Query gi|254781160|ref|YP_003065573.1| 16S rRNA m3U1498 methyltransferase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 245
No_of_seqs 113 out of 2755
Neff 7.5
Searched_HMMs 39220
Date Mon May 30 05:53:51 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781160.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11713 16S rRNA m3U1498 meth 100.0 0 0 441.0 20.2 235 7-245 1-243 (243)
2 COG1385 Uncharacterized protei 100.0 0 0 421.9 18.7 237 5-243 1-246 (246)
3 pfam04452 Methyltrans_RNA RNA 100.0 0 0 402.6 15.5 217 22-239 1-225 (225)
4 TIGR00046 TIGR00046 conserved 100.0 0 0 384.0 18.4 236 5-244 2-256 (258)
5 PRK02135 hypothetical protein; 93.8 0.12 3.1E-06 31.3 4.8 79 150-235 113-191 (199)
6 pfam04013 DUF358 Protein of un 93.0 0.21 5.3E-06 29.8 4.8 79 150-235 113-192 (199)
7 pfam00588 SpoU_methylase SpoU 91.6 0.48 1.2E-05 27.5 5.2 112 85-210 6-118 (142)
8 COG1901 Uncharacterized conser 90.5 1.1 2.8E-05 25.1 6.3 89 142-237 103-192 (197)
9 TIGR02775 TrbG_Ti P-type conju 84.9 2.3 5.9E-05 23.0 5.0 19 189-207 177-196 (220)
10 pfam02590 SPOUT_MTase Predicte 83.6 2.9 7.4E-05 22.4 5.1 76 157-237 62-142 (155)
11 pfam02598 DUF171 Uncharacteriz 81.0 2.1 5.2E-05 23.4 3.5 98 136-238 170-283 (283)
12 COG1756 Mra1 Uncharacterized c 79.0 5.6 0.00014 20.5 5.5 83 150-242 137-221 (223)
13 PRK01191 rpl24p 50S ribosomal 78.3 3.3 8.5E-05 22.0 3.9 51 23-73 31-83 (119)
14 TIGR02203 MsbA_lipidA lipid A 75.7 1.4 3.5E-05 24.5 1.3 40 7-50 408-451 (603)
15 PRK00103 SPOUT methyltransfera 74.9 6.4 0.00016 20.2 4.6 75 158-237 63-141 (156)
16 PRK11181 23S rRNA (guanosine-2 74.6 0.26 6.8E-06 29.1 -2.5 140 82-241 97-238 (244)
17 PRK10864 putative methyltransf 74.1 7.6 0.00019 19.6 5.1 141 80-241 200-342 (348)
18 PRK11081 tRNA guanosine-2'-O-m 73.9 2.8 7.2E-05 22.4 2.6 118 78-210 16-135 (229)
19 KOG3079 consensus 73.4 4.3 0.00011 21.3 3.4 79 78-156 6-103 (195)
20 cd05828 Sortase_D_4 Sortase D 67.5 9.3 0.00024 19.1 4.1 69 18-89 42-110 (127)
21 PTZ00194 60S ribosomal protein 65.1 6.9 0.00018 19.9 3.0 52 23-74 31-84 (143)
22 COG4080 SpoU rRNA Methylase fa 61.9 3.6 9.1E-05 21.8 1.1 100 132-242 37-144 (147)
23 CHL00194 ycf39 Ycf39; Provisio 61.9 12 0.0003 18.4 3.8 112 96-209 92-217 (319)
24 pfam09895 DUF2122 RecB-family 60.3 11 0.00027 18.7 3.3 77 150-240 26-104 (105)
25 cd05827 Sortase_C_3 Sortase C 58.0 16 0.0004 17.6 3.8 69 18-91 43-118 (131)
26 PRK11572 copper homeostasis pr 57.1 8.3 0.00021 19.4 2.3 131 91-228 72-206 (248)
27 TIGR00513 accA acetyl-CoA carb 56.7 13 0.00034 18.1 3.2 109 81-199 68-209 (329)
28 cd06165 Sortase_A_1 Sortase A 56.0 12 0.00031 18.3 3.0 68 20-92 42-116 (127)
29 cd05830 Sortase_D_5 Sortase D 55.8 17 0.00043 17.4 4.0 74 18-92 43-125 (137)
30 TIGR01080 rplX_A_E ribosomal p 52.9 19 0.00048 17.1 4.5 70 6-75 6-80 (116)
31 TIGR00630 uvra excinuclease AB 50.7 9.2 0.00024 19.1 1.6 17 91-107 215-231 (956)
32 PTZ00066 pyruvate kinase; Prov 49.8 21 0.00054 16.8 4.2 72 36-110 152-228 (513)
33 PRK04980 hypothetical protein; 49.8 19 0.00048 17.1 3.1 45 11-62 11-56 (102)
34 cd00004 Sortase Sortases are c 48.3 14 0.00036 17.9 2.3 68 19-91 42-116 (128)
35 TIGR02851 spore_V_T stage V sp 48.0 10 0.00026 18.8 1.6 28 32-59 21-49 (184)
36 cd01724 Sm_D1 The eukaryotic S 47.6 23 0.00058 16.5 4.5 66 32-97 2-67 (90)
37 cd06166 Sortase_D_5 Sortase D 46.5 24 0.0006 16.4 4.1 68 19-91 42-116 (126)
38 cd01721 Sm_D3 The eukaryotic S 46.4 24 0.00061 16.4 3.7 65 33-97 2-66 (70)
39 KOG3172 consensus 45.3 25 0.00063 16.3 3.5 65 33-97 7-71 (119)
40 TIGR02109 PQQ_syn_pqqE coenzym 43.3 21 0.00053 16.8 2.5 74 79-152 145-231 (363)
41 cd05829 Sortase_E Sortase E (S 42.3 27 0.0007 16.0 3.2 70 19-90 49-126 (144)
42 PRK10039 hypothetical protein; 41.5 18 0.00046 17.2 2.0 18 195-212 78-95 (127)
43 TIGR03531 selenium_SpcS O-phos 39.9 20 0.00052 16.8 2.0 23 94-116 191-213 (444)
44 pfam02844 GARS_N Phosphoribosy 39.7 27 0.0007 16.0 2.7 29 191-222 64-92 (99)
45 TIGR00699 GABAtrns_euk 4-amino 36.5 17 0.00044 17.3 1.2 14 195-208 154-167 (469)
46 cd00429 RPE Ribulose-5-phospha 35.7 16 0.00042 17.5 1.0 137 78-228 58-202 (211)
47 pfam04203 Sortase Sortase fami 35.3 35 0.00089 15.3 4.2 69 18-90 37-110 (122)
48 COG3097 Uncharacterized protei 35.1 35 0.0009 15.3 3.4 45 11-62 12-57 (106)
49 TIGR01672 AphA HAD superfamily 34.3 25 0.00065 16.2 1.8 33 20-53 112-144 (248)
50 TIGR00958 3a01208 antigen pept 32.7 31 0.00078 15.7 2.0 15 186-200 557-571 (770)
51 PRK13885 conjugal transfer pro 29.3 23 0.00059 16.5 0.9 20 188-207 241-261 (299)
52 COG1660 Predicted P-loop-conta 28.2 18 0.00046 17.2 0.2 15 186-200 240-254 (286)
53 PRK05784 phosphoribosylamine-- 27.0 48 0.0012 14.5 2.2 22 124-145 318-339 (485)
54 pfam05896 NQRA Na(+)-transloca 26.7 49 0.0012 14.4 5.6 97 17-117 24-135 (257)
55 PRK04171 ribosome biogenesis p 26.4 49 0.0013 14.4 5.0 90 142-242 128-219 (221)
56 pfam01081 Aldolase KDPG and KH 26.4 49 0.0013 14.3 5.2 95 127-227 89-183 (196)
57 PRK10433 putative RNA methyltr 25.6 51 0.0013 14.3 2.8 25 186-210 104-129 (228)
58 pfam00834 Ribul_P_3_epim Ribul 25.4 41 0.001 14.9 1.6 136 77-226 57-200 (201)
59 TIGR00223 panD aspartate 1-dec 25.0 52 0.0013 14.2 4.8 57 3-63 6-63 (127)
60 KOG2925 consensus 25.0 39 0.00099 15.0 1.4 60 6-68 2-62 (167)
61 pfam06003 SMN Survival motor n 24.9 53 0.0013 14.2 3.9 37 36-72 67-105 (264)
62 PRK10358 putative tRNA/rRNA me 24.6 53 0.0014 14.1 3.7 132 82-234 4-141 (157)
63 pfam07236 Phytoreo_S7 Phytoreo 24.5 43 0.0011 14.7 1.6 20 191-210 283-302 (506)
64 pfam01079 Hint Hint module. Th 24.4 54 0.0014 14.1 5.0 45 17-64 14-59 (214)
65 COG2106 Uncharacterized conser 23.6 53 0.0014 14.1 1.9 96 142-241 165-266 (272)
66 TIGR02311 HpaI 2,4-dihydroxyhe 22.9 26 0.00067 16.1 0.2 25 94-118 73-98 (249)
67 cd01733 LSm10 The eukaryotic S 22.7 58 0.0015 13.9 3.8 68 29-96 7-74 (78)
68 cd00452 KDPG_aldolase KDPG and 22.5 58 0.0015 13.9 4.6 90 127-223 85-174 (190)
69 PRK13210 putative L-xylulose 5 22.5 43 0.0011 14.7 1.3 72 92-163 94-176 (284)
70 PRK13668 hypothetical protein; 22.1 59 0.0015 13.8 3.4 10 131-140 145-154 (266)
71 PRK12281 rplX 50S ribosomal pr 22.0 60 0.0015 13.8 3.4 27 36-62 5-31 (77)
72 PRK00885 phosphoribosylamine-- 21.7 60 0.0015 13.8 2.2 35 21-55 154-194 (424)
73 PRK08745 ribulose-phosphate 3- 21.7 34 0.00087 15.4 0.6 136 77-228 62-207 (223)
74 pfam05113 DUF693 Protein of un 20.8 63 0.0016 13.7 2.5 11 202-212 222-232 (311)
75 TIGR02609 doc_partner putative 20.5 64 0.0016 13.6 4.0 39 21-63 11-51 (77)
76 TIGR00185 rRNA_methyl_2 RNA me 20.4 56 0.0014 14.0 1.5 95 94-205 15-116 (161)
77 KOG2589 consensus 20.2 55 0.0014 14.1 1.4 42 11-53 199-241 (453)
78 TIGR01213 TIGR01213 conserved 20.1 65 0.0017 13.6 2.6 22 188-209 338-359 (450)
79 CHL00141 rpl24 ribosomal prote 20.0 66 0.0017 13.5 3.4 29 34-62 8-36 (90)
No 1
>PRK11713 16S rRNA m3U1498 methyltransferase; Provisional
Probab=100.00 E-value=0 Score=440.96 Aligned_cols=235 Identities=37% Similarity=0.565 Sum_probs=203.8
Q ss_pred CCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCC-CEEEEEEEECCC-CCCCCCEE
Q ss_conf 8777408544788889987798759987035789888999977998798753023555-238997541355-55443135
Q gi|254781160|r 7 LKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKS-IRFKVEYQSRSQ-TKQSDVQY 84 (245)
Q Consensus 7 m~R~f~~~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~-~~~~i~~~~~~~-~~~~~i~l 84 (245)
|||||++.++..+..+.|+++++|||.+|||+++||.|.+|||+|+.|.|+|++++|+ +.+.+......+ .++++++|
T Consensus 1 m~r~fi~~~l~~~~~i~L~~~~~~Hl~~VlR~k~gd~i~v~dg~g~~~~a~I~~i~k~~~~~~i~~~~~~~~~~~~~i~L 80 (243)
T PRK11713 1 MPRLFVDAPLAAGETVILTGEEAHHLVRVLRLKEGDELRLFDGRGGEYLAEITEIGKKSVEVEILEKLEVEREPPLRLTL 80 (243)
T ss_pred CCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEEECCEEEEEEECCCCCCCCCCCEEEE
T ss_conf 97699687678999999788998899981608999999999798979999999955998999995122367899970799
Q ss_pred EECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 413445411567775444456656555542022011------22122335788999975123443433200000011233
Q gi|254781160|r 85 IFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNT------HYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKN 158 (245)
Q Consensus 85 ~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~------~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~ 158 (245)
++|++|+++|||+|||+|||||++|+|+.++||+++ .++++||++|+++|||||||+++|+|+.+.+|+++++.
T Consensus 81 ~~al~K~~~~e~il~k~tElGV~~i~p~~s~rs~~~~~~~~~~~k~eR~~~i~~eA~eQs~r~~lP~i~~~~~l~~~l~~ 160 (243)
T PRK11713 81 AQALPKGDRLELIIQKATELGVSAIIPLITERSVVKLDGERADKKLERWQKIAIEAAEQSGRTRIPEIRPPVSLKELLEA 160 (243)
T ss_pred EEEECCCHHHHHHHHHHHHHCCCEEEEEEHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEECCCCCHHHHHHH
T ss_conf 99600755899999999872877799997000545212105666699999999999997099828776576799999953
Q ss_pred CCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf 32233321263000121102221003678835999888888888999999957995586368874004489999999999
Q gi|254781160|r 159 WDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQ 238 (245)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i~als~~~ 238 (245)
.......+++++.... ..........++++++||||||||++|+++|.++|| .++|||++|||||||+++|+|+++
T Consensus 161 ~~~~~~~~i~~~~~~~---~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~g~-~~vsLG~~ILR~ETA~i~als~l~ 236 (243)
T PRK11713 161 LADGDLRLVLHPEANL---AAALKSLKPAGKVLLLIGPEGGFSPEEIELLREAGF-TPVSLGPRILRTETAALAALAALQ 236 (243)
T ss_pred CCCCCCEEEECCCCCC---CCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHCCC-EEEECCCCCCHHHHHHHHHHHHHH
T ss_conf 8677828998688775---432011257885899987888999999999998898-898679991357749999999999
Q ss_pred HHHCCCC
Q ss_conf 9847869
Q gi|254781160|r 239 AICGDWY 245 (245)
Q Consensus 239 ~~~g~~~ 245 (245)
+++|+|-
T Consensus 237 ~~~~~~~ 243 (243)
T PRK11713 237 ALLGDLG 243 (243)
T ss_pred HHHCCCC
T ss_conf 9855799
No 2
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=0 Score=421.88 Aligned_cols=237 Identities=37% Similarity=0.554 Sum_probs=207.6
Q ss_pred CCCCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCC-CEEEEEEEECC-CCCCCCC
Q ss_conf 778777408544788889987798759987035789888999977998798753023555-23899754135-5554431
Q gi|254781160|r 5 SHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKS-IRFKVEYQSRS-QTKQSDV 82 (245)
Q Consensus 5 ~~m~R~f~~~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~-~~~~i~~~~~~-~~~~~~i 82 (245)
++|+|+|++.++..+..+.++++++||+.+|||+++||++.+|||.|+.|.|+|..++|+ +.+.+...... ...+.++
T Consensus 1 ~~~~~~~v~~~~~~~~~~~l~~~~~~Hl~~VlRl~~gd~l~l~~g~g~~~~a~i~~~~kk~~~~~i~~~~~~~~e~~~~i 80 (246)
T COG1385 1 MRMPRLFVDEELAEGATVILTGDEAHHLKRVLRLKEGDELRLFDGSGGEFLAEITKIGKKEALLKIVEQLEPNPELPLKI 80 (246)
T ss_pred CCCEEEEECCCCCCCCEEEECCHHHHHHHHEEECCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEECCCCCCCCCCEE
T ss_conf 97406863464467977997632443267446667899899995899699999810467716999864145677888607
Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHH--H---HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf 354134454115677754444566565555420220112--2---12233578899997512344343320000001123
Q gi|254781160|r 83 QYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTH--Y---NMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLK 157 (245)
Q Consensus 83 ~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~--~---k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~ 157 (245)
+|+++++|+++||+++||+|||||+.|+|++|+||+.+. . |++||++|+++|||||||+.+|+|..+.+|.++++
T Consensus 81 ~l~~~~~kg~k~d~iiqkatELGv~~i~p~~ter~~~k~~~~~~~kler~~ki~ieAaEQs~R~~vP~I~~~~~~~~~l~ 160 (246)
T COG1385 81 TLAQAIPKGDKLELIIQKATELGVSKIIPLITERSVVKLDGKKAAKLERWQKIAIEAAEQSGRNVVPEIKPPESLKELLK 160 (246)
T ss_pred EEEEECCCHHHHHHHHHHHHHHCCCEEEEEEECEEEEEHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECHHHHHHHHH
T ss_conf 99996275188999999998718011798850126772001103689999999999998649986982623130999998
Q ss_pred CCCCCC--CCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHH
Q ss_conf 332233--321263000121102221003678835999888888888999999957995586368874004489999999
Q gi|254781160|r 158 NWDHNC--QIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMA 235 (245)
Q Consensus 158 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i~als 235 (245)
.++.++ .+.+++....+....... .....++++++||||||||++|++.|+.+|| .+|+|||||||||||+++|+|
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~iiIGPEGGfs~~Ei~~l~~~g~-~~v~LGprILRtETA~l~ala 238 (246)
T COG1385 161 EIDDEDALKLIYEEKAKEGLLALPLL-EALPEGKVLLIIGPEGGFSEDEIELLREAGF-TPVSLGPRILRTETAALAALA 238 (246)
T ss_pred HCCCHHHHHHEECCCCCCCCCCCHHH-HCCCCCCEEEEECCCCCCCHHHHHHHHHCCC-EEECCCCCEEEHHHHHHHHHH
T ss_conf 54630013322254454454333012-0156773899988998999899999997798-581378972007789999999
Q ss_pred HHHHHHCC
Q ss_conf 99998478
Q gi|254781160|r 236 LVQAICGD 243 (245)
Q Consensus 236 ~~~~~~g~ 243 (245)
++++.+||
T Consensus 239 ~i~~~~~~ 246 (246)
T COG1385 239 ALQALLGD 246 (246)
T ss_pred HHHHHHCC
T ss_conf 99997349
No 3
>pfam04452 Methyltrans_RNA RNA methyltransferase. RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation.
Probab=100.00 E-value=0 Score=402.61 Aligned_cols=217 Identities=35% Similarity=0.554 Sum_probs=186.0
Q ss_pred EEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCC-CEEEEEEEECC-CCCCCCCEEEECCCCCCHHHHHHH
Q ss_conf 9987798759987035789888999977998798753023555-23899754135-555443135413445411567775
Q gi|254781160|r 22 GKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKS-IRFKVEYQSRS-QTKQSDVQYIFSPIKTNRLDYMIQ 99 (245)
Q Consensus 22 i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~-~~~~i~~~~~~-~~~~~~i~l~~~~~k~~~~~~ilq 99 (245)
|.|+++++|||.||||+++||.|.+|||+|+.|.|+|++++++ +.+.+...... ..++++++|++|++|+++|||+||
T Consensus 1 i~L~~~~~hHl~kVlR~k~gd~i~v~dg~g~~~~~~I~~i~~~~~~~~i~~~~~~~~~~~~~i~l~~al~K~~~~~~il~ 80 (225)
T pfam04452 1 VTLTDEEAHHLVRVLRLKEGDEIKLFDGDGGEYLAEIEEISKKSVLVKILEKLEVNKELPLKITLAQALPKGDRLELILQ 80 (225)
T ss_pred CCCCHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEECCCCEEEEEEHHCCCCCCCCCEEEEEEEEECCHHHHHHHH
T ss_conf 99868998899981858999999999798989999999951881899650002467899971799995007278999999
Q ss_pred HHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHC
Q ss_conf 444456656555542022011------22122335788999975123443433200000011233322333212630001
Q gi|254781160|r 100 KSVEMGMGAIRPVITRYTQNT------HYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCG 173 (245)
Q Consensus 100 k~tELGV~~I~p~~~~rs~~~------~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~ 173 (245)
|+|||||++|+|++++||+.+ .++.+||++|+++|||||||+++|+|+.+.+|+++++.++....++++++...
T Consensus 81 k~tElGV~~i~p~~~ers~~k~~~~~~~~k~~R~~~i~~~A~eQs~r~~lP~I~~~~~l~~~l~~~~~~~~~i~~~~~~~ 160 (225)
T pfam04452 81 KATELGVDRIVPLISERSVVKLDGKRADKKLERWQKIAIEAAEQSGRTRLPEVLPPISLKELLEELDDADKLILHEEAAK 160 (225)
T ss_pred HHHHHCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCHHHHHHHCCCCCEEEEECCCCC
T ss_conf 99862876579998403545443034666599999999999997199828777266899999961866888999266554
Q ss_pred CCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf 211022210036788359998888888889999999579955863688740044899999999999
Q gi|254781160|r 174 SENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQA 239 (245)
Q Consensus 174 ~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i~als~~~~ 239 (245)
..............++++++||||||||++|+++|+++|| .+++||++|||||||+++|+|++++
T Consensus 161 ~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~g~-~~v~LG~~ILR~ETA~i~als~l~~ 225 (225)
T pfam04452 161 SLGELSELLASLKGGKVLLIIGPEGGFSPEEIELLKEAGF-TPVSLGPRILRTETAALAALSALQA 225 (225)
T ss_pred CCCCCHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHCCC-EEEECCCCCCCHHHHHHHHHHHHCC
T ss_conf 4321012321035784589988988999999999998899-8984799946078599999999619
No 4
>TIGR00046 TIGR00046 conserved hypothetical protein TIGR00046; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry are predicted to belong to the family of Mtases, based on a crystal structure showing close structural homology to known methyltransferases ..
Probab=100.00 E-value=0 Score=384.05 Aligned_cols=236 Identities=27% Similarity=0.404 Sum_probs=199.2
Q ss_pred CCCCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEEC-CCCEEEEEEECCCCC-CEEEEEEEECCC-CCCCC
Q ss_conf 778777408544788889987798759987035789888999977-998798753023555-238997541355-55443
Q gi|254781160|r 5 SHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNG-KDGEWLSKISYVGKS-IRFKVEYQSRSQ-TKQSD 81 (245)
Q Consensus 5 ~~m~R~f~~~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg-~g~~~~~~I~~~~k~-~~~~i~~~~~~~-~~~~~ 81 (245)
++|+++|.+..+....++.|+++++|||.|||||+.||.+.++|+ +|..|.|++.+.+|+ +.+.+....... ..+.+
T Consensus 2 m~~~~~~~~~~~~~~~~i~l~~~~~~Hl~rVlR~~~gd~l~~~~~~~g~~y~~~~~~~~k~~~~~~~~~~~~~~~~~~~~ 81 (258)
T TIGR00046 2 MRMRLVLHPEQLEEALIISLTEEEAHHLVRVLRLKKGDKLKLLDGKDGFIYKCEIKKISKKFVKVKLLEGESEERELPLK 81 (258)
T ss_pred CEEEEEECCCCCCCCCEEEEEHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEECCCCEEEEEEEEEEHHCCCCCCC
T ss_conf 04777734200156525898000344346542158787145667589807987776414668899987100211457762
Q ss_pred CEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC--
Q ss_conf 135413445411567775444456656555542022011------221223357889999751234434332000000--
Q gi|254781160|r 82 VQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNT------HYNMDRVRTYTISAAEQCDILTLPFIYPPTTLE-- 153 (245)
Q Consensus 82 i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~------~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~-- 153 (245)
++++++++|+.+||+|||++|||||..|.|++||||..+ .+|++||++|+++|||||+|.++|+|..+.+|.
T Consensus 82 ~~~~~~~~~g~~~e~ii~~~~eLGv~~~~p~~~ers~~k~~~~~~~~K~~rw~KI~~eA~eQs~r~~~P~i~~~~~l~ql 161 (258)
T TIGR00046 82 IHLAIVLIKGKKMEKIIRKLTELGVSKIIPLNAERSVVKLDIERAIKKLERWQKIVIEAAEQSGRNIVPEIKVPKNLKQL 161 (258)
T ss_pred EEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH
T ss_conf 89999753212342565456764678998888865304855778875778889999999862779989843205678999
Q ss_pred -------CCCCCCCC-CCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf -------11233322-3332126300012110222100367883599988888888899999995799558636887400
Q gi|254781160|r 154 -------FLLKNWDH-NCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILR 225 (245)
Q Consensus 154 -------~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR 225 (245)
+++..... .....++... ......+.+..+.+++.|+||||||||++|+.++.+.|| ++|+|||+|||
T Consensus 162 lqr~Q~~e~~~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~~GPEGGfse~E~~~~~~~~f-~~~~L~~~~LR 237 (258)
T TIGR00046 162 LQRMQDVEKLAESEEEALKLNFHPEA---SPLSANLEQIEQAGKIVIIIGPEGGFSEKEIQLLKEKGF-TPVLLGPRILR 237 (258)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCC---CHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHCCC-EECCCCCCCCH
T ss_conf 99865687641001013232210033---111200122005570489981699968889999988298-24137887021
Q ss_pred HHHHHHHHHHHHHHHHCCC
Q ss_conf 4489999999999984786
Q gi|254781160|r 226 SDTAAVAAMALVQAICGDW 244 (245)
Q Consensus 226 ~ETA~i~als~~~~~~g~~ 244 (245)
||||+++|+|++++.++|+
T Consensus 238 tETA~~~a~s~~~~~l~~l 256 (258)
T TIGR00046 238 TETAPVAALSILQALLEDL 256 (258)
T ss_pred HHHHHHHHHHHHHHHHHHC
T ss_conf 2268999999999986303
No 5
>PRK02135 hypothetical protein; Provisional
Probab=93.85 E-value=0.12 Score=31.32 Aligned_cols=79 Identities=23% Similarity=0.347 Sum_probs=55.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHH
Q ss_conf 00001123332233321263000121102221003678835999888888888999999957995586368874004489
Q gi|254781160|r 150 TTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTA 229 (245)
Q Consensus 150 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA 229 (245)
.+|++.+..+.....+++.++...+. .......+.+++.|=-=||+++|.+.+...|. ..+||||..|=+..+
T Consensus 113 ~~~e~~l~e~~~~~~~~~Ld~~G~~i------~~~~~~~~~~FILsDh~~~~~~e~~~L~~~g~-~~iSLGp~~L~a~~c 185 (199)
T PRK02135 113 GSFEDLLQELAEDGQLYYLHEDGEDI------RDVEFPANPVFVLGDHIGMTKEEENLLKRLGA-EKISLGPKMLHADHC 185 (199)
T ss_pred CCHHHHHHHHHCCCCEEEECCCCCCH------HCCCCCCCCEEEEECCCCCCHHHHHHHHHCCC-CEEEECCHHHHHHHH
T ss_conf 89999999985379799988999950------00568999879962899988789999987088-316547388765058
Q ss_pred HHHHHH
Q ss_conf 999999
Q gi|254781160|r 230 AVAAMA 235 (245)
Q Consensus 230 ~i~als 235 (245)
.+.+--
T Consensus 186 I~iiH~ 191 (199)
T PRK02135 186 ITLIHN 191 (199)
T ss_pred HHHHHH
T ss_conf 999999
No 6
>pfam04013 DUF358 Protein of unknown function (DUF358). The proteins in this family are around 200 amino acids long with the exception of the Archaeoglobus fulgidus protein AF_1056 that has an additional 100 amino acids at its amino terminus. The function of these bacterial protein is unknown, however, they do contain several conserved histidines and aspartates that might form a metal binding site.
Probab=92.97 E-value=0.21 Score=29.83 Aligned_cols=79 Identities=18% Similarity=0.259 Sum_probs=53.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCC-CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHH
Q ss_conf 000011233322333212630001211022210036-7883599988888888899999995799558636887400448
Q gi|254781160|r 150 TTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIA-HIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDT 228 (245)
Q Consensus 150 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ET 228 (245)
.+|++++..+.....+++.++...+.. ... ...+.+++.|=-=||+++|.+.++..+. ..+||||..|=+..
T Consensus 113 ~~fe~ll~e~~e~~~~~~Ld~~G~~i~------~~~~~~~~~~FiL~Dh~~~~~~e~~~L~~~~~-~~iSLGp~~L~a~h 185 (199)
T pfam04013 113 MGFEALIRELSEFKPLYYLHEDGGDIS------NVKIPPNNPVFILGDHIGLPEEDEKFLERILA-LKVSLGPLSLHASH 185 (199)
T ss_pred CCHHHHHHHHHCCCCEEEECCCCCCCC------CCCCCCCCCEEEECCCCCCCHHHHHHHHHCCC-CEEEECCHHHHHHH
T ss_conf 899999999855897999978898432------35577889769855999988678888864488-21553738888757
Q ss_pred HHHHHHH
Q ss_conf 9999999
Q gi|254781160|r 229 AAVAAMA 235 (245)
Q Consensus 229 A~i~als 235 (245)
+.+.+--
T Consensus 186 cI~ivH~ 192 (199)
T pfam04013 186 CITLVHN 192 (199)
T ss_pred HHHHHHH
T ss_conf 9999999
No 7
>pfam00588 SpoU_methylase SpoU rRNA Methylase family. This family of proteins probably use S-AdoMet.
Probab=91.59 E-value=0.48 Score=27.47 Aligned_cols=112 Identities=21% Similarity=0.236 Sum_probs=64.4
Q ss_pred EECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 41344541156777544445665655554202201122122335788999975123443433200000011233322333
Q gi|254781160|r 85 IFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQ 164 (245)
Q Consensus 85 ~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~~~~ 164 (245)
+-.+-.+..+-.+++-+.-.|++.++.... ++. +-|...+..++.- ..-++| +....+++++++.......
T Consensus 6 L~~i~~p~NlG~i~Rta~~fG~~~v~l~~~-~~~------~~~~~~~~r~s~g-a~~~i~-~~~~~~~~~~~~~~~~~~~ 76 (142)
T pfam00588 6 LDEPQDPGNLGAIARTAAAFGADGLILVEP-RCA------DLYNPKAIRASAG-ALFHLP-LVIVDNLEEALKDLKEAGY 76 (142)
T ss_pred EECCCCCCHHHHHHHHHHHHCCCCCCCCCC-CCC------CCCCHHHHHHHCC-CCCCCC-CEEECCHHHHHHHHHHCCC
T ss_conf 957988776999999999839996435578-767------9777899999767-752378-3284339999999887495
Q ss_pred CCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCC-CCCCHHHHHHHHH
Q ss_conf 212630001211022210036788359998888-8888899999995
Q gi|254781160|r 165 IVFADETCGSENSLEKLHAIAHIPNVAILIGPE-GGYHSEEKETLHS 210 (245)
Q Consensus 165 ~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPE-GGfs~~E~~~l~~ 210 (245)
.++.-+. .+ +.+......+++.+++|+| .|.|+++.+....
T Consensus 77 ~i~~~~~-~~----~~~~~~~~~~~~~lv~G~E~~Gls~~~l~~~d~ 118 (142)
T pfam00588 77 WIIATSL-KG----KPLYEIDFPKKVALVFGNEGTGLSNEVLELCDR 118 (142)
T ss_pred EEECCCC-CC----CCHHHHCCCCCEEEEECCCCCCCCHHHHHHCCE
T ss_conf 0111344-67----487781468872899778778989999986997
No 8
>COG1901 Uncharacterized conserved protein [Function unknown]
Probab=90.50 E-value=1.1 Score=25.09 Aligned_cols=89 Identities=24% Similarity=0.340 Sum_probs=61.0
Q ss_pred CCCCCCC-CCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf 4343320-000001123332233321263000121102221003678835999888888888999999957995586368
Q gi|254781160|r 142 TLPFIYP-PTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLG 220 (245)
Q Consensus 142 ~lP~i~~-~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG 220 (245)
..|=+.- -.+|+.++........+++..+...+.. .....++.+++.|--=|+++++...++..+. ..+|||
T Consensus 103 ~~pGi~V~~~~~e~ll~~l~~~~~ly~L~E~G~DI~------~v~~~~np~FIlGDH~g~t~e~~k~L~r~~~-~~ISlG 175 (197)
T COG1901 103 VTPGIYVRNGGFEALLAELAEGRSLYYLHEDGRDIS------EVDLIPNPVFILGDHIGLTEEDEKLLERHAA-KKISLG 175 (197)
T ss_pred CCCCEEEECCCHHHHHHHHHCCCCEEEECCCCCCHH------HCCCCCCCEEEEECCCCCCHHHHHHHHHHHC-CEEEEC
T ss_conf 379879925789999999865584799925786475------5556899669961788989789999998648-536727
Q ss_pred CCCCCHHHHHHHHHHHH
Q ss_conf 87400448999999999
Q gi|254781160|r 221 PRILRSDTAAVAAMALV 237 (245)
Q Consensus 221 ~~ILR~ETA~i~als~~ 237 (245)
|.-|-|+.+.+++-..+
T Consensus 176 P~~lha~hcit~~h~~L 192 (197)
T COG1901 176 PLSLHADHCITLLHNLL 192 (197)
T ss_pred CHHHHHHHHHHHHHHHH
T ss_conf 66888888999999877
No 9
>TIGR02775 TrbG_Ti P-type conjugative transfer protein TrbG; InterPro: IPR014142 The TrbG protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbG is a homologue of the F-type TraK protein (which is believed to be an outer membrane pore-forming secretin, IPR014126 from INTERPRO) as well as the vir system VirB9 protein , ..
Probab=84.92 E-value=2.3 Score=23.03 Aligned_cols=19 Identities=32% Similarity=0.821 Sum_probs=15.0
Q ss_pred CEEEEECCCCC-CCHHHHHH
Q ss_conf 35999888888-88899999
Q gi|254781160|r 189 NVAILIGPEGG-YHSEEKET 207 (245)
Q Consensus 189 ~i~i~IGPEGG-fs~~E~~~ 207 (245)
..+++|||+|| |++++-++
T Consensus 177 P~LfVv~~~GGlftdd~~~L 196 (220)
T TIGR02775 177 PPLFVVGPDGGLFTDDENEL 196 (220)
T ss_pred CEEEEEECCCCEEECCCCCE
T ss_conf 70168826886456378636
No 10
>pfam02590 SPOUT_MTase Predicted SPOUT methyltransferase. This family of proteins are predicted to be SPOUT methyltransferases.
Probab=83.56 E-value=2.9 Score=22.37 Aligned_cols=76 Identities=17% Similarity=0.159 Sum_probs=48.2
Q ss_pred CCCCCCCCCCCCCCHHCCCCCHHH---HHCC--CCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHH
Q ss_conf 333223332126300012110222---1003--67883599988888888899999995799558636887400448999
Q gi|254781160|r 157 KNWDHNCQIVFADETCGSENSLEK---LHAI--AHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAV 231 (245)
Q Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~--~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i 231 (245)
+..+.++.+++.|+.....++.+- +... ...+++.++||.--||++.=.+ .+. ..+|||+-++--+-|.+
T Consensus 62 ~~i~~~~~~I~LDe~Gk~~sS~~fa~~i~~~~~~g~~~i~FiIGGa~G~~~~~~~---~a~--~~~Sls~mT~pH~larv 136 (155)
T pfam02590 62 AAIPPGSYVIALDERGKELSSEEFAKLLEDLRLKGKSDITFVIGGSDGLSEEVLK---RAN--EKLSLSKMTLPHQLVRL 136 (155)
T ss_pred HHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHH---HHH--HEEECCCCCCCHHHHHH
T ss_conf 7379999899993799837879999999999833897559998379886989997---566--63441367650899999
Q ss_pred HHHHHH
Q ss_conf 999999
Q gi|254781160|r 232 AAMALV 237 (245)
Q Consensus 232 ~als~~ 237 (245)
+++=++
T Consensus 137 ~l~EQi 142 (155)
T pfam02590 137 LLAEQI 142 (155)
T ss_pred HHHHHH
T ss_conf 999999
No 11
>pfam02598 DUF171 Uncharacterized ACR, COG2106.
Probab=80.99 E-value=2.1 Score=23.35 Aligned_cols=98 Identities=10% Similarity=0.152 Sum_probs=53.6
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCHHCCCCCH-HHHHCCCCCCCEEEEECCCCCCCHHHHH-----
Q ss_conf 75123443433200000011233322---33321263000121102-2210036788359998888888889999-----
Q gi|254781160|r 136 EQCDILTLPFIYPPTTLEFLLKNWDH---NCQIVFADETCGSENSL-EKLHAIAHIPNVAILIGPEGGYHSEEKE----- 206 (245)
Q Consensus 136 eQsgr~~lP~i~~~~~l~~~l~~~~~---~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~i~IGPEGGfs~~E~~----- 206 (245)
...|-.|=-.+....+|.+++...+. ++..+...+........ .......+.+.++++.| ||.+.+..
T Consensus 170 ~~~~~YwGY~Vr~a~sl~~v~~~~~~~~gYd~~I~tS~~G~~~~~~~~~~~~~~~~~~~lvVFG---~~~~~~~~~~~~~ 246 (283)
T pfam02598 170 YGEGLYWGYKVRIASSLSDVFKKSPFPEGYDVTIGTSRRGKDISEAELEIKLMENFKHILLVFG---GWEPLKGSDEILK 246 (283)
T ss_pred CCCCCCCCEEEEEECCHHHHHHCCCCCCCCCEEEEECCCCCCCCHHHHCCCCCCCCCCEEEEEC---CCHHHHHHHHHHC
T ss_conf 6678877757998368999962387678888699989999646310001145567784899979---9436510344411
Q ss_pred ------HHHHC-CCCEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf ------99957-995586368874004489999999999
Q gi|254781160|r 207 ------TLHSL-PFVTPLSLGPRILRSDTAAVAAMALVQ 238 (245)
Q Consensus 207 ------~l~~~-~~~~~vsLG~~ILR~ETA~i~als~~~ 238 (245)
.|... ++ +-+-|.+..|+|-|...+||+++
T Consensus 247 ~~~~~~~fD~~lN~--~P~Qgs~tIRtEEAv~itLa~Ln 283 (283)
T pfam02598 247 DQGPKELFDGYLNT--PPNQGSRTIRTEEAVLIALSILN 283 (283)
T ss_pred CCCCHHHCCEEEEC--CCCCCCCCEEHHHHHHHHHHHCC
T ss_conf 35625437878976--89988761367889999886119
No 12
>COG1756 Mra1 Uncharacterized conserved protein [Function unknown]
Probab=79.02 E-value=5.6 Score=20.50 Aligned_cols=83 Identities=17% Similarity=0.205 Sum_probs=48.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEEC--CCCCCCHHHHHHHHHCCCCEEEECCCCCCCHH
Q ss_conf 0000112333223332126300012110222100367883599988--88888889999999579955863688740044
Q gi|254781160|r 150 TTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIG--PEGGYHSEEKETLHSLPFVTPLSLGPRILRSD 227 (245)
Q Consensus 150 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IG--PEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~E 227 (245)
.++.++++..+ ...++|++. .....+.+........ ++++|| |+|.|+.+-.... ..+|+|+-=|-+.
T Consensus 137 ~~l~d~l~~~~-~~~ill~e~-G~~~~p~~~~~~l~~~--i~v~iG~fp~Gdf~~~~~~~~------~~~si~~~pL~a~ 206 (223)
T COG1756 137 NPLTDLLPENN-KVTILLHEK-GELIPPKELISLLLKG--IAVIIGGFPHGDFREETEFVA------EKYSIYDEPLSAW 206 (223)
T ss_pred CCHHHHCCCCC-CEEEEECCC-CCCCCHHHHHHHHCCC--CEEEEECCCCCCCHHHHHHHH------HEEEECCCCCCHH
T ss_conf 73888506347-638998578-8826889998640248--559995167773024443110------1355158876499
Q ss_pred HHHHHHHHHHHHHHC
Q ss_conf 899999999999847
Q gi|254781160|r 228 TAAVAAMALVQAICG 242 (245)
Q Consensus 228 TA~i~als~~~~~~g 242 (245)
|++--.+......+|
T Consensus 207 ~v~~ki~~~~E~~~g 221 (223)
T COG1756 207 SVCSKIVYAYERALG 221 (223)
T ss_pred HHHHHHHHHHHHHHC
T ss_conf 999999999999865
No 13
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=78.29 E-value=3.3 Score=21.98 Aligned_cols=51 Identities=24% Similarity=0.228 Sum_probs=35.2
Q ss_pred EECHHH-HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC-CCCEEEEEEEE
Q ss_conf 987798-7599870357898889999779987987530235-55238997541
Q gi|254781160|r 23 KASGDQ-YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG-KSIRFKVEYQS 73 (245)
Q Consensus 23 ~L~~~~-~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~-k~~~~~i~~~~ 73 (245)
.|+.+. ..|=++-++++.||+|.|.-|+..--.+.|..++ ++..+.++...
T Consensus 31 ~LSkeLr~ky~~Rs~~IrkgD~V~V~rG~~kG~~GkV~~V~~k~~~V~VEgv~ 83 (119)
T PRK01191 31 PLSKELREKYGIRSLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRYRIYVEGVT 83 (119)
T ss_pred CCCHHHHHHHCCCCCCEECCCEEEEEECCCCCCCCEEEEEECCCCEEEEEEEE
T ss_conf 47988999848874435469999995527789623189997368899994369
No 14
>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA; InterPro: IPR011917 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes .; GO: 0005524 ATP binding, 0006869 lipid transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=75.68 E-value=1.4 Score=24.51 Aligned_cols=40 Identities=23% Similarity=0.300 Sum_probs=32.7
Q ss_pred CCEEEECCCCCCCCEEEECHHH-HHHHHHHCCCC---CCCEEEEEECC
Q ss_conf 8777408544788889987798-75998703578---98889999779
Q gi|254781160|r 7 LKRLFVDFPLCIKTQGKASGDQ-YHYLAHVLRMK---EGDNILLFNGK 50 (245)
Q Consensus 7 m~R~f~~~~l~~~~~i~L~~~~-~hHl~kVlRlk---~Gd~i~i~dg~ 50 (245)
+||||-++ .+.|.|||.+ .||..+-||-+ +++.|.+||+.
T Consensus 408 lPRFy~p~----~G~IllDG~~l~d~~L~~LR~q~alVsQ~V~LFdDT 451 (603)
T TIGR02203 408 LPRFYEPD----SGQILLDGVDLQDYTLADLRRQVALVSQDVVLFDDT 451 (603)
T ss_pred CCCCCCCC----CCCEEECCCHHHHCCHHHHHHHHHHHCCCEEECCCC
T ss_conf 23660458----885652784044302663562300021523720532
No 15
>PRK00103 SPOUT methyltransferase superfamily protein; Provisional
Probab=74.90 E-value=6.4 Score=20.15 Aligned_cols=75 Identities=16% Similarity=0.096 Sum_probs=46.4
Q ss_pred CCCCCCCCCCCCCHHCCCCCHHH---HHCC-CCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHH
Q ss_conf 33223332126300012110222---1003-6788359998888888889999999579955863688740044899999
Q gi|254781160|r 158 NWDHNCQIVFADETCGSENSLEK---LHAI-AHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAA 233 (245)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i~a 233 (245)
..+..+.+++.|+.....++.+- +... ...+.+.++||.--||+++=.+. +. ..+|||+-++--+-|-+++
T Consensus 63 ~~~~~~~~I~LDe~Gk~~sS~~fa~~l~~~~~~g~~i~FiIGGa~G~~~~~~~~---a~--~~lSlS~mTfpH~lar~il 137 (156)
T PRK00103 63 AIPKGARVVALDIRGKPWTSEQFAKELERWRLDGRDVTFVIGGPEGLSPAVKKR---AD--QSWSLSKLTLPHQLVRLVL 137 (156)
T ss_pred HCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHH---HH--HEEEECCCCCCHHHHHHHH
T ss_conf 479999899991799805769999999999863996699997888769899974---32--2887136766289999999
Q ss_pred HHHH
Q ss_conf 9999
Q gi|254781160|r 234 MALV 237 (245)
Q Consensus 234 ls~~ 237 (245)
+=++
T Consensus 138 ~EQi 141 (156)
T PRK00103 138 AEQL 141 (156)
T ss_pred HHHH
T ss_conf 9999
No 16
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=74.61 E-value=0.26 Score=29.14 Aligned_cols=140 Identities=11% Similarity=0.099 Sum_probs=74.5
Q ss_pred CEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 13541344541156777544445665655554202201122122335788999975123443433200000011233322
Q gi|254781160|r 82 VQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDH 161 (245)
Q Consensus 82 i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~ 161 (245)
+-++=.+-.+..+-.|++-|.-.||+.|+ +..+++..-... .++.| +|-.+...+....++.++++.+..
T Consensus 97 il~LD~I~DP~NlGaIiRsA~afGv~~vi-l~~~~~~~~~~~------v~k~S---~Ga~~~~pi~~~~nl~~~l~~lk~ 166 (244)
T PRK11181 97 LLILDGVTDPHNLGACLRSADAAGVHAVI-VPKDRSAQLTAT------AKKVA---CGAAETVPLIRVTNLARTMRMLQE 166 (244)
T ss_pred EEEECCCCCCCHHHHHHHHHHHCCCCEEE-ECCCCCCCCCHH------HHHHH---HCHHHCCCEEEECCHHHHHHHHHH
T ss_conf 99981887873899999999981998999-789977854258------88874---142321881695899999999886
Q ss_pred CCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCCEEEECCCCCCCHHH-HHHHHHHHHHH
Q ss_conf 3332126300012110222100367883599988888-888899999995799558636887400448-99999999999
Q gi|254781160|r 162 NCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG-GYHSEEKETLHSLPFVTPLSLGPRILRSDT-AAVAAMALVQA 239 (245)
Q Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~~~~~~~vsLG~~ILR~ET-A~i~als~~~~ 239 (245)
....++..+... . ..+.+.....++.+++|-|| |.++.= .+.+...-.+-+...+ |. -+-+|.+++.|
T Consensus 167 ~g~~i~g~~~~~-~---~~~~~~~~~~~~alvlGsE~~Gl~~~~---~~~~d~~v~Ip~~g~~---~SLNVsvAa~I~ly 236 (244)
T PRK11181 167 KNVWIVGTAGEA-D---HTLYQSKLTGPLALVMGAEGEGMRRLT---REHCDELISIPMAGSV---SSLNVSVATGICLF 236 (244)
T ss_pred CCEEEEEECCCC-C---CCCCHHCCCCCEEEEECCCCCCCCHHH---HHHCCEEEEECCCCCC---CCHHHHHHHHHHHH
T ss_conf 596999524666-7---664101057876999877766658999---9759989980799998---55879999999999
Q ss_pred HH
Q ss_conf 84
Q gi|254781160|r 240 IC 241 (245)
Q Consensus 240 ~~ 241 (245)
.+
T Consensus 237 E~ 238 (244)
T PRK11181 237 EA 238 (244)
T ss_pred HH
T ss_conf 99
No 17
>PRK10864 putative methyltransferase; Provisional
Probab=74.09 E-value=7.6 Score=19.64 Aligned_cols=141 Identities=9% Similarity=0.063 Sum_probs=74.4
Q ss_pred CCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 43135413445411567775444456656555542022011221223357889999751234434332000000112333
Q gi|254781160|r 80 SDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNW 159 (245)
Q Consensus 80 ~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~ 159 (245)
+.+-++=.+-.+..+--||+-|.-.||+.|+. .+++... .. ..++.|+ .+-.++|-+ ...++..+++.+
T Consensus 200 ~~lL~LDgV~DP~NlGAIiRSAaafGv~gVIl--~~~~~~~---s~---~avr~Sa--Ga~e~vpv~-~v~nl~~aL~~L 268 (348)
T PRK10864 200 DCVLALEDVGNPHNLGGIMRSCAHFGVKGVVV--QDAALLE---SG---AAIRTAE--GGAEHVQPI-TGDSIVDVLDDF 268 (348)
T ss_pred CEEEEECCCCCCCHHHHHHHHHHHHCCCEEEE--CCCCCCC---CH---HHHHHHC--CHHCCCCEE-EECCHHHHHHHH
T ss_conf 85999789779715889999999858988997--9998774---37---8896633--222006359-977899999999
Q ss_pred CCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCCEEEECCCCCCCHHH-HHHHHHHHH
Q ss_conf 223332126300012110222100367883599988888-888899999995799558636887400448-999999999
Q gi|254781160|r 160 DHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG-GYHSEEKETLHSLPFVTPLSLGPRILRSDT-AAVAAMALV 237 (245)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~~~~~~~vsLG~~ILR~ET-A~i~als~~ 237 (245)
......++.-..... ..+......+++.|++|.|| |.|+.-.+. +.+...+.+-.. +|. =+-+|.+++
T Consensus 269 k~aG~~Ivg~s~~~~----~~l~~~~l~~~~vLVlGsEg~GLs~~v~~~---cD~~V~IPm~g~---veSLNVSVAagIl 338 (348)
T PRK10864 269 RQAGYTIVTTSSHKG----KPLFKAELPAKMVLVLGQEYDGLSDAARSP---GDLSVKIDGTGN---VESLNVSVATGVL 338 (348)
T ss_pred HHCCCEEEEECCCCC----CCHHHCCCCCCEEEEECCCCCCCCHHHHHH---CCEEEECCCCCC---CCCHHHHHHHHHH
T ss_conf 988968998547788----647563678988999899885506999975---888998279999---8578899999999
Q ss_pred HHHH
Q ss_conf 9984
Q gi|254781160|r 238 QAIC 241 (245)
Q Consensus 238 ~~~~ 241 (245)
.|.+
T Consensus 339 LyE~ 342 (348)
T PRK10864 339 LAEW 342 (348)
T ss_pred HHHH
T ss_conf 9999
No 18
>PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional
Probab=73.92 E-value=2.8 Score=22.45 Aligned_cols=118 Identities=14% Similarity=0.184 Sum_probs=64.6
Q ss_pred CCCCCEEEEC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 5443135413-445411567775444456656555542022011221223357889999751234434332000000112
Q gi|254781160|r 78 KQSDVQYIFS-PIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLL 156 (245)
Q Consensus 78 ~~~~i~l~~~-~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l 156 (245)
+.+.++|+.- +-|+..+--|++-|--.||+.++.+......+. ..+ +-+.-..|+|. ....++.+.+
T Consensus 16 Rq~dL~vvLD~V~dP~NlGAIiRTadA~Gv~~V~~v~~~~~~~~------~~~-----ta~Gs~~wv~v-~~~~~i~~~i 83 (229)
T PRK11081 16 RQPDLTVCLEQVHKPHNVSAIIRTADAVGVHEVHAVWPGSRMRT------MGS-----TAAGSNSWVQV-KTHRTIGDAV 83 (229)
T ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCCCCHHH------HHH-----HHHHHHCEEEE-EEECCHHHHH
T ss_conf 58986999768899850999999999838974689678752011------114-----43034400455-7847899999
Q ss_pred CCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCC-CCCHHHHHHHHH
Q ss_conf 333223332126300012110222100367883599988888-888899999995
Q gi|254781160|r 157 KNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG-GYHSEEKETLHS 210 (245)
Q Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~ 210 (245)
..+.....-++..+.. ..+.. +.+..-.++.+|++|.|+ |.|++=.+....
T Consensus 84 ~~Lk~~G~~I~at~l~--~~avd-~~~~d~t~ptalVlGnE~~GiS~~~~~~aD~ 135 (229)
T PRK11081 84 AHLKAQGMQILATHLS--DKAVD-FREIDYTRPTAILMGQEKTGISQEALALADQ 135 (229)
T ss_pred HHHHHCCCEEEEEECC--CCCCC-HHHHCCCCCEEEEECCCCCCCCHHHHHHCCC
T ss_conf 9999749989999368--88640-7670456876999858777759999982895
No 19
>KOG3079 consensus
Probab=73.36 E-value=4.3 Score=21.28 Aligned_cols=79 Identities=8% Similarity=0.088 Sum_probs=40.1
Q ss_pred CCCCCEEEECCC---CCCHHHHHHHHH--HHHHHHHHHHHHHHC--CCHH-----HH------HHHHHHHHHHHHHHHHC
Q ss_conf 544313541344---541156777544--445665655554202--2011-----22------12233578899997512
Q gi|254781160|r 78 KQSDVQYIFSPI---KTNRLDYMIQKS--VEMGMGAIRPVITRY--TQNT-----HY------NMDRVRTYTISAAEQCD 139 (245)
Q Consensus 78 ~~~~i~l~~~~~---k~~~~~~ilqk~--tELGV~~I~p~~~~r--s~~~-----~~------k~eR~~~ii~eA~eQsg 139 (245)
..++|..+++-| |+..++.|++|- |-|.+..+---..++ |+.- .. -.+=....+.+|+.||+
T Consensus 6 ~~~~IifVlGGPGsgKgTqC~kiv~ky~ftHlSaGdLLR~E~~~~gse~g~~I~~~i~~G~iVP~ei~~~LL~~am~~~~ 85 (195)
T KOG3079 6 DKPPIIFVLGGPGSGKGTQCEKIVEKYGFTHLSAGDLLRAEIASAGSERGALIKEIIKNGDLVPVEITLSLLEEAMRSSG 85 (195)
T ss_pred CCCCEEEEECCCCCCCCHHHHHHHHHCCCEEECHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 57988999768988822699999997695463287999998805467678999999986996748999999999999657
Q ss_pred C-CCCCCCCCCCCCCCCC
Q ss_conf 3-4434332000000112
Q gi|254781160|r 140 I-LTLPFIYPPTTLEFLL 156 (245)
Q Consensus 140 r-~~lP~i~~~~~l~~~l 156 (245)
. .++-.=-.|.+.+++.
T Consensus 86 ~~~~fLIDGyPR~~~q~~ 103 (195)
T KOG3079 86 DSNGFLIDGYPRNVDQLV 103 (195)
T ss_pred CCCEEEECCCCCCHHHHH
T ss_conf 788388658988768899
No 20
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=67.49 E-value=9.3 Score=19.08 Aligned_cols=69 Identities=10% Similarity=0.024 Sum_probs=42.6
Q ss_pred CCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCC
Q ss_conf 888899877987599870357898889999779987987530235552389975413555544313541344
Q gi|254781160|r 18 IKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPI 89 (245)
Q Consensus 18 ~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~~~~~i~~~~~~~~~~~~i~l~~~~~ 89 (245)
.+..+.|-|....|..+.-+++.||.|.+.+. ++.|..+|.+..- .-.-......+.+...++|+=|.|
T Consensus 42 ~~GN~viaGH~~~~F~~L~~l~~GD~I~l~~~-~~~y~Y~V~~~~v--v~p~d~~~~~~~~~~~LTLiTC~P 110 (127)
T cd05828 42 EGGNIVIAGHRDTHFRFLGELEPGDIITLQTL-GGTYTYRVTSTRI--VDADDTSVLAPSDDPTLTLITCYP 110 (127)
T ss_pred CCCCEEEEEECCCCCCCHHHCCCCCEEEEEEC-CEEEEEEEEEEEE--ECCCCCEECCCCCCCEEEEECCCC
T ss_conf 88869999506887767455747999999978-8399999977999--998771872579998799993688
No 21
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=65.13 E-value=6.9 Score=19.90 Aligned_cols=52 Identities=12% Similarity=0.151 Sum_probs=33.9
Q ss_pred EECHHH-HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC-CCCEEEEEEEEC
Q ss_conf 987798-7599870357898889999779987987530235-552389975413
Q gi|254781160|r 23 KASGDQ-YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG-KSIRFKVEYQSR 74 (245)
Q Consensus 23 ~L~~~~-~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~-k~~~~~i~~~~~ 74 (245)
.|+.+. ..|=++-++++.||+|.|.-|.-.--.++|+.++ ++..+.++....
T Consensus 31 ~LSkELr~ky~~Rs~pIRkgDeV~V~RG~fkG~eGKV~~V~~kk~~I~VEgvt~ 84 (143)
T PTZ00194 31 PLSKELRAKYNVRAMPVRKDDEVIVKRGAFKGREGKVTACYRLKWVIHIDKVNR 84 (143)
T ss_pred CCCHHHHHHHCCCCCCCCCCCEEEEEECCCCCCCCEEEEEEEEEEEEEEEEEEE
T ss_conf 269999998496310011599999985553687765999995000999951789
No 22
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only]
Probab=61.92 E-value=3.6 Score=21.77 Aligned_cols=100 Identities=17% Similarity=0.139 Sum_probs=51.2
Q ss_pred HHHHHHHCCCCCCCCC--------CCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHH
Q ss_conf 9999751234434332--------00000011233322333212630001211022210036788359998888888889
Q gi|254781160|r 132 ISAAEQCDILTLPFIY--------PPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSE 203 (245)
Q Consensus 132 ~eA~eQsgr~~lP~i~--------~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~ 203 (245)
..++-|||-+...++. ....++++++..+.+..++.. .....+..++....+.. .-..++-|-|+||+..
T Consensus 37 ~g~AAQsGIp~~~kla~k~G~~vlvf~dL~DAlevL~P~v~ll~~-~~~~~ek~~dp~e~ie~-~vliVf~ga~~gl~k~ 114 (147)
T COG4080 37 KGSAAQSGIPEVLKLAFKLGKPVLVFPDLDDALEVLRPDVTLLVG-SASEGEKKLDPNEKIEG-RVLIVFSGAEPGLTKR 114 (147)
T ss_pred CCHHHHHCCHHHHHHHHHHCCCEEEEHHHHHHHHHCCCCEEEEEC-CCCCCCCCCCCCCCCCC-EEEEEEECCCCCCCHH
T ss_conf 547666356889999998399479852277899745975699814-76443234794312463-3799992688775866
Q ss_pred HHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf 999999579955863688740044899999999999847
Q gi|254781160|r 204 EKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICG 242 (245)
Q Consensus 204 E~~~l~~~~~~~~vsLG~~ILR~ETA~i~als~~~~~~g 242 (245)
|.+. |-.. + -+-..+--++.+++++-|.++
T Consensus 115 El~l----g~~~--~---y~ve~~VG~~g~lAi~Lyell 144 (147)
T COG4080 115 ELEL----GADL--R---YIVEADVGELGALAIFLYELL 144 (147)
T ss_pred HCCC----CCCE--E---EEEECCCHHHHHHHHHHHHHH
T ss_conf 6056----7727--9---998446417888999999987
No 23
>CHL00194 ycf39 Ycf39; Provisional
Probab=61.88 E-value=12 Score=18.36 Aligned_cols=112 Identities=13% Similarity=0.121 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCC
Q ss_conf 777544445665655554202201-12212233578899997512344343320000001123332----2333212630
Q gi|254781160|r 96 YMIQKSVEMGMGAIRPVITRYTQN-THYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWD----HNCQIVFADE 170 (245)
Q Consensus 96 ~ilqk~tELGV~~I~p~~~~rs~~-~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~----~~~~~~~~~~ 170 (245)
.+++-|-+-||.+++.+..-.... .....-+++.-.....++||-+|. .+.+..-+..++.++. ....++....
T Consensus 92 ~li~AAk~aGVkr~V~lS~lga~~~~~~p~~~~K~~~E~~L~~Sgl~~T-IlRPs~F~q~l~~~~a~pi~~~~~v~~~~~ 170 (319)
T CHL00194 92 ALIEAAKAAKVKRFIFFSILNAEQYPQVPLMKIKSDIEEKLKQSGINYT-IFRLAGFFQGLISQYAIPILDSQTIWITGE 170 (319)
T ss_pred HHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHHHHHHCCCCEEECCC
T ss_conf 9999999849988999613566668875677879999999986799859-984739999889987677630785776699
Q ss_pred H---------HCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHH
Q ss_conf 0---------01211022210036788359998888888889999999
Q gi|254781160|r 171 T---------CGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLH 209 (245)
Q Consensus 171 ~---------~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~ 209 (245)
. .-+......+........+.-+.||| -||.+|+-.+-
T Consensus 171 ~~~ia~I~~~DVA~~~a~aL~~~~~~gk~y~L~GP~-a~T~~EIa~l~ 217 (319)
T CHL00194 171 STPIAYIDTQDAAKFALKSLSLPETKNKTFPLVGPK-SWNSSEIISLC 217 (319)
T ss_pred CCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEECCC-CCCHHHHHHHH
T ss_conf 875288779999999999958977589899954986-38999999999
No 24
>pfam09895 DUF2122 RecB-family nuclease (DUF2122). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=60.34 E-value=11 Score=18.66 Aligned_cols=77 Identities=17% Similarity=0.225 Sum_probs=43.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCC-EEEEECCCCCCCHHHHHHHHHCCC-CEEEECCCCCCCHH
Q ss_conf 0000112333223332126300012110222100367883-599988888888899999995799-55863688740044
Q gi|254781160|r 150 TTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPN-VAILIGPEGGYHSEEKETLHSLPF-VTPLSLGPRILRSD 227 (245)
Q Consensus 150 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-i~i~IGPEGGfs~~E~~~l~~~~~-~~~vsLG~~ILR~E 227 (245)
..++++++.+..+..+++......... + ..+...+ ..++-|-|.|||..|.+. |- +.... +..+
T Consensus 26 ~dl~DAiEvL~P~~v~~i~~~~~~~~~--~---~l~~~~rvllvf~G~e~gfsk~El~~----g~~v~~~~-----v~~~ 91 (105)
T pfam09895 26 PDLKDAIELLKPDVVYLLSRAAEGIKK--E---VLKVEGRVLLVFSGAEPGFSKIELEL----GEAVYIKG-----VESD 91 (105)
T ss_pred CCHHHHHHHHCCCEEEEECCCCCCCCH--H---HHHCCCCEEEEECCCCCCCCHHHHCC----CCEEEEEC-----CCCC
T ss_conf 877889987298779997576656203--4---55305838999818988979656148----84478603-----6556
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 8999999999998
Q gi|254781160|r 228 TAAVAAMALVQAI 240 (245)
Q Consensus 228 TA~i~als~~~~~ 240 (245)
.-++..++++-|.
T Consensus 92 iG~ig~~Ai~Ly~ 104 (105)
T pfam09895 92 VGPIGALAIILYL 104 (105)
T ss_pred CCCHHHHHHHHHH
T ss_conf 6628899999950
No 25
>cd05827 Sortase_C_3 Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Sortase C cleaves surface proteins at the LPXTG motif between Thr and Gly and catalyzes the formation of an amide bond between the carboxyl group of Thr and the amino group of cell-wall cross bridges. It is a narrow-range enzyme required for anchoring a few substrates. It plays a role in Streptococcus pneumoniae pathogenesis and is required in the assembly of pili on the surface of Corynebacterium diphtheriae. Sortase C is
Probab=57.97 E-value=16 Score=17.60 Aligned_cols=69 Identities=9% Similarity=0.098 Sum_probs=41.2
Q ss_pred CCCEEEECHHH----HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC---CCCEEEEEEEECCCCCCCCCEEEECCCC
Q ss_conf 88889987798----7599870357898889999779987987530235---5523899754135555443135413445
Q gi|254781160|r 18 IKTQGKASGDQ----YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG---KSIRFKVEYQSRSQTKQSDVQYIFSPIK 90 (245)
Q Consensus 18 ~~~~i~L~~~~----~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~---k~~~~~i~~~~~~~~~~~~i~l~~~~~k 90 (245)
.+....|.+.. ..|..+.-+++.||+|.+.+. ++.|..+|.+.. .+ ... .......+..++|+=|.|.
T Consensus 43 ~g~n~viaGH~~~~~~~~F~~L~~l~~GD~I~l~~~-~~~y~Y~V~~~~iV~p~-d~~---~l~~~~~~~~LTLiTC~p~ 117 (131)
T cd05827 43 KGTHSVITGHRGLPNAKLFTDLDKLKKGDKFYIHVL-GETLAYQVDQIEVVLPD-DTD---KLKIVPGKDLVTLLTCTPY 117 (131)
T ss_pred CCCEEEEECCCCCCCCCCCCHHHCCCCCCEEEEEEC-CEEEEEEEEEEEEECCC-CCE---EEEECCCCCEEEEEEECCC
T ss_conf 767899980799999951010343878999999979-90999999889999976-225---8601599878999977799
Q ss_pred C
Q ss_conf 4
Q gi|254781160|r 91 T 91 (245)
Q Consensus 91 ~ 91 (245)
+
T Consensus 118 ~ 118 (131)
T cd05827 118 G 118 (131)
T ss_pred C
T ss_conf 9
No 26
>PRK11572 copper homeostasis protein CutC; Provisional
Probab=57.09 E-value=8.3 Score=19.40 Aligned_cols=131 Identities=13% Similarity=0.098 Sum_probs=63.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH---HCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 41156777544445665655554202201122122335788999975---123443433200000011233322333212
Q gi|254781160|r 91 TNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQ---CDILTLPFIYPPTTLEFLLKNWDHNCQIVF 167 (245)
Q Consensus 91 ~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQ---sgr~~lP~i~~~~~l~~~l~~~~~~~~~~~ 167 (245)
-+.|..=++.+-++|++.|.+-.-. ..-..+.++.++++..|--. -+|.+=-.-++...++++++. ..+.++-
T Consensus 72 ~~~M~~dI~~~~~~Ga~GvV~G~L~--~dg~iD~~~~~~Li~~a~~l~vTFHRAfD~~~dp~~ale~Li~l--G~~rILT 147 (248)
T PRK11572 72 FAAMLEDIRTVRELGFPGLVTGVLD--VDGHVDMPRMEKIMAAAGPLAVTFHRAFDMCANPLNALKNLAEL--GVARILT 147 (248)
T ss_pred HHHHHHHHHHHHHCCCCEEEEEEEC--CCCCCCHHHHHHHHHHHCCCEEEEECHHHCCCCHHHHHHHHHHC--CCCEEEC
T ss_conf 9999999999998699967996688--99984999999999974898079862022149999999999975--9998988
Q ss_pred CCCHHCCCCCHHHHHCCCC-CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHH
Q ss_conf 6300012110222100367-883599988888888899999995799558636887400448
Q gi|254781160|r 168 ADETCGSENSLEKLHAIAH-IPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDT 228 (245)
Q Consensus 168 ~~~~~~~~~~~~~~~~~~~-~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ET 228 (245)
.-........++.+..... .... + |=|-||.+++-+..|.+.|+ +.+++..+.-|..+
T Consensus 148 SG~~~~A~~G~~~L~~L~~~a~~~-i-Im~GgGV~~~Ni~~~~~tG~-~eiH~Sak~~~~s~ 206 (248)
T PRK11572 148 SGQQSDAEQGLSLIMELIAQGDAP-I-IMAGAGVRAENLQKFLDAGV-REVHSSAGAWQPSP 206 (248)
T ss_pred CCCCCCHHHHHHHHHHHHHHCCCC-E-EEECCCCCHHHHHHHHHCCC-CEEEECCCCCCCCC
T ss_conf 999787778899999999844996-8-98789989999999997597-78973578644787
No 27
>TIGR00513 accA acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; InterPro: IPR001095 This entry contains the alpha subunit the acetyl coenzyme A carboxylase complex (). It catalyzes the first step in the synthesis of long-chain fatty acids which involves the carboxylation of acetyl-CoA to malonyl-CoA. The acetyl-CoA carboxylase complex () is a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps: Biotin carrier protein + ATP + HCO_3^- -> Carboxybiotin carrier protein + ADP + P_i Carboxybiotin carrier protein + Acetyl-CoA -> Malonyl-CoA + Biotin carrier protein ; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=56.67 E-value=13 Score=18.07 Aligned_cols=109 Identities=23% Similarity=0.356 Sum_probs=58.0
Q ss_pred CCEEEECCCCCCHHHHHHHHHHHH-----------------HHHHHH--HHHH---HCCCHHHHH---------HHHHHH
Q ss_conf 313541344541156777544445-----------------665655--5542---022011221---------223357
Q gi|254781160|r 81 DVQYIFSPIKTNRLDYMIQKSVEM-----------------GMGAIR--PVIT---RYTQNTHYN---------MDRVRT 129 (245)
Q Consensus 81 ~i~l~~~~~k~~~~~~ilqk~tEL-----------------GV~~I~--p~~~---~rs~~~~~k---------~eR~~~ 129 (245)
.+.|+=-+-||..||+|=--.+|- ||.+|- |+.- ++....+-| .+-+|+
T Consensus 68 ~~qlARhP~RP~tLDYI~~i~~df~E~~GDRay~DD~AiVGG~Arldg~PV~viGhqKGr~tKek~~RNFGMP~P~GYRK 147 (329)
T TIGR00513 68 RLQLARHPDRPYTLDYIELIFDDFFELHGDRAYADDKAIVGGVARLDGRPVVVIGHQKGRDTKEKLLRNFGMPAPEGYRK 147 (329)
T ss_pred HHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEEECCCCEEEEECCCCCCCHHHCCCCCCCCCCCCHHH
T ss_conf 99973088889768899998612200036778897822343211337812488621357540342112579887960479
Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCC--CCCCCEEEEECCCCC
Q ss_conf 8899997512344343320000001123332233321263000121102221003--678835999888888
Q gi|254781160|r 130 YTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAI--AHIPNVAILIGPEGG 199 (245)
Q Consensus 130 ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i~i~IGPEGG 199 (245)
+.-=++|+.|.-+|.|.+..|= -.++. +=+++..-++.-..++... -..+.|+++|| |||
T Consensus 148 -ALrLm~~AerF~~PIi~fiDT~----GAYPG----igAEerGQsEAIA~NL~Ema~L~VPvic~vIG-EGG 209 (329)
T TIGR00513 148 -ALRLMKMAERFNLPIITFIDTP----GAYPG----IGAEERGQSEAIAKNLREMARLKVPVICTVIG-EGG 209 (329)
T ss_pred -HHHHHHHHHHCCCCEEEEECCC----CCCCC----CHHHHHCCHHHHHHHHHHHHCCCCCEEEEEEC-CCC
T ss_conf -9999987776179858865388----88756----20445052789999989971099887999852-686
No 28
>cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra
Probab=56.03 E-value=12 Score=18.30 Aligned_cols=68 Identities=16% Similarity=0.196 Sum_probs=40.1
Q ss_pred CEEEECHHHHHH----HHHHCCCCCCCEEEEEECCCCEEEEEEECCC---CCCEEEEEEEECCCCCCCCCEEEECCCCCC
Q ss_conf 889987798759----9870357898889999779987987530235---552389975413555544313541344541
Q gi|254781160|r 20 TQGKASGDQYHY----LAHVLRMKEGDNILLFNGKDGEWLSKISYVG---KSIRFKVEYQSRSQTKQSDVQYIFSPIKTN 92 (245)
Q Consensus 20 ~~i~L~~~~~hH----l~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~---k~~~~~i~~~~~~~~~~~~i~l~~~~~k~~ 92 (245)
..+.|.|....| ..+.-++++||.|.+.+.. +.|..+|.+.. .+ ...+ .......+.++|+=|.|.+.
T Consensus 42 gN~viaGH~~~~~~~~F~~L~~l~~GD~I~v~~~~-~~~~Y~V~~~~iV~p~-d~~~---l~~~~~~~~lTLiTC~P~~~ 116 (127)
T cd06165 42 GNYALAGHNMRNKGVLFSPLYKVKVGDKIYLTDKD-NVYEYKVTSKKIVDPT-RVDV---IDDVPGKKLITLITCDDATD 116 (127)
T ss_pred CCEEEEECCCCCCCCCCCCHHHCCCCCEEEEEECC-CEEEEEEEEEEEECCC-CCEE---ECCCCCCCEEEEEEECCCCC
T ss_conf 86999936588676546676568999999999899-3999999489999988-7779---63169987899996589999
No 29
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=55.78 E-value=17 Score=17.36 Aligned_cols=74 Identities=11% Similarity=0.073 Sum_probs=43.7
Q ss_pred CCCEEEECHHHHHH---HHHHCCCCCCCEEEEEECCCCEEEEEEECC---CCCCEEEEE---EEECCCCCCCCCEEEECC
Q ss_conf 88889987798759---987035789888999977998798753023---555238997---541355554431354134
Q gi|254781160|r 18 IKTQGKASGDQYHY---LAHVLRMKEGDNILLFNGKDGEWLSKISYV---GKSIRFKVE---YQSRSQTKQSDVQYIFSP 88 (245)
Q Consensus 18 ~~~~i~L~~~~~hH---l~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~---~k~~~~~i~---~~~~~~~~~~~i~l~~~~ 88 (245)
.+..+.|.|....| ..+--++++||.|.+.++. +.|..+|+.. +..-.-.+. ...........++|+=|.
T Consensus 43 ~~Gn~viaGHr~~~~~~F~~L~~l~~GD~I~v~~~~-~~~~Y~V~~~~iV~p~d~~vl~p~~~~~~~~~~~~~lTLiTC~ 121 (137)
T cd05830 43 EVGNFAVAGHRTTYGAPFNDLDKLRPGDKIVVETAD-GWYTYVVRSSEIVLPTDVEVIAPVPGQPGAEPTDRYLTLTTCH 121 (137)
T ss_pred CCCEEEEEECCCCCCCCCCCHHCCCCCCEEEEEECC-EEEEEEEEEEEEECCCCCEEECCCCCCCCCCCCCCEEEEEEEC
T ss_conf 997199997228977556013538999999999999-8999999749998976366873367745658998889999257
Q ss_pred CCCC
Q ss_conf 4541
Q gi|254781160|r 89 IKTN 92 (245)
Q Consensus 89 ~k~~ 92 (245)
|.+.
T Consensus 122 P~~~ 125 (137)
T cd05830 122 PKFS 125 (137)
T ss_pred CCCC
T ss_conf 9999
No 30
>TIGR01080 rplX_A_E ribosomal protein L24; InterPro: IPR005756 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein L24 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. This entry represents the archaeal and eukaryotic branch of these proteins, known as the L26 family.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=52.94 E-value=19 Score=17.07 Aligned_cols=70 Identities=20% Similarity=0.293 Sum_probs=46.0
Q ss_pred CCCEEEECCCCCCCC---EEEECHHH-HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC-CCCEEEEEEEECC
Q ss_conf 787774085447888---89987798-7599870357898889999779987987530235-5523899754135
Q gi|254781160|r 6 HLKRLFVDFPLCIKT---QGKASGDQ-YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG-KSIRFKVEYQSRS 75 (245)
Q Consensus 6 ~m~R~f~~~~l~~~~---~i~L~~~~-~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~-k~~~~~i~~~~~~ 75 (245)
+-+++++..|+..-. +-.|+.+. ..|=.+.|+++.||.|.|.=|+=.-.+|+|..++ +...+.++..+..
T Consensus 6 K~Rk~~f~Apl~~Rr~lmsA~LSkeLr~~y~~r~lP~RkgD~V~i~RG~fkG~EGkv~~Vd~kr~~i~ve~~t~~ 80 (116)
T TIGR01080 6 KQRKALFTAPLHVRRKLMSAPLSKELREKYGVRALPVRKGDKVRIVRGDFKGHEGKVLEVDLKRYRIYVEGVTKE 80 (116)
T ss_pred CCCCEEEECCHHHHHHHHCCCCCHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEECCCCCC
T ss_conf 325135607722303222230246889872865376123987899746625875516887303888988131010
No 31
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=50.68 E-value=9.2 Score=19.10 Aligned_cols=17 Identities=18% Similarity=0.413 Sum_probs=7.6
Q ss_pred CCHHHHHHHHHHHHHHH
Q ss_conf 41156777544445665
Q gi|254781160|r 91 TNRLDYMIQKSVEMGMG 107 (245)
Q Consensus 91 ~~~~~~ilqk~tELGV~ 107 (245)
..|+-.-+|++=++|-.
T Consensus 215 ~~RL~eSvEtaL~~~~G 231 (956)
T TIGR00630 215 RSRLAESVETALRLSEG 231 (956)
T ss_pred CCHHHHHHHHHHHCCCC
T ss_conf 21168999999850587
No 32
>PTZ00066 pyruvate kinase; Provisional
Probab=49.83 E-value=21 Score=16.76 Aligned_cols=72 Identities=18% Similarity=0.187 Sum_probs=37.1
Q ss_pred CCCCCCCEEEEEECCCCEEEEEEECCCCC-CEEEEEEE--ECC--CCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 35789888999977998798753023555-23899754--135--55544313541344541156777544445665655
Q gi|254781160|r 36 LRMKEGDNILLFNGKDGEWLSKISYVGKS-IRFKVEYQ--SRS--QTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIR 110 (245)
Q Consensus 36 lRlk~Gd~i~i~dg~g~~~~~~I~~~~k~-~~~~i~~~--~~~--~~~~~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~ 110 (245)
--+++||.|.+-|| ....+|.+++.+ +.+++..- ... .-.-|...+-++.+-..-.+.+++-+.+.||+-|.
T Consensus 152 ~~v~~Gd~IlidDG---~I~l~V~~v~~~~v~~~V~~gG~L~s~KgVnlP~~~l~lp~lTekD~~dil~fa~~~~vD~Ia 228 (513)
T PTZ00066 152 QSVKVGNIILIADG---SLSCEVLEVHDDHIVVKVLNSATIGERKNMNLPGVKVELPVIGEKDKNDILNFAIPMNCDFIA 228 (513)
T ss_pred HHCCCCCEEEEECC---EEEEEEEEECCCEEEEEEEECCEEECCCCEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEE
T ss_conf 56788988999799---799999982297799999748397478643358986675547636889999999875999999
No 33
>PRK04980 hypothetical protein; Provisional
Probab=49.80 E-value=19 Score=17.09 Aligned_cols=45 Identities=18% Similarity=0.214 Sum_probs=34.9
Q ss_pred EECCCCCCCCEEEE-CHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC
Q ss_conf 40854478888998-77987599870357898889999779987987530235
Q gi|254781160|r 11 FVDFPLCIKTQGKA-SGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG 62 (245)
Q Consensus 11 f~~~~l~~~~~i~L-~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~ 62 (245)
|-+..++...+|.+ |.+|+|+ ++|+.+.++.-..+.|.|.|...+
T Consensus 11 fe~dIlsG~KTITIRD~SEsh~-------~~G~~l~V~t~E~~~~fc~IeIls 56 (102)
T PRK04980 11 FEADILAGRKTITIRDESESHF-------KPGDVLRVGTFEDDRYFCTIEVLS 56 (102)
T ss_pred HHHHHHCCCCEEEECCCCCCCC-------CCCCEEEEEECCCCCEEEEEEEEE
T ss_conf 1678865984699525310456-------799889989835897899999999
No 34
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=48.29 E-value=14 Score=17.92 Aligned_cols=68 Identities=15% Similarity=0.171 Sum_probs=41.4
Q ss_pred CCEEEECHHHH----HHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC---CCCEEEEEEEECCCCCCCCCEEEECCCCC
Q ss_conf 88899877987----599870357898889999779987987530235---55238997541355554431354134454
Q gi|254781160|r 19 KTQGKASGDQY----HYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG---KSIRFKVEYQSRSQTKQSDVQYIFSPIKT 91 (245)
Q Consensus 19 ~~~i~L~~~~~----hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~---k~~~~~i~~~~~~~~~~~~i~l~~~~~k~ 91 (245)
+..+.|.+... .|..+.-++++||.|.+.++ ++.|..+|.+.. ..-. .....+...+.++|+=|.+.+
T Consensus 42 ~gN~vIaGH~~~~~~~~F~~L~~l~~GD~i~i~~~-~~~y~Y~V~~~~iv~p~d~----~~~~~~~~~~~LTLiTC~p~~ 116 (128)
T cd00004 42 NGNTVIAGHRGGDSGTVFSDLDNLKKGDKIYLTDG-GKTYVYKVTSILTVTPTDV----VVVNPPTGDPILTLITCTPPG 116 (128)
T ss_pred CCCEEEEEEECCCCCCCCCCHHHCCCCCEEEEEEC-CEEEEEEEEEEEEECCCCC----EEECCCCCCCEEEEEEECCCC
T ss_conf 96099999818998844365545768998999999-9899999988999898864----781146998679999878999
No 35
>TIGR02851 spore_V_T stage V sporulation protein T; InterPro: IPR014213 Members of this protein entry include the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB..
Probab=48.03 E-value=10 Score=18.77 Aligned_cols=28 Identities=32% Similarity=0.512 Sum_probs=19.5
Q ss_pred HHHHCCCCCCCEEEEEE-CCCCEEEEEEE
Q ss_conf 98703578988899997-79987987530
Q gi|254781160|r 32 LAHVLRMKEGDNILLFN-GKDGEWLSKIS 59 (245)
Q Consensus 32 l~kVlRlk~Gd~i~i~d-g~g~~~~~~I~ 59 (245)
+.|.||+++||-+.+|. -+|...+=+.+
T Consensus 21 IRRTLRIrEGDPLEIF~Dr~GevILKKYS 49 (184)
T TIGR02851 21 IRRTLRIREGDPLEIFVDREGEVILKKYS 49 (184)
T ss_pred CCCCCCCCCCCCCEEEEECCCCEEEEECC
T ss_conf 41101012599714888078978987107
No 36
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=47.56 E-value=23 Score=16.53 Aligned_cols=66 Identities=14% Similarity=0.105 Sum_probs=40.3
Q ss_pred HHHHCCCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCHHHHH
Q ss_conf 987035789888999977998798753023555238997541355554431354134454115677
Q gi|254781160|r 32 LAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYM 97 (245)
Q Consensus 32 l~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~~~~~i~~~~~~~~~~~~i~l~~~~~k~~~~~~i 97 (245)
|++-|+--.|+.|.|=--+|..|.+.+.+++....+.............+..+-...+|+....++
T Consensus 2 LV~fL~~l~g~~VtVELKng~~~~G~L~~vd~~MN~~L~~v~~t~~~~~~~~l~~~~IRGs~IRyi 67 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYF 67 (90)
T ss_pred HHHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCEEEEEEEEEECCCCCEEECCEEEECCCCEEEE
T ss_conf 769787668987999987997999999881378201898899977999877877499957738999
No 37
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=46.53 E-value=24 Score=16.43 Aligned_cols=68 Identities=13% Similarity=0.191 Sum_probs=40.2
Q ss_pred CCEEEECHHH----HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC---CCCEEEEEEEECCCCCCCCCEEEECCCCC
Q ss_conf 8889987798----7599870357898889999779987987530235---55238997541355554431354134454
Q gi|254781160|r 19 KTQGKASGDQ----YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG---KSIRFKVEYQSRSQTKQSDVQYIFSPIKT 91 (245)
Q Consensus 19 ~~~i~L~~~~----~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~---k~~~~~i~~~~~~~~~~~~i~l~~~~~k~ 91 (245)
+..+.|.|.. ..|..+.-+++.||+|.+.++ ++.|..+|.+.. .. ...+ .........++|+=|.|.+
T Consensus 42 ~gN~viaGH~~~~~~~~F~~L~~l~~GD~I~l~~~-~~~y~Y~V~~~~iV~p~-d~~~---l~~~~~~~~LTL~TC~p~~ 116 (126)
T cd06166 42 NGNFAIAGHRSYTYGRIFNRLDEVEKGDEIKVTTK-NGTYKYKITSIFVVEPT-DTDV---LNQDKSKKEITLITCTPDG 116 (126)
T ss_pred CCCEEEEEEECCCCCCCCCCHHHCCCCCEEEEEEC-CEEEEEEEEEEEEECCC-CCEE---ECCCCCCCEEEEEEECCCC
T ss_conf 96299997508887855200551858999999999-98999999779999976-5568---1347998889999747999
No 38
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=46.39 E-value=24 Score=16.42 Aligned_cols=65 Identities=9% Similarity=0.100 Sum_probs=40.6
Q ss_pred HHHCCCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCHHHHH
Q ss_conf 87035789888999977998798753023555238997541355554431354134454115677
Q gi|254781160|r 33 AHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYM 97 (245)
Q Consensus 33 ~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~~~~~i~~~~~~~~~~~~i~l~~~~~k~~~~~~i 97 (245)
.++|+-..|..|.+=--+|..|.+.+..++.+..+.+..............+-...+|+....++
T Consensus 2 l~lL~~a~g~~VtVELKnG~~y~G~L~~~d~~MN~~L~~v~~t~~~g~~~~l~~v~IRGs~Ir~i 66 (70)
T cd01721 2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFF 66 (70)
T ss_pred HHHHHHCCCCEEEEEECCCEEEEEEEEEEECCCCCEEEEEEEECCCCCEEECCEEEECCCEEEEE
T ss_conf 41675579988999988994999999887023674998999998899897566599907658999
No 39
>KOG3172 consensus
Probab=45.28 E-value=25 Score=16.31 Aligned_cols=65 Identities=8% Similarity=0.105 Sum_probs=39.3
Q ss_pred HHHCCCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCHHHHH
Q ss_conf 87035789888999977998798753023555238997541355554431354134454115677
Q gi|254781160|r 33 AHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYM 97 (245)
Q Consensus 33 ~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~~~~~i~~~~~~~~~~~~i~l~~~~~k~~~~~~i 97 (245)
+|+|--.+|-.|.+-.-.|..|.+++.+.+.+..+...........-.--++-+.+++++...|+
T Consensus 7 iKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFl 71 (119)
T KOG3172 7 IKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFL 71 (119)
T ss_pred EEEEECCCCCEEEEEECCCCEEEEEEEEECCCCCEEEEEEEEECCCCCCEEEEEEEEECCEEEEE
T ss_conf 21210156718999933786660046783056440877789973588300202589706657899
No 40
>TIGR02109 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E; InterPro: IPR011843 This entry describes coenzyme PQQ biosynthesis protein E, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.; GO: 0051539 4 iron 4 sulfur cluster binding, 0018189 pyrroloquinoline quinone biosynthetic process.
Probab=43.35 E-value=21 Score=16.78 Aligned_cols=74 Identities=12% Similarity=0.099 Sum_probs=53.6
Q ss_pred CCCCEEEECCCCC--CHHHHHHHHHHHHHHHHHHHHHHHCC----CHH------HHHHHHHHHHHHHHHHHH-CCCCCCC
Q ss_conf 4431354134454--11567775444456656555542022----011------221223357889999751-2344343
Q gi|254781160|r 79 QSDVQYIFSPIKT--NRLDYMIQKSVEMGMGAIRPVITRYT----QNT------HYNMDRVRTYTISAAEQC-DILTLPF 145 (245)
Q Consensus 79 ~~~i~l~~~~~k~--~~~~~ilqk~tELGV~~I~p~~~~rs----~~~------~~k~eR~~~ii~eA~eQs-gr~~lP~ 145 (245)
-.+++|=+.+=|. ++.+.||+.|.|||+++|=.=.+++= .++ ...+++-.+++.+|-|-- |...+++
T Consensus 145 g~PltLN~V~HR~Ni~~i~~~i~La~~L~AdrvE~A~~QyYGWA~~NR~aLlPt~~Ql~~a~r~V~~aRer~~g~~~~~~ 224 (363)
T TIGR02109 145 GLPLTLNFVLHRHNIDQIPEIIELAIELGADRVELATTQYYGWALLNRAALLPTREQLEEATRIVEEARERLKGQGNPLS 224 (363)
T ss_pred CCCEEEEHCCCCCHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf 89817602002420213678999998638984888740202256774542489889999999999999999860799823
Q ss_pred CCCCCCC
Q ss_conf 3200000
Q gi|254781160|r 146 IYPPTTL 152 (245)
Q Consensus 146 i~~~~~l 152 (245)
|..+..-
T Consensus 225 l~yV~PD 231 (363)
T TIGR02109 225 LDYVVPD 231 (363)
T ss_pred EEEECCC
T ss_conf 6763487
No 41
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=42.35 E-value=27 Score=16.02 Aligned_cols=70 Identities=13% Similarity=0.106 Sum_probs=40.8
Q ss_pred CCEEEECHHHHHH-----HHHHCCCCCCCEEEEEECCCCEEEEEEECCC---CCCEEEEEEEECCCCCCCCCEEEECCCC
Q ss_conf 8889987798759-----9870357898889999779987987530235---5523899754135555443135413445
Q gi|254781160|r 19 KTQGKASGDQYHY-----LAHVLRMKEGDNILLFNGKDGEWLSKISYVG---KSIRFKVEYQSRSQTKQSDVQYIFSPIK 90 (245)
Q Consensus 19 ~~~i~L~~~~~hH-----l~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~---k~~~~~i~~~~~~~~~~~~i~l~~~~~k 90 (245)
.....|.|.--.| ..+.-++++||.|.+.+..|..+..+++... |.. +.. ...-....+..++|+-|-..
T Consensus 49 ~Gn~ViaGH~d~~~~p~~F~~L~~l~~GD~I~v~~~~G~~~~Y~V~~~~~v~~~~-~p~-~~v~~~~~~~~LtLITC~g~ 126 (144)
T cd05829 49 KGTAVLAGHVDSRGGPAVFFRLGDLRKGDKVEVTRADGQTATFRVDRVEVYPKDA-FPT-DAVYGDTGPPRLRLITCGGP 126 (144)
T ss_pred CCCEEEEEEECCCCCCCHHHHHHCCCCCCEEEEEECCCCEEEEEEEEEEEECCHH-CCC-CEEECCCCCCEEEEEEECCC
T ss_conf 9889999970689987023244248999999999789959999998899987120-884-33676899986999970898
No 42
>PRK10039 hypothetical protein; Provisional
Probab=41.55 E-value=18 Score=17.23 Aligned_cols=18 Identities=39% Similarity=0.549 Sum_probs=15.0
Q ss_pred CCCCCCCHHHHHHHHHCC
Q ss_conf 888888889999999579
Q gi|254781160|r 195 GPEGGYHSEEKETLHSLP 212 (245)
Q Consensus 195 GPEGGfs~~E~~~l~~~~ 212 (245)
=+|||+|+-|...|++..
T Consensus 78 ~~EGGlSqVE~R~~~Ela 95 (127)
T PRK10039 78 MNEGGLSQVEERILHELA 95 (127)
T ss_pred CCCCCCCHHHHHHHHHHH
T ss_conf 577882299999999997
No 43
>TIGR03531 selenium_SpcS O-phosphoseryl-tRNA(Sec) selenium transferase. In the archaea and eukaryotes, the conversion of the mischarged serine to selenocysteine (Sec) on its tRNA is accomplished in two steps. This enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase, acts second, after a phosphophorylation step catalyzed by a homolog of the bacterial SelA protein.
Probab=39.89 E-value=20 Score=16.84 Aligned_cols=23 Identities=17% Similarity=0.182 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 56777544445665655554202
Q gi|254781160|r 94 LDYMIQKSVEMGMGAIRPVITRY 116 (245)
Q Consensus 94 ~~~ilqk~tELGV~~I~p~~~~r 116 (245)
++.+-++.-|+|.++|..+.|--
T Consensus 191 v~~ie~~i~~~g~~~i~cVlSTT 213 (444)
T TIGR03531 191 VEDIERAIEEIGPENILCVLSTT 213 (444)
T ss_pred HHHHHHHHHHHCCCCEEEEEECC
T ss_conf 99999999982867647998536
No 44
>pfam02844 GARS_N Phosphoribosylglycinamide synthetase, N domain. Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam00289).
Probab=39.67 E-value=27 Score=16.01 Aligned_cols=29 Identities=24% Similarity=0.575 Sum_probs=24.2
Q ss_pred EEEECCCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf 99988888888899999995799558636887
Q gi|254781160|r 191 AILIGPEGGYHSEEKETLHSLPFVTPLSLGPR 222 (245)
Q Consensus 191 ~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ 222 (245)
+++||||.=...-=.+.|.++|. +| .||.
T Consensus 64 lviiGPE~pL~~Gl~D~l~~~gi--~v-fGP~ 92 (99)
T pfam02844 64 LVVVGPEAPLVAGIVDALRAAGI--PV-FGPS 92 (99)
T ss_pred EEEECCCHHHHHHHHHHHHHCCC--EE-ECCC
T ss_conf 99989606778788999986899--17-9928
No 45
>TIGR00699 GABAtrns_euk 4-aminobutyrate aminotransferase; InterPro: IPR004631 4-aminobutyrate aminotransferase eukaryotic (2.6.1.19 from EC) is a class III pyridoxal-phosphate-dependent aminotransferase. The enzyme catalyses the conversion of 4-aminobutanoate and 2-oxoglutarate into succinate semialdehyde and L-glutamate. The degree of sequence difference between this set and known bacterial examples is greater than the distance between either set the most similar enzyme with distinct function, and so the prokaryotic and eukaryotic sets have been placed into separate families. This family describes known eukaryotic examples of the enzyme. Alternate names include GABA transaminase, gamma-amino-N-butyrate transaminase, and beta-alanine--oxoglutarate aminotransferase.; GO: 0003867 4-aminobutyrate transaminase activity, 0009448 gamma-aminobutyric acid metabolic process.
Probab=36.45 E-value=17 Score=17.30 Aligned_cols=14 Identities=43% Similarity=0.800 Sum_probs=8.5
Q ss_pred CCCCCCCHHHHHHH
Q ss_conf 88888888999999
Q gi|254781160|r 195 GPEGGYHSEEKETL 208 (245)
Q Consensus 195 GPEGGfs~~E~~~l 208 (245)
||++|||++|.+..
T Consensus 154 Gp~~~Fs~eE~~s~ 167 (469)
T TIGR00699 154 GPERDFSEEENESC 167 (469)
T ss_pred CCCCCCCHHHHHHH
T ss_conf 88753117887764
No 46
>cd00429 RPE Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose phosphate pathway. In the Calvin cycle Ru5P is phosphorylated by phosphoribulose kinase to ribulose-1,5-bisphosphate, which in turn is used by RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) to incorporate CO2 as the central step in carbohydrate synthesis.
Probab=35.70 E-value=16 Score=17.47 Aligned_cols=137 Identities=21% Similarity=0.234 Sum_probs=78.8
Q ss_pred CCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf 54431354134454115677754444566565555420220112212233578899997512344343320000001123
Q gi|254781160|r 78 KQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLK 157 (245)
Q Consensus 78 ~~~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~ 157 (245)
-+..+||.+--| +..+++..+.|++.|. +..|-+ ....++-..+++.-..+|=..-|.- +...+..+++
T Consensus 58 ~~~DvHLMv~~P-----~~~i~~~~~~g~d~I~-~H~E~~----~~~~~~i~~ik~~g~~~Glal~p~T-~~~~l~~~l~ 126 (211)
T cd00429 58 LPLDVHLMVENP-----ERYIEAFAKAGADIIT-FHAEAT----DHLHRTIQLIKELGMKAGVALNPGT-PVEVLEPYLD 126 (211)
T ss_pred CCEEEEEEECCH-----HHHHHHHHHHCCCEEE-ECCCCC----CCHHHHHHHHHHCCCCCEEEECCCC-CHHHHHHHHH
T ss_conf 970589987188-----7769999970998899-864322----0899999999973987235754899-9899999997
Q ss_pred CCCCCCCCCCCCC-HHCC----CCCHHHHHCCC---CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHH
Q ss_conf 3322333212630-0012----11022210036---7883599988888888899999995799558636887400448
Q gi|254781160|r 158 NWDHNCQIVFADE-TCGS----ENSLEKLHAIA---HIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDT 228 (245)
Q Consensus 158 ~~~~~~~~~~~~~-~~~~----~~~~~~~~~~~---~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ET 228 (245)
..+. .+++.-+ ...+ ...++++...+ ......+.|.=.||-+.+-+..+.++|. ..+-.|..|.+.+.
T Consensus 127 ~~D~--vliMtV~PGf~GQ~f~~~~~~ki~~l~~~~~~~~~~~~I~vDGGI~~~~i~~l~~~Ga-d~~V~GS~iF~~~d 202 (211)
T cd00429 127 EVDL--VLVMSVNPGFGGQKFIPEVLEKIRKLRELIPENNLNLLIEVDGGINLETIPLLAEAGA-DVLVAGSALFGSDD 202 (211)
T ss_pred HHCE--EEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCCC-CEEEECHHHHCCCC
T ss_conf 5152--2798746887887545679999999999998649985999967859899999998599-99997937758999
No 47
>pfam04203 Sortase Sortase family. The founder member of this family is S.aureus sortase, a transpeptidase that attaches surface proteins by the threonine of an LPXTG motif to the cell wall.
Probab=35.34 E-value=35 Score=15.31 Aligned_cols=69 Identities=10% Similarity=0.080 Sum_probs=38.8
Q ss_pred CCCEEEECHHH--HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECC---CCCCEEEEEEEECCCCCCCCCEEEECCCC
Q ss_conf 88889987798--759987035789888999977998798753023---55523899754135555443135413445
Q gi|254781160|r 18 IKTQGKASGDQ--YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYV---GKSIRFKVEYQSRSQTKQSDVQYIFSPIK 90 (245)
Q Consensus 18 ~~~~i~L~~~~--~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~---~k~~~~~i~~~~~~~~~~~~i~l~~~~~k 90 (245)
.+....|.|.. --|..+.-.++.||.|.+.+..|..|..+|... ++.-. . .......++.++|.=|.+.
T Consensus 37 ~~gn~viaGH~~~~~~F~~L~~l~~Gd~i~l~~~~~~~~~Y~V~~~~iv~~~~~-~---~~~~~~~~~~LtLiTC~p~ 110 (122)
T pfam04203 37 EGGNTVIAGHRGGGTMFSRLDKLKKGDKIYVTTLDGKTYTYRVTSVEVVDPTDV-E---VLDPTPGDRLLTLITCTPF 110 (122)
T ss_pred CCCCEEEEEEECCCCHHHHHHCCCCCCEEEEEECCCCEEEEEEEEEEEECCCCC-E---EECCCCCCCEEEEEEECCC
T ss_conf 987299998738992133565288999999997999799999999999987876-5---8623799988999975898
No 48
>COG3097 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.14 E-value=35 Score=15.29 Aligned_cols=45 Identities=18% Similarity=0.211 Sum_probs=33.8
Q ss_pred EECCCCCCCCEEEE-CHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC
Q ss_conf 40854478888998-77987599870357898889999779987987530235
Q gi|254781160|r 11 FVDFPLCIKTQGKA-SGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG 62 (245)
Q Consensus 11 f~~~~l~~~~~i~L-~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~ 62 (245)
|-+..++...+|.+ |.+++|+ ++||.+.|+.-+...|.|.|....
T Consensus 12 fe~dilagrKTITIRD~SEShf-------~~g~vlrV~r~Ed~~~fc~I~vl~ 57 (106)
T COG3097 12 FEADILAGRKTITIRDKSESHF-------KPGDVLRVGRFEDDRYFCTIEVLA 57 (106)
T ss_pred CCHHHHCCCCEEEEECCCHHCC-------CCCCEEEEEEECCCCEEEEEEEEE
T ss_conf 0077767872689703632037-------888789999924784899999987
No 49
>TIGR01672 AphA HAD superfamily (subfamily IIIB) phosphatase, TIGR01672; InterPro: IPR010025 This family of proteins is a member of the IIIB subfamily (IPR001001 from INTERPRO) of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of subfamily III and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs , all of which are found conserved in this family. AphA is a periplasmic acid phosphatase of Escherichia coli belonging to class B bacterial phosphatases , which is part of the DDDD superfamily of phosphohydrolases. The crystal structure of AphA has been determined at 2.2A and its resolution extended to 1.7A. Despite the lack of sequence homology, the AphA structure reveals a haloacid dehalogenase-like fold. This finding suggests that this fold could be conserved among members of the DDDD superfamily of phosphohydrolases. The active enzyme is a homotetramer built by using an extended N-terminal arm intertwining the four monomers. The active site of the native enzyme hosts a magnesium ion, which can be replaced by other metal ions. The structure explains the non-specific behaviour of AphA towards substrates, while a structure-based alignment with other phosphatases provides clues about the catalytic mechanism . ; GO: 0003993 acid phosphatase activity, 0030288 outer membrane-bounded periplasmic space.
Probab=34.28 E-value=25 Score=16.22 Aligned_cols=33 Identities=18% Similarity=0.305 Sum_probs=18.1
Q ss_pred CEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCE
Q ss_conf 8899877987599870357898889999779987
Q gi|254781160|r 20 TQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGE 53 (245)
Q Consensus 20 ~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~ 53 (245)
+...+..+-++.|+ -|-.+-||.|..+.|+..-
T Consensus 112 D~~SIPKe~A~qLI-~MH~~RGD~i~F~TGRt~g 144 (248)
T TIGR01672 112 DKYSIPKEVAKQLI-DMHQKRGDKIFFVTGRTAG 144 (248)
T ss_pred CCCCCCHHHHHHHH-HHHHHHCCEEEEEECCCCC
T ss_conf 87777578999999-9887609879998468764
No 50
>TIGR00958 3a01208 antigen peptide transporter 2; InterPro: IPR005293 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Proteins of this family are involved in the transport of antigens from the cytoplasm to a membrane-bound compartment for association with MHC class I molecules.; GO: 0005215 transporter activity, 0006810 transport.
Probab=32.72 E-value=31 Score=15.69 Aligned_cols=15 Identities=33% Similarity=0.541 Sum_probs=6.7
Q ss_pred CCCCEEEEECCCCCC
Q ss_conf 788359998888888
Q gi|254781160|r 186 HIPNVAILIGPEGGY 200 (245)
Q Consensus 186 ~~~~i~i~IGPEGGf 200 (245)
.+.++.-+|||-|+=
T Consensus 557 ~PG~vvALVGPsGsG 571 (770)
T TIGR00958 557 EPGEVVALVGPSGSG 571 (770)
T ss_pred CCCEEEEEECCCCCC
T ss_conf 386259986589983
No 51
>PRK13885 conjugal transfer protein TrbG; Provisional
Probab=29.33 E-value=23 Score=16.48 Aligned_cols=20 Identities=20% Similarity=0.506 Sum_probs=14.5
Q ss_pred CCEEEEECCCCC-CCHHHHHH
Q ss_conf 835999888888-88899999
Q gi|254781160|r 188 PNVAILIGPEGG-YHSEEKET 207 (245)
Q Consensus 188 ~~i~i~IGPEGG-fs~~E~~~ 207 (245)
-..+++|||+|| |+++|-++
T Consensus 241 aP~LfVvg~dGgl~~d~e~~L 261 (299)
T PRK13885 241 APTLLVVRKEGGLFTDDETVM 261 (299)
T ss_pred CCCEEEECCCCCCCCCCCCEE
T ss_conf 882899837887466784317
No 52
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=28.20 E-value=18 Score=17.18 Aligned_cols=15 Identities=33% Similarity=0.437 Sum_probs=11.7
Q ss_pred CCCCEEEEECCCCCC
Q ss_conf 788359998888888
Q gi|254781160|r 186 HIPNVAILIGPEGGY 200 (245)
Q Consensus 186 ~~~~i~i~IGPEGGf 200 (245)
+..-++|+||+-||=
T Consensus 240 gks~lTIaIGCTGGq 254 (286)
T COG1660 240 GKSYLTIAIGCTGGQ 254 (286)
T ss_pred CCEEEEEEECCCCCC
T ss_conf 974999997147986
No 53
>PRK05784 phosphoribosylamine--glycine ligase; Provisional
Probab=27.00 E-value=48 Score=14.45 Aligned_cols=22 Identities=9% Similarity=-0.241 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 2233578899997512344343
Q gi|254781160|r 124 MDRVRTYTISAAEQCDILTLPF 145 (245)
Q Consensus 124 ~eR~~~ii~eA~eQsgr~~lP~ 145 (245)
+-|++.=+.+-+..|-...++.
T Consensus 318 Lp~L~sDl~~l~~a~~~g~L~~ 339 (485)
T PRK05784 318 LYLYEGDFYELFELAATGKLHK 339 (485)
T ss_pred HHHHHCCHHHHHHHHHCCCCCC
T ss_conf 9874263999999998199887
No 54
>pfam05896 NQRA Na(+)-translocating NADH-quinone reductase subunit A (NQRA). This family consists of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration.
Probab=26.68 E-value=49 Score=14.38 Aligned_cols=97 Identities=13% Similarity=0.133 Sum_probs=54.0
Q ss_pred CCCCEEEECHHHHHHHHHHCCCCCCCEEE----EE-ECC--CCEE----EEEEECCC---CCCEEEEEEEEC-CCCCCCC
Q ss_conf 78888998779875998703578988899----99-779--9879----87530235---552389975413-5555443
Q gi|254781160|r 17 CIKTQGKASGDQYHYLAHVLRMKEGDNIL----LF-NGK--DGEW----LSKISYVG---KSIRFKVEYQSR-SQTKQSD 81 (245)
Q Consensus 17 ~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~----i~-dg~--g~~~----~~~I~~~~---k~~~~~i~~~~~-~~~~~~~ 81 (245)
....++.+.++++|.++=-|-+++||+|. || |=+ +-.| .++|.++. |...+.++-+.. .....+.
T Consensus 24 ~~~~~~ai~p~Df~glkPkl~VkeGD~Vk~G~pLF~dK~np~i~f~SPvsG~V~~I~RG~kR~ilsivI~~d~~~~~~~~ 103 (257)
T pfam05896 24 PAVRTVALLGEDYVGMKPKMLVKEGDKVKAGQPLFEDKKNPGVKFTAPASGTVVAINRGAKRVLQSVVIEVDGDEAVTFE 103 (257)
T ss_pred CCCCEEEECCCCCCCCCEEEEEECCCEEECCCEEEEEECCCCCEEECCCCEEEEEECCCCCCCEEEEEEEECCCCCCCCC
T ss_conf 98757998460148873269983499985587579973698846856787389501056751015999993687430000
Q ss_pred CEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 135413445411567775444456656555542022
Q gi|254781160|r 82 VQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYT 117 (245)
Q Consensus 82 i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs 117 (245)
-.=...+.+ -.-|.+.+.+.+-| .||++-+|=
T Consensus 104 ~~~~~~~~~-ls~e~i~~~Ll~sG---lW~~~rqRP 135 (257)
T pfam05896 104 KYSAKDLSS-LSREAVKENLLESG---LWTALRTRP 135 (257)
T ss_pred CCCCCCHHH-CCHHHHHHHHHHCC---CHHHHHCCC
T ss_conf 157224324-79999999998669---706754264
No 55
>PRK04171 ribosome biogenesis protein; Provisional
Probab=26.44 E-value=49 Score=14.35 Aligned_cols=90 Identities=22% Similarity=0.248 Sum_probs=49.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEEC--CCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf 434332000000112333223332126300012110222100367883599988--888888899999995799558636
Q gi|254781160|r 142 TLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIG--PEGGYHSEEKETLHSLPFVTPLSL 219 (245)
Q Consensus 142 ~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IG--PEGGfs~~E~~~l~~~~~~~~vsL 219 (245)
.|.++.. .++.+++.. ...+++...+........+..... ..++++|| |-|.|+.+-.+.. . ..+|+
T Consensus 128 ~Ll~v~k-~~l~~~l~~--~~~kii~ls~~g~~~~~~~~~~~~---~~~~~vIGaf~~G~f~~~~~~~~---d--~~~SI 196 (221)
T PRK04171 128 PLLELED-KSLSELLEE--NPGKIILLSEKGEPVKPKELAKEL---ENPVVVIGGFPHGDFSSEVLEKA---D--KKYSI 196 (221)
T ss_pred CCEEEEC-CCHHHHHCC--CCCEEEEECCCCCCCCHHHHHHHC---CCCEEEEEECCCCCCCCCCHHCC---C--CEEEE
T ss_conf 0015663-868997065--898599983588672899997422---79769983016987660000136---8--48998
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf 88740044899999999999847
Q gi|254781160|r 220 GPRILRSDTAAVAAMALVQAICG 242 (245)
Q Consensus 220 G~~ILR~ETA~i~als~~~~~~g 242 (245)
++.-|-|-+++--.++..-..||
T Consensus 197 s~~~Lsa~~v~~ri~~a~E~~~G 219 (221)
T PRK04171 197 YNEPLDAWTVVSRIIAAAERALG 219 (221)
T ss_pred ECCCHHHHHHHHHHHHHHHHHHC
T ss_conf 48876999999999999999867
No 56
>pfam01081 Aldolase KDPG and KHG aldolase. This family includes the following members: 4-hydroxy-2-oxoglutarate aldolase (KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate aldolase (KDPG-aldolase)
Probab=26.40 E-value=49 Score=14.35 Aligned_cols=95 Identities=19% Similarity=0.262 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHH
Q ss_conf 35788999975123443433200000011233322333212630001211022210036788359998888888889999
Q gi|254781160|r 127 VRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKE 206 (245)
Q Consensus 127 ~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~ 206 (245)
+..-+.++|.+.+-+++|=+..|.......+.=-.. ..+|.-...+....++.+.. ..+.+-++ |=||.+.+-..
T Consensus 89 ~~~~v~~~a~~~~i~~iPGv~TpsEi~~A~~~G~~~-vKlFPA~~~Gg~~~lkal~~--p~p~~~f~--ptGGv~~~N~~ 163 (196)
T pfam01081 89 LTADLLKHAVDVKIPLIPGVSTPSEIMLGLDLGLTR-FKFFPAEASGGVPAIKALAG--PFPQVRFC--PTGGIHPANVR 163 (196)
T ss_pred CHHHHHHHHHHCCCCEECCCCCHHHHHHHHHCCCCE-EEECCCHHCCCHHHHHHHHC--CCCCCEEE--EECCCCHHHHH
T ss_conf 639999999973996637859999999999879998-99787310184999999857--79998699--80798988899
Q ss_pred HHHHCCCCEEEECCCCCCCHH
Q ss_conf 999579955863688740044
Q gi|254781160|r 207 TLHSLPFVTPLSLGPRILRSD 227 (245)
Q Consensus 207 ~l~~~~~~~~vsLG~~ILR~E 227 (245)
.+-++|. ..+-.|..+..-+
T Consensus 164 ~yl~~g~-v~~~~GS~l~~~~ 183 (196)
T pfam01081 164 DYLALPN-ILCVGGSWLVPAS 183 (196)
T ss_pred HHHHCCC-EEEEECHHHCCHH
T ss_conf 9996898-6999893648988
No 57
>PRK10433 putative RNA methyltransferase; Provisional
Probab=25.65 E-value=51 Score=14.26 Aligned_cols=25 Identities=24% Similarity=0.401 Sum_probs=19.7
Q ss_pred CCCCEEEEECCCC-CCCHHHHHHHHH
Q ss_conf 7883599988888-888899999995
Q gi|254781160|r 186 HIPNVAILIGPEG-GYHSEEKETLHS 210 (245)
Q Consensus 186 ~~~~i~i~IGPEG-Gfs~~E~~~l~~ 210 (245)
..+++.++.|+|. |.|.+|++.+..
T Consensus 104 ~~~~valvFG~E~~GLsneEl~~C~~ 129 (228)
T PRK10433 104 WMSHAALVFGREDSGLTNEELALADV 129 (228)
T ss_pred CCCCEEEEECCCCCCCCHHHHHHCCE
T ss_conf 47847999888668989899986797
No 58
>pfam00834 Ribul_P_3_epim Ribulose-phosphate 3 epimerase family. This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.
Probab=25.44 E-value=41 Score=14.87 Aligned_cols=136 Identities=18% Similarity=0.266 Sum_probs=73.1
Q ss_pred CCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 55443135413445411567775444456656555542022011221223357889999751234434332000000112
Q gi|254781160|r 77 TKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLL 156 (245)
Q Consensus 77 ~~~~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l 156 (245)
.-+..+||.+.-| +..+++..+.|++.|. +..|-+. ...+.-..++++-.++|=..-|. .+...++.++
T Consensus 57 ~~~~DvHLMv~~P-----~~~i~~~~~~g~d~i~-~H~E~~~----~~~~~i~~ik~~g~k~GlAlnP~-T~~~~l~~~l 125 (201)
T pfam00834 57 ELPLDVHLMVEEP-----DRIIPDFAEAGADIIS-FHAEASD----HPHRTIQLIKEAGAKAGLVLNPA-TPLDAIEYLL 125 (201)
T ss_pred CCCEEEEEEEECH-----HHHHHHHHHCCCCEEE-ECHHHHH----CHHHHHHHHHHCCCEEEEEECCC-CCCHHHHHHH
T ss_conf 9963899998377-----6639999873998899-7544413----79999999986497268885699-8602888767
Q ss_pred CCCCCCCCCCCCCCH-HCC----CCCHHHHHCCC---CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCH
Q ss_conf 333223332126300-012----11022210036---78835999888888888999999957995586368874004
Q gi|254781160|r 157 KNWDHNCQIVFADET-CGS----ENSLEKLHAIA---HIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRS 226 (245)
Q Consensus 157 ~~~~~~~~~~~~~~~-~~~----~~~~~~~~~~~---~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ 226 (245)
+..+.- +++.-+. ..+ ...++++...+ ..+...+.|.=.||-+.+-+..+.++|. ..+=.|.-|.++
T Consensus 126 ~~iD~V--LvMtV~PGf~GQ~f~~~~l~KI~~lr~~~~~~~~~~~I~vDGGIn~~ti~~l~~~Ga-d~~V~GSaiF~s 200 (201)
T pfam00834 126 DDLDLV--LLMSVNPGFGGQSFIPSVLPKIRKVRKMIDEGGLDTLIEVDGGVNLDNIPQIAEAGA-DVLVAGSAVFGA 200 (201)
T ss_pred HHCCEE--EEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCCC-CEEEECCEECCC
T ss_conf 427989--998866898876456779999999999998269980799989888999999998799-999978002459
No 59
>TIGR00223 panD aspartate 1-decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process.
Probab=25.00 E-value=52 Score=14.18 Aligned_cols=57 Identities=19% Similarity=0.214 Sum_probs=41.5
Q ss_pred CCCCCCEEEEC-CCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCC
Q ss_conf 76778777408-54478888998779875998703578988899997799879875302355
Q gi|254781160|r 3 IHSHLKRLFVD-FPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGK 63 (245)
Q Consensus 3 ~~~~m~R~f~~-~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k 63 (245)
...|+||.-+- -+|..-.++.+|.|-. +.-.+.+|++|.+.|-++|.-..+..-.+|
T Consensus 6 l~gKlHRa~vT~AnLnY~GSitIDeDl~----daag~lenekv~IvnvnNG~RfsTY~I~gk 63 (127)
T TIGR00223 6 LSGKLHRATVTEANLNYVGSITIDEDLL----DAAGLLENEKVDIVNVNNGKRFSTYVIAGK 63 (127)
T ss_pred CCCCCCEEEEEECCCCEEEEEEHHHHHH----HHHHCCCCCEEEEEECCCCCCEEEEEECCC
T ss_conf 2176221576323674365332546799----985128998489986689971234665142
No 60
>KOG2925 consensus
Probab=24.96 E-value=39 Score=15.03 Aligned_cols=60 Identities=13% Similarity=0.127 Sum_probs=41.7
Q ss_pred CCCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEE-CCCCCCEEE
Q ss_conf 787774085447888899877987599870357898889999779987987530-235552389
Q gi|254781160|r 6 HLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKIS-YVGKSIRFK 68 (245)
Q Consensus 6 ~m~R~f~~~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~-~~~k~~~~~ 68 (245)
.|.|=|+.+. ..+..+.|...+.- .+|++++-...+.|.|.+|..+.+..- ...|++.++
T Consensus 2 atkkry~~q~-v~de~~~le~~q~I--aqVvqlrGsnlheV~danGq~~lvsmP~KfRksiWiR 62 (167)
T KOG2925 2 ATKKRYLKQA-VSDEDFTLEECQSI--AQVVQLRGSNLHEVMDANGQNSLVSMPAKFRKSIWIR 62 (167)
T ss_pred CCCHHHHCCC-CCCCCCCHHHHHHH--HHHHHCCCCCHHHHHHCCCCEEEEECCHHHHHCEEEE
T ss_conf 6311111000-25887431242568--9998457842323665177243001777651025785
No 61
>pfam06003 SMN Survival motor neuron protein (SMN). This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.
Probab=24.90 E-value=53 Score=14.17 Aligned_cols=37 Identities=16% Similarity=0.107 Sum_probs=27.0
Q ss_pred CCCCCCCEEEEEE-CCCCEEEEEEECCC-CCCEEEEEEE
Q ss_conf 3578988899997-79987987530235-5523899754
Q gi|254781160|r 36 LRMKEGDNILLFN-GKDGEWLSKISYVG-KSIRFKVEYQ 72 (245)
Q Consensus 36 lRlk~Gd~i~i~d-g~g~~~~~~I~~~~-k~~~~~i~~~ 72 (245)
..-++||.....- .+|..|.|+|.+|+ |..++.+...
T Consensus 67 ~~wkVGD~C~A~yseDG~~YeAtI~SId~k~gtCvV~Y~ 105 (264)
T pfam06003 67 KEWQVGDSCNAVWSEDGNLYTATITSIDQKRGTCVVFYT 105 (264)
T ss_pred CEEECCCEEEEEECCCCCCCEEEEEEECCCCCCEEEEEE
T ss_conf 201118856766525785201367775267870689982
No 62
>PRK10358 putative tRNA/rRNA methyltransferase YibK; Provisional
Probab=24.63 E-value=53 Score=14.14 Aligned_cols=132 Identities=8% Similarity=0.077 Sum_probs=61.2
Q ss_pred CEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHHHHHHHCCCCC--CCCCCCCCCCCCCCC
Q ss_conf 1354134454115677754444566565555420220-1122122335788999975123443--433200000011233
Q gi|254781160|r 82 VQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQ-NTHYNMDRVRTYTISAAEQCDILTL--PFIYPPTTLEFLLKN 158 (245)
Q Consensus 82 i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~-~~~~k~eR~~~ii~eA~eQsgr~~l--P~i~~~~~l~~~l~~ 158 (245)
|.|+.+ -.+...-.|++-|.-.|+. ++.+.. .+- -.++++. . +|-.+. ..+....+++.+++.
T Consensus 4 IVL~~P-~iP~N~G~i~R~ca~~g~~-L~LV~P-~gf~~~dk~lr-------R----Agldy~~~~~~~~~~~~~~f~~~ 69 (157)
T PRK10358 4 IVLYEP-EIPPNTGNIIRLCANTGFR-LHIIEP-MGFAWDDKRLR-------R----AGLDYHEFTAVTRHHDYAAFLEA 69 (157)
T ss_pred EEEECC-CCCCCHHHHHHHHHHCCCE-EEEEEC-CCCCCCCHHHH-------H----HCCCCHHEEEEEECCCHHHHHHH
T ss_conf 999589-8888289999999963998-999806-88787426665-------3----31630212689980899999974
Q ss_pred CCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCCEEEECCCC--CCCHHHHHHHHH
Q ss_conf 3223332126300012110222100367883599988888-888899999995799558636887--400448999999
Q gi|254781160|r 159 WDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG-GYHSEEKETLHSLPFVTPLSLGPR--ILRSDTAAVAAM 234 (245)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~~~~~~~vsLG~~--ILR~ETA~i~al 234 (245)
......+.+.... ..... ...-.+.-.++.|||+ |.+++..+.+.....+ .+-+-+. -|=-.+|+.+++
T Consensus 70 ~~~~r~~~~tt~~---~~~~~---~~~~~~~d~llFG~Es~GLp~e~l~~~~~~~~i-~IPm~~~~rSLNLs~AvaIvl 141 (157)
T PRK10358 70 ENPQRLFALTTKG---TPAHS---AVSYQDGDYLMFGPETRGLPASILDALPAEQKI-RIPMVPDSRSMNLSNAVSVVV 141 (157)
T ss_pred CCCCEEEEEECCC---CCCCH---HCCCCCCCEEEECCCCCCCCHHHHHCCCCCEEE-EEECCCCCCCHHHHHHHHHHH
T ss_conf 3897289972577---87610---023578988997776789899999517777499-830897985142999999999
No 63
>pfam07236 Phytoreo_S7 Phytoreovirus S7 protein. This family consists of several Phytoreovirus S7 proteins which are thought to be viral core proteins.
Probab=24.49 E-value=43 Score=14.73 Aligned_cols=20 Identities=20% Similarity=0.388 Sum_probs=14.3
Q ss_pred EEEECCCCCCCHHHHHHHHH
Q ss_conf 99988888888899999995
Q gi|254781160|r 191 AILIGPEGGYHSEEKETLHS 210 (245)
Q Consensus 191 ~i~IGPEGGfs~~E~~~l~~ 210 (245)
-++|--++=||.+|.+.+.+
T Consensus 283 evFie~d~vFs~eE~s~lde 302 (506)
T pfam07236 283 EVFIEIDSVFSKEEHSKLDE 302 (506)
T ss_pred CEEEECCCCCCHHHHHHHHH
T ss_conf 10460445656677878887
No 64
>pfam01079 Hint Hint module. This is an alignment of the Hint module in the Hedgehog proteins. It does not include any Inteins which also possess the Hint module.
Probab=24.40 E-value=54 Score=14.11 Aligned_cols=45 Identities=9% Similarity=0.097 Sum_probs=30.7
Q ss_pred CCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEE-ECCCCC
Q ss_conf 788889987798759987035789888999977998798753-023555
Q gi|254781160|r 17 CIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKI-SYVGKS 64 (245)
Q Consensus 17 ~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I-~~~~k~ 64 (245)
..+.++.+.+.... .+--+++||.|...|.+|......+ ...+++
T Consensus 14 pg~a~V~l~~G~~k---~m~~L~~GD~Vla~d~~G~~~yS~Vi~Fldr~ 59 (214)
T pfam01079 14 PGDATVTLEDGGTK---PMSDLRIGDRVLAADSDGKLVYSPVILFLDRD 59 (214)
T ss_pred CCCCEEEECCCCEE---EHHHCCCCCEEEEECCCCCEEEEEEEEEEEEC
T ss_conf 99878993799888---93776888889986589999888579998217
No 65
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=23.55 E-value=53 Score=14.14 Aligned_cols=96 Identities=20% Similarity=0.260 Sum_probs=47.7
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHH-----HHH-HCCCCE
Q ss_conf 43433200000011233322333212630001211022210036788359998888888889999-----999-579955
Q gi|254781160|r 142 TLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKE-----TLH-SLPFVT 215 (245)
Q Consensus 142 ~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~-----~l~-~~~~~~ 215 (245)
|==.+....+|.++++..+.+..++.... .+.....+.. .....+....+-||+.|.-+-... .+. -.++ .
T Consensus 165 wGY~V~~~~~L~e~~~~~~~~~vvi~tsr-~g~~~~~e~~-~~~~~~~~~~fg~P~~gv~~~~~~~~~~~~~d~~~N~-~ 241 (272)
T COG2106 165 WGYKVRIAKSLNELLKGFDLDVVVIATSR-YGPLDVRETE-APLKSKVTLVFGGPEKGVLEILKVGGVKLEFDIVVNF-I 241 (272)
T ss_pred CCEEEEEHHHHHHHHHCCCCCCEEEEECC-CCCCEEEECC-CCCCCCCEEEECCCCCCHHEECCCCCCCCCCCEEEEE-C
T ss_conf 74799861458877633688735998435-5865001225-6667760589648655700011445666433615773-4
Q ss_pred EEECCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 86368874004489999999999984
Q gi|254781160|r 216 PLSLGPRILRSDTAAVAAMALVQAIC 241 (245)
Q Consensus 216 ~vsLG~~ILR~ETA~i~als~~~~~~ 241 (245)
+ .=|...-|+|-|.++.+++++.+.
T Consensus 242 p-~Qg~~~vrtEEavlatl~~ln~~~ 266 (272)
T COG2106 242 P-GQGTETVRTEEAVLATLSILNILL 266 (272)
T ss_pred C-CCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 8-755324660466788888888998
No 66
>TIGR02311 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; InterPro: IPR012689 This entry represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway.; GO: 0018802 24-dihydroxyhept-2-ene-17-dioate aldolase activity, 0010124 phenylacetate catabolic process.
Probab=22.91 E-value=26 Score=16.13 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHCCC
Q ss_conf 5677754444566565-555420220
Q gi|254781160|r 94 LDYMIQKSVEMGMGAI-RPVITRYTQ 118 (245)
Q Consensus 94 ~~~ilqk~tELGV~~I-~p~~~~rs~ 118 (245)
-=++|.+.=-+|+..+ .|++-.+-+
T Consensus 73 ~~~lIK~lLDIGAQTLLvPmi~~aeq 98 (249)
T TIGR02311 73 DPVLIKQLLDIGAQTLLVPMIETAEQ 98 (249)
T ss_pred CCEEEEHHHHHHHHHHHHHHHCCHHH
T ss_conf 82021013223456643103037789
No 67
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=22.69 E-value=58 Score=13.90 Aligned_cols=68 Identities=12% Similarity=0.087 Sum_probs=42.6
Q ss_pred HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCHHHH
Q ss_conf 75998703578988899997799879875302355523899754135555443135413445411567
Q gi|254781160|r 29 YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDY 96 (245)
Q Consensus 29 ~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~~~~~i~~~~~~~~~~~~i~l~~~~~k~~~~~~ 96 (245)
.+-|...|.--.|..+.+=--+|..+.+++.+++....+....-........+..+-...+++....+
T Consensus 7 ~~tLv~lL~~l~g~~VtVELkNg~~~~G~L~~vD~~MN~~L~~v~~t~~~g~~~~l~~~~IRGs~IRy 74 (78)
T cd01733 7 ENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRY 74 (78)
T ss_pred HCCHHHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEEEEEECCCCCEEECCEEEECCCEEEE
T ss_conf 46199999873897899997699899999998744626699459999379987787779991766899
No 68
>cd00452 KDPG_aldolase KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.
Probab=22.54 E-value=58 Score=13.88 Aligned_cols=90 Identities=20% Similarity=0.296 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHH
Q ss_conf 35788999975123443433200000011233322333212630001211022210036788359998888888889999
Q gi|254781160|r 127 VRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKE 206 (245)
Q Consensus 127 ~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~ 206 (245)
+..-+.+.|.+.+-+++|-+..|..+...++.=-+..+ +|.-+.. ..+-++.+... .+.+.++ |=||.+.+-..
T Consensus 85 ~~~~v~~~a~~~~~~~iPGv~TpsEi~~A~~~G~~~vK-~FPa~~~-G~~~lkal~~p--fp~~~~~--ptGGI~~~N~~ 158 (190)
T cd00452 85 LDPEVVKAANRAGIPLLPGVATPTEIMQALELGADIVK-LFPAEAV-GPAYIKALKGP--FPQVRFM--PTGGVSLDNAA 158 (190)
T ss_pred CCHHHHHHHHHCCCCEECCCCCHHHHHHHHHCCCCEEE-ECCCCCC-CHHHHHHHHCC--CCCCCEE--EECCCCHHHHH
T ss_conf 99999999998299665787999999999987999899-8955114-99999998554--8999389--96799988899
Q ss_pred HHHHCCCCEEEECCCCC
Q ss_conf 99957995586368874
Q gi|254781160|r 207 TLHSLPFVTPLSLGPRI 223 (245)
Q Consensus 207 ~l~~~~~~~~vsLG~~I 223 (245)
.+-+.| +..|.+|...
T Consensus 159 ~yl~~g-v~avG~g~~l 174 (190)
T cd00452 159 EWLAAG-VVAVGGGSLL 174 (190)
T ss_pred HHHHCC-CEEEEECHHC
T ss_conf 999689-9899954125
No 69
>PRK13210 putative L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=22.50 E-value=43 Score=14.73 Aligned_cols=72 Identities=15% Similarity=0.153 Sum_probs=37.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHCCCCC---------CCCCCCCCCCCCCCCCC
Q ss_conf 115677754444566565555420--2201122122335788999975123443---------43320000001123332
Q gi|254781160|r 92 NRLDYMIQKSVEMGMGAIRPVITR--YTQNTHYNMDRVRTYTISAAEQCDILTL---------PFIYPPTTLEFLLKNWD 160 (245)
Q Consensus 92 ~~~~~ilqk~tELGV~~I~p~~~~--rs~~~~~k~eR~~~ii~eA~eQsgr~~l---------P~i~~~~~l~~~l~~~~ 160 (245)
+.++..++-|..||+..|...-.+ +........+|+..-+..+++.+.+.-+ |-+..+..+..+++..+
T Consensus 94 e~l~kaI~lA~~LGi~~I~l~g~dv~~~~~~~~~~~rf~e~l~~~~~~Ae~~gV~L~iE~~~~~f~~t~~~~~~~i~~v~ 173 (284)
T PRK13210 94 EIMKKAIRLAQDLGIRTIQLAGYDVYYEEKDEETRQRFIEGLAWAVEQAAAAQVMLAVEIMDTPFMNSISKWKKWDEEID 173 (284)
T ss_pred HHHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEECCCCCCCCHHHHHHHHHHCC
T ss_conf 99999999999809978996887666686988999999999999999999839989999567655477999999999649
Q ss_pred CCC
Q ss_conf 233
Q gi|254781160|r 161 HNC 163 (245)
Q Consensus 161 ~~~ 163 (245)
+..
T Consensus 174 sp~ 176 (284)
T PRK13210 174 SPW 176 (284)
T ss_pred CCC
T ss_conf 983
No 70
>PRK13668 hypothetical protein; Provisional
Probab=22.11 E-value=59 Score=13.82 Aligned_cols=10 Identities=10% Similarity=-0.449 Sum_probs=3.5
Q ss_pred HHHHHHHHCC
Q ss_conf 8999975123
Q gi|254781160|r 131 TISAAEQCDI 140 (245)
Q Consensus 131 i~eA~eQsgr 140 (245)
+.+.+.+--|
T Consensus 145 i~E~A~fNlr 154 (266)
T PRK13668 145 IREMALFNVR 154 (266)
T ss_pred HHHHHHHHHH
T ss_conf 9999998886
No 71
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=21.96 E-value=60 Score=13.80 Aligned_cols=27 Identities=30% Similarity=0.368 Sum_probs=21.9
Q ss_pred CCCCCCCEEEEEECCCCEEEEEEECCC
Q ss_conf 357898889999779987987530235
Q gi|254781160|r 36 LRMKEGDNILLFNGKDGEWLSKISYVG 62 (245)
Q Consensus 36 lRlk~Gd~i~i~dg~g~~~~~~I~~~~ 62 (245)
|+++.||.|.+.-|+..--.++|..+.
T Consensus 5 ~kIkkGD~V~VisGkdKGk~G~Vl~v~ 31 (77)
T PRK12281 5 LHVKKGDMVKVIAGDDKGKTGKVLAVL 31 (77)
T ss_pred EEEECCCEEEEEECCCCCCCEEEEEEE
T ss_conf 487589999994667899727899998
No 72
>PRK00885 phosphoribosylamine--glycine ligase; Provisional
Probab=21.74 E-value=60 Score=13.77 Aligned_cols=35 Identities=9% Similarity=0.006 Sum_probs=14.8
Q ss_pred EEEECHHHHH-HHHHHCCCC----CCCEEEEEE-CCCCEEE
Q ss_conf 8998779875-998703578----988899997-7998798
Q gi|254781160|r 21 QGKASGDQYH-YLAHVLRMK----EGDNILLFN-GKDGEWL 55 (245)
Q Consensus 21 ~i~L~~~~~h-Hl~kVlRlk----~Gd~i~i~d-g~g~~~~ 55 (245)
.|.=+.+++. .+..+|.-+ .|+.|.+=. -.|.++.
T Consensus 154 ~V~~~~~ea~~al~~i~~~~~fg~ag~~VvIEE~L~G~E~S 194 (424)
T PRK00885 154 VVAMTLEEAEAAVDDMLAGNKFGDAGARVVIEEFLDGEEAS 194 (424)
T ss_pred EEECCHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCEEE
T ss_conf 76378999999999985033234568728999705883179
No 73
>PRK08745 ribulose-phosphate 3-epimerase; Provisional
Probab=21.67 E-value=34 Score=15.41 Aligned_cols=136 Identities=19% Similarity=0.308 Sum_probs=73.6
Q ss_pred CCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 55443135413445411567775444456656555542022011221223357889999751234434332000000112
Q gi|254781160|r 77 TKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLL 156 (245)
Q Consensus 77 ~~~~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l 156 (245)
..+..+||.+.. -+..+++..+.|++.|. +..|-+ ....+.-..++++=.++|=.--|. .++..++.++
T Consensus 62 ~~plDvHLMv~~-----P~~~i~~~~~aGad~i~-~H~Ea~----~~~~~~i~~ik~~g~k~GlalnP~-T~~~~l~~~l 130 (223)
T PRK08745 62 TAPIDVHLMVEP-----VDRIVPDFADAGATTIS-FHPEAS----RHVHRTIQLIKSHGCQAGLVLNPA-TPVDILDWVL 130 (223)
T ss_pred CCCEEEEEEECC-----HHHHHHHHHHCCCCEEE-EEECCC----CCHHHHHHHHHHCCCCEEEEECCC-CCHHHHHHHH
T ss_conf 975377898339-----89999999973997899-960644----299999999998398446774699-9879999988
Q ss_pred CCCCCCCCCCCCCCH-HCCC----CCHHHHHCCC-----CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCH
Q ss_conf 333223332126300-0121----1022210036-----78835999888888888999999957995586368874004
Q gi|254781160|r 157 KNWDHNCQIVFADET-CGSE----NSLEKLHAIA-----HIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRS 226 (245)
Q Consensus 157 ~~~~~~~~~~~~~~~-~~~~----~~~~~~~~~~-----~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ 226 (245)
...+.- +++.-+. ..++ ..++++.... ....+. |.=-||.+.+-+..+.++|. ..+=.|.-|++.
T Consensus 131 ~~~D~V--liMtV~PGf~GQ~f~~~~l~KI~~l~~~~~~~~~~~~--I~VDGGI~~~ti~~l~~aGa-d~~V~GSaiF~~ 205 (223)
T PRK08745 131 PELDLV--LVMSVNPGFGGQAFIPSALDKLRAIRKKIDALGKPIR--LEIDGGVKADNIGAIAAAGA-DTFVAGSAIFNA 205 (223)
T ss_pred HHCCEE--EEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCE--EEEECCCCHHHHHHHHHCCC-CEEEECHHHHCC
T ss_conf 647989--9987569988754568899999999999986499945--99978879899999998699-999974177579
Q ss_pred HH
Q ss_conf 48
Q gi|254781160|r 227 DT 228 (245)
Q Consensus 227 ET 228 (245)
+-
T Consensus 206 ~d 207 (223)
T PRK08745 206 PD 207 (223)
T ss_pred CC
T ss_conf 99
No 74
>pfam05113 DUF693 Protein of unknown function (DUF693). This family consists of several uncharacterized proteins from Borrelia burgdorferi (Lyme disease spirochete).
Probab=20.84 E-value=63 Score=13.65 Aligned_cols=11 Identities=18% Similarity=0.229 Sum_probs=4.3
Q ss_pred HHHHHHHHHCC
Q ss_conf 89999999579
Q gi|254781160|r 202 SEEKETLHSLP 212 (245)
Q Consensus 202 ~~E~~~l~~~~ 212 (245)
+.+-+.|+..|
T Consensus 222 ~~~yk~LEDyg 232 (311)
T pfam05113 222 NAEYKALEDYG 232 (311)
T ss_pred CCCHHHHHHHC
T ss_conf 52323366504
No 75
>TIGR02609 doc_partner putative addiction module antidote; InterPro: IPR013432 This entry contains putative addiction module antidote proteins encoded by genes that appear recurrently in two-gene operons where the other gene encodes a Doc (death-on-curing) protein IPR006440 from INTERPRO. Note that these proteins tend to be found on bacterial chromosomes, not on plasmids..
Probab=20.55 E-value=64 Score=13.61 Aligned_cols=39 Identities=23% Similarity=0.262 Sum_probs=27.0
Q ss_pred EEEECHHHHHHHHHHCCCCCCCEE--EEEECCCCEEEEEEECCCC
Q ss_conf 899877987599870357898889--9997799879875302355
Q gi|254781160|r 21 QGKASGDQYHYLAHVLRMKEGDNI--LLFNGKDGEWLSKISYVGK 63 (245)
Q Consensus 21 ~i~L~~~~~hHl~kVlRlk~Gd~i--~i~dg~g~~~~~~I~~~~k 63 (245)
-+.|+.+- ..-|+++.||+| .++--+|+.-......+.+
T Consensus 11 vv~lpKE~----l~~L~~~~GDtl~i~~~~~~~g~~~~~~~~~~~ 51 (77)
T TIGR02609 11 VVTLPKEV----LESLGLKEGDTLEIYVDEEEGGLRLKRADEVEK 51 (77)
T ss_pred EEEECHHH----HHHCCCCCCCEEEEEEEECCCCEEEEEECCCHH
T ss_conf 26747488----974689999827899870799568998656723
No 76
>TIGR00185 rRNA_methyl_2 RNA methyltransferase, TrmH family, group 2; InterPro: IPR004440 The RNA methyltransferase, TrmH family, group 2 are part of the trmH (spoU) family of rRNA methylases that are involved in tRNA and rRNA base modification.; GO: 0008173 RNA methyltransferase activity, 0009451 RNA modification.
Probab=20.44 E-value=56 Score=13.97 Aligned_cols=95 Identities=8% Similarity=0.126 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHH--HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCCCCCCCCCCCCCCCC-CCCC
Q ss_conf 5677754444566--56555542022011221223357889999751234434--33200000011233322333-2126
Q gi|254781160|r 94 LDYMIQKSVEMGM--GAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLP--FIYPPTTLEFLLKNWDHNCQ-IVFA 168 (245)
Q Consensus 94 ~~~ilqk~tELGV--~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP--~i~~~~~l~~~l~~~~~~~~-~~~~ 168 (245)
---|++-|+--|. +=|-|+-+.-..+.-++ +|=.+-+ .+..+.+++++++....... +++.
T Consensus 15 TGNI~R~Caat~~~LHLi~PlGF~~~DK~L~R--------------AGLdyw~fv~~~~H~s~E~fle~~~~~~~nlf~l 80 (161)
T TIGR00185 15 TGNIVRTCAATGTRLHLIKPLGFELDDKRLKR--------------AGLDYWEFVQLFYHKSWEEFLEAEKPQKGNLFLL 80 (161)
T ss_pred CCHHHHHHHCCCCEEEEECCCCCCCCCCEEEE--------------CCCCCCCCEEEEECCCHHHHHHHCCCCCEEEEEE
T ss_conf 41120101115862456605786207814231--------------4787445232356255688886338997168888
Q ss_pred CCHHC-CCCCHHHHHCCCCCCCEEEEECCCC-CCCHHHH
Q ss_conf 30001-2110222100367883599988888-8888999
Q gi|254781160|r 169 DETCG-SENSLEKLHAIAHIPNVAILIGPEG-GYHSEEK 205 (245)
Q Consensus 169 ~~~~~-~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~ 205 (245)
..... ..+... -+........++.|+|- |. |..+
T Consensus 81 T~~G~~t~~~~~--~~~~~~d~~yl~fG~ET~GL-P~~~ 116 (161)
T TIGR00185 81 TKKGDKTPDHIS--VTYQDGDELYLVFGQETKGL-PKSL 116 (161)
T ss_pred EECCCCCCCCEE--EEECCCCCEEEEECCCCCCC-HHHH
T ss_conf 403887745046--65437861699836877551-2899
No 77
>KOG2589 consensus
Probab=20.24 E-value=55 Score=14.05 Aligned_cols=42 Identities=21% Similarity=0.312 Sum_probs=29.4
Q ss_pred EECCCCCCCCEEEECHHHHHHHHHHCC-CCCCCEEEEEECCCCE
Q ss_conf 408544788889987798759987035-7898889999779987
Q gi|254781160|r 11 FVDFPLCIKTQGKASGDQYHYLAHVLR-MKEGDNILLFNGKDGE 53 (245)
Q Consensus 11 f~~~~l~~~~~i~L~~~~~hHl~kVlR-lk~Gd~i~i~dg~g~~ 53 (245)
|++.+=..|=.+.-.|.+.-|+ |||| +++||+|.+|-|.|..
T Consensus 199 fINHDCrpnCkFvs~g~~tacv-kvlRDIePGeEITcFYgs~fF 241 (453)
T KOG2589 199 FINHDCRPNCKFVSTGRDTACV-KVLRDIEPGEEITCFYGSGFF 241 (453)
T ss_pred HHCCCCCCCCEEECCCCCEEEE-EHHHCCCCCCEEEEEECCCCC
T ss_conf 6267778886650689860320-041227778536786225656
No 78
>TIGR01213 TIGR01213 conserved hypothetical protein TIGR01213; InterPro: IPR005912 The members of this family of conserved hypothetical proteins show a low level of similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs. .
Probab=20.09 E-value=65 Score=13.55 Aligned_cols=22 Identities=18% Similarity=0.143 Sum_probs=10.1
Q ss_pred CCEEEEECCCCCCCHHHHHHHH
Q ss_conf 8359998888888889999999
Q gi|254781160|r 188 PNVAILIGPEGGYHSEEKETLH 209 (245)
Q Consensus 188 ~~i~i~IGPEGGfs~~E~~~l~ 209 (245)
|..--+|=-++|-|++|++.+.
T Consensus 338 KvYrALV~~~~~v~d~dl~~l~ 359 (450)
T TIGR01213 338 KVYRALVEVDDPVSDEDLEELV 359 (450)
T ss_pred EEEEEEEEECCCCCHHHHHHHH
T ss_conf 1588868875997889999999
No 79
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=20.04 E-value=66 Score=13.54 Aligned_cols=29 Identities=21% Similarity=0.418 Sum_probs=22.8
Q ss_pred HHCCCCCCCEEEEEECCCCEEEEEEECCC
Q ss_conf 70357898889999779987987530235
Q gi|254781160|r 34 HVLRMKEGDNILLFNGKDGEWLSKISYVG 62 (245)
Q Consensus 34 kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~ 62 (245)
+=|+++.||.|.+.-|+..--.++|..+.
T Consensus 8 ~K~kIkkGD~V~VisGkdKGk~G~Vl~v~ 36 (90)
T CHL00141 8 KKMHVKKGDTVQVISGKDKGKIGEVLKII 36 (90)
T ss_pred CCEEEECCCEEEEEECCCCCCCEEEEEEE
T ss_conf 14067089999991667899735799998
Done!