Query psy7740
Match_columns 184
No_of_seqs 187 out of 1092
Neff 5.8
Searched_HMMs 46136
Date Fri Aug 16 17:36:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7740.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7740hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3477|consensus 100.0 4.9E-36 1.1E-40 217.1 5.7 86 1-86 1-87 (97)
2 PLN02496 probable phosphopanto 99.9 2.7E-26 5.9E-31 191.5 5.6 100 74-182 17-116 (209)
3 KOG0672|consensus 99.9 3.6E-26 7.7E-31 187.3 3.5 105 74-182 18-122 (218)
4 PRK07313 phosphopantothenoylcy 99.9 4.2E-25 9.2E-30 180.7 5.7 95 76-182 1-97 (182)
5 TIGR02113 coaC_strep phosphopa 99.9 5.5E-24 1.2E-28 173.5 6.0 94 77-182 1-96 (177)
6 PRK08305 spoVFB dipicolinate s 99.9 1.2E-22 2.7E-27 168.2 5.1 90 75-182 4-104 (196)
7 PRK05579 bifunctional phosphop 99.9 1.1E-22 2.4E-27 183.8 5.0 96 75-182 5-102 (399)
8 PRK13982 bifunctional SbtC-lik 99.9 1.7E-22 3.6E-27 186.0 5.4 96 75-182 69-166 (475)
9 PRK05920 aromatic acid decarbo 99.9 2.3E-22 5.1E-27 167.5 5.7 97 75-182 2-113 (204)
10 PF02441 Flavoprotein: Flavopr 99.9 1.7E-22 3.8E-27 155.6 3.8 93 77-182 1-93 (129)
11 PRK06029 3-octaprenyl-4-hydrox 99.8 8.1E-22 1.7E-26 162.0 3.6 88 77-182 2-98 (185)
12 TIGR00521 coaBC_dfp phosphopan 99.8 2.2E-21 4.7E-26 175.0 4.6 95 75-182 2-98 (390)
13 TIGR00421 ubiX_pad polyprenyl 99.8 2.9E-21 6.2E-26 158.0 2.9 87 78-182 1-95 (181)
14 TIGR02700 flavo_MJ0208 archaeo 99.8 5.1E-20 1.1E-24 155.4 5.5 94 78-182 1-105 (234)
15 COG0452 Dfp Phosphopantothenoy 99.8 7.9E-20 1.7E-24 165.0 5.4 94 76-182 4-99 (392)
16 TIGR02852 spore_dpaB dipicolin 99.8 1.2E-19 2.6E-24 149.5 3.8 88 77-182 1-99 (187)
17 TIGR02699 archaeo_AfpA archaeo 99.6 2.4E-16 5.3E-21 128.5 4.8 91 78-182 1-98 (174)
18 COG0163 UbiX 3-polyprenyl-4-hy 99.5 7.9E-15 1.7E-19 120.2 3.8 89 77-182 3-100 (191)
19 COG1036 Archaeal flavoproteins 99.2 6.6E-12 1.4E-16 101.6 3.4 96 73-182 5-108 (187)
20 PF06747 CHCH: CHCH domain; I 98.7 7E-09 1.5E-13 63.0 2.4 35 29-63 1-35 (35)
21 KOG4695|consensus 94.9 0.026 5.6E-07 43.3 3.1 36 26-61 45-80 (122)
22 PF05676 NDUF_B7: NADH-ubiquin 93.5 0.054 1.2E-06 37.9 2.0 49 20-68 13-61 (66)
23 PF08991 DUF1903: Domain of un 87.0 0.83 1.8E-05 31.9 3.2 36 28-63 3-38 (67)
24 PF08583 Cmc1: Cytochrome c ox 81.4 1.1 2.4E-05 30.2 1.9 39 27-65 11-50 (69)
25 KOG3468|consensus 68.4 3.8 8.3E-05 31.6 2.0 51 22-72 50-100 (128)
26 KOG4618|consensus 68.4 6.1 0.00013 28.0 2.8 37 27-63 22-58 (74)
27 cd00926 Cyt_c_Oxidase_VIb Cyto 64.0 9.9 0.00022 26.9 3.3 31 28-58 22-52 (75)
28 PF10200 Ndufs5: NADH:ubiquino 63.5 14 0.00031 27.6 4.2 48 22-69 26-75 (96)
29 KOG4083|consensus 55.2 9.4 0.0002 31.8 2.2 37 25-61 144-180 (192)
30 KOG4090|consensus 53.3 16 0.00034 29.7 3.1 43 21-63 110-152 (157)
31 PF05051 COX17: Cytochrome C o 49.5 21 0.00045 23.6 2.7 30 29-60 12-41 (49)
32 PF03033 Glyco_transf_28: Glyc 47.7 18 0.0004 26.6 2.6 45 80-132 2-47 (139)
33 TIGR02536 eut_hyp ethanolamine 45.8 17 0.00036 30.6 2.3 22 161-182 52-73 (207)
34 PF10203 Pet191_N: Cytochrome 45.5 16 0.00034 25.5 1.8 27 38-64 31-58 (68)
35 PF05051 COX17: Cytochrome C o 41.3 45 0.00098 22.0 3.3 19 28-46 30-48 (49)
36 PF02297 COX6B: Cytochrome oxi 40.8 22 0.00049 24.8 2.0 33 29-61 12-54 (76)
37 PRK03971 putative deoxyhypusin 40.6 49 0.0011 29.9 4.6 39 76-123 66-104 (334)
38 KOG3458|consensus 40.0 18 0.00039 29.4 1.6 37 28-64 77-114 (170)
39 PF09623 Cas_NE0113: CRISPR-as 39.4 33 0.00071 29.2 3.2 43 77-125 2-44 (224)
40 cd08437 PBP2_MleR The substrat 36.4 47 0.001 24.7 3.4 35 79-119 2-36 (198)
41 TIGR00661 MJ1255 conserved hyp 35.3 40 0.00088 29.0 3.2 44 79-131 2-47 (321)
42 COG0378 HypB Ni2+-binding GTPa 35.3 86 0.0019 26.5 5.0 76 49-132 33-115 (202)
43 cd08440 PBP2_LTTR_like_4 TThe 33.2 56 0.0012 23.8 3.3 34 79-118 2-35 (197)
44 KOG4110|consensus 31.9 69 0.0015 24.7 3.5 53 17-69 23-78 (120)
45 COG0794 GutQ Predicted sugar p 31.5 72 0.0016 26.8 3.9 25 79-103 89-113 (202)
46 cd08470 PBP2_CrgA_like_1 The C 31.2 47 0.001 24.6 2.6 35 79-119 3-37 (197)
47 KOG3481|consensus 31.0 80 0.0017 23.2 3.6 37 27-63 11-55 (87)
48 cd08471 PBP2_CrgA_like_2 The C 29.7 53 0.0011 24.4 2.7 35 79-119 3-37 (201)
49 cd08422 PBP2_CrgA_like The C-t 29.3 51 0.0011 24.1 2.5 35 79-119 3-37 (197)
50 PF07956 DUF1690: Protein of U 29.2 73 0.0016 25.2 3.4 36 25-60 105-140 (142)
51 cd08472 PBP2_CrgA_like_3 The C 28.9 62 0.0013 24.0 2.9 34 79-118 3-36 (202)
52 PLN03079 Uncharacterized prote 28.6 82 0.0018 23.4 3.4 36 28-63 17-60 (91)
53 KOG1502|consensus 28.2 55 0.0012 29.5 2.9 31 80-119 8-38 (327)
54 PF09001 DUF1890: Domain of un 27.9 81 0.0018 25.1 3.4 30 91-128 15-44 (139)
55 cd08475 PBP2_CrgA_like_6 The C 27.9 61 0.0013 23.9 2.7 40 79-124 3-42 (199)
56 cd08434 PBP2_GltC_like The sub 27.8 73 0.0016 23.2 3.1 36 79-120 2-37 (195)
57 PF01171 ATP_bind_3: PP-loop f 27.6 70 0.0015 25.3 3.1 26 78-103 1-26 (182)
58 PF07802 GCK: GCK domain; Int 27.1 73 0.0016 22.8 2.8 36 26-61 11-51 (76)
59 PF13460 NAD_binding_10: NADH( 27.0 77 0.0017 24.3 3.2 29 80-120 3-31 (183)
60 PRK07667 uridine kinase; Provi 26.9 48 0.001 26.6 2.1 28 76-103 15-45 (193)
61 cd08460 PBP2_DntR_like_1 The C 26.7 68 0.0015 24.0 2.8 34 79-118 2-35 (200)
62 cd08448 PBP2_LTTR_aromatics_li 26.6 88 0.0019 22.9 3.4 34 79-118 2-35 (197)
63 cd08456 PBP2_LysR The C-termin 26.5 75 0.0016 23.4 3.0 37 79-121 2-38 (196)
64 cd08438 PBP2_CidR The C-termin 26.4 65 0.0014 23.6 2.6 34 79-118 2-35 (197)
65 PF01916 DS: Deoxyhypusine syn 26.2 29 0.00063 30.8 0.8 40 76-124 37-76 (299)
66 KOG3584|consensus 26.2 36 0.00079 30.5 1.3 14 28-41 305-318 (348)
67 KOG3057|consensus 26.0 89 0.0019 24.0 3.2 31 28-58 57-87 (112)
68 cd03785 GT1_MurG MurG is an N- 25.9 68 0.0015 27.1 3.0 36 78-121 1-37 (350)
69 cd08435 PBP2_GbpR The C-termin 25.8 84 0.0018 23.1 3.2 34 79-118 2-35 (201)
70 cd08416 PBP2_MdcR The C-termin 25.6 76 0.0017 23.4 2.9 36 79-120 2-37 (199)
71 PF15628 RRM_DME: RRM in Demet 25.3 30 0.00065 26.2 0.6 8 17-24 11-18 (103)
72 cd08482 PBP2_TrpI The C-termin 25.3 72 0.0016 23.8 2.7 35 79-119 2-36 (195)
73 cd08458 PBP2_NocR The C-termin 25.0 81 0.0018 23.6 3.0 37 79-121 2-38 (196)
74 COG4081 Uncharacterized protei 24.8 63 0.0014 25.8 2.3 29 92-128 21-49 (148)
75 PF02670 DXP_reductoisom: 1-de 24.8 51 0.0011 25.7 1.8 21 80-101 3-23 (129)
76 cd08486 PBP2_CbnR The C-termin 24.7 79 0.0017 23.9 2.9 35 79-119 3-37 (198)
77 PHA00680 hypothetical protein 24.6 18 0.00039 27.7 -0.8 30 154-183 72-102 (143)
78 PF13439 Glyco_transf_4: Glyco 24.6 1.3E+02 0.0029 21.9 4.0 30 86-123 12-41 (177)
79 TIGR00321 dhys deoxyhypusine s 23.8 62 0.0014 28.8 2.4 38 77-123 46-83 (301)
80 KOG3584|consensus 23.4 27 0.00059 31.3 0.0 23 39-61 295-317 (348)
81 cd08459 PBP2_DntR_NahR_LinR_li 23.4 85 0.0018 23.4 2.8 34 79-118 2-35 (201)
82 cd05564 PTS_IIB_chitobiose_lic 23.3 2.8E+02 0.006 19.9 5.4 18 162-179 46-63 (96)
83 cd08420 PBP2_CysL_like C-termi 23.0 1E+02 0.0022 22.4 3.2 35 79-119 2-36 (201)
84 cd08441 PBP2_MetR The C-termin 22.9 96 0.0021 23.0 3.0 34 79-118 2-35 (198)
85 cd03789 GT1_LPS_heptosyltransf 22.7 1E+02 0.0022 25.7 3.4 45 79-129 2-47 (279)
86 cd08446 PBP2_Chlorocatechol Th 22.3 99 0.0022 22.8 3.0 34 79-118 3-36 (198)
87 cd05560 Xcc1710_like Xcc1710_l 22.0 60 0.0013 24.2 1.6 44 77-128 53-96 (109)
88 cd08427 PBP2_LTTR_like_2 The C 21.9 1E+02 0.0023 22.5 3.0 44 79-128 2-47 (195)
89 cd00248 Mth938-like Mth938-lik 21.7 60 0.0013 24.1 1.6 44 77-128 53-96 (109)
90 cd08469 PBP2_PnbR The C-termin 21.6 1E+02 0.0022 23.5 3.0 36 79-120 2-37 (221)
91 PRK09982 universal stress prot 21.6 84 0.0018 23.6 2.5 26 77-102 4-29 (142)
92 PRK10696 tRNA 2-thiocytidine b 21.5 90 0.002 26.4 2.8 36 67-102 20-55 (258)
93 TIGR02584 cas_NE0113 CRISPR-as 21.4 1.1E+02 0.0024 26.0 3.2 45 79-127 1-45 (209)
94 cd03784 GT1_Gtf_like This fami 21.4 93 0.002 27.2 3.0 46 78-131 2-48 (401)
95 PF13579 Glyco_trans_4_4: Glyc 21.3 1.4E+02 0.0031 21.2 3.6 26 88-121 3-28 (160)
96 PF08583 Cmc1: Cytochrome c ox 21.1 56 0.0012 21.7 1.2 29 21-49 27-55 (69)
97 PRK02301 putative deoxyhypusin 21.0 84 0.0018 28.2 2.6 39 76-123 57-95 (316)
98 cd08477 PBP2_CrgA_like_8 The C 20.9 96 0.0021 22.8 2.6 35 79-119 3-37 (197)
99 cd08488 PBP2_AmpR The C-termin 20.9 1E+02 0.0022 22.9 2.8 34 80-119 3-36 (191)
100 KOG3496|consensus 20.8 91 0.002 22.0 2.2 20 27-46 52-71 (72)
101 TIGR01133 murG undecaprenyldip 20.7 1E+02 0.0022 26.0 3.0 36 78-121 2-38 (348)
102 cd08487 PBP2_BlaA The C-termin 20.7 92 0.002 22.9 2.5 34 80-119 3-36 (189)
103 cd08467 PBP2_SyrM The C-termin 20.7 1.6E+02 0.0035 22.1 3.9 33 80-118 3-35 (200)
104 cd08421 PBP2_LTTR_like_1 The C 20.6 1.2E+02 0.0026 22.3 3.1 34 79-118 2-35 (198)
105 cd08429 PBP2_NhaR The C-termin 20.5 1.3E+02 0.0029 23.1 3.4 35 80-120 3-37 (204)
106 cd08474 PBP2_CrgA_like_5 The C 20.5 96 0.0021 23.0 2.5 35 78-118 4-38 (202)
107 cd08485 PBP2_ClcR The C-termin 20.3 1.3E+02 0.0027 22.7 3.2 34 79-118 3-36 (198)
108 PRK00805 putative deoxyhypusin 20.1 86 0.0019 28.3 2.5 39 76-123 46-84 (329)
109 cd08449 PBP2_XapR The C-termin 20.1 1.1E+02 0.0025 22.3 2.9 34 79-118 2-35 (197)
No 1
>KOG3477|consensus
Probab=100.00 E-value=4.9e-36 Score=217.07 Aligned_cols=86 Identities=41% Similarity=0.742 Sum_probs=78.9
Q ss_pred CCC-cCCCCCCcccCCCCCCCCCCCCCCccHHHHHHHHHHHhhcCCCChhhHHHhhhhhhccchhhhhhhhhhhhhhhhh
Q psy7740 1 MSS-MTFGQKKFIPTAPDKGSFPLDHYGDCKAFMTKYMICIKKNNSDSSACRDEIKDYLGCRMEKELMAKEDWEKLEFNI 79 (184)
Q Consensus 1 ~~~-~~~~~~~~~~~~p~~g~fpldh~~~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~crm~~~Lm~k~~~~~LGf~i 79 (184)
||+ ..-+.+..+|+|||||||||||+|||+.+|..||.||+....+++.||.+||.||+|||+++||.+++|++|||..
T Consensus 1 MS~~g~~~~r~lrp~pPekGsFPLDH~geC~~em~eYl~Cl~~k~e~~~eCR~laK~YlqCRMdh~Lmdkdd~~~LG~~~ 80 (97)
T KOG3477|consen 1 MSTGGAGGNRGLRPIPPEKGSFPLDHLGECTAEMKEYLGCLKSKAENSEECRLLAKKYLQCRMDHGLMDKDDMAELGFSG 80 (97)
T ss_pred CCCCCCCCcccccCCCcccCCcCCCcccccHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhhhcccccHHHHHHcCCCc
Confidence 777 4466899999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred hhcCCCc
Q psy7740 80 LLCCTGS 86 (184)
Q Consensus 80 llg~tGS 86 (184)
+-.++++
T Consensus 81 ~k~ls~~ 87 (97)
T KOG3477|consen 81 VKELSST 87 (97)
T ss_pred cccCcCC
Confidence 5555544
No 2
>PLN02496 probable phosphopantothenoylcysteine decarboxylase
Probab=99.93 E-value=2.7e-26 Score=191.55 Aligned_cols=100 Identities=43% Similarity=0.744 Sum_probs=89.2
Q ss_pred hhhhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCCCCCeeeeCCccchhcccCCCC
Q psy7740 74 KLEFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHKPNIRFYSDDDEWISWEKRGDP 153 (184)
Q Consensus 74 ~LGf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~~~~~V~~d~de~~~~~~~~~~ 153 (184)
..+++|++|+|||+|++|++++++.|++ | + +|+|++|++|++|+++++++...+||+|.++|..|...+.+
T Consensus 17 ~~~k~IllgVtGSIAAyk~~~lvr~L~~-g--~------~V~VvmT~~A~~FI~p~~l~~~~~v~td~~~~~~~~~~~~~ 87 (209)
T PLN02496 17 PRKPRILLAASGSVAAIKFGNLCHCFSE-W--A------EVRAVVTKASLHFIDRASLPKDVTLYTDEDEWSSWNKIGDS 87 (209)
T ss_pred CCCCEEEEEEeCHHHHHHHHHHHHHhcC-C--C------eEEEEEChhHhhhcCHHHcCCCCcEEeCcccccccccCCCC
Confidence 3467899999999999999999999985 6 7 99999999999999999886445799998888666555678
Q ss_pred cccccccccccEEEEcccccHHHHHHhcC
Q psy7740 154 VLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 154 ~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
+.||+|++|+|+|||||||||||||+|+|
T Consensus 88 ~~HI~La~wAD~~vVaPaTaNtlaKiA~G 116 (209)
T PLN02496 88 VLHIELRRWADVMVIAPLSANTLGKIAGG 116 (209)
T ss_pred cchhHhhhhhCEEEEEeCCHHHHHHHHcc
Confidence 99999999999999999999999999997
No 3
>KOG0672|consensus
Probab=99.92 E-value=3.6e-26 Score=187.34 Aligned_cols=105 Identities=50% Similarity=0.881 Sum_probs=96.0
Q ss_pred hhhhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCCCCCeeeeCCccchhcccCCCC
Q psy7740 74 KLEFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHKPNIRFYSDDDEWISWEKRGDP 153 (184)
Q Consensus 74 ~LGf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~~~~~V~~d~de~~~~~~~~~~ 153 (184)
..+|++|+|+|||+|++|++.+|+.|.+.. +.|+| .|+||+|++|.+|+..+.+.....+|+|.|+|..|++.++|
T Consensus 18 d~K~hvL~gaTGSvA~iK~~~li~kL~ei~-G~dki---~iqvvvT~~a~~f~~~~~l~~~v~~~~d~DeW~~W~~r~dp 93 (218)
T KOG0672|consen 18 DGKFHVLLGATGSVAVIKLPLLIKKLEEIY-GRDKI---SIQVVVTKSATHFLEKLKLNKHVQLYTDEDEWKMWKSRSDP 93 (218)
T ss_pred CCceeEEEEeccccceeehHHHHHHHHHhc-CCcce---eEEEEEechHHHHHhhcccccceeeecChHHhhhhhhcCCc
Confidence 457899999999999999999999999963 24443 79999999999999988877678999999999999999999
Q ss_pred cccccccccccEEEEcccccHHHHHHhcC
Q psy7740 154 VLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 154 ~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
+.||+|+||||++||||.|||||||||+|
T Consensus 94 VLHIeLRrWADilliAPLsANTlaKiA~G 122 (218)
T KOG0672|consen 94 VLHIELRRWADILLIAPLSANTLAKIANG 122 (218)
T ss_pred eeeehHhhhhhhheecccCcchHHHHHhh
Confidence 99999999999999999999999999997
No 4
>PRK07313 phosphopantothenoylcysteine decarboxylase; Validated
Probab=99.91 E-value=4.2e-25 Score=180.66 Aligned_cols=95 Identities=35% Similarity=0.431 Sum_probs=84.4
Q ss_pred hhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCC--CCCeeeeCCccchhcccCCCC
Q psy7740 76 EFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHK--PNIRFYSDDDEWISWEKRGDP 153 (184)
Q Consensus 76 Gf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~--~~~~V~~d~de~~~~~~~~~~ 153 (184)
++||++|+|||++++|++++++.|++.| + +|+|++|++|++|++++.++ ++++|++|.+.+ ...++
T Consensus 1 ~k~Ill~vtGsiaa~~~~~li~~L~~~g--~------~V~vv~T~~A~~fi~~~~l~~l~~~~v~~~~~~~----~~~~~ 68 (182)
T PRK07313 1 MKNILLAVSGSIAAYKAADLTSQLTKRG--Y------QVTVLMTKAATKFITPLTLQVLSKNPVHLDVMDE----HDPKL 68 (182)
T ss_pred CCEEEEEEeChHHHHHHHHHHHHHHHCC--C------EEEEEEChhHHHHcCHHHHHHHhCCceEeccccc----cccCC
Confidence 3689999999999999999999999988 7 99999999999999988776 578999986432 12346
Q ss_pred cccccccccccEEEEcccccHHHHHHhcC
Q psy7740 154 VLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 154 ~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
.+||++++|+|+|||+|||+|||||||+|
T Consensus 69 ~~hi~l~~~aD~~vIaPaTantlakiA~G 97 (182)
T PRK07313 69 MNHIELAKRADLFLVAPATANTIAKLAHG 97 (182)
T ss_pred ccccccccccCEEEEeeCCHhHHHHHHcc
Confidence 78999999999999999999999999997
No 5
>TIGR02113 coaC_strep phosphopantothenoylcysteine decarboxylase, streptococcal. In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis (see TIGR00521). These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This model describes proteins from the genera Streptococcus and Enterococcus homologous to the N-terminal region of TIGR00521, corresponding to phosphopantothenoylcysteine decarboxylase activity.
Probab=99.89 E-value=5.5e-24 Score=173.48 Aligned_cols=94 Identities=34% Similarity=0.451 Sum_probs=82.2
Q ss_pred hhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCC--CCCeeeeCCccchhcccCCCCc
Q psy7740 77 FNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHK--PNIRFYSDDDEWISWEKRGDPV 154 (184)
Q Consensus 77 f~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~--~~~~V~~d~de~~~~~~~~~~~ 154 (184)
+||++|+|||++++|++++++.|++.| + +|+||+|++|++|++++.++ ++++|+++. |.. ..+..+
T Consensus 1 k~I~lgvtGs~~a~~~~~ll~~L~~~g--~------~V~vi~T~~A~~fi~~~~l~~l~~~~v~~~~--~~~--~~~~~~ 68 (177)
T TIGR02113 1 KKILLAVTGSIAAYKAADLTSQLTKLG--Y------DVTVLMTQAATQFITPLTLQVLSKNPVHLDV--MDE--HDPKVI 68 (177)
T ss_pred CEEEEEEcCHHHHHHHHHHHHHHHHCC--C------EEEEEEChHHHhhccHhhHHHHhCCCeEeec--ccc--ccCCCc
Confidence 378999999999999999999999988 7 99999999999999998876 678898874 211 122457
Q ss_pred ccccccccccEEEEcccccHHHHHHhcC
Q psy7740 155 LHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 155 ~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
.|+++++|+|+|||+|||||||||||+|
T Consensus 69 ~hi~l~~~aD~~vVaPaSanTlakiA~G 96 (177)
T TIGR02113 69 NHIELAKKADLFLVAPASANTIAHLAHG 96 (177)
T ss_pred ccceechhhCEEEEEeCCHHHHHHHHcC
Confidence 8999999999999999999999999997
No 6
>PRK08305 spoVFB dipicolinate synthase subunit B; Reviewed
Probab=99.86 E-value=1.2e-22 Score=168.21 Aligned_cols=90 Identities=21% Similarity=0.143 Sum_probs=77.8
Q ss_pred hhhhhhhcCCCchHHhH-HHHHHHHHHhccccccccccceEEEEcCchHHHhcCcC--------CCC--CCCeeeeCCcc
Q psy7740 75 LEFNILLCCTGSVATIK-LPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDL--------PHK--PNIRFYSDDDE 143 (184)
Q Consensus 75 LGf~illg~tGSiaa~k-~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~--------~l~--~~~~V~~d~de 143 (184)
.|++|++|+|||+|++| ++++++.|++.| + +|+|++|++|++|+.+. .++ ++++|+++..+
T Consensus 4 ~~k~IllgVTGsiaa~k~a~~lir~L~k~G--~------~V~vv~T~aA~~~~~~~~~~~~~~~~l~~ls~~~v~~~~~~ 75 (196)
T PRK08305 4 KGKRIGFGLTGSHCTYDEVMPEIEKLVDEG--A------EVTPIVSYTVQTTDTRFGKAEEWIKKIEEITGNKVINTIVE 75 (196)
T ss_pred CCCEEEEEEcCHHHHHHHHHHHHHHHHhCc--C------EEEEEECHhHHHHhhhcCChHHHHHHHHHHHCCCcEEecCC
Confidence 47799999999999999 799999999998 8 99999999999997642 133 57888877311
Q ss_pred chhcccCCCCcccccccccccEEEEcccccHHHHHHhcC
Q psy7740 144 WISWEKRGDPVLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 144 ~~~~~~~~~~~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
..|+++++|+|+|||||||||||||||+|
T Consensus 76 ----------~~~isls~~aD~mvIAPaSanTLAKiA~G 104 (196)
T PRK08305 76 ----------AEPLGPKKLLDCMVIAPCTGNTMAKLANA 104 (196)
T ss_pred ----------CccCccccccCEEEEEeCCHhHHHHHHcc
Confidence 45889999999999999999999999997
No 7
>PRK05579 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated
Probab=99.86 E-value=1.1e-22 Score=183.77 Aligned_cols=96 Identities=32% Similarity=0.489 Sum_probs=85.0
Q ss_pred hhhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCC--CCCeeeeCCccchhcccCCC
Q psy7740 75 LEFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHK--PNIRFYSDDDEWISWEKRGD 152 (184)
Q Consensus 75 LGf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~--~~~~V~~d~de~~~~~~~~~ 152 (184)
.|++|++|+|||+++++++++++.|++.| + +|+|++|++|++|++++.++ ++++||++. |.. ..+.
T Consensus 5 ~~k~IllgvTGsiaa~k~~~lv~~L~~~g--~------~V~vv~T~~A~~fi~~~~l~~l~~~~V~~~~--~~~--~~~~ 72 (399)
T PRK05579 5 AGKRIVLGVSGGIAAYKALELVRRLRKAG--A------DVRVVMTEAAKKFVTPLTFQALSGNPVSTDL--WDP--AAEA 72 (399)
T ss_pred CCCeEEEEEeCHHHHHHHHHHHHHHHhCC--C------EEEEEECHhHHHHHhHHHHHHhhCCceEccc--ccc--ccCC
Confidence 36789999999999999999999999998 8 99999999999999999887 688999873 421 1234
Q ss_pred CcccccccccccEEEEcccccHHHHHHhcC
Q psy7740 153 PVLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 153 ~~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
+++||++.+|+|+|||||||||||||||+|
T Consensus 73 ~~~hi~l~~~aD~~vVaPaTaNtlaKiA~G 102 (399)
T PRK05579 73 AMGHIELAKWADLVLIAPATADLIAKLAHG 102 (399)
T ss_pred CcchhhcccccCEEEEeeCCHHHHHHHHcc
Confidence 578999999999999999999999999997
No 8
>PRK13982 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional
Probab=99.86 E-value=1.7e-22 Score=186.03 Aligned_cols=96 Identities=30% Similarity=0.418 Sum_probs=85.1
Q ss_pred hhhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCC--CCCeeeeCCccchhcccCCC
Q psy7740 75 LEFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHK--PNIRFYSDDDEWISWEKRGD 152 (184)
Q Consensus 75 LGf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~--~~~~V~~d~de~~~~~~~~~ 152 (184)
.|++|++|+||||++||++++++.|++.| + +|+|+||++|++|++++.++ ++++||+|. |.. ..+.
T Consensus 69 ~~k~IllgVtGsIAayka~~lvr~L~k~G--~------~V~VvmT~sA~~fv~p~~~~~ls~~~V~~d~--~~~--~~~~ 136 (475)
T PRK13982 69 ASKRVTLIIGGGIAAYKALDLIRRLKERG--A------HVRCVLTKAAQQFVTPLTASALSGQRVYTDL--FDP--ESEF 136 (475)
T ss_pred CCCEEEEEEccHHHHHHHHHHHHHHHhCc--C------EEEEEECcCHHHHhhHHHHHHhcCCceEecC--CCc--cccc
Confidence 46899999999999999999999999998 8 99999999999999998876 689999874 321 1123
Q ss_pred CcccccccccccEEEEcccccHHHHHHhcC
Q psy7740 153 PVLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 153 ~~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
.++|+++++|+|+|||||||||||||||+|
T Consensus 137 ~~~Hi~la~~aD~~vVAPATANTIAKiA~G 166 (475)
T PRK13982 137 DAGHIRLARDCDLIVVAPATADLMAKMANG 166 (475)
T ss_pred CccchhhhhhcCEEEEeeCCHHHHHHHHcc
Confidence 578999999999999999999999999997
No 9
>PRK05920 aromatic acid decarboxylase; Validated
Probab=99.86 E-value=2.3e-22 Score=167.46 Aligned_cols=97 Identities=21% Similarity=0.207 Sum_probs=80.6
Q ss_pred hhhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCC--CCCeeeeCCccchhcccCCC
Q psy7740 75 LEFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHK--PNIRFYSDDDEWISWEKRGD 152 (184)
Q Consensus 75 LGf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~--~~~~V~~d~de~~~~~~~~~ 152 (184)
.++||++|||||+|++|++++++.|++.| + +|+|++|++|++|++++... .+++++++. .|..+ .+.
T Consensus 2 ~~krIllgITGsiaa~ka~~lvr~L~~~g--~------~V~vi~T~~A~~fv~~~~~~~l~~~~v~~~~-~~~~~--~~~ 70 (204)
T PRK05920 2 KMKRIVLAITGASGAIYGVRLLECLLAAD--Y------EVHLVISKAAQKVLATETGLKLPAVPDLAEA-FLREQ--LGA 70 (204)
T ss_pred CCCEEEEEEeCHHHHHHHHHHHHHHHHCC--C------EEEEEEChhHHHHHHHHhCCCCCCCeeecch-hhhhc--ccc
Confidence 35789999999999999999999999998 7 99999999999999987665 467888774 23222 123
Q ss_pred Cccccccc-------------ccccEEEEcccccHHHHHHhcC
Q psy7740 153 PVLHIELS-------------KWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 153 ~~~Hi~l~-------------~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
..+|+++. +|+|+|||||||+|||||||+|
T Consensus 71 ~~~hi~l~~~~d~~a~~~sgs~~aD~~vVaPaTantlakiA~G 113 (204)
T PRK05920 71 AAGQLRVHGKDDWGAPIASGSFRTDGMVIAPCSMGTLAAIAHG 113 (204)
T ss_pred ccCceeEcccccccCccccCccccCEEEEeeCCHhHHHHHHcc
Confidence 45677664 7999999999999999999997
No 10
>PF02441 Flavoprotein: Flavoprotein; InterPro: IPR003382 This entry contains a diverse range of flavoprotein enzymes, including epidermin biosynthesis protein, EpiD, which has been shown to be a flavoprotein that binds FMN []. This enzyme catalyzes the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance []. Dipicolinate synthase catalyses the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenylacrylic acid decarboxylase 4.1.1 from EC [].; GO: 0003824 catalytic activity; PDB: 3QJG_L 1G63_G 1G5Q_L 1P3Y_1 1QZU_A 1E20_A 1MVN_A 1MVL_A 3ZQU_A 2EJB_A ....
Probab=99.86 E-value=1.7e-22 Score=155.61 Aligned_cols=93 Identities=43% Similarity=0.729 Sum_probs=80.3
Q ss_pred hhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCCCCCeeeeCCccchhcccCCCCccc
Q psy7740 77 FNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHKPNIRFYSDDDEWISWEKRGDPVLH 156 (184)
Q Consensus 77 f~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~~~~~V~~d~de~~~~~~~~~~~~H 156 (184)
+||++++|||++++++++++++|++.| + +|+|++|++|++|++++. ..+++|+.+ |..| ..+...+|
T Consensus 1 k~i~l~vtGs~~~~~~~~~l~~L~~~g--~------~v~vv~S~~A~~~~~~~~-~~~~~v~~~---~~~~-~~~~~~~~ 67 (129)
T PF02441_consen 1 KRILLGVTGSIAAYKAPDLLRRLKRAG--W------EVRVVLSPSAERFVTPEG-LTGEPVYTD---WDTW-DRGDPAEH 67 (129)
T ss_dssp -EEEEEE-SSGGGGGHHHHHHHHHTTT--S------EEEEEESHHHHHHSHHHG-HCCSCEECT---HCTC-STTTTTCH
T ss_pred CEEEEEEECHHHHHHHHHHHHHHhhCC--C------EEEEEECCcHHHHhhhhc-cccchhhhc---cccC-CCCCCcCc
Confidence 479999999999999999999999998 7 999999999999999988 446788887 2111 23456899
Q ss_pred ccccccccEEEEcccccHHHHHHhcC
Q psy7740 157 IELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 157 i~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
+++++|+|+|||+|||+||+||+|+|
T Consensus 68 ~~~~~~~D~~vVaPaT~NtlaKiA~G 93 (129)
T PF02441_consen 68 IELSRWADAMVVAPATANTLAKIANG 93 (129)
T ss_dssp HHHHHTESEEEEEEEEHHHHHHHHTT
T ss_pred ccccccCCEEEEcccCHHHHHHHHhC
Confidence 99999999999999999999999998
No 11
>PRK06029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
Probab=99.84 E-value=8.1e-22 Score=162.00 Aligned_cols=88 Identities=18% Similarity=0.130 Sum_probs=71.5
Q ss_pred hhhhhcCCCchHHhHHHHHHHHHHh-ccccccccccceEEEEcCchHHHhcCcCC------CC-CCCeeeeCCccchhcc
Q psy7740 77 FNILLCCTGSVATIKLPELIEQIEQ-LQYEFNKIMIINLNVVMTKHAFHFVPDLP------HK-PNIRFYSDDDEWISWE 148 (184)
Q Consensus 77 f~illg~tGSiaa~k~~~li~~L~~-~g~~~~~~~~~~V~VilT~sA~~fv~~~~------l~-~~~~V~~d~de~~~~~ 148 (184)
+||++|+|||+|++|++++++.|++ .| + +|+|++|++|++|++++. +. ...+++.+.+.
T Consensus 2 k~IllgVTGsiaa~ka~~l~~~L~k~~g--~------~V~vv~T~~A~~fv~~~~~~~~~~~~~l~~~v~~~~~~----- 68 (185)
T PRK06029 2 KRLIVGISGASGAIYGVRLLQVLRDVGE--I------ETHLVISQAARQTLAHETDFSLRDVQALADVVHDVRDI----- 68 (185)
T ss_pred CEEEEEEECHHHHHHHHHHHHHHHhhcC--C------eEEEEECHHHHHHHHHHHCCChhhHHHhcCcccChhhc-----
Confidence 4799999999999999999999999 46 7 999999999999999872 11 12345543221
Q ss_pred cCCCCccccccc-ccccEEEEcccccHHHHHHhcC
Q psy7740 149 KRGDPVLHIELS-KWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 149 ~~~~~~~Hi~l~-~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
..||+++ +|+|+|||||||||||||||+|
T Consensus 69 -----~~~i~~~s~~aD~~vIaPaTaNtlAKiA~G 98 (185)
T PRK06029 69 -----GASIASGSFGTDGMVIAPCSMKTLAKIAHG 98 (185)
T ss_pred -----ccChhhcCchhCEEEEeeCCHhHHHHHHcc
Confidence 2366663 6999999999999999999997
No 12
>TIGR00521 coaBC_dfp phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase, prokaryotic. This model represents a bifunctional enzyme that catalyzes the second and third steps (cysteine ligation, EC 6.3.2.5, and decarboxylation, EC 4.1.1.36) in the biosynthesis of coenzyme A (CoA) from pantothenate in bacteria. In early descriptions of this flavoprotein, a ts mutation in one region of the protein appeared to cause a defect in DNA metaobolism rather than an increased need for the pantothenate precursor beta-alanine. This protein was then called dfp, for DNA/pantothenate metabolism flavoprotein. The authors responsible for detecting phosphopantothenate--cysteine ligase activity suggest renaming this bifunctional protein coaBC for its role in CoA biosynthesis. This enzyme contains the FMN cofactor, but no FAD or pyruvoyl group. The amino-terminal region contains the phosphopantothenoylcysteine decarboxylase activity.
Probab=99.83 E-value=2.2e-21 Score=175.01 Aligned_cols=95 Identities=33% Similarity=0.524 Sum_probs=81.9
Q ss_pred hhhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCC--CCCeeeeCCccchhcccCCC
Q psy7740 75 LEFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHK--PNIRFYSDDDEWISWEKRGD 152 (184)
Q Consensus 75 LGf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~--~~~~V~~d~de~~~~~~~~~ 152 (184)
.|++|++|+|||+++++++++++.|++.| + +|+|++|++|++|++++.++ ++++|+++. |.. ...
T Consensus 2 ~~k~IllgiTGSiaa~~~~~ll~~L~~~g--~------~V~vv~T~~A~~fv~~~~l~~~~~~~v~~~~--~~~---~~~ 68 (390)
T TIGR00521 2 ENKKILLGVTGGIAAYKTVELVRELVRQG--A------EVKVIMTEAAKKFITPLTLEALSGHKVVTEL--WGP---IEH 68 (390)
T ss_pred CCCEEEEEEeCHHHHHHHHHHHHHHHhCC--C------EEEEEECHhHHHHHHHHHHHHhhCCceeehh--ccc---ccc
Confidence 36799999999999999999999999988 7 99999999999999999876 577888773 321 111
Q ss_pred CcccccccccccEEEEcccccHHHHHHhcC
Q psy7740 153 PVLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 153 ~~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
...||++++|+|+|||||||+|||||||+|
T Consensus 69 ~~~hi~l~~~aD~~vVaPaTanTlaKiA~G 98 (390)
T TIGR00521 69 NALHIDLAKWADLILIAPATANTISKIAHG 98 (390)
T ss_pred ccchhhcccccCEEEEecCCHHHHHHHHcc
Confidence 122999999999999999999999999997
No 13
>TIGR00421 ubiX_pad polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases. In E.coli, the protein UbiX (3-octaprenyl-4-hydroxybenzoate carboxy-lyase) has been shown to be involved in the third step of ubiquinone biosynthesis. It catalyzes the reaction [3-octaprenyl-4-hydroxybenzoate = 2-octaprenylphenol + CO2]. The knockout of the homologous protein in yeast confers sensitivity to phenylacrylic acid. Members are not restricted to ubiquinone-synthesizing species. This family represents a distinct clade within the flavoprotein family of Pfam model pfam02441.
Probab=99.82 E-value=2.9e-21 Score=158.01 Aligned_cols=87 Identities=21% Similarity=0.243 Sum_probs=69.7
Q ss_pred hhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCC------CCC-CCeeeeCCccchhcccC
Q psy7740 78 NILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLP------HKP-NIRFYSDDDEWISWEKR 150 (184)
Q Consensus 78 ~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~------l~~-~~~V~~d~de~~~~~~~ 150 (184)
||++|+|||||++|++++++.|++.| + +|+|++|++|++|++++. ++. ...++.+
T Consensus 1 ~illgvtGsiaa~ka~~lir~L~~~g--~------~V~vv~T~~A~~fv~~e~~~~~~~l~~~~~~~~~~---------- 62 (181)
T TIGR00421 1 RIVVAMTGASGVIYGIRLLEVLKEAG--V------EVHLVISDWAKETIKYETDIDPGEVEELATKYYDA---------- 62 (181)
T ss_pred CEEEEEECHHHHHHHHHHHHHHHHCC--C------EEEEEECccHHHHHHHHHCCCHHHHHHHhhhhCCC----------
Confidence 58899999999999999999999998 7 999999999999998643 111 1112211
Q ss_pred CCCcccccc-cccccEEEEcccccHHHHHHhcC
Q psy7740 151 GDPVLHIEL-SKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 151 ~~~~~Hi~l-~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
.+...|+++ ++|+|+|||||||||||||||+|
T Consensus 63 ~~~~~~i~~~s~~aD~~vIaPATantiAkiA~G 95 (181)
T TIGR00421 63 DDFAAPIASGSFPFDGMVVVPCSMKTLSAIANG 95 (181)
T ss_pred cccccccccCCchhCEEEEecCCHhHHHHHHcc
Confidence 112357764 78999999999999999999997
No 14
>TIGR02700 flavo_MJ0208 archaeoflavoprotein, MJ0208 family. This model describes one of two paralogous families of archaealflavoprotein. The other, described by TIGR02699 and typified by the partially characterized AF1518 of Archaeoglobus fulgidus, is a homodimeric FMN-containing flavoprotein that accepts electrons from ferredoxin and can transfer them to various oxidoreductases. The function of this protein family is unknown.
Probab=99.80 E-value=5.1e-20 Score=155.43 Aligned_cols=94 Identities=17% Similarity=0.262 Sum_probs=75.4
Q ss_pred hhhhcCCCchHH-hHHHHHHHHHHhc--cccccccccceEEEEcCchHHHhcCcCC----CC--CCCeeeeCCccchhcc
Q psy7740 78 NILLCCTGSVAT-IKLPELIEQIEQL--QYEFNKIMIINLNVVMTKHAFHFVPDLP----HK--PNIRFYSDDDEWISWE 148 (184)
Q Consensus 78 ~illg~tGSiaa-~k~~~li~~L~~~--g~~~~~~~~~~V~VilT~sA~~fv~~~~----l~--~~~~V~~d~de~~~~~ 148 (184)
||++|||||+.+ ++++++++.|++. | + +|+|+||++|++|++++. ++ ++++|+++. |..-.
T Consensus 1 ~i~~~itGs~~~~~~~~~l~~~L~~~~~g--~------~V~vv~T~~a~~~i~~~~~~~~~~~~~~~~v~~~~--~~~~~ 70 (234)
T TIGR02700 1 RIGWGITGAGHLLVESFQVMKELKREIEE--L------RVSTFVSRAGEEVVRMYGLWDDLREISPGGYYEEV--FTESE 70 (234)
T ss_pred CeEEEEeCccHhHHHHHHHHHHHHhhcCC--C------eEEEEEChhHHhHHhhhhhHHHHHHHhCCCcchhc--ccccc
Confidence 588999996555 7999999999998 7 7 999999999999999984 33 478888773 21000
Q ss_pred cC--CCCcccccccccccEEEEcccccHHHHHHhcC
Q psy7740 149 KR--GDPVLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 149 ~~--~~~~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
+. +-..+|+++++ +|+|||||||||||||||+|
T Consensus 71 ~~~~~~~~~~i~~~~-~D~~vIaPaTantlakiA~G 105 (234)
T TIGR02700 71 EGASSPIIGRFALGK-YDLLIVSPATANTVAKIAHG 105 (234)
T ss_pred ccccCCccceeeccc-cCEEEEecCChhHHHHHHcc
Confidence 00 11367999887 89999999999999999997
No 15
>COG0452 Dfp Phosphopantothenoylcysteine synthetase/decarboxylase [Coenzyme metabolism]
Probab=99.79 E-value=7.9e-20 Score=165.02 Aligned_cols=94 Identities=37% Similarity=0.505 Sum_probs=84.2
Q ss_pred hhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCC--CCCeeeeCCccchhcccCCCC
Q psy7740 76 EFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHK--PNIRFYSDDDEWISWEKRGDP 153 (184)
Q Consensus 76 Gf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~--~~~~V~~d~de~~~~~~~~~~ 153 (184)
|++|+++||||||+||.+++++.|++.| + +|+|++|++|.+|+++++++ ++++|++ . |. ......
T Consensus 4 ~k~ill~v~gsiaayk~~~l~r~L~~~g--a------~v~vvmt~~a~~fv~p~~~~~~s~~~v~t-~--~~--~~~~~~ 70 (392)
T COG0452 4 GKRILLGVTGSIAAYKSVELVRLLRRSG--A------EVRVVMTESARKFITPLTFQALSGNPVYT-L--LD--EELTGS 70 (392)
T ss_pred CceEEEEecCchhhhhHHHHHHHHhhCC--C------eeEEEcchhhhhhcCcccHHHhhCCCccc-c--cc--cccccc
Confidence 4589999999999999999999999999 8 99999999999999999987 6889998 2 21 123456
Q ss_pred cccccccccccEEEEcccccHHHHHHhcC
Q psy7740 154 VLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 154 ~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
++||+|++|+|++||+|||+|||+|+|+|
T Consensus 71 ~~HI~l~~~adl~lvaPaTan~i~Kla~g 99 (392)
T COG0452 71 VEHIELARWADLLLVAPATANTIAKLAVG 99 (392)
T ss_pred ccHhhhhhccCEEEecCCChhHHHHHHHh
Confidence 89999999999999999999999999986
No 16
>TIGR02852 spore_dpaB dipicolinic acid synthetase, B subunit. Members of this family represent the B subunit of dipicolinic acid synthetase, an enzyme that synthesizes a small molecule that appears to confer heat stability to bacterial endospores such as those of Bacillus subtilis. The A and B subunits are together in what was originally designated the spoVF locus for stage V of endospore formation.
Probab=99.77 E-value=1.2e-19 Score=149.47 Aligned_cols=88 Identities=18% Similarity=0.112 Sum_probs=71.6
Q ss_pred hhhhhcCCCchHHhHHH-HHHHHHHhccccccccccceEEEEcCchHHHhcCcC--------CCC--CCCeeeeCCccch
Q psy7740 77 FNILLCCTGSVATIKLP-ELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDL--------PHK--PNIRFYSDDDEWI 145 (184)
Q Consensus 77 f~illg~tGSiaa~k~~-~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~--------~l~--~~~~V~~d~de~~ 145 (184)
+||++|+|||+|+++++ ++++.|++.| + +|+||+|++|+++.+.. .++ ++++++++.+++
T Consensus 1 ~~I~lgITGs~~a~~a~~~ll~~L~~~g--~------~V~vI~S~~A~~~~~~~g~~~~~i~~l~~~tg~~v~~~~~~~- 71 (187)
T TIGR02852 1 KRIGFGLTGSHCTLEAVMPQLEKLVDEG--A------EVTPIVSETVQTTDTRFGKGADWIKKIEEITGRPAINTIVEA- 71 (187)
T ss_pred CEEEEEEecHHHHHHHHHHHHHHHHhCc--C------EEEEEEchhHHHHHHHcCChHHHHHHHHHHHCCCCEEECCCC-
Confidence 36899999999999997 9999999998 8 99999999999665532 122 577888774322
Q ss_pred hcccCCCCcccccccccccEEEEcccccHHHHHHhcC
Q psy7740 146 SWEKRGDPVLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 146 ~~~~~~~~~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
..++.++|+|+|||||||+|||||||+|
T Consensus 72 ---------~~~~~s~~~D~mVIaPcTanTLAKiA~G 99 (187)
T TIGR02852 72 ---------EPFGPKVPLDCMVIAPLTGNSMSKLANA 99 (187)
T ss_pred ---------cccCCchhhCEEEEEeCCHhHHHHHHcc
Confidence 1134578999999999999999999997
No 17
>TIGR02699 archaeo_AfpA archaeoflavoprotein AfpA. The prototypical member of this archaeal protein family is AF1518 from Archaeoglobus fulgidus. This homodimer with two non-covalently bound FMN cofactors can receive electrons from ferredoxin, but not from a number of other electron donors such as NADH or rubredoxin. It can then donate electrons to various reductases.
Probab=99.63 E-value=2.4e-16 Score=128.52 Aligned_cols=91 Identities=21% Similarity=0.215 Sum_probs=66.4
Q ss_pred hhhhcCCCchHHh-HHHHHHHHHHhc-cccccccccceEEEEcCchHHHhcCcCCC-C--CCC--eeeeCCccchhcccC
Q psy7740 78 NILLCCTGSVATI-KLPELIEQIEQL-QYEFNKIMIINLNVVMTKHAFHFVPDLPH-K--PNI--RFYSDDDEWISWEKR 150 (184)
Q Consensus 78 ~illg~tGSiaa~-k~~~li~~L~~~-g~~~~~~~~~~V~VilT~sA~~fv~~~~l-~--~~~--~V~~d~de~~~~~~~ 150 (184)
||+||+|||+... ..+++++.|++. | + +|+|++|++|++|++.+.+ + .+. .++.+. +. . .
T Consensus 1 ~i~~gitGsg~~l~e~v~~l~~L~~~~g--~------eV~vv~S~~A~~vi~~~~~~~~l~~~~~~~~~~~-~~---~-~ 67 (174)
T TIGR02699 1 RIAWGITGSGDKLPETYSIMKDVKNRYG--D------EIDVFLSKAGEQVVKWYKLWDKLENDFPNFRVEI-NA---N-S 67 (174)
T ss_pred CEEEEEEccHHHHHHHHHHHHHHHHhcC--C------EEEEEECHhHHHHHHHHHhHHHHhccCCcccccC-CC---C-C
Confidence 5889999995554 488888888754 5 7 9999999999999987754 2 111 123221 11 1 1
Q ss_pred CCCcccccccccccEEEEcccccHHHHHHhcC
Q psy7740 151 GDPVLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 151 ~~~~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
+...+|+.+.+ +|+|||||||+|||||||+|
T Consensus 68 p~~sg~~~l~~-~D~~vVaPaTaNtlakiA~G 98 (174)
T TIGR02699 68 PFLAGQLQMGK-YDFLLIAPATANTVAKIAYG 98 (174)
T ss_pred ccccCcccccc-cCEEEEEeCCHHHHHHHHcc
Confidence 12357888764 89999999999999999997
No 18
>COG0163 UbiX 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism]
Probab=99.51 E-value=7.9e-15 Score=120.24 Aligned_cols=89 Identities=20% Similarity=0.223 Sum_probs=72.6
Q ss_pred hhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCC--CCC-------CCeeeeCCccchhc
Q psy7740 77 FNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLP--HKP-------NIRFYSDDDEWISW 147 (184)
Q Consensus 77 f~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~--l~~-------~~~V~~d~de~~~~ 147 (184)
.++++|+||+++++++.++++.|++.+ + ++++++|++|++.+..|. ... ...+|.+.
T Consensus 3 ~riivgisGASG~iygvrlLe~L~~~~--~------e~hlviS~~a~~~~~~E~~~~~~~~~~~~~a~~~~~~~------ 68 (191)
T COG0163 3 KRIIVGISGASGAIYGVRLLEVLRELG--V------ETHLVISKAAKKTLKYETGNDESLGEVLALADVVHDEK------ 68 (191)
T ss_pred cEEEEEEeccccHHHHHHHHHHHHhcC--c------eEEEEEcHHHHHHHHHHhCcchhhHHHhhhcceecCHH------
Confidence 478999999999999999999999998 7 999999999999887776 221 22344332
Q ss_pred ccCCCCcccccccccccEEEEcccccHHHHHHhcC
Q psy7740 148 EKRGDPVLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 148 ~~~~~~~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
+.++++++.+ ...|.|+|+|||+.|||+||+|
T Consensus 69 -D~~A~iASGS--~~~~gMiI~PCSmkTla~IA~G 100 (191)
T COG0163 69 -DIGAPIASGS--FRTDGMIIAPCSMKTLAAIAHG 100 (191)
T ss_pred -HccCcccCCC--CCcCcEEEEeCcHHHHHHHHhc
Confidence 2356777664 5789999999999999999997
No 19
>COG1036 Archaeal flavoproteins [Energy production and conversion]
Probab=99.22 E-value=6.6e-12 Score=101.56 Aligned_cols=96 Identities=20% Similarity=0.197 Sum_probs=67.1
Q ss_pred hhhhhhhhhcCCCchHHhH-HHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCC-----CCCeeeeCCccchh
Q psy7740 73 EKLEFNILLCCTGSVATIK-LPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHK-----PNIRFYSDDDEWIS 146 (184)
Q Consensus 73 ~~LGf~illg~tGSiaa~k-~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~-----~~~~V~~d~de~~~ 146 (184)
++++.||.||+|||.--+- ..+++..+++..+.+ +|.+.+|++|++++..+.|. ....++.+.+
T Consensus 5 ~~~~~rIaWgITGaG~~L~Et~~imk~lk~~~~~~------~v~v~lSkageeVvk~YgL~~~l~~~~~~~~~e~~---- 74 (187)
T COG1036 5 EKKKKRIAWGITGAGHLLPETYQIMKELKKEYGDV------EVDVFLSKAGEEVVKMYGLWDKLEKIFGGLEVEIG---- 74 (187)
T ss_pred ccccceEEEEEeccccccHHHHHHHHHHHhhcCCc------eEEEeehhhHHHHHHHHHHHHHHHHHcCCeEeecC----
Confidence 3567789999999954332 444555555553234 89999999999999887643 1112333321
Q ss_pred cccCCCC--cccccccccccEEEEcccccHHHHHHhcC
Q psy7740 147 WEKRGDP--VLHIELSKWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 147 ~~~~~~~--~~Hi~l~~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
.+.| ++.+++.+ +|+++|+|||+||+||||+|
T Consensus 75 ---ansPfi~GrlqlGk-YD~llvaPaTsNTvAKIa~G 108 (187)
T COG1036 75 ---ANSPFIAGRLQLGK-YDFLLVAPATSNTVAKIAYG 108 (187)
T ss_pred ---CCCCceecceeccc-ccEEEEcccccchHHHHHhh
Confidence 1223 56778877 99999999999999999986
No 20
>PF06747 CHCH: CHCH domain; InterPro: IPR010625 A conserved motif was identified in the LOC118487 protein was called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11 kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation []. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit []. The CHCH domain was previously called DUF657 []. ; PDB: 2ZXT_A 3A3C_A 2L0Y_A 2K3J_A.
Probab=98.72 E-value=7e-09 Score=63.04 Aligned_cols=35 Identities=49% Similarity=0.937 Sum_probs=32.8
Q ss_pred cHHHHHHHHHHHhhcCCCChhhHHHhhhhhhccch
Q psy7740 29 CKAFMTKYMICIKKNNSDSSACRDEIKDYLGCRME 63 (184)
Q Consensus 29 c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~crm~ 63 (184)
|..+|..||.||++|+++.++||.++++|++|||+
T Consensus 1 C~~e~~~~~~Cl~~n~~~~~~C~~~~~~~~~C~~~ 35 (35)
T PF06747_consen 1 CAEEMKAYLACLKENNFDWSKCRKEFKAYKECRMK 35 (35)
T ss_dssp THHHHHHHHHHHHCH-SSTCCCHHHHHHHHHHHCC
T ss_pred CHHHHHHHHHHHHHCCCcHHhhHHHHHHHHHHhhC
Confidence 88999999999999999999999999999999985
No 21
>KOG4695|consensus
Probab=94.92 E-value=0.026 Score=43.26 Aligned_cols=36 Identities=33% Similarity=0.722 Sum_probs=34.3
Q ss_pred CCccHHHHHHHHHHHhhcCCCChhhHHHhhhhhhcc
Q psy7740 26 YGDCKAFMTKYMICIKKNNSDSSACRDEIKDYLGCR 61 (184)
Q Consensus 26 ~~~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~cr 61 (184)
+-.|..+|.-.+.|||.|++.+..||.+..-|+.|-
T Consensus 45 ~~tC~qEm~vlfaClK~nEF~d~~C~Kei~~f~dC~ 80 (122)
T KOG4695|consen 45 EATCIQEMSVLFACLKQNEFRDDACRKEIQGFLDCA 80 (122)
T ss_pred chHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHH
Confidence 678999999999999999999999999999999984
No 22
>PF05676 NDUF_B7: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7); InterPro: IPR008698 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of several NADH-ubiquinone oxidoreductase B18 subunit proteins from different eukaryotic organisms. Oxidative phosphorylation is the well-characterised process in which ATP, the principal carrier of chemical energy of individual cells, is produced due to a mitochondrial proton gradient formed by the transfer of electrons from NADH and FADH2 to molecular oxygen. The oxidative phosphorylation (OXPHOS) system is located in the mitochondrial inner membrane and consists of five multi-subunit enzyme complexes and two small electron carriers: coenzyme Q10 and cytochrome C. At least 70 structural proteins involved in the formation of the whole OXPHOS system are encoded by nuclear genes, whereas 13 structural proteins are encoded by the mitochondrial genome. Deficiency of NADH ubiquinone oxidoreductase, the first enzyme complex of the mitochondrial respiratory chain, is one of the most frequent causes of Homo sapiens mitochondrial encephalomyopathies [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=93.50 E-value=0.054 Score=37.85 Aligned_cols=49 Identities=20% Similarity=0.427 Sum_probs=43.7
Q ss_pred CCCCCCCCccHHHHHHHHHHHhhcCCCChhhHHHhhhhhhccchhhhhh
Q psy7740 20 SFPLDHYGDCKAFMTKYMICIKKNNSDSSACRDEIKDYLGCRMEKELMA 68 (184)
Q Consensus 20 ~fpldh~~~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~crm~~~Lm~ 68 (184)
--||..-.-|-+..+.|.+|++++....-+|..+--+|..|.-+.-++.
T Consensus 13 ~lPl~~RDyCAh~Li~l~kCrr~~~p~~~~C~~erH~y~~C~y~dy~~R 61 (66)
T PF05676_consen 13 KLPLQYRDYCAHLLIPLNKCRRDNFPFPWKCEHERHEYEKCQYDDYVMR 61 (66)
T ss_pred CCChhhhhhHHHHHHHHHHHHHhCCCCcccCCcchhhHHHccHHHHHHH
Confidence 3588889999999999999999998888999999999999998776643
No 23
>PF08991 DUF1903: Domain of unknown function (DUF1903); InterPro: IPR009069 The mature-T-cell-proliferation (MTCP1) putative oncogene was identified for its involvement in t(X:14)(q28;q11)-associated T-cell leukaemia []. MTCP1 is alternatively spliced to produce two completely distinct proteins: the small mitochondrial protein, p8MTCP1, and the protein p13MTCP1, which shows strong homology to another oncogene product, p14TCL1. While p13MTCP1 expression appears to be restricted to mature T-cell proliferation with t(X,14) translocations, the mitochondrial p8MTCP1 is expressed at low levels in most human tissues, and is over-expressed in the proliferating T-cells. The biological function of p8MTCP1 is still unknown, but it appears to play a role in oncogenesis. The structure of p8MTCP1 reveals a disulphide-rich, irregular array of three helices [].; PDB: 2HP8_A 1EI0_A 1HP8_A.
Probab=87.04 E-value=0.83 Score=31.93 Aligned_cols=36 Identities=28% Similarity=0.565 Sum_probs=31.7
Q ss_pred ccHHHHHHHHHHHhhcCCCChhhHHHhhhhhhccch
Q psy7740 28 DCKAFMTKYMICIKKNNSDSSACRDEIKDYLGCRME 63 (184)
Q Consensus 28 ~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~crm~ 63 (184)
-|+.+--.-..||..|+++.+.|.+...+|-.|.-.
T Consensus 3 PC~~~Ac~iq~CL~~N~Yd~~kC~~~i~~l~~Cck~ 38 (67)
T PF08991_consen 3 PCQKEACAIQKCLQRNNYDESKCQDYIDALYECCKK 38 (67)
T ss_dssp TTHHHHHHHHHHHHHTTT-CCCTHHHHHHHHHHHTT
T ss_pred chHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 488888889999999999999999999999999754
No 24
>PF08583 Cmc1: Cytochrome c oxidase biogenesis protein Cmc1 like; InterPro: IPR013892 Cmc1 is a metallo-chaperone like protein which is known to localise to the inner mitochondrial membrane in Saccharomyces cerevisiae. It is essential for full expression of cytochrome c oxidase and respiration []. Cmc1 contains two Cx9C motifs and is able to bind copper(I). Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase.
Probab=81.43 E-value=1.1 Score=30.24 Aligned_cols=39 Identities=23% Similarity=0.435 Sum_probs=32.9
Q ss_pred CccHHHHHHHHHHHhhcC-CCChhhHHHhhhhhhccchhh
Q psy7740 27 GDCKAFMTKYMICIKKNN-SDSSACRDEIKDYLGCRMEKE 65 (184)
Q Consensus 27 ~~c~~~~~~y~~cl~~~~-~~~~~cr~~~k~yl~crm~~~ 65 (184)
-.|..++..|..|.+... ..-+.||++.++.-.|--...
T Consensus 11 ~~C~~~i~~~~~C~~~~~~~~~~~C~~~~~~m~~Cl~~~~ 50 (69)
T PF08583_consen 11 KKCADEIEAFAECHKDRTFKFVGKCREEKKAMNECLKEER 50 (69)
T ss_pred HHhHHHHHHHHHHHhcchHHHHHhhhHHHHHHHHHHHHHH
Confidence 579999999999999944 456899999999999976543
No 25
>KOG3468|consensus
Probab=68.42 E-value=3.8 Score=31.61 Aligned_cols=51 Identities=20% Similarity=0.352 Sum_probs=41.7
Q ss_pred CCCCCCccHHHHHHHHHHHhhcCCCChhhHHHhhhhhhccchhhhhhhhhh
Q psy7740 22 PLDHYGDCKAFMTKYMICIKKNNSDSSACRDEIKDYLGCRMEKELMAKEDW 72 (184)
Q Consensus 22 pldh~~~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~crm~~~Lm~k~~~ 72 (184)
+|-----|-+..+.|++|-..+--+.-+|-++--+|+.|-.+.-+|.=.++
T Consensus 50 ~l~~RDyCAH~lI~l~kCr~~~fp~~~kC~~erh~~dkCEyed~vmRmkef 100 (128)
T KOG3468|consen 50 ALGSRDYCAHLLIPLNKCRQDEFPFPWKCEDERHVYDKCEYEDYVMRMKEF 100 (128)
T ss_pred CcchHHHHHHHHHHHHHhhcccCCcchhccccccchhhhhHHHHHHHHHHH
Confidence 344445699999999999999988889999999999999988877654443
No 26
>KOG4618|consensus
Probab=68.39 E-value=6.1 Score=28.04 Aligned_cols=37 Identities=27% Similarity=0.518 Sum_probs=33.2
Q ss_pred CccHHHHHHHHHHHhhcCCCChhhHHHhhhhhhccch
Q psy7740 27 GDCKAFMTKYMICIKKNNSDSSACRDEIKDYLGCRME 63 (184)
Q Consensus 27 ~~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~crm~ 63 (184)
.-|-+.-..-++||.+|+.|-++|-+-=-.|=+|+--
T Consensus 22 nPCl~es~aSfkCLeennyDRsKCq~yFd~YkeCKkf 58 (74)
T KOG4618|consen 22 NPCLLESSASFKCLEENNYDRSKCQDYFDVYKECKKF 58 (74)
T ss_pred ChHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHHHHH
Confidence 5688899999999999999999999999999999743
No 27
>cd00926 Cyt_c_Oxidase_VIb Cytochrome c oxidase subunit VIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex.
Probab=63.99 E-value=9.9 Score=26.94 Aligned_cols=31 Identities=29% Similarity=0.545 Sum_probs=27.0
Q ss_pred ccHHHHHHHHHHHhhcCCCChhhHHHhhhhh
Q psy7740 28 DCKAFMTKYMICIKKNNSDSSACRDEIKDYL 58 (184)
Q Consensus 28 ~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl 58 (184)
.|-.--..|..||+.++.+.+.|..+-+.|=
T Consensus 22 ~Cw~~y~~y~~Cl~~~ged~~~C~~~~~~~e 52 (75)
T cd00926 22 HCWQRYVDYHRCIKAKGEDASPCKKFRRVYE 52 (75)
T ss_pred HHHHHHHHHHHHHHHcCCchHHHHHHHHHHH
Confidence 4666778899999999999999999999873
No 28
>PF10200 Ndufs5: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa; InterPro: IPR019342 Proteins in this entry form part of the NADH:ubiquinone oxidoreductase complex I. Complex I is the first multisubunit inner membrane protein complex of the mitochondrial electron transport chain and it transfers two electrons from NADH to ubiquinone. The mammalian complex I is composed of 45 different subunits. The proteins in this entry represent a component of the iron-sulphur (IP) fragment of the enzyme, that is not involved in catalysis. These proteins carry four highly conserved cysteine residues, but these do not appear to be in a configuration which would favour metal binding, so the exact function of the protein is uncertain [].
Probab=63.46 E-value=14 Score=27.57 Aligned_cols=48 Identities=21% Similarity=0.576 Sum_probs=38.7
Q ss_pred CCCCCCccHHHHHHHHHHHhhcCC--CChhhHHHhhhhhhccchhhhhhh
Q psy7740 22 PLDHYGDCKAFMTKYMICIKKNNS--DSSACRDEIKDYLGCRMEKELMAK 69 (184)
Q Consensus 22 pldh~~~c~~~~~~y~~cl~~~~~--~~~~cr~~~k~yl~crm~~~Lm~k 69 (184)
|--..+.|-.+-..||.|....+. ...+|+.+--+|++|..-.+.+.+
T Consensus 26 ~~~~~~RC~~FE~e~i~C~~~~G~~r~kKeC~~e~EDy~EClh~~Ke~~R 75 (96)
T PF10200_consen 26 PYKQPSRCHPFEKEWIECAEAYGQTRGKKECKLELEDYYECLHHTKEMKR 75 (96)
T ss_pred CCCCCCchHHHHHHHHHHHHHHcccchhhhchhHHhHHHHHHhhHHHHHH
Confidence 344568899999999999988774 356999999999999987665444
No 29
>KOG4083|consensus
Probab=55.24 E-value=9.4 Score=31.83 Aligned_cols=37 Identities=14% Similarity=0.475 Sum_probs=34.7
Q ss_pred CCCccHHHHHHHHHHHhhcCCCChhhHHHhhhhhhcc
Q psy7740 25 HYGDCKAFMTKYMICIKKNNSDSSACRDEIKDYLGCR 61 (184)
Q Consensus 25 h~~~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~cr 61 (184)
.+.-|.......+.|.++|-...-+|-.+++.|..|-
T Consensus 144 ~~pvCqdlq~qil~Cyr~~p~e~LkC~~lv~af~~Cv 180 (192)
T KOG4083|consen 144 REPVCQDLQAQILRCYRENPGEVLKCSPLVAAFMKCV 180 (192)
T ss_pred cCCcccccHHHHHHHHhcCCCccccccHHHHHHHHHH
Confidence 6778999999999999999999999999999999995
No 30
>KOG4090|consensus
Probab=53.34 E-value=16 Score=29.65 Aligned_cols=43 Identities=19% Similarity=0.386 Sum_probs=35.2
Q ss_pred CCCCCCCccHHHHHHHHHHHhhcCCCChhhHHHhhhhhhccch
Q psy7740 21 FPLDHYGDCKAFMTKYMICIKKNNSDSSACRDEIKDYLGCRME 63 (184)
Q Consensus 21 fpldh~~~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~crm~ 63 (184)
-|---.+-|..+...|+.|+..++.|.+.|.-...-.-+|+-.
T Consensus 110 q~~q~~~~C~~e~kqF~dCa~~~~~d~slC~~f~e~Lk~Ck~~ 152 (157)
T KOG4090|consen 110 QPAQQQQPCFIEIKQFLDCAQNQGSDISLCEGYNEMLKQCKKN 152 (157)
T ss_pred chhhhcCchHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHH
Confidence 3434466799999999999999999999998887777777644
No 31
>PF05051 COX17: Cytochrome C oxidase copper chaperone (COX17); InterPro: IPR007745 Cox17p is essential for the assembly of functional cytochrome c oxidase (CCO) and for delivery of copper ions to the mitochondrion for insertion into the enzyme in Saccharomyces cerevisiae [].; GO: 0005507 copper ion binding, 0016531 copper chaperone activity, 0006825 copper ion transport, 0005758 mitochondrial intermembrane space; PDB: 1U97_A 1U96_A 1Z2G_A 2RNB_A 2RN9_A 2LGQ_A 2L0Y_B.
Probab=49.51 E-value=21 Score=23.57 Aligned_cols=30 Identities=23% Similarity=0.489 Sum_probs=15.2
Q ss_pred cHHHHHHHHHHHhhcCCCChhhHHHhhhhhhc
Q psy7740 29 CKAFMTKYMICIKKNNSDSSACRDEIKDYLGC 60 (184)
Q Consensus 29 c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~c 60 (184)
|......-=.|+=.++.++ |+++..+|-+|
T Consensus 12 CpetK~aRDeC~l~~g~e~--C~~~Ieahk~C 41 (49)
T PF05051_consen 12 CPETKKARDECILFNGEED--CKELIEAHKAC 41 (49)
T ss_dssp SHHHHHHHHHHHHHC-CCC--CHHHHHHHHHH
T ss_pred ChhHHHHhHhhHHhcChHH--HHHHHHHHHHH
Confidence 4445555555555554444 55555555555
No 32
>PF03033 Glyco_transf_28: Glycosyltransferase family 28 N-terminal domain; InterPro: IPR004276 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 28 GT28 from CAZY comprises enzymes with a number of known activities; 1,2-diacylglycerol 3-beta-galactosyltransferase (2.4.1.46 from EC); 1,2-diacylglycerol 3-beta-glucosyltransferase (2.4.1.157 from EC); beta-N-acetylglucosamine transferase (2.4.1 from EC).; GO: 0016758 transferase activity, transferring hexosyl groups, 0005975 carbohydrate metabolic process, 0030259 lipid glycosylation; PDB: 2IYF_B 2YJN_A 2P6P_A 1PNV_A 3H4T_A 3H4I_A 1PN3_B 3IA7_B 1NLM_B 1F0K_B ....
Probab=47.72 E-value=18 Score=26.61 Aligned_cols=45 Identities=9% Similarity=0.095 Sum_probs=31.7
Q ss_pred hhcCCCchHHhH-HHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCCC
Q psy7740 80 LLCCTGSVATIK-LPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPHK 132 (184)
Q Consensus 80 llg~tGSiaa~k-~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l~ 132 (184)
++...|+-|=+. ..-+.++|+++| + +|.+..++.....+....++
T Consensus 2 li~~~Gt~Ghv~P~lala~~L~~rG--h------~V~~~~~~~~~~~v~~~Gl~ 47 (139)
T PF03033_consen 2 LIATGGTRGHVYPFLALARALRRRG--H------EVRLATPPDFRERVEAAGLE 47 (139)
T ss_dssp EEEEESSHHHHHHHHHHHHHHHHTT---------EEEEEETGGGHHHHHHTT-E
T ss_pred EEEEcCChhHHHHHHHHHHHHhccC--C------eEEEeecccceecccccCce
Confidence 344455555444 778999999999 7 99988888888887665544
No 33
>TIGR02536 eut_hyp ethanolamine utilization protein. This family of proteins is found in operons for the polyhedral organelle-based degradation of ethanolamine. This family is not found in proteobacterial species which otherwise have the same suite of genes in the eut operon. Proteobacteria have two genes that are not found in non-proteobacteria which may complement this genes function, a phosphotransacetylase (pfam01515) and the EutJ protein (TIGR02529) of unknown function.
Probab=45.82 E-value=17 Score=30.63 Aligned_cols=22 Identities=23% Similarity=0.407 Sum_probs=20.6
Q ss_pred ccccEEEEcccccHHHHHHhcC
Q psy7740 161 KWCDIIVLAPLDANTLAKLATY 182 (184)
Q Consensus 161 ~~aD~~VVaPaSaNTlAKiA~~ 182 (184)
+.+|.+||-=.|.|+|+|||+|
T Consensus 52 ~~~dillv~~Lt~n~lskIAlG 73 (207)
T TIGR02536 52 KLADILLVSRLSIKELNNISHG 73 (207)
T ss_pred hcCCEEEEccCCHHHHHHHHcc
Confidence 5799999999999999999997
No 34
>PF10203 Pet191_N: Cytochrome c oxidase assembly protein PET191; InterPro: IPR018793 This entry represents a family of conserved proteins found from nematodes to humans. Cytochrome c oxidase assembly protein Pet191 carries six highly conserved cysteine residues. Pet191 is required for the assembly of active cytochrome c oxidase but does not form part of the final assembled complex [].
Probab=45.50 E-value=16 Score=25.53 Aligned_cols=27 Identities=19% Similarity=0.485 Sum_probs=18.8
Q ss_pred HHHhhcC-CCChhhHHHhhhhhhccchh
Q psy7740 38 ICIKKNN-SDSSACRDEIKDYLGCRMEK 64 (184)
Q Consensus 38 ~cl~~~~-~~~~~cr~~~k~yl~crm~~ 64 (184)
.||+... .-...|..+-++|.+|+...
T Consensus 31 ~Cl~~~~~~~p~eC~~lr~~f~eCKrg~ 58 (68)
T PF10203_consen 31 DCLKDPSDELPEECQQLRKAFFECKRGM 58 (68)
T ss_pred HHHcCCCCcCCHHHHHHHHHHHHHhccc
Confidence 3444442 23469999999999999753
No 35
>PF05051 COX17: Cytochrome C oxidase copper chaperone (COX17); InterPro: IPR007745 Cox17p is essential for the assembly of functional cytochrome c oxidase (CCO) and for delivery of copper ions to the mitochondrion for insertion into the enzyme in Saccharomyces cerevisiae [].; GO: 0005507 copper ion binding, 0016531 copper chaperone activity, 0006825 copper ion transport, 0005758 mitochondrial intermembrane space; PDB: 1U97_A 1U96_A 1Z2G_A 2RNB_A 2RN9_A 2LGQ_A 2L0Y_B.
Probab=41.33 E-value=45 Score=21.99 Aligned_cols=19 Identities=21% Similarity=0.590 Sum_probs=16.8
Q ss_pred ccHHHHHHHHHHHhhcCCC
Q psy7740 28 DCKAFMTKYMICIKKNNSD 46 (184)
Q Consensus 28 ~c~~~~~~y~~cl~~~~~~ 46 (184)
.|++++..|-.||+.-+++
T Consensus 30 ~C~~~Ieahk~Cmr~~GF~ 48 (49)
T PF05051_consen 30 DCKELIEAHKACMRGEGFK 48 (49)
T ss_dssp CCHHHHHHHHHHHHHHTCC
T ss_pred HHHHHHHHHHHHHHHcCCC
Confidence 3999999999999988764
No 36
>PF02297 COX6B: Cytochrome oxidase c subunit VIb; InterPro: IPR003213 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex that is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptide subunits. One of these subunits is the potentially haem-binding subunit, VIb, which is encoded in the nucleus []. ; GO: 0004129 cytochrome-c oxidase activity, 0005739 mitochondrion; PDB: 1OCC_U 1OCR_U 2DYS_H 3ASO_H 3AG3_U 2EIL_H 2EIJ_U 3AG2_U 3ABM_U 2EIN_U ....
Probab=40.78 E-value=22 Score=24.85 Aligned_cols=33 Identities=36% Similarity=0.707 Sum_probs=26.8
Q ss_pred cHHHHHHHHHHHhhcCC---------CChhhHHHhhhhhh-cc
Q psy7740 29 CKAFMTKYMICIKKNNS---------DSSACRDEIKDYLG-CR 61 (184)
Q Consensus 29 c~~~~~~y~~cl~~~~~---------~~~~cr~~~k~yl~-cr 61 (184)
|=.---.|-.||..++. +...|..+-+.|-+ |-
T Consensus 12 Cw~arD~y~~Cl~~~~~~~~~~~~~~~~~~C~~~~~~ye~~Cp 54 (76)
T PF02297_consen 12 CWQARDDYFKCLDKNGEPDSEKEKKKDESACKYFRKNYESNCP 54 (76)
T ss_dssp HHHHHHHHHHHHHHHHH------TTTTGGGGHHHHHHHHHHS-
T ss_pred HHHHHHHHHHHHHHcCccccccccccchhhhHHHHHHHHHhCc
Confidence 55666789999999987 78899999999865 64
No 37
>PRK03971 putative deoxyhypusine synthase; Provisional
Probab=40.65 E-value=49 Score=29.93 Aligned_cols=39 Identities=21% Similarity=0.317 Sum_probs=33.3
Q ss_pred hhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHH
Q psy7740 76 EFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAF 123 (184)
Q Consensus 76 Gf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~ 123 (184)
+-++.++.||+..+.-..++|+.|.+.+ -|++|+|-.|-
T Consensus 66 ~~~ifL~~tg~misaGlr~~i~~Li~~~---------~Vd~iVtTgan 104 (334)
T PRK03971 66 EATVFLGYTSNIVSSGLREIIAYLVKEK---------KVDVIVTTAGG 104 (334)
T ss_pred CCeEEEEccccccchhHHHHHHHHHHcC---------CeeEEEeCCCc
Confidence 4577899999999998999999999998 59999986653
No 38
>KOG3458|consensus
Probab=39.99 E-value=18 Score=29.36 Aligned_cols=37 Identities=30% Similarity=0.618 Sum_probs=30.0
Q ss_pred ccHHHHHHHHHHHhhcC-CCChhhHHHhhhhhhccchh
Q psy7740 28 DCKAFMTKYMICIKKNN-SDSSACRDEIKDYLGCRMEK 64 (184)
Q Consensus 28 ~c~~~~~~y~~cl~~~~-~~~~~cr~~~k~yl~crm~~ 64 (184)
.|-..|.+|..|+-... +.=+.||++-+++-.|--++
T Consensus 77 ~C~~e~~~y~~C~dysst~~f~~Crk~Q~~fdkcv~~k 114 (170)
T KOG3458|consen 77 SCLEEFTKYATCMDYSSTNEFSHCRKEQEAFDKCVPDK 114 (170)
T ss_pred HhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhHhh
Confidence 58889999999998885 45579999999888886543
No 39
>PF09623 Cas_NE0113: CRISPR-associated protein NE0113 (Cas_NE0113); InterPro: IPR019092 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a Cas protein family found in both bacteria and arachaea. The function of these proteins is unknown.
Probab=39.38 E-value=33 Score=29.22 Aligned_cols=43 Identities=21% Similarity=0.238 Sum_probs=32.4
Q ss_pred hhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHh
Q psy7740 77 FNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHF 125 (184)
Q Consensus 77 f~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~f 125 (184)
+++|++++|.+..+ +.+-+..|...|+ +.++|+|+-|.++..-
T Consensus 2 k~iLlatlG~sPqV-VTETL~aL~~~g~-----~p~EV~vitT~~~~~~ 44 (224)
T PF09623_consen 2 KNILLATLGTSPQV-VTETLYALAQQGE-----IPDEVHVITTRDGAVR 44 (224)
T ss_pred ceEEEEecCCCchH-HHHHHHHHHcCCC-----CCCEEEEEECCChHHH
Confidence 57899999997764 5666788888763 2459999999877643
No 40
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=36.38 E-value=47 Score=24.74 Aligned_cols=35 Identities=6% Similarity=0.126 Sum_probs=26.9
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
+-+|++.+.+...++.++..+.+..++. ++++..+
T Consensus 2 l~Ig~~~~~~~~~l~~~l~~~~~~~P~v------~i~~~~~ 36 (198)
T cd08437 2 LRFGLPPIIGNYYFPKLAKDLIKTGLMI------QIDTYEG 36 (198)
T ss_pred eEEeeChHHHHHHhHHHHHHHHHhCCce------EEEEEEc
Confidence 4568888888888999999999986555 6666543
No 41
>TIGR00661 MJ1255 conserved hypothetical protein. This model represents nearly the full length of MJ1255 from Methanococcus jannaschii and of an unpublished protein from Vibrio cholerae, as well as the C-terminal half of a protein from Methanobacterium thermoautotrophicum. A small region (~50 amino acids) within the domain appears related to a family of sugar transferases.
Probab=35.35 E-value=40 Score=28.99 Aligned_cols=44 Identities=11% Similarity=0.249 Sum_probs=31.8
Q ss_pred hhhcCC--CchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCC
Q psy7740 79 ILLCCT--GSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPH 131 (184)
Q Consensus 79 illg~t--GSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l 131 (184)
|+++++ |-.-+..+..++++|++ | + +|.++.|..+..++....+
T Consensus 2 il~~~~g~G~GH~~r~~ala~~L~~-g--~------ev~~~~~~~~~~~~~~~~~ 47 (321)
T TIGR00661 2 ILYSVCGEGFGHTTRSVAIGEALKN-D--Y------EVSYIASGRSKNYISKYGF 47 (321)
T ss_pred EEEEEeccCccHHHHHHHHHHHHhC-C--C------eEEEEEcCCHHHhhhhhcC
Confidence 445444 43345678889999998 8 7 9999988888887765533
No 42
>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]
Probab=35.30 E-value=86 Score=26.49 Aligned_cols=76 Identities=17% Similarity=0.117 Sum_probs=54.4
Q ss_pred hhHHHhhhhhhccchhhhhhhhhhhh----hhhhhhhcCCCchH---HhHHHHHHHHHHhccccccccccceEEEEcCch
Q psy7740 49 ACRDEIKDYLGCRMEKELMAKEDWEK----LEFNILLCCTGSVA---TIKLPELIEQIEQLQYEFNKIMIINLNVVMTKH 121 (184)
Q Consensus 49 ~cr~~~k~yl~crm~~~Lm~k~~~~~----LGf~illg~tGSia---a~k~~~li~~L~~~g~~~~~~~~~~V~VilT~s 121 (184)
.||.+.++|=-+-+.+.+-.+++-+. .|-+++-+.||-.+ +....+-|.+|.... - ++.+++.++
T Consensus 33 ~~~~L~~~~~~aVI~~Di~t~~Da~~l~~~~g~~i~~v~TG~~CH~da~m~~~ai~~l~~~~--~------~~Dll~iEs 104 (202)
T COG0378 33 TLRALKDEYKIAVITGDIYTKEDADRLRKLPGEPIIGVETGKGCHLDASMNLEAIEELVLDF--P------DLDLLFIES 104 (202)
T ss_pred HHHHHHhhCCeEEEeceeechhhHHHHHhCCCCeeEEeccCCccCCcHHHHHHHHHHHhhcC--C------cCCEEEEec
Confidence 48999999888888877755555443 45578888888554 455667777788775 2 588899888
Q ss_pred HHHhcCcCCCC
Q psy7740 122 AFHFVPDLPHK 132 (184)
Q Consensus 122 A~~fv~~~~l~ 132 (184)
+-..+-+.+..
T Consensus 105 ~GNL~~~~sp~ 115 (202)
T COG0378 105 VGNLVCPFSPD 115 (202)
T ss_pred CcceecccCcc
Confidence 87777666655
No 43
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=33.25 E-value=56 Score=23.81 Aligned_cols=34 Identities=12% Similarity=0.186 Sum_probs=25.9
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+.+...++.++..+.+..++. +|++..
T Consensus 2 l~Ig~~~~~~~~~l~~~l~~~~~~~p~v------~i~i~~ 35 (197)
T cd08440 2 VRVAALPSLAATLLPPVLAAFRRRHPGI------RVRLRD 35 (197)
T ss_pred eEEEeccchhhhHHHHHHHHHHHhCCCc------EEEEEe
Confidence 4568888888888999999999876545 666654
No 44
>KOG4110|consensus
Probab=31.91 E-value=69 Score=24.70 Aligned_cols=53 Identities=25% Similarity=0.545 Sum_probs=44.4
Q ss_pred CCCCCCCCCCCc-cHHHHHHHHHHHhhcCC--CChhhHHHhhhhhhccchhhhhhh
Q psy7740 17 DKGSFPLDHYGD-CKAFMTKYMICIKKNNS--DSSACRDEIKDYLGCRMEKELMAK 69 (184)
Q Consensus 17 ~~g~fpldh~~~-c~~~~~~y~~cl~~~~~--~~~~cr~~~k~yl~crm~~~Lm~k 69 (184)
+-++-|+-|-|- |-.|-.++|.|...-+. -.-.|+.+-..+-+|-.-++.|.+
T Consensus 23 ds~~~p~~~q~r~cg~FE~e~~eC~eayG~~~g~keC~ie~~dFqECv~~qKqmrr 78 (120)
T KOG4110|consen 23 DSTEQPYKHQGRDCGKFEKEWMECAEAYGLERGEKECAIEYDDFQECVLMQKQMRR 78 (120)
T ss_pred ccccCccccccccccHHHHHHHHHHHHHhhHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 678899999999 99999999999998884 345899999999999755554433
No 45
>COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]
Probab=31.49 E-value=72 Score=26.85 Aligned_cols=25 Identities=24% Similarity=0.367 Sum_probs=22.1
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhcc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQ 103 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g 103 (184)
++++++||.-+-.+..++..+++.|
T Consensus 89 vviaiS~SGeT~el~~~~~~aK~~g 113 (202)
T COG0794 89 VVIAISGSGETKELLNLAPKAKRLG 113 (202)
T ss_pred EEEEEeCCCcHHHHHHHHHHHHHcC
Confidence 6788999999888999999999987
No 46
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=31.19 E-value=47 Score=24.61 Aligned_cols=35 Identities=11% Similarity=0.256 Sum_probs=26.4
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
+-+|++.+.+...++.++..+++..|+. ++++..+
T Consensus 3 l~Ig~~~~~~~~~l~~~l~~f~~~~P~v------~l~i~~~ 37 (197)
T cd08470 3 LRITCPVAYGERFIAPLVNDFMQRYPKL------EVDIELT 37 (197)
T ss_pred EEEEcCHHHHHHHHHHHHHHHHHHCCCe------EEEEEec
Confidence 4567888888888999999999986555 6666543
No 47
>KOG3481|consensus
Probab=31.03 E-value=80 Score=23.20 Aligned_cols=37 Identities=24% Similarity=0.531 Sum_probs=29.7
Q ss_pred CccHHHHHHHHHHHhh------cC--CCChhhHHHhhhhhhccch
Q psy7740 27 GDCKAFMTKYMICIKK------NN--SDSSACRDEIKDYLGCRME 63 (184)
Q Consensus 27 ~~c~~~~~~y~~cl~~------~~--~~~~~cr~~~k~yl~crm~ 63 (184)
.+|.+...+|=+|-.+ .. .....|-.+=|.|.+|--.
T Consensus 11 ~eCt~lk~~YD~CFn~Wf~eKflKG~~~~~pC~~l~k~Y~~Cv~k 55 (87)
T KOG3481|consen 11 PECTDLKQKYDQCFNEWFSEKFLKGDSSGEPCSRLFKVYKQCVQK 55 (87)
T ss_pred ccchHHHHHHHHHHHHHHHHHhcCCccccCcHHHHHHHHHHHHHH
Confidence 4899999999999764 22 3456999999999999643
No 48
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=29.74 E-value=53 Score=24.35 Aligned_cols=35 Identities=6% Similarity=0.129 Sum_probs=26.7
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
+-+|++.+.+...++.++..+++..|+. +|++..+
T Consensus 3 l~Ig~~~~~~~~~l~~~l~~~~~~~P~v------~i~i~~~ 37 (201)
T cd08471 3 LTVTAPVLFGRLHVLPIITDFLDAYPEV------SVRLLLL 37 (201)
T ss_pred EEEEccHHHHHHHHHHHHHHHHHHCCCc------EEEEEEc
Confidence 5578888888888999999999876545 6666533
No 49
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=29.29 E-value=51 Score=24.10 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=26.4
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
+-+|++.+++...++.++..+.+..++. ++++..+
T Consensus 3 l~Ig~~~~~~~~~l~~~l~~~~~~~P~v------~i~i~~~ 37 (197)
T cd08422 3 LRISAPVSFGRLHLAPLLAEFLARYPDV------RLELVLS 37 (197)
T ss_pred EEEEecHHHHHHHHHHHHHHHHHhCCce------EEEEecC
Confidence 4568888888888999999999986545 5666543
No 50
>PF07956 DUF1690: Protein of Unknown function (DUF1690) ; InterPro: IPR012471 Family of uncharacterised fungal proteins.
Probab=29.22 E-value=73 Score=25.20 Aligned_cols=36 Identities=11% Similarity=0.359 Sum_probs=31.7
Q ss_pred CCCccHHHHHHHHHHHhhcCCCChhhHHHhhhhhhc
Q psy7740 25 HYGDCKAFMTKYMICIKKNNSDSSACRDEIKDYLGC 60 (184)
Q Consensus 25 h~~~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl~c 60 (184)
|..+|+..-..-..||+.|..-.=.|-.+..++=.|
T Consensus 105 ~~~~v~~aR~~vv~CL~~N~~rPLnCw~EVe~FKk~ 140 (142)
T PF07956_consen 105 NSEEVEKARSAVVRCLRENDGRPLNCWEEVEAFKKE 140 (142)
T ss_pred cchhhHHHHHHHHHHHHHCCCCCCchHHHHHHHHHH
Confidence 667899999999999999999999999998886554
No 51
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=28.93 E-value=62 Score=24.00 Aligned_cols=34 Identities=15% Similarity=0.174 Sum_probs=25.8
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+++...++.++..+.+..++. +|.+..
T Consensus 3 l~Ig~~~~~~~~~l~~~l~~~~~~~P~i------~v~~~~ 36 (202)
T cd08472 3 LRVDVPGSLARLLLIPALPDFLARYPDI------ELDLGV 36 (202)
T ss_pred EEEeccHHHHHHHHHHHHHHHHHHCCCc------EEEEEE
Confidence 4468888888888999999999886555 666643
No 52
>PLN03079 Uncharacterized protein At4g33100; Provisional
Probab=28.56 E-value=82 Score=23.35 Aligned_cols=36 Identities=28% Similarity=0.598 Sum_probs=28.9
Q ss_pred ccHHHHHHHHHHHhhc------CC--CChhhHHHhhhhhhccch
Q psy7740 28 DCKAFMTKYMICIKKN------NS--DSSACRDEIKDYLGCRME 63 (184)
Q Consensus 28 ~c~~~~~~y~~cl~~~------~~--~~~~cr~~~k~yl~crm~ 63 (184)
+|+..+.+|=+|-..- ++ ....|..+=+.|-+|...
T Consensus 17 eCtelK~~YD~CFN~WYsEkFLKG~~~~~eC~~~w~~Yq~Cv~~ 60 (91)
T PLN03079 17 PCAELRTAYHNCFNRWYSEKFVKGQWDKEDCVAEWHKYRACLSE 60 (91)
T ss_pred ccHHHHHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHHHH
Confidence 6999999999997632 12 346899999999999764
No 53
>KOG1502|consensus
Probab=28.23 E-value=55 Score=29.51 Aligned_cols=31 Identities=10% Similarity=0.215 Sum_probs=24.7
Q ss_pred hhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 80 LLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 80 llg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
.+.|||++| +-+-++++.|.++| + .|+-.+-
T Consensus 8 ~VcVTGAsG-fIgswivk~LL~rG--Y------~V~gtVR 38 (327)
T KOG1502|consen 8 KVCVTGASG-FIGSWIVKLLLSRG--Y------TVRGTVR 38 (327)
T ss_pred EEEEeCCch-HHHHHHHHHHHhCC--C------EEEEEEc
Confidence 467899977 55889999999999 6 8886653
No 54
>PF09001 DUF1890: Domain of unknown function (DUF1890); InterPro: IPR012033 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. The structure of the Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) protein has been determined but no evidence as to the function is available yet.; PDB: 1KJN_B.
Probab=27.92 E-value=81 Score=25.13 Aligned_cols=30 Identities=13% Similarity=0.105 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhccccccccccceEEEEcCchHHHhcCc
Q psy7740 91 KLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPD 128 (184)
Q Consensus 91 k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~ 128 (184)
.+..+...|++.| + +|.|.-|++|.+.+.-
T Consensus 15 ~alYl~~~Lk~~G--~------~v~Va~npAA~kLl~v 44 (139)
T PF09001_consen 15 SALYLSYKLKKKG--F------EVVVAGNPAALKLLEV 44 (139)
T ss_dssp HHHHHHHHHHCTT--E------EEEEEE-HHHHHHHHH
T ss_pred HHHHHHHHHHhcC--C------eEEEecCHHHHhHhhh
Confidence 4678889999999 7 9999999999988653
No 55
>cd08475 PBP2_CrgA_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=27.86 E-value=61 Score=23.89 Aligned_cols=40 Identities=8% Similarity=0.161 Sum_probs=27.9
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHH
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFH 124 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~ 124 (184)
+-+|++.+++...++.++..+++..++. +|++..+....+
T Consensus 3 l~Ig~~~~~~~~~l~~~l~~~~~~~P~v------~i~i~~~~~~~~ 42 (199)
T cd08475 3 LRIDLPVAFGRLCVAPLLLELARRHPEL------ELELSFSDRFVD 42 (199)
T ss_pred EEEechHHHHHhhHHHHHHHHHHHCCCe------EEEEEeccchhh
Confidence 4567788888888999999999886545 666653333333
No 56
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=27.75 E-value=73 Score=23.21 Aligned_cols=36 Identities=17% Similarity=0.190 Sum_probs=26.9
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTK 120 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~ 120 (184)
+-+|++.+++...++.++..+.+..++. +|++..+.
T Consensus 2 l~Ig~~~~~~~~~l~~~l~~~~~~~P~i------~i~i~~~~ 37 (195)
T cd08434 2 VRLGFLHSLGTSLVPDLIRAFRKEYPNV------TFELHQGS 37 (195)
T ss_pred eEEEecchhhhhhhHHHHHHHHHhCCCe------EEEEecCc
Confidence 4568888888888999999999875445 66666543
No 57
>PF01171 ATP_bind_3: PP-loop family; InterPro: IPR011063 This entry represents the PP-loop motif superfamily [,]. The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, Escherichia coli NtrL, and Bacillus subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain.; PDB: 3A2K_A 2E89_B 2E21_D 1WY5_B 1NI5_A.
Probab=27.56 E-value=70 Score=25.31 Aligned_cols=26 Identities=19% Similarity=0.465 Sum_probs=19.6
Q ss_pred hhhhcCCCchHHhHHHHHHHHHHhcc
Q psy7740 78 NILLCCTGSVATIKLPELIEQIEQLQ 103 (184)
Q Consensus 78 ~illg~tGSiaa~k~~~li~~L~~~g 103 (184)
|+++|++|+.=+.-+..++..+.+..
T Consensus 1 ki~va~SGG~DS~~Ll~~l~~~~~~~ 26 (182)
T PF01171_consen 1 KILVAVSGGKDSMALLHLLKELRRRN 26 (182)
T ss_dssp EEEEE--SSHHHHHHHHHHHHHHTTT
T ss_pred CEEEEEcCCHHHHHHHHHHHHHHHhc
Confidence 57899999988888888888888753
No 58
>PF07802 GCK: GCK domain; InterPro: IPR012891 This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways (such as IPR001806 from INTERPRO) indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this family (such as Q9LMF3 from SWISSPROT); this may indicate that these domains are able to interact with one another, raising the possibility that this domain mediates heterodimerisation.
Probab=27.06 E-value=73 Score=22.76 Aligned_cols=36 Identities=19% Similarity=0.410 Sum_probs=26.8
Q ss_pred CCccHHHHHHHHHHHhhcCC-----CChhhHHHhhhhhhcc
Q psy7740 26 YGDCKAFMTKYMICIKKNNS-----DSSACRDEIKDYLGCR 61 (184)
Q Consensus 26 ~~~c~~~~~~y~~cl~~~~~-----~~~~cr~~~k~yl~cr 61 (184)
-|-||.....+-.|..+... ...+|+..--..-.|-
T Consensus 11 gG~Cke~F~awe~C~~ea~~~~~~d~v~kC~e~~~~L~kCM 51 (76)
T PF07802_consen 11 GGGCKESFTAWEDCVDEAEKNKEEDFVEKCFEATAALRKCM 51 (76)
T ss_pred CCChhHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHH
Confidence 48999999999999954432 2359998776666663
No 59
>PF13460 NAD_binding_10: NADH(P)-binding ; PDB: 3OH8_A 3E8X_A 3GPI_A 3QVO_A 2Q46_B 1YBM_B 1XQ6_B 2Q4B_B 3EW7_A 3IUS_B ....
Probab=26.98 E-value=77 Score=24.27 Aligned_cols=29 Identities=17% Similarity=0.272 Sum_probs=21.6
Q ss_pred hhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCc
Q psy7740 80 LLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTK 120 (184)
Q Consensus 80 llg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~ 120 (184)
++|.||-+| ..+++.|.+.+ + +|+++...
T Consensus 3 V~GatG~vG----~~l~~~L~~~~--~------~V~~~~R~ 31 (183)
T PF13460_consen 3 VFGATGFVG----RALAKQLLRRG--H------EVTALVRS 31 (183)
T ss_dssp EETTTSHHH----HHHHHHHHHTT--S------EEEEEESS
T ss_pred EECCCChHH----HHHHHHHHHCC--C------EEEEEecC
Confidence 566777766 45788888888 7 89988754
No 60
>PRK07667 uridine kinase; Provisional
Probab=26.94 E-value=48 Score=26.62 Aligned_cols=28 Identities=25% Similarity=0.245 Sum_probs=19.8
Q ss_pred hhhhhhcCCCchHHhH---HHHHHHHHHhcc
Q psy7740 76 EFNILLCCTGSVATIK---LPELIEQIEQLQ 103 (184)
Q Consensus 76 Gf~illg~tGSiaa~k---~~~li~~L~~~g 103 (184)
+.+.++|++|..|+=| +-.+.+.|.+.|
T Consensus 15 ~~~~iIgI~G~~gsGKStla~~L~~~l~~~~ 45 (193)
T PRK07667 15 ENRFILGIDGLSRSGKTTFVANLKENMKQEG 45 (193)
T ss_pred CCCEEEEEECCCCCCHHHHHHHHHHHHHhCC
Confidence 4568899999998887 444556666555
No 61
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=26.73 E-value=68 Score=24.02 Aligned_cols=34 Identities=12% Similarity=0.101 Sum_probs=26.6
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+.+....+.++..+.+..++. +|++..
T Consensus 2 ~~i~~~~~~~~~~l~~~l~~~~~~~P~v------~v~l~~ 35 (200)
T cd08460 2 FTIRANDGFVAAFGPALLAAVAAEAPGV------RLRFVP 35 (200)
T ss_pred EEEEechhHHHHHHHHHHHHHHHHCCCC------EEEEec
Confidence 4467888888889999999999986555 677764
No 62
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=26.61 E-value=88 Score=22.88 Aligned_cols=34 Identities=12% Similarity=0.161 Sum_probs=26.4
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+++...++.++..+.+..++. +|++..
T Consensus 2 l~i~~~~~~~~~~l~~~l~~~~~~~P~i------~i~i~~ 35 (197)
T cd08448 2 LRIGFVGSMLYRGLPRILRAFRAEYPGI------EVALHE 35 (197)
T ss_pred eEEEEchhHHHHHHHHHHHHHHHHCCCC------eEEEEe
Confidence 3467888888888999999999876555 677664
No 63
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=26.47 E-value=75 Score=23.40 Aligned_cols=37 Identities=11% Similarity=0.183 Sum_probs=27.3
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCch
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKH 121 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~s 121 (184)
+-+|++.+++...++.++..+.+..++. +|++..+.+
T Consensus 2 l~Ig~~~~~~~~~l~~~l~~~~~~~P~i------~~~i~~~~~ 38 (196)
T cd08456 2 LRIAVLPALSQSFLPRAIKAFLQRHPDV------TISIHTRDS 38 (196)
T ss_pred eEEEecHHHHHhhHHHHHHHHHHHCCCc------EEEEEeCCH
Confidence 4467777888888999999999876545 677765443
No 64
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=26.39 E-value=65 Score=23.59 Aligned_cols=34 Identities=15% Similarity=0.132 Sum_probs=25.9
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+++...++.++..+.+..++. +|++..
T Consensus 2 l~Ig~~~~~~~~~l~~~l~~~~~~~p~v------~i~i~~ 35 (197)
T cd08438 2 LRLGLPPLGGSLLFAPLLAAFRQRYPNI------ELELVE 35 (197)
T ss_pred eEEEecchhhhhhcHHHHHHHHHHCcCe------EEEEEE
Confidence 4467888888888999999999876545 666664
No 65
>PF01916 DS: Deoxyhypusine synthase; InterPro: IPR002773 Eukaryotic initiation factor 5A (eIF-5A), now considered to be an elongation factor (see IPR001884 from INTERPRO), contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalysed by the enzyme deoxyhypusine synthase (DS) 2.5.1.46 from EC. The enzyme catalyses the following reaction: Spermidine + [eIF-5A]-lysine = 1,3-diaminopropane + [eIF-5A]-deoxyhypusine The modified version of eIF-5A, and DS, are required for eukaryotic cell proliferation []. The structure is known for this enzyme [] in complex with its NAD+ cofactor.; GO: 0008612 peptidyl-lysine modification to hypusine; PDB: 1RQD_A 1RLZ_A 1DHS_A 1ROZ_B.
Probab=26.23 E-value=29 Score=30.78 Aligned_cols=40 Identities=20% Similarity=0.315 Sum_probs=31.0
Q ss_pred hhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHH
Q psy7740 76 EFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFH 124 (184)
Q Consensus 76 Gf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~ 124 (184)
.-++.++.||+....-...+|..|.+.+ -|+||+|-.|--
T Consensus 37 ~~tifLt~aGamvsaGLr~ii~~LIr~g---------~Vd~IvtTganl 76 (299)
T PF01916_consen 37 DCTIFLTFAGAMVSAGLRGIIADLIRNG---------YVDVIVTTGANL 76 (299)
T ss_dssp SSEEEEEE-THHHHSTHHHHHHHHHHTT-----------SEEEE-HHHH
T ss_pred CCeEEEEcccccccccHHHHHHHHHhCC---------ceEEEEeCCCch
Confidence 4578899999999999999999999998 599999876653
No 66
>KOG3584|consensus
Probab=26.16 E-value=36 Score=30.51 Aligned_cols=14 Identities=21% Similarity=0.849 Sum_probs=8.8
Q ss_pred ccHHHHHHHHHHHh
Q psy7740 28 DCKAFMTKYMICIK 41 (184)
Q Consensus 28 ~c~~~~~~y~~cl~ 41 (184)
||+..+.+|.+||.
T Consensus 305 ECRRKKKEYVKCLE 318 (348)
T KOG3584|consen 305 ECRRKKKEYVKCLE 318 (348)
T ss_pred HHHHhHhHHHHHHH
Confidence 56666666666664
No 67
>KOG3057|consensus
Probab=25.96 E-value=89 Score=24.02 Aligned_cols=31 Identities=29% Similarity=0.550 Sum_probs=26.4
Q ss_pred ccHHHHHHHHHHHhhcCCCChhhHHHhhhhh
Q psy7740 28 DCKAFMTKYMICIKKNNSDSSACRDEIKDYL 58 (184)
Q Consensus 28 ~c~~~~~~y~~cl~~~~~~~~~cr~~~k~yl 58 (184)
.|=.--..|-+|++.+..|-..|..+.+.|=
T Consensus 57 hCf~~y~dyhrC~~~~geD~~~Ck~f~~~y~ 87 (112)
T KOG3057|consen 57 HCFQRYVDYHRCIKAKGEDANPCKKFQKVYR 87 (112)
T ss_pred HHHHHHHHHHHHHHHhcccchhHHHHHHHHH
Confidence 3555677888999999999999999999884
No 68
>cd03785 GT1_MurG MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide (NAM). The resulting disaccharide is then transported across the cell membrane, where it is polymerized into NAG-NAM cell-wall repeat structure. MurG belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains, each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=25.93 E-value=68 Score=27.12 Aligned_cols=36 Identities=22% Similarity=0.215 Sum_probs=26.3
Q ss_pred hhhhcCCCchHHhH-HHHHHHHHHhccccccccccceEEEEcCch
Q psy7740 78 NILLCCTGSVATIK-LPELIEQIEQLQYEFNKIMIINLNVVMTKH 121 (184)
Q Consensus 78 ~illg~tGSiaa~k-~~~li~~L~~~g~~~~~~~~~~V~VilT~s 121 (184)
+|++..+|..+... +..+++.|.+.| + +|+|+.+..
T Consensus 1 ~~~~~~~~~gG~~~~~~~la~~l~~~G--~------ev~v~~~~~ 37 (350)
T cd03785 1 RILIAGGGTGGHIFPALALAEELRERG--A------EVLFLGTKR 37 (350)
T ss_pred CEEEEecCchhhhhHHHHHHHHHHhCC--C------EEEEEECCC
Confidence 35566666666665 668999999998 7 999886654
No 69
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=25.83 E-value=84 Score=23.08 Aligned_cols=34 Identities=18% Similarity=0.249 Sum_probs=25.8
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+.+...+++++..+++..++. ++++..
T Consensus 2 l~Ig~~~~~~~~~l~~~l~~~~~~~P~v------~i~i~~ 35 (201)
T cd08435 2 VRVGAVPAAAPVLLPPAIARLLARHPRL------TVRVVE 35 (201)
T ss_pred eEEEechHHHHHHHHHHHHHHHHHCCCe------EEEEEe
Confidence 3467888888888999999999976545 566554
No 70
>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom
Probab=25.57 E-value=76 Score=23.42 Aligned_cols=36 Identities=14% Similarity=0.248 Sum_probs=27.0
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTK 120 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~ 120 (184)
+-+|++.+++...++.++..+++..++. +|++....
T Consensus 2 l~ig~~~~~~~~~l~~~l~~~~~~~P~i------~l~i~~~~ 37 (199)
T cd08416 2 LRLGSLYSLTVNTVPRIIMGLKLRRPEL------DIELTLGS 37 (199)
T ss_pred EEEEechHHHHhhhHHHHHHHHHhCCCe------EEEEEEcC
Confidence 4468888888888999999999876555 66666443
No 71
>PF15628 RRM_DME: RRM in Demeter
Probab=25.31 E-value=30 Score=26.17 Aligned_cols=8 Identities=63% Similarity=1.219 Sum_probs=5.9
Q ss_pred CCCCCCCC
Q psy7740 17 DKGSFPLD 24 (184)
Q Consensus 17 ~~g~fpld 24 (184)
-||+|||.
T Consensus 11 mrg~FPLn 18 (103)
T PF15628_consen 11 MRGSFPLN 18 (103)
T ss_pred hCCccccC
Confidence 47888884
No 72
>cd08482 PBP2_TrpI The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold. TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cy
Probab=25.26 E-value=72 Score=23.76 Aligned_cols=35 Identities=17% Similarity=0.327 Sum_probs=25.4
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
+-+|++++.+...++.++..+++..++. +|++..+
T Consensus 2 l~Ig~~~~~~~~~l~~~i~~f~~~~P~v------~i~~~~~ 36 (195)
T cd08482 2 LVLSCSGSLLMRWLIPRLPAFQAALPDI------DLQLSAS 36 (195)
T ss_pred eEEEecHHHHHHHHHhhHHHHHHHCCCc------eEEEEec
Confidence 3467888888888889999999876544 5665543
No 73
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=25.00 E-value=81 Score=23.56 Aligned_cols=37 Identities=8% Similarity=0.099 Sum_probs=28.0
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCch
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKH 121 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~s 121 (184)
+-+|++.+.+...++.++..+.+..++. +|++....+
T Consensus 2 l~ig~~~~~~~~~l~~~l~~f~~~~P~v------~i~~~~~~~ 38 (196)
T cd08458 2 LRVACYTAPALSFMSGVIQTFIADRPDV------SVYLDTVPS 38 (196)
T ss_pred eEEEEcchhhhhhhHHHHHHHHHHCCCc------EEEEeccCh
Confidence 4467888888888999999999886555 677765443
No 74
>COG4081 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.83 E-value=63 Score=25.78 Aligned_cols=29 Identities=17% Similarity=0.261 Sum_probs=24.8
Q ss_pred HHHHHHHHHhccccccccccceEEEEcCchHHHhcCc
Q psy7740 92 LPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPD 128 (184)
Q Consensus 92 ~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~ 128 (184)
+..+-.+|++.| + +|.|..|++|.+.+.-
T Consensus 21 aiYls~klkkkg--f------~v~VaateAa~kLlev 49 (148)
T COG4081 21 AIYLSHKLKKKG--F------DVTVAATEAALKLLEV 49 (148)
T ss_pred HHHHHHHhhccC--c------cEEEecCHhhheeeee
Confidence 566778899998 8 9999999999998754
No 75
>PF02670 DXP_reductoisom: 1-deoxy-D-xylulose 5-phosphate reductoisomerase; InterPro: IPR013512 1-deoxy-D-xylulose 5-phosphate reductoisomerase synthesises 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose 5-phosphate in a single step by intramolecular rearrangement and reduction and is responsible for terpenoid biosynthesis in some organisms []. In Arabidopsis thaliana 1-deoxy-D-xylulose 5-phosphate reductoisomerase is the first committed enzyme of the non-mevalonate pathway for isoprenoid biosynthesis. The enzyme requires Mn2+, Co2+ or Mg2+ for activity, with the first being most effective. This domain is found at the N terminus of bacterial and plant 1-deoxy-D-xylulose 5-phosphate reductoisomerases.; GO: 0070402 NADPH binding, 0055114 oxidation-reduction process; PDB: 1R0K_D 1R0L_C 3A14_A 3A06_A 3AUA_A 3AU9_B 3AU8_B 3IIE_A 2Y1D_B 4AIC_A ....
Probab=24.80 E-value=51 Score=25.68 Aligned_cols=21 Identities=29% Similarity=0.458 Sum_probs=15.0
Q ss_pred hhcCCCchHHhHHHHHHHHHHh
Q psy7740 80 LLCCTGSVATIKLPELIEQIEQ 101 (184)
Q Consensus 80 llg~tGSiaa~k~~~li~~L~~ 101 (184)
++|.||||+. ..++++++...
T Consensus 3 ILGsTGSIG~-qtLdVi~~~~d 23 (129)
T PF02670_consen 3 ILGSTGSIGT-QTLDVIRKHPD 23 (129)
T ss_dssp EESTTSHHHH-HHHHHHHHCTT
T ss_pred EEcCCcHHHH-HHHHHHHhCCC
Confidence 6789999984 56677666643
No 76
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=24.74 E-value=79 Score=23.89 Aligned_cols=35 Identities=11% Similarity=0.108 Sum_probs=25.9
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
+-+|++.+.+...++.++..+++..++. +|++...
T Consensus 3 l~Ig~~~~~~~~~l~~~l~~f~~~~P~v------~i~i~~~ 37 (198)
T cd08486 3 LSVAYFGTPIYRSLPLLLRAFLTSTPTA------TVSLTHM 37 (198)
T ss_pred EEEEEechhhHHHHHHHHHHHHHhCCCe------EEEEEEC
Confidence 4567788877777899999999876555 6666543
No 77
>PHA00680 hypothetical protein
Probab=24.60 E-value=18 Score=27.73 Aligned_cols=30 Identities=30% Similarity=0.485 Sum_probs=21.9
Q ss_pred cccccccccccEEEEccc-ccHHHHHHhcCC
Q psy7740 154 VLHIELSKWCDIIVLAPL-DANTLAKLATYD 183 (184)
Q Consensus 154 ~~Hi~l~~~aD~~VVaPa-SaNTlAKiA~~~ 183 (184)
++...++.-+|+|+|-|| |+..+..+|.+|
T Consensus 72 iepgalaqlcdamligpantaallnalaaad 102 (143)
T PHA00680 72 IEPGALAQLCDAMLIGPANTAALLNALAAAD 102 (143)
T ss_pred CCchHHHHHhHHHhcCcccHHHHHHHHHhhc
Confidence 444567788999999997 455666777665
No 78
>PF13439 Glyco_transf_4: Glycosyltransferase Family 4; PDB: 2JJM_E 3MBO_C 2GEJ_A 2GEK_A.
Probab=24.56 E-value=1.3e+02 Score=21.86 Aligned_cols=30 Identities=13% Similarity=0.011 Sum_probs=21.8
Q ss_pred chHHhHHHHHHHHHHhccccccccccceEEEEcCchHH
Q psy7740 86 SVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAF 123 (184)
Q Consensus 86 Siaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~ 123 (184)
+.+...+.++++.|.+.| + +|+|+......
T Consensus 12 GG~e~~~~~l~~~l~~~G--~------~v~v~~~~~~~ 41 (177)
T PF13439_consen 12 GGAERVVLNLARALAKRG--H------EVTVVSPGVKD 41 (177)
T ss_dssp SHHHHHHHHHHHHHHHTT---------EEEEEESS-TT
T ss_pred ChHHHHHHHHHHHHHHCC--C------EEEEEEcCCCc
Confidence 334567899999999998 7 99999665433
No 79
>TIGR00321 dhys deoxyhypusine synthase. This family of apparent orthologs has an unusual UPGMA difference tree, in which the members from the archaea M. jannaschii and P. horikoshii cluster with the known eukaryotic deoxyhypusine synthases. Separated by a fairly deep branch, although still strongly related, is a small cluster of proteins from Methanobacterium thermoautotrophicum and Archeoglobus fulgidus, the latter of which has two.
Probab=23.76 E-value=62 Score=28.82 Aligned_cols=38 Identities=18% Similarity=0.285 Sum_probs=32.7
Q ss_pred hhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHH
Q psy7740 77 FNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAF 123 (184)
Q Consensus 77 f~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~ 123 (184)
-++.++.||+..+.-..++|..|.+.+ -|++++|-.|-
T Consensus 46 ~~ifLt~tg~mvsaGlr~ii~~Li~~g---------~Vd~ivtTgan 83 (301)
T TIGR00321 46 ITIFMGYAGNLVPSGMREIIAYLIQHG---------MIDALVTTGAN 83 (301)
T ss_pred CeEEEEeccccchhhHHHHHHHHHHcC---------CeeEEEeCCCc
Confidence 467899999999999999999999998 59999986653
No 80
>KOG3584|consensus
Probab=23.39 E-value=27 Score=31.26 Aligned_cols=23 Identities=30% Similarity=0.667 Sum_probs=18.7
Q ss_pred HHhhcCCCChhhHHHhhhhhhcc
Q psy7740 39 CIKKNNSDSSACRDEIKDYLGCR 61 (184)
Q Consensus 39 cl~~~~~~~~~cr~~~k~yl~cr 61 (184)
-|..|+....+||-..|+|.+|.
T Consensus 295 RLmKNREAARECRRKKKEYVKCL 317 (348)
T KOG3584|consen 295 RLMKNREAARECRRKKKEYVKCL 317 (348)
T ss_pred HHHhhHHHHHHHHHhHhHHHHHH
Confidence 35556666779999999999996
No 81
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=23.38 E-value=85 Score=23.35 Aligned_cols=34 Identities=12% Similarity=0.199 Sum_probs=26.2
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+.+...++.++..+.+..++. +|++..
T Consensus 2 l~I~~~~~~~~~~l~~~l~~~~~~~P~v------~v~i~~ 35 (201)
T cd08459 2 FRIAMSDIGEMYFLPRLLAALREVAPGV------RIETVR 35 (201)
T ss_pred eEEEeChHHHHHHHHHHHHHHHHHCCCC------eEEEEe
Confidence 4567888888888999999999886555 666664
No 82
>cd05564 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins from chbA, chbB, and chbC of the chb operon (formerly the cel (cellulose) operon). In the lichenan system, these subunits are expressed from licA, licB, and licC of the lic operon. The lic operon of Bacillus subtilis is required for the transport and degradation of oligomeric beta-glucosides, which are produced by extracellular enzymes on substrates such as lichenan or barley glucan. The lic operon is transcribed from a gammaA-dependent promoter and is inducible by lichenan, lichenan hydrolysate, and cellobiose. The IIB d
Probab=23.25 E-value=2.8e+02 Score=19.91 Aligned_cols=18 Identities=22% Similarity=0.366 Sum_probs=11.3
Q ss_pred cccEEEEcccccHHHHHH
Q psy7740 162 WCDIIVLAPLDANTLAKL 179 (184)
Q Consensus 162 ~aD~~VVaPaSaNTlAKi 179 (184)
.+|+++++|=.+.-+.++
T Consensus 46 ~~Diil~~Pqv~~~~~~i 63 (96)
T cd05564 46 DADVVLLGPQVRYMLDEV 63 (96)
T ss_pred CCCEEEEChhHHHHHHHH
Confidence 357777777666655554
No 83
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=23.00 E-value=1e+02 Score=22.43 Aligned_cols=35 Identities=11% Similarity=0.293 Sum_probs=25.9
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
+-+|++.+.+...++.++..+.+..++. +|++...
T Consensus 2 l~i~~~~~~~~~~l~~~l~~~~~~~P~~------~l~~~~~ 36 (201)
T cd08420 2 LRIGASTTIGEYLLPRLLARFRKRYPEV------RVSLTIG 36 (201)
T ss_pred eEEeeccchhhhhhHHHHHHHHHHCCCc------eEEEEeC
Confidence 4567888888888999999999876545 6666543
No 84
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=22.87 E-value=96 Score=22.98 Aligned_cols=34 Identities=9% Similarity=0.072 Sum_probs=25.4
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+++...++.++..+.+..++. +|++..
T Consensus 2 l~Ig~~~~~~~~~~~~~l~~~~~~~P~i------~i~i~~ 35 (198)
T cd08441 2 LRIAVECHSCFDWLMPVLDQFRERWPDV------ELDLSS 35 (198)
T ss_pred EEEEeeccchhhhhHHHHHHHHHhCCCe------EEEEEe
Confidence 4467888888888899999999876544 566554
No 85
>cd03789 GT1_LPS_heptosyltransferase Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from ADP-heptose to 3-deoxy-D-manno-octulosonic acid (KDO), a part of the inner core component of LPS. This family belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=22.74 E-value=1e+02 Score=25.72 Aligned_cols=45 Identities=9% Similarity=0.096 Sum_probs=33.6
Q ss_pred hhhcCCCchHHh-HHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcC
Q psy7740 79 ILLCCTGSVATI-KLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDL 129 (184)
Q Consensus 79 illg~tGSiaa~-k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~ 129 (184)
||+.-++++|-. ...-+++.|++..|+. +|+++.++....+++..
T Consensus 2 ILii~~~~iGD~i~~~p~l~~Lk~~~P~~------~I~~l~~~~~~~l~~~~ 47 (279)
T cd03789 2 ILVIRLSWIGDVVLATPLLRALKARYPDA------RITVLAPPWFAPLLELM 47 (279)
T ss_pred EEEEecccHHHHHHHHHHHHHHHHHCCCC------EEEEEEChhhHHHHhcC
Confidence 455556666654 4677889999987667 99999999888887653
No 86
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=22.26 E-value=99 Score=22.82 Aligned_cols=34 Identities=12% Similarity=0.147 Sum_probs=25.9
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+++...++.++..+.+..++. +|++..
T Consensus 3 l~ig~~~~~~~~~l~~~i~~~~~~~P~v------~l~i~~ 36 (198)
T cd08446 3 LDVGYFGSAILDTVPRLLRAFLTARPDV------TVSLHN 36 (198)
T ss_pred EEEEechHHHHHHHHHHHHHHHHHCCCe------EEEEee
Confidence 4468888888888999999999876545 566654
No 87
>cd05560 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
Probab=21.99 E-value=60 Score=24.24 Aligned_cols=44 Identities=18% Similarity=0.175 Sum_probs=35.9
Q ss_pred hhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCc
Q psy7740 77 FNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPD 128 (184)
Q Consensus 77 f~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~ 128 (184)
..+++--||.-....-+++.+.|++.| . .|.+.-|++|.+..+.
T Consensus 53 peiliiGTG~~~~~~~~~~~~~l~~~g--i------~vE~m~T~~AcrTyN~ 96 (109)
T cd05560 53 PEVILLGTGERQRFPPPALLAPLLARG--I------GVEVMDTQAACRTYNI 96 (109)
T ss_pred CCEEEEecCCCCCcCCHHHHHHHHHcC--C------eEEEECHHHHHHHHHH
Confidence 346666688888777888999999998 6 9999999999887653
No 88
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=21.86 E-value=1e+02 Score=22.49 Aligned_cols=44 Identities=16% Similarity=0.242 Sum_probs=29.5
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc--CchHHHhcCc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM--TKHAFHFVPD 128 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil--T~sA~~fv~~ 128 (184)
+-+|++.+++...++.++..+.+..++. +|++.. +......+..
T Consensus 2 l~Ig~~~~~~~~~l~~~l~~~~~~~P~i------~l~~~~~~~~~~~~~l~~ 47 (195)
T cd08427 2 LRLGAIATVLTGLLPRALARLRRRHPDL------EVHIVPGLSAELLARVDA 47 (195)
T ss_pred EEEEeeHHHHHHHhHHHHHHHHHHCCCc------eEEEEeCCcHHHHHHHHC
Confidence 3457778888888999999998876545 676665 3333344433
No 89
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=21.74 E-value=60 Score=24.13 Aligned_cols=44 Identities=20% Similarity=0.129 Sum_probs=34.8
Q ss_pred hhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcCc
Q psy7740 77 FNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPD 128 (184)
Q Consensus 77 f~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~ 128 (184)
..+++--||.-....-+++.+.|++.| . .|.+.=|++|.+..+.
T Consensus 53 peiliiGTG~~~~~~~~~~~~~l~~~g--I------~vE~m~T~aAcrTyNi 96 (109)
T cd00248 53 PDILLIGTGAEIAFLPRALRAALRAAG--I------GVEVMSTGAACRTYNV 96 (109)
T ss_pred CCEEEEcCCCCCCcCCHHHHHHHHHcC--C------eEEEeCcHHHHHHHHH
Confidence 345666688877666788999999998 6 9999999999887653
No 90
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=21.59 E-value=1e+02 Score=23.54 Aligned_cols=36 Identities=17% Similarity=0.347 Sum_probs=26.7
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTK 120 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~ 120 (184)
+-+|++.+++...+++++..+++..++. +|++....
T Consensus 2 ~~Ig~~~~~~~~~l~~~l~~f~~~~P~v------~l~i~~~~ 37 (221)
T cd08469 2 FVIAANDYVTAVLLPALVRRLETEAPGI------DLRIRPVT 37 (221)
T ss_pred EEEEEChHHHHHHHHHHHHHHHHHCCCc------EEEEeeCC
Confidence 3467888888888999999999876545 66666443
No 91
>PRK09982 universal stress protein UspD; Provisional
Probab=21.59 E-value=84 Score=23.57 Aligned_cols=26 Identities=12% Similarity=0.059 Sum_probs=22.1
Q ss_pred hhhhhcCCCchHHhHHHHHHHHHHhc
Q psy7740 77 FNILLCCTGSVATIKLPELIEQIEQL 102 (184)
Q Consensus 77 f~illg~tGSiaa~k~~~li~~L~~~ 102 (184)
.+||+++-||..+.++.+....|.+.
T Consensus 4 k~ILvavD~S~~s~~al~~A~~lA~~ 29 (142)
T PRK09982 4 KHIGVAISGNEEDALLVNKALELARH 29 (142)
T ss_pred eEEEEEecCCcchHHHHHHHHHHHHH
Confidence 47999999999999999888877764
No 92
>PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
Probab=21.50 E-value=90 Score=26.38 Aligned_cols=36 Identities=11% Similarity=0.281 Sum_probs=26.8
Q ss_pred hhhhhhhhhhhhhhhcCCCchHHhHHHHHHHHHHhc
Q psy7740 67 MAKEDWEKLEFNILLCCTGSVATIKLPELIEQIEQL 102 (184)
Q Consensus 67 m~k~~~~~LGf~illg~tGSiaa~k~~~li~~L~~~ 102 (184)
+.+..+-.-|-+++++++|+.-+.-+..++..+++.
T Consensus 20 i~~~~li~~~~kilVa~SGG~DS~~LL~ll~~l~~~ 55 (258)
T PRK10696 20 IADFNMIEEGDRVMVCLSGGKDSYTLLDILLNLQKR 55 (258)
T ss_pred HHHcCCCCCCCEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 334444445679999999999988888888877764
No 93
>TIGR02584 cas_NE0113 CRISPR-associated protein, NE0113 family. Members of this minor CRISPR-associated (Cas) protein family are found in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum.
Probab=21.45 E-value=1.1e+02 Score=26.02 Aligned_cols=45 Identities=24% Similarity=0.361 Sum_probs=30.6
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHHHhcC
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVP 127 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~ 127 (184)
||++++|....+ +-+-+..|...|+. ...++|+||-|..+.+-+.
T Consensus 1 ILvat~G~sPQV-VTETLyaL~~~g~~---~~pdEi~vItT~~g~~~~~ 45 (209)
T TIGR02584 1 ILLCVSGMSPQI-ITETIYALAQESPP---VVPEEIHVITTSDGKRDIQ 45 (209)
T ss_pred CEEEecCCCCch-HHHHHHHHHhcCCC---CCCCeEEEEEccCcHHHHH
Confidence 678899987765 45556667766632 2345999999998854433
No 94
>cd03784 GT1_Gtf_like This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the oxidatively cross-linked heptapeptide core of vancomycin group antibiotics. The core structure is important for the bioactivity of the antibiotics.
Probab=21.38 E-value=93 Score=27.17 Aligned_cols=46 Identities=15% Similarity=0.158 Sum_probs=33.6
Q ss_pred hhhhcCCCchHHh-HHHHHHHHHHhccccccccccceEEEEcCchHHHhcCcCCC
Q psy7740 78 NILLCCTGSVATI-KLPELIEQIEQLQYEFNKIMIINLNVVMTKHAFHFVPDLPH 131 (184)
Q Consensus 78 ~illg~tGSiaa~-k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~~fv~~~~l 131 (184)
||++...|+.|=+ -...+.++|++.| + +|.++.++.-..++....+
T Consensus 2 rIl~~~~p~~GHv~P~l~la~~L~~rG--h------~V~~~t~~~~~~~v~~~G~ 48 (401)
T cd03784 2 RVLITTIGSRGDVQPLVALAWALRAAG--H------EVRVATPPEFADLVEAAGL 48 (401)
T ss_pred eEEEEeCCCcchHHHHHHHHHHHHHCC--C------eEEEeeCHhHHHHHHHcCC
Confidence 4566555554444 4888999999999 7 9999999876666665444
No 95
>PF13579 Glyco_trans_4_4: Glycosyl transferase 4-like domain; PDB: 3C4Q_B 3C4V_A 3C48_B 1Z2T_A.
Probab=21.26 E-value=1.4e+02 Score=21.23 Aligned_cols=26 Identities=15% Similarity=0.152 Sum_probs=19.2
Q ss_pred HHhHHHHHHHHHHhccccccccccceEEEEcCch
Q psy7740 88 ATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKH 121 (184)
Q Consensus 88 aa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~s 121 (184)
+...+.++++.|.+.| + +|+|+....
T Consensus 3 ~~~~~~~l~~~L~~~G--~------~V~v~~~~~ 28 (160)
T PF13579_consen 3 IERYVRELARALAARG--H------EVTVVTPQP 28 (160)
T ss_dssp HHHHHHHHHHHHHHTT---------EEEEEEE--
T ss_pred HHHHHHHHHHHHHHCC--C------EEEEEecCC
Confidence 3456889999999998 7 999887543
No 96
>PF08583 Cmc1: Cytochrome c oxidase biogenesis protein Cmc1 like; InterPro: IPR013892 Cmc1 is a metallo-chaperone like protein which is known to localise to the inner mitochondrial membrane in Saccharomyces cerevisiae. It is essential for full expression of cytochrome c oxidase and respiration []. Cmc1 contains two Cx9C motifs and is able to bind copper(I). Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase.
Probab=21.11 E-value=56 Score=21.69 Aligned_cols=29 Identities=17% Similarity=0.369 Sum_probs=24.3
Q ss_pred CCCCCCCccHHHHHHHHHHHhhcCCCChh
Q psy7740 21 FPLDHYGDCKAFMTKYMICIKKNNSDSSA 49 (184)
Q Consensus 21 fpldh~~~c~~~~~~y~~cl~~~~~~~~~ 49 (184)
+.+--.|.|.........||+....+...
T Consensus 27 ~~~~~~~~C~~~~~~m~~Cl~~~~~~~~~ 55 (69)
T PF08583_consen 27 RTFKFVGKCREEKKAMNECLKEERNDERF 55 (69)
T ss_pred chHHHHHhhhHHHHHHHHHHHHHHhhHHH
Confidence 55566799999999999999999876655
No 97
>PRK02301 putative deoxyhypusine synthase; Provisional
Probab=20.99 E-value=84 Score=28.23 Aligned_cols=39 Identities=10% Similarity=0.242 Sum_probs=33.4
Q ss_pred hhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHH
Q psy7740 76 EFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAF 123 (184)
Q Consensus 76 Gf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~ 123 (184)
+-++.++.||+..+.-..++|+.|.+.+ -|++|+|-.|-
T Consensus 57 ~~~ifL~~tg~mvsaGlr~ii~~Li~~~---------~VD~iVtTgan 95 (316)
T PRK02301 57 DVTKFFGLAGAMVPAGMRGIVSDLIRDG---------HIDVLVTTGAN 95 (316)
T ss_pred CCeEEEEcccchhHHHHHHHHHHHHHcC---------CeeEEEcCCCc
Confidence 4567899999999999999999999998 59999986653
No 98
>cd08477 PBP2_CrgA_like_8 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=20.94 E-value=96 Score=22.82 Aligned_cols=35 Identities=6% Similarity=0.129 Sum_probs=25.4
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
+-+|++-+++...++.++..+++..++. ++++..+
T Consensus 3 l~Ig~~~~~~~~~l~~~l~~~~~~~P~i------~l~i~~~ 37 (197)
T cd08477 3 LRISAPVTFGSHVLTPALAEYLARYPDV------RVDLVLS 37 (197)
T ss_pred EEEeCCHHHHHHHHHHHHHHHHHHCCCc------EEEEEec
Confidence 4467777777778899999998876555 6666643
No 99
>cd08488 PBP2_AmpR The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold. AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsibl
Probab=20.90 E-value=1e+02 Score=22.87 Aligned_cols=34 Identities=12% Similarity=0.074 Sum_probs=25.5
Q ss_pred hhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 80 LLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 80 llg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
-+|++.+++...++.++..+.+..|+. +|++..+
T Consensus 3 ~Ig~~~~~~~~~l~~~l~~f~~~~P~v------~i~~~~~ 36 (191)
T cd08488 3 HVGAVGTFAVGWLLPRLADFQNRHPFI------DLRLSTN 36 (191)
T ss_pred EEEecHHHHHHHHHhHHHHHHHHCCCc------EEEEEec
Confidence 357778888878888999999886555 6776643
No 100
>KOG3496|consensus
Probab=20.80 E-value=91 Score=22.04 Aligned_cols=20 Identities=10% Similarity=0.378 Sum_probs=17.3
Q ss_pred CccHHHHHHHHHHHhhcCCC
Q psy7740 27 GDCKAFMTKYMICIKKNNSD 46 (184)
Q Consensus 27 ~~c~~~~~~y~~cl~~~~~~ 46 (184)
-.|+++++.|-.|+|..+++
T Consensus 52 e~C~~lIEahk~CMr~~GF~ 71 (72)
T KOG3496|consen 52 EKCGKLIEAHKECMRAYGFE 71 (72)
T ss_pred HHHHHHHHHHHHHHHHcCCC
Confidence 46999999999999988764
No 101
>TIGR01133 murG undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase. RL J Bacteriol 1993 Mar;175(6):1841-3
Probab=20.73 E-value=1e+02 Score=26.01 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=24.8
Q ss_pred hhhhcCCCchHHhHH-HHHHHHHHhccccccccccceEEEEcCch
Q psy7740 78 NILLCCTGSVATIKL-PELIEQIEQLQYEFNKIMIINLNVVMTKH 121 (184)
Q Consensus 78 ~illg~tGSiaa~k~-~~li~~L~~~g~~~~~~~~~~V~VilT~s 121 (184)
+|++.+.|..+-... ..+++.|.+.| + +|+|+..+.
T Consensus 2 ~i~~~~g~~~g~~~~~~~La~~L~~~g--~------eV~vv~~~~ 38 (348)
T TIGR01133 2 KVVLAAGGTGGHIFPALAVAEELIKRG--V------EVLWLGTKR 38 (348)
T ss_pred eEEEEeCccHHHHhHHHHHHHHHHhCC--C------EEEEEeCCC
Confidence 455555555554443 58999999998 7 999985433
No 102
>cd08487 PBP2_BlaA The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold. This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is
Probab=20.67 E-value=92 Score=22.88 Aligned_cols=34 Identities=18% Similarity=0.132 Sum_probs=24.5
Q ss_pred hhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcC
Q psy7740 80 LLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMT 119 (184)
Q Consensus 80 llg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT 119 (184)
-+|++.+++....+..+..+++..|+. +|++..+
T Consensus 3 ~Ig~~~~~~~~~l~~~l~~f~~~~P~i------~l~i~~~ 36 (189)
T cd08487 3 TVGAVGTFAVGWLLPRLAEFRQLHPFI------ELRLRTN 36 (189)
T ss_pred EEEecHHHHHHHHhHHHHHHHHHCCCc------eEEeeec
Confidence 467777777777888899998876555 6666543
No 103
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=20.66 E-value=1.6e+02 Score=22.05 Aligned_cols=33 Identities=15% Similarity=0.209 Sum_probs=24.8
Q ss_pred hhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 80 LLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 80 llg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
-+|++.+.+....+.++..+++..++. ++++..
T Consensus 3 ~I~~~~~~~~~~l~~~l~~~~~~~P~i------~l~~~~ 35 (200)
T cd08467 3 TLAMPDYAEVALLPRLAPRLRERAPGL------DLRLCP 35 (200)
T ss_pred EEEechhhHHHHHHHHHHHHHhhCCCC------EEEEec
Confidence 356777777888999999999876555 666664
No 104
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=20.60 E-value=1.2e+02 Score=22.30 Aligned_cols=34 Identities=15% Similarity=0.138 Sum_probs=25.4
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+.+...++.++..+++..++. +|++..
T Consensus 2 l~I~~~~~~~~~~l~~~l~~~~~~~P~i------~i~~~~ 35 (198)
T cd08421 2 VRLLANTSAIVEFLPEDLASFLAAHPDV------RIDLEE 35 (198)
T ss_pred EEEEeccchhhhhhHHHHHHHHHHCCCc------eEEEEe
Confidence 4467788888888899999999876545 666653
No 105
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=20.47 E-value=1.3e+02 Score=23.05 Aligned_cols=35 Identities=17% Similarity=0.068 Sum_probs=26.1
Q ss_pred hhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCc
Q psy7740 80 LLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTK 120 (184)
Q Consensus 80 llg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~ 120 (184)
-+|++.+++...++.++..+.+..++. +|.+....
T Consensus 3 ~ig~~~~~~~~~l~~~l~~f~~~~P~v------~l~i~~~~ 37 (204)
T cd08429 3 RVGVADAVPKSIAYRLLEPAMDLHEPI------RLVCREGK 37 (204)
T ss_pred eEEcchhhhHHHHHHHHHHHHHhCCCc------EEEEEeCC
Confidence 367788888888999999999876545 66666543
No 106
>cd08474 PBP2_CrgA_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=20.46 E-value=96 Score=23.00 Aligned_cols=35 Identities=14% Similarity=0.216 Sum_probs=26.6
Q ss_pred hhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 78 NILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 78 ~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
++-+|++.+.+...++.++..+++..++. ++++..
T Consensus 4 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v------~i~~~~ 38 (202)
T cd08474 4 TLRINAPRVAARLLLAPLLARFLARYPDI------RLELVV 38 (202)
T ss_pred EEEEeCcHHHHHHHHHHHHHHHHHHCCCe------EEEEEe
Confidence 35678888888888999999999876544 566553
No 107
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=20.31 E-value=1.3e+02 Score=22.66 Aligned_cols=34 Identities=18% Similarity=0.273 Sum_probs=26.3
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+.+...++.++..+++..++. +|+++.
T Consensus 3 l~ig~~~~~~~~~l~~~l~~~~~~~P~i------~l~~~~ 36 (198)
T cd08485 3 LRVAYFGTVVLHTLPLLLRQLLSVAPSA------TVSLTQ 36 (198)
T ss_pred EEEEEeccchhHHHHHHHHHHHHhCCCc------EEEEEE
Confidence 4568888888888999999998876555 676664
No 108
>PRK00805 putative deoxyhypusine synthase; Provisional
Probab=20.10 E-value=86 Score=28.32 Aligned_cols=39 Identities=13% Similarity=0.274 Sum_probs=33.3
Q ss_pred hhhhhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEcCchHH
Q psy7740 76 EFNILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVMTKHAF 123 (184)
Q Consensus 76 Gf~illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~VilT~sA~ 123 (184)
+-++.++.||+..+.-...+|+.|.+.+ -|++|+|-.|-
T Consensus 46 ~~~ifL~~tg~mvsaGlr~~i~~Li~~g---------~VD~iVTTgan 84 (329)
T PRK00805 46 DNTIFMGLSGAMVPAGMRKIIKWLIRNR---------YVDVLVSTGAN 84 (329)
T ss_pred CCeEEEEeccchHHHHHHHHHHHHHHcC---------CeeEEEeCCCc
Confidence 4577899999999998999999999998 59999986653
No 109
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=20.09 E-value=1.1e+02 Score=22.30 Aligned_cols=34 Identities=12% Similarity=0.042 Sum_probs=25.5
Q ss_pred hhhcCCCchHHhHHHHHHHHHHhccccccccccceEEEEc
Q psy7740 79 ILLCCTGSVATIKLPELIEQIEQLQYEFNKIMIINLNVVM 118 (184)
Q Consensus 79 illg~tGSiaa~k~~~li~~L~~~g~~~~~~~~~~V~Vil 118 (184)
+-+|++.+++...++.++..+++..++. +|++..
T Consensus 2 l~ig~~~~~~~~~l~~~l~~~~~~~P~i------~i~~~~ 35 (197)
T cd08449 2 LNIGMVGSVLWGGLGPALRRFKRQYPNV------TVRFHE 35 (197)
T ss_pred eEEEEechHhhhhHHHHHHHHHHHCCCe------EEEEEE
Confidence 3468888888888999999999876544 555553
Done!