No 29
>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=62.61 E-value=7.3 Score=28.31 Aligned_cols=31 Identities=19% Similarity=0.263 Sum_probs=26.0
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~SfG 34 (190)
-.+.++|.+ .+||..+-..|+..|| +|..|-
T Consensus 79 ~~iv~yc~~-g~~s~~~~~~l~~~G~~~v~~l~ 110 (118)
T cd01449 79 KPVIVYCGS-GVTACVLLLALELLGYKNVRLYD 110 (118)
T ss_pred CCEEEECCc-HHHHHHHHHHHHHcCCCCeeeeC
Confidence 367899987 5799999999999999 577775
No 30
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=62.46 E-value=4.7 Score=35.11 Aligned_cols=59 Identities=2% Similarity=-0.192 Sum_probs=51.0
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccc-cCCCCHHHH
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVY-EFGTPYKQM 61 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY-~FgT~Y~~I 61 (190)
..+|++|-++.++||++|+...-.+-.+-|+++=...++|++-|+.++.+ .+.--|++.
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 36899999999999999999999999999999999999999999998875 333445544
No 31
>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=61.53 E-value=23 Score=26.83 Aligned_cols=132 Identities=13% Similarity=0.135 Sum_probs=73.3
Q ss_pred EEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHh----hcC----------h-
Q 029616 6 AMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLR----RKD----------P- 70 (190)
Q Consensus 6 AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~----~kD----------~- 70 (190)
|++......-+.++...+.+.|.++.+++++..... ..|+++.+++++.+....+. ++. .
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 56788888877665444332 211 0
Q ss_pred HH--HHhcCchhhhhccc-------CCCCCccc-ccc----ccCCCcccEEEecccchHHHHHHHHhcCCCCCCCeEEEE
Q 029616 71 EL--YKRNGILPMLKRNI-------GVKAAPQR-WQD----NALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVI 136 (190)
Q Consensus 71 ~l--Y~~NGlL~MLdRNr-------~IK~~PER-fQ~----~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVI 136 (190)
.. =+.+|+-.-+.++. .....++. ++. .......|+||++....-..+++.+...+-. .+.+.||
T Consensus 136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~~~~a~~~~~~~~~~g~~-~~~~~ii 214 (269)
T cd01391 136 AYGRERLEGFKAALKKAGIEVVAIEYGDLDTEKGFQALLQLLKAAPKPDAIFACNDEMAAGALKAAREAGLT-PGDISII 214 (269)
T ss_pred chhhHHHHHHHHHHHhcCcEEEeccccCCCccccHHHHHHHHhcCCCCCEEEEcCchHHHHHHHHHHHcCCC-CCCCEEE
Confidence 00 01122222222221 11111100 111 1111147888888887778888888887655 5667777
Q ss_pred EeeccCC
Q 029616 137 NLEVKDN 143 (190)
Q Consensus 137 NvDIkDn 143 (190)
-.|--..
T Consensus 215 ~~~~~~~ 221 (269)
T cd01391 215 GFDGSPA 221 (269)
T ss_pred ecccccc
Confidence 7665433
No 32
>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains.
Probab=61.09 E-value=15 Score=26.30 Aligned_cols=31 Identities=29% Similarity=0.507 Sum_probs=24.9
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~SfG 34 (190)
..+-++|.+. +||-.+=..|.+.|| +|..+-
T Consensus 59 ~~vv~~c~~g-~rs~~~~~~l~~~G~~~v~~l~ 90 (101)
T cd01528 59 KDIVVLCHHG-GRSMQVAQWLLRQGFENVYNLQ 90 (101)
T ss_pred CeEEEEeCCC-chHHHHHHHHHHcCCccEEEec
Confidence 3678899874 899999999999999 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=59.65 E-value=11 Score=26.73 Aligned_cols=30 Identities=27% Similarity=0.464 Sum_probs=24.4
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCC-Ceeee
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGF-DVSSY 33 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~Sf 33 (190)
..+.++|.+ .+||..+=..|++.|| +|..|
T Consensus 67 ~~ivv~c~~-g~~s~~~~~~l~~~G~~~v~~~ 97 (106)
T cd01519 67 KELIFYCKA-GVRSKAAAELARSLGYENVGNY 97 (106)
T ss_pred CeEEEECCC-cHHHHHHHHHHHHcCCccceec
Confidence 367888886 6799999999999999 46655
No 34
>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=59.30 E-value=13 Score=26.35 Aligned_cols=30 Identities=23% Similarity=0.202 Sum_probs=24.2
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~SfG 34 (190)
.+.++|.+ .+||-.+=..|++.|| +|..+-
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 58899974 6899888889999999 676653
No 35
>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=56.47 E-value=20 Score=23.93 Aligned_cols=31 Identities=32% Similarity=0.510 Sum_probs=25.0
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeeec
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSYG 34 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~-V~SfG 34 (190)
..+.++| .+.+||..+-..|++.||. |.-+-
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 3678899 5688999999999999996 66553
No 36
>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=56.36 E-value=8 Score=28.98 Aligned_cols=25 Identities=32% Similarity=0.642 Sum_probs=16.5
Q ss_pred CeeeecCCCceecCCC-CCCCCccccC
Q 029616 29 DVSSYGTGAHVKLPGP-SLREPNVYEF 54 (190)
Q Consensus 29 ~V~SfGTGs~VkLPGp-s~dkPNvY~F 54 (190)
+|+||||-.+ +=++| -+..+.||+|
T Consensus 37 nVr~fGTEgR-~~~~~~ipp~~~vyd~ 62 (74)
T cd01736 37 NVRSFGTEGR-PTDGPEIPPSDEVYDY 62 (74)
T ss_pred eeEeecccCC-CCCCCccCCCCcceeE
Confidence 7999999887 22233 3455667765
No 37
>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=54.64 E-value=16 Score=29.74 Aligned_cols=32 Identities=19% Similarity=0.270 Sum_probs=23.2
Q ss_pred ceEEEEccCCCCcch-----HHHHhHHhCCCCeeeecC
Q 029616 3 YRYAMVCSSNQNRSM-----EAHYLLKRHGFDVSSYGT 35 (190)
Q Consensus 3 l~~AvVCaSN~NRSM-----EAH~~L~k~Gf~V~SfGT 35 (190)
.++||+|+|+.+-.. |.=+.|.++|+.|.| |-
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 589999999854332 222568899998888 64
No 38
>PRK05320 rhodanese superfamily protein; Provisional
Probab=53.18 E-value=16 Score=31.97 Aligned_cols=28 Identities=21% Similarity=0.310 Sum_probs=24.2
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-ee
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VS 31 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~-V~ 31 (190)
.++.|+|++- +||.+|=..|++.||+ |.
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 54
No 39
>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=52.69 E-value=36 Score=28.79 Aligned_cols=43 Identities=12% Similarity=0.070 Sum_probs=35.3
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHH
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~i 154 (190)
.+.+...+++++.+++-..++|-++-.|.+.+++.|...++.+
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 3667889999999998889999999999998888877655443
No 40
>PRK01415 hypothetical protein; Validated
Probab=51.80 E-value=15 Score=32.44 Aligned_cols=30 Identities=37% Similarity=0.561 Sum_probs=25.3
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeee
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSY 33 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~-V~Sf 33 (190)
.+++|.|++- .||..|-+.|++.||. |.+.
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 4799999776 7999999999999995 6554
No 41
>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=51.63 E-value=24 Score=24.44 Aligned_cols=27 Identities=30% Similarity=0.471 Sum_probs=23.0
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Cee
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVS 31 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~ 31 (190)
.+-++|+ +-.||+.|-..|++.|| +|.
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 5778898 77899999999999999 454
No 42
>COG4822 CbiK Cobalamin biosynthesis protein CbiK, Co2+ chelatase [Coenzyme metabolism]
Probab=51.07 E-value=8.2 Score=34.87 Aligned_cols=58 Identities=19% Similarity=0.333 Sum_probs=31.4
Q ss_pred cccCCCCHHH--------HHHHHhhcChHH-----HHhcCchhhhh-cccCCCCCccc-cccccCCCcccEEE
Q 029616 51 VYEFGTPYKQ--------MFDDLRRKDPEL-----YKRNGILPMLK-RNIGVKAAPQR-WQDNALDGSFDIVF 108 (190)
Q Consensus 51 vY~FgT~Y~~--------Iy~dL~~kD~~l-----Y~~NGlL~MLd-RNr~IK~~PER-fQ~~~~~~~fDvIi 108 (190)
|-.|||+|.+ |-+++..+=+++ ||.+-|+.-|. |.--+=.-|.+ -+..++.|.=+|||
T Consensus 7 iVsFGTty~dtre~tIda~e~~va~efpDydvfrAfTS~kIIkkLK~rdgi~~dTP~~aL~klk~~gy~evii 79 (265)
T COG4822 7 IVSFGTTYNDTRELTIDAIEEKVADEFPDYDVFRAFTSRKIIKKLKERDGIDFDTPIQALNKLKDQGYEEVII 79 (265)
T ss_pred EEEcCCccchhHHhhHHHHHHHHHHhCccHHHHHHHhHHHHHHHHHhhcCcccCCHHHHHHHHHHccchheee
Confidence 3457777765 555665543333 88888887764 43333344655 23333333345554
No 43
>PRK10147 phnH carbon-phosphorus lyase complex subunit; Validated
Probab=50.88 E-value=23 Score=30.44 Aligned_cols=26 Identities=23% Similarity=0.459 Sum_probs=21.4
Q ss_pred CCeeeecCCCceecCCCCCCCCcccc
Q 029616 28 FDVSSYGTGAHVKLPGPSLREPNVYE 53 (190)
Q Consensus 28 f~V~SfGTGs~VkLPGps~dkPNvY~ 53 (190)
..|.|++.|..++|=||-|.+.+...
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 44
>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.
Probab=50.26 E-value=27 Score=24.67 Aligned_cols=30 Identities=13% Similarity=0.077 Sum_probs=23.4
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~SfG 34 (190)
.+.++|.+ .+||-.+=..|.+.|| +|..+.
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 57778876 5778899899999998 676653
No 45
>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=48.74 E-value=7.5 Score=29.47 Aligned_cols=60 Identities=17% Similarity=0.202 Sum_probs=43.6
Q ss_pred CCeeeecCC----CceecCCCCCCCCccccCC-CCHHHHHHHHhhcChHH-H--HhcCchhhhhcccC
Q 029616 28 FDVSSYGTG----AHVKLPGPSLREPNVYEFG-TPYKQMFDDLRRKDPEL-Y--KRNGILPMLKRNIG 87 (190)
Q Consensus 28 f~V~SfGTG----s~VkLPGps~dkPNvY~Fg-T~Y~~Iy~dL~~kD~~l-Y--~~NGlL~MLdRNr~ 87 (190)
+.+..|..| ...++||..--.+-+-.|| +++.++++=+.+=.... - ++++.+.+||++..
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 345556455 4569999998888899999 78888877766422111 1 79999999999983
No 46
>KOG1530 consensus Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=48.58 E-value=19 Score=29.89 Aligned_cols=29 Identities=31% Similarity=0.571 Sum_probs=23.7
Q ss_pred EEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029616 5 YAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (190)
Q Consensus 5 ~AvVCaSN~NRSMEAH~~L~k~Gf-~V~SfG 34 (190)
+-+-|+|- +||.+|-.+|..+|| +|.-|+
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 47
>KOG0239 consensus Kinesin (KAR3 subfamily) [Cytoskeleton]
Probab=47.98 E-value=16 Score=36.64 Aligned_cols=45 Identities=22% Similarity=0.635 Sum_probs=35.4
Q ss_pred CCCCeeee-----cCCCceecCCCCCCCCc--------------------cccCCCCHHHHHH----HHhhcCh
Q 029616 26 HGFDVSSY-----GTGAHVKLPGPSLREPN--------------------VYEFGTPYKQMFD----DLRRKDP 70 (190)
Q Consensus 26 ~Gf~V~Sf-----GTGs~VkLPGps~dkPN--------------------vY~FgT~Y~~Iy~----dL~~kD~ 70 (190)
-||||+.| |+|-...+=||+++.|- -|++.+++-+||+ ||...+.
T Consensus 390 DGYnVCIFAYGQTGSGKTyTM~G~~~~~~Giipral~~lF~~~~~~~~g~~y~~~~s~~EIYNe~i~DlL~~~~ 463 (670)
T KOG0239|consen 390 DGYNVCIFAYGQTGSGKTYTMSGPTPEDPGIIPRALEKLFRTITSLKSGWKYDKTVSMLEIYNEAIRDLLSDES 463 (670)
T ss_pred cCcceeEEEecccCCCccccccCCCcccCCccHHHHHHHHHHHHhhccCceEEeeeehhHHHHHHHHHhccccc
Confidence 39999998 78888899998777665 4788899999997 4555554
No 48
>COG3625 PhnH Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=47.94 E-value=30 Score=30.30 Aligned_cols=58 Identities=21% Similarity=0.367 Sum_probs=40.2
Q ss_pred CCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhhhhcccCCCCCccccccccCCCcccEE
Q 029616 28 FDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPMLKRNIGVKAAPQRWQDNALDGSFDIV 107 (190)
Q Consensus 28 f~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY~~NGlL~MLdRNr~IK~~PERfQ~~~~~~~fDvI 107 (190)
..|.||--|..++|-||-|..-++-.=|-|.-=+ +-+. .+|+.|- .-.|||
T Consensus 128 iQV~sl~~G~~l~l~GPGI~~~~~Iap~LP~~f~------------------~~w~------~n~~~fP-----rGiDvi 178 (196)
T COG3625 128 IQVASLEGGRPLRLTGPGIAESRIIAPGLPDHFW------------------HFWA------ENRAIFP-----RGIDVI 178 (196)
T ss_pred EEecccCCCCceEeECCCcccccccCCCCchHHH------------------HHHH------hCccccC-----CcceEE
Confidence 3689999999999999999887766555553322 1121 2344441 138999
Q ss_pred Eecccch
Q 029616 108 FTFEEKV 114 (190)
Q Consensus 108 iTcEERv 114 (190)
+||+|++
T Consensus 179 lt~ge~~ 185 (196)
T COG3625 179 LTAGEAL 185 (196)
T ss_pred EecCcee
Confidence 9999987
No 49
>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=46.41 E-value=16 Score=23.98 Aligned_cols=24 Identities=29% Similarity=0.439 Sum_probs=17.7
Q ss_pred HHHHhHHhCCCCeeeecCCCceecC
Q 029616 18 EAHYLLKRHGFDVSSYGTGAHVKLP 42 (190)
Q Consensus 18 EAH~~L~k~Gf~V~SfGTGs~VkLP 42 (190)
|.-++|.+.||.+..= +||++++=
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 50
>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=45.66 E-value=56 Score=27.96 Aligned_cols=42 Identities=10% Similarity=0.166 Sum_probs=35.1
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHH
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~i 154 (190)
..++..++++|.+++-..+||-+|..|.+-+++.|...++.+
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 456888999999999999999999999999988876555443
No 51
>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=45.56 E-value=39 Score=23.92 Aligned_cols=30 Identities=17% Similarity=0.155 Sum_probs=23.3
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCC-Ceeeec
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGF-DVSSYG 34 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~SfG 34 (190)
.+.++|.+. +||..+=..|+..|| +|..+-
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 577888765 589888889999999 476653
No 52
>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=44.19 E-value=28 Score=24.38 Aligned_cols=32 Identities=25% Similarity=0.367 Sum_probs=24.3
Q ss_pred eEEEEccCCCCcchHH----HHhHHhCCCCeeeecC
Q 029616 4 RYAMVCSSNQNRSMEA----HYLLKRHGFDVSSYGT 35 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEA----H~~L~k~Gf~V~SfGT 35 (190)
|+-+||++-+.-|+-+ -+.+++.|+.+.++-.
T Consensus 1 kIlvvC~~Gi~TS~~~~~~i~~~~~~~gi~~~~~~~ 36 (90)
T PF02302_consen 1 KILVVCGSGIGTSLMVANKIKKALKELGIEVEVSAG 36 (90)
T ss_dssp EEEEEESSSSHHHHHHHHHHHHHHHHTTECEEEEEE
T ss_pred CEEEECCChHHHHHHHHHHHHHHHHhccCceEEEEe
Confidence 6789999999999877 4456678987776543
No 53
>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=43.75 E-value=66 Score=27.79 Aligned_cols=43 Identities=9% Similarity=0.034 Sum_probs=35.3
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHH
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTF 155 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~il 155 (190)
+-....+|++|..++-..++|-+|=.|-+-++++|...++.++
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 4467789999999998899999999999999888876665543
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=42.60 E-value=31 Score=28.40 Aligned_cols=41 Identities=12% Similarity=0.091 Sum_probs=34.0
Q ss_pred EEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCC
Q 029616 6 AMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLR 47 (190)
Q Consensus 6 AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~d 47 (190)
|++|+ |-.-.+.+-+.|+++|+.|.+|+....-.+|+|.+.
T Consensus 186 aI~~~-nd~~A~gv~~al~~~gisIvGfD~~~~~~~~~p~lt 226 (265)
T cd06354 186 VIFAA-AGGTGNGVFQAAKEAGVYAIGVDSDQYYLAPGVVLT 226 (265)
T ss_pred EEEEC-CCCCchHHHHHHHhcCCeEEEecCcccccCCCcEEE
Confidence 55555 667788999999999999999999888888887654
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=42.23 E-value=49 Score=24.23 Aligned_cols=31 Identities=13% Similarity=0.096 Sum_probs=25.0
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeee
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSY 33 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~-V~Sf 33 (190)
..+.+.|.+-..||-.+-..|+..||+ |..+
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
>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=41.16 E-value=65 Score=27.16 Aligned_cols=43 Identities=7% Similarity=0.139 Sum_probs=33.8
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHH
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~i 154 (190)
.+.+...+|+++..++-.+++|-++-.|-+.+++.|...+..+
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 4678899999999988888998888888888877766555433
No 57
>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=40.83 E-value=56 Score=28.04 Aligned_cols=44 Identities=5% Similarity=0.077 Sum_probs=35.9
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHH
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFD 156 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ile 156 (190)
+-+...+++++..++...++|.++-.|.+.+++.|...++.+++
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 58
>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=39.64 E-value=45 Score=25.34 Aligned_cols=24 Identities=13% Similarity=0.124 Sum_probs=20.3
Q ss_pred ceEEEEccCCCCcchHHHHhHHhC
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRH 26 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~ 26 (190)
..+.+.|....+||..|-..|++.
T Consensus 69 ~~vv~yC~~sg~rs~~aa~~L~~~ 92 (121)
T cd01530 69 RVLIFHCEFSSKRGPRMARHLRNL 92 (121)
T ss_pred CEEEEECCCccccHHHHHHHHHHH
Confidence 358889987779999999999985
No 59
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=39.29 E-value=20 Score=29.78 Aligned_cols=20 Identities=40% Similarity=0.609 Sum_probs=17.1
Q ss_pred CCcchHHHHhHHhCCCCeee
Q 029616 13 QNRSMEAHYLLKRHGFDVSS 32 (190)
Q Consensus 13 ~NRSMEAH~~L~k~Gf~V~S 32 (190)
.-|+=|||++|.++||-|+-
T Consensus 49 V~~~d~A~~~Lee~gF~Vr~ 68 (142)
T COG4747 49 VDRPDEAHSVLEEAGFTVRE 68 (142)
T ss_pred cCChHHHHHHHHHCCcEEEe
Confidence 46888999999999997763
No 60
>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=39.20 E-value=81 Score=27.46 Aligned_cols=45 Identities=4% Similarity=0.002 Sum_probs=37.1
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHH
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFD 156 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ile 156 (190)
.+-+...+++++.+++-..+++-++-.|.+-+++.|...++.+++
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 456788899999999988999999999999888888776665553
No 61
>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=37.85 E-value=92 Score=27.10 Aligned_cols=43 Identities=12% Similarity=0.024 Sum_probs=35.6
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHH
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTF 155 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~il 155 (190)
+-.+..++++|.+++-..+||-++-.|-+-+++.|...++.++
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 4668889999999998899999999998888888876666554
No 62
>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=36.67 E-value=45 Score=31.76 Aligned_cols=52 Identities=21% Similarity=0.265 Sum_probs=40.8
Q ss_pred EEEccCCCCcchHHHHhHHh-CCCCeeeecCCCceecCCCCCCCCccccCCCCH
Q 029616 6 AMVCSSNQNRSMEAHYLLKR-HGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPY 58 (190)
Q Consensus 6 AvVCaSN~NRSMEAH~~L~k-~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y 58 (190)
+||.|+-.=-|-+.-.-|++ .|+.+..||+|+.-|+=|.|+|---+| |.+.|
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 63
>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=36.24 E-value=73 Score=26.50 Aligned_cols=41 Identities=10% Similarity=0.121 Sum_probs=30.6
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHH
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRL 153 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ 153 (190)
+.+..-+++++.+++-..++|-++-.|.+-+.+.|.-.+..
T Consensus 23 ~g~~~a~~~~N~~ggi~G~~i~l~~~D~~~~~~~a~~~~~~ 63 (343)
T PF13458_consen 23 RGAELAVDEINAAGGINGRKIELVVYDDGGDPAQAVQAARK 63 (343)
T ss_dssp HHHHHHHHHHHHTTEETTEEEEEEEEE-TT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCcCCccceeeeccCCCChHHHHHHHHH
Confidence 45678889999988878899999999888887777544443
No 64
>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=36.19 E-value=83 Score=26.67 Aligned_cols=42 Identities=12% Similarity=-0.065 Sum_probs=33.8
Q ss_pred hHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHH
Q 029616 114 VFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTF 155 (190)
Q Consensus 114 vfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~il 155 (190)
-....+++++.+++..++++-+|-.|-+.+++.|...+..+.
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 65
>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=36.17 E-value=36 Score=21.33 Aligned_cols=21 Identities=29% Similarity=0.309 Sum_probs=18.6
Q ss_pred hHHHHhHHhCCCCeeeecCCC
Q 029616 17 MEAHYLLKRHGFDVSSYGTGA 37 (190)
Q Consensus 17 MEAH~~L~k~Gf~V~SfGTGs 37 (190)
.-.|.+....|+...|.|+|.
T Consensus 31 ~~vH~la~~~~L~s~s~g~~~ 51 (59)
T cd02325 31 KLIHDLAEYYGLKSESEGEGP 51 (59)
T ss_pred HHHHHHHHHCCCEEEEecCCC
Confidence 458999999999999999984
No 66
>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=36.11 E-value=32 Score=24.30 Aligned_cols=23 Identities=26% Similarity=0.482 Sum_probs=19.7
Q ss_pred HHHhHHhCCCCeeeecCCCceec
Q 029616 19 AHYLLKRHGFDVSSYGTGAHVKL 41 (190)
Q Consensus 19 AH~~L~k~Gf~V~SfGTGs~VkL 41 (190)
-|.++++.|+.-.|+|.|.+=||
T Consensus 34 ~H~~v~~~~l~s~S~G~ep~Rrv 56 (60)
T cd02645 34 QHDLVERYQLRSESFGSEPNRRL 56 (60)
T ss_pred HHHHHHHCCCeEEEecCCCCcEE
Confidence 69999999999999999976443
No 67
>PRK01175 phosphoribosylformylglycinamidine synthase I; Provisional
Probab=35.61 E-value=53 Score=28.98 Aligned_cols=34 Identities=18% Similarity=0.124 Sum_probs=29.4
Q ss_pred CCceEEEEccCCCCcchHHHHhHHhCCCCeeeec
Q 029616 1 MKYRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYG 34 (190)
Q Consensus 1 ~~l~~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfG 34 (190)
+++|+||++..-.|.-+|+-..|+++|+.|.-..
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 4679999999999988999999999999886543
No 68
>PRK00142 putative rhodanese-related sulfurtransferase; Provisional
Probab=35.08 E-value=47 Score=29.89 Aligned_cols=30 Identities=27% Similarity=0.444 Sum_probs=24.8
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCC-eeee
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFD-VSSY 33 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~-V~Sf 33 (190)
.++.|.|++- .||..|=.+|+++||+ |..+
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 4799999864 8999999999999994 6554
No 69
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=34.36 E-value=34 Score=27.60 Aligned_cols=39 Identities=28% Similarity=0.263 Sum_probs=29.4
Q ss_pred HhhHHHHHHHHHHHHhhhhh---HHHHHhhhhcccceeeeeecc
Q 029616 148 AIGGRLTFDLCQEVCLLLFF---IVSLVYHLKHHCTFTGLCIDR 188 (190)
Q Consensus 148 ~~Ga~~ileLc~~l~~~~~~---~~~~~~~~~~~~~~~~~~~~~ 188 (190)
.+||..+-+||+.|..+.++ +-.+..|.-.|+| .|--||
T Consensus 12 ~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t--~L~~dR 53 (135)
T PF01857_consen 12 KLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHT--ELMKDR 53 (135)
T ss_dssp HHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSG--GGGTTS
T ss_pred HHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhH--HHHhcc
Confidence 57899999999999988887 4556777776663 555555
No 70
>PRK08762 molybdopterin biosynthesis protein MoeB; Validated
Probab=33.50 E-value=53 Score=29.75 Aligned_cols=30 Identities=30% Similarity=0.502 Sum_probs=25.2
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCC-Ceeee
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGF-DVSSY 33 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~Sf 33 (190)
..+.++|.+ .+||..|-..|++.|| +|..+
T Consensus 58 ~~IvvyC~~-G~rs~~aa~~L~~~G~~~v~~l 88 (376)
T PRK08762 58 REIVLICAS-GTRSAHAAATLRELGYTRVASV 88 (376)
T ss_pred CeEEEEcCC-CcHHHHHHHHHHHcCCCceEee
Confidence 357889986 5799999999999999 68766
No 71
>COG3414 SgaB Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism]
Probab=33.20 E-value=54 Score=24.97 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=23.9
Q ss_pred CceEEEEccCCCCcc----hHHHHhHHhCCC
Q 029616 2 KYRYAMVCSSNQNRS----MEAHYLLKRHGF 28 (190)
Q Consensus 2 ~l~~AvVCaSN~NRS----MEAH~~L~k~Gf 28 (190)
..||-+||-+-++-| |..-.+|++.|+
T Consensus 1 ~~KIL~aCG~GvgSS~~ik~kve~~l~~~gi 31 (93)
T COG3414 1 MIKILAACGNGVGSSTMIKMKVEEVLKELGI 31 (93)
T ss_pred CcEEEEECCCCccHHHHHHHHHHHHHHHcCC
Confidence 368999999999999 567889999999
No 72
>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=32.97 E-value=1.1e+02 Score=27.51 Aligned_cols=44 Identities=11% Similarity=0.115 Sum_probs=36.7
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHH
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTF 155 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~il 155 (190)
.+-.+.-+|++|..++...++|-+|-.|-+-+++.|...++.++
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 73
>PRK01220 malonate decarboxylase subunit delta; Provisional
Probab=32.80 E-value=46 Score=26.20 Aligned_cols=46 Identities=20% Similarity=0.251 Sum_probs=34.7
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHHHHHHHHhhh
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEVCLLL 165 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ileLc~~l~~~~ 165 (190)
..+|.+|++++..|.... =.+|+|-|. ...=|-.-|+|.|.++...
T Consensus 52 ~~~Wqavl~rf~~~~~~~-----~~~i~InD~---GATP~VV~LRL~QA~e~~~ 97 (99)
T PRK01220 52 AARWKALFERFFTAQTPP-----AANIDIHDF---GATPGVVRLRLEQALEEIG 97 (99)
T ss_pred HHHHHHHHHHHHhhCCCC-----ccEEEEeCC---CCCcHhhhhHHHHHHHHHh
Confidence 568999999999985322 357888898 4555677889999998653
No 74
>PRK11784 tRNA 2-selenouridine synthase; Provisional
Probab=32.66 E-value=54 Score=30.07 Aligned_cols=66 Identities=21% Similarity=0.198 Sum_probs=43.9
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCCCeeeecCCC----cee---cCCC-CCCCCcccc--CCCCHHHHHHHHhhc
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGA----HVK---LPGP-SLREPNVYE--FGTPYKQMFDDLRRK 68 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs----~Vk---LPGp-s~dkPNvY~--FgT~Y~~Iy~dL~~k 68 (190)
..+.|.|..+.+||.-+-.+|+..||+|....-|- ..- +.+. ..-..-+.. =|+...+|...|..+
T Consensus 89 ~~ivvyC~rgG~RS~~aa~~L~~~G~~v~~L~GG~~awr~~~~~~~~~~~~~~~~ivl~G~TGsGKT~iL~~L~~~ 164 (345)
T PRK11784 89 PRGLLYCWRGGLRSGSVQQWLKEAGIDVPRLEGGYKAYRRFVIDTLEEAPAQFPLVVLGGNTGSGKTELLQALANA 164 (345)
T ss_pred CeEEEEECCCChHHHHHHHHHHHcCCCcEEEcCCHHHHHHhhHHHHhhhcccCceEecCCCCcccHHHHHHHHHhc
Confidence 46889998888999999999999999988775441 100 1111 111111222 257899999999875
No 75
>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=32.62 E-value=1e+02 Score=26.16 Aligned_cols=41 Identities=15% Similarity=0.053 Sum_probs=29.1
Q ss_pred cchHHHHHHHHhcCC-CCCCCeEEEEEeeccCCHHHHHhhHH
Q 029616 112 EKVFDTVVEDLNTRE-QPFMKTVLVINLEVKDNHEEAAIGGR 152 (190)
Q Consensus 112 ERvfD~Vvedl~~R~-~~~~~pVHVINvDIkDnhEeA~~Ga~ 152 (190)
++.+...+|+++.++ .-.++++.++-.|.+.+++.|..++.
T Consensus 18 ~~~~~lAv~~iN~~gg~~~g~~i~~~~~D~~~~~~~a~~~a~ 59 (350)
T cd06366 18 LPAIEMALEDVNADNSILPGYRLVLHVRDSKCDPVQAASAAL 59 (350)
T ss_pred HHHHHHHHHHHhcCCCcCCCcEEEEEecCCCCCHHHHHHHHH
Confidence 467788899999997 44578887777776666655544443
No 76
>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=32.51 E-value=1.3e+02 Score=23.65 Aligned_cols=43 Identities=21% Similarity=0.230 Sum_probs=30.8
Q ss_pred HHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHH
Q 029616 18 EAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFD 63 (190)
Q Consensus 18 EAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~ 63 (190)
.+...+.++|.+|.+++++... ++. ...||+|...+++.+...
T Consensus 81 ~~~~~~~~~~ip~i~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~ 123 (298)
T cd06268 81 AAAPVAEEAGVPLISPGATSPA-LTG--KGNPYVFRTAPSDAQQAA 123 (298)
T ss_pred hhHHHHHhCCCcEEccCCCCcc-ccc--CCCceEEEcccCcHHHHH
Confidence 5678899999999999887542 111 346899998887755444
No 77
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=32.41 E-value=40 Score=28.67 Aligned_cols=89 Identities=21% Similarity=0.344 Sum_probs=57.3
Q ss_pred CceEEEEccCCCCcchHHHHhHH----hCCC----CeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhhcChHHH
Q 029616 2 KYRYAMVCSSNQNRSMEAHYLLK----RHGF----DVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRRKDPELY 73 (190)
Q Consensus 2 ~l~~AvVCaSN~NRSMEAH~~L~----k~Gf----~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY 73 (190)
+.+++.||--|.=||=-|-.+++ |+|+ +|-|+||+..=- |.++|. -.. .--
T Consensus 6 ~~svlFvclGNiCRSP~AEaVFr~~v~K~~l~~~~~iDSagt~~yh~--G~~PD~-----------R~~--------s~l 64 (159)
T KOG3217|consen 6 TKSVLFVCLGNICRSPIAEAVFRDLVKKRNLSEEWHIDSAGTSGYHT--GRSPDP-----------RTL--------SIL 64 (159)
T ss_pred ceEEEEEEecccccCHHHHHHHHHHHHHcCcceeeeecccccccccc--CCCCCh-----------HHH--------HHH
Confidence 45788999999999977776654 6664 779999987432 444432 111 124
Q ss_pred HhcCchhhhhcccCCCCCccccccccCCCcccEEEecccchHHHHHHHHhc
Q 029616 74 KRNGILPMLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNT 124 (190)
Q Consensus 74 ~~NGlL~MLdRNr~IK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~ 124 (190)
+++||= +=-+-|.||+ +=| . .||.|++-+|.. ++||+.
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 5555555553 223 1 499999999755 556655
No 78
>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=32.36 E-value=75 Score=29.18 Aligned_cols=94 Identities=11% Similarity=0.201 Sum_probs=56.6
Q ss_pred ccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCC-C-----HHHHHHHHhhcChHHHHhcCchhhh
Q 029616 9 CSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGT-P-----YKQMFDDLRRKDPELYKRNGILPML 82 (190)
Q Consensus 9 CaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT-~-----Y~~Iy~dL~~kD~~lY~~NGlL~ML 82 (190)
|..||--|----..|.++||.+.+. .+...|+-..| + .+++|+.+.+ |.+.|. ...
T Consensus 9 C~~N~~ds~~~~~~l~~~g~~~~~~------------~~~aD~viinTC~v~~~a~~~~~~~i~~-----~~~~~~-~vv 70 (430)
T TIGR01125 9 CPKNLVDSEVMLGILREAGYEVTPN------------YEDADYVIVNTCGFIEDARQESIDTIGE-----LADAGK-KVI 70 (430)
T ss_pred CCCcHHHHHHHHHHHHHCcCEECCC------------cccCCEEEEeCCCccchHHHHHHHHHHH-----HHhcCC-CEE
Confidence 9999999988889999999987762 23456776665 2 3445555432 332232 010
Q ss_pred hcccCCCCCccccccccCCCcccEEEecccchHHHHHHHHhc
Q 029616 83 KRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNT 124 (190)
Q Consensus 83 dRNr~IK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~ 124 (190)
==.=-....||....... ..|+|+ .|..|.++++++..
T Consensus 71 vgGc~a~~~pee~~~~~~--~vd~v~--g~~~~~~l~~~~~~ 108 (430)
T TIGR01125 71 VTGCLVQRYKEELKEEIP--EVHAIT--GSGDVENILNAIES 108 (430)
T ss_pred EECCccccchHHHHhhCC--CCcEEE--CCCCHHHHHHHHHH
Confidence 001112334665533222 378877 56789999998865
No 79
>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=32.36 E-value=55 Score=29.60 Aligned_cols=65 Identities=22% Similarity=0.241 Sum_probs=43.6
Q ss_pred eEEEEccCCCCcchHHHHhHHhCCCCeeeecCCC-------c---eecCCCCCC-CCccccCCCCHHHHHHHHhhcC
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGA-------H---VKLPGPSLR-EPNVYEFGTPYKQMFDDLRRKD 69 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs-------~---VkLPGps~d-kPNvY~FgT~Y~~Iy~dL~~kD 69 (190)
++-++|..+-.||--+-.+|++.||+|....-|- . -..|+|..- .|+ =.=|+...++.+-|...+
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 4889998888999999999999999997765442 1 111222211 111 123478999999987663
No 80
>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=31.97 E-value=42 Score=23.69 Aligned_cols=21 Identities=29% Similarity=0.588 Sum_probs=18.7
Q ss_pred HHHHhHHhCCCCeeeecCCCc
Q 029616 18 EAHYLLKRHGFDVSSYGTGAH 38 (190)
Q Consensus 18 EAH~~L~k~Gf~V~SfGTGs~ 38 (190)
-.|.+-.+.|+.-.|+|.|..
T Consensus 33 ~vH~~a~~~gL~s~S~G~g~~ 53 (60)
T cd02640 33 LIHQIAQKYGLKSRSYGSGND 53 (60)
T ss_pred HHHHHHHHcCCceeeEeCCCC
Confidence 479999999999999999874
No 81
>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=31.76 E-value=1.3e+02 Score=25.43 Aligned_cols=41 Identities=17% Similarity=0.160 Sum_probs=32.2
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHH
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRL 153 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ 153 (190)
+-.+..+++++..++..+++|-++-.|-+-+++.|...+..
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 34677889999999888999999888888887776554443
No 82
>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=31.23 E-value=1.7e+02 Score=23.23 Aligned_cols=38 Identities=16% Similarity=0.128 Sum_probs=32.9
Q ss_pred ccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeecc
Q 029616 104 FDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVK 141 (190)
Q Consensus 104 fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDIk 141 (190)
+|.|+|+.......+++-+..++-...+.+.||-+|-.
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 89999999999999999999887666678999998843
No 83
>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=31.08 E-value=1.1e+02 Score=26.05 Aligned_cols=45 Identities=11% Similarity=0.135 Sum_probs=32.1
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHHHHH
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQ 159 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ileLc~ 159 (190)
++.+...+++++.+++-..++|-++=.|.+-++++| ...+.+|.+
T Consensus 20 ~~g~~~a~~~iN~~GGi~G~~i~l~~~D~~~~p~~a---~~~a~~lv~ 64 (342)
T cd06329 20 RRGLQLAADEINAKGGVDGRPIELVEEDNKGSPQEA---LRKAQKAID 64 (342)
T ss_pred HHHHHHHHHHHHhcCCcCCeEEEEEeccCCCChHHH---HHHHHHHHH
Confidence 467788999999998888888777766666665555 444555544
No 84
>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=30.31 E-value=43 Score=23.59 Aligned_cols=21 Identities=29% Similarity=0.499 Sum_probs=18.9
Q ss_pred HHHHhHHhCCCCeeeecCCCc
Q 029616 18 EAHYLLKRHGFDVSSYGTGAH 38 (190)
Q Consensus 18 EAH~~L~k~Gf~V~SfGTGs~ 38 (190)
-.|.+-.+.|+.-.|+|.|..
T Consensus 32 ~vH~~a~~~gL~s~S~G~g~~ 52 (59)
T cd06007 32 VIHRLCRKLGLKSKSKGKGSN 52 (59)
T ss_pred HHHHHHHHcCCCceeecCCCC
Confidence 479999999999999999874
No 85
>PRK02103 malonate decarboxylase subunit delta; Provisional
Probab=29.93 E-value=53 Score=26.12 Aligned_cols=45 Identities=22% Similarity=0.321 Sum_probs=33.7
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHHHHHHHHhh
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEVCLL 164 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ileLc~~l~~~ 164 (190)
..+|.+|++++..|.+ .-=.+|+|-|. ...=|-.-|+|.|.++..
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 4689999999999863 22357788888 445566778899988864
No 86
>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=29.71 E-value=41 Score=25.33 Aligned_cols=24 Identities=21% Similarity=0.664 Sum_probs=19.4
Q ss_pred ccccCCCCHHHHHHHHhhcChHHH
Q 029616 50 NVYEFGTPYKQMFDDLRRKDPELY 73 (190)
Q Consensus 50 NvY~FgT~Y~~Iy~dL~~kD~~lY 73 (190)
..|+.+++|+.||+++.++|+.+-
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 346778999999999999999875
No 87
>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=29.63 E-value=48 Score=26.04 Aligned_cols=44 Identities=20% Similarity=0.273 Sum_probs=32.8
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHHHHHHHHh
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQEVCL 163 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ileLc~~l~~ 163 (190)
..+|.+|++++..|.+ .-=.+++|-|. ...=|-.-|+|.|.++.
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 5689999999999853 22356788888 44556677889988875
No 88
>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=29.54 E-value=49 Score=23.20 Aligned_cols=26 Identities=27% Similarity=0.470 Sum_probs=18.4
Q ss_pred eEEEEccCCCCcchHHHH----hHHhCCCC
Q 029616 4 RYAMVCSSNQNRSMEAHY----LLKRHGFD 29 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~----~L~k~Gf~ 29 (190)
|+++||++.++-|+=... .+.+.|+.
T Consensus 1 kilvvC~~G~~tS~ll~~kl~~~f~~~~i~ 30 (86)
T cd05563 1 KILAVCGSGLGSSLMLKMNVEKVLKELGIE 30 (86)
T ss_pred CEEEECCCCccHHHHHHHHHHHHHHHCCCc
Confidence 589999999998865553 34466663
No 89
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=29.18 E-value=20 Score=32.10 Aligned_cols=37 Identities=24% Similarity=0.304 Sum_probs=24.3
Q ss_pred HHHHhhHHHHHHHHHHHHhh-----hhh----H-HHHHhhhhcccce
Q 029616 145 EEAAIGGRLTFDLCQEVCLL-----LFF----I-VSLVYHLKHHCTF 181 (190)
Q Consensus 145 EeA~~Ga~~ileLc~~l~~~-----~~~----~-~~~~~~~~~~~~~ 181 (190)
||.||.|+.+-++-.-|-++ .|| | -.|..||+||..+
T Consensus 97 EetTISAKvm~~ikavLgaTKiDLPVDINDPYDlGLLLRhLRHHSNL 143 (238)
T PF02084_consen 97 EETTISAKVMEDIKAVLGATKIDLPVDINDPYDLGLLLRHLRHHSNL 143 (238)
T ss_pred CCccccHHHHHHHHHHhcccccccccccCChhhHHHHHHHHHHHHHH
Confidence 47788888777665444333 233 1 2688999999764
No 90
>cd01531 Acr2p Eukaryotic arsenate resistance proteins are members of the Rhodanese Homology Domain superfamily. Included in this CD is the Saccharomyces cerevisiae arsenate reductase protein, Acr2p, and other yeast and plant homologs.
Probab=28.96 E-value=93 Score=22.70 Aligned_cols=33 Identities=21% Similarity=0.200 Sum_probs=24.1
Q ss_pred eEEEEccCCCCcchHHHHhHHh--------CCC-CeeeecCC
Q 029616 4 RYAMVCSSNQNRSMEAHYLLKR--------HGF-DVSSYGTG 36 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~k--------~Gf-~V~SfGTG 36 (190)
.+-+.|++...||..|=+.|.+ .|| +|....-|
T Consensus 64 ~iv~yC~~~~~r~~~aa~~l~~~~~~~~~~~G~~~v~~l~gG 105 (113)
T cd01531 64 TVVFHCALSQVRGPSAARKFLRYLDEEDLETSKFEVYVLHGG 105 (113)
T ss_pred eEEEEeecCCcchHHHHHHHHHHHHHhccccCCCeEEEEcCh
Confidence 6888999777899999777654 366 67665444
No 91
>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=28.41 E-value=2e+02 Score=22.94 Aligned_cols=40 Identities=13% Similarity=0.067 Sum_probs=33.1
Q ss_pred cccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeeccC
Q 029616 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKD 142 (190)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDIkD 142 (190)
.+|.||+.....-..++.-|...+-...+.+.|+-+|--+
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 4899999999998899999998886666778899887544
No 92
>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=28.09 E-value=96 Score=25.24 Aligned_cols=56 Identities=7% Similarity=-0.015 Sum_probs=40.4
Q ss_pred EEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHHhh
Q 029616 6 AMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDLRR 67 (190)
Q Consensus 6 AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~~ 67 (190)
|++| +|..-.+.+-..|+++|..|.+|+....-... .|.+.....++.+|......
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 66667888999999999888888875544444 46677777788777766554
No 93
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=27.93 E-value=1.5e+02 Score=22.33 Aligned_cols=51 Identities=12% Similarity=0.350 Sum_probs=33.9
Q ss_pred HHHHhHHhCCCCeeeecCCCc------eecCCCC----------CCCCccccCCCCHHHHHHHHhhc
Q 029616 18 EAHYLLKRHGFDVSSYGTGAH------VKLPGPS----------LREPNVYEFGTPYKQMFDDLRRK 68 (190)
Q Consensus 18 EAH~~L~k~Gf~V~SfGTGs~------VkLPGps----------~dkPNvY~FgT~Y~~Iy~dL~~k 68 (190)
.....|+++||.|.++++.+. +=.-|-. ..-|-|=.=|-|=++|++.|+++
T Consensus 12 ~v~~~L~~~GyeVv~l~~~~~~~~~daiVvtG~~~n~mg~~d~~~~~pVInA~G~T~eEI~~~v~~r 78 (80)
T PF03698_consen 12 NVKEALREKGYEVVDLENEQDLQNVDAIVVTGQDTNMMGIQDTSTKVPVINASGLTAEEIVQEVEER 78 (80)
T ss_pred HHHHHHHHCCCEEEecCCccccCCcCEEEEECCCcccccccccccCceEEecCCCCHHHHHHHHHHh
Confidence 566789999999999998871 1122333 23344444555668888888754
No 94
>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=27.87 E-value=1.4e+02 Score=20.07 Aligned_cols=33 Identities=15% Similarity=0.231 Sum_probs=21.7
Q ss_pred eEEEEccCCCCcchHH--HHhHHhCCCCe--eeecCC
Q 029616 4 RYAMVCSSNQNRSMEA--HYLLKRHGFDV--SSYGTG 36 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEA--H~~L~k~Gf~V--~SfGTG 36 (190)
.+++|-....+...-+ -..|.++|.+| .|+|+.
T Consensus 3 ~VsvVG~~~~~~~~~~~i~~aL~~~~I~v~~i~~g~s 39 (65)
T cd04918 3 IISLIGNVQRSSLILERAFHVLYTKGVNVQMISQGAS 39 (65)
T ss_pred EEEEECCCCCCccHHHHHHHHHHHCCCCEEEEEecCc
Confidence 5677776333333433 34489999999 888774
No 95
>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=27.77 E-value=1.7e+02 Score=24.35 Aligned_cols=37 Identities=8% Similarity=0.042 Sum_probs=29.7
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHh
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAI 149 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~ 149 (190)
+..+..++++|.+++..+.+|-++..|-+.+++.+..
T Consensus 22 ~~~~~a~~~iN~~ggi~G~~v~l~~~D~~~d~~~~~~ 58 (336)
T cd06326 22 AGAQAYFDAVNAAGGVNGRKIELVTLDDGYEPERTVA 58 (336)
T ss_pred HHHHHHHHHHHhcCCcCCceEEEEEeCCCCChHHHHH
Confidence 4567889999999988889999999997766666543
No 96
>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=27.37 E-value=28 Score=29.00 Aligned_cols=47 Identities=26% Similarity=0.473 Sum_probs=31.6
Q ss_pred EEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHH
Q 029616 7 MVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQM 61 (190)
Q Consensus 7 vVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~I 61 (190)
+..++|.+.-.|+-.+|...|+.|.|+ ..++.+..+-|-+ +++|.++
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 467899999999999999999999888 4566554444433 7777765
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=27.34 E-value=37 Score=28.60 Aligned_cols=36 Identities=22% Similarity=0.394 Sum_probs=26.7
Q ss_pred CchhhhhcccCCCCCccccccc--cCCCcccEEEecccch
Q 029616 77 GILPMLKRNIGVKAAPQRWQDN--ALDGSFDIVFTFEEKV 114 (190)
Q Consensus 77 GlL~MLdRNr~IK~~PERfQ~~--~~~~~fDvIiTcEERv 114 (190)
-.||++..+.=+ ..|| |.+. .+++.|-|=||-||.|
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 356666665544 5799 8887 4557899999999987
No 98
>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=27.22 E-value=1.2e+02 Score=26.54 Aligned_cols=43 Identities=5% Similarity=-0.202 Sum_probs=34.8
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHH
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~i 154 (190)
.+-+...++++|..++-..++|-+|-.|-+-+++.|...++.+
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 3456778999999999889999999999999988886555433
No 99
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=27.16 E-value=57 Score=23.23 Aligned_cols=22 Identities=27% Similarity=0.540 Sum_probs=19.3
Q ss_pred hHHHHhHHhCCCCeeeecCCCc
Q 029616 17 MEAHYLLKRHGFDVSSYGTGAH 38 (190)
Q Consensus 17 MEAH~~L~k~Gf~V~SfGTGs~ 38 (190)
.-.|.+++.-|+.-.|+|.|..
T Consensus 50 ~~iH~~a~~~~l~s~S~g~g~~ 71 (79)
T smart00393 50 KIVHELAEKYGLESESFGEGPK 71 (79)
T ss_pred HHHHHHHHHcCCEEEEEcCCCC
Confidence 3589999999999999999864
No 100
>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=26.97 E-value=62 Score=26.53 Aligned_cols=53 Identities=11% Similarity=0.127 Sum_probs=35.8
Q ss_pred EEEccCCCCcchHHHHhHHhCCCC------eeeecCCCceecCCCCCCCCccccCCCCHHHHHHH
Q 029616 6 AMVCSSNQNRSMEAHYLLKRHGFD------VSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDD 64 (190)
Q Consensus 6 AvVCaSN~NRSMEAH~~L~k~Gf~------V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~d 64 (190)
|++|+|..- .+-+-+.|+++|++ |.+|+-...-++ -.|.+..+..|+++|=+.
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 788875543 56677888899984 677775533333 445566788899888543
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=26.39 E-value=47 Score=21.82 Aligned_cols=18 Identities=33% Similarity=0.357 Sum_probs=14.4
Q ss_pred chHHHHhHHhCCCCeeee
Q 029616 16 SMEAHYLLKRHGFDVSSY 33 (190)
Q Consensus 16 SMEAH~~L~k~Gf~V~Sf 33 (190)
+.-=|++|++.||+|.+.
T Consensus 20 t~lk~r~L~~~G~~Vi~I 37 (58)
T PF08373_consen 20 TKLKHRHLKALGYKVISI 37 (58)
T ss_pred HHHHHHHHHHCCCEEEEe
Confidence 455688999999999864
No 102
>smart00267 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria
Probab=26.34 E-value=2.2e+02 Score=20.04 Aligned_cols=51 Identities=16% Similarity=0.278 Sum_probs=31.1
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHH-HH----HhhHHHHHHHHHHHHh
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHE-EA----AIGGRLTFDLCQEVCL 163 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhE-eA----~~Ga~~ileLc~~l~~ 163 (190)
+-|...++.+..+......++.++.++|.+-.+ .. ..+...+-++++.|..
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~l~~i~i~~~~~~~~~~g~~~~~~~l~~i~~~l~~ 70 (163)
T smart00267 15 RYFEEELEQELQRAQRQGSPFALLLIDLDNFKDINDTYGHAVGDELLQEVAQRLSS 70 (163)
T ss_pred HHHHHHHHHHHHHhhccCCeEEEEEEEccccchhhhccCchhHHHHHHHHHHHHHH
Confidence 445666655555555555678999999965332 11 2355666667776654
No 103
>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=26.28 E-value=58 Score=22.97 Aligned_cols=28 Identities=29% Similarity=0.484 Sum_probs=19.9
Q ss_pred ceEEEEccCCCCcc-hH---HHHhHHhCCCCe
Q 029616 3 YRYAMVCSSNQNRS-ME---AHYLLKRHGFDV 30 (190)
Q Consensus 3 l~~AvVCaSN~NRS-ME---AH~~L~k~Gf~V 30 (190)
.|+++||++.++-| |= .-+.+++.|+.+
T Consensus 1 ~~ilivC~~G~~tS~~l~~~i~~~~~~~~i~~ 32 (89)
T cd05566 1 KKILVACGTGVATSTVVASKVKELLKENGIDV 32 (89)
T ss_pred CEEEEECCCCccHHHHHHHHHHHHHHHCCCce
Confidence 47999999999988 32 334556777743
No 104
>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=25.23 E-value=82 Score=20.83 Aligned_cols=29 Identities=34% Similarity=0.437 Sum_probs=22.6
Q ss_pred ceEEEEccCCCCcchHHHHhHHhCCC-Ceee
Q 029616 3 YRYAMVCSSNQNRSMEAHYLLKRHGF-DVSS 32 (190)
Q Consensus 3 l~~AvVCaSN~NRSMEAH~~L~k~Gf-~V~S 32 (190)
-.+-++|++ ..+|..+=..|++.|| +|..
T Consensus 51 ~~vv~~c~~-~~~a~~~~~~l~~~G~~~v~~ 80 (89)
T cd00158 51 KPIVVYCRS-GNRSARAAKLLRKAGGTNVYN 80 (89)
T ss_pred CeEEEEeCC-CchHHHHHHHHHHhCcccEEE
Confidence 357788988 5788899999999997 4543
No 105
>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=24.79 E-value=84 Score=22.02 Aligned_cols=36 Identities=25% Similarity=0.421 Sum_probs=25.9
Q ss_pred EccCCCCcchHHHHhHHhCCCCeee--------ecCCCceecCC
Q 029616 8 VCSSNQNRSMEAHYLLKRHGFDVSS--------YGTGAHVKLPG 43 (190)
Q Consensus 8 VCaSN~NRSMEAH~~L~k~Gf~V~S--------fGTGs~VkLPG 43 (190)
+=-.|.+..|.|.++|+++|++++- -|=|-.+|++.
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 3345667899999999999998764 44455555553
No 106
>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=24.77 E-value=2e+02 Score=22.89 Aligned_cols=45 Identities=16% Similarity=0.086 Sum_probs=24.7
Q ss_pred HHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHHHHHH
Q 029616 115 FDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLCQE 160 (190)
Q Consensus 115 fD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ileLc~~ 160 (190)
|+.|++.+.........+ ..+|+|||....+..-....++++++.
T Consensus 62 l~evl~~~~~~~~~~~~~-~~l~iEiK~~~~~~~~~~~~~~~~~~~ 106 (179)
T cd08555 62 LEEVLELIADYLKNPDYT-IILSLEIKQDSPEYDEFLAKVLKELRV 106 (179)
T ss_pred HHHHHHHHHhhhhcCCCc-eEEEEEeCCCCCcchHHHHHHHHHHHH
Confidence 677777665533322233 479999997754222223344444443
No 107
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=24.62 E-value=1.3e+02 Score=21.42 Aligned_cols=48 Identities=17% Similarity=0.239 Sum_probs=33.8
Q ss_pred CCCCccccCCCCHHHHHHHHhhcChHHHHhcCchhhhhcccCCCCCccccccc
Q 029616 46 LREPNVYEFGTPYKQMFDDLRRKDPELYKRNGILPMLKRNIGVKAAPQRWQDN 98 (190)
Q Consensus 46 ~dkPNvY~FgT~Y~~Iy~dL~~kD~~lY~~NGlL~MLdRNr~IK~~PERfQ~~ 98 (190)
++-|+++..|-|+++-...++.-=. +|-. .+++-|+.|+..|+.+|..
T Consensus 21 Pdlpgc~s~G~T~eea~~n~~eai~-l~~e----~~~~~~~~iP~~~~~~~~~ 68 (73)
T COG1598 21 PDLPGCHSQGETLEEALQNAKEAIE-LHLE----ALLEEGEPIPAAPESFQRV 68 (73)
T ss_pred CCCCCccccCCCHHHHHHHHHHHHH-HHHH----HHHhcCCcCCCccccccee
Confidence 5889999999999998887765322 2222 1566667777788887754
No 108
>PF06288 DUF1040: Protein of unknown function (DUF1040); InterPro: IPR009383 This family consists of several bacterial YihD proteins of unknown function [].; PDB: 2KO6_A.
Probab=24.45 E-value=80 Score=24.47 Aligned_cols=11 Identities=45% Similarity=0.597 Sum_probs=9.7
Q ss_pred HHHHHhhhhcc
Q 029616 168 IVSLVYHLKHH 178 (190)
Q Consensus 168 ~~~~~~~~~~~ 178 (190)
|++|.||+|..
T Consensus 47 DdvLIYhLKMr 57 (86)
T PF06288_consen 47 DDVLIYHLKMR 57 (86)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHhc
Confidence 99999999854
No 109
>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=24.30 E-value=1.4e+02 Score=23.96 Aligned_cols=38 Identities=11% Similarity=0.173 Sum_probs=32.5
Q ss_pred cccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeec
Q 029616 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEV 140 (190)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDI 140 (190)
.+|.|||+.....-.++.-+..++-...+.+-|+.+|-
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 48999999999998999999988766667799999974
No 110
>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=24.14 E-value=2.9e+02 Score=21.79 Aligned_cols=40 Identities=13% Similarity=0.200 Sum_probs=32.9
Q ss_pred cccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeeccC
Q 029616 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKD 142 (190)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDIkD 142 (190)
.+|.||+........++..|...+....+-+.|+-+|-.+
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 4899999999999999999998876555678888887554
No 111
>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=24.09 E-value=2e+02 Score=22.15 Aligned_cols=129 Identities=12% Similarity=0.081 Sum_probs=70.9
Q ss_pred EEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHH----hhcC-hH--------
Q 029616 5 YAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDL----RRKD-PE-------- 71 (190)
Q Consensus 5 ~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL----~~kD-~~-------- 71 (190)
-|+|+++-.+.++.+=..|.++|.+|..++++... .++.+.+++.+.++-..+ .++- ++
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 36777776666655446677899999999988642 244455555443333322 2211 00
Q ss_pred -----HHHhcCchhhhhcccCCC---CCcccc---------ccccCC-CcccEEEecccchHHHHHHHHhcCCCCCCCeE
Q 029616 72 -----LYKRNGILPMLKRNIGVK---AAPQRW---------QDNALD-GSFDIVFTFEEKVFDTVVEDLNTREQPFMKTV 133 (190)
Q Consensus 72 -----lY~~NGlL~MLdRNr~IK---~~PERf---------Q~~~~~-~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pV 133 (190)
--+.+|+...+...-.++ ..+..| +..... ...|+|++......-.++..+...+..-.+.+
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 EEEEeecc
Q 029616 134 LVINLEVK 141 (190)
Q Consensus 134 HVINvDIk 141 (190)
.++-.|-.
T Consensus 209 ~i~~~d~~ 216 (264)
T cd01537 209 SVIGFDGT 216 (264)
T ss_pred EEEeecCc
Confidence 88877643
No 112
>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=23.83 E-value=2e+02 Score=24.20 Aligned_cols=41 Identities=12% Similarity=-0.044 Sum_probs=32.4
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHH
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRL 153 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ 153 (190)
+-.+..+++++..++..++++-++-.|.+.+++++...+..
T Consensus 21 ~g~~~a~~~~N~~Ggi~G~~i~lv~~D~~~~~~~~~~~~~~ 61 (341)
T cd06341 21 AGADAAAGYANAAGGIAGRPIEYVWCDDQGDPASAAACARD 61 (341)
T ss_pred HHHHHHHHHHHhcCCcCCceEEEEEecCCCChhHHHHHHHH
Confidence 44578889999888888889999989998888877655443
No 113
>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=23.71 E-value=1.2e+02 Score=22.43 Aligned_cols=36 Identities=11% Similarity=0.165 Sum_probs=30.7
Q ss_pred ccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEee
Q 029616 104 FDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLE 139 (190)
Q Consensus 104 fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvD 139 (190)
+|.|||..+.+.-.|+..|..++-...+-+.||-+|
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 689999999999999999999987666666777766
No 114
>smart00280 KAZAL Kazal type serine protease inhibitors. Kazal type serine protease inhibitors and follistatin-like domains.
Probab=23.66 E-value=58 Score=20.75 Aligned_cols=29 Identities=21% Similarity=0.320 Sum_probs=18.1
Q ss_pred EEEEccCCCCcc------hHHHHhHHhCCCCeeeec
Q 029616 5 YAMVCSSNQNRS------MEAHYLLKRHGFDVSSYG 34 (190)
Q Consensus 5 ~AvVCaSN~NRS------MEAH~~L~k~Gf~V~SfG 34 (190)
+.-||+|+ +++ |++++......+.+.++|
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 35689998 455 555555555566666666
No 115
>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=23.55 E-value=3.3e+02 Score=22.05 Aligned_cols=38 Identities=13% Similarity=0.050 Sum_probs=32.6
Q ss_pred cccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeec
Q 029616 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEV 140 (190)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDI 140 (190)
.+|.|||+...+--.|+.-|..++-...+.+.|+-+|-
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 48999999999999999999988876667788888864
No 116
>PHA02576 3 tail completion and sheath stabilizer protein; Provisional
Probab=23.54 E-value=29 Score=29.75 Aligned_cols=62 Identities=16% Similarity=0.247 Sum_probs=42.9
Q ss_pred CceecCCCCC-CCCccccCC-----CCHHHHHHHHhhcC----------hHHHHhcCchhhhhcccCCCCCccccccc
Q 029616 37 AHVKLPGPSL-REPNVYEFG-----TPYKQMFDDLRRKD----------PELYKRNGILPMLKRNIGVKAAPQRWQDN 98 (190)
Q Consensus 37 s~VkLPGps~-dkPNvY~Fg-----T~Y~~Iy~dL~~kD----------~~lY~~NGlL~MLdRNr~IK~~PERfQ~~ 98 (190)
..+++||... -.|-+-.|- ..|-+||+=+.+-. ..=|.+++.||+|++|.+-=-+-=+|.++
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 677777774 58999999887643 22356789999999994311122236654
No 117
>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=23.53 E-value=1.8e+02 Score=24.58 Aligned_cols=57 Identities=12% Similarity=0.163 Sum_probs=37.8
Q ss_pred EEEEccCCCCcchHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHH
Q 029616 5 YAMVCSSNQNRSMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFD 63 (190)
Q Consensus 5 ~AvVCaSN~NRSMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~ 63 (190)
.||+-...-.-++.+..++.+.|..+.|.++++.- |.++. ..|++|.++.++.+.-.
T Consensus 68 ~aviG~~~s~~~~a~~~~~~~~~vp~i~~~s~~~~-~~~~~-~~~~~f~~~~~~~~~~~ 124 (334)
T cd06327 68 DMIVGGPNSAVALAVQEVAREKKKIYIVTGAGSDD-LTGKD-CSPYTFHWAYDTYMLAN 124 (334)
T ss_pred eEEECCccHHHHHHHHHHHHHhCceEEecCCCccc-cccCC-CCCceEEccCChHHHHH
Confidence 34554333233567778899999999999887643 33332 46999999987765433
No 118
>PF13399 LytR_C: LytR cell envelope-related transcriptional attenuator
Probab=23.52 E-value=1.4e+02 Score=21.12 Aligned_cols=36 Identities=17% Similarity=0.298 Sum_probs=28.3
Q ss_pred CceEEEEccCCCCc-chHHHHhHHhCCCCeeeecCCC
Q 029616 2 KYRYAMVCSSNQNR-SMEAHYLLKRHGFDVSSYGTGA 37 (190)
Q Consensus 2 ~l~~AvVCaSN~NR-SMEAH~~L~k~Gf~V~SfGTGs 37 (190)
..+|.|.-+|..+. -=.+-..|+++||.|.+.|...
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 35778888887654 3567789999999999988876
No 119
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=23.41 E-value=51 Score=25.68 Aligned_cols=26 Identities=19% Similarity=0.074 Sum_probs=19.6
Q ss_pred HhHHhCCCCeeeecCCCceecCCCCCC
Q 029616 21 YLLKRHGFDVSSYGTGAHVKLPGPSLR 47 (190)
Q Consensus 21 ~~L~k~Gf~V~SfGTGs~VkLPGps~d 47 (190)
.+++++|||+.|.-.| ....||-|.-
T Consensus 27 glFsRRgyNIeSLtvg-~te~~~iSRm 52 (96)
T PRK08178 27 GLFARRAFNVEGILCL-PIQDGDKSRI 52 (96)
T ss_pred HHHhcCCcCeeeEEEe-ecCCCCceEE
Confidence 4678999999999886 4556665543
No 120
>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=23.39 E-value=87 Score=26.04 Aligned_cols=32 Identities=22% Similarity=0.318 Sum_probs=22.4
Q ss_pred ceEEEEccCCC--Ccc-----hHHHHhHHhCCCCeeeec
Q 029616 3 YRYAMVCSSNQ--NRS-----MEAHYLLKRHGFDVSSYG 34 (190)
Q Consensus 3 l~~AvVCaSN~--NRS-----MEAH~~L~k~Gf~V~SfG 34 (190)
.+|||.|+|.. +-+ .|.=+.|.++|+.+..=|
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 222 233367889999887544
No 121
>cd05567 PTS_IIB_mannitol PTS_IIB_mannitol: subunit IIB of enzyme II (EII) of the mannitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a mannitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIA, IIB, and IIC domains are expressed from the mtlA gene as a single protein, also known as the mannitol PTS permease, the mtl transporter, or MtlA. MtlA is only functional as a dimer with the dimer contacts occuring between the IIC domains. MtlA takes up exogenous mannitol releasing the phosphate ester into the cytoplasm in preparation for oxidation to fructose-6-phosphate by the NAD-dependent mannitol-P dehydrogenase (MtlD). 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 mannitol, chitobiose/lichenan, ascorbate, lactose, galactitol, fructose, and a s
Probab=23.25 E-value=1.2e+02 Score=21.73 Aligned_cols=27 Identities=19% Similarity=0.366 Sum_probs=20.4
Q ss_pred ceEEEEccCCCCcchH----HHHhHHhCCCC
Q 029616 3 YRYAMVCSSNQNRSME----AHYLLKRHGFD 29 (190)
Q Consensus 3 l~~AvVCaSN~NRSME----AH~~L~k~Gf~ 29 (190)
.++++||.+.+.-|+- .-+.+++.|..
T Consensus 1 ~kilvvCg~G~gtS~ml~~ki~~~~~~~~~~ 31 (87)
T cd05567 1 KKIVFACDAGMGSSAMGASVLRKKLKKAGLE 31 (87)
T ss_pred CEEEEECCCCccHHHHHHHHHHHHHHHCCCc
Confidence 3789999999998865 44666677763
No 122
>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=23.06 E-value=80 Score=22.02 Aligned_cols=22 Identities=27% Similarity=0.415 Sum_probs=19.3
Q ss_pred hHHHHhHHhCCCCeeeecCCCc
Q 029616 17 MEAHYLLKRHGFDVSSYGTGAH 38 (190)
Q Consensus 17 MEAH~~L~k~Gf~V~SfGTGs~ 38 (190)
.-.|.+-.+.|+.-.|+|.|..
T Consensus 32 ~~vH~lA~~~gL~s~S~G~g~~ 53 (60)
T cd02641 32 LLVHELAEELGLRHESTGEGSD 53 (60)
T ss_pred HHHHHHHHHcCCceEeeCCCCc
Confidence 4579999999999999999874
No 123
>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=23.03 E-value=2e+02 Score=24.56 Aligned_cols=43 Identities=7% Similarity=-0.184 Sum_probs=33.0
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHH
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~i 154 (190)
.+-++..+++.|.+++-..++|-++-.|-+.+++.|...+..+
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 3567788899999888889999988888888777765544443
No 124
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=22.93 E-value=3.5e+02 Score=23.17 Aligned_cols=84 Identities=14% Similarity=0.184 Sum_probs=58.9
Q ss_pred CCCHHHHHHHHhhcChHHHHhcCchhhhhcccCCCCCccccccccCCCcccEEEecccchHHHHHHHHhcCCCCCCCeEE
Q 029616 55 GTPYKQMFDDLRRKDPELYKRNGILPMLKRNIGVKAAPQRWQDNALDGSFDIVFTFEEKVFDTVVEDLNTREQPFMKTVL 134 (190)
Q Consensus 55 gT~Y~~Iy~dL~~kD~~lY~~NGlL~MLdRNr~IK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVH 134 (190)
+-||...|+-|..+|+++=|=.-|+.-+ |.++ .. +.+.|=-+|+- ..|+|.+..+....+.-..
T Consensus 40 nIP~StLYKil~G~dpr~~tl~~I~kti---r~~e-------k~-en~~fiA~IAA-----R~vL~~i~~~kk~i~gk~~ 103 (170)
T COG4800 40 NIPLSTLYKILKGSDPRYDTLTRIFKTI---RSYE-------KK-ENIGFIALIAA-----RYVLEEIKFGKKGINGKSY 103 (170)
T ss_pred CCCHHHHHHHHhCCCccHHHHHHHHHHH---HHHH-------hc-cCCCeeeeeeh-----HHHHHHHHhhhccccCcee
Confidence 4599999999999999986655455443 2222 12 22235444542 6789999988877777777
Q ss_pred EEEeeccCCHHHHHhhHHHH
Q 029616 135 VINLEVKDNHEEAAIGGRLT 154 (190)
Q Consensus 135 VINvDIkDnhEeA~~Ga~~i 154 (190)
.|-.=--.+.|||.++|-.+
T Consensus 104 ~ireYpa~slEeaIvAaVrA 123 (170)
T COG4800 104 LIREYPASSLEEAIVAAVRA 123 (170)
T ss_pred EEEecccccHHHHHHHHHHh
Confidence 77777788999999987653
No 125
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=22.85 E-value=3.6e+02 Score=22.16 Aligned_cols=40 Identities=10% Similarity=0.079 Sum_probs=32.2
Q ss_pred cccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeeccC
Q 029616 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKD 142 (190)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDIkD 142 (190)
.+|.|||+.+...-.|+..|...+-...+-+-||-+|-..
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 126
>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=22.05 E-value=1e+02 Score=18.93 Aligned_cols=21 Identities=33% Similarity=0.395 Sum_probs=18.0
Q ss_pred hHHHHhHHhCCCCeeeecCCC
Q 029616 17 MEAHYLLKRHGFDVSSYGTGA 37 (190)
Q Consensus 17 MEAH~~L~k~Gf~V~SfGTGs 37 (190)
-+|...|.++||.+..-|.|.
T Consensus 11 ~~a~~~l~~~g~~~~~~~~g~ 31 (55)
T cd06576 11 EEAKKELKEAGLQPVVIGNGK 31 (55)
T ss_pred HHHHHHHHHCCCEEEEeCCCC
Confidence 368899999999998888876
No 127
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=22.02 E-value=2.2e+02 Score=26.35 Aligned_cols=64 Identities=16% Similarity=0.258 Sum_probs=41.9
Q ss_pred EEEccCCCCcchHHHHhHHhCCCC-eeeecCCCceecCCCCC----------CCCc--cccCCCCHHHHHHHHhhcChH
Q 029616 6 AMVCSSNQNRSMEAHYLLKRHGFD-VSSYGTGAHVKLPGPSL----------REPN--VYEFGTPYKQMFDDLRRKDPE 71 (190)
Q Consensus 6 AvVCaSN~NRSMEAH~~L~k~Gf~-V~SfGTGs~VkLPGps~----------dkPN--vY~FgT~Y~~Iy~dL~~kD~~ 71 (190)
-|+|+|..-.+ ...++++-|+. -.-.--|+.|-.|.--. ..++ +..||.||.+|-.-|..--.+
T Consensus 37 vVlaTGRt~~e--v~~l~~~Lgl~~p~I~eNGA~I~~p~~~~~~~~~~~~~~~~~~~~~~~lg~~y~~ir~~L~~l~~~ 113 (302)
T PRK12702 37 LVLYSLRTRAQ--LEHLCRQLRLEHPFICEDGSAIYVPEHYFPAGILDEQWQHRPPYYVCALGLPYPCLRHILQQVRQD 113 (302)
T ss_pred EEEEcCCCHHH--HHHHHHHhCCCCeEEEeCCcEEEEccccccccccccccccCCCceEEecCCCHHHHHHHHHHHHHH
Confidence 36788876664 45577777875 23334677887774322 3344 778999999999888664333
No 128
>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=21.73 E-value=2.8e+02 Score=21.78 Aligned_cols=37 Identities=16% Similarity=0.210 Sum_probs=27.0
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHh
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAI 149 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~ 149 (190)
+.+...+++++.+++..++++.++-.|.+.+.+.+.-
T Consensus 21 ~g~~~a~~~~n~~gg~~g~~v~~~~~d~~~~~~~~~~ 57 (298)
T cd06268 21 NGAELAVEEINAAGGILGRKIELVVEDTQGDPEAAAA 57 (298)
T ss_pred HHHHHHHHHHHhcCCCCCeEEEEEEecCCCCHHHHHH
Confidence 4566778888888877778888887777776665543
No 129
>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=21.68 E-value=3.1e+02 Score=21.65 Aligned_cols=61 Identities=13% Similarity=0.104 Sum_probs=42.9
Q ss_pred cccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHH------------HHhhHHHHHHHHHHHHh
Q 029616 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEE------------AAIGGRLTFDLCQEVCL 163 (190)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEe------------A~~Ga~~ileLc~~l~~ 163 (190)
.+|.|+++.......++..|...+-...+.+-||-+|=.+-.+. ..+|...+-.|.++|+.
T Consensus 177 ~~~ai~~~~d~~a~~~~~~l~~~g~~~p~di~vig~d~~~~~~~~~~~itti~~~~~~~g~~a~~~l~~~i~~ 249 (268)
T cd01575 177 DLDAVFCSNDDLALGALFECQRRGISVPEDIAIAGFGDLEIAAALPPALTTVRTPRREIGRRAAELLLARLAG 249 (268)
T ss_pred CCCEEEECCcHHHHHHHHHHHHhCCCCCcceEEEecCCchhhhccCCCceeeeCCHHHHHHHHHHHHHHHhcC
Confidence 48999999999999999999988766667788888773322221 13555566666666664
No 130
>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=21.45 E-value=2.6e+02 Score=23.28 Aligned_cols=47 Identities=23% Similarity=0.291 Sum_probs=31.7
Q ss_pred chHHHHhHHhCCCCeeeecCCCceecCCCCCCCCccccCCCCHHHHHHHH
Q 029616 16 SMEAHYLLKRHGFDVSSYGTGAHVKLPGPSLREPNVYEFGTPYKQMFDDL 65 (190)
Q Consensus 16 SMEAH~~L~k~Gf~V~SfGTGs~VkLPGps~dkPNvY~FgT~Y~~Iy~dL 65 (190)
++.+..++.+.+.++.+++.++.. +-+ ...|++|.+..++.+....+
T Consensus 81 ~~~~~~~~~~~~iP~i~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~~~ 127 (336)
T cd06326 81 TAAALPLLEEAGVPLVGPFTGASS-LRD--PPDRNVFNVRASYADEIAAI 127 (336)
T ss_pred HHHHHHHHHHcCCeEEEecCCcHH-hcC--CCCCceEEeCCChHHHHHHH
Confidence 456678889999999998766531 111 23578888887776655543
No 131
>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=21.31 E-value=1.3e+02 Score=24.96 Aligned_cols=29 Identities=21% Similarity=0.316 Sum_probs=25.0
Q ss_pred EEccCCCCcchHHHHhHHhCCCCeeeecC
Q 029616 7 MVCSSNQNRSMEAHYLLKRHGFDVSSYGT 35 (190)
Q Consensus 7 vVCaSN~NRSMEAH~~L~k~Gf~V~SfGT 35 (190)
+..++|.+.--|+-.+|...|+.|.++..
T Consensus 2 ~~aT~N~~K~~E~~~il~~~~i~v~~~~~ 30 (183)
T cd00515 2 VFATGNKGKLKEFKEILAPFGIEVVSLKD 30 (183)
T ss_pred EEECCCHHHHHHHHHHHhhcCcEEEEcCc
Confidence 46799999999999999988888877664
No 132
>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=21.27 E-value=2.4e+02 Score=23.87 Aligned_cols=44 Identities=9% Similarity=-0.032 Sum_probs=29.9
Q ss_pred cchHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHHHHHH
Q 029616 112 EKVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLTFDLC 158 (190)
Q Consensus 112 ERvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~ileLc 158 (190)
++-....+|+++.+++-..++|-++=.|-+-++++| ...+.+|.
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 356678899999999888888776666555555444 44444444
No 133
>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=21.26 E-value=2.1e+02 Score=18.33 Aligned_cols=52 Identities=12% Similarity=0.082 Sum_probs=31.3
Q ss_pred eEEEEccCCCCcc---hHHHHhHHhCCCCeeeecCC-CceecCCCCCCCCccccCCCCHHHHHHHHh
Q 029616 4 RYAMVCSSNQNRS---MEAHYLLKRHGFDVSSYGTG-AHVKLPGPSLREPNVYEFGTPYKQMFDDLR 66 (190)
Q Consensus 4 ~~AvVCaSN~NRS---MEAH~~L~k~Gf~V~SfGTG-s~VkLPGps~dkPNvY~FgT~Y~~Iy~dL~ 66 (190)
.+++|+.-..++. -+.-..|.++|.+|.....| +. +-+.|-.+.++.-+-+.
T Consensus 3 ~isvvg~~~~~~~~~~~~i~~~l~~~~I~v~~i~~~~s~-----------~~is~~v~~~~~~~~~~ 58 (66)
T cd04922 3 ILALVGDGMAGTPGVAATFFSALAKANVNIRAIAQGSSE-----------RNISAVIDEDDATKALR 58 (66)
T ss_pred EEEEECCCCCCCccHHHHHHHHHHHCCCCEEEEEecCcc-----------cEEEEEEeHHHHHHHHH
Confidence 4778887655543 23455678999999544332 22 34667777766544433
No 134
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=20.93 E-value=51 Score=36.53 Aligned_cols=88 Identities=26% Similarity=0.390 Sum_probs=64.5
Q ss_pred EEEEccCCC-CcchHHHHhHHhCCCCeeee-cCCCceecCCCCCCCCccccCC-CCHHHHHHHHhhcChHHHHhcCchhh
Q 029616 5 YAMVCSSNQ-NRSMEAHYLLKRHGFDVSSY-GTGAHVKLPGPSLREPNVYEFG-TPYKQMFDDLRRKDPELYKRNGILPM 81 (190)
Q Consensus 5 ~AvVCaSN~-NRSMEAH~~L~k~Gf~V~Sf-GTGs~VkLPGps~dkPNvY~Fg-T~Y~~Iy~dL~~kD~~lY~~NGlL~M 81 (190)
+-||=+|+. |+-||--++-- ||+|.+| |+--.-|.--.--.|||-|.-= |+|+..++|+.+ |=+.+==.=+
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 456666664 99999777654 9999885 8877777777778899999886 999999999875 2222222345
Q ss_pred hhcccCCCC-Cccccccc
Q 029616 82 LKRNIGVKA-APQRWQDN 98 (190)
Q Consensus 82 LdRNr~IK~-~PERfQ~~ 98 (190)
||--.+||- .-+|||..
T Consensus 743 LDEaqnIKnfksqrWQAl 760 (1958)
T KOG0391|consen 743 LDEAQNIKNFKSQRWQAL 760 (1958)
T ss_pred hhhhhhhcchhHHHHHHH
Confidence 777778885 45679864
No 135
>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=20.76 E-value=2.2e+02 Score=24.03 Aligned_cols=42 Identities=12% Similarity=0.164 Sum_probs=33.2
Q ss_pred chHHHHHHHHhcCCCCCCCeEEEEEeeccCCHHHHHhhHHHH
Q 029616 113 KVFDTVVEDLNTREQPFMKTVLVINLEVKDNHEEAAIGGRLT 154 (190)
Q Consensus 113 RvfD~Vvedl~~R~~~~~~pVHVINvDIkDnhEeA~~Ga~~i 154 (190)
+.....+++++..++-..+++.++-.|-+.+++.|...+..+
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 455778899999988888999999999998887776554433
No 136
>TIGR02553 SipD_IpaD_SspD type III effector protein IpaD/SipD/SspD. These proteins are found within type III secretion operons and have been shown to be secreted by that system.
Probab=20.52 E-value=67 Score=29.85 Aligned_cols=56 Identities=25% Similarity=0.249 Sum_probs=39.8
Q ss_pred hHHHHhHHhCCCCee---eecCCCceecCCCCCCCCccccCC-CCHHHHHHHHhhcChHHHHhcCchhhhhcccCCCCCc
Q 029616 17 MEAHYLLKRHGFDVS---SYGTGAHVKLPGPSLREPNVYEFG-TPYKQMFDDLRRKDPELYKRNGILPMLKRNIGVKAAP 92 (190)
Q Consensus 17 MEAH~~L~k~Gf~V~---SfGTGs~VkLPGps~dkPNvY~Fg-T~Y~~Iy~dL~~kD~~lY~~NGlL~MLdRNr~IK~~P 92 (190)
-||-.++++-|+.|. -++.| .| .|+ +||++||++|-.... +| .++.-.
T Consensus 198 ~Ea~~W~keLg~~v~~~~~~~~G-~I-------------~~dl~~i~~m~~sl~~~g~-----g~---------~~~~~~ 249 (308)
T TIGR02553 198 ADARRWRKELGLPVSCLQISDSG-VV-------------TVDPTPLIKMRDDLPPLGT-----GT---------ELEWDN 249 (308)
T ss_pred HHHHHHHHHhCCCCccccccCCC-eE-------------EeChHHHHHHHHhcCCCCC-----CC---------cccccH
Confidence 478899999999887 57777 55 344 699999999965432 12 345566
Q ss_pred cccccccC
Q 029616 93 QRWQDNAL 100 (190)
Q Consensus 93 ERfQ~~~~ 100 (190)
.+||.|..
T Consensus 250 A~YQAWqA 257 (308)
T TIGR02553 250 AKYQAWQS 257 (308)
T ss_pred HHHHHHHH
Confidence 78888753
No 137
>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor
Probab=20.52 E-value=4.3e+02 Score=21.02 Aligned_cols=40 Identities=10% Similarity=0.031 Sum_probs=33.4
Q ss_pred cccEEEecccchHHHHHHHHhcCCCCCCCeEEEEEeeccC
Q 029616 103 SFDIVFTFEEKVFDTVVEDLNTREQPFMKTVLVINLEVKD 142 (190)
Q Consensus 103 ~fDvIiTcEERvfD~Vvedl~~R~~~~~~pVHVINvDIkD 142 (190)
.+|.|+|+.....-.++..+...+-...+.+-|+-+|-.+
T Consensus 172 ~~~ai~~~~d~~a~~~~~~l~~~g~~vp~dv~vvg~d~~~ 211 (261)
T cd06272 172 LPTAIICGSYDIALGVLSALNKQGISIPEDIEIISYDNIP 211 (261)
T ss_pred CCCEEEECCcHHHHHHHHHHHHhCCCCCCceEEEeeCChh
Confidence 4899999999999999999988876666788888888654
No 138
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=20.42 E-value=57 Score=18.30 Aligned_cols=13 Identities=31% Similarity=0.708 Sum_probs=10.3
Q ss_pred HHHHHhhhhcccc
Q 029616 168 IVSLVYHLKHHCT 180 (190)
Q Consensus 168 ~~~~~~~~~~~~~ 180 (190)
...|..|++.||.
T Consensus 14 ~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 14 LSALREHKRSHCS 26 (27)
T ss_dssp HHHHHHHHCTTTT
T ss_pred hhHHHHHhHHhcC
Confidence 4578899999984
No 139
>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=20.35 E-value=1.2e+02 Score=24.38 Aligned_cols=25 Identities=12% Similarity=0.187 Sum_probs=19.9
Q ss_pred EEEEccCCCCcchHHHHhHHhCCCCee
Q 029616 5 YAMVCSSNQNRSMEAHYLLKRHGFDVS 31 (190)
Q Consensus 5 ~AvVCaSN~NRSMEAH~~L~k~Gf~V~ 31 (190)
-|++|++.. .+-+.+.|+++|+++-
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 9999999999998643
No 140
>cd06392 PBP1_iGluR_delta_1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 may be closer related to non-NMDA receptors. In contrast to GluRdelta2, GluRdel
Probab=20.35 E-value=1.2e+02 Score=28.19 Aligned_cols=46 Identities=17% Similarity=0.245 Sum_probs=28.0
Q ss_pred ccchHHHHHHHHhcCCCCCCCeEEEEEeec-cCCHHHHHhhHHHHHHHH
Q 029616 111 EEKVFDTVVEDLNTREQPFMKTVLVINLEV-KDNHEEAAIGGRLTFDLC 158 (190)
Q Consensus 111 EERvfD~Vvedl~~R~~~~~~pVHVINvDI-kDnhEeA~~Ga~~ileLc 158 (190)
+|+.|..-|++++.......+ +=++++| .|+..+.-.|++.+|+|-
T Consensus 13 ~~~af~~Av~~~N~~~~~l~~--~~L~~~~~~~~~~d~F~~~~~ac~l~ 59 (400)
T cd06392 13 DDRVFQLAVSDLSLNDDILQS--EKITYSIKSIEANNPFQAVQEACDLM 59 (400)
T ss_pred HHHHHHHHHHHhccCccccCC--ceEEEEEEecCCCChhHHHHHHHHHH
Confidence 789999999999964422111 1233444 445555666667666554
No 141
>cd01443 Cdc25_Acr2p Cdc25 enzymes are members of the Rhodanese Homology Domain (RHOD) superfamily. Also included in this CD are eukaryotic arsenate resistance proteins such as Saccharomyces cerevisiae Acr2p and similar proteins. Cdc25 phosphatases 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. The Cdc25 and Acr2p RHOD domains have the signature motif (H/YCxxxxxR).
Probab=20.19 E-value=1.6e+02 Score=21.54 Aligned_cols=25 Identities=24% Similarity=0.276 Sum_probs=18.1
Q ss_pred eEEEEccCCCCcchHHHHhHH----hCCC
Q 029616 4 RYAMVCSSNQNRSMEAHYLLK----RHGF 28 (190)
Q Consensus 4 ~~AvVCaSN~NRSMEAH~~L~----k~Gf 28 (190)
.+-++|.+...||..|=..|. +.||
T Consensus 68 ~iv~~C~~~g~rs~~a~~~l~~~l~~~G~ 96 (113)
T cd01443 68 LAIFYCGSSQGRGPRAARWFADYLRKVGE 96 (113)
T ss_pred EEEEECCCCCcccHHHHHHHHHHHhccCC
Confidence 477889988899977655544 4576
Done!