Query psy9210
Match_columns 234
No_of_seqs 108 out of 187
Neff 2.5
Searched_HMMs 46136
Date Fri Aug 16 21:43:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9210.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9210hhsearch_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 4E-105 8E-110 684.5 16.1 190 4-234 1-195 (195)
2 KOG2424|consensus 100.0 3.8E-98 8E-103 640.6 18.8 192 2-234 3-195 (195)
3 COG5211 SSU72 RNA polymerase I 100.0 6.4E-83 1.4E-87 543.8 18.1 191 3-234 5-197 (197)
4 COG0394 Wzb Protein-tyrosine-p 96.4 0.026 5.7E-07 46.0 8.9 38 4-41 2-42 (139)
5 PRK13530 arsenate reductase; P 95.5 0.063 1.4E-06 42.8 6.9 98 4-116 3-130 (133)
6 TIGR02691 arsC_pI258_fam arsen 95.2 0.054 1.2E-06 43.0 5.8 89 7-110 1-125 (129)
7 PRK11391 etp phosphotyrosine-p 93.7 0.072 1.6E-06 43.0 3.4 37 5-41 3-41 (144)
8 PF01451 LMWPc: Low molecular 93.0 0.089 1.9E-06 40.6 2.8 35 7-41 1-42 (138)
9 PRK10126 tyrosine phosphatase; 92.9 0.096 2.1E-06 42.0 3.0 37 5-41 3-41 (147)
10 TIGR02689 ars_reduc_gluta arse 90.6 0.21 4.5E-06 39.0 2.4 34 5-38 1-37 (126)
11 cd01523 RHOD_Lact_B Member of 89.2 0.72 1.6E-05 33.4 4.2 35 4-39 61-95 (100)
12 cd00115 LMWPc Substituted upda 88.5 0.44 9.6E-06 37.3 2.8 35 5-39 1-39 (141)
13 smart00226 LMWPc Low molecular 88.4 0.31 6.7E-06 37.8 2.0 33 7-39 1-36 (140)
14 COG0607 PspE Rhodanese-related 85.4 1.5 3.2E-05 31.5 4.0 31 2-33 59-89 (110)
15 PLN02160 thiosulfate sulfurtra 83.9 1.4 3.1E-05 35.1 3.6 34 4-38 81-115 (136)
16 cd01534 4RHOD_Repeat_3 Member 81.9 2.1 4.6E-05 30.9 3.6 33 5-38 57-89 (95)
17 cd01447 Polysulfide_ST Polysul 79.5 2.3 5E-05 30.3 3.1 34 4-38 61-95 (103)
18 cd01518 RHOD_YceA Member of th 78.8 2.8 6.1E-05 30.5 3.4 34 4-38 61-95 (101)
19 cd01521 RHOD_PspE2 Member of t 74.1 6.8 0.00015 29.2 4.4 37 2-38 62-99 (110)
20 TIGR03746 conj_TIGR03746 integ 73.9 3.1 6.7E-05 37.3 2.9 71 104-182 101-180 (202)
21 cd01526 RHOD_ThiF Member of th 73.8 5 0.00011 30.5 3.7 34 4-38 72-107 (122)
22 cd01533 4RHOD_Repeat_2 Member 73.2 5.2 0.00011 29.6 3.6 34 5-39 67-102 (109)
23 PF13399 LytR_C: LytR cell env 70.9 13 0.00029 27.0 5.2 40 2-41 1-41 (90)
24 TIGR02981 phageshock_pspE phag 70.5 6.7 0.00015 30.1 3.7 31 4-35 58-89 (101)
25 PRK00162 glpE thiosulfate sulf 70.0 8.3 0.00018 28.5 4.0 34 4-38 58-92 (108)
26 cd01520 RHOD_YbbB Member of th 69.8 9.2 0.0002 29.5 4.4 36 4-39 86-121 (128)
27 cd01524 RHOD_Pyr_redox Member 68.8 9.4 0.0002 27.2 4.0 34 4-38 51-84 (90)
28 cd01529 4RHOD_Repeats Member o 66.8 9.5 0.0002 27.5 3.7 35 3-38 55-90 (96)
29 TIGR00725 conserved hypothetic 66.6 7.9 0.00017 32.1 3.7 36 5-41 2-42 (159)
30 PRK08395 fumarate hydratase; P 66.2 8.1 0.00017 33.4 3.7 63 20-128 33-95 (162)
31 cd01528 RHOD_2 Member of the R 66.1 12 0.00026 27.2 4.1 34 4-38 58-92 (101)
32 cd01444 GlpE_ST GlpE sulfurtra 65.4 12 0.00027 26.3 4.0 33 2-35 54-87 (96)
33 cd01519 RHOD_HSP67B2 Member of 65.0 9.5 0.00021 27.5 3.4 32 4-36 66-98 (106)
34 cd01449 TST_Repeat_2 Thiosulfa 64.6 7.7 0.00017 28.6 2.9 32 4-36 78-110 (118)
35 smart00450 RHOD Rhodanese Homo 63.1 17 0.00037 24.6 4.2 35 3-38 55-90 (100)
36 PRK01415 hypothetical protein; 62.1 8.6 0.00019 34.6 3.3 35 3-38 170-205 (247)
37 PRK10287 thiosulfate:cyanide s 60.7 11 0.00023 29.2 3.2 29 5-34 61-90 (104)
38 PRK05320 rhodanese superfamily 60.4 9.6 0.00021 34.0 3.3 57 4-74 175-232 (257)
39 cd01527 RHOD_YgaP Member of th 60.1 18 0.00039 26.0 4.1 35 3-38 53-88 (99)
40 cd01448 TST_Repeat_1 Thiosulfa 58.9 21 0.00046 26.6 4.5 35 4-38 79-114 (122)
41 PF02302 PTS_IIB: PTS system, 57.0 13 0.00028 26.6 2.9 33 6-38 1-37 (90)
42 PRK10310 PTS system galactitol 55.3 14 0.00031 28.1 3.1 30 4-33 2-35 (94)
43 cd01525 RHOD_Kc Member of the 52.0 25 0.00054 25.3 3.7 34 4-38 65-99 (105)
44 PRK08228 L(+)-tartrate dehydra 47.5 27 0.00059 31.3 4.0 76 20-139 36-118 (204)
45 TIGR00723 ttdB_fumA_fumB hydro 47.4 21 0.00045 31.0 3.2 68 20-127 24-94 (168)
46 PF11823 DUF3343: Protein of u 45.1 27 0.00058 25.1 3.0 42 9-59 5-46 (73)
47 cd06331 PBP1_AmiC_like Type I 43.8 85 0.0018 26.9 6.3 41 152-193 20-60 (333)
48 COG1011 Predicted hydrolase (H 43.5 35 0.00077 27.4 3.8 46 141-195 138-191 (229)
49 KOG1530|consensus 43.3 26 0.00056 30.0 3.0 30 6-36 91-121 (136)
50 cd01144 BtuF Cobalamin binding 43.1 1.7E+02 0.0037 24.0 7.8 70 143-223 57-129 (245)
51 cd01530 Cdc25 Cdc25 phosphatas 42.8 42 0.0009 26.0 3.9 25 4-28 68-92 (121)
52 TIGR03292 PhnH_redo phosphonat 41.5 24 0.00053 30.5 2.7 14 81-94 120-133 (174)
53 PRK00142 putative rhodanese-re 41.2 30 0.00066 31.7 3.4 34 4-38 171-205 (314)
54 cd05563 PTS_IIB_ascorbate PTS_ 41.1 24 0.00052 25.3 2.2 26 6-31 1-30 (86)
55 COG3414 SgaB Phosphotransferas 40.3 35 0.00075 26.7 3.2 26 5-30 2-31 (93)
56 smart00393 R3H Putative single 39.8 36 0.00079 24.8 3.0 23 19-41 50-72 (79)
57 COG0473 LeuB Isocitrate/isopro 38.7 65 0.0014 31.2 5.3 116 85-218 178-320 (348)
58 PRK06043 fumarate hydratase; P 38.3 35 0.00075 30.4 3.2 69 20-129 35-108 (192)
59 cd02325 R3H R3H domain. The na 38.0 45 0.00097 21.3 3.0 23 19-41 31-53 (59)
60 PRK14329 (dimethylallyl)adenos 37.6 46 0.00099 31.8 4.1 48 3-57 22-72 (467)
61 PRK10147 phnH carbon-phosphoru 36.2 32 0.0007 30.3 2.7 15 81-95 138-152 (196)
62 cd05566 PTS_IIB_galactitol PTS 35.8 33 0.00072 24.7 2.3 28 5-32 1-32 (89)
63 PRK14326 (dimethylallyl)adenos 35.1 51 0.0011 32.0 4.1 49 2-57 11-62 (502)
64 COG0614 FepB ABC-type Fe3+-hyd 34.7 2E+02 0.0043 24.2 7.1 71 143-223 115-186 (319)
65 PRK08762 molybdopterin biosynt 34.1 57 0.0012 30.1 4.0 34 4-38 57-91 (376)
66 cd01391 Periplasmic_Binding_Pr 33.9 2.1E+02 0.0046 21.7 10.1 40 143-184 182-221 (269)
67 cd01574 PBP1_LacI Ligand-bindi 33.1 1.5E+02 0.0031 23.9 5.8 37 144-181 175-211 (264)
68 cd00158 RHOD Rhodanese Homolog 32.6 67 0.0014 21.6 3.3 32 3-35 49-81 (89)
69 TIGR03167 tRNA_sel_U_synt tRNA 32.3 58 0.0013 30.0 3.8 35 5-39 75-109 (311)
70 PRK11784 tRNA 2-selenouridine 32.2 62 0.0013 30.3 4.0 44 4-50 88-131 (345)
71 cd02645 R3H_AAA R3H domain of 30.7 56 0.0012 23.8 2.7 21 21-41 34-54 (60)
72 KOG3085|consensus 30.7 17 0.00037 32.8 0.1 109 100-231 118-234 (237)
73 cd06356 PBP1_Amide_Urea_BP_lik 30.3 1.4E+02 0.0029 26.0 5.5 41 153-194 21-61 (334)
74 COG4747 ACT domain-containing 30.1 35 0.00075 29.4 1.8 20 15-34 49-68 (142)
75 cd04918 ACT_AK1-AT_2 ACT domai 29.9 1.1E+02 0.0024 21.1 4.0 35 6-40 3-41 (65)
76 PRK03379 vitamin B12-transport 29.5 2.9E+02 0.0062 23.7 7.3 69 143-222 72-143 (260)
77 PF08885 GSCFA: GSCFA family; 29.4 51 0.0011 29.8 2.9 60 20-109 94-156 (251)
78 PF03698 UPF0180: Uncharacteri 28.8 71 0.0015 24.8 3.2 20 20-39 12-31 (80)
79 KOG2424|consensus 28.6 42 0.00092 30.2 2.2 38 4-41 8-45 (195)
80 cd01736 LSm14_N LSm14 (also kn 28.3 45 0.00097 25.8 2.0 27 8-41 21-47 (74)
81 COG1794 RacX Aspartate racemas 28.2 83 0.0018 28.9 4.0 78 154-231 18-105 (230)
82 cd05565 PTS_IIB_lactose PTS_II 27.8 80 0.0017 24.8 3.4 29 5-33 1-32 (99)
83 cd06346 PBP1_ABC_ligand_bindin 27.2 1.5E+02 0.0033 25.3 5.2 40 152-192 20-59 (312)
84 cd06392 PBP1_iGluR_delta_1 N-t 26.8 78 0.0017 30.0 3.7 74 151-229 13-91 (400)
85 cd01141 TroA_d Periplasmic bin 26.7 3E+02 0.0065 21.8 6.5 70 143-223 69-144 (186)
86 PRK07188 nicotinate phosphorib 26.7 79 0.0017 30.0 3.7 38 6-45 280-317 (352)
87 COG1838 FumA Tartrate dehydrat 26.1 56 0.0012 29.2 2.5 83 20-142 34-118 (184)
88 PRK01175 phosphoribosylformylg 26.0 1.3E+02 0.0028 27.1 4.8 34 4-37 3-36 (261)
89 cd06344 PBP1_ABC_ligand_bindin 25.8 1.6E+02 0.0035 25.2 5.2 40 154-194 21-60 (332)
90 cd06354 PBP1_BmpA_PnrA_like Pe 25.6 91 0.002 26.0 3.5 33 8-41 186-218 (265)
91 cd00636 TroA-like Helical back 25.6 2.5E+02 0.0053 19.8 7.2 76 143-224 61-136 (148)
92 TIGR00730 conserved hypothetic 25.6 74 0.0016 27.0 3.0 31 6-36 2-39 (178)
93 cd06355 PBP1_FmdD_like Peripla 25.5 1.9E+02 0.0041 25.3 5.6 42 153-195 21-62 (348)
94 PLN00123 isocitrate dehydrogen 24.8 1.3E+02 0.0027 29.1 4.7 118 85-218 190-334 (360)
95 PRK14333 (dimethylallyl)adenos 24.3 91 0.002 29.5 3.6 48 3-57 5-55 (448)
96 COG4551 Predicted protein tyro 24.2 73 0.0016 26.4 2.6 37 5-41 2-39 (109)
97 PRK09548 PTS system ascorbate- 24.2 75 0.0016 32.6 3.3 30 3-32 505-538 (602)
98 cd00133 PTS_IIB PTS_IIB: subun 23.7 62 0.0013 21.6 1.8 25 6-30 1-29 (84)
99 PF05845 PhnH: Bacterial phosp 23.7 40 0.00087 29.4 1.1 16 81-96 135-150 (192)
100 cd06335 PBP1_ABC_ligand_bindin 23.5 1.6E+02 0.0036 25.6 4.8 74 153-229 21-96 (347)
101 cd06343 PBP1_ABC_ligand_bindin 23.4 2.5E+02 0.0053 24.3 5.8 41 152-193 27-67 (362)
102 cd01522 RHOD_1 Member of the R 22.9 1.6E+02 0.0036 22.3 4.2 34 4-38 64-98 (117)
103 cd05567 PTS_IIB_mannitol PTS_I 22.9 85 0.0018 23.0 2.6 25 6-30 2-30 (87)
104 COG1598 Predicted nuclease of 22.6 1.6E+02 0.0036 21.5 4.0 48 87-140 21-68 (73)
105 PF01424 R3H: R3H domain; Int 22.5 98 0.0021 21.2 2.7 28 14-41 29-56 (63)
106 cd06296 PBP1_CatR_like Ligand- 22.2 3.2E+02 0.007 22.0 6.0 41 142-183 177-217 (270)
107 cd06366 PBP1_GABAb_receptor Li 22.1 2E+02 0.0042 24.8 5.0 72 152-229 18-95 (350)
108 KOG3217|consensus 21.8 90 0.002 27.4 2.8 96 4-167 6-109 (159)
109 PF13458 Peripla_BP_6: Peripla 21.6 2.3E+02 0.005 23.8 5.2 36 153-189 23-58 (343)
110 cd04509 PBP1_ABC_transporter_G 21.4 3.7E+02 0.008 21.3 6.0 75 152-229 20-96 (299)
111 PRK14862 rimO ribosomal protei 21.3 1.3E+02 0.0028 28.6 4.0 48 3-57 6-56 (440)
112 cd06328 PBP1_SBP_like_2 Peripl 21.1 2.4E+02 0.0053 24.4 5.4 43 153-195 21-63 (333)
113 TIGR03407 urea_ABC_UrtA urea A 21.0 2.6E+02 0.0057 24.7 5.6 43 153-196 22-64 (359)
114 cd06357 PBP1_AmiC Periplasmic 21.0 2.4E+02 0.0051 25.0 5.4 44 152-196 20-63 (360)
115 cd01443 Cdc25_Acr2p Cdc25 enzy 20.9 1.6E+02 0.0035 21.9 3.8 34 5-38 67-107 (113)
116 cd06293 PBP1_LacI_like_11 Liga 20.9 1.8E+02 0.0039 23.6 4.3 39 142-181 176-214 (269)
117 PF13361 UvrD_C: UvrD-like hel 20.8 1.1E+02 0.0025 25.4 3.2 34 5-39 78-111 (351)
118 cd01535 4RHOD_Repeat_4 Member 20.6 1.6E+02 0.0034 23.8 3.9 37 2-39 47-84 (145)
119 TIGR01578 MiaB-like-B MiaB-lik 20.6 78 0.0017 29.7 2.4 41 11-58 9-49 (420)
120 cd01575 PBP1_GntR Ligand-bindi 20.5 3.6E+02 0.0078 21.6 5.8 39 142-181 176-214 (268)
121 cd02640 R3H_NRF R3H domain of 20.2 81 0.0018 22.9 1.9 21 20-40 33-53 (60)
122 cd00861 ProRS_anticodon_short 20.1 1.6E+02 0.0034 20.8 3.4 41 5-45 2-47 (94)
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=3.7e-105 Score=684.47 Aligned_cols=190 Identities=63% Similarity=1.041 Sum_probs=168.3
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCceeeccCCCCCCccccceeeeeccccccccccccccceeeeeeecccccccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVFVFQISVNLFFQSIT 83 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lP 83 (234)
+||||||||||||||||||++|+|+||+|+|||||++| |||
T Consensus 1 ~l~~avVCasN~NRSMEAH~~L~~~G~~V~SfGTGs~V---------------------------------------kLP 41 (195)
T PF04722_consen 1 KLRFAVVCASNQNRSMEAHNVLKKAGFNVRSFGTGSHV---------------------------------------KLP 41 (195)
T ss_dssp -SEEEEEESSSSSHHHHHHHHHHHTT-EEEEEE-SSSE---------------------------------------EEE
T ss_pred CceEEEEccCCCCcCHHHHHHHHHCCCceEeecCCCcc---------------------------------------cCC
Confidence 58999999999999999999999999999999999999 999
Q ss_pred CCCCCCCceecCCCCcHHHHHHHHHhccHHHHhhcchhhhhhhcccCcCCCccccccCCC--ccEEEEecchhHHHHHHh
Q psy9210 84 GTAMDKPNVYDFHTTTYEDIYQDLMNKDKAFYTRNGLLHMLERNKRIKLKPEKFQESKDK--FDIIITCEERVYDQVLEH 161 (234)
Q Consensus 84 G~a~dkPNvY~F~~TtY~~Iy~dL~~kD~~~Yt~NGlL~MLdRN~rIK~~PErfQe~~~~--fDvIiTcEERvyD~V~Ed 161 (234)
|||+|+||||+|| |||++||+||++||++|||+||||+||+||++||++|||||++++. |||||||||||||+|+||
T Consensus 42 Gps~d~PnvY~Fg-T~Y~~iy~dL~~kd~~lY~~NGlL~ML~RN~~iK~~PERfQ~~~~~~~fDvIiTcEERvfD~Vved 120 (195)
T PF04722_consen 42 GPSIDKPNVYDFG-TPYDDIYNDLLRKDKELYTQNGLLHMLDRNRRIKPAPERFQDCKEKGKFDVIITCEERVFDQVVED 120 (195)
T ss_dssp ESSTTCEEEE-TT-S-HHHHHHHHHHHHHHHHHHTSHHHHHHHHHCH-SS--BGGG-------SEEEESSHHHHHHHHHH
T ss_pred CCCCCCCcccCCC-CcHHHHHHHHHHhCHHHHHHcCcHHHHhcCccccCCccchhcCCCCcceeEEEEechHHHHHHHHH
Confidence 9999999999999 9999999999999999999999999999999999999999999998 999999999999999999
Q ss_pred HhhhcccCCCceeEEEEeecCCCHHHHhhhHHHHHHHHHHhh--cchhhHHHHHHHHHHHHHHc-CCCceeeeccC
Q psy9210 162 FDNQMISLENTPVHLINIDIQDNQEEATLGAFLASELMSMFI--KCEDLDNEIDEIMQEFEEKC-SRPLLHTILFY 234 (234)
Q Consensus 162 l~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~eL~~~l~--~~eDld~~ideil~~feek~-~r~~Lhtv~fY 234 (234)
|.+ |++.+++|||||||||+||||||++||++||+||++|+ +++|||++|++||++||+|+ ++|+|||||||
T Consensus 121 l~~-R~~~~~~pvHVINvDIkDnhEeA~~Ga~~ileLc~~l~~~~~~d~e~~i~~il~~fe~k~p~~~~Lhtv~fY 195 (195)
T PF04722_consen 121 LNS-REQETNQPVHVINVDIKDNHEEATIGAFLILELCQMLEEEASEDLEDEIDEILQEFEEKHPGRPLLHTVCFY 195 (195)
T ss_dssp HHC-S--SS-EEEEEEEE---SSHHHHHHHHHHHHHHHHHHH--TSSSHHHHHHHHHHHHHHHH-T--EEEEEEEE
T ss_pred HHh-ccccCCceEEEEEeeccCCHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHcCCCCceEEEecC
Confidence 999 99999999999999999999999999999999999999 99999999999999999999 89999999998
No 2
>KOG2424|consensus
Probab=100.00 E-value=3.8e-98 Score=640.56 Aligned_cols=192 Identities=59% Similarity=0.988 Sum_probs=190.6
Q ss_pred CCCceEEEEecCCCccchHHHHHHhhCCCceeeccCCCCCCccccceeeeeccccccccccccccceeeeeeeccccccc
Q psy9210 2 PSNLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVFVFQISVNLFFQS 81 (234)
Q Consensus 2 ~s~lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (234)
+++||+|||||||||||||||.+|+++|++|+|||||++| |
T Consensus 3 ~~~l~~avvC~sN~NRSMeaH~~L~~~G~~v~S~GTg~~v---------------------------------------k 43 (195)
T KOG2424|consen 3 SSNLRVAVVCASNQNRSMEAHNILKKKGLNVRSFGTGSHV---------------------------------------K 43 (195)
T ss_pred CccceeeeeehhcccchHHHHHHHHHcCCcceeecCCCce---------------------------------------e
Confidence 6789999999999999999999999999999999999999 9
Q ss_pred CCCCCCCCCceecCCCCcHHHHHHHHHhccHHHHhhcchhhhhhhcccCcCCCccccccCCCccEEEEecchhHHHHHHh
Q psy9210 82 ITGTAMDKPNVYDFHTTTYEDIYQDLMNKDKAFYTRNGLLHMLERNKRIKLKPEKFQESKDKFDIIITCEERVYDQVLEH 161 (234)
Q Consensus 82 lPG~a~dkPNvY~F~~TtY~~Iy~dL~~kD~~~Yt~NGlL~MLdRN~rIK~~PErfQe~~~~fDvIiTcEERvyD~V~Ed 161 (234)
||||++||||||+|| |||++||+||.+||+++||+|||||||+||||||++|||||++++.|||||||||||||+|+||
T Consensus 44 lPG~~~dkPNvY~Fg-t~Y~~iy~dL~~kd~~~Y~~nGiL~mldRNrriK~~Per~q~~t~~FDvV~TcEErvyD~VvEd 122 (195)
T KOG2424|consen 44 LPGPSPDKPNVYDFG-TTYKQIYNDLLRKDRELYTRNGILHMLDRNRRIKPAPERFQECTEVFDVVFTCEERVFDSVVED 122 (195)
T ss_pred CCCCCCCCCCccccC-CcHHHHHHHHHhhhHHHHhhcccchhhhcccccccCCcchhhccccceEEEEehhHHHHHHHHH
Confidence 999999999999999 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcccCCCceeEEEEeecCCCHHHHhhhHHHHHHHHHHhh-cchhhHHHHHHHHHHHHHHcCCCceeeeccC
Q psy9210 162 FDNQMISLENTPVHLINIDIQDNQEEATLGAFLASELMSMFI-KCEDLDNEIDEIMQEFEEKCSRPLLHTILFY 234 (234)
Q Consensus 162 l~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~eL~~~l~-~~eDld~~ideil~~feek~~r~~Lhtv~fY 234 (234)
|.+ |++.+++||||||+|||||+|||++|||+|||||++|+ +++|||+.||+||++|||++|+++|||||||
T Consensus 123 l~~-re~~~~qpVhviN~DI~Dn~EdA~~Gaf~I~elcq~l~~~s~d~Ed~ideil~~~ee~~~~~~Lhtv~fy 195 (195)
T KOG2424|consen 123 LNS-REQSLNQPVHVINVDIKDNHEDATLGAFLILELCQCLQAQSDDLEDNIDEILLEFEEKHGRSLLHTVCFY 195 (195)
T ss_pred HHh-cccccCCceEEEEeecccCHHhhhhhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhcCCeeEEeeecC
Confidence 999 99999999999999999999999999999999999999 9999999999999999999999999999998
No 3
>COG5211 SSU72 RNA polymerase II-interacting protein involved in transcription start site selection [Transcription]
Probab=100.00 E-value=6.4e-83 Score=543.80 Aligned_cols=191 Identities=43% Similarity=0.734 Sum_probs=187.1
Q ss_pred CCceEEEEecCCCccchHHHHHHhhCCCceeeccCCCCCCccccceeeeeccccccccccccccceeeeeeecccccccC
Q psy9210 3 SNLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVFVFQISVNLFFQSI 82 (234)
Q Consensus 3 s~lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 82 (234)
++||+||+||||||||||+|.+|+++|++|+|||||++| ||
T Consensus 5 ~nlk~~v~CAsNqNRSMetH~vL~~aGy~V~SfGTgsav---------------------------------------rL 45 (197)
T COG5211 5 PNLKLAVTCASNQNRSMETHDVLAKAGYPVKSFGTGSAV---------------------------------------RL 45 (197)
T ss_pred CCceEEeeeccCCCcchHHHHHHHHcCCcccccCCCcce---------------------------------------eC
Confidence 589999999999999999999999999999999999999 99
Q ss_pred CCCCCCCCceecCCCCcHHHHHHHHHhccHHHHhhcchhhhhhhcccCcCCCccccccCCCccEEEEecchhHHHHHHhH
Q psy9210 83 TGTAMDKPNVYDFHTTTYEDIYQDLMNKDKAFYTRNGLLHMLERNKRIKLKPEKFQESKDKFDIIITCEERVYDQVLEHF 162 (234)
Q Consensus 83 PG~a~dkPNvY~F~~TtY~~Iy~dL~~kD~~~Yt~NGlL~MLdRN~rIK~~PErfQe~~~~fDvIiTcEERvyD~V~Edl 162 (234)
||++|||||||.|| +||++||+||..|+.+.|+.||||.|||||||||.+|||||+....||+||||||||||+|+||+
T Consensus 46 PG~siDKPNvY~FG-~pY~~IY~dL~~q~~d~Y~~nGlL~mLdRNrrvK~aPe~wq~~~~~fd~ViTCEERcfdaicEdl 124 (197)
T COG5211 46 PGESIDKPNVYNFG-VPYQQIYDDLCMQNEDHYRENGLLYMLDRNRRVKEAPENWQQRSEDFDLVITCEERCFDAICEDL 124 (197)
T ss_pred CCCCCCCCCeeecC-CcHHHHHHHHHhhhhhhhhhccHHHHHHhcchhhhCchhhhhccccccEEEEehHHHHHHHHHHH
Confidence 99999999999999 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcccCCCceeEEEEeecCCCHHHHhhhHHHHHHHHHHhhcchh-hHHHHHHHHHHHHHHc-CCCceeeeccC
Q psy9210 163 DNQMISLENTPVHLINIDIQDNQEEATLGAFLASELMSMFIKCED-LDNEIDEIMQEFEEKC-SRPLLHTILFY 234 (234)
Q Consensus 163 ~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~eL~~~l~~~eD-ld~~ideil~~feek~-~r~~Lhtv~fY 234 (234)
.+ |++..|++||+||+||+|++|+|.+||++|+||+.+|.+.++ ||.-++.||.+|++.+ |.|+|+|+.||
T Consensus 125 y~-rg~~ln~~v~~iNvDIkD~~e~A~~G~kaILelvd~L~~~~e~lE~~~~sil~~~qsnh~~lp~Lyt~~~~ 197 (197)
T COG5211 125 YA-RGPSLNQCVFMINVDIKDTPEDAIAGAKAILELVDVLAKEEERLEYAVDSILRRYQSNHKGLPLLYTVVNL 197 (197)
T ss_pred Hh-cCccccccEEEEEeeccCChhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEEeeccC
Confidence 99 999999999999999999999999999999999999988765 9999999999999977 99999999987
No 4
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=96.44 E-value=0.026 Score=45.95 Aligned_cols=38 Identities=42% Similarity=0.558 Sum_probs=33.5
Q ss_pred CceEEEEecCCCccchHHHHHHhhC---CCceeeccCCCCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKK---GVDVKSFGTGDKK 41 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~---G~~V~SfGTG~~v 41 (234)
..||.+||..|-=||=-|-+++++. ++.|.|-|||.++
T Consensus 2 ~~kVLFVC~gN~cRSpmAE~l~~~~~~~~~~v~SAGt~~~~ 42 (139)
T COG0394 2 MMKVLFVCTGNICRSPMAEALLRHLAPDNVEVDSAGTGGHP 42 (139)
T ss_pred CceEEEEcCCCcccCHHHHHHHHHhccCCeEEECCccCCCC
Confidence 3799999999999999999998875 7999999999743
No 5
>PRK13530 arsenate reductase; Provisional
Probab=95.48 E-value=0.063 Score=42.80 Aligned_cols=98 Identities=16% Similarity=0.272 Sum_probs=64.3
Q ss_pred CceEEEEecCCCccchHHHHHHhh---CCCceeeccCCC--------------------CCCcccc-------ceeeeec
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSK---KGVDVKSFGTGD--------------------KKPQQWE-------SVVIFHC 53 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k---~G~~V~SfGTG~--------------------~v~~~~~-------~~~~~~~ 53 (234)
+.||-.||..|--||--|.+++++ .++.|.|-||.. +.|+|+. .+||--|
T Consensus 3 ~~~vLFvC~~N~cRS~mAEal~~~~~~~~~~v~SAG~~~~~~~~~a~~~l~e~Gi~~~~~~s~~l~~~~~~~~D~ii~m~ 82 (133)
T PRK13530 3 KKTIYFLCTGNSCRSQMAEGWGKQYLGDKWNVYSAGIEAHGVNPNAIKAMKEVGIDISNQTSDIIDNDILNNADLVVTLC 82 (133)
T ss_pred CCEEEEEcCCchhHHHHHHHHHHHhcCCCEEEECCCCCCCCCCHHHHHHHHHcCCCcCCCccccCChhHhccCCEEEEec
Confidence 679999999999999999999986 357889999832 3445543 3444444
Q ss_pred cccccccccccccceeeeeeecccccccCCCCCCCCCceecCCCCcHHHHHHHHHhccHHHHh
Q psy9210 54 CDFCSELIPLFFHKVFVFQISVNLFFQSITGTAMDKPNVYDFHTTTYEDIYQDLMNKDKAFYT 116 (234)
Q Consensus 54 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lPG~a~dkPNvY~F~~TtY~~Iy~dL~~kD~~~Yt 116 (234)
+--.++.|.+..++.... + . ++.| |.=+...|+++|+++.+.=+.|..
T Consensus 83 -~~~~~~~~~~p~~~~~~~------w-~-----i~DP--~~~~~~~f~~~~~~I~~~v~~l~~ 130 (133)
T PRK13530 83 -SHADDVCPSTPPHVKRVH------W-G-----FDDP--AGKEWSEFQRVRDEIGERIKRFAE 130 (133)
T ss_pred -hHhhhhccccCCCceEEE------C-C-----CCCC--CCCcHHHHHHHHHHHHHHHHHHHH
Confidence 544677787765443221 1 2 3334 322235788999888877666644
No 6
>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=95.23 E-value=0.054 Score=42.97 Aligned_cols=89 Identities=17% Similarity=0.244 Sum_probs=57.8
Q ss_pred EEEEecCCCccchHHHHHHhh---CCCceeeccCC-C-------------------CCCcccc-------ceeeeecccc
Q psy9210 7 VAVVCSSNMNRSMEAHAYLSK---KGVDVKSFGTG-D-------------------KKPQQWE-------SVVIFHCCDF 56 (234)
Q Consensus 7 ~AvVCsSN~NRSMEAH~~L~k---~G~~V~SfGTG-~-------------------~v~~~~~-------~~~~~~~~~~ 56 (234)
|-.||..|.-||--|.+++++ .++.|.|-||. . +.|+|+. .+||--| +-
T Consensus 1 iLFvC~~N~~RS~mAea~~~~~~~~~~~v~SaG~~~~~~~~~a~~~l~e~Gid~~~~~~~~l~~~~~~~~D~vitm~-~~ 79 (129)
T TIGR02691 1 IYFLCTGNSCRSQMAEGWGKKYLGDEWEVYSAGIEAHGLNPNAVKAMKEVGIDISNQTSDLIDLDILNKADLVVTLC-GD 79 (129)
T ss_pred CEEEcCCchHHHHHHHHHHHHhcCCCEEEEcCCCCCCCcCHHHHHHHHHcCCCcCCcccccCChhhcccCCEEEEeC-ch
Confidence 457999999999999999987 35788999983 1 3344442 3455454 88
Q ss_pred ccccccccccceeeeeeecccccccCCCCCCCCCceecCC------CCcHHHHHHHHHhc
Q psy9210 57 CSELIPLFFHKVFVFQISVNLFFQSITGTAMDKPNVYDFH------TTTYEDIYQDLMNK 110 (234)
Q Consensus 57 ~~~~~~~~~~~~~~~~~~~~~~~~~lPG~a~dkPNvY~F~------~TtY~~Iy~dL~~k 110 (234)
+.++.|.+-.++...-. .++.| |.-+ ...|+.+|+.|.++
T Consensus 80 ~~~~~~~~p~~~~~~~w------------~i~DP--~~~~g~~~~~~~~~~~~~~~I~~~ 125 (129)
T TIGR02691 80 ARDKCPATPPHVKREHW------------GLDDP--ARAEGTEEEKWAVFRRVRDEIKER 125 (129)
T ss_pred hccCCCccCCCCeEEEC------------CCCCC--CCCCCCHHHHHHHHHHHHHHHHHH
Confidence 88888887765543211 23444 3333 23577777777654
No 7
>PRK11391 etp phosphotyrosine-protein phosphatase; Provisional
Probab=93.73 E-value=0.072 Score=43.00 Aligned_cols=37 Identities=38% Similarity=0.487 Sum_probs=32.8
Q ss_pred ceEEEEecCCCccchHHHHHHhhC--CCceeeccCCCCC
Q psy9210 5 LKVAVVCSSNMNRSMEAHAYLSKK--GVDVKSFGTGDKK 41 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~L~k~--G~~V~SfGTG~~v 41 (234)
.||.+||..|.-||--|.++|++. ++.|.|-||...+
T Consensus 3 ~~ILfVC~gN~cRSpmAEa~~~~~~~~~~v~SaG~~~~~ 41 (144)
T PRK11391 3 NSILVVCTGNICRSPIGERLLRKRLPGVKVKSAGVHGLV 41 (144)
T ss_pred CeEEEEcCCcHhHHHHHHHHHHHhcCCeEEEcccccCCC
Confidence 589999999999999999999974 6899999997554
No 8
>PF01451 LMWPc: Low molecular weight phosphotyrosine protein phosphatase; InterPro: IPR023485 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents the low molecular weight (LMW) protein-tyrosine phosphatases (or acid phosphatase), which act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates [, ]. The structure of a LMW PTPase has been solved by X-ray crystallography [] and is found to form a single structural domain. It belongs to the alpha/beta class, with 6 alpha-helices and 4 beta-strands forming a 3-layer alpha-beta-alpha sandwich architecture.; PDB: 3RH0_B 1JL3_B 2IPA_B 1Z2D_A 1Z2E_A 2CWD_D 2L18_A 2L17_A 2L19_A 1BVH_A ....
Probab=92.97 E-value=0.089 Score=40.64 Aligned_cols=35 Identities=34% Similarity=0.409 Sum_probs=30.4
Q ss_pred EEEEecCCCccchHHHHHHhhC-------CCceeeccCCCCC
Q psy9210 7 VAVVCSSNMNRSMEAHAYLSKK-------GVDVKSFGTGDKK 41 (234)
Q Consensus 7 ~AvVCsSN~NRSMEAH~~L~k~-------G~~V~SfGTG~~v 41 (234)
|..||..|-=||--|+++|++. ++.|.|-||....
T Consensus 1 ILFvC~~N~cRS~mAEai~~~~~~~~~~~~~~v~SAG~~~~~ 42 (138)
T PF01451_consen 1 ILFVCTGNICRSPMAEAILRHLLKQRLGDRFEVESAGTEAWP 42 (138)
T ss_dssp EEEEESSSSSHHHHHHHHHHHHHHHTHTTTEEEEEEESSSTT
T ss_pred CEEEeCCCcchHHHHHHHHHHhccccccCCcEEEEEeecccc
Confidence 5789999999999999999887 8899999997543
No 9
>PRK10126 tyrosine phosphatase; Provisional
Probab=92.95 E-value=0.096 Score=42.00 Aligned_cols=37 Identities=32% Similarity=0.439 Sum_probs=32.5
Q ss_pred ceEEEEecCCCccchHHHHHHhh--CCCceeeccCCCCC
Q psy9210 5 LKVAVVCSSNMNRSMEAHAYLSK--KGVDVKSFGTGDKK 41 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~L~k--~G~~V~SfGTG~~v 41 (234)
.||..||..|.-||=-|.++|++ .++.|.|-||...+
T Consensus 3 ~~iLFVC~gN~cRSpmAEa~~~~~~~~~~v~SAG~~~~~ 41 (147)
T PRK10126 3 NNILVVCVGNICRSPTAERLLQRYHPELKVESAGLGALV 41 (147)
T ss_pred CeEEEEcCCcHhHHHHHHHHHHHhcCCeEEEeeeccCCC
Confidence 58999999999999999999998 45899999997654
No 10
>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=90.58 E-value=0.21 Score=39.03 Aligned_cols=34 Identities=32% Similarity=0.390 Sum_probs=29.7
Q ss_pred ceEEEEecCCCccchHHHHHHhhC---CCceeeccCC
Q psy9210 5 LKVAVVCSSNMNRSMEAHAYLSKK---GVDVKSFGTG 38 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~L~k~---G~~V~SfGTG 38 (234)
.||..||..|--||--|.++|++. ++.|.|-||.
T Consensus 1 ~~vlfvC~~N~cRS~mAEa~~~~~~~~~~~v~SAG~~ 37 (126)
T TIGR02689 1 KKVMFVCKRNSCRSQMAEGFAKTLGAGNIAVTSAGLE 37 (126)
T ss_pred CeEEEEcCCcHHHHHHHHHHHHHhcCCCEEEEcCcCC
Confidence 378999999999999999999974 3788999985
No 11
>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=89.24 E-value=0.72 Score=33.45 Aligned_cols=35 Identities=26% Similarity=0.467 Sum_probs=29.4
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCceeeccCCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGD 39 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~ 39 (234)
.-+|.++|++. +||..|=..|++.||+|...-.|-
T Consensus 61 ~~~ivv~C~~G-~rs~~aa~~L~~~G~~~~~l~GG~ 95 (100)
T cd01523 61 DQEVTVICAKE-GSSQFVAELLAERGYDVDYLAGGM 95 (100)
T ss_pred CCeEEEEcCCC-CcHHHHHHHHHHcCceeEEeCCcH
Confidence 45789999875 699999999999999988876664
No 12
>cd00115 LMWPc Substituted updates: Aug 22, 2001
Probab=88.47 E-value=0.44 Score=37.25 Aligned_cols=35 Identities=37% Similarity=0.489 Sum_probs=30.2
Q ss_pred ceEEEEecCCCccchHHHHHHhhC----CCceeeccCCC
Q psy9210 5 LKVAVVCSSNMNRSMEAHAYLSKK----GVDVKSFGTGD 39 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~L~k~----G~~V~SfGTG~ 39 (234)
.||-.||..|--||==|.++|++. ++.|.|-||..
T Consensus 1 ~~iLfvc~~N~~RS~mAEai~~~~~~~~~~~v~SaG~~~ 39 (141)
T cd00115 1 KKVLFVCTGNICRSPMAEAIFRHLAPKLDIEVDSAGTSG 39 (141)
T ss_pred CeEEEEecChhhhhHHHHHHHHHHhhhCCEEEECCCCCC
Confidence 379999999999999999999874 68888988854
No 13
>smart00226 LMWPc Low molecular weight phosphatase family.
Probab=88.44 E-value=0.31 Score=37.85 Aligned_cols=33 Identities=36% Similarity=0.530 Sum_probs=28.0
Q ss_pred EEEEecCCCccchHHHHHHhhC---CCceeeccCCC
Q psy9210 7 VAVVCSSNMNRSMEAHAYLSKK---GVDVKSFGTGD 39 (234)
Q Consensus 7 ~AvVCsSN~NRSMEAH~~L~k~---G~~V~SfGTG~ 39 (234)
|-.||..|.-||--|.++|++. ++.|.|-||..
T Consensus 1 vLFVC~~N~cRSpmAEa~~~~~~~~~~~v~SAG~~~ 36 (140)
T smart00226 1 ILFVCTGNICRSPMAEALFKAIVGDRVKIDSAGTGA 36 (140)
T ss_pred CEEEeCChhhhHHHHHHHHHHhcCCCEEEEcCcccC
Confidence 4579999999999999999874 38899998864
No 14
>COG0607 PspE Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=85.43 E-value=1.5 Score=31.46 Aligned_cols=31 Identities=32% Similarity=0.353 Sum_probs=26.6
Q ss_pred CCCceEEEEecCCCccchHHHHHHhhCCCcee
Q psy9210 2 PSNLKVAVVCSSNMNRSMEAHAYLSKKGVDVK 33 (234)
Q Consensus 2 ~s~lk~AvVCsSN~NRSMEAH~~L~k~G~~V~ 33 (234)
+..-++.|+|+| .+||..|=..|+++||...
T Consensus 59 ~~~~~ivv~C~~-G~rS~~aa~~L~~~G~~~~ 89 (110)
T COG0607 59 PDDDPIVVYCAS-GVRSAAAAAALKLAGFTNV 89 (110)
T ss_pred CCCCeEEEEeCC-CCChHHHHHHHHHcCCccc
Confidence 345689999987 5899999999999999776
No 15
>PLN02160 thiosulfate sulfurtransferase
Probab=83.91 E-value=1.4 Score=35.05 Aligned_cols=34 Identities=32% Similarity=0.463 Sum_probs=28.6
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCC-ceeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG 38 (234)
.-+|.++|.|. +||..|=..|.+.|| +|..+.-|
T Consensus 81 ~~~IivyC~sG-~RS~~Aa~~L~~~G~~~v~~l~GG 115 (136)
T PLN02160 81 ADDILVGCQSG-ARSLKATTELVAAGYKKVRNKGGG 115 (136)
T ss_pred CCcEEEECCCc-HHHHHHHHHHHHcCCCCeeecCCc
Confidence 34788999866 999999999999999 69888555
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=81.90 E-value=2.1 Score=30.88 Aligned_cols=33 Identities=15% Similarity=0.238 Sum_probs=27.1
Q ss_pred ceEEEEecCCCccchHHHHHHhhCCCceeeccCC
Q psy9210 5 LKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTG 38 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG 38 (234)
-+|.+.|.+ -+||..|-..|++.||+|.++-.|
T Consensus 57 ~~iv~~c~~-G~rs~~aa~~L~~~G~~v~~l~GG 89 (95)
T cd01534 57 ARIVLADDD-GVRADMTASWLAQMGWEVYVLEGG 89 (95)
T ss_pred CeEEEECCC-CChHHHHHHHHHHcCCEEEEecCc
Confidence 368888877 678999999999999998777444
No 17
>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=79.46 E-value=2.3 Score=30.30 Aligned_cols=34 Identities=26% Similarity=0.282 Sum_probs=27.7
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCc-eeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVD-VKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~-V~SfGTG 38 (234)
.-++.|.|++ .+||..+=..|.+.|++ |..+-.|
T Consensus 61 ~~~ivv~c~~-g~~s~~~~~~l~~~G~~~v~~l~Gg 95 (103)
T cd01447 61 DKPFVFYCAS-GWRSALAGKTLQDMGLKPVYNIEGG 95 (103)
T ss_pred CCeEEEEcCC-CCcHHHHHHHHHHcChHHhEeecCc
Confidence 3478999987 68999999999999996 8877433
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=78.75 E-value=2.8 Score=30.50 Aligned_cols=34 Identities=32% Similarity=0.515 Sum_probs=27.1
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCC-ceeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG 38 (234)
.-++-|+|.+ .+||..|=..|++.|| +|...--|
T Consensus 61 ~~~ivvyC~~-G~rs~~a~~~L~~~G~~~v~~l~GG 95 (101)
T cd01518 61 GKKVLMYCTG-GIRCEKASAYLKERGFKNVYQLKGG 95 (101)
T ss_pred CCEEEEECCC-chhHHHHHHHHHHhCCcceeeechh
Confidence 3468899976 5999999999999999 48766433
No 19
>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=74.10 E-value=6.8 Score=29.17 Aligned_cols=37 Identities=24% Similarity=0.263 Sum_probs=29.8
Q ss_pred CCCceEEEEecCCC-ccchHHHHHHhhCCCceeeccCC
Q psy9210 2 PSNLKVAVVCSSNM-NRSMEAHAYLSKKGVDVKSFGTG 38 (234)
Q Consensus 2 ~s~lk~AvVCsSN~-NRSMEAH~~L~k~G~~V~SfGTG 38 (234)
+..-+|.+.|++.. +||..+=..|.+.|++|..+-.|
T Consensus 62 ~~~~~vvvyc~~g~~~~s~~~a~~l~~~G~~v~~l~GG 99 (110)
T cd01521 62 DKEKLFVVYCDGPGCNGATKAALKLAELGFPVKEMIGG 99 (110)
T ss_pred CCCCeEEEEECCCCCchHHHHHHHHHHcCCeEEEecCC
Confidence 34567999999875 79999999999999998877333
No 20
>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=73.91 E-value=3.1 Score=37.31 Aligned_cols=71 Identities=14% Similarity=0.240 Sum_probs=52.3
Q ss_pred HHHHHhccHHHHhhcchhhhhhhcccCcCCCccccccC-------CC--ccEEEEecchhHHHHHHhHhhhcccCCCcee
Q psy9210 104 YQDLMNKDKAFYTRNGLLHMLERNKRIKLKPEKFQESK-------DK--FDIIITCEERVYDQVLEHFDNQMISLENTPV 174 (234)
Q Consensus 104 y~dL~~kD~~~Yt~NGlL~MLdRN~rIK~~PErfQe~~-------~~--fDvIiTcEERvyD~V~Edl~~~r~~~~~~pV 174 (234)
+++++.||-+++++||=| -+|.|.+-.=|.|+-+.+ +. .-+.++-+|+.=.+++.+-.- .-|+
T Consensus 101 c~~~L~~d~~~R~~~geL--r~R~R~vyEIpgrgy~~~rV~~~s~d~W~V~LDl~~~E~~~~e~VK~~~v------RYpL 172 (202)
T TIGR03746 101 CRAFLQQDYELRRSNGEL--RQRVRGVYEIPGRGYSENRVIVHSDDSWTVNLDLSVDEYYGGEPVKRALV------RYPL 172 (202)
T ss_pred HHHHHHHHHHHHhhcchH--hhheeeeEecCCCCCCccceEEeCCCceEEEEEEEEEeeeCCcchhhhhc------ccce
Confidence 577889999999999955 699999999999985432 21 445566678776666655443 4799
Q ss_pred EEEEeecC
Q psy9210 175 HLINIDIQ 182 (234)
Q Consensus 175 HvINiDI~ 182 (234)
+|+-.|+-
T Consensus 173 ~VVR~d~D 180 (202)
T TIGR03746 173 RVVRWDVD 180 (202)
T ss_pred EEEEecCC
Confidence 99988873
No 21
>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=73.76 E-value=5 Score=30.53 Aligned_cols=34 Identities=29% Similarity=0.361 Sum_probs=28.0
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCC--ceeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGV--DVKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~--~V~SfGTG 38 (234)
.-.+.++|.+. +||..|=..|++.|| +|..+--|
T Consensus 72 ~~~ivv~C~~G-~rs~~aa~~L~~~G~~~~v~~l~GG 107 (122)
T cd01526 72 DSPIYVVCRRG-NDSQTAVRKLKELGLERFVRDIIGG 107 (122)
T ss_pred CCcEEEECCCC-CcHHHHHHHHHHcCCccceeeecch
Confidence 45789999886 699999999999999 68887433
No 22
>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=73.23 E-value=5.2 Score=29.57 Aligned_cols=34 Identities=24% Similarity=0.452 Sum_probs=27.6
Q ss_pred ceEEEEecCCCccchHHHHHHhhCCC-c-eeeccCCC
Q psy9210 5 LKVAVVCSSNMNRSMEAHAYLSKKGV-D-VKSFGTGD 39 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~L~k~G~-~-V~SfGTG~ 39 (234)
-.+.|+|.+. +||..|-..|++.|| + |.+.-.|-
T Consensus 67 ~~ivv~C~~G-~rs~~a~~~L~~~G~~~~v~~l~gG~ 102 (109)
T cd01533 67 TPIVVNCAGR-TRSIIGAQSLINAGLPNPVAALRNGT 102 (109)
T ss_pred CeEEEECCCC-chHHHHHHHHHHCCCCcceeEecCCH
Confidence 4688999875 589889999999999 4 88876553
No 23
>PF13399 LytR_C: LytR cell envelope-related transcriptional attenuator
Probab=70.87 E-value=13 Score=27.00 Aligned_cols=40 Identities=20% Similarity=0.400 Sum_probs=33.8
Q ss_pred CCCceEEEEecCCCcc-chHHHHHHhhCCCceeeccCCCCC
Q psy9210 2 PSNLKVAVVCSSNMNR-SMEAHAYLSKKGVDVKSFGTGDKK 41 (234)
Q Consensus 2 ~s~lk~AvVCsSN~NR-SMEAH~~L~k~G~~V~SfGTG~~v 41 (234)
|+.++|.|.-+|..+. .=.+-..|+++||.|.+.|..+..
T Consensus 1 P~~v~V~VlNgt~~~GlA~~~a~~L~~~Gf~v~~~~n~~~~ 41 (90)
T PF13399_consen 1 PSDVRVEVLNGTGVSGLAARVADALRNRGFTVVEVGNAPSS 41 (90)
T ss_pred CCceEEEEEECcCCcCHHHHHHHHHHHCCCceeecCCCCCC
Confidence 7889999999998754 456788999999999999888744
No 24
>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=70.49 E-value=6.7 Score=30.06 Aligned_cols=31 Identities=23% Similarity=0.264 Sum_probs=25.5
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCc-eeec
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVD-VKSF 35 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~-V~Sf 35 (234)
.-++.++|++. +||..|=..|++.||+ |...
T Consensus 58 ~~~vvlyC~~G-~rS~~aa~~L~~~G~~~v~~~ 89 (101)
T TIGR02981 58 NDTVKLYCNAG-RQSGMAKDILLDMGYTHAENA 89 (101)
T ss_pred CCeEEEEeCCC-HHHHHHHHHHHHcCCCeEEec
Confidence 34688999885 7999999999999995 6654
No 25
>PRK00162 glpE thiosulfate sulfurtransferase; Validated
Probab=69.95 E-value=8.3 Score=28.45 Aligned_cols=34 Identities=38% Similarity=0.563 Sum_probs=27.0
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCc-eeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVD-VKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~-V~SfGTG 38 (234)
.-.+.++|.+. +||..|-..|++.||+ |..+.-|
T Consensus 58 ~~~ivv~c~~g-~~s~~a~~~L~~~G~~~v~~l~GG 92 (108)
T PRK00162 58 DTPVMVMCYHG-NSSQGAAQYLLQQGFDVVYSIDGG 92 (108)
T ss_pred CCCEEEEeCCC-CCHHHHHHHHHHCCchheEEecCC
Confidence 44688999865 6999999999999995 7766544
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=69.80 E-value=9.2 Score=29.50 Aligned_cols=36 Identities=25% Similarity=0.321 Sum_probs=30.2
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCceeeccCCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGD 39 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~ 39 (234)
.-+|-|.|.+.-.||..|-..|+..||+|...-.|-
T Consensus 86 ~~~vvvyC~~~G~rs~~a~~~L~~~G~~v~~L~GG~ 121 (128)
T cd01520 86 DPKLLIYCARGGMRSQSLAWLLESLGIDVPLLEGGY 121 (128)
T ss_pred CCeEEEEeCCCCccHHHHHHHHHHcCCceeEeCCcH
Confidence 457899998767889999999999999998886663
No 27
>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=68.82 E-value=9.4 Score=27.25 Aligned_cols=34 Identities=26% Similarity=0.429 Sum_probs=27.4
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCceeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG 38 (234)
.-++.++|++ -+||..+=..|++.|++|..+--|
T Consensus 51 ~~~vvl~c~~-g~~a~~~a~~L~~~G~~v~~l~GG 84 (90)
T cd01524 51 DKEIIVYCAV-GLRGYIAARILTQNGFKVKNLDGG 84 (90)
T ss_pred CCcEEEEcCC-ChhHHHHHHHHHHCCCCEEEecCC
Confidence 4568888886 578999999999999998887443
No 28
>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=66.79 E-value=9.5 Score=27.47 Aligned_cols=35 Identities=17% Similarity=0.118 Sum_probs=27.4
Q ss_pred CCceEEEEecCCCccchHHHHHHhhCCC-ceeeccCC
Q psy9210 3 SNLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTG 38 (234)
Q Consensus 3 s~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG 38 (234)
..-+|.++|.+ .+||-.+=..|++.|+ +|..+-.|
T Consensus 55 ~~~~ivv~c~~-g~~s~~~~~~l~~~G~~~v~~l~GG 90 (96)
T cd01529 55 RATRYVLTCDG-SLLARFAAQELLALGGKPVALLDGG 90 (96)
T ss_pred CCCCEEEEeCC-hHHHHHHHHHHHHcCCCCEEEeCCC
Confidence 34578999975 5899888889999999 68777544
No 29
>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=66.62 E-value=7.9 Score=32.07 Aligned_cols=36 Identities=25% Similarity=0.296 Sum_probs=25.5
Q ss_pred ceEEEEecCCCccch-----HHHHHHhhCCCceeeccCCCCC
Q psy9210 5 LKVAVVCSSNMNRSM-----EAHAYLSKKGVDVKSFGTGDKK 41 (234)
Q Consensus 5 lk~AvVCsSN~NRSM-----EAH~~L~k~G~~V~SfGTG~~v 41 (234)
.+|||+|||+.+-.. |.=+.|.++|+.|.| |-+.-+
T Consensus 2 ~~I~V~gss~~~~~~~~~A~~lg~~La~~g~~lv~-Gg~~Gl 42 (159)
T TIGR00725 2 VQIGVIGSSNKSEELYEIAYRLGKELAKKGHILIN-GGRTGV 42 (159)
T ss_pred eEEEEEeCCCCChHHHHHHHHHHHHHHHCCCEEEc-CCchhH
Confidence 489999999864432 222568899999998 765433
No 30
>PRK08395 fumarate hydratase; Provisional
Probab=66.19 E-value=8.1 Score=33.37 Aligned_cols=63 Identities=21% Similarity=0.334 Sum_probs=45.0
Q ss_pred HHHHHHhhCCCceeeccCCCCCCccccceeeeeccccccccccccccceeeeeeecccccccCCCCCCCCCceecCCCCc
Q psy9210 20 EAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVFVFQISVNLFFQSITGTAMDKPNVYDFHTTT 99 (234)
Q Consensus 20 EAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lPG~a~dkPNvY~F~~Tt 99 (234)
.||+.|.+.| .|-.++.-+|||| ||+..++.+-.+|.||
T Consensus 33 aah~rl~e~~-----------lP~dl~g~~iy~~------------------------------GP~~~~~~igs~GPTT 71 (162)
T PRK08395 33 LAHRRFLSEG-----------FPFNPEGAVIYHC------------------------------GPLVKNKKIVSAGPTT 71 (162)
T ss_pred HHHHHHHhcC-----------CCccccCCEEEEe------------------------------cCCCCCCCeEEECCcc
Confidence 7999998744 7888999999998 6777777888899887
Q ss_pred HHHHHHHHHhccHHHHhhcchhhhhhhcc
Q psy9210 100 YEDIYQDLMNKDKAFYTRNGLLHMLERNK 128 (234)
Q Consensus 100 Y~~Iy~dL~~kD~~~Yt~NGlL~MLdRN~ 128 (234)
=.-| ..=-+.+.. .|+--|+..-.
T Consensus 72 S~RM----d~~~~~l~~-~Gv~~iIGKG~ 95 (162)
T PRK08395 72 SARM----NKYLDFLFS-LGVRGIIGKGG 95 (162)
T ss_pred hHHH----HHhHHHHHH-CCCeEEEEcCC
Confidence 6654 111233454 58888876443
No 31
>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains.
Probab=66.11 E-value=12 Score=27.20 Aligned_cols=34 Identities=26% Similarity=0.596 Sum_probs=27.9
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCC-ceeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG 38 (234)
.-++-++|.+. +||-.+=..|++.|+ +|..+-.|
T Consensus 58 ~~~vv~~c~~g-~rs~~~~~~l~~~G~~~v~~l~GG 92 (101)
T cd01528 58 DKDIVVLCHHG-GRSMQVAQWLLRQGFENVYNLQGG 92 (101)
T ss_pred CCeEEEEeCCC-chHHHHHHHHHHcCCccEEEecCC
Confidence 45788999874 899999999999999 58877555
No 32
>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=65.41 E-value=12 Score=26.32 Aligned_cols=33 Identities=30% Similarity=0.408 Sum_probs=26.6
Q ss_pred CCCceEEEEecCCCccchHHHHHHhhCCC-ceeec
Q psy9210 2 PSNLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSF 35 (234)
Q Consensus 2 ~s~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~Sf 35 (234)
|..-++-++|+ +..||+.|-..|.+.|+ +|..+
T Consensus 54 ~~~~~ivv~c~-~g~~s~~a~~~l~~~G~~~v~~l 87 (96)
T cd01444 54 DRDRPVVVYCY-HGNSSAQLAQALREAGFTDVRSL 87 (96)
T ss_pred CCCCCEEEEeC-CCChHHHHHHHHHHcCCceEEEc
Confidence 34457889999 77899999999999999 47644
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=64.97 E-value=9.5 Score=27.47 Aligned_cols=32 Identities=19% Similarity=0.277 Sum_probs=26.3
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCC-ceeecc
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFG 36 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfG 36 (234)
.-.|.++|.+ .+||..|=..|++.|+ +|..+=
T Consensus 66 ~~~ivv~c~~-g~~s~~~~~~l~~~G~~~v~~~~ 98 (106)
T cd01519 66 DKELIFYCKA-GVRSKAAAELARSLGYENVGNYP 98 (106)
T ss_pred CCeEEEECCC-cHHHHHHHHHHHHcCCccceecC
Confidence 4578888886 6799999999999999 577764
No 34
>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=64.61 E-value=7.7 Score=28.59 Aligned_cols=32 Identities=22% Similarity=0.224 Sum_probs=27.5
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCC-ceeecc
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFG 36 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfG 36 (234)
.-.|.++|.+ -+||..+-..|...|+ +|..+.
T Consensus 78 ~~~iv~yc~~-g~~s~~~~~~l~~~G~~~v~~l~ 110 (118)
T cd01449 78 DKPVIVYCGS-GVTACVLLLALELLGYKNVRLYD 110 (118)
T ss_pred CCCEEEECCc-HHHHHHHHHHHHHcCCCCeeeeC
Confidence 4578999987 5799999999999999 588886
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=63.15 E-value=17 Score=24.61 Aligned_cols=35 Identities=31% Similarity=0.384 Sum_probs=27.9
Q ss_pred CCceEEEEecCCCccchHHHHHHhhCCCc-eeeccCC
Q psy9210 3 SNLKVAVVCSSNMNRSMEAHAYLSKKGVD-VKSFGTG 38 (234)
Q Consensus 3 s~lk~AvVCsSN~NRSMEAH~~L~k~G~~-V~SfGTG 38 (234)
..-++.++| .+.+||..+-..|.+.|++ |.-+--|
T Consensus 55 ~~~~iv~~c-~~g~~a~~~~~~l~~~G~~~v~~l~GG 90 (100)
T smart00450 55 KDKPVVVYC-RSGNRSAKAAWLLRELGFKNVYLLDGG 90 (100)
T ss_pred CCCeEEEEe-CCCcHHHHHHHHHHHcCCCceEEecCC
Confidence 345788999 5688999999999999997 7766544
No 36
>PRK01415 hypothetical protein; Validated
Probab=62.12 E-value=8.6 Score=34.63 Aligned_cols=35 Identities=26% Similarity=0.447 Sum_probs=29.2
Q ss_pred CCceEEEEecCCCccchHHHHHHhhCCC-ceeeccCC
Q psy9210 3 SNLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTG 38 (234)
Q Consensus 3 s~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG 38 (234)
.+-+|+|.|++. .||..|-++|++.|| +|.+.-.|
T Consensus 170 k~k~Iv~yCtgG-iRs~kAa~~L~~~Gf~~Vy~L~GG 205 (247)
T PRK01415 170 KGKKIAMVCTGG-IRCEKSTSLLKSIGYDEVYHLKGG 205 (247)
T ss_pred CCCeEEEECCCC-hHHHHHHHHHHHcCCCcEEEechH
Confidence 345899999776 799999999999999 48887555
No 37
>PRK10287 thiosulfate:cyanide sulfurtransferase; Provisional
Probab=60.70 E-value=11 Score=29.24 Aligned_cols=29 Identities=24% Similarity=0.368 Sum_probs=23.9
Q ss_pred ceEEEEecCCCccchHHHHHHhhCCCc-eee
Q psy9210 5 LKVAVVCSSNMNRSMEAHAYLSKKGVD-VKS 34 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~L~k~G~~-V~S 34 (234)
-.+.++|++. +||..|=..|.+.|++ |..
T Consensus 61 ~~IVlyC~~G-~rS~~aa~~L~~~G~~~v~~ 90 (104)
T PRK10287 61 DTVKLYCNAG-RQSGQAKEILSEMGYTHAEN 90 (104)
T ss_pred CeEEEEeCCC-hHHHHHHHHHHHcCCCeEEe
Confidence 4689999865 8999999999999995 555
No 38
>PRK05320 rhodanese superfamily protein; Provisional
Probab=60.42 E-value=9.6 Score=33.97 Aligned_cols=57 Identities=19% Similarity=0.306 Sum_probs=39.6
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCC-ceeeccCCCCCCccccceeeeeccccccccccccccceeeeeee
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVFVFQIS 74 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 (234)
.-+|.++|++. +||.+|-++|++.|| +|...-.| . ..|..-+ .+ .+|--|-|||-=-
T Consensus 175 dk~IvvyC~~G-~Rs~~Aa~~L~~~Gf~~V~~L~GG-i--~~w~~~~--------~~--~~~~G~~fVFD~R 232 (257)
T PRK05320 175 GKTVVSFCTGG-IRCEKAAIHMQEVGIDNVYQLEGG-I--LKYFEEV--------GG--AHYDGDCFVFDYR 232 (257)
T ss_pred CCeEEEECCCC-HHHHHHHHHHHHcCCcceEEeccC-H--HHHHHhC--------CC--CeeeeeeeeecCe
Confidence 35799999885 899999999999999 48877444 3 2464322 11 1366778888543
No 39
>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.
Probab=60.06 E-value=18 Score=25.99 Aligned_cols=35 Identities=14% Similarity=0.177 Sum_probs=27.1
Q ss_pred CCceEEEEecCCCccchHHHHHHhhCCC-ceeeccCC
Q psy9210 3 SNLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTG 38 (234)
Q Consensus 3 s~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG 38 (234)
..-+|.++|.+ .+||-.+=..|.+.|+ +|..+.-|
T Consensus 53 ~~~~iv~~c~~-g~~s~~~~~~L~~~g~~~v~~l~gG 88 (99)
T cd01527 53 GANAIIFHCRS-GMRTQQNAERLAAISAGEAYVLEGG 88 (99)
T ss_pred CCCcEEEEeCC-CchHHHHHHHHHHcCCccEEEeeCC
Confidence 34578888886 5778899889999999 68777555
No 40
>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=58.89 E-value=21 Score=26.55 Aligned_cols=35 Identities=20% Similarity=0.076 Sum_probs=28.2
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCc-eeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVD-VKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~-V~SfGTG 38 (234)
.-.|.+.|.+...||-.+-..|++.|++ |..+-.|
T Consensus 79 ~~~vv~~c~~g~~~a~~~~~~l~~~G~~~v~~l~GG 114 (122)
T cd01448 79 DDTVVVYDDGGGFFAARAWWTLRYFGHENVRVLDGG 114 (122)
T ss_pred CCEEEEECCCCCccHHHHHHHHHHcCCCCEEEecCC
Confidence 4578999988666888999999999996 8877544
No 41
>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=57.05 E-value=13 Score=26.56 Aligned_cols=33 Identities=27% Similarity=0.470 Sum_probs=26.0
Q ss_pred eEEEEecCCCccchHH----HHHHhhCCCceeeccCC
Q psy9210 6 KVAVVCSSNMNRSMEA----HAYLSKKGVDVKSFGTG 38 (234)
Q Consensus 6 k~AvVCsSN~NRSMEA----H~~L~k~G~~V~SfGTG 38 (234)
|+-+||++-+.-|+-+ -+.+.+.|+++.+.-..
T Consensus 1 kIlvvC~~Gi~TS~~~~~~i~~~~~~~gi~~~~~~~~ 37 (90)
T PF02302_consen 1 KILVVCGSGIGTSLMVANKIKKALKELGIEVEVSAGS 37 (90)
T ss_dssp EEEEEESSSSHHHHHHHHHHHHHHHHTTECEEEEEEE
T ss_pred CEEEECCChHHHHHHHHHHHHHHHHhccCceEEEEec
Confidence 7889999999999877 45566789887766554
No 42
>PRK10310 PTS system galactitol-specific transporter subunit IIB; Provisional
Probab=55.31 E-value=14 Score=28.05 Aligned_cols=30 Identities=20% Similarity=0.362 Sum_probs=24.2
Q ss_pred CceEEEEecCCCccch----HHHHHHhhCCCcee
Q psy9210 4 NLKVAVVCSSNMNRSM----EAHAYLSKKGVDVK 33 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSM----EAH~~L~k~G~~V~ 33 (234)
+.|+.+||.|-+.-|+ ....+|+++|+++.
T Consensus 2 k~kILvvCgsG~~TS~m~~~ki~~~l~~~gi~~~ 35 (94)
T PRK10310 2 KRKIIVACGGAVATSTMAAEEIKELCQSHNIPVE 35 (94)
T ss_pred CCeEEEECCCchhHHHHHHHHHHHHHHHCCCeEE
Confidence 3589999999998884 45678999999754
No 43
>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=52.01 E-value=25 Score=25.35 Aligned_cols=34 Identities=26% Similarity=0.312 Sum_probs=26.0
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCc-eeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVD-VKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~-V~SfGTG 38 (234)
.-.|.++|.+. +||..+=..|...|++ |...-.|
T Consensus 65 ~~~vv~~c~~g-~~s~~~a~~L~~~G~~~v~~l~GG 99 (105)
T cd01525 65 GKIIVIVSHSH-KHAALFAAFLVKCGVPRVCILDGG 99 (105)
T ss_pred CCeEEEEeCCC-ccHHHHHHHHHHcCCCCEEEEeCc
Confidence 34677888765 5898888899999994 8777555
No 44
>PRK08228 L(+)-tartrate dehydratase subunit beta; Validated
Probab=47.54 E-value=27 Score=31.32 Aligned_cols=76 Identities=24% Similarity=0.286 Sum_probs=47.6
Q ss_pred HHHHHHhhCCCceeeccCCCCCCccccceeeeeccccccccccccccceeeeeeecccccccCCCCCCCC---Ccee---
Q psy9210 20 EAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVFVFQISVNLFFQSITGTAMDK---PNVY--- 93 (234)
Q Consensus 20 EAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lPG~a~dk---PNvY--- 93 (234)
.||+.|.+ .|...|-.++.-+|||| ||++.+ |.=|
T Consensus 36 aAHkrl~e---------~g~~lP~dl~g~~Iyh~------------------------------GP~~~~~~~~g~~~~g 76 (204)
T PRK08228 36 VAHRRLIE---------LGRELPVDLNGGAIFHA------------------------------GPIVRPKKNDDKFEMV 76 (204)
T ss_pred HHHHHHHH---------cCCCCCcCCCCCEEEEe------------------------------CCCCCccCCCCCcEEE
Confidence 78999886 35558999999999998 777776 4424
Q ss_pred cCCCCcHHHHHHHHHhcc-HHHHhhcchhhhhhhcccCcCCCccccc
Q psy9210 94 DFHTTTYEDIYQDLMNKD-KAFYTRNGLLHMLERNKRIKLKPEKFQE 139 (234)
Q Consensus 94 ~F~~TtY~~Iy~dL~~kD-~~~Yt~NGlL~MLdRN~rIK~~PErfQe 139 (234)
.+|.||=--| ++- +.+-.+.|+.-|+..-.+-+.--|=+++
T Consensus 77 s~GPTTS~RM-----d~y~~~~l~~~G~~~~IGKG~~~~~~~~a~k~ 118 (204)
T PRK08228 77 SVGPTTSMRM-----EKFEKEFIEQTGVKLIVGKGGMGPGTEEGCQE 118 (204)
T ss_pred EeCCCcHHHh-----hhhHHHHHHhCCcEEEEECCCCCHHHHHHHHH
Confidence 5666653321 111 3455556777777665554433333443
No 45
>TIGR00723 ttdB_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase. This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of archaeal proteins in this subfamily has not been established.
Probab=47.38 E-value=21 Score=31.04 Aligned_cols=68 Identities=24% Similarity=0.359 Sum_probs=45.4
Q ss_pred HHHHHHhhCCCceeeccCCCCCCccccceeeeeccccccccccccccceeeeeeecccccccCCCCCCCCCc---eecCC
Q psy9210 20 EAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVFVFQISVNLFFQSITGTAMDKPN---VYDFH 96 (234)
Q Consensus 20 EAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lPG~a~dkPN---vY~F~ 96 (234)
.||+.|.+.. ..|...|-.++.-+|||| ||++.+|+ +-.+|
T Consensus 24 ~ah~rl~e~~------~~g~~lP~dl~g~~Iy~~------------------------------GP~~~~~g~~~~gs~G 67 (168)
T TIGR00723 24 EAHARLLELI------DEGKELPFDLNGSVIYHA------------------------------GPIVTKNGEWEVVSVG 67 (168)
T ss_pred HHHHHHHHHH------HcCCCCCcCCCCCEEEEe------------------------------CCCCCCCCCceeEEeC
Confidence 6888887421 135668999999999998 77777776 45788
Q ss_pred CCcHHHHHHHHHhccHHHHhhcchhhhhhhc
Q psy9210 97 TTTYEDIYQDLMNKDKAFYTRNGLLHMLERN 127 (234)
Q Consensus 97 ~TtY~~Iy~dL~~kD~~~Yt~NGlL~MLdRN 127 (234)
.||=..|= .=-+.+..+.|+.-|+...
T Consensus 68 PTTS~RMd----~y~~~ll~~~Gv~~~IGKG 94 (168)
T TIGR00723 68 PTTSARMN----PFEPELLEKLGVMAIIGKG 94 (168)
T ss_pred CChHHHHH----HhHHHHHHhCCcEEEEECC
Confidence 77654431 1114466667888888544
No 46
>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=45.15 E-value=27 Score=25.11 Aligned_cols=42 Identities=19% Similarity=0.313 Sum_probs=31.3
Q ss_pred EEecCCCccchHHHHHHhhCCCceeeccCCCCCCccccceeeeeccccccc
Q psy9210 9 VVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSE 59 (234)
Q Consensus 9 vVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~~~ 59 (234)
++=-.|.+..|.|++.|+++|++++-..|=..+ -.+|..|-.
T Consensus 5 ~i~F~st~~a~~~ek~lk~~gi~~~liP~P~~i---------~~~CG~al~ 46 (73)
T PF11823_consen 5 LITFPSTHDAMKAEKLLKKNGIPVRLIPTPREI---------SAGCGLALR 46 (73)
T ss_pred EEEECCHHHHHHHHHHHHHCCCcEEEeCCChhc---------cCCCCEEEE
Confidence 333456678999999999999999988775554 456776653
No 47
>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=43.83 E-value=85 Score=26.89 Aligned_cols=41 Identities=15% Similarity=0.094 Sum_probs=32.5
Q ss_pred chhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHH
Q psy9210 152 ERVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAF 193 (234)
Q Consensus 152 ERvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~ 193 (234)
.+.+...+++++. +++..+++|-++-.|.+.+++.|...+.
T Consensus 20 ~~g~~~a~~~iN~-~gGi~G~~i~l~~~D~~~~p~~a~~~a~ 60 (333)
T cd06331 20 RNAALLAIEEINA-AGGILGRPLELVVEDPASDPAFAAKAAR 60 (333)
T ss_pred HHHHHHHHHHHHh-cCCCCCeEEEEEEECCCCCHHHHHHHHH
Confidence 3567888999998 7777889999999998888777765443
No 48
>COG1011 Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=43.49 E-value=35 Score=27.35 Aligned_cols=46 Identities=26% Similarity=0.450 Sum_probs=33.5
Q ss_pred CCCccEEEEecc--------hhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHH
Q psy9210 141 KDKFDIIITCEE--------RVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLA 195 (234)
Q Consensus 141 ~~~fDvIiTcEE--------RvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i 195 (234)
.+.||.|+++++ +.|..+++.+.. .|-+++=|| |+.+.-..||..+
T Consensus 138 ~~~Fd~v~~s~~~g~~KP~~~~f~~~~~~~g~-------~p~~~l~Vg--D~~~~di~gA~~~ 191 (229)
T COG1011 138 LDYFDAVFISEDVGVAKPDPEIFEYALEKLGV-------PPEEALFVG--DSLENDILGARAL 191 (229)
T ss_pred hhhhheEEEecccccCCCCcHHHHHHHHHcCC-------CcceEEEEC--CChhhhhHHHHhc
Confidence 367999999976 789999998776 255555554 7777776777653
No 49
>KOG1530|consensus
Probab=43.27 E-value=26 Score=29.99 Aligned_cols=30 Identities=27% Similarity=0.471 Sum_probs=24.6
Q ss_pred eEEEEecCCCccchHHHHHHhhCCC-ceeecc
Q psy9210 6 KVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFG 36 (234)
Q Consensus 6 k~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfG 36 (234)
-+-+-|+|. +||.+|-..|..+|| +|.-|+
T Consensus 91 eiIf~C~SG-~Rs~~A~~~l~s~Gyknv~ny~ 121 (136)
T KOG1530|consen 91 EIIFGCASG-VRSLKATKILVSAGYKNVGNYP 121 (136)
T ss_pred cEEEEeccC-cchhHHHHHHHHcCcccccccC
Confidence 356779885 699999999999999 666664
No 50
>cd01144 BtuF Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=43.11 E-value=1.7e+02 Score=24.02 Aligned_cols=70 Identities=13% Similarity=0.230 Sum_probs=39.8
Q ss_pred CccEEEEecchhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHHHHHHHHhhc---chhhHHHHHHHHHHH
Q psy9210 143 KFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLASELMSMFIK---CEDLDNEIDEIMQEF 219 (234)
Q Consensus 143 ~fDvIiTcEERvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~eL~~~l~~---~eDld~~ideil~~f 219 (234)
+.|+||+....--+...+.|.. ..-||-+ ++ .++.++.. ..+..|++.+.+ ++.+-+++++.+++.
T Consensus 57 ~PDlIi~~~~~~~~~~~~~l~~-----~gi~v~~--~~-~~~~~~~~---~~~~~lg~~~g~~~~a~~~~~~~~~~~~~~ 125 (245)
T cd01144 57 KPDLVIAWDDCNVCAVVDQLRA-----AGIPVLV--SE-PQTLDDIL---ADIRRLGTLAGRPARAEELAEALRRRLAAL 125 (245)
T ss_pred CCCEEEEecCCCHHHHHHHHHH-----cCCcEEE--eC-CCCHHHHH---HHHHHHHHHhCChhHHHHHHHHHHHHHHHH
Confidence 5899999765433334666665 2223333 33 22333322 345556665544 455777777888888
Q ss_pred HHHc
Q psy9210 220 EEKC 223 (234)
Q Consensus 220 eek~ 223 (234)
.++.
T Consensus 126 ~~~~ 129 (245)
T cd01144 126 RKQY 129 (245)
T ss_pred HHHh
Confidence 7775
No 51
>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=42.79 E-value=42 Score=26.00 Aligned_cols=25 Identities=12% Similarity=0.082 Sum_probs=21.3
Q ss_pred CceEEEEecCCCccchHHHHHHhhC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKK 28 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~ 28 (234)
.-.|.+.|....+||..|-..|++.
T Consensus 68 ~~~vv~yC~~sg~rs~~aa~~L~~~ 92 (121)
T cd01530 68 RRVLIFHCEFSSKRGPRMARHLRNL 92 (121)
T ss_pred CCEEEEECCCccccHHHHHHHHHHH
Confidence 4578899986779999999999985
No 52
>TIGR03292 PhnH_redo phosphonate C-P lyase system protein PhnH. PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on Pfam model pfam05845.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context.
Probab=41.55 E-value=24 Score=30.46 Aligned_cols=14 Identities=14% Similarity=0.361 Sum_probs=12.2
Q ss_pred cCCCCCCCCCceec
Q psy9210 81 SITGTAMDKPNVYD 94 (234)
Q Consensus 81 ~lPG~a~dkPNvY~ 94 (234)
+|.||-|...+...
T Consensus 120 ~L~GPGI~~~~~i~ 133 (174)
T TIGR03292 120 TLTGPGIATERTIA 133 (174)
T ss_pred EEECCCcCCceeEc
Confidence 89999999888775
No 53
>PRK00142 putative rhodanese-related sulfurtransferase; Provisional
Probab=41.16 E-value=30 Score=31.70 Aligned_cols=34 Identities=26% Similarity=0.523 Sum_probs=28.7
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCC-ceeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG 38 (234)
.-+|.|.|++. .||..|=.+|+++|| +|...--|
T Consensus 171 dk~IvvyC~~G-~Rs~~aa~~L~~~Gf~~V~~L~GG 205 (314)
T PRK00142 171 DKKVVMYCTGG-IRCEKASAWMKHEGFKEVYQLEGG 205 (314)
T ss_pred cCeEEEECCCC-cHHHHHHHHHHHcCCCcEEEecch
Confidence 35899999864 899999999999999 59888655
No 54
>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=41.10 E-value=24 Score=25.26 Aligned_cols=26 Identities=27% Similarity=0.539 Sum_probs=18.8
Q ss_pred eEEEEecCCCccchHHHHH----HhhCCCc
Q psy9210 6 KVAVVCSSNMNRSMEAHAY----LSKKGVD 31 (234)
Q Consensus 6 k~AvVCsSN~NRSMEAH~~----L~k~G~~ 31 (234)
|+++||++.++-|.=...- +.+.|+.
T Consensus 1 kilvvC~~G~~tS~ll~~kl~~~f~~~~i~ 30 (86)
T cd05563 1 KILAVCGSGLGSSLMLKMNVEKVLKELGIE 30 (86)
T ss_pred CEEEECCCCccHHHHHHHHHHHHHHHCCCc
Confidence 6899999999988655533 4556653
No 55
>COG3414 SgaB Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism]
Probab=40.35 E-value=35 Score=26.72 Aligned_cols=26 Identities=23% Similarity=0.553 Sum_probs=23.6
Q ss_pred ceEEEEecCCCccc----hHHHHHHhhCCC
Q psy9210 5 LKVAVVCSSNMNRS----MEAHAYLSKKGV 30 (234)
Q Consensus 5 lk~AvVCsSN~NRS----MEAH~~L~k~G~ 30 (234)
.||-+||-+-++-| |..-.+|+++|+
T Consensus 2 ~KIL~aCG~GvgSS~~ik~kve~~l~~~gi 31 (93)
T COG3414 2 IKILAACGNGVGSSTMIKMKVEEVLKELGI 31 (93)
T ss_pred cEEEEECCCCccHHHHHHHHHHHHHHHcCC
Confidence 68999999999999 567789999999
No 56
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=39.83 E-value=36 Score=24.78 Aligned_cols=23 Identities=35% Similarity=0.593 Sum_probs=20.5
Q ss_pred hHHHHHHhhCCCceeeccCCCCC
Q psy9210 19 MEAHAYLSKKGVDVKSFGTGDKK 41 (234)
Q Consensus 19 MEAH~~L~k~G~~V~SfGTG~~v 41 (234)
.-.|.+++.-|+.-.|+|.|..-
T Consensus 50 ~~iH~~a~~~~l~s~S~g~g~~R 72 (79)
T smart00393 50 KIVHELAEKYGLESESFGEGPKR 72 (79)
T ss_pred HHHHHHHHHcCCEEEEEcCCCCc
Confidence 46899999999999999999864
No 57
>COG0473 LeuB Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]
Probab=38.73 E-value=65 Score=31.16 Aligned_cols=116 Identities=20% Similarity=0.401 Sum_probs=86.7
Q ss_pred CCCCCCceecCCCCcHHHHHHHHHhcc------HHHHhhcchhhhhhhcccCcCCCccccccCCCccEEEEecchhHHHH
Q psy9210 85 TAMDKPNVYDFHTTTYEDIYQDLMNKD------KAFYTRNGLLHMLERNKRIKLKPEKFQESKDKFDIIITCEERVYDQV 158 (234)
Q Consensus 85 ~a~dkPNvY~F~~TtY~~Iy~dL~~kD------~~~Yt~NGlL~MLdRN~rIK~~PErfQe~~~~fDvIiTcEERvyD~V 158 (234)
++++|.||-.+.+--+.++.+++. |+ ..+|--|.-.+|. .+|++ ||||+| +..|-.+
T Consensus 178 Tsv~KaNVl~~s~~lwrev~~eva-~~yPdv~~~~~~VD~aam~lV-------~~P~~-------FDViVt--~NlFGDI 240 (348)
T COG0473 178 TSVHKANVLKLSDGLWREVVEEVA-KEYPDVELDHMYVDAAAMQLV-------RNPEQ-------FDVIVT--SNLFGDI 240 (348)
T ss_pred EEEehhhhhhhhhHHHHHHHHHHh-hcCCCcchhHHhHHHHHHHHh-------hCccc-------cCEEEE--ccchhHH
Confidence 688999999998789999999998 44 2345556555554 35765 689998 5689999
Q ss_pred HHhHhhhcc-----------------cCCCceeEEEEeecC----CCHHHHhhhHHHHHHHHHHhhcchhhHHHHHHHHH
Q psy9210 159 LEHFDNQMI-----------------SLENTPVHLINIDIQ----DNQEEATLGAFLASELMSMFIKCEDLDNEIDEIMQ 217 (234)
Q Consensus 159 ~Edl~~~r~-----------------~~~~~pVHvINiDI~----Dn~EeA~~Ga~~i~eL~~~l~~~eDld~~ideil~ 217 (234)
+-|+-+ .. .....|||=---||. =|+=-+.+.+-.+++-.-..+.++.+|+.|.+.|+
T Consensus 241 LSD~aa-~l~GslGl~PSAnig~~~~~~lfEPvHGSAPDIAGkgiANPiA~IlS~aMML~~~g~~~~A~~Ie~Av~~vl~ 319 (348)
T COG0473 241 LSDEAA-ALTGSLGLAPSANLGDERGPALFEPVHGSAPDIAGKGIANPIATILSAAMMLRHLGEKEAADAIENAVEKVLA 319 (348)
T ss_pred HHhHHH-HhcCccccCccCccCCCCCCceeecCCCCcccccCCCccChHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHH
Confidence 999886 31 235678998888886 46777777777777666666677778888888887
Q ss_pred H
Q psy9210 218 E 218 (234)
Q Consensus 218 ~ 218 (234)
+
T Consensus 320 ~ 320 (348)
T COG0473 320 E 320 (348)
T ss_pred c
Confidence 6
No 58
>PRK06043 fumarate hydratase; Provisional
Probab=38.33 E-value=35 Score=30.37 Aligned_cols=69 Identities=26% Similarity=0.389 Sum_probs=43.7
Q ss_pred HHHHHHhhCCCceeeccCCCCCCccccceeeeeccccccccccccccceeeeeeecccccccCCCCCCCCC----ceecC
Q psy9210 20 EAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVFVFQISVNLFFQSITGTAMDKP----NVYDF 95 (234)
Q Consensus 20 EAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lPG~a~dkP----NvY~F 95 (234)
.||+.|.+.. ..|...|..++.-+|||| ||++.|| -+-.+
T Consensus 35 aaH~rl~e~~------~~G~~lP~dl~g~~Iyh~------------------------------GP~~~k~~~g~~~gs~ 78 (192)
T PRK06043 35 EAHARILEMK------EKGKELPFSLEGAVIYHC------------------------------GPLMKKTDEGWKVVSA 78 (192)
T ss_pred HHHHHHHHHH------hcCCCCCcCcCCCEEEEe------------------------------cCCCccCCCCCeeeee
Confidence 6888887522 236678999999999998 6665554 34467
Q ss_pred CCCcHHHHHHHHHhcc-HHHHhhcchhhhhhhccc
Q psy9210 96 HTTTYEDIYQDLMNKD-KAFYTRNGLLHMLERNKR 129 (234)
Q Consensus 96 ~~TtY~~Iy~dL~~kD-~~~Yt~NGlL~MLdRN~r 129 (234)
|.||=.-| .+- +.|-.+.|+.-|+..-.|
T Consensus 79 GPTTS~RM-----d~y~~~l~~~~G~~~~IGKG~r 108 (192)
T PRK06043 79 GPTTSARM-----SKMTPKLLEKVEVRAIIGKGGM 108 (192)
T ss_pred CCChHHHh-----hhhHHHHHHhCCcEEEEEcCCC
Confidence 76664432 111 234444577777766655
No 59
>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=38.01 E-value=45 Score=21.28 Aligned_cols=23 Identities=22% Similarity=0.274 Sum_probs=20.0
Q ss_pred hHHHHHHhhCCCceeeccCCCCC
Q psy9210 19 MEAHAYLSKKGVDVKSFGTGDKK 41 (234)
Q Consensus 19 MEAH~~L~k~G~~V~SfGTG~~v 41 (234)
.-.|.+....|+...|.|+|..-
T Consensus 31 ~~vH~la~~~~L~s~s~g~~~~r 53 (59)
T cd02325 31 KLIHDLAEYYGLKSESEGEGPNR 53 (59)
T ss_pred HHHHHHHHHCCCEEEEecCCCCc
Confidence 46899999999999999999544
No 60
>PRK14329 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=37.61 E-value=46 Score=31.85 Aligned_cols=48 Identities=17% Similarity=0.270 Sum_probs=37.3
Q ss_pred CCceEEEE---ecCCCccchHHHHHHhhCCCceeeccCCCCCCccccceeeeeccccc
Q psy9210 3 SNLKVAVV---CSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFC 57 (234)
Q Consensus 3 s~lk~AvV---CsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~ 57 (234)
...||+++ |..|+--|---...|.++||.+.+. ..+..+||+..|-+=
T Consensus 22 ~~~~~~i~t~GC~~N~~dse~~~~~l~~~G~~~~~~-------~~~ADiviiNTC~v~ 72 (467)
T PRK14329 22 NTKKLFIESYGCQMNFADSEIVASILQMAGYNTTEN-------LEEADLVLVNTCSIR 72 (467)
T ss_pred CCCEEEEEecCCCCcHHHHHHHHHHHHHCcCEECCC-------cccCCEEEEeCccee
Confidence 34467776 9999999977788999999998762 334577889988775
No 61
>PRK10147 phnH carbon-phosphorus lyase complex subunit; Validated
Probab=36.18 E-value=32 Score=30.29 Aligned_cols=15 Identities=7% Similarity=0.213 Sum_probs=12.0
Q ss_pred cCCCCCCCCCceecC
Q psy9210 81 SITGTAMDKPNVYDF 95 (234)
Q Consensus 81 ~lPG~a~dkPNvY~F 95 (234)
+|.||-|.+.+...-
T Consensus 138 ~L~GPGI~~~~~i~~ 152 (196)
T PRK10147 138 RLRGPGIEAEERIAA 152 (196)
T ss_pred EEECCCcCCcceecC
Confidence 899999987776654
No 62
>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=35.78 E-value=33 Score=24.68 Aligned_cols=28 Identities=29% Similarity=0.582 Sum_probs=20.4
Q ss_pred ceEEEEecCCCccch----HHHHHHhhCCCce
Q psy9210 5 LKVAVVCSSNMNRSM----EAHAYLSKKGVDV 32 (234)
Q Consensus 5 lk~AvVCsSN~NRSM----EAH~~L~k~G~~V 32 (234)
.|+++||++.++-|. ..-+.+++.|+.+
T Consensus 1 ~~ilivC~~G~~tS~~l~~~i~~~~~~~~i~~ 32 (89)
T cd05566 1 KKILVACGTGVATSTVVASKVKELLKENGIDV 32 (89)
T ss_pred CEEEEECCCCccHHHHHHHHHHHHHHHCCCce
Confidence 489999999999882 2345567788743
No 63
>PRK14326 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=35.11 E-value=51 Score=32.01 Aligned_cols=49 Identities=22% Similarity=0.325 Sum_probs=37.3
Q ss_pred CCCceEEEE---ecCCCccchHHHHHHhhCCCceeeccCCCCCCccccceeeeeccccc
Q psy9210 2 PSNLKVAVV---CSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFC 57 (234)
Q Consensus 2 ~s~lk~AvV---CsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~ 57 (234)
+..-||+++ |..|+--|.--...|.++||.+.+.... ..|+|+..|-+=
T Consensus 11 ~~~~~~~i~T~GC~~N~~dse~~~~~L~~~G~~~~~~~e~-------ADvvviNTCtv~ 62 (502)
T PRK14326 11 RGARTYQVRTYGCQMNVHDSERLAGLLEAAGYVRAAEGQD-------ADVVVFNTCAVR 62 (502)
T ss_pred CCCCEEEEEecCCCCcHHHHHHHHHHHHHCCCEECCCcCC-------CCEEEEECCCee
Confidence 444567766 9999999999999999999988775432 256788887653
No 64
>COG0614 FepB ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=34.67 E-value=2e+02 Score=24.24 Aligned_cols=71 Identities=21% Similarity=0.320 Sum_probs=39.6
Q ss_pred CccEEEEecchhHHHHHHhHhhhcccCCCceeEEEEee-cCCCHHHHhhhHHHHHHHHHHhhcchhhHHHHHHHHHHHHH
Q psy9210 143 KFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINID-IQDNQEEATLGAFLASELMSMFIKCEDLDNEIDEIMQEFEE 221 (234)
Q Consensus 143 ~fDvIiTcEERvyD~V~Edl~~~r~~~~~~pVHvINiD-I~Dn~EeA~~Ga~~i~eL~~~l~~~eDld~~ideil~~fee 221 (234)
++|+||+... -.+..+.++.+ ..-||-++.-. ..+-.+.-.. +-++...=++++.|-+++++-+++..+
T Consensus 115 kPDlIi~~~~-~~~~~~~~~~~-----~~~pvv~~~~~~~~~~~~~i~~----lg~~~g~e~~A~~li~~~~~~~~~~~~ 184 (319)
T COG0614 115 KPDLIIASSS-SQDDLIYKLLS-----LGAPVVVVDYGSLDDIKEQIRL----LGKALGKEEKAEELIAEYDQRLAALRA 184 (319)
T ss_pred CCCEEEEecc-cchhHHHHHHh-----cCCCEEEECCcchhhHHHHHHH----HHHHhCcHHHHHHHHHHHHHHHHHHHH
Confidence 4899999987 44566666666 45666665544 2222222222 222222224456666667777777777
Q ss_pred Hc
Q psy9210 222 KC 223 (234)
Q Consensus 222 k~ 223 (234)
+.
T Consensus 185 ~~ 186 (319)
T COG0614 185 RT 186 (319)
T ss_pred Hh
Confidence 66
No 65
>PRK08762 molybdopterin biosynthesis protein MoeB; Validated
Probab=34.07 E-value=57 Score=30.06 Aligned_cols=34 Identities=32% Similarity=0.483 Sum_probs=27.7
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCC-ceeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG 38 (234)
.-.|.+.|.+ .+||..|-..|.+.|| +|..+--|
T Consensus 57 ~~~IvvyC~~-G~rs~~aa~~L~~~G~~~v~~l~GG 91 (376)
T PRK08762 57 DREIVLICAS-GTRSAHAAATLRELGYTRVASVAGG 91 (376)
T ss_pred CCeEEEEcCC-CcHHHHHHHHHHHcCCCceEeecCc
Confidence 4568899986 5799999999999999 68877444
No 66
>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=33.86 E-value=2.1e+02 Score=21.73 Aligned_cols=40 Identities=18% Similarity=0.206 Sum_probs=29.8
Q ss_pred CccEEEEecchhHHHHHHhHhhhcccCCCceeEEEEeecCCC
Q psy9210 143 KFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDIQDN 184 (234)
Q Consensus 143 ~fDvIiTcEERvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn 184 (234)
..|+||++....-..+++.+.. ++-. ...+.+|-.|-.+.
T Consensus 182 ~~~~i~~~~~~~a~~~~~~~~~-~g~~-~~~~~ii~~~~~~~ 221 (269)
T cd01391 182 KPDAIFACNDEMAAGALKAARE-AGLT-PGDISIIGFDGSPA 221 (269)
T ss_pred CCCEEEEcCchHHHHHHHHHHH-cCCC-CCCCEEEecccccc
Confidence 5899999998888889898888 4433 45678887765443
No 67
>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=33.10 E-value=1.5e+02 Score=23.90 Aligned_cols=37 Identities=11% Similarity=0.104 Sum_probs=30.1
Q ss_pred ccEEEEecchhHHHHHHhHhhhcccCCCceeEEEEeec
Q psy9210 144 FDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDI 181 (234)
Q Consensus 144 fDvIiTcEERvyD~V~Edl~~~r~~~~~~pVHvINiDI 181 (234)
+|.|+|+..+....+++.+.. ++-...+.+.||-+|-
T Consensus 175 ~~ai~~~~d~~a~g~~~~~~~-~g~~ip~~i~ii~~d~ 211 (264)
T cd01574 175 PTAVFAANDQMALGVLRALHE-LGLRVPDDVSVVGFDD 211 (264)
T ss_pred CcEEEEcCcHHHHHHHHHHHH-cCCCCccceEEecccC
Confidence 899999999999999999987 5444455789998874
No 68
>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=32.63 E-value=67 Score=21.61 Aligned_cols=32 Identities=34% Similarity=0.449 Sum_probs=24.6
Q ss_pred CCceEEEEecCCCccchHHHHHHhhCCC-ceeec
Q psy9210 3 SNLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSF 35 (234)
Q Consensus 3 s~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~Sf 35 (234)
..-+|.++|++ ..||..+=..|++.|+ +|..+
T Consensus 49 ~~~~vv~~c~~-~~~a~~~~~~l~~~G~~~v~~l 81 (89)
T cd00158 49 KDKPIVVYCRS-GNRSARAAKLLRKAGGTNVYNL 81 (89)
T ss_pred CCCeEEEEeCC-CchHHHHHHHHHHhCcccEEEe
Confidence 44578899988 5788899999999987 45433
No 69
>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=32.26 E-value=58 Score=30.05 Aligned_cols=35 Identities=20% Similarity=0.145 Sum_probs=30.0
Q ss_pred ceEEEEecCCCccchHHHHHHhhCCCceeeccCCC
Q psy9210 5 LKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGD 39 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~ 39 (234)
-++-++|..+..||--|-..|.+.|++|.....|-
T Consensus 75 ~~vvvyC~~gG~RS~~aa~~L~~~G~~v~~L~GG~ 109 (311)
T TIGR03167 75 PQPLLYCWRGGMRSGSLAWLLAQIGFRVPRLEGGY 109 (311)
T ss_pred CcEEEEECCCChHHHHHHHHHHHcCCCEEEecChH
Confidence 35899998888999999999999999998876563
No 70
>PRK11784 tRNA 2-selenouridine synthase; Provisional
Probab=32.18 E-value=62 Score=30.31 Aligned_cols=44 Identities=27% Similarity=0.391 Sum_probs=35.0
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCceeeccCCCCCCccccceee
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVI 50 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~ 50 (234)
.-+|.|.|..+.+||.-+-..|...|++|....-|-+- |...++
T Consensus 88 ~~~ivvyC~rgG~RS~~aa~~L~~~G~~v~~L~GG~~a---wr~~~~ 131 (345)
T PRK11784 88 NPRGLLYCWRGGLRSGSVQQWLKEAGIDVPRLEGGYKA---YRRFVI 131 (345)
T ss_pred CCeEEEEECCCChHHHHHHHHHHHcCCCcEEEcCCHHH---HHHhhH
Confidence 45799999888899999999999999999888666433 655443
No 71
>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=30.72 E-value=56 Score=23.78 Aligned_cols=21 Identities=19% Similarity=0.447 Sum_probs=19.1
Q ss_pred HHHHHhhCCCceeeccCCCCC
Q psy9210 21 AHAYLSKKGVDVKSFGTGDKK 41 (234)
Q Consensus 21 AH~~L~k~G~~V~SfGTG~~v 41 (234)
-|.++++.|+.-.|.|.|..-
T Consensus 34 ~H~~v~~~~l~s~S~G~ep~R 54 (60)
T cd02645 34 QHDLVERYQLRSESFGSEPNR 54 (60)
T ss_pred HHHHHHHCCCeEEEecCCCCc
Confidence 699999999999999999875
No 72
>KOG3085|consensus
Probab=30.69 E-value=17 Score=32.83 Aligned_cols=109 Identities=26% Similarity=0.354 Sum_probs=65.5
Q ss_pred HHHHHHHHHhccHHHHhhcchhhhhhhcccCcCCCccccccCCCccEEEEe-c-------chhHHHHHHhHhhhcccCCC
Q psy9210 100 YEDIYQDLMNKDKAFYTRNGLLHMLERNKRIKLKPEKFQESKDKFDIIITC-E-------ERVYDQVLEHFDNQMISLEN 171 (234)
Q Consensus 100 Y~~Iy~dL~~kD~~~Yt~NGlL~MLdRN~rIK~~PErfQe~~~~fDvIiTc-E-------ERvyD~V~Edl~~~r~~~~~ 171 (234)
=.+..+.|..++ +.=|++.+.|+-.+.=+.|=+. ...||.|++. | .|+|.-++|++..
T Consensus 118 ~~~~lq~lR~~g----~~l~iisN~d~r~~~~l~~~~l---~~~fD~vv~S~e~g~~KPDp~If~~al~~l~v------- 183 (237)
T KOG3085|consen 118 MQELLQKLRKKG----TILGIISNFDDRLRLLLLPLGL---SAYFDFVVESCEVGLEKPDPRIFQLALERLGV------- 183 (237)
T ss_pred HHHHHHHHHhCC----eEEEEecCCcHHHHHHhhccCH---HHhhhhhhhhhhhccCCCChHHHHHHHHHhCC-------
Confidence 346777777777 6667777776654422222111 2568877764 3 4899999999988
Q ss_pred ceeEEEEeecCCCHHHHhhhHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHcCCCceeee
Q psy9210 172 TPVHLINIDIQDNQEEATLGAFLASELMSMFIKCEDLDNEIDEIMQEFEEKCSRPLLHTI 231 (234)
Q Consensus 172 ~pVHvINiDI~Dn~EeA~~Ga~~i~eL~~~l~~~eDld~~ideil~~feek~~r~~Lhtv 231 (234)
+|.+++-|| |+.+.-..||+.+= -.+-=+++.+ .-+.+.+.+.+..++|+.
T Consensus 184 ~Pee~vhIg--D~l~nD~~gA~~~G------~~ailv~~~~-~~~~~~~~~~~~~l~~~~ 234 (237)
T KOG3085|consen 184 KPEECVHIG--DLLENDYEGARNLG------WHAILVDNSI-TALKELEYKLGIDLLNLP 234 (237)
T ss_pred ChHHeEEec--CccccccHhHHHcC------CEEEEEcccc-chhhhhhhcccccccccc
Confidence 488887765 88777666665431 0111123333 334455666666666653
No 73
>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=30.28 E-value=1.4e+02 Score=26.01 Aligned_cols=41 Identities=15% Similarity=0.137 Sum_probs=32.7
Q ss_pred hhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHH
Q psy9210 153 RVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFL 194 (234)
Q Consensus 153 RvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~ 194 (234)
+..+..+++++. +++...+||-++..|-+-+++.|.-.+..
T Consensus 21 ~g~~la~~~iNa-~gGi~Gr~v~lv~~D~~~~p~~a~~~~~~ 61 (334)
T cd06356 21 HATQLAVDEINA-SGGILGREVELVDYDTQSDNERYQQYAQR 61 (334)
T ss_pred HHHHHHHHHHHh-cCCCCCceEEEEEECCCCCHHHHHHHHHH
Confidence 456788899988 78888999999999998888777554433
No 74
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=30.14 E-value=35 Score=29.38 Aligned_cols=20 Identities=35% Similarity=0.599 Sum_probs=17.1
Q ss_pred CccchHHHHHHhhCCCceee
Q psy9210 15 MNRSMEAHAYLSKKGVDVKS 34 (234)
Q Consensus 15 ~NRSMEAH~~L~k~G~~V~S 34 (234)
.-|+=|||+.|.++||-|+-
T Consensus 49 V~~~d~A~~~Lee~gF~Vr~ 68 (142)
T COG4747 49 VDRPDEAHSVLEEAGFTVRE 68 (142)
T ss_pred cCChHHHHHHHHHCCcEEEe
Confidence 35788999999999998863
No 75
>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=29.92 E-value=1.1e+02 Score=21.12 Aligned_cols=35 Identities=20% Similarity=0.241 Sum_probs=23.2
Q ss_pred eEEEEecCCCccchHH--HHHHhhCCCce--eeccCCCC
Q psy9210 6 KVAVVCSSNMNRSMEA--HAYLSKKGVDV--KSFGTGDK 40 (234)
Q Consensus 6 k~AvVCsSN~NRSMEA--H~~L~k~G~~V--~SfGTG~~ 40 (234)
.|++|-.-..+...-+ -..|+++|.+| .|+||...
T Consensus 3 ~VsvVG~~~~~~~~~~~i~~aL~~~~I~v~~i~~g~s~~ 41 (65)
T cd04918 3 IISLIGNVQRSSLILERAFHVLYTKGVNVQMISQGASKV 41 (65)
T ss_pred EEEEECCCCCCccHHHHHHHHHHHCCCCEEEEEecCccc
Confidence 5778887333333444 44489999999 88887643
No 76
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=29.51 E-value=2.9e+02 Score=23.73 Aligned_cols=69 Identities=9% Similarity=0.128 Sum_probs=34.9
Q ss_pred CccEEEEecchhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHHHHHHHHhhc---chhhHHHHHHHHHHH
Q psy9210 143 KFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLASELMSMFIK---CEDLDNEIDEIMQEF 219 (234)
Q Consensus 143 ~fDvIiTcEERvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~eL~~~l~~---~eDld~~ideil~~f 219 (234)
+.|+||+...---...++.|.. .+-||.+++. ++.++.. ..+..|.+.+.+ .+.+-+++++-+++.
T Consensus 72 ~PDlVi~~~~~~~~~~~~~L~~-----~gi~v~~~~~---~~~~~~~---~~i~~lg~~~g~~~~A~~li~~~~~~l~~i 140 (260)
T PRK03379 72 KPDLVLAWRGGNAERQVDQLAS-----LGIKVMWVDA---TSIEQIA---NALRQLAPWSPQPEKAEQAAQSLLQQYAAL 140 (260)
T ss_pred CCCEEEEecCCCcHHHHHHHHH-----CCCCEEEeCC---CCHHHHH---HHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence 5899998643112345566655 4568877763 3444321 123344444433 333444444444444
Q ss_pred HHH
Q psy9210 220 EEK 222 (234)
Q Consensus 220 eek 222 (234)
+++
T Consensus 141 ~~~ 143 (260)
T PRK03379 141 KAQ 143 (260)
T ss_pred HHH
Confidence 444
No 77
>PF08885 GSCFA: GSCFA family; InterPro: IPR014982 This group of proteins are functionally uncharacterised. They have been named GSCFA after a highly conserved N-terminal motif in the alignment, they are functionally uncharacterised.
Probab=29.42 E-value=51 Score=29.80 Aligned_cols=60 Identities=23% Similarity=0.478 Sum_probs=42.3
Q ss_pred HHHHHHhhCCCceeeccCCCCCCccccce---eeeeccccccccccccccceeeeeeecccccccCCCCCCCCCceecCC
Q psy9210 20 EAHAYLSKKGVDVKSFGTGDKKPQQWESV---VIFHCCDFCSELIPLFFHKVFVFQISVNLFFQSITGTAMDKPNVYDFH 96 (234)
Q Consensus 20 EAH~~L~k~G~~V~SfGTG~~v~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lPG~a~dkPNvY~F~ 96 (234)
++++.|.++.+=|-.+||--. |+.. .++-.|. ++||.. -.|..|.|.
T Consensus 94 ~~~~~l~~ad~~iiTLGtaev----w~~~~~g~vv~nc~-------------------------k~p~~~-F~~~~~~f~ 143 (251)
T PF08885_consen 94 EVREALEEADVFIITLGTAEV----WRDRETGRVVANCH-------------------------KVPAGQ-FDPERYEFR 143 (251)
T ss_pred HHHHHHHhCCEEEEeCCcHHH----heeCCCCEEEecCC-------------------------Cccccc-cchhhhhhc
Confidence 568889999999999998432 2221 2222332 555554 368899999
Q ss_pred CCcHHHHHHHHHh
Q psy9210 97 TTTYEDIYQDLMN 109 (234)
Q Consensus 97 ~TtY~~Iy~dL~~ 109 (234)
..+|+||.++|.+
T Consensus 144 ~ls~~ei~~~l~~ 156 (251)
T PF08885_consen 144 NLSVEEILEDLEA 156 (251)
T ss_pred cCCHHHHHHHHHH
Confidence 9999999999975
No 78
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=28.76 E-value=71 Score=24.75 Aligned_cols=20 Identities=20% Similarity=0.331 Sum_probs=18.3
Q ss_pred HHHHHHhhCCCceeeccCCC
Q psy9210 20 EAHAYLSKKGVDVKSFGTGD 39 (234)
Q Consensus 20 EAH~~L~k~G~~V~SfGTG~ 39 (234)
.....|+++||.|.++++++
T Consensus 12 ~v~~~L~~~GyeVv~l~~~~ 31 (80)
T PF03698_consen 12 NVKEALREKGYEVVDLENEQ 31 (80)
T ss_pred HHHHHHHHCCCEEEecCCcc
Confidence 56789999999999999987
No 79
>KOG2424|consensus
Probab=28.61 E-value=42 Score=30.23 Aligned_cols=38 Identities=3% Similarity=-0.243 Sum_probs=35.3
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCceeeccCCCCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKK 41 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v 41 (234)
-..+|++|-++.++|+++|+...-++-.+-|+++=...
T Consensus 8 ~avvC~sN~NRSMeaH~~L~~~G~~v~S~GTg~~vklP 45 (195)
T KOG2424|consen 8 VAVVCASNQNRSMEAHNILKKKGLNVRSFGTGSHVKLP 45 (195)
T ss_pred eeeeehhcccchHHHHHHHHHcCCcceeecCCCceeCC
Confidence 35799999999999999999999999999999998888
No 80
>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=28.27 E-value=45 Score=25.83 Aligned_cols=27 Identities=33% Similarity=0.517 Sum_probs=17.7
Q ss_pred EEEecCCCccchHHHHHHhhCCCceeeccCCCCC
Q psy9210 8 AVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKK 41 (234)
Q Consensus 8 AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v 41 (234)
++..+-|...|+=| |+ +|+||||-...
T Consensus 21 GiL~~In~~~sTi~---L~----nVr~fGTEgR~ 47 (74)
T cd01736 21 GILYTINTEDSTIA---LK----NVRSFGTEGRP 47 (74)
T ss_pred EEEEeeccccCEEE---ee----eeEeecccCCC
Confidence 45555566555432 33 69999998876
No 81
>COG1794 RacX Aspartate racemase [Cell envelope biogenesis, outer membrane]
Probab=28.21 E-value=83 Score=28.90 Aligned_cols=78 Identities=17% Similarity=0.281 Sum_probs=57.3
Q ss_pred hHHHHHHhHhhhcccCCCceeEEEEeecCCC-----HHHHhhhHHHHHHHHHHhhcch-h----hHHHHHHHHHHHHHHc
Q psy9210 154 VYDQVLEHFDNQMISLENTPVHLINIDIQDN-----QEEATLGAFLASELMSMFIKCE-D----LDNEIDEIMQEFEEKC 223 (234)
Q Consensus 154 vyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn-----~EeA~~Ga~~i~eL~~~l~~~e-D----ld~~ideil~~feek~ 223 (234)
-|..+.|.-..+|++.--..+++.|+|+.|- +.+---.+..+.+-+..|+++. | --|-+-.+.++-|+..
T Consensus 18 yyr~ine~~~~~~g~~h~~~i~~~s~~f~~~~~~q~~~~w~~~~~~L~~~a~~Le~~GAd~i~l~~NT~H~~~d~iq~~~ 97 (230)
T COG1794 18 YYRKINEAVRAKLGGLHSAELLLYSVDFPEIETLQRAGEWDEAGEILIDAAKKLERAGADFIVLPTNTMHKVADDIQKAV 97 (230)
T ss_pred HHHHHHHHHHHHhCCcCcchhheecCCcccHHHHHccCccccHHHHHHHHHHHHHhcCCCEEEEeCCcHHHHHHHHHHhc
Confidence 4778888888878888777888999999886 3333344566677777777753 3 2566677777888899
Q ss_pred CCCceeee
Q psy9210 224 SRPLLHTI 231 (234)
Q Consensus 224 ~r~~Lhtv 231 (234)
+.|+||.+
T Consensus 98 ~iPllhIi 105 (230)
T COG1794 98 GIPLLHII 105 (230)
T ss_pred CCCeehHH
Confidence 99999954
No 82
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. 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 lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=27.81 E-value=80 Score=24.81 Aligned_cols=29 Identities=24% Similarity=0.428 Sum_probs=23.1
Q ss_pred ceEEEEecCCCccchHHH---HHHhhCCCcee
Q psy9210 5 LKVAVVCSSNMNRSMEAH---AYLSKKGVDVK 33 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH---~~L~k~G~~V~ 33 (234)
|||-++|++-+--||=+. .+++++|+++.
T Consensus 1 ~~Ill~C~~GaSSs~la~km~~~a~~~gi~~~ 32 (99)
T cd05565 1 LNVLVLCAGGGTSGLLANALNKGAKERGVPLE 32 (99)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHCCCcEE
Confidence 688999999988887654 56788999765
No 83
>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=27.24 E-value=1.5e+02 Score=25.29 Aligned_cols=40 Identities=15% Similarity=0.229 Sum_probs=30.3
Q ss_pred chhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhH
Q psy9210 152 ERVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGA 192 (234)
Q Consensus 152 ERvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga 192 (234)
.+..+..+|+++. .++..++++-++-.|-+.+.+.|.-.+
T Consensus 20 ~~g~~lA~~~iN~-~ggi~G~~iel~~~D~~~~p~~a~~~a 59 (312)
T cd06346 20 ADAAELAVKEVNA-AGGVLGEPVTLVTADTQTDPAAGVAAA 59 (312)
T ss_pred HHHHHHHHHHHHH-hCCCCCceEEEEECCCCCCHHHHHHHH
Confidence 4678889999998 777778898888877777766654433
No 84
>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=26.81 E-value=78 Score=29.96 Aligned_cols=74 Identities=15% Similarity=0.213 Sum_probs=46.4
Q ss_pred cchhHHHHHHhHhhhcccCCCceeEEEEeec-CCCHHHHhhhHHHHHHHHHH----hhcchhhHHHHHHHHHHHHHHcCC
Q psy9210 151 EERVYDQVLEHFDNQMISLENTPVHLINIDI-QDNQEEATLGAFLASELMSM----FIKCEDLDNEIDEIMQEFEEKCSR 225 (234)
Q Consensus 151 EERvyD~V~Edl~~~r~~~~~~pVHvINiDI-~Dn~EeA~~Ga~~i~eL~~~----l~~~eDld~~ideil~~feek~~r 225 (234)
+|+.|...++++++-+....++ =++++| +|+..+.-.|+..+|+|++. |.-.. ......+++.+=.+...
T Consensus 13 ~~~af~~Av~~~N~~~~~l~~~---~L~~~~~~~~~~d~F~~~~~ac~l~~~gV~AI~Gp~--s~~~a~~v~sic~~l~V 87 (400)
T cd06392 13 DDRVFQLAVSDLSLNDDILQSE---KITYSIKSIEANNPFQAVQEACDLMTQGILALVTST--GCASANALQSLTDAMHI 87 (400)
T ss_pred HHHHHHHHHHHhccCccccCCc---eEEEEEEecCCCChhHHHHHHHHHHhcCeEEEECCC--chhHHHHHHHHhccCcC
Confidence 7999999999999623333332 233455 55666677777888777643 11122 33555677777777777
Q ss_pred Ccee
Q psy9210 226 PLLH 229 (234)
Q Consensus 226 ~~Lh 229 (234)
|++-
T Consensus 88 P~is 91 (400)
T cd06392 88 PHLF 91 (400)
T ss_pred CcEe
Confidence 7664
No 85
>cd01141 TroA_d Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=26.75 E-value=3e+02 Score=21.78 Aligned_cols=70 Identities=16% Similarity=0.182 Sum_probs=36.2
Q ss_pred CccEEEEecchhHHH-HHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHHHHHHHHh-----hcchhhHHHHHHHH
Q psy9210 143 KFDIIITCEERVYDQ-VLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLASELMSMF-----IKCEDLDNEIDEIM 216 (234)
Q Consensus 143 ~fDvIiTcEERvyD~-V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~eL~~~l-----~~~eDld~~ideil 216 (234)
+.|+||+-.. -.++ ..+.|.. .+-||..+... .+..+. . ..+..+.+.+ ++++.+=+++++-+
T Consensus 69 ~PDlii~~~~-~~~~~~~~~l~~-----~gIpvv~i~~~--~~~~~~-~--~~i~~~g~~~g~~~~~~a~~~i~~~~~~~ 137 (186)
T cd01141 69 KPDLVILYGG-FQAQTILDKLEQ-----LGIPVLYVNEY--PSPLGR-A--EWIKFAAAFYGVGKEDKADEAFAQIAGRY 137 (186)
T ss_pred CCCEEEEecC-CCchhHHHHHHH-----cCCCEEEeCCC--CChhhH-H--HHHHHHHHHcCCchHHHHHHHHHHHHHHH
Confidence 5899998542 2343 6676665 33466666431 122221 1 1234444545 34455555666666
Q ss_pred HHHHHHc
Q psy9210 217 QEFEEKC 223 (234)
Q Consensus 217 ~~feek~ 223 (234)
++..++.
T Consensus 138 ~~i~~~~ 144 (186)
T cd01141 138 RDLAKKV 144 (186)
T ss_pred HHHHHHh
Confidence 6666555
No 86
>PRK07188 nicotinate phosphoribosyltransferase; Provisional
Probab=26.72 E-value=79 Score=29.99 Aligned_cols=38 Identities=18% Similarity=0.283 Sum_probs=28.4
Q ss_pred eEEEEecCCCccchHHHHHHhhCCCceeeccCCCCCCccc
Q psy9210 6 KVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQW 45 (234)
Q Consensus 6 k~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~ 45 (234)
.+-++.|+.-|- +-=+-|.+.|..|.+||.|+++...|
T Consensus 280 ~vkI~aSgGine--~~I~~~~~~g~piD~~GVGt~l~~~~ 317 (352)
T PRK07188 280 HVKIIVSSGFDA--KKIREFEAQNVPVDIYGVGSSLLKIN 317 (352)
T ss_pred CcEEEEeCCCCH--HHHHHHHHcCCCccEEecCcccccCc
Confidence 456777888874 33345788999999999999994433
No 87
>COG1838 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]
Probab=26.12 E-value=56 Score=29.15 Aligned_cols=83 Identities=20% Similarity=0.215 Sum_probs=58.2
Q ss_pred HHHHHHhhCCCceeeccCCCCCCccccceeeeeccccccccccccccceeeeeeecccccccCCCCCCCCC--ceecCCC
Q psy9210 20 EAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVFVFQISVNLFFQSITGTAMDKP--NVYDFHT 97 (234)
Q Consensus 20 EAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lPG~a~dkP--NvY~F~~ 97 (234)
.||+.|.+.+= .|...|...+.-+|+|| ||...+| -+=..|.
T Consensus 34 ~AH~ri~e~~~------~ge~lP~dl~g~~Iy~a------------------------------GP~~~~~~~~v~s~GP 77 (184)
T COG1838 34 AAHKRLLEMLD------RGEELPVDLKGHIIYYA------------------------------GPVKTKDGWVVGSAGP 77 (184)
T ss_pred HHHHHHHHHHh------cCCCCCccCCCCEEEEe------------------------------ccccCCCCceeeccCC
Confidence 68888776542 46677888888888887 4444443 3555676
Q ss_pred CcHHHHHHHHHhccHHHHhhcchhhhhhhcccCcCCCccccccCC
Q psy9210 98 TTYEDIYQDLMNKDKAFYTRNGLLHMLERNKRIKLKPEKFQESKD 142 (234)
Q Consensus 98 TtY~~Iy~dL~~kD~~~Yt~NGlL~MLdRN~rIK~~PErfQe~~~ 142 (234)
||=-.|=.- -..++.+-|++-|+..+.+.+...|-+++.+.
T Consensus 78 TTs~RMd~~----~~~~l~~~G~~~~iGKG~~~~~~~ea~~~~ka 118 (184)
T COG1838 78 TTSGRMDKF----TDELLEQTGVLAMIGKGGRGPETVEACKKHKA 118 (184)
T ss_pred cchhhhhhh----HHHHHHhcCeEEEEecCCcCHHHHHHHHHcCe
Confidence 764433111 13478888999999999999999999998764
No 88
>PRK01175 phosphoribosylformylglycinamidine synthase I; Provisional
Probab=25.97 E-value=1.3e+02 Score=27.12 Aligned_cols=34 Identities=21% Similarity=0.226 Sum_probs=29.4
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCCceeeccC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGT 37 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGT 37 (234)
..||||++....|.-+|+-+.|+++|+.|.-...
T Consensus 3 ~~kvaVl~~pG~n~d~e~~~Al~~aG~~v~~v~~ 36 (261)
T PRK01175 3 SIRVAVLRMEGTNCEDETVKAFRRLGVEPEYVHI 36 (261)
T ss_pred CCEEEEEeCCCCCCHHHHHHHHHHCCCcEEEEee
Confidence 4799999999999889999999999998865543
No 89
>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=25.80 E-value=1.6e+02 Score=25.25 Aligned_cols=40 Identities=10% Similarity=-0.062 Sum_probs=30.8
Q ss_pred hHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHH
Q psy9210 154 VYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFL 194 (234)
Q Consensus 154 vyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~ 194 (234)
-....+++++. +++..++|+.+|-.|-+++.+.|...+..
T Consensus 21 g~~lA~~~iNa-~ggi~G~~ielv~~D~~~~p~~a~~~a~~ 60 (332)
T cd06344 21 GVAQAQTEINL-QGGINGKLLKVVIANDGNDPEIAKKVADE 60 (332)
T ss_pred HHHHHHHHHHh-cCCCCCCeEEEEEECCCCChHHHHHHHHH
Confidence 34566788887 78888999999999999888777654443
No 90
>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=25.61 E-value=91 Score=26.04 Aligned_cols=33 Identities=6% Similarity=0.004 Sum_probs=24.6
Q ss_pred EEEecCCCccchHHHHHHhhCCCceeeccCCCCC
Q psy9210 8 AVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKK 41 (234)
Q Consensus 8 AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v 41 (234)
||+|+ |-.-.+.+-+.|+++|+.|.+|+....-
T Consensus 186 aI~~~-nd~~A~gv~~al~~~gisIvGfD~~~~~ 218 (265)
T cd06354 186 VIFAA-AGGTGNGVFQAAKEAGVYAIGVDSDQYY 218 (265)
T ss_pred EEEEC-CCCCchHHHHHHHhcCCeEEEecCcccc
Confidence 55555 6667788889999999877788775555
No 91
>cd00636 TroA-like Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between two globular domains linked by a single helix. Many of these proteins also possess a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). The TroA-like proteins differ in their fold and ligand-binding mechanism from the PBPI and PBPII proteins, but are structurally similar, however, to the beta-subunit of the nitrogenase molybdenum-iron protein MoFe. Most TroA-like proteins are encoded by ABC-type operons and appear to function as periplasmic components of ABC transporters in metal ion uptake.
Probab=25.59 E-value=2.5e+02 Score=19.82 Aligned_cols=76 Identities=20% Similarity=0.236 Sum_probs=44.5
Q ss_pred CccEEEEecchhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHHHHHHHHhhcchhhHHHHHHHHHHHHHH
Q psy9210 143 KFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLASELMSMFIKCEDLDNEIDEIMQEFEEK 222 (234)
Q Consensus 143 ~fDvIiTcEERvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~eL~~~l~~~eDld~~ideil~~feek 222 (234)
..|+||+... ..+...+.+.. .+ -|+-.++.....+.++...-...+-++...-++++.+-+.+++.++...++
T Consensus 61 ~pDlvi~~~~-~~~~~~~~l~~-~~----i~~~~~~~~~~~~~~~~~~~i~~lg~~~~~~~~a~~~~~~~~~~~~~i~~~ 134 (148)
T cd00636 61 KPDLIIANGS-GLEAWLDKLSK-IA----IPVVVVDEASELSLENIKESIRLIGKALGKEENAEELIAELDARLAELRAK 134 (148)
T ss_pred CCCEEEEecc-cchhHHHHHHH-hC----CCEEEECCCCcCCHHHHHHHHHHHHHHHCChHHHHHHHHHHHHHHHHHHHH
Confidence 6899999874 33445565655 22 344444332111455554444555555544466677888888888887776
Q ss_pred cC
Q psy9210 223 CS 224 (234)
Q Consensus 223 ~~ 224 (234)
.+
T Consensus 135 ~~ 136 (148)
T cd00636 135 LA 136 (148)
T ss_pred Hh
Confidence 63
No 92
>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=25.56 E-value=74 Score=27.05 Aligned_cols=31 Identities=35% Similarity=0.468 Sum_probs=22.0
Q ss_pred eEEEEecCCC--ccch-----HHHHHHhhCCCceeecc
Q psy9210 6 KVAVVCSSNM--NRSM-----EAHAYLSKKGVDVKSFG 36 (234)
Q Consensus 6 k~AvVCsSN~--NRSM-----EAH~~L~k~G~~V~SfG 36 (234)
+|||.|+|.. +.+. |.=+.|.++|+.+.+=|
T Consensus 2 ~i~V~~~s~~~~~~~~~~~A~~lG~~la~~g~~lV~GG 39 (178)
T TIGR00730 2 TVCVYCGSSPGGNAAYKELAAELGAYLAGQGWGLVYGG 39 (178)
T ss_pred EEEEECcCCCCCCcHHHHHHHHHHHHHHHCCCEEEECC
Confidence 7999999986 2222 23356889999887544
No 93
>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=25.53 E-value=1.9e+02 Score=25.32 Aligned_cols=42 Identities=7% Similarity=-0.114 Sum_probs=32.5
Q ss_pred hhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHH
Q psy9210 153 RVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLA 195 (234)
Q Consensus 153 RvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i 195 (234)
+-....+|+++. .++..+++|-+|-.|-+-++++|.-.+..+
T Consensus 21 ~g~~la~~~iN~-~GGi~G~~ielv~~D~~~~p~~a~~~a~~L 62 (348)
T cd06355 21 DAELLAIEEINA-AGGVLGRKIEAVVEDGASDWPTFAEKARKL 62 (348)
T ss_pred HHHHHHHHHHHh-cCCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Confidence 456778899988 777778999999888888887776555443
No 94
>PLN00123 isocitrate dehydrogenase (NAD+)
Probab=24.82 E-value=1.3e+02 Score=29.06 Aligned_cols=118 Identities=14% Similarity=0.262 Sum_probs=69.0
Q ss_pred CCCCCCceecCCCCcHHHHHHHHHhccHH-----HHhhcchhhhhhhcccCcCCCccccccCCCccEEEEecchhHHHHH
Q psy9210 85 TAMDKPNVYDFHTTTYEDIYQDLMNKDKA-----FYTRNGLLHMLERNKRIKLKPEKFQESKDKFDIIITCEERVYDQVL 159 (234)
Q Consensus 85 ~a~dkPNvY~F~~TtY~~Iy~dL~~kD~~-----~Yt~NGlL~MLdRN~rIK~~PErfQe~~~~fDvIiTcEERvyD~V~ 159 (234)
++.+|.||..+..--+.+++++..++=+. .|--+-..+|.. +|+ .||||+| +..|=.++
T Consensus 190 t~v~KaNvl~~t~glf~~~~~eva~eyPdV~~~~~~VDa~~~~Lv~-------~P~-------~fDViVt--~NlfGDIL 253 (360)
T PLN00123 190 TAVHKANIMKLADGLFLESCREVAKKYPGIKYNEIIVDNCCMQLVS-------KPE-------QFDVMVT--PNLYGNLV 253 (360)
T ss_pred EEEECCccccchhhHHHHHHHHHHhhCCCceEeeeeHHHHHHHHhh-------Ccc-------cCcEEEE--cCcccchh
Confidence 56899999997545799999888653221 133444444432 454 4799988 46899999
Q ss_pred HhHhhhccc--------------CCCceeEEEE----eecC----CCHHHHhhhHHHHHHHHHHhhcchhhHHHHHHHHH
Q psy9210 160 EHFDNQMIS--------------LENTPVHLIN----IDIQ----DNQEEATLGAFLASELMSMFIKCEDLDNEIDEIMQ 217 (234)
Q Consensus 160 Edl~~~r~~--------------~~~~pVHvIN----iDI~----Dn~EeA~~Ga~~i~eL~~~l~~~eDld~~ideil~ 217 (234)
-|+-..-.+ ....|||.== =||. =|+=-+.++|-.+++-...-+.++-+++.|...++
T Consensus 254 SDlaa~l~GglGl~pSanig~~~a~FEpvh~hGSA~~PdIAGk~iANP~a~IlS~amML~~lG~~~~A~~I~~AV~~~l~ 333 (360)
T PLN00123 254 ANTAAGIAGGTGVMPGGNVGADHAVFEQGASAGNVGNEKLVEQKKANPVALLLSSAMMLRHLQFPSFADRLETAVKRVIA 333 (360)
T ss_pred hhHHHHhcCCcCccceEeeCCCceEEEecccCCCcCCccccCCCccChHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHH
Confidence 999863311 2334766211 2442 24545555555555544333444456666666664
Q ss_pred H
Q psy9210 218 E 218 (234)
Q Consensus 218 ~ 218 (234)
+
T Consensus 334 ~ 334 (360)
T PLN00123 334 E 334 (360)
T ss_pred c
Confidence 3
No 95
>PRK14333 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=24.29 E-value=91 Score=29.51 Aligned_cols=48 Identities=17% Similarity=0.236 Sum_probs=36.3
Q ss_pred CCceEEEE---ecCCCccchHHHHHHhhCCCceeeccCCCCCCccccceeeeeccccc
Q psy9210 3 SNLKVAVV---CSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFC 57 (234)
Q Consensus 3 s~lk~AvV---CsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~ 57 (234)
++-||+++ |..|+.-|---...|.++||.+.+...+ ..++|+.-|-+=
T Consensus 5 ~~~~~~i~t~GC~~N~~ds~~~~~~l~~~G~~~~~~~~~-------ADiiiiNTC~v~ 55 (448)
T PRK14333 5 SRRSYWITTFGCQMNKADSERMAGILEDMGYQWAEDELQ-------ADLVLYNTCTIR 55 (448)
T ss_pred CCcEEEEEEcCCCCcHHHHHHHHHHHHHCcCEECCCccc-------CCEEEEEeeeee
Confidence 34477766 9999999988888999999988875332 256777777663
No 96
>COG4551 Predicted protein tyrosine phosphatase [General function prediction only]
Probab=24.18 E-value=73 Score=26.41 Aligned_cols=37 Identities=27% Similarity=0.428 Sum_probs=33.0
Q ss_pred ceEEEEecCCCccchHHHHHHhh-CCCceeeccCCCCC
Q psy9210 5 LKVAVVCSSNMNRSMEAHAYLSK-KGVDVKSFGTGDKK 41 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~L~k-~G~~V~SfGTG~~v 41 (234)
.|+-.+||-|.=||=-|-.+++. .|+.+.|-|+..--
T Consensus 2 ~r~lficsrnrlrsptae~~Fa~~~~vetdSAGl~~dA 39 (109)
T COG4551 2 KRILFICSRNRLRSPTAEVMFATWPGVETDSAGLAHDA 39 (109)
T ss_pred ceEEEEeccccccCcchhHHhhcCCCCccccccccccc
Confidence 47889999999999999999887 79999999998766
No 97
>PRK09548 PTS system ascorbate-specific transporter subunits IICB; Provisional
Probab=24.16 E-value=75 Score=32.63 Aligned_cols=30 Identities=27% Similarity=0.647 Sum_probs=26.0
Q ss_pred CCceEEEEecCCCccc----hHHHHHHhhCCCce
Q psy9210 3 SNLKVAVVCSSNMNRS----MEAHAYLSKKGVDV 32 (234)
Q Consensus 3 s~lk~AvVCsSN~NRS----MEAH~~L~k~G~~V 32 (234)
.++|+-+||-|-+--| |...++|+++|+++
T Consensus 505 k~mKILvaCGsGiGTStmva~kIkk~Lke~GI~v 538 (602)
T PRK09548 505 KPVRILAVCGQGQGSSMMMKMKIKKYLDKRGIPI 538 (602)
T ss_pred cccEEEEECCCCchHHHHHHHHHHHHHHHcCCCe
Confidence 4689999999999999 56788999999964
No 98
>cd00133 PTS_IIB PTS_IIB: subunit IIB of enzyme II (EII) is the central energy-coupling domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In the multienzyme PTS complex, EII is a carbohydrate-specific permease consisting of two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC 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 chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. The PTS is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, polyols, amino sugars, and other sugar derivatives. The four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB), can phosphorylate or interact with numerous non-PTS proteins thereby r
Probab=23.73 E-value=62 Score=21.61 Aligned_cols=25 Identities=28% Similarity=0.420 Sum_probs=16.8
Q ss_pred eEEEEecCCCccchHHHH----HHhhCCC
Q psy9210 6 KVAVVCSSNMNRSMEAHA----YLSKKGV 30 (234)
Q Consensus 6 k~AvVCsSN~NRSMEAH~----~L~k~G~ 30 (234)
|+++||.+.+.-|.-+-. .+++.|+
T Consensus 1 ~il~vc~~G~~~s~~l~~~l~~~~~~~~~ 29 (84)
T cd00133 1 KILVVCGSGIGSSSMLAEKLEKAAKELGI 29 (84)
T ss_pred CEEEECCCcHhHHHHHHHHHHHHHHHCCC
Confidence 578999999877754433 3445666
No 99
>PF05845 PhnH: Bacterial phosphonate metabolism protein (PhnH); InterPro: IPR008772 This family consists of several bacterial PhnH sequences, which is a component of the C-P lyase system (GenProp0232 from GENPROP) for the catabolism of phosphonate compounds []. The specific function of this component is unknown.; GO: 0015716 phosphonate transport; PDB: 2FSU_A.
Probab=23.72 E-value=40 Score=29.43 Aligned_cols=16 Identities=6% Similarity=0.297 Sum_probs=5.0
Q ss_pred cCCCCCCCCCceecCC
Q psy9210 81 SITGTAMDKPNVYDFH 96 (234)
Q Consensus 81 ~lPG~a~dkPNvY~F~ 96 (234)
+|.||-|...+...-.
T Consensus 135 ~LsGPGI~~~~~i~~~ 150 (192)
T PF05845_consen 135 TLSGPGIKGERTIAVD 150 (192)
T ss_dssp EEE-------EEE---
T ss_pred EEEcCccccceEEccc
Confidence 8999999988876644
No 100
>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=23.54 E-value=1.6e+02 Score=25.56 Aligned_cols=74 Identities=14% Similarity=0.114 Sum_probs=45.3
Q ss_pred hhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHHHHH--HHHhhcchhhHHHHHHHHHHHHHHcCCCcee
Q psy9210 153 RVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLASEL--MSMFIKCEDLDNEIDEIMQEFEEKCSRPLLH 229 (234)
Q Consensus 153 RvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~eL--~~~l~~~eDld~~ideil~~feek~~r~~Lh 229 (234)
+-....+|+++. .++...++|.++-.|.+.+.+.|.-.|+.+.+- +..+.-. +......-+..+-++.+.|++.
T Consensus 21 ~g~~la~~~iN~-~gGi~G~~i~lv~~D~~~~p~~a~~~a~~Li~~~~V~aiiG~--~~s~~~~a~~~~~~~~~vp~i~ 96 (347)
T cd06335 21 RGARLAIDEINA-AGGVLGRKLELVERDDRGNPARGLQNAQELAADEKVVAVLGG--LHTPVALANLEFIQQNKIPLIG 96 (347)
T ss_pred HHHHHHHHHHHh-cCCcCCeEEEEEeccCCCCcHHHHHHHHHHhccCCeEEEEcC--CCCHHHHhhhHHHHhcCCcEEe
Confidence 456778888877 777778999999998888877776555443321 1112211 2223333444555666788775
No 101
>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=23.37 E-value=2.5e+02 Score=24.34 Aligned_cols=41 Identities=7% Similarity=-0.083 Sum_probs=29.9
Q ss_pred chhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHH
Q psy9210 152 ERVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAF 193 (234)
Q Consensus 152 ERvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~ 193 (234)
.+-++..+++.+. +++..+++|-++-.|-+.+.+.|...+.
T Consensus 27 ~~g~~~a~~~~Na-~gGi~G~~i~l~~~D~~~~~~~a~~~a~ 67 (362)
T cd06343 27 RTGAAYFFMINND-QGGINGRKIELIVEDDGYSPPKTVEQTR 67 (362)
T ss_pred HHHHHHHHHHHHh-cCCcCCeEEEEEEecCCCChHHHHHHHH
Confidence 3556777888877 7778889999998888777666554443
No 102
>cd01522 RHOD_1 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins.
Probab=22.92 E-value=1.6e+02 Score=22.28 Aligned_cols=34 Identities=29% Similarity=0.452 Sum_probs=25.7
Q ss_pred CceEEEEecCCCccchHHHHHHhhCCC-ceeeccCC
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTG 38 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG 38 (234)
.-++.++|.+. .||-.+=..|.+.|| +|..+--|
T Consensus 64 ~~~ivv~C~~G-~rs~~aa~~L~~~G~~~v~~l~gG 98 (117)
T cd01522 64 DRPVLLLCRSG-NRSIAAAEAAAQAGFTNVYNVLEG 98 (117)
T ss_pred CCeEEEEcCCC-ccHHHHHHHHHHCCCCeEEECcCc
Confidence 45688888775 788888889999999 47766444
No 103
>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=22.91 E-value=85 Score=22.97 Aligned_cols=25 Identities=28% Similarity=0.508 Sum_probs=19.0
Q ss_pred eEEEEecCCCccchHH----HHHHhhCCC
Q psy9210 6 KVAVVCSSNMNRSMEA----HAYLSKKGV 30 (234)
Q Consensus 6 k~AvVCsSN~NRSMEA----H~~L~k~G~ 30 (234)
|+++||.+.+.-|+=+ -+.+++.|.
T Consensus 2 kilvvCg~G~gtS~ml~~ki~~~~~~~~~ 30 (87)
T cd05567 2 KIVFACDAGMGSSAMGASVLRKKLKKAGL 30 (87)
T ss_pred EEEEECCCCccHHHHHHHHHHHHHHHCCC
Confidence 7999999999988653 455566665
No 104
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=22.57 E-value=1.6e+02 Score=21.48 Aligned_cols=48 Identities=25% Similarity=0.252 Sum_probs=34.0
Q ss_pred CCCCceecCCCCcHHHHHHHHHhccHHHHhhcchhhhhhhcccCcCCCcccccc
Q psy9210 87 MDKPNVYDFHTTTYEDIYQDLMNKDKAFYTRNGLLHMLERNKRIKLKPEKFQES 140 (234)
Q Consensus 87 ~dkPNvY~F~~TtY~~Iy~dL~~kD~~~Yt~NGlL~MLdRN~rIK~~PErfQe~ 140 (234)
++-|+++..| -|+++..+.+..-=.- |- =.+++-|+.|+..|+++|..
T Consensus 21 Pdlpgc~s~G-~T~eea~~n~~eai~l-~~----e~~~~~~~~iP~~~~~~~~~ 68 (73)
T COG1598 21 PDLPGCHSQG-ETLEEALQNAKEAIEL-HL----EALLEEGEPIPAAPESFQRV 68 (73)
T ss_pred CCCCCccccC-CCHHHHHHHHHHHHHH-HH----HHHHhcCCcCCCccccccee
Confidence 3889999999 8999988877653222 22 22667777787788888754
No 105
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=22.45 E-value=98 Score=21.24 Aligned_cols=28 Identities=25% Similarity=0.247 Sum_probs=22.2
Q ss_pred CCccchHHHHHHhhCCCceeeccCCCCC
Q psy9210 14 NMNRSMEAHAYLSKKGVDVKSFGTGDKK 41 (234)
Q Consensus 14 N~NRSMEAH~~L~k~G~~V~SfGTG~~v 41 (234)
|...-.-.|.+....|+.-.|.|.|..-
T Consensus 29 ~~~~R~~iH~~a~~~gL~s~S~g~~~~R 56 (63)
T PF01424_consen 29 NSFERKLIHELAEYYGLKSKSEGEGPNR 56 (63)
T ss_dssp -SHHHHHHHHHHHHCTEEEEEESSSSSS
T ss_pred CHHHHHHHHHHHHHCCCEEEEecCCCCe
Confidence 3333467999999999999999998765
No 106
>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=22.23 E-value=3.2e+02 Score=21.99 Aligned_cols=41 Identities=10% Similarity=-0.027 Sum_probs=30.9
Q ss_pred CCccEEEEecchhHHHHHHhHhhhcccCCCceeEEEEeecCC
Q psy9210 142 DKFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDIQD 183 (234)
Q Consensus 142 ~~fDvIiTcEERvyD~V~Edl~~~r~~~~~~pVHvINiDI~D 183 (234)
..+|.|++.....-..++.-+.. .+-.-...+.|+-+|-.+
T Consensus 177 ~~~~ai~~~~d~~a~~~~~~l~~-~g~~~p~~i~v~~~d~~~ 217 (270)
T cd06296 177 ERPTAIFAGNDLMALGVYEAARE-RGLRIPEDLSVVGFDDLP 217 (270)
T ss_pred CCCcEEEEcCcHHHHHHHHHHHH-hCCCCCCceEEEEECChh
Confidence 45899999998888888988887 554444568888886443
No 107
>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=22.12 E-value=2e+02 Score=24.83 Aligned_cols=72 Identities=19% Similarity=0.163 Sum_probs=41.4
Q ss_pred chhHHHHHHhHhhhcc-cCCCceeEEEEeecCCCHHHHhhhHHHHHHHHHH-----hhcchhhHHHHHHHHHHHHHHcCC
Q psy9210 152 ERVYDQVLEHFDNQMI-SLENTPVHLINIDIQDNQEEATLGAFLASELMSM-----FIKCEDLDNEIDEIMQEFEEKCSR 225 (234)
Q Consensus 152 ERvyD~V~Edl~~~r~-~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~eL~~~-----l~~~eDld~~ideil~~feek~~r 225 (234)
++..+..+|+++. ++ ...++++.++-.|.+.+...| +..+.+|... +.- -.....-..+..+-++.+.
T Consensus 18 ~~~~~lAv~~iN~-~gg~~~g~~i~~~~~D~~~~~~~a---~~~a~~l~~~~~v~~viG--~~~s~~~~a~~~~~~~~~i 91 (350)
T cd06366 18 LPAIEMALEDVNA-DNSILPGYRLVLHVRDSKCDPVQA---ASAALDLLENKPVVAIIG--PQCSSVAEFVAEVANEWNV 91 (350)
T ss_pred HHHHHHHHHHHhc-CCCcCCCcEEEEEecCCCCCHHHH---HHHHHHHhccCCceEEEC--CCcHHHHHHHHHHhhcCCe
Confidence 4677888999998 65 556788877776666555544 4444444432 111 1233333444455556666
Q ss_pred Ccee
Q psy9210 226 PLLH 229 (234)
Q Consensus 226 ~~Lh 229 (234)
|++-
T Consensus 92 p~i~ 95 (350)
T cd06366 92 PVLS 95 (350)
T ss_pred eEEe
Confidence 6553
No 108
>KOG3217|consensus
Probab=21.82 E-value=90 Score=27.44 Aligned_cols=96 Identities=27% Similarity=0.403 Sum_probs=62.9
Q ss_pred CceEEEEecCCCccchHHHHHH----hhCCC----ceeeccCCCCCCccccceeeeeccccccccccccccceeeeeeec
Q psy9210 4 NLKVAVVCSSNMNRSMEAHAYL----SKKGV----DVKSFGTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVFVFQISV 75 (234)
Q Consensus 4 ~lk~AvVCsSN~NRSMEAH~~L----~k~G~----~V~SfGTG~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (234)
+.+|+.||--|-=||=-|-+++ .|+|. .|-|+||++.=
T Consensus 6 ~~svlFvclGNiCRSP~AEaVFr~~v~K~~l~~~~~iDSagt~~yh---------------------------------- 51 (159)
T KOG3217|consen 6 TKSVLFVCLGNICRSPIAEAVFRDLVKKRNLSEEWHIDSAGTSGYH---------------------------------- 51 (159)
T ss_pred ceEEEEEEecccccCHHHHHHHHHHHHHcCcceeeeeccccccccc----------------------------------
Confidence 4678999999999997777665 45664 67999998866
Q ss_pred ccccccCCCCCCCCCceecCCCCcHHHHHHHHHhccHHHHhhcchhhhhhhcccCcCCCccccccCCCccEEEEecchhH
Q psy9210 76 NLFFQSITGTAMDKPNVYDFHTTTYEDIYQDLMNKDKAFYTRNGLLHMLERNKRIKLKPEKFQESKDKFDIIITCEERVY 155 (234)
Q Consensus 76 ~~~~~~lPG~a~dkPNvY~F~~TtY~~Iy~dL~~kD~~~Yt~NGlL~MLdRN~rIK~~PErfQe~~~~fDvIiTcEERvy 155 (234)
.|.++|.. +- .--+++||= +=-+-|.|+ |+-| ..||.|++-+|...
T Consensus 52 -------~G~~PD~R--------~~------------s~lK~hGI~-~~H~aRqit--~~DF----~~FDYI~~MDesN~ 97 (159)
T KOG3217|consen 52 -------TGRSPDPR--------TL------------SILKKHGIK-IDHLARQIT--TSDF----REFDYILAMDESNL 97 (159)
T ss_pred -------cCCCCChH--------HH------------HHHHHcCCc-chhhccccc--HhHh----hhcceeEEecHHHH
Confidence 47776641 11 124556753 444455554 3444 46999999998766
Q ss_pred HHHHHhHhhhcc
Q psy9210 156 DQVLEHFDNQMI 167 (234)
Q Consensus 156 D~V~Edl~~~r~ 167 (234)
..+.+-.-+|+.
T Consensus 98 ~dL~~~a~~~~~ 109 (159)
T KOG3217|consen 98 RDLLRKASNQPK 109 (159)
T ss_pred HHHHHHhccCCC
Confidence 555554334343
No 109
>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=21.59 E-value=2.3e+02 Score=23.84 Aligned_cols=36 Identities=11% Similarity=0.192 Sum_probs=26.0
Q ss_pred hhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHh
Q psy9210 153 RVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEAT 189 (234)
Q Consensus 153 RvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~ 189 (234)
+.+...+++++. +++..++||-++-.|-+-+.+.|.
T Consensus 23 ~g~~~a~~~~N~-~ggi~G~~i~l~~~D~~~~~~~a~ 58 (343)
T PF13458_consen 23 RGAELAVDEINA-AGGINGRKIELVVYDDGGDPAQAV 58 (343)
T ss_dssp HHHHHHHHHHHH-TTEETTEEEEEEEEE-TT-HHHHH
T ss_pred HHHHHHHHHHHH-hCCcCCccceeeeccCCCChHHHH
Confidence 456777888888 677778999999888777666654
No 110
>cd04509 PBP1_ABC_transporter_GCPR_C_like Family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. This CD includes members of the family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. The family C GPCR includes glutamate/glycine-gated ion channels such as the NMDA receptor, G-protein-coupled receptors, metabotropic glutamate, GABA-B, calcium sensing, phermone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. The glutamate receptors that form cation-selective ion channels, iGluR, can be classified into three different subgroups according to their binding-affinity for the agonists NMDA (N-methyl-D-asparate), AMPA (alpha-amino-3-dihydro-5-methyl-3-oxo-4-isoxazolepropionic acid), and kainate. L-glutamate is a major neurotransmitter in the brain of vertebrates and acts th
Probab=21.37 E-value=3.7e+02 Score=21.32 Aligned_cols=75 Identities=12% Similarity=0.087 Sum_probs=42.9
Q ss_pred chhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHHHHH--HHHhhcchhhHHHHHHHHHHHHHHcCCCcee
Q psy9210 152 ERVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLASEL--MSMFIKCEDLDNEIDEIMQEFEEKCSRPLLH 229 (234)
Q Consensus 152 ERvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~eL--~~~l~~~eDld~~ideil~~feek~~r~~Lh 229 (234)
.+.....+++++. +++..+.++.++-.|.+.+.+.+...+..+++- +..+.-.. .......+.+.-+..+.|++-
T Consensus 20 ~~~~~~a~~~~n~-~~g~~g~~~~~~~~d~~~~~~~~~~~~~~l~~~~~v~~iig~~--~~~~~~~~~~~~~~~~iP~i~ 96 (299)
T cd04509 20 LAGAQLAVEEINA-KGGIPGRKLELVIYDDQSDPARALAAARRLCQQEGVDALVGPV--SSGVALAVAPVAEALKIPLIS 96 (299)
T ss_pred HHHHHHHHHHHHh-cCCCCCcEEEEEEecCCCCHHHHHHHHHHHhcccCceEEEcCC--CcHHHHHHHHHHhhCCceEEe
Confidence 4566778888888 667778888888888777665554443333321 22232221 112223445555666777654
No 111
>PRK14862 rimO ribosomal protein S12 methylthiotransferase; Provisional
Probab=21.32 E-value=1.3e+02 Score=28.58 Aligned_cols=48 Identities=21% Similarity=0.368 Sum_probs=34.2
Q ss_pred CCceEEEE---ecCCCccchHHHHHHhhCCCceeeccCCCCCCccccceeeeeccccc
Q psy9210 3 SNLKVAVV---CSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFC 57 (234)
Q Consensus 3 s~lk~AvV---CsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~ 57 (234)
...||+++ |..|+--|----..|.++||.+.++.. +.. ++|+.-|.+=
T Consensus 6 ~~~~~~i~t~GC~~N~~dse~~~~~l~~~G~~~~~~~~------~aD-~ivinTC~v~ 56 (440)
T PRK14862 6 AAPKIGFVSLGCPKALVDSERILTQLRAEGYEISPSYD------GAD-LVIVNTCGFI 56 (440)
T ss_pred CCCEEEEEEcCCCCcHHHHHHHHHHHHHCcCEECCCcc------cCC-EEEEeccccc
Confidence 34567765 999999998888899999999987643 222 3455566553
No 112
>cd06328 PBP1_SBP_like_2 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=21.14 E-value=2.4e+02 Score=24.45 Aligned_cols=43 Identities=21% Similarity=0.101 Sum_probs=30.5
Q ss_pred hhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHH
Q psy9210 153 RVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLA 195 (234)
Q Consensus 153 RvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i 195 (234)
+-.+..+++++|..++..++|+-++-.|-+-+++.|...+..+
T Consensus 21 ~g~~lav~~inn~~ggi~G~~i~lv~~D~~~~p~~a~~~~~~l 63 (333)
T cd06328 21 TGFMLGLEYATGGTMQVDGRPIEVIVKDDAGNPEVAVSLAREL 63 (333)
T ss_pred HHHHHHHHHHHhcCCCcCCEEEEEEEecCCCChHHHHHHHHHH
Confidence 4456678888665677788999888887777777666555433
No 113
>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=20.99 E-value=2.6e+02 Score=24.66 Aligned_cols=43 Identities=7% Similarity=-0.132 Sum_probs=32.6
Q ss_pred hhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHHH
Q psy9210 153 RVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLAS 196 (234)
Q Consensus 153 RvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~ 196 (234)
+-.+..+++++. +++..++||-++-.|-+-+++.|...++.+.
T Consensus 22 ~g~~lav~~iN~-~GGi~G~~i~l~~~Dd~~~p~~a~~~a~~Lv 64 (359)
T TIGR03407 22 DAELMAIEEINA-SGGVLGKKIEPVVEDGASDWPTFAEKARKLI 64 (359)
T ss_pred HHHHHHHHHHHh-cCCCCCcEEEEEEeCCCCCHHHHHHHHHHHH
Confidence 456778899988 7888889999988888877777765554443
No 114
>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=20.97 E-value=2.4e+02 Score=24.95 Aligned_cols=44 Identities=7% Similarity=-0.093 Sum_probs=33.5
Q ss_pred chhHHHHHHhHhhhcccCCCceeEEEEeecCCCHHHHhhhHHHHH
Q psy9210 152 ERVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLAS 196 (234)
Q Consensus 152 ERvyD~V~Edl~~~r~~~~~~pVHvINiDI~Dn~EeA~~Ga~~i~ 196 (234)
.+-+...+++++. +++..++|+-++..|-+-+++.|.-.++.+.
T Consensus 20 ~~g~~la~~~iN~-~GGi~G~~ielv~~D~~~~p~~a~~~a~~li 63 (360)
T cd06357 20 RNGALLAIEEINA-AGGVLGRELEPVEYDPGGDPDAYRALAERLL 63 (360)
T ss_pred HHHHHHHHHHHhh-cCCCCCeEEEEEEECCCCCHHHHHHHHHHHH
Confidence 3456778899998 7878889999998888888777766555444
No 115
>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=20.91 E-value=1.6e+02 Score=21.88 Aligned_cols=34 Identities=24% Similarity=0.283 Sum_probs=23.2
Q ss_pred ceEEEEecCCCccchHHHHH----HhhCCC---ceeeccCC
Q psy9210 5 LKVAVVCSSNMNRSMEAHAY----LSKKGV---DVKSFGTG 38 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~----L~k~G~---~V~SfGTG 38 (234)
-.+-++|.+...||..|=.. |++.|+ +|.+..-|
T Consensus 67 ~~iv~~C~~~g~rs~~a~~~l~~~l~~~G~~~~~v~~l~GG 107 (113)
T cd01443 67 KLAIFYCGSSQGRGPRAARWFADYLRKVGESLPKSYILTGG 107 (113)
T ss_pred CEEEEECCCCCcccHHHHHHHHHHHhccCCCCCeEEEECCh
Confidence 46888999888999776555 445686 56665433
No 116
>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=20.89 E-value=1.8e+02 Score=23.61 Aligned_cols=39 Identities=15% Similarity=0.088 Sum_probs=30.9
Q ss_pred CCccEEEEecchhHHHHHHhHhhhcccCCCceeEEEEeec
Q psy9210 142 DKFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDI 181 (234)
Q Consensus 142 ~~fDvIiTcEERvyD~V~Edl~~~r~~~~~~pVHvINiDI 181 (234)
..+|.|+++..+..-.++.-+.. ++-.-.+.+.|+-+|-
T Consensus 176 ~~~~ai~~~~d~~a~g~~~al~~-~g~~vp~di~i~g~d~ 214 (269)
T cd06293 176 DPPTAIFAASDEIAIGLLEVLRE-RGLSIPGDMSLVGFDD 214 (269)
T ss_pred CCCCEEEEcCcHHHHHHHHHHHH-cCCCCccceEEEeecC
Confidence 45899999999998889988887 5544445689998863
No 117
>PF13361 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 1UAA_B 3U4Q_A 3U44_A 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A ....
Probab=20.81 E-value=1.1e+02 Score=25.38 Aligned_cols=34 Identities=21% Similarity=0.320 Sum_probs=25.6
Q ss_pred ceEEEEecCCCccchHHHHHHhhCCCceeeccCCC
Q psy9210 5 LKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGD 39 (234)
Q Consensus 5 lk~AvVCsSN~NRSMEAH~~L~k~G~~V~SfGTG~ 39 (234)
=.+||+|-+| ....+-...|.++|+.+..-|.++
T Consensus 78 ~diAVL~R~~-~~~~~i~~~L~~~gIp~~~~~~~~ 111 (351)
T PF13361_consen 78 SDIAVLVRTN-SQIKEIEDALKEAGIPYRISGSKS 111 (351)
T ss_dssp GGEEEEESSG-GHHHHHHHHHHHTTS-EEESSSSB
T ss_pred ccEEEEEECc-hhHHHHHHHHhhhcceeEeccccc
Confidence 3599999993 345677999999999997776643
No 118
>cd01535 4RHOD_Repeat_4 Member of the Rhodanese Homology Domain superfamily, repeat 4. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 4th repeat which, in general, contains the putative catalytic Cys residue.
Probab=20.65 E-value=1.6e+02 Score=23.76 Aligned_cols=37 Identities=24% Similarity=0.232 Sum_probs=27.7
Q ss_pred CCCceEEEEecCCCccchHHHHHHhhCCC-ceeeccCCC
Q psy9210 2 PSNLKVAVVCSSNMNRSMEAHAYLSKKGV-DVKSFGTGD 39 (234)
Q Consensus 2 ~s~lk~AvVCsSN~NRSMEAH~~L~k~G~-~V~SfGTG~ 39 (234)
+..-++-|+|++. .+|--+=..|++.|+ +|...=.|-
T Consensus 47 ~~~~~vVv~c~~g-~~a~~aa~~L~~~G~~~v~~L~GG~ 84 (145)
T cd01535 47 PAAERYVLTCGSS-LLARFAAADLAALTVKPVFVLEGGT 84 (145)
T ss_pred CCCCCEEEEeCCC-hHHHHHHHHHHHcCCcCeEEecCcH
Confidence 3445799999995 566666678999999 788875554
No 119
>TIGR01578 MiaB-like-B MiaB-like tRNA modifying enzyme, archaeal-type. This clade is a member of a subfamily (TIGR00089) and spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this clade, while eukaryotes have sequences described by this model as well as ones falling within the scope of the MiaB equivalog model.
Probab=20.60 E-value=78 Score=29.68 Aligned_cols=41 Identities=17% Similarity=0.259 Sum_probs=31.9
Q ss_pred ecCCCccchHHHHHHhhCCCceeeccCCCCCCccccceeeeecccccc
Q psy9210 11 CSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCS 58 (234)
Q Consensus 11 CsSN~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~~~~~~~~~~~~~~ 58 (234)
|.-|+--|----..|.++||.+.+. ..+..++|+..|-+=.
T Consensus 9 C~~N~~ds~~~~~~l~~~G~~~~~~-------~~~ADviiinTC~v~~ 49 (420)
T TIGR01578 9 CTLNNGDSEIMKNSLAAYGHELVNN-------AEEADLAILNTCTVKN 49 (420)
T ss_pred CCCcHHHHHHHHHHHHHCCCEECCC-------cccCCEEEEEeeeeee
Confidence 9999998877788999999988752 2345788888887643
No 120
>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=20.45 E-value=3.6e+02 Score=21.56 Aligned_cols=39 Identities=5% Similarity=-0.026 Sum_probs=30.4
Q ss_pred CCccEEEEecchhHHHHHHhHhhhcccCCCceeEEEEeec
Q psy9210 142 DKFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDI 181 (234)
Q Consensus 142 ~~fDvIiTcEERvyD~V~Edl~~~r~~~~~~pVHvINiDI 181 (234)
...|.|+++..+....++..+.. .+-....-+.||-+|=
T Consensus 176 ~~~~ai~~~~d~~a~~~~~~l~~-~g~~~p~di~vig~d~ 214 (268)
T cd01575 176 PDLDAVFCSNDDLALGALFECQR-RGISVPEDIAIAGFGD 214 (268)
T ss_pred CCCCEEEECCcHHHHHHHHHHHH-hCCCCCcceEEEecCC
Confidence 45899999999999999999987 5544455677887763
No 121
>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=20.15 E-value=81 Score=22.90 Aligned_cols=21 Identities=29% Similarity=0.586 Sum_probs=19.2
Q ss_pred HHHHHHhhCCCceeeccCCCC
Q psy9210 20 EAHAYLSKKGVDVKSFGTGDK 40 (234)
Q Consensus 20 EAH~~L~k~G~~V~SfGTG~~ 40 (234)
-.|.+-.+.|+.-+|+|.|..
T Consensus 33 ~vH~~a~~~gL~s~S~G~g~~ 53 (60)
T cd02640 33 LIHQIAQKYGLKSRSYGSGND 53 (60)
T ss_pred HHHHHHHHcCCceeeEeCCCC
Confidence 579999999999999999975
No 122
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=20.07 E-value=1.6e+02 Score=20.78 Aligned_cols=41 Identities=17% Similarity=0.169 Sum_probs=25.9
Q ss_pred ceEEEEecCC-----CccchHHHHHHhhCCCceeeccCCCCCCccc
Q psy9210 5 LKVAVVCSSN-----MNRSMEAHAYLSKKGVDVKSFGTGDKKPQQW 45 (234)
Q Consensus 5 lk~AvVCsSN-----~NRSMEAH~~L~k~G~~V~SfGTG~~v~~~~ 45 (234)
.+++++..++ ....++.-..|.++|++|.-.-.+.....++
T Consensus 2 ~qv~i~p~~~~~~~~~~~a~~la~~Lr~~g~~v~~d~~~~~l~k~i 47 (94)
T cd00861 2 FDVVIIPMNMKDEVQQELAEKLYAELQAAGVDVLLDDRNERPGVKF 47 (94)
T ss_pred eEEEEEEcCCCcHHHHHHHHHHHHHHHHCCCEEEEECCCCCcccch
Confidence 5777777654 2344555667888999997754555543333
Done!