Query 032606
Match_columns 137
No_of_seqs 129 out of 1102
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 03:37:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032606.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032606hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11630 hypothetical protein; 99.6 1.1E-16 2.5E-21 126.9 4.9 55 81-135 4-59 (206)
2 COG0009 SUA5 Putative translat 99.6 6.5E-16 1.4E-20 124.9 5.7 56 81-136 3-59 (211)
3 TIGR00057 Sua5/YciO/YrdC/YwlC 99.6 6.6E-16 1.4E-20 121.5 3.9 53 84-136 1-54 (201)
4 PRK10634 tRNA(ANN) t(6)A37 thr 99.5 3.9E-15 8.4E-20 116.9 4.0 48 89-136 5-53 (190)
5 TIGR00143 hypF [NiFe] hydrogen 98.9 2.2E-09 4.7E-14 99.3 7.4 44 91-134 162-206 (711)
6 KOG3051 RNA binding/translatio 96.6 0.00049 1.1E-08 58.5 0.1 43 93-135 18-61 (261)
7 COG0068 HypF Hydrogenase matur 91.6 0.3 6.5E-06 47.0 5.0 42 93-134 199-241 (750)
8 KOG3051 RNA binding/translatio 87.2 0.047 1E-06 46.7 -3.5 68 50-117 16-83 (261)
9 PLN02476 O-methyltransferase 63.4 4 8.6E-05 34.7 1.4 41 80-121 196-238 (278)
10 COG4122 Predicted O-methyltran 50.3 17 0.00037 30.0 2.9 56 80-135 134-191 (219)
11 TIGR00322 diphth2_R diphthamid 49.3 22 0.00047 30.7 3.6 32 94-126 34-67 (332)
12 PF01866 Diphthamide_syn: Puta 47.1 23 0.00049 29.8 3.3 33 94-127 9-42 (307)
13 PF05951 Peptidase_M15_2: Bact 43.3 28 0.00061 27.6 3.1 33 81-113 106-138 (152)
14 PF09843 DUF2070: Predicted me 41.2 54 0.0012 25.6 4.4 45 77-121 73-119 (179)
15 COG1867 TRM1 N2,N2-dimethylgua 41.0 36 0.00078 30.8 3.8 34 80-113 123-157 (380)
16 TIGR00272 DPH2 diphthamide bio 40.9 27 0.00059 32.0 3.0 34 94-128 66-104 (496)
17 KOG1253 tRNA methyltransferase 39.7 35 0.00075 32.2 3.5 31 80-110 185-215 (525)
18 PF08351 DUF1726: Domain of un 38.5 21 0.00046 25.4 1.6 35 78-113 13-47 (92)
19 PF09837 DUF2064: Uncharacteri 37.9 41 0.00089 24.8 3.1 58 63-120 46-106 (122)
20 cd00733 GlyRS_alpha_core Class 34.4 47 0.001 29.1 3.3 85 18-118 32-125 (279)
21 cd07988 LPLAT_ABO13168-like Ly 34.3 61 0.0013 24.5 3.6 35 81-116 71-108 (163)
22 TIGR00308 TRM1 tRNA(guanine-26 33.9 50 0.0011 29.0 3.5 35 80-114 116-151 (374)
23 PLN02589 caffeoyl-CoA O-methyl 33.7 35 0.00076 28.3 2.4 42 80-121 158-200 (247)
24 PF03279 Lip_A_acyltrans: Bact 33.4 37 0.00081 27.4 2.4 22 94-115 181-202 (295)
25 COG0144 Sun tRNA and rRNA cyto 31.8 29 0.00062 29.9 1.6 36 92-132 269-306 (355)
26 PF09180 ProRS-C_1: Prolyl-tRN 31.4 56 0.0012 22.0 2.7 18 94-111 1-18 (68)
27 TIGR00446 nop2p NOL1/NOP2/sun 30.9 31 0.00066 28.1 1.6 36 92-131 180-216 (264)
28 PRK09348 glyQ glycyl-tRNA synt 30.5 57 0.0012 28.6 3.2 85 18-118 36-129 (283)
29 COG1736 DPH2 Diphthamide synth 30.4 48 0.001 29.4 2.8 36 92-128 37-75 (347)
30 PRK11933 yebU rRNA (cytosine-C 30.2 32 0.00069 31.2 1.7 36 92-131 223-259 (470)
31 PF08241 Methyltransf_11: Meth 30.2 23 0.0005 22.3 0.6 19 91-109 77-95 (95)
32 TIGR02464 ribofla_fusion conse 29.3 83 0.0018 24.1 3.6 22 100-121 102-126 (153)
33 PF13684 Dak1_2: Dihydroxyacet 29.2 58 0.0013 27.8 3.0 32 83-114 147-179 (313)
34 TIGR00091 tRNA (guanine-N(7)-) 28.8 48 0.001 25.4 2.3 23 92-114 113-135 (194)
35 PF02005 TRM: N2,N2-dimethylgu 28.7 32 0.00069 30.3 1.4 36 78-113 121-157 (377)
36 PRK15018 1-acyl-sn-glycerol-3- 28.5 62 0.0013 26.4 3.0 35 81-115 113-151 (245)
37 cd07985 LPLAT_GPAT Lysophospho 27.7 75 0.0016 26.7 3.4 43 89-131 99-150 (235)
38 KOG1663 O-methyltransferase [S 26.8 37 0.00079 29.0 1.4 44 78-121 149-193 (237)
39 cd07992 LPLAT_AAK14816-like Ly 25.1 1.1E+02 0.0025 23.3 3.7 24 92-115 98-122 (203)
40 smart00563 PlsC Phosphate acyl 24.6 92 0.002 20.4 2.8 30 89-118 60-90 (118)
41 COG0204 PlsC 1-acyl-sn-glycero 23.8 1E+02 0.0022 23.4 3.2 36 80-115 113-150 (255)
42 TIGR03682 arCOG04112 arCOG0411 23.3 81 0.0018 26.9 2.9 30 97-127 20-51 (308)
43 KOG1122 tRNA and rRNA cytosine 23.2 39 0.00085 31.4 1.0 22 93-114 353-374 (460)
44 PRK14901 16S rRNA methyltransf 22.8 49 0.0011 28.9 1.5 23 91-113 364-386 (434)
45 PF14258 DUF4350: Domain of un 21.7 2.2E+02 0.0047 18.2 4.1 33 77-109 34-68 (70)
46 cd01452 VWA_26S_proteasome_sub 21.0 3.7E+02 0.008 21.5 6.0 64 63-131 95-159 (187)
47 COG0220 Predicted S-adenosylme 20.8 73 0.0016 26.2 2.0 21 93-113 146-166 (227)
48 TIGR02208 lipid_A_msbB lipid A 20.8 98 0.0021 25.6 2.8 25 92-116 180-204 (305)
49 TIGR00563 rsmB ribosomal RNA s 20.7 58 0.0013 28.3 1.5 37 91-131 348-385 (426)
50 PF00316 FBPase: Fructose-1-6- 20.6 93 0.002 27.3 2.7 23 93-115 239-261 (324)
51 PF14399 Transpep_BrtH: NlpC/p 20.5 1E+02 0.0022 24.8 2.7 26 90-115 74-99 (317)
52 PF10446 DUF2457: Protein of u 20.2 58 0.0013 30.2 1.5 30 31-66 274-303 (458)
53 COG3108 Uncharacterized protei 20.1 82 0.0018 26.1 2.2 32 82-113 139-170 (185)
54 COG1560 HtrB Lauroyl/myristoyl 20.0 1.1E+02 0.0023 26.4 3.0 29 92-120 182-210 (308)
No 1
>PRK11630 hypothetical protein; Provisional
Probab=99.65 E-value=1.1e-16 Score=126.85 Aligned_cols=55 Identities=20% Similarity=0.348 Sum_probs=51.9
Q ss_pred EEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606 81 YVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF 135 (137)
Q Consensus 81 ~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~ 135 (137)
++++++++++.+.+++++++|++||+|+|||||+||||||+ |++|++|||++|+-
T Consensus 4 ~~~~~~~~~~~~~i~~a~~~L~~G~vi~~PTdTvYgL~~d~~n~~Av~~l~~lK~R 59 (206)
T PRK11630 4 FFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQL 59 (206)
T ss_pred eEecCCCCCCHHHHHHHHHHHHCCCEEEEeCCChHhhhcCCCCHHHHHHHHHHcCC
Confidence 67789999998889999999999999999999999999999 99999999999974
No 2
>COG0009 SUA5 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]
Probab=99.61 E-value=6.5e-16 Score=124.89 Aligned_cols=56 Identities=23% Similarity=0.290 Sum_probs=52.6
Q ss_pred EEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCCC
Q 032606 81 YVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPFS 136 (137)
Q Consensus 81 ~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~~ 136 (137)
++.+++.+++.+.++++++.|++|++|+|||||||||||++ |++|++|||++|+.+
T Consensus 3 ~~~~~~~~~~~~~~~~a~~~l~~G~vVa~PTeTVYGLg~~~~~~~Av~~i~~~K~Rp 59 (211)
T COG0009 3 IFMIHPENPQPRAIEKAVEALRKGGVVAYPTDTVYGLGADATNEEAVERLYEIKQRP 59 (211)
T ss_pred eeecCccccchHHHHHHHHHHHcCCEEEEEccchheeecCCCCHHHHHHHHHHhCCC
Confidence 56788888888999999999999999999999999999999 999999999999864
No 3
>TIGR00057 Sua5/YciO/YrdC/YwlC family protein. partial match to sua5, which is involved in regulation of translation initiation. 3' end of sua5 has matches to sua5, BS3690, and weakly to AF0781 and BB0734.
Probab=99.59 E-value=6.6e-16 Score=121.48 Aligned_cols=53 Identities=23% Similarity=0.342 Sum_probs=49.5
Q ss_pred ecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCCC
Q 032606 84 ADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPFS 136 (137)
Q Consensus 84 vdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~~ 136 (137)
+|+++++.+.+++++++|++||||+|||||+|||+|++ |++|++|||++|+-+
T Consensus 1 ~~~~~~~~~~i~~a~~~L~~G~ii~~PTdTvYgL~~~~~~~~av~ri~~iK~R~ 54 (201)
T TIGR00057 1 IHPENPSQRGIEQAVKILRKGGIVVYPTDTVYGIGADALDEDAVRRLYRIKGRP 54 (201)
T ss_pred CCcCCCCHHHHHHHHHHHHCCCEEEEeCCCHHHhhcCCCCHHHHHHHHHHhCCC
Confidence 57888888889999999999999999999999999999 999999999999743
No 4
>PRK10634 tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; Provisional
Probab=99.54 E-value=3.9e-15 Score=116.85 Aligned_cols=48 Identities=17% Similarity=0.146 Sum_probs=44.5
Q ss_pred CCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCCC
Q 032606 89 ADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPFS 136 (137)
Q Consensus 89 pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~~ 136 (137)
++.+.++++++.|++||||+|||||||||||++ |++|++|||++|+-+
T Consensus 5 ~~~~~i~~a~~~L~~G~vv~~PTdTvYgL~~~~~n~~Av~ri~~iK~R~ 53 (190)
T PRK10634 5 LQGDAIAAAVDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRP 53 (190)
T ss_pred ccHHHHHHHHHHHHCCCEEEEeCCchhhhhcCCCCHHHHHHHHHHhCCC
Confidence 456789999999999999999999999999999 999999999999743
No 5
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=98.93 E-value=2.2e-09 Score=99.26 Aligned_cols=44 Identities=23% Similarity=0.180 Sum_probs=42.0
Q ss_pred cccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCC
Q 032606 91 SWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEP 134 (137)
Q Consensus 91 ~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~ 134 (137)
.+.++++++.|++|+||++||||+|||+||+ |++||+|||++|+
T Consensus 162 ~~~i~~aa~~L~~G~IVaipt~ggy~L~cda~n~~AV~rLr~~K~ 206 (711)
T TIGR00143 162 DDALLEAAKLLKKGKIIAIKGIGGFHLACDARNDEVVERLRLRKN 206 (711)
T ss_pred hHHHHHHHHHHhCCCEEEEEcCCcceeecCCCCHHHHHHHHHHhC
Confidence 4679999999999999999999999999999 9999999999986
No 6
>KOG3051 consensus RNA binding/translational regulation protein of the SUA5 family [Translation, ribosomal structure and biogenesis]
Probab=96.63 E-value=0.00049 Score=58.51 Aligned_cols=43 Identities=12% Similarity=0.087 Sum_probs=36.3
Q ss_pred cHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606 93 KLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF 135 (137)
Q Consensus 93 ~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~ 135 (137)
.++.+.-+-+.++.+++||||+||+|+++ +..++.+||.+|..
T Consensus 18 ~~~aa~~~r~~~~~va~pT~t~yg~g~~~~~~~av~~v~~~K~r 61 (261)
T KOG3051|consen 18 LYDAALIVRRTDKRVAFPTETVYGLGASAYNEVAVLRLYKLKNR 61 (261)
T ss_pred hhhhhhheeccCCceecCchhhhhhhhhhhccccchhhhhhhcC
Confidence 34444556678999999999999999999 99999999998763
No 7
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=91.62 E-value=0.3 Score=46.97 Aligned_cols=42 Identities=19% Similarity=0.156 Sum_probs=39.3
Q ss_pred cHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCC
Q 032606 93 KLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEP 134 (137)
Q Consensus 93 ~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~ 134 (137)
.+.++++.|+.|++|++--=-.|.|+||+ |.++|++|++-++
T Consensus 199 ai~~a~klL~~G~IvAIKGiGGFhLaCda~~~eaV~~LR~rk~ 241 (750)
T COG0068 199 AIRKAAKLLKVGKIVAIKGIGGFHLACDARNEEAVAKLRKRKN 241 (750)
T ss_pred HHHHHHHHHhhCCEEEEeecCceeeeecCCchHHHHHHHHhcC
Confidence 67899999999999999999999999999 9999999998654
No 8
>KOG3051 consensus RNA binding/translational regulation protein of the SUA5 family [Translation, ribosomal structure and biogenesis]
Probab=87.23 E-value=0.047 Score=46.71 Aligned_cols=68 Identities=19% Similarity=0.126 Sum_probs=61.9
Q ss_pred CceeeeeeeeccCcccccccccceeecCceEEEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEe
Q 032606 50 SRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYAT 117 (137)
Q Consensus 50 ~r~~~~~~~~~r~~krlky~~~~~~~~~~~~~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGL 117 (137)
+++...+.++++..|+.+|.++++.+..+..|.+.++..-..|+...+.+.|.-+-.-+.+++++|..
T Consensus 16 ~~~~~aa~~~r~~~~~va~pT~t~yg~g~~~~~~~av~~v~~~K~rP~~~pL~~~~~s~~~~~~v~~~ 83 (261)
T KOG3051|consen 16 PALYDAALIVRRTDKRVAFPTETVYGLGASAYNEVAVLRLYKLKNRPADNPLIVHVSSVDQLKRVVAI 83 (261)
T ss_pred hhhhhhhhheeccCCceecCchhhhhhhhhhhccccchhhhhhhcCccccchhhccccHHHHHHHHhh
Confidence 56677999999999999999999999988889999999999999999999999999999999999876
No 9
>PLN02476 O-methyltransferase
Probab=63.40 E-value=4 Score=34.66 Aligned_cols=41 Identities=17% Similarity=0.194 Sum_probs=30.1
Q ss_pred EEEEecCCCCC-cccHHHHHHHHhcCCeEEeccCCee-EeeecC
Q 032606 80 MYVEADPSGAD-SWKLEPVVELLKEGAVGVIPTDTLY-ATAICL 121 (137)
Q Consensus 80 ~~levdp~~pd-~~~l~~aa~~Lr~GgVVa~PTDTVY-GLgcda 121 (137)
-++.+|.+..+ ...++.+.+.|+.||+|++ .++.| |..++.
T Consensus 196 D~VFIDa~K~~Y~~y~e~~l~lL~~GGvIV~-DNvL~~G~V~d~ 238 (278)
T PLN02476 196 DFAFVDADKRMYQDYFELLLQLVRVGGVIVM-DNVLWHGRVADP 238 (278)
T ss_pred CEEEECCCHHHHHHHHHHHHHhcCCCcEEEE-ecCccCCcccCc
Confidence 45677777655 3457888999999999988 56666 666665
No 10
>COG4122 Predicted O-methyltransferase [General function prediction only]
Probab=50.35 E-value=17 Score=30.05 Aligned_cols=56 Identities=23% Similarity=0.135 Sum_probs=34.1
Q ss_pred EEEEecCCCCC-cccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHhcCCC
Q 032606 80 MYVEADPSGAD-SWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRFEEPF 135 (137)
Q Consensus 80 ~~levdp~~pd-~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~I~~~ 135 (137)
-++.+|.+..+ +..++.+.+.|+.||+||+=-=-.=|...+. -+.+-.....+|+|
T Consensus 134 DliFIDadK~~yp~~le~~~~lLr~GGliv~DNvl~~G~v~~~~~~~~~~~~~~~~~~ 191 (219)
T COG4122 134 DLVFIDADKADYPEYLERALPLLRPGGLIVADNVLFGGRVADPSIRDARTQVRGVRDF 191 (219)
T ss_pred cEEEEeCChhhCHHHHHHHHHHhCCCcEEEEeecccCCccCCccchhHHHHHHHHHHH
Confidence 35666776665 5678999999999999987433333433443 23444444444433
No 11
>TIGR00322 diphth2_R diphthamide biosynthesis protein 2-related domain. Because archaeal species are known to have the diphthamide modification to the conserved His of archaeal and eukaryotic EF-2, it may be that the lone homolog of YKL191W in M. jannaschii, A. fulgidus, and M. thermoautotrophicum is orthologous. However, each of these is considerably shorter than YKL191W and seems more closely related to the uncharacterized protein YIL103W than to YKL191W.
Probab=49.30 E-value=22 Score=30.73 Aligned_cols=32 Identities=22% Similarity=0.321 Sum_probs=23.1
Q ss_pred HHHHHHHHhc--CCeEEeccCCeeEeeecCCHHHH
Q 032606 94 LEPVVELLKE--GAVGVIPTDTLYATAICLSRSVC 126 (137)
Q Consensus 94 l~~aa~~Lr~--GgVVa~PTDTVYGLgcdan~~AV 126 (137)
..++++.|++ |.=+++=.||.|| +||.+..+.
T Consensus 34 a~~ia~~l~~~~~~~v~IlaD~~YG-aCcvdd~~a 67 (332)
T TIGR00322 34 ALEIAEIIEQFCGVETVISGDTSFG-ACDIDDFTA 67 (332)
T ss_pred HHHHHHHHHhccCceEEEEcCCcee-cCCCCHHHH
Confidence 3456777764 7889999999999 777744433
No 12
>PF01866 Diphthamide_syn: Putative diphthamide synthesis protein; InterPro: IPR002728 Members of this family include Q16439 from SWISSPROT, a candidate tumour suppressor gene [], and DPH2 from yeast P32461 from SWISSPROT [], which confers resistance to diphtheria toxin and has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a posttranslationally modified histidine residue present in EF2. The exact function of the members of this family is unknown.; GO: 0017183 peptidyl-diphthamide biosynthetic process from peptidyl-histidine, 0005737 cytoplasm; PDB: 3LZD_B 3LZC_A.
Probab=47.10 E-value=23 Score=29.79 Aligned_cols=33 Identities=21% Similarity=0.337 Sum_probs=17.1
Q ss_pred HHHHHHHHhcC-CeEEeccCCeeEeeecCCHHHHH
Q 032606 94 LEPVVELLKEG-AVGVIPTDTLYATAICLSRSVCN 127 (137)
Q Consensus 94 l~~aa~~Lr~G-gVVa~PTDTVYGLgcdan~~AVe 127 (137)
..++++.|++. .=+.+=.||.|| +||.+..+.+
T Consensus 9 a~~ia~~L~~~~~~v~IlaDttYG-aCcvD~~~a~ 42 (307)
T PF01866_consen 9 AVEIASILESTGVEVYILADTTYG-ACCVDEVAAE 42 (307)
T ss_dssp HHHHHHHHHTTT-EEEEE-S-B---TTS--HHHHH
T ss_pred HHHHHHHHHcCCceEEEEeCCccc-CCCcCHHHHh
Confidence 34567777644 358888999999 7777554443
No 13
>PF05951 Peptidase_M15_2: Bacterial protein of unknown function (DUF882); InterPro: IPR010275 This family consists of proteins related to metallopeptidases belong to MEROPS peptidase family M15A. They are classed as non-peptidase homologues (M15A.UNA) and include A3D3U2 from SWISSPROT, where the metal ligands (marked by *) are conserved but the catalytic Asn has been replaced by Asp (+): 70 80 90 100 110 120 A3D3U2: QSKVLNDFNHLLRDHRQNVAAPMDKRLFDLLYSLKTTLNVDDEIHVISGYRSPKTNAMLA : .:. .:. : :.: ::.:: . :: . B1W1A6: PELNTCNSTWAGGKVAAGTARANALSSMWKLEALRHALG-DRSIRVTSGFRSASCNAAV- 20 30 40 50 60 70 * 130 * 140 150 160 170 * + A3D3U2: SNSGGVAKKSYHMRGMAMDIAIPSVKLKTLREAALSLKLGGV---GYYPNSGFVHVDCGP :: :..: :: : :.:.. .: :: . : . :. :: .. :::. :: B1W1A6: ---GG-ASNSRHMYGDAVDLGASPHSLCTLAKQARYHGFRGILGPGYVGHNDHVHVNQGP 80 90 100 110 120 B1W1A6 from SWISSPROT belongs to IPR013230 from INTERPRO, whcih contains peptidases belonging to the M15A family. The function of the proteins in this entry are not known.
Probab=43.35 E-value=28 Score=27.55 Aligned_cols=33 Identities=21% Similarity=0.314 Sum_probs=27.4
Q ss_pred EEEecCCCCCcccHHHHHHHHhcCCeEEeccCC
Q 032606 81 YVEADPSGADSWKLEPVVELLKEGAVGVIPTDT 113 (137)
Q Consensus 81 ~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDT 113 (137)
=+.+.-.+-+...+.+++..|+.|||..||+..
T Consensus 106 AiDi~ipgv~~~~l~~~A~~l~~GGVG~Yp~s~ 138 (152)
T PF05951_consen 106 AIDIRIPGVPLRQLRRAALSLQRGGVGYYPRSG 138 (152)
T ss_pred EEEEecCCCCHHHHHHHHHHcCCCeEEeeCCCC
Confidence 356666677788899999999999999999854
No 14
>PF09843 DUF2070: Predicted membrane protein (DUF2070); InterPro: IPR019204 This domain of unknown function is found in various bacterial and archael hypothetical proteins, as well as in prokaryotic polyketide synthase.
Probab=41.25 E-value=54 Score=25.56 Aligned_cols=45 Identities=24% Similarity=0.164 Sum_probs=36.1
Q ss_pred CceEEEEecCCCCCcccHHHHHHHHh--cCCeEEeccCCeeEeeecC
Q 032606 77 GGLMYVEADPSGADSWKLEPVVELLK--EGAVGVIPTDTLYATAICL 121 (137)
Q Consensus 77 ~~~~~levdp~~pd~~~l~~aa~~Lr--~GgVVa~PTDTVYGLgcda 121 (137)
+...|+-+|.+|.++..-+++.+.+. -..+.++-|||.+--+-..
T Consensus 73 ~~~~lv~~DsNNm~~~lr~~i~~~~~~~~d~~ev~TTDtH~~~~~~~ 119 (179)
T PF09843_consen 73 QRSALVLADSNNMEPGLREKIREALGDVVDEVEVMTTDTHFVNGESG 119 (179)
T ss_pred cEEEEEEEECCCCCHHHHHHHHHHHhhhcceeEEecCcccEEccEEC
Confidence 35678899999999988888888877 4589999999987655543
No 15
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=41.04 E-value=36 Score=30.82 Aligned_cols=34 Identities=24% Similarity=0.392 Sum_probs=29.4
Q ss_pred EEEEecCCCCCcccHHHHHHHHhcCCeEEe-ccCC
Q 032606 80 MYVEADPSGADSWKLEPVVELLKEGAVGVI-PTDT 113 (137)
Q Consensus 80 ~~levdp~~pd~~~l~~aa~~Lr~GgVVa~-PTDT 113 (137)
-+|.|||-+.-...++.|++.+++||++.+ -|||
T Consensus 123 d~IDiDPFGSPaPFlDaA~~s~~~~G~l~vTATD~ 157 (380)
T COG1867 123 DVIDIDPFGSPAPFLDAALRSVRRGGLLCVTATDT 157 (380)
T ss_pred cEEecCCCCCCchHHHHHHHHhhcCCEEEEEeccc
Confidence 478999999988899999999999888765 5776
No 16
>TIGR00272 DPH2 diphthamide biosynthesis protein 2. This protein has been shown in Saccharomyces cerevisiae to be one of several required for the modification of a particular histidine residue of translation elongation factor 2 to diphthamide. This modified site can then become the target for ADP-ribosylation by diphtheria toxin.
Probab=40.89 E-value=27 Score=32.01 Aligned_cols=34 Identities=24% Similarity=0.333 Sum_probs=23.6
Q ss_pred HHHHHHHHhc-----CCeEEeccCCeeEeeecCCHHHHHH
Q 032606 94 LEPVVELLKE-----GAVGVIPTDTLYATAICLSRSVCNS 128 (137)
Q Consensus 94 l~~aa~~Lr~-----GgVVa~PTDTVYGLgcdan~~AVer 128 (137)
...+++.|++ |-=+++=-||.|| +|+.+.-+.+.
T Consensus 66 a~~va~~L~~~~~~~~~~v~IlaDtsYG-aCCVDevaA~h 104 (496)
T TIGR00272 66 SSKVVRLLQSKFPHGKIKFWVLADTAYS-SCCVDEVAAEH 104 (496)
T ss_pred HHHHHHHHHhhcccCCceEEEEeCCccc-ccccCHHHHhh
Confidence 4456777766 5778888999999 66664444443
No 17
>KOG1253 consensus tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=39.69 E-value=35 Score=32.16 Aligned_cols=31 Identities=23% Similarity=0.408 Sum_probs=27.7
Q ss_pred EEEEecCCCCCcccHHHHHHHHhcCCeEEec
Q 032606 80 MYVEADPSGADSWKLEPVVELLKEGAVGVIP 110 (137)
Q Consensus 80 ~~levdp~~pd~~~l~~aa~~Lr~GgVVa~P 110 (137)
-.|.+||-+.....|+.|++.+++||++.+-
T Consensus 185 DvIDLDPyGs~s~FLDsAvqav~~gGLL~vT 215 (525)
T KOG1253|consen 185 DVIDLDPYGSPSPFLDSAVQAVRDGGLLCVT 215 (525)
T ss_pred ceEecCCCCCccHHHHHHHHHhhcCCEEEEE
Confidence 3578999999999999999999999998763
No 18
>PF08351 DUF1726: Domain of unknown function (DUF1726); InterPro: IPR013562 This entry represents a protein of unknown function and is found towards the N terminus of putative ATPases (IPR007807 from INTERPRO). ; PDB: 2ZPA_B.
Probab=38.48 E-value=21 Score=25.43 Aligned_cols=35 Identities=17% Similarity=0.261 Sum_probs=22.1
Q ss_pred ceEEEEecCCCCCcccHHHHHHHHhcCCeEEeccCC
Q 032606 78 GLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDT 113 (137)
Q Consensus 78 ~~~~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDT 113 (137)
.+.++.. -++-++..+..++..++.||++++-+..
T Consensus 13 ~~~i~d~-~~g~~pnal~a~~gtv~gGGllill~p~ 47 (92)
T PF08351_consen 13 DLLIFDA-FEGFDPNALAALAGTVRGGGLLILLLPP 47 (92)
T ss_dssp SSEEEE--SS---HHHHHHHHTTB-TT-EEEEEES-
T ss_pred CEEEEEc-cCCCCHHHHHHHhcceecCeEEEEEcCC
Confidence 4455555 4566788999999999999999987665
No 19
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=37.89 E-value=41 Score=24.83 Aligned_cols=58 Identities=17% Similarity=0.198 Sum_probs=33.4
Q ss_pred cccccccccceeecC-ceEEEEecCCCCCcccHHHHHHHHhcCCeEEeccCC--eeEeeec
Q 032606 63 PKRLKYSAPQFTKEG-GLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDT--LYATAIC 120 (137)
Q Consensus 63 ~krlky~~~~~~~~~-~~~~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDT--VYGLgcd 120 (137)
-+|+.+......++- .+++|=.|.-.-+...+++|.+.|+++.+|+-|++- .|-||..
T Consensus 46 G~Rm~~a~~~~~~g~~~vvliGsD~P~l~~~~l~~A~~~L~~~d~VlgPa~DGGy~LiG~~ 106 (122)
T PF09837_consen 46 GERMANAFQQAARGYEPVVLIGSDCPDLTPDDLEQAFEALQRHDVVLGPAEDGGYYLIGLR 106 (122)
T ss_dssp HHHHHHHHHHHHTT-SEEEEE-SS-TT--HHHHHHHHHHTTT-SEEEEEBTTSSEEEEEEE
T ss_pred HHHHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHHHhccCCEEEeeccCCCEEEEecC
Confidence 355555444431111 334444444444577899999999999999999863 3555553
No 20
>cd00733 GlyRS_alpha_core Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. This alignment contains only sequences from the GlyRS form which heterotetramerizes. The homodimer form of GlyRS is in a different family of class II aaRS. Class II assignment is based upon structure and the presence of three characteristic sequence motifs.
Probab=34.38 E-value=47 Score=29.06 Aligned_cols=85 Identities=24% Similarity=0.326 Sum_probs=51.4
Q ss_pred ccCCcchhhhhhhhcccCCCceeeecCCCCCCCceeeeeeeeccCcccccccccceeecCceEEEEecCCCCCcccHHHH
Q 032606 18 HSHSHSHFLEAATRRAAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPV 97 (137)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~r~~krlky~~~~~~~~~~~~~levdp~~pd~~~l~~a 97 (137)
-+|+.++ -|+..|-|-.+-+.+|.+.|--.+ +-.||.||---. |.-++++-.|.|.|.--++..
T Consensus 32 T~hPaTf-----lr~Lgpepw~vAYVqPsrRP~DGR-----YGeNPNRLq~y~------QfQViiKPsP~niQelYL~SL 95 (279)
T cd00733 32 TFHPATF-----LRALGPEPWNVAYVEPSRRPTDGR-----YGENPNRLQHYY------QFQVIIKPSPDNIQELYLESL 95 (279)
T ss_pred cCCHHHH-----HHhcCCCcceeccccCCCCCCCCC-----cCCCchhhhhhe------eeEEEECCCCccHHHHHHHHH
Confidence 3566777 677889999999999998887666 677888873211 122455555555554444332
Q ss_pred HHH---HhcCCeEEe------ccCCeeEee
Q 032606 98 VEL---LKEGAVGVI------PTDTLYATA 118 (137)
Q Consensus 98 a~~---Lr~GgVVa~------PTDTVYGLg 118 (137)
..+ +++..+-.+ ||=.-||||
T Consensus 96 ~~lGid~~~hDIRFVEDnWEsPTLGAwGLG 125 (279)
T cd00733 96 EALGINPKEHDIRFVEDNWESPTLGAWGLG 125 (279)
T ss_pred HHhCCCccccCeeEeecCCCCCcccccccc
Confidence 221 244444433 555566665
No 21
>cd07988 LPLAT_ABO13168-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are uncharacterized phospholipid/glycerol acyltransferases such as the Acinetobacter baumannii ATCC 17978 locus ABO13168 putative acyltransferase, and similar proteins.
Probab=34.28 E-value=61 Score=24.46 Aligned_cols=35 Identities=26% Similarity=0.264 Sum_probs=25.3
Q ss_pred EEEecCCCCCcccHHHHHHHHhcCC---eEEeccCCeeE
Q 032606 81 YVEADPSGADSWKLEPVVELLKEGA---VGVIPTDTLYA 116 (137)
Q Consensus 81 ~levdp~~pd~~~l~~aa~~Lr~Gg---VVa~PTDTVYG 116 (137)
.+.|+.+++ ...++.+.+.|++|+ +++||--|--.
T Consensus 71 ~i~V~r~~~-~~~~~~~~~~l~~g~~~~l~IFPEGtR~~ 108 (163)
T cd07988 71 GIPVDRSRA-GGLVEQVVEEFRRREEFVLAIAPEGTRSK 108 (163)
T ss_pred CEEeEcCCc-ccHHHHHHHHHHhCCCcEEEEeCCCCCCC
Confidence 456666664 336788888899863 89999888654
No 22
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=33.93 E-value=50 Score=28.98 Aligned_cols=35 Identities=20% Similarity=0.295 Sum_probs=27.1
Q ss_pred EEEEecCCCCCcccHHHHHHHHhcCCeEEe-ccCCe
Q 032606 80 MYVEADPSGADSWKLEPVVELLKEGAVGVI-PTDTL 114 (137)
Q Consensus 80 ~~levdp~~pd~~~l~~aa~~Lr~GgVVa~-PTDTV 114 (137)
-+|.+||-+.....++.+.+.+++||++.+ -|||-
T Consensus 116 DvIdlDPfGs~~~fld~al~~~~~~glL~vTaTD~~ 151 (374)
T TIGR00308 116 HVIDIDPFGTPAPFVDSAIQASAERGLLLVTATDTS 151 (374)
T ss_pred CEEEeCCCCCcHHHHHHHHHhcccCCEEEEEecccH
Confidence 578889976555789999999999886655 47874
No 23
>PLN02589 caffeoyl-CoA O-methyltransferase
Probab=33.68 E-value=35 Score=28.29 Aligned_cols=42 Identities=12% Similarity=0.122 Sum_probs=28.2
Q ss_pred EEEEecCCCCC-cccHHHHHHHHhcCCeEEeccCCeeEeeecC
Q 032606 80 MYVEADPSGAD-SWKLEPVVELLKEGAVGVIPTDTLYATAICL 121 (137)
Q Consensus 80 ~~levdp~~pd-~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda 121 (137)
-++.+|.+..+ ...++.+.+.|+.||+|++----..|..++.
T Consensus 158 D~iFiDadK~~Y~~y~~~~l~ll~~GGviv~DNvl~~G~v~~~ 200 (247)
T PLN02589 158 DFIFVDADKDNYINYHKRLIDLVKVGGVIGYDNTLWNGSVVAP 200 (247)
T ss_pred cEEEecCCHHHhHHHHHHHHHhcCCCeEEEEcCCCCCCcccCc
Confidence 35566666444 4457788999999999998433334666665
No 24
>PF03279 Lip_A_acyltrans: Bacterial lipid A biosynthesis acyltransferase; InterPro: IPR004960 Bacterial lipopolysachharides (LPS) are glycolipids that make up the outer monolayer of the outer membranes of most Gram-negative bacteria. Though LPS moleculesare variable, they all show the same general features: an outer polysaccharide which is attached to the lipid component, termed lipid A []. The polysaccharide component consists of a variable repeat-structure polysaccharide known as the O-antigen, and a highly conserved short core oligosaccharide which connects the O-antigen to lipid A. Lipid A is a glucosamine-based phospholipid that makes up the membrane anchor region of LPS []. The structure of lipid A is relatively invariant between species, presumably reflecting its fundamental role in membrane integrity. Recognition of lipid A by the innate immune system can lead to a response even at picomolar levels. In some genera, such as Neisseria and Haemophilus, lipooligosaccharides (LOS) are the predominant glycolipids []. These are analogous to LPS except that they lack O-antigens, with the LOS oligosaccharide structures limited to 10 saccharide units. The bacterial lipid A biosynthesis protein, or lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase 2.3.1 from EC, transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA during lipopolysaccharide core biosynthesis.; GO: 0016746 transferase activity, transferring acyl groups, 0009244 lipopolysaccharide core region biosynthetic process, 0016021 integral to membrane
Probab=33.41 E-value=37 Score=27.38 Aligned_cols=22 Identities=23% Similarity=0.277 Sum_probs=19.9
Q ss_pred HHHHHHHHhcCCeEEeccCCee
Q 032606 94 LEPVVELLKEGAVGVIPTDTLY 115 (137)
Q Consensus 94 l~~aa~~Lr~GgVVa~PTDTVY 115 (137)
+.++++.|++|++|++-.|-.+
T Consensus 181 ~~~~~~~Lk~g~~v~~l~Dq~~ 202 (295)
T PF03279_consen 181 IRELIRALKEGGIVGLLGDQDP 202 (295)
T ss_pred HHHHHHHhccCCEEEEEECCCC
Confidence 8889999999999999999655
No 25
>COG0144 Sun tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]
Probab=31.83 E-value=29 Score=29.94 Aligned_cols=36 Identities=28% Similarity=0.231 Sum_probs=26.6
Q ss_pred ccHHHHHHHHhcCCeEEeccCCeeEeeecC--CHHHHHHHHhc
Q 032606 92 WKLEPVVELLKEGAVGVIPTDTLYATAICL--SRSVCNSLRFE 132 (137)
Q Consensus 92 ~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda--n~~AVerIy~I 132 (137)
..|+.+.+.|+.||+++|-|=|+ .+ |++.|++..+-
T Consensus 269 ~iL~~a~~~lk~GG~LVYSTCS~-----~~eENE~vV~~~L~~ 306 (355)
T COG0144 269 EILAAALKLLKPGGVLVYSTCSL-----TPEENEEVVERFLER 306 (355)
T ss_pred HHHHHHHHhcCCCCEEEEEccCC-----chhcCHHHHHHHHHh
Confidence 45778899999999999987443 12 77777776643
No 26
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=31.38 E-value=56 Score=21.98 Aligned_cols=18 Identities=22% Similarity=0.409 Sum_probs=15.1
Q ss_pred HHHHHHHHhcCCeEEecc
Q 032606 94 LEPVVELLKEGAVGVIPT 111 (137)
Q Consensus 94 l~~aa~~Lr~GgVVa~PT 111 (137)
++++.+.|++||++.+|=
T Consensus 1 ~eE~k~~i~~gg~v~~pw 18 (68)
T PF09180_consen 1 YEEFKEAIEKGGFVLVPW 18 (68)
T ss_dssp HHHHHHHHHTSSEEEEEE
T ss_pred ChHHHHHHhCCCEEEEEc
Confidence 467888999999999983
No 27
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=30.94 E-value=31 Score=28.05 Aligned_cols=36 Identities=25% Similarity=0.162 Sum_probs=25.0
Q ss_pred ccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHh
Q 032606 92 WKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRF 131 (137)
Q Consensus 92 ~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~ 131 (137)
..++.+.+.|+.||.++|-|=|+. .. |++.|+++.+
T Consensus 180 ~iL~~a~~~lkpgG~lvYstcs~~----~~Ene~vv~~~l~ 216 (264)
T TIGR00446 180 ELIDSAFDALKPGGVLVYSTCSLE----PEENEAVVDYLLE 216 (264)
T ss_pred HHHHHHHHhcCCCCEEEEEeCCCC----hHHHHHHHHHHHH
Confidence 367788899999999997664421 12 5667776654
No 28
>PRK09348 glyQ glycyl-tRNA synthetase subunit alpha; Validated
Probab=30.50 E-value=57 Score=28.61 Aligned_cols=85 Identities=20% Similarity=0.270 Sum_probs=51.0
Q ss_pred ccCCcchhhhhhhhcccCCCceeeecCCCCCCCceeeeeeeeccCcccccccccceeecCceEEEEecCCCCCcccHHHH
Q 032606 18 HSHSHSHFLEAATRRAAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPV 97 (137)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~r~~krlky~~~~~~~~~~~~~levdp~~pd~~~l~~a 97 (137)
-+++.++ -|+..|-|-.+-+.+|.+.|--.+ +-.||.||-.-. |.-++++-.|+|.+.--++..
T Consensus 36 T~~P~Tf-----lr~Lgpepw~vaYvqPsRRP~DGR-----YGeNPNRLq~y~------QfQVilKPsP~niQelYL~SL 99 (283)
T PRK09348 36 TFHPATF-----LRALGPEPWNAAYVQPSRRPTDGR-----YGENPNRLQHYY------QFQVILKPSPDNIQELYLGSL 99 (283)
T ss_pred cCCHHHH-----HHhcCCCccccccccCCCCCCCCC-----cCCCchhhhhhe------eeEEEEcCCCccHHHHHHHHH
Confidence 3566777 677889999999999988887666 567888874322 122455555555554444432
Q ss_pred HHH---HhcCCeEEe------ccCCeeEee
Q 032606 98 VEL---LKEGAVGVI------PTDTLYATA 118 (137)
Q Consensus 98 a~~---Lr~GgVVa~------PTDTVYGLg 118 (137)
..+ +++..|-.+ ||=.-||||
T Consensus 100 ~~lGid~~~hDIRFVEDnWEsPTLGAwGlG 129 (283)
T PRK09348 100 EALGIDPLEHDIRFVEDNWESPTLGAWGLG 129 (283)
T ss_pred HHhCCCccccceeEeecCCCCCcccccccc
Confidence 222 233333333 555566665
No 29
>COG1736 DPH2 Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis]
Probab=30.41 E-value=48 Score=29.44 Aligned_cols=36 Identities=17% Similarity=0.210 Sum_probs=25.0
Q ss_pred ccHHHHHHHHhcC--CeEEeccCCeeEeeecC-CHHHHHH
Q 032606 92 WKLEPVVELLKEG--AVGVIPTDTLYATAICL-SRSVCNS 128 (137)
Q Consensus 92 ~~l~~aa~~Lr~G--gVVa~PTDTVYGLgcda-n~~AVer 128 (137)
+...++++.|++- -=+++-+|++|| +||. +.++...
T Consensus 37 ~~~~~ia~~le~~~~~~v~i~gd~~yG-ACdi~~~~a~~~ 75 (347)
T COG1736 37 RYAIEIADILEANLGAEVIISGDPVYG-ACDIDDLKAKDV 75 (347)
T ss_pred HHHHHHHHHHHHhhCceEEEeCCcccc-cccCCHHHHhhc
Confidence 3445566666665 678889999999 8888 5555443
No 30
>PRK11933 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
Probab=30.18 E-value=32 Score=31.24 Aligned_cols=36 Identities=31% Similarity=0.248 Sum_probs=25.2
Q ss_pred ccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHh
Q 032606 92 WKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRF 131 (137)
Q Consensus 92 ~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~ 131 (137)
.+++.|.+.|+.||.+||-|=|+- .- |++.|+.+.+
T Consensus 223 ~iL~~A~~~LkpGG~LVYSTCT~~----~eENE~vV~~~L~ 259 (470)
T PRK11933 223 ELIESAFHALKPGGTLVYSTCTLN----REENQAVCLWLKE 259 (470)
T ss_pred HHHHHHHHHcCCCcEEEEECCCCC----HHHHHHHHHHHHH
Confidence 357788999999999999874421 12 6666766654
No 31
>PF08241 Methyltransf_11: Methyltransferase domain; InterPro: IPR013216 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Arsenite methyltransferase (2.1.1.137 from EC) which converts arsenical compounds to their methylated forms [] Biotin synthesis protein bioC, which is involved in the early stages of biotin biosyntheis [] Arginine N-methyltransferase 1, an arginine-methylating enzyme which acts on residues present in a glycine and argine-rich domain and can methylate histones [] Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Sterol 24-C-methyltransferase (2.1.1.41 from EC), shown to participate in ergosterol biosynthesis [] 3-demethylubiquinone-9 3-methyltransferase (2.1.1.64 from EC) involved in ubiquinone biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ]. ; GO: 0008168 methyltransferase activity, 0008152 metabolic process; PDB: 3CGG_B 3CCF_B 3BKW_B 2PXX_A 3I9F_A 2YQZ_B 2YR0_A 3BUS_A 3EGE_A 3G5L_B ....
Probab=30.18 E-value=23 Score=22.27 Aligned_cols=19 Identities=32% Similarity=0.336 Sum_probs=16.4
Q ss_pred cccHHHHHHHHhcCCeEEe
Q 032606 91 SWKLEPVVELLKEGAVGVI 109 (137)
Q Consensus 91 ~~~l~~aa~~Lr~GgVVa~ 109 (137)
...++++.+.|+.||.+++
T Consensus 77 ~~~l~e~~rvLk~gG~l~~ 95 (95)
T PF08241_consen 77 EAALREIYRVLKPGGRLVI 95 (95)
T ss_dssp HHHHHHHHHHEEEEEEEEE
T ss_pred HHHHHHHHHHcCcCeEEeC
Confidence 4578999999999999886
No 32
>TIGR02464 ribofla_fusion conserved hypothetical protein, ribA/ribD-fused. This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from E. coli currently is named YbiA. The function(s) of members of this family is unknown.
Probab=29.28 E-value=83 Score=24.13 Aligned_cols=22 Identities=23% Similarity=0.543 Sum_probs=16.6
Q ss_pred HHhcCCeEEe---ccCCeeEeeecC
Q 032606 100 LLKEGAVGVI---PTDTLYATAICL 121 (137)
Q Consensus 100 ~Lr~GgVVa~---PTDTVYGLgcda 121 (137)
+|.-|+-+++ |.|.+||+|++.
T Consensus 102 Ll~Tg~~~LVE~s~~D~~WG~g~~~ 126 (153)
T TIGR02464 102 LLSTGGKKLVEASPNDKIWGIGLDA 126 (153)
T ss_pred HHhcCCcEEEecCCCCCeeecCCCC
Confidence 3444666554 999999999987
No 33
>PF13684 Dak1_2: Dihydroxyacetone kinase family
Probab=29.18 E-value=58 Score=27.78 Aligned_cols=32 Identities=25% Similarity=0.311 Sum_probs=15.6
Q ss_pred EecCCCCCcc-cHHHHHHHHhcCCeEEeccCCe
Q 032606 83 EADPSGADSW-KLEPVVELLKEGAVGVIPTDTL 114 (137)
Q Consensus 83 evdp~~pd~~-~l~~aa~~Lr~GgVVa~PTDTV 114 (137)
-+-|+|.+.. ..+++++.+++..|+++||.|+
T Consensus 147 ivLPNn~ni~~aa~qa~~~~~~~~v~VipTks~ 179 (313)
T PF13684_consen 147 IVLPNNKNIILAAEQAARLSEDKNVVVIPTKSI 179 (313)
T ss_pred EEEeCCchHHHHHHHHHHHhcCCCEEEEecCCH
Confidence 3444444433 3444455554444666666654
No 34
>TIGR00091 tRNA (guanine-N(7)-)-methyltransferase. In E. coli, this protein flanks the DNA repair protein MutY, also called micA.
Probab=28.76 E-value=48 Score=25.38 Aligned_cols=23 Identities=30% Similarity=0.291 Sum_probs=20.2
Q ss_pred ccHHHHHHHHhcCCeEEeccCCe
Q 032606 92 WKLEPVVELLKEGAVGVIPTDTL 114 (137)
Q Consensus 92 ~~l~~aa~~Lr~GgVVa~PTDTV 114 (137)
..++++.+.|+.||.+++=||..
T Consensus 113 ~~l~~~~r~LkpgG~l~~~td~~ 135 (194)
T TIGR00091 113 HFLKEYANVLKKGGVIHFKTDNE 135 (194)
T ss_pred HHHHHHHHHhCCCCEEEEEeCCH
Confidence 35888999999999999988875
No 35
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=28.75 E-value=32 Score=30.25 Aligned_cols=36 Identities=25% Similarity=0.423 Sum_probs=25.0
Q ss_pred ceEEEEecCCCCCcccHHHHHHHHhcCCeEEe-ccCC
Q 032606 78 GLMYVEADPSGADSWKLEPVVELLKEGAVGVI-PTDT 113 (137)
Q Consensus 78 ~~~~levdp~~pd~~~l~~aa~~Lr~GgVVa~-PTDT 113 (137)
.--+|.+||-+.-...++.|++.+++||++.+ -|||
T Consensus 121 ~fD~IDlDPfGSp~pfldsA~~~v~~gGll~vTaTD~ 157 (377)
T PF02005_consen 121 RFDVIDLDPFGSPAPFLDSALQAVKDGGLLCVTATDT 157 (377)
T ss_dssp -EEEEEE--SS--HHHHHHHHHHEEEEEEEEEEE--H
T ss_pred cCCEEEeCCCCCccHhHHHHHHHhhcCCEEEEecccc
Confidence 44689999999999999999999999998765 4554
No 36
>PRK15018 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional
Probab=28.49 E-value=62 Score=26.42 Aligned_cols=35 Identities=17% Similarity=0.174 Sum_probs=25.8
Q ss_pred EEEecCCCCCc--ccHHHHHHHHhcCC--eEEeccCCee
Q 032606 81 YVEADPSGADS--WKLEPVVELLKEGA--VGVIPTDTLY 115 (137)
Q Consensus 81 ~levdp~~pd~--~~l~~aa~~Lr~Gg--VVa~PTDTVY 115 (137)
.+.||.+++.. ..++++.+.|+++| +++||.-|--
T Consensus 113 ~i~VdR~~~~~~~~~l~~~~~~l~~~g~sv~IFPEGTRs 151 (245)
T PRK15018 113 NLLIDRNNRTKAHGTIAEVVNHFKKRRISIWMFPEGTRS 151 (245)
T ss_pred CeEEeCCCHHHHHHHHHHHHHHHHhCCCEEEEECCccCC
Confidence 46778776643 36788889998755 7899988754
No 37
>cd07985 LPLAT_GPAT Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT. Lysophospholipid acyltransferase (LPLAT) superfamily member: glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB). LPLATs are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. This subgroup includes glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB).
Probab=27.65 E-value=75 Score=26.74 Aligned_cols=43 Identities=23% Similarity=0.170 Sum_probs=28.2
Q ss_pred CCcccHHHHHHHHhcCCe--EEeccCCeeE------eeecC-CHHHHHHHHh
Q 032606 89 ADSWKLEPVVELLKEGAV--GVIPTDTLYA------TAICL-SRSVCNSLRF 131 (137)
Q Consensus 89 pd~~~l~~aa~~Lr~GgV--Va~PTDTVYG------Lgcda-n~~AVerIy~ 131 (137)
.+...++.+.+.|++|+. .|||-=|-.= +.-.. +.++++....
T Consensus 99 ~~~~alk~~~~lLk~G~~~i~IfPEGtR~r~~~~g~~~p~~Fd~~~~~~~~~ 150 (235)
T cd07985 99 ANLATLKEMQQLLNEGGQLIWVAPSGGRDRPDANGEWYPDPFDPSAVEMMRL 150 (235)
T ss_pred ccHHHHHHHHHHHHcCCeEEEEcCCCCCCCCCCCCCccCCccchHHHHHHHH
Confidence 556678899999999985 5888754431 11123 6666665544
No 38
>KOG1663 consensus O-methyltransferase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=26.81 E-value=37 Score=28.96 Aligned_cols=44 Identities=16% Similarity=0.094 Sum_probs=32.4
Q ss_pred ceEEEEecCCCCCc-ccHHHHHHHHhcCCeEEeccCCeeEeeecC
Q 032606 78 GLMYVEADPSGADS-WKLEPVVELLKEGAVGVIPTDTLYATAICL 121 (137)
Q Consensus 78 ~~~~levdp~~pd~-~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda 121 (137)
..-++.+|.+-..- ...++.+++|+.|||+++=-=--+|..|++
T Consensus 149 tfDfaFvDadK~nY~~y~e~~l~Llr~GGvi~~DNvl~~G~v~~p 193 (237)
T KOG1663|consen 149 TFDFAFVDADKDNYSNYYERLLRLLRVGGVIVVDNVLWPGVVADP 193 (237)
T ss_pred ceeEEEEccchHHHHHHHHHHHhhcccccEEEEeccccCCcccCc
Confidence 34455666665442 468899999999999999776777866766
No 39
>cd07992 LPLAT_AAK14816-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown AAK14816-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are uncharacterized glycerol-3-phosphate acyltransferases such as the Plasmodium falciparum locus AAK14816 putative acyltransferase, and similar proteins.
Probab=25.10 E-value=1.1e+02 Score=23.32 Aligned_cols=24 Identities=29% Similarity=0.452 Sum_probs=19.0
Q ss_pred ccHHHHHHHHhcCC-eEEeccCCee
Q 032606 92 WKLEPVVELLKEGA-VGVIPTDTLY 115 (137)
Q Consensus 92 ~~l~~aa~~Lr~Gg-VVa~PTDTVY 115 (137)
..++.+.+.|++|. ++|||--|..
T Consensus 98 ~~~~~~~~~l~~G~~l~IFPEGtr~ 122 (203)
T cd07992 98 AVFDAVGEALKAGGAIGIFPEGGSH 122 (203)
T ss_pred HHHHHHHHHHhCCCEEEEeCCCCCC
Confidence 46778899999987 5789988853
No 40
>smart00563 PlsC Phosphate acyltransferases. Function in phospholipid biosynthesis and have either glycerolphosphate, 1-acylglycerolphosphate, or 2-acylglycerolphosphoethanolamine acyltransferase activities. Tafazzin, the product of the gene mutated in patients with Barth syndrome, is a member of this family.
Probab=24.58 E-value=92 Score=20.38 Aligned_cols=30 Identities=23% Similarity=0.336 Sum_probs=21.3
Q ss_pred CCcccHHHHHHHHhcCC-eEEeccCCeeEee
Q 032606 89 ADSWKLEPVVELLKEGA-VGVIPTDTLYATA 118 (137)
Q Consensus 89 pd~~~l~~aa~~Lr~Gg-VVa~PTDTVYGLg 118 (137)
.+...++++.+.|++|+ +++||-.+.+--.
T Consensus 60 ~~~~~~~~~~~~l~~~~~~~ifPeG~~~~~~ 90 (118)
T smart00563 60 LARAALREAVRLLRDGGWLLIFPEGTRSRPG 90 (118)
T ss_pred HHHHHHHHHHHHHhCCCEEEEeCCcccCCCC
Confidence 34557788888898877 5888887754433
No 41
>COG0204 PlsC 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]
Probab=23.83 E-value=1e+02 Score=23.36 Aligned_cols=36 Identities=25% Similarity=0.300 Sum_probs=29.3
Q ss_pred EEEEecCCCCCcccHHHHHHHHhcC--CeEEeccCCee
Q 032606 80 MYVEADPSGADSWKLEPVVELLKEG--AVGVIPTDTLY 115 (137)
Q Consensus 80 ~~levdp~~pd~~~l~~aa~~Lr~G--gVVa~PTDTVY 115 (137)
-.+.++.++++...+..+++.+++| .+++||.=|-.
T Consensus 113 ~~i~v~r~~~~~~~~~~~~~~~~~~g~~l~iFPEGtr~ 150 (255)
T COG0204 113 GAIPVDRENPDDETLRAAVARLKAGGRSLVIFPEGTRS 150 (255)
T ss_pred CeeEecCCCCcHHHHHHHHHHHHhCCcEEEECCCcCcC
Confidence 4688999999888888888888885 68899987763
No 42
>TIGR03682 arCOG04112 arCOG04112 universal archaeal diphthamide biosynthesis domain protein. This family of proteins has been observed universally in archaeal genomes and contains a match to the TIGR00322 model for the diphthamide biosynthesis protein 2-related domain.
Probab=23.35 E-value=81 Score=26.93 Aligned_cols=30 Identities=20% Similarity=0.295 Sum_probs=21.2
Q ss_pred HHHHHh-cCCeEEeccCCeeEeeecC-CHHHHH
Q 032606 97 VVELLK-EGAVGVIPTDTLYATAICL-SRSVCN 127 (137)
Q Consensus 97 aa~~Lr-~GgVVa~PTDTVYGLgcda-n~~AVe 127 (137)
+++.|+ .|-=+++=-||.|| +||. +..|.+
T Consensus 20 ia~~l~~~~~~v~I~gD~tYG-aCcV~D~~a~~ 51 (308)
T TIGR03682 20 IAQKLEEKGYEVIISGEPCYG-ACDLADDEALE 51 (308)
T ss_pred HHHHHHhCCceEEEEcCCcee-eccCChHHHHh
Confidence 444443 46668888999999 7778 776643
No 43
>KOG1122 consensus tRNA and rRNA cytosine-C5-methylase (nucleolar protein NOL1/NOP2) [RNA processing and modification]
Probab=23.22 E-value=39 Score=31.37 Aligned_cols=22 Identities=32% Similarity=0.413 Sum_probs=18.4
Q ss_pred cHHHHHHHHhcCCeEEeccCCe
Q 032606 93 KLEPVVELLKEGAVGVIPTDTL 114 (137)
Q Consensus 93 ~l~~aa~~Lr~GgVVa~PTDTV 114 (137)
.+..|++.++.||+++|-|=|+
T Consensus 353 LllsAi~lv~~GGvLVYSTCSI 374 (460)
T KOG1122|consen 353 LLLSAIDLVKAGGVLVYSTCSI 374 (460)
T ss_pred HHHHHHhhccCCcEEEEEeeec
Confidence 4678999999999999988443
No 44
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=22.85 E-value=49 Score=28.92 Aligned_cols=23 Identities=39% Similarity=0.325 Sum_probs=18.6
Q ss_pred cccHHHHHHHHhcCCeEEeccCC
Q 032606 91 SWKLEPVVELLKEGAVGVIPTDT 113 (137)
Q Consensus 91 ~~~l~~aa~~Lr~GgVVa~PTDT 113 (137)
...++.+.+.|+.||.++|-|=|
T Consensus 364 ~~iL~~a~~~lkpgG~lvystcs 386 (434)
T PRK14901 364 AELLESLAPLLKPGGTLVYATCT 386 (434)
T ss_pred HHHHHHHHHhcCCCCEEEEEeCC
Confidence 34588889999999999987644
No 45
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=21.65 E-value=2.2e+02 Score=18.24 Aligned_cols=33 Identities=15% Similarity=0.186 Sum_probs=23.7
Q ss_pred CceEEEEecCC-CCCc-ccHHHHHHHHhcCCeEEe
Q 032606 77 GGLMYVEADPS-GADS-WKLEPVVELLKEGAVGVI 109 (137)
Q Consensus 77 ~~~~~levdp~-~pd~-~~l~~aa~~Lr~GgVVa~ 109 (137)
+.-.+|-+.|. ..+. ..+++..+.+.+||-+++
T Consensus 34 ~~~tll~i~~~~~~~~~~~~~~l~~~v~~G~~lvl 68 (70)
T PF14258_consen 34 DDGTLLVIGPDLRLSEPEEAEALLEWVEAGNTLVL 68 (70)
T ss_pred CCCEEEEEeCCCCCCchHHHHHHHHHHHcCCEEEE
Confidence 33455667777 5553 778888888999998875
No 46
>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.
Probab=21.03 E-value=3.7e+02 Score=21.48 Aligned_cols=64 Identities=14% Similarity=0.069 Sum_probs=44.4
Q ss_pred cccccccccceeecCceEEEEecCCCCCcccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHh
Q 032606 63 PKRLKYSAPQFTKEGGLMYVEADPSGADSWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRF 131 (137)
Q Consensus 63 ~krlky~~~~~~~~~~~~~levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~ 131 (137)
..+||+.... ..++.++++-..+...++..+.++++.|++.+|-+. +.|+|..- |.+-++.+.+
T Consensus 95 ~~~L~~~~~~-~~~~rivi~v~S~~~~d~~~i~~~~~~lkk~~I~v~----vI~~G~~~~~~~~l~~~~~ 159 (187)
T cd01452 95 QLALKHRQNK-NQKQRIVAFVGSPIEEDEKDLVKLAKRLKKNNVSVD----IINFGEIDDNTEKLTAFID 159 (187)
T ss_pred HHHHhcCCCc-CCcceEEEEEecCCcCCHHHHHHHHHHHHHcCCeEE----EEEeCCCCCCHHHHHHHHH
Confidence 3455554332 122466777777766777778889999999999885 78998877 7776666554
No 47
>COG0220 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]
Probab=20.84 E-value=73 Score=26.18 Aligned_cols=21 Identities=33% Similarity=0.267 Sum_probs=19.0
Q ss_pred cHHHHHHHHhcCCeEEeccCC
Q 032606 93 KLEPVVELLKEGAVGVIPTDT 113 (137)
Q Consensus 93 ~l~~aa~~Lr~GgVVa~PTDT 113 (137)
.++..++.|+.||++-+-||-
T Consensus 146 fl~~~a~~Lk~gG~l~~aTD~ 166 (227)
T COG0220 146 FLKLYARKLKPGGVLHFATDN 166 (227)
T ss_pred HHHHHHHHccCCCEEEEEecC
Confidence 488899999999999999994
No 48
>TIGR02208 lipid_A_msbB lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase. This family consists of MsbB in E. coli and closely related proteins in other species. MsbB is homologous to HtrB (TIGR02207) and acts immediately after it in the biosynthesis of KDO-2 lipid A (also called Re LPS and Re endotoxin). These two enzymes act after creation of KDO-2 lipid IV-A by addition of the KDO sugars.
Probab=20.80 E-value=98 Score=25.55 Aligned_cols=25 Identities=20% Similarity=0.212 Sum_probs=21.6
Q ss_pred ccHHHHHHHHhcCCeEEeccCCeeE
Q 032606 92 WKLEPVVELLKEGAVGVIPTDTLYA 116 (137)
Q Consensus 92 ~~l~~aa~~Lr~GgVVa~PTDTVYG 116 (137)
..+.++++.|++|++|++-.|-.+|
T Consensus 180 ~~~r~i~~aLk~g~~v~il~Dq~~~ 204 (305)
T TIGR02208 180 AGIKALLASLKRGESGYYLPDEDHG 204 (305)
T ss_pred hhHHHHHHHHhCCCeEEEeCCCCCC
Confidence 3578899999999999999998763
No 49
>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.
Probab=20.67 E-value=58 Score=28.34 Aligned_cols=37 Identities=22% Similarity=0.156 Sum_probs=27.0
Q ss_pred cccHHHHHHHHhcCCeEEeccCCeeEeeecC-CHHHHHHHHh
Q 032606 91 SWKLEPVVELLKEGAVGVIPTDTLYATAICL-SRSVCNSLRF 131 (137)
Q Consensus 91 ~~~l~~aa~~Lr~GgVVa~PTDTVYGLgcda-n~~AVerIy~ 131 (137)
...++.+.+.|+.||.++|-|=|+.- - |++.|+++.+
T Consensus 348 ~~lL~~a~~~LkpgG~lvystcs~~~----~Ene~~v~~~l~ 385 (426)
T TIGR00563 348 SEILDAIWPLLKTGGTLVYATCSVLP----EENSEQIKAFLQ 385 (426)
T ss_pred HHHHHHHHHhcCCCcEEEEEeCCCCh----hhCHHHHHHHHH
Confidence 34678889999999999998765531 2 6777766654
No 50
>PF00316 FBPase: Fructose-1-6-bisphosphatase; InterPro: IPR000146 This entry represents the fructose-1,6-bisphosphatase (FBPase) class 1 family. FBPase is a critical regulatory enzyme in gluconeogenesis that catalyses the removal of 1-phosphate from fructose 1,6-bis-phosphate to form fructose 6-phosphate [, ]. It is involved in many different metabolic pathways and found in most organisms. FBPase requires metal ions for catalysis (Mg2+ and Mn2+ being preferred) and the enzyme is potently inhibited by Li+. The fold of fructose-1,6-bisphosphatase was noted to be identical to that of inositol-1-phosphatase (IMPase) []. Inositol polyphosphate 1-phosphatase (IPPase), IMPase and FBPase share a sequence motif (Asp-Pro-Ile/Leu-Asp-Gly/Ser-Thr/Ser) which has been shown to bind metal ions and participate in catalysis. This motif is also found in the distantly-related fungal, bacterial and yeast IMPase homologues. It has been suggested that these proteins define an ancient structurally conserved family involved in diverse metabolic pathways, including inositol signalling, gluconeogenesis, sulphate assimilation and possibly quinone metabolism []. This entry also includes sedoheptulose-1,7-bisphosphatase, which is a member of the FBPase class 1 family.; GO: 0042578 phosphoric ester hydrolase activity, 0005975 carbohydrate metabolic process; PDB: 2GQ1_A 2QVR_A 2Q8M_B 2OX3_A 2OWZ_A 3KC0_C 2WBB_A 1FTA_C 2VT5_F 2Y5L_F ....
Probab=20.56 E-value=93 Score=27.28 Aligned_cols=23 Identities=26% Similarity=0.468 Sum_probs=19.3
Q ss_pred cHHHHHHHHhcCCeEEeccCCee
Q 032606 93 KLEPVVELLKEGAVGVIPTDTLY 115 (137)
Q Consensus 93 ~l~~aa~~Lr~GgVVa~PTDTVY 115 (137)
.+.++-++|-.|||..||.|.-|
T Consensus 239 mVaD~HRiL~~GGif~YP~d~~~ 261 (324)
T PF00316_consen 239 MVADVHRILLKGGIFLYPADKKY 261 (324)
T ss_dssp HHHHHHHHHHHTCEEEE-SBSSB
T ss_pred cchhHHHHHhhCcEEECCCCCCC
Confidence 47788899999999999999864
No 51
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=20.47 E-value=1e+02 Score=24.82 Aligned_cols=26 Identities=23% Similarity=0.239 Sum_probs=21.6
Q ss_pred CcccHHHHHHHHhcCCeEEeccCCee
Q 032606 90 DSWKLEPVVELLKEGAVGVIPTDTLY 115 (137)
Q Consensus 90 d~~~l~~aa~~Lr~GgVVa~PTDTVY 115 (137)
....++.+.+.|.+|..|++.+|..|
T Consensus 74 ~~~~~~~l~~~l~~g~pv~~~~D~~~ 99 (317)
T PF14399_consen 74 PDEAWEELKEALDAGRPVIVWVDMYY 99 (317)
T ss_pred HHHHHHHHHHHHhCCCceEEEecccc
Confidence 35578889999999998888899876
No 52
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=20.23 E-value=58 Score=30.25 Aligned_cols=30 Identities=37% Similarity=0.558 Sum_probs=17.3
Q ss_pred hcccCCCceeeecCCCCCCCceeeeeeeeccCcccc
Q 032606 31 RRAAPFPGRVSSVSPNPKPSRYRILAMTVKRSPKRL 66 (137)
Q Consensus 31 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~r~~krl 66 (137)
+.-+|.+|.-++.||+||+.|. .-+|||||
T Consensus 274 ~k~s~~~SPkR~~SPPP~~Rk~------~g~SPrrl 303 (458)
T PF10446_consen 274 RKKSPRTSPKRLRSPPPKRRKL------RGRSPRRL 303 (458)
T ss_pred cccCCCCCcccccCCCchhhhc------cCCCCccc
Confidence 3446666777777755543322 34566666
No 53
>COG3108 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.13 E-value=82 Score=26.06 Aligned_cols=32 Identities=22% Similarity=0.492 Sum_probs=26.5
Q ss_pred EEecCCCCCcccHHHHHHHHhcCCeEEeccCC
Q 032606 82 VEADPSGADSWKLEPVVELLKEGAVGVIPTDT 113 (137)
Q Consensus 82 levdp~~pd~~~l~~aa~~Lr~GgVVa~PTDT 113 (137)
..+.-.+-..|.|.+++.-++.|||.-|||--
T Consensus 139 mD~~i~gV~l~~lr~~~~~~~~GGVGyYp~s~ 170 (185)
T COG3108 139 MDFQIPGVSLWELRNAALSMQGGGVGYYPHSN 170 (185)
T ss_pred eeeecCCccHHHHHHHHHhCcCCceeeccCCC
Confidence 34455677789999999999999999999854
No 54
>COG1560 HtrB Lauroyl/myristoyl acyltransferase [Cell envelope biogenesis, outer membrane]
Probab=20.02 E-value=1.1e+02 Score=26.44 Aligned_cols=29 Identities=17% Similarity=0.181 Sum_probs=25.1
Q ss_pred ccHHHHHHHHhcCCeEEeccCCeeEeeec
Q 032606 92 WKLEPVVELLKEGAVGVIPTDTLYATAIC 120 (137)
Q Consensus 92 ~~l~~aa~~Lr~GgVVa~PTDTVYGLgcd 120 (137)
..+.+.++.|++|+.|.|..|-.||-+-.
T Consensus 182 ~~ir~li~~Lk~G~~v~~lpDqd~~~~~~ 210 (308)
T COG1560 182 EGIRQLIKALKQGEAVGYLPDQDYGPGES 210 (308)
T ss_pred hhHHHHHHHHhcCCeEEEecCcccCCCCC
Confidence 45889999999999999999998886654
Done!