Query gi|254780688|ref|YP_003065101.1| putative flagellar motor switch protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 147
No_of_seqs 169 out of 872
Neff 5.6
Searched_HMMs 39220
Date Sun May 29 20:16:00 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780688.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06782 flagellar motor switc 100.0 1.7E-31 4.4E-36 199.5 9.4 95 47-144 453-547 (547)
2 PRK08119 flagellar motor switc 100.0 2.7E-30 6.9E-35 192.7 11.0 87 58-147 297-383 (390)
3 PRK05698 fliN flagellar motor 100.0 6.6E-30 1.7E-34 190.5 9.2 80 65-147 69-148 (155)
4 PRK08916 flagellar motor switc 100.0 2.7E-28 6.9E-33 181.3 13.2 93 52-147 20-112 (114)
5 PRK08432 flagellar motor switc 100.0 2E-28 5.1E-33 182.0 10.3 85 60-147 189-273 (281)
6 PRK08983 fliN flagellar motor 100.0 4.4E-28 1.1E-32 180.1 10.9 86 59-147 34-119 (126)
7 TIGR02480 fliN flagellar motor 100.0 3.3E-28 8.4E-33 180.8 10.1 77 68-147 1-77 (77)
8 PRK07963 fliN flagellar motor 100.0 6.3E-28 1.6E-32 179.2 10.3 83 62-147 47-129 (137)
9 PRK06788 flagellar motor switc 99.9 1.1E-27 2.9E-32 177.7 10.5 87 58-147 17-103 (119)
10 PRK08433 flagellar motor switc 99.9 1.2E-26 3.1E-31 171.9 10.4 84 61-147 18-101 (111)
11 PRK06033 hypothetical protein; 99.9 1.3E-24 3.3E-29 160.3 11.1 78 65-145 4-81 (87)
12 COG1886 FliN Flagellar motor s 99.9 5.5E-24 1.4E-28 156.7 12.1 82 59-143 55-136 (136)
13 PRK06666 fliM flagellar motor 99.8 8.7E-19 2.2E-23 127.0 11.1 75 70-147 252-326 (336)
14 TIGR02551 SpaO_YscQ type III s 99.8 1.4E-18 3.5E-23 125.9 11.2 72 69-143 254-326 (326)
15 pfam01052 SpoA Surface present 99.7 4.5E-17 1.2E-21 117.2 11.6 75 70-147 3-77 (77)
16 PRK06933 type III secretion sy 99.7 1.1E-15 2.8E-20 109.4 10.3 74 70-146 231-304 (307)
17 PRK08158 surface presentation 99.7 5.9E-16 1.5E-20 110.9 8.8 75 69-146 224-298 (303)
18 PRK12795 fliM flagellar motor 99.5 7.5E-14 1.9E-18 98.9 9.5 74 70-146 287-360 (378)
19 PRK05933 type III secretion sy 99.4 2.2E-12 5.7E-17 90.5 9.7 63 78-143 309-371 (371)
20 COG1868 FliM Flagellar motor s 99.4 2.6E-12 6.6E-17 90.1 9.6 74 70-146 248-321 (332)
21 PRK08035 type III secretion sy 99.3 1.7E-11 4.3E-16 85.5 8.4 74 68-144 244-317 (326)
22 PRK06789 flagellar motor switc 98.1 5.3E-06 1.4E-10 54.1 5.8 59 82-143 1-59 (61)
23 TIGR01397 fliM_switch flagella 98.1 1.1E-05 2.9E-10 52.2 6.5 73 69-144 254-327 (328)
24 PRK05933 type III secretion sy 96.8 0.0072 1.8E-07 36.3 7.4 67 70-138 207-280 (371)
25 PRK06933 type III secretion sy 96.1 0.018 4.6E-07 34.0 5.8 54 73-126 153-208 (307)
26 PRK08158 surface presentation 95.9 0.024 6.1E-07 33.3 5.8 50 72-124 145-194 (303)
27 TIGR02551 SpaO_YscQ type III s 93.0 0.15 3.8E-06 28.8 4.1 44 69-112 136-179 (326)
28 TIGR02305 HpaG-N-term 4-hydrox 55.3 13 0.00033 17.7 3.0 32 89-121 162-193 (206)
29 TIGR01439 lp_hng_hel_AbrB tran 49.5 15 0.00038 17.4 2.6 27 89-115 15-41 (44)
30 pfam06622 SepQ SepQ protein. T 42.4 27 0.00068 15.9 7.9 63 78-143 240-303 (305)
31 TIGR01570 A_thal_3588 uncharac 41.9 14 0.00035 17.5 1.4 13 112-124 71-83 (172)
32 PRK09555 feoA ferrous iron tra 41.7 27 0.0007 15.9 4.0 30 94-123 29-60 (75)
33 TIGR01196 edd phosphogluconate 40.6 7.6 0.00019 19.0 -0.1 46 91-137 541-590 (614)
34 TIGR02303 HpaG-C-term 4-hydrox 40.4 26 0.00066 16.0 2.6 47 67-122 188-234 (249)
35 TIGR00409 proS_fam_II prolyl-t 33.3 2.7 6.9E-05 21.6 -3.3 56 86-146 442-498 (620)
36 pfam10071 DUF2310 Zn-ribbon-co 32.1 39 0.001 15.0 2.6 24 115-140 32-55 (259)
37 cd00982 gltB_C gltb_C. This do 26.9 44 0.0011 14.7 2.0 19 117-141 124-142 (251)
38 COG1838 FumA Tartrate dehydrat 26.1 45 0.0012 14.6 1.9 15 91-105 11-25 (184)
39 pfam09956 DUF2190 Uncharacteri 25.2 53 0.0013 14.2 3.6 20 121-143 19-38 (106)
40 pfam11399 DUF3192 Protein of u 24.0 52 0.0013 14.3 1.9 16 112-127 83-98 (102)
41 COG0070 GltB Glutamate synthas 23.5 55 0.0014 14.1 2.0 19 124-142 151-169 (301)
42 COG0469 PykF Pyruvate kinase [ 23.5 53 0.0013 14.2 1.9 77 67-145 54-142 (477)
43 pfam04023 FeoA FeoA domain. Th 23.3 57 0.0015 14.0 3.5 31 94-124 30-62 (73)
44 TIGR01021 rpsE_bact ribosomal 22.9 58 0.0015 14.0 3.2 29 112-140 15-43 (157)
45 pfam00577 Usher Fimbrial Usher 22.7 59 0.0015 14.0 4.4 10 117-126 729-738 (784)
46 cd00288 Pyruvate_Kinase Pyruva 22.1 60 0.0015 13.9 2.9 70 73-144 57-139 (480)
47 COG3887 Predicted signaling pr 20.5 65 0.0017 13.7 1.9 57 68-124 252-309 (655)
48 PRK04424 fatty acid biosynthes 20.2 67 0.0017 13.7 4.6 28 114-143 139-166 (185)
49 pfam02837 Glyco_hydro_2_N Glyc 20.1 67 0.0017 13.7 2.6 42 82-125 62-103 (159)
No 1
>PRK06782 flagellar motor switch protein; Reviewed
Probab=99.97 E-value=1.7e-31 Score=199.48 Aligned_cols=95 Identities=23% Similarity=0.489 Sum_probs=84.5
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEE
Q ss_conf 77711234445433342310002343055138999992134429999457978899847778880699999989999999
Q gi|254780688|r 47 VDNISEPISSDSNNILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEI 126 (147)
Q Consensus 47 ~~~~~~~~~~~~~~~~~~~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GEl 126 (147)
..+..+|.++......+....++++|+|||++++|+||||+++|+|+|.|.+|++|+|||.+++||+|+|||++||+||+
T Consensus 453 ~~p~vqP~~~~~~~~~~~~~~n~~lLlDVPL~VtVeLGRTKksIKdILel~~GSIIELDKLAgEPVDILVNGklIAkGEV 532 (547)
T PRK06782 453 VEPVVQPIEFKEVKQMEPVYMDTSILQNVEMNVKFVFGSTVKTIQDILSLQENEAVVLDEDIDEPIRIYVNDVLVAYGEL 532 (547)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHCCCCEEEEEEECCCCCCHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEE
T ss_conf 99877876556666567666444651426607999964765509997267999779850016997289998889987759
Q ss_pred EEECCCCCEEEEEEEEEE
Q ss_conf 995688870558999731
Q gi|254780688|r 127 TIMEEDDTHFGVRVIEIL 144 (147)
Q Consensus 127 v~v~e~~~~~gvrIt~ii 144 (147)
|+||| |||||||+.+
T Consensus 533 VVIDE---NFGVRITE~~ 547 (547)
T PRK06782 533 VNVDG---FFGVKVTKSL 547 (547)
T ss_pred EEECC---CCCEEEEECC
T ss_conf 99878---8646776139
No 2
>PRK08119 flagellar motor switch protein; Validated
Probab=99.97 E-value=2.7e-30 Score=192.67 Aligned_cols=87 Identities=34% Similarity=0.708 Sum_probs=80.5
Q ss_pred CCCCCCCCHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEE
Q ss_conf 43334231000234305513899999213442999945797889984777888069999998999999999568887055
Q gi|254780688|r 58 SNNILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFG 137 (147)
Q Consensus 58 ~~~~~~~~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~g 137 (147)
........++|+++|+|||++++|+|||++++++|+|+|++|+||+||+.+++||+|+|||++|||||+|++++ |||
T Consensus 297 ~~~~~~~~~~~~~~~~dvpl~~~v~lg~t~~~i~~~l~l~~g~vi~l~~~~~ep~~i~vng~~ia~gevv~~~~---~fg 373 (390)
T PRK08119 297 EPSLASTEPRNLDLILDVPLQITVELGRTKKSIKDILELGPGSIIELDKLAGEPVDILVNGKLVAKGEVVVIDE---NFG 373 (390)
T ss_pred CCCCCCCCCHHHHHHCCCCEEEEEEEECCEEEHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECC---CCE
T ss_conf 55434455122455313752899998031567999736799977982444799769999999999765999888---403
Q ss_pred EEEEEEECCC
Q ss_conf 8999731679
Q gi|254780688|r 138 VRVIEILNAQ 147 (147)
Q Consensus 138 vrIt~iis~~ 147 (147)
||||+|++++
T Consensus 374 vrit~iv~~~ 383 (390)
T PRK08119 374 VRITDIVSPA 383 (390)
T ss_pred EEEEEECCHH
T ss_conf 7898626989
No 3
>PRK05698 fliN flagellar motor switch protein; Validated
Probab=99.96 E-value=6.6e-30 Score=190.46 Aligned_cols=80 Identities=36% Similarity=0.743 Sum_probs=76.6
Q ss_pred CHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEE
Q ss_conf 10002343055138999992134429999457978899847778880699999989999999995688870558999731
Q gi|254780688|r 65 STDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEIL 144 (147)
Q Consensus 65 ~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~ii 144 (147)
..+|+++|+||||+++|+|||++|+|++||+|++|+||+|++.+++||+|+|||++||+||+|++++ |||||||+|+
T Consensus 69 ~~~nld~ilDIPV~isVElGrt~m~I~elL~L~~GSVIeLdr~agEPvdI~VNg~liA~GEVVVv~d---~fGVRIteIi 145 (155)
T PRK05698 69 EGPNLDVILDIPVSISMEVGSTDINIRNLLQLNQGSVIELDRLAGEPLDVLVNGTLIAHGEVVVVNE---KFGIRLTDVI 145 (155)
T ss_pred CCCCCCEEEECEEEEEEEEECCEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECC---EEEEEEEEEC
T ss_conf 6778327983306999999433227999854599978981566999548999999999886999999---7789999845
Q ss_pred CCC
Q ss_conf 679
Q gi|254780688|r 145 NAQ 147 (147)
Q Consensus 145 s~~ 147 (147)
|+.
T Consensus 146 sp~ 148 (155)
T PRK05698 146 SPS 148 (155)
T ss_pred CHH
T ss_conf 989
No 4
>PRK08916 flagellar motor switch protein; Reviewed
Probab=99.96 E-value=2.7e-28 Score=181.25 Aligned_cols=93 Identities=29% Similarity=0.674 Sum_probs=85.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECC
Q ss_conf 23444543334231000234305513899999213442999945797889984777888069999998999999999568
Q gi|254780688|r 52 EPISSDSNNILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEE 131 (147)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e 131 (147)
++..+.++...+....|+++|+||||+++|+|||++|++++||+|++|+||+|++.+++|++|+|||++||+||+|++|+
T Consensus 20 ~~~~~~~~~~~~~~~~nl~~l~DIpV~vtVeLGrt~m~i~elL~L~~GsVIeLdr~~gepvdI~VNg~liArGEvVvv~d 99 (114)
T PRK08916 20 DDVGYNEEEQASRIAADLEAVFDVPVQVSAVLGRSKMDVGQLLKLGPGAVLELDRKVGEAIDIYVNNRLVARGEVVLVED 99 (114)
T ss_pred CCCCCCCCCCCCCCCCCHHHHCCCCEEEEEEEEEEEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECC
T ss_conf 74555665679863237466146737999999312648999845699988983576899589999999999886999999
Q ss_pred CCCEEEEEEEEEECCC
Q ss_conf 8870558999731679
Q gi|254780688|r 132 DDTHFGVRVIEILNAQ 147 (147)
Q Consensus 132 ~~~~~gvrIt~iis~~ 147 (147)
|||||||+|++++
T Consensus 100 ---~~GVRIteIv~~e 112 (114)
T PRK08916 100 ---KLGVTMTEIIKAE 112 (114)
T ss_pred ---EEEEEEEEEECCC
T ss_conf ---7889999841544
No 5
>PRK08432 flagellar motor switch protein FliY; Validated
Probab=99.95 E-value=2e-28 Score=182.02 Aligned_cols=85 Identities=22% Similarity=0.560 Sum_probs=79.5
Q ss_pred CCCCCCHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEE
Q ss_conf 33423100023430551389999921344299994579788998477788806999999899999999956888705589
Q gi|254780688|r 60 NILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVR 139 (147)
Q Consensus 60 ~~~~~~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvr 139 (147)
.....+.+|+++|+|||++++|+|||++|+++|+|+|.+|+||+|++.+++|++|+|||++|||||+|++++ |||||
T Consensus 189 ~l~~~~~~n~~ll~Dv~l~v~VelGrt~m~ikdiL~l~~GsvveLdk~a~ep~di~vn~~liA~GEvVvv~~---~fGvr 265 (281)
T PRK08432 189 SLSSEEIKNINLIMDVRLPVKVRIGQKKMLLKDVLSMDIGSVVELNQLANDPLEILVDDKVIAKGEVVIVDG---NFGIQ 265 (281)
T ss_pred CCCCHHHCCCCEEEECCEEEEEEECCCEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECC---CCEEE
T ss_conf 557610146105894543899997763047999852799967985223799648999999998762999878---40289
Q ss_pred EEEEECCC
Q ss_conf 99731679
Q gi|254780688|r 140 VIEILNAQ 147 (147)
Q Consensus 140 It~iis~~ 147 (147)
||+|+|++
T Consensus 266 it~I~s~~ 273 (281)
T PRK08432 266 ITDIGTKK 273 (281)
T ss_pred EEEECCHH
T ss_conf 99836989
No 6
>PRK08983 fliN flagellar motor switch protein; Validated
Probab=99.95 E-value=4.4e-28 Score=180.07 Aligned_cols=86 Identities=31% Similarity=0.692 Sum_probs=79.8
Q ss_pred CCCCCCCHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEE
Q ss_conf 33342310002343055138999992134429999457978899847778880699999989999999995688870558
Q gi|254780688|r 59 NNILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGV 138 (147)
Q Consensus 59 ~~~~~~~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gv 138 (147)
........+|+++|+||||+++|+|||++|++++||+|++|+||+|++.+++||+|+|||++||+||+|++|+ ||||
T Consensus 34 ~~~~~~~~~nld~llDIpv~vsVelGrt~m~i~elL~L~~GsVIeLdr~~gepvdI~VNg~liA~GEvVvv~d---~fGV 110 (126)
T PRK08983 34 APITEDEARKLDTILDIPVTISMEVGRSFISIRNLLQLNQGSVVELDRVAGEPLDVMVNGTLIAHGEVVVVND---KFGI 110 (126)
T ss_pred CCCCCCCCCCCCEEECCCEEEEEEEECEEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECC---EEEE
T ss_conf 8767666667215870527999999121758999853699989993875899589999999999988999999---8899
Q ss_pred EEEEEECCC
Q ss_conf 999731679
Q gi|254780688|r 139 RVIEILNAQ 147 (147)
Q Consensus 139 rIt~iis~~ 147 (147)
|||+|+|++
T Consensus 111 RIteIvs~~ 119 (126)
T PRK08983 111 RLTDVISQT 119 (126)
T ss_pred EEEEECCHH
T ss_conf 999845989
No 7
>TIGR02480 fliN flagellar motor switch protein FliN; InterPro: IPR012826 Proteins that consist largely of this domain can be designated flagellar motor switch proteins: FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside of this family, are associated with type III secretion systems (TTSS) and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.; GO: 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0016020 membrane, 0044461 flagellin-based flagellum part.
Probab=99.95 E-value=3.3e-28 Score=180.78 Aligned_cols=77 Identities=42% Similarity=0.826 Sum_probs=74.3
Q ss_pred HHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEECCC
Q ss_conf 02343055138999992134429999457978899847778880699999989999999995688870558999731679
Q gi|254780688|r 68 NFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNAQ 147 (147)
Q Consensus 68 ~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~iis~~ 147 (147)
++++|+|||+++++||||++|+++||++|..||||+|||.++||+||+|||++||+||+|+++| |||||||+|.++.
T Consensus 1 ~~~~~~Dipv~l~velG~~~i~l~dll~l~~GsVieLDk~agepldI~VNG~~ia~GEvvV~~d---k~Giri~ei~~~~ 77 (77)
T TIGR02480 1 NIDLILDIPVELTVELGRTRITLKDLLKLGEGSVIELDKLAGEPLDILVNGRLIARGEVVVVED---KFGIRITEIVDSS 77 (77)
T ss_pred CCCCEEECCEEEEEEEEEEEECHHHHHCCCCCCEEEECCCCCCEEEEEECCCEEEEEEEEEECC---CEEEEEEEEECCC
T ss_conf 9784110105888888656603688843899849996477889215988892788898998679---6008989854179
No 8
>PRK07963 fliN flagellar motor switch protein FliN; Validated
Probab=99.95 E-value=6.3e-28 Score=179.18 Aligned_cols=83 Identities=39% Similarity=0.730 Sum_probs=78.3
Q ss_pred CCCCHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEE
Q ss_conf 42310002343055138999992134429999457978899847778880699999989999999995688870558999
Q gi|254780688|r 62 LEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVI 141 (147)
Q Consensus 62 ~~~~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt 141 (147)
.....+++++|+||||+++|+|||++|++++||+|++|+||+|++.+++|++|+|||++||+||+|++++ |||||||
T Consensus 47 ~~~~~~dldlilDIpV~itVeLGrt~m~i~eLL~L~~GsVIeLdr~agepvdI~VNg~liA~GEVVvv~d---k~GVRIt 123 (137)
T PRK07963 47 VSGTLQDIDLIMDIPVKLTVELGRTRMTIKELLRLTQGSVVALDGLAGEPLDILINGYLIAQGEVVVVAD---KYGVRIT 123 (137)
T ss_pred CCCCCCCCCEEECCEEEEEEEEECCEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECC---EEEEEEE
T ss_conf 6686557226861417999999033208999845699988984775999569999999999987999998---7889999
Q ss_pred EEECCC
Q ss_conf 731679
Q gi|254780688|r 142 EILNAQ 147 (147)
Q Consensus 142 ~iis~~ 147 (147)
+|++++
T Consensus 124 eIisp~ 129 (137)
T PRK07963 124 DIITPS 129 (137)
T ss_pred EECCHH
T ss_conf 855989
No 9
>PRK06788 flagellar motor switch protein; Validated
Probab=99.95 E-value=1.1e-27 Score=177.72 Aligned_cols=87 Identities=28% Similarity=0.555 Sum_probs=80.0
Q ss_pred CCCCCCCCHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEE
Q ss_conf 43334231000234305513899999213442999945797889984777888069999998999999999568887055
Q gi|254780688|r 58 SNNILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFG 137 (147)
Q Consensus 58 ~~~~~~~~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~g 137 (147)
.....+....|+++|+|||++++++|||++|+++|+|+|.+|+||+|++.+|+|++|+|||++||+||+|++|| |||
T Consensus 17 ~~~~~~~~~~nldll~DV~v~vsVELGrt~m~ikdlL~L~~GsVVELdk~AGepvDi~VNgkliArGEVVVvde---~fG 93 (119)
T PRK06788 17 AGKRNEASKAHIDTVSDISIELGVKLGKASITLGDVKQLKVGDVLEVEKNLGHKVDVYLSNMKVGIGEAIVMDE---KFG 93 (119)
T ss_pred CCCCCCCCCCCCCEEEECEEEEEEEECCEEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECC---CCE
T ss_conf 68877676346556971206999997542568999745799868998434899679999999998775999858---606
Q ss_pred EEEEEEECCC
Q ss_conf 8999731679
Q gi|254780688|r 138 VRVIEILNAQ 147 (147)
Q Consensus 138 vrIt~iis~~ 147 (147)
||||+|-+.+
T Consensus 94 VRITeI~~~k 103 (119)
T PRK06788 94 IIISEIEADK 103 (119)
T ss_pred EEEEEECCHH
T ss_conf 8999844456
No 10
>PRK08433 flagellar motor switch protein; Validated
Probab=99.94 E-value=1.2e-26 Score=171.87 Aligned_cols=84 Identities=31% Similarity=0.571 Sum_probs=79.5
Q ss_pred CCCCCHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEE
Q ss_conf 34231000234305513899999213442999945797889984777888069999998999999999568887055899
Q gi|254780688|r 61 ILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRV 140 (147)
Q Consensus 61 ~~~~~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrI 140 (147)
..+...+|+++|+|||++++++|||++|+++++|+|.+|+||+|++.+|+|++++|||++||+||+|++++ ||||||
T Consensus 18 ~~e~~~~~~e~llDi~v~v~vELGrt~m~i~elL~L~~GSVIeLdk~aGEPvDI~VNgrlIArGEVVVv~e---~fGVRI 94 (111)
T PRK08433 18 YLEGLICDYKNLLDMEVDFSAELGTTQISLLEILKFEKGSVIDLEKPAGESVETYINGRIIGKGEVMVYEK---NLAIRI 94 (111)
T ss_pred HHHHHHHHHHHHCCCEEEEEEEEECCEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEECEEEECC---EEEEEE
T ss_conf 99998751786254338999997030568999845799988995455899679999899999647899998---578999
Q ss_pred EEEECCC
Q ss_conf 9731679
Q gi|254780688|r 141 IEILNAQ 147 (147)
Q Consensus 141 t~iis~~ 147 (147)
|+|+++.
T Consensus 95 TeIi~s~ 101 (111)
T PRK08433 95 NEILDSN 101 (111)
T ss_pred EEEECCC
T ss_conf 9983672
No 11
>PRK06033 hypothetical protein; Validated
Probab=99.92 E-value=1.3e-24 Score=160.30 Aligned_cols=78 Identities=27% Similarity=0.475 Sum_probs=74.7
Q ss_pred CHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEE
Q ss_conf 10002343055138999992134429999457978899847778880699999989999999995688870558999731
Q gi|254780688|r 65 STDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEIL 144 (147)
Q Consensus 65 ~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~ii 144 (147)
...+++.|.|||++++++|||++|++++||+|.+|+||+||+.+++||+|++||++||+||+|++|| |||||||+|+
T Consensus 4 g~~~l~~l~~V~v~vsV~LGrt~m~i~~lL~L~~GsVIeLD~~~gepvdi~vN~~liArGEVvV~~d---~~gVriTeIv 80 (87)
T PRK06033 4 GSPFVSTLDKVSVDLMVVLGTTSMPIHQVLRLSRGAIIELDATEADEVKILANNHPIASGVVLVDRN---RIAVEVKRML 80 (87)
T ss_pred CCHHHHHHHCCCEEEEEEECCCEEEHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECC---EEEEEEEEEE
T ss_conf 7213567617617999998555119999735589868986567899489999999998885999898---8899999930
Q ss_pred C
Q ss_conf 6
Q gi|254780688|r 145 N 145 (147)
Q Consensus 145 s 145 (147)
.
T Consensus 81 ~ 81 (87)
T PRK06033 81 P 81 (87)
T ss_pred C
T ss_conf 4
No 12
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=99.91 E-value=5.5e-24 Score=156.67 Aligned_cols=82 Identities=41% Similarity=0.799 Sum_probs=75.5
Q ss_pred CCCCCCCHHHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEE
Q ss_conf 33342310002343055138999992134429999457978899847778880699999989999999995688870558
Q gi|254780688|r 59 NNILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGV 138 (147)
Q Consensus 59 ~~~~~~~~~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gv 138 (147)
....+....+++.++|||++++|+|||++|++++|++|++||||+|++.+++||+|++||++|||||+|++++ ||||
T Consensus 55 ~~~~~~~~~~~~~l~dipv~v~velGr~~~~l~eLl~l~~Gsvi~Ld~~~~e~VdI~vNg~~Ig~GEvVvvdd---~~GV 131 (136)
T COG1886 55 STVLESLNESIDLLLDIPVRLSVELGRTKMPLGELLALGKGSVIELDKLAGEPVDILVNGRLIGRGEVVVVDD---KFGV 131 (136)
T ss_pred CCCCCCCCCCCHHHCCCCEEEEEEEEEEEEEHHHHHHCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECC---EEEE
T ss_conf 7733345434100215856999999313124999971189988976776899669999998997776999988---6789
Q ss_pred EEEEE
Q ss_conf 99973
Q gi|254780688|r 139 RVIEI 143 (147)
Q Consensus 139 rIt~i 143 (147)
|||+|
T Consensus 132 rItei 136 (136)
T COG1886 132 RITEI 136 (136)
T ss_pred EEEEC
T ss_conf 99859
No 13
>PRK06666 fliM flagellar motor switch protein FliM; Validated
Probab=99.79 E-value=8.7e-19 Score=127.04 Aligned_cols=75 Identities=16% Similarity=0.347 Sum_probs=71.6
Q ss_pred HHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEECCC
Q ss_conf 343055138999992134429999457978899847778880699999989999999995688870558999731679
Q gi|254780688|r 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNAQ 147 (147)
Q Consensus 70 ~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~iis~~ 147 (147)
+.|.++||+++++||+++++++||++|++||||+|++.+++||+|+|||+++|+|++++.|+ |+|||||+++..+
T Consensus 252 ~~l~~v~v~v~a~Lg~~~~tl~ell~L~vGDVI~L~~~~~~~v~v~V~g~~~f~g~~G~~~~---~~Av~I~e~i~~~ 326 (336)
T PRK06666 252 EQVQQVEVELVANLGEIKLTLREILNLKVGDVIPLEKPIDDPLTVKVDGKPKFTCQYGKSNG---RKALQIEELIERI 326 (336)
T ss_pred HHHCCCCEEEEEEECCCEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECC---EEEEEEEEECCCC
T ss_conf 98616827999998344478999857999998995798999879999999999999988999---9999998830663
No 14
>TIGR02551 SpaO_YscQ type III secretion apparatus protein, YscQ/HrcQ family; InterPro: IPR013385 Proteins in this entry are encoded within type III secretion operons and are involved in many different functions. For example, YscQ in Yersinia is essential for YOPs secretion , while SpaO in Shigella is involved in the Surface Presentation of Antigens apparatus found on the virulence plasmid , and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae .; GO: 0030254 protein secretion by the type III secretion system.
Probab=99.79 E-value=1.4e-18 Score=125.91 Aligned_cols=72 Identities=24% Similarity=0.490 Sum_probs=68.6
Q ss_pred HHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCC-CCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEE
Q ss_conf 2343055138999992134429999457978899847778-88069999998999999999568887055899973
Q gi|254780688|r 69 FDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRV-GESVDITINNQKIAKGEITIMEEDDTHFGVRVIEI 143 (147)
Q Consensus 69 ~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~-~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~i 143 (147)
..-+.++||+|+|||||..|++.+|.+|++|+||+|...+ +.+|+|++||+.||+||||.||+ ++||||+++
T Consensus 254 ~~~l~~Lpv~l~fE~~r~~l~L~~L~~L~pG~vL~L~~~~~~~~V~l~~nG~~~G~GeLV~~~~---~LGVri~~l 326 (326)
T TIGR02551 254 LVDLDQLPVTLEFELGRLTLTLAELAALQPGSVLELNVPVRDGPVRLRANGRLLGRGELVDVGG---RLGVRILRL 326 (326)
T ss_pred CCCCCCCCEEEEEEEEEEEECHHHHHHCCCCCEEECCCCCCCCCEEEEECCEEEEEEEEEEECC---EEEEEEEEC
T ss_conf 7775642215999997777157999732887432168768877558998775887677898988---875787409
No 15
>pfam01052 SpoA Surface presentation of antigens (SPOA). This family includes the C-terminal region of flagellar motor switch proteins FliN and FliM. It is associated with family FliM, pfam02154.
Probab=99.73 E-value=4.5e-17 Score=117.25 Aligned_cols=75 Identities=31% Similarity=0.650 Sum_probs=71.3
Q ss_pred HHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEECCC
Q ss_conf 343055138999992134429999457978899847778880699999989999999995688870558999731679
Q gi|254780688|r 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNAQ 147 (147)
Q Consensus 70 ~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~iis~~ 147 (147)
+.|.++|++++++||+.+++++||++|++||+|+|++.+++++++++||+++|+|+++.+++ +|||||+++++.+
T Consensus 3 ~~l~~~~v~l~~~l~~~~l~l~~l~~L~~Gdvl~l~~~~~~~v~l~v~~~~~~~g~~g~~~~---~~av~I~~~~~~~ 77 (77)
T pfam01052 3 EELSDVPVELEAVLGRTELTLGELLNLKVGDVIPLDKPAEDPVELYVNGRPIFRGELGVIGG---KLAVRITELLEPE 77 (77)
T ss_pred HHHCCCCEEEEEEEEEEEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECC---EEEEEEEEEECCC
T ss_conf 27617838999999510878999845899999994898999779999999999999999999---9999999840899
No 16
>PRK06933 type III secretion system protein; Validated
Probab=99.65 E-value=1.1e-15 Score=109.40 Aligned_cols=74 Identities=22% Similarity=0.442 Sum_probs=69.8
Q ss_pred HHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEECC
Q ss_conf 34305513899999213442999945797889984777888069999998999999999568887055899973167
Q gi|254780688|r 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNA 146 (147)
Q Consensus 70 ~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~iis~ 146 (147)
.-+.++||+++|++||..+++.+|..|++|++|+|+..++.+|+|++||++||+||+|.|++ |+||||+++...
T Consensus 231 tdldqLpV~l~Fevgrqt~tL~~L~sL~pG~lidL~~pi~g~V~i~ANg~~lG~GeLV~I~~---rLGVRV~~L~~~ 304 (307)
T PRK06933 231 TDLNQLPVQVSFEVGRQTLDLHTLTSLQPGSLIDLTTPVDGEVRLLANGRLLGHGRLVEIQG---RLGVRVERLFGV 304 (307)
T ss_pred CCHHHCCEEEEEEECCEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEECCEEEEEECC---EEEEEEEEEECC
T ss_conf 64421846899996662644999840589857866899887479998775851115998778---535899984245
No 17
>PRK08158 surface presentation of antigens protein SpaO; Validated
Probab=99.65 E-value=5.9e-16 Score=110.90 Aligned_cols=75 Identities=23% Similarity=0.433 Sum_probs=70.5
Q ss_pred HHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEECC
Q ss_conf 234305513899999213442999945797889984777888069999998999999999568887055899973167
Q gi|254780688|r 69 FDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNA 146 (147)
Q Consensus 69 ~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~iis~ 146 (147)
+.-+.|+||+|+|+||+.++++.+|-++.+|.+++|+..+...|+|++||+++|+||+|.|++ ++||+|++.++.
T Consensus 224 l~d~~~LpV~l~FvL~~~~~tl~eL~~l~pG~vl~L~~~~e~~V~I~aNg~l~g~GELV~i~d---~LgVEI~~w~~~ 298 (303)
T PRK08158 224 LPGLNQLPVKLEFVLYRKNVTLAELEELCQQQLLSLPTNAELNVEIRANGALLGNGELVQMDD---TLGVEIHEWLSG 298 (303)
T ss_pred CCCHHHCCEEEEEEECCCEECHHHHHHCCCCCEECCCCCCCCEEEEEECCEEEEEEEEEEECC---EEEEEEHHHHCC
T ss_conf 787532925899997374885999963089847617999764089999998986665999888---366877665546
No 18
>PRK12795 fliM flagellar motor switch protein FliM; Reviewed
Probab=99.53 E-value=7.5e-14 Score=98.91 Aligned_cols=74 Identities=20% Similarity=0.324 Sum_probs=67.8
Q ss_pred HHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEECC
Q ss_conf 34305513899999213442999945797889984777888069999998999999999568887055899973167
Q gi|254780688|r 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNA 146 (147)
Q Consensus 70 ~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~iis~ 146 (147)
+.|.+.+|+++++||+++++++|+++|++||||+|+....++|.++|+|.++++|...+. ++|++|||++.+..
T Consensus 287 ~eI~~a~V~l~A~Lg~~~itL~dvL~LkvGDVI~Ld~~~d~~v~v~v~gvp~F~g~~G~~---~g~~AvqIt~~l~~ 360 (378)
T PRK12795 287 TEIWQTDVEVDAVLDEQTLPLKQVMALKVGDTLPLDARPDALVTLRCGSVPLFEGRMGRV---GDRVAVRVEKPLRK 360 (378)
T ss_pred HHHHCCEEEEEEEEECCEEEHHHHHCCCCCCEEEECCCCCCEEEEEECCEEEEEEECCCC---CCEEEEEEEECCCC
T ss_conf 998359228999993548889998579999989967999960799999999899724748---99899998514789
No 19
>PRK05933 type III secretion system protein; Validated
Probab=99.40 E-value=2.2e-12 Score=90.48 Aligned_cols=63 Identities=25% Similarity=0.558 Sum_probs=60.7
Q ss_pred EEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEE
Q ss_conf 899999213442999945797889984777888069999998999999999568887055899973
Q gi|254780688|r 78 KMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEI 143 (147)
Q Consensus 78 ~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~i 143 (147)
++++|+||.+|+++++++|.+|++++|+-.....|||.+||+.+||||++.+|| -+|||+.++
T Consensus 309 kl~~Ev~R~~ltv~~~lkL~pGs~L~l~vhP~~GvdlilnG~kVgRgei~~lgd---vLGiRVLEv 371 (371)
T PRK05933 309 KLVVEVARYSLSVGEFLKLEPGSILELGVHPTLGVDIILNGAKVGRGEIIALGD---VLGIRVLEV 371 (371)
T ss_pred EEEEEEEEEEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCCEECCCEEEEECC---EEEEEEEEC
T ss_conf 367786533566988733699877762577565613897252641300686403---002578509
No 20
>COG1868 FliM Flagellar motor switch protein [Cell motility and secretion]
Probab=99.40 E-value=2.6e-12 Score=90.13 Aligned_cols=74 Identities=19% Similarity=0.437 Sum_probs=68.3
Q ss_pred HHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEECC
Q ss_conf 34305513899999213442999945797889984777888069999998999999999568887055899973167
Q gi|254780688|r 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNA 146 (147)
Q Consensus 70 ~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~iis~ 146 (147)
..+..++|++.+.+|..++++++|++|.+||||+|++.+.+++.++|+|++++.|+.... ++||+|||++.++.
T Consensus 248 ~~v~~v~V~l~A~l~~~~ltl~~il~L~vGDVI~l~~~~~d~v~v~v~g~~~f~c~~G~~---g~~~aVkI~~~i~~ 321 (332)
T COG1868 248 QQVQRVEVELEARLGEISLTLREILRLEVGDVIPLEKPADDRVTVSVGGKPKFLCQYGKS---GGQYAVKILELINS 321 (332)
T ss_pred HHHHCCCEEEEEEEECCEEEHHHHHCCCCCCEEECCCCCCCEEEEEECCEEEEEEECCCC---CCEEEEEEEEECCC
T ss_conf 997118668999960435469998589888679778877760799999989899811651---87789998310476
No 21
>PRK08035 type III secretion system protein; Validated
Probab=99.28 E-value=1.7e-11 Score=85.47 Aligned_cols=74 Identities=23% Similarity=0.388 Sum_probs=69.8
Q ss_pred HHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEE
Q ss_conf 02343055138999992134429999457978899847778880699999989999999995688870558999731
Q gi|254780688|r 68 NFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEIL 144 (147)
Q Consensus 68 ~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~ii 144 (147)
....|.++|..+.+|+||.++++++|.+|++|+++++...+...|.|+.||+.||.|+++.+|+ .|-|||++..
T Consensus 244 ~~v~L~~lPQtLl~EIGRlsL~lg~L~QLavG~~L~~~t~fygeV~IRLnGq~iG~G~Ll~Cd~---~l~VRI~rW~ 317 (326)
T PRK08035 244 SSVELEQLPQQVLFEIGRLSLEIGQLRQLAVGDVLPVGGCFAPEVTIRLNGQIIGQGELIACDN---ELMVRITRWY 317 (326)
T ss_pred CCHHHHHCCCEEEEEEEEEEEEHHHHHHCCCCCEECCCCEECCEEEEEECCEEECCCCEEEECC---EEEEEEEEEE
T ss_conf 3201554761118773066300677540055657201241623689998891852530784088---5699987621
No 22
>PRK06789 flagellar motor switch protein; Validated
Probab=98.14 E-value=5.3e-06 Score=54.14 Aligned_cols=59 Identities=22% Similarity=0.479 Sum_probs=55.0
Q ss_pred EEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEE
Q ss_conf 99213442999945797889984777888069999998999999999568887055899973
Q gi|254780688|r 82 ILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEI 143 (147)
Q Consensus 82 eLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~i 143 (147)
||||++..+.+||.++.|.++.|..+...-|.|.+.|..|++||+..-+ |++=|+|+++
T Consensus 1 ElG~Tkq~v~~LL~i~KGT~~RLE~ST~N~Vki~i~~~~IG~G~ILTKd---GKm~V~Iv~L 59 (61)
T PRK06789 1 EIGNTKKKIEDLLHITKGTLYRLENSTKNTVRLMLENEEIGTGKILTKN---GKMYVEIVEL 59 (61)
T ss_pred CCCCCCCHHHHHHEECCCEEEEEECCCCCEEEEEECCCEEEEEEEECCC---CEEEEEEEEE
T ss_conf 9773224023341202555999733788899999826466100587028---8399999983
No 23
>TIGR01397 fliM_switch flagellar motor switch protein FliM; InterPro: IPR001689 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour . The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour . CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN . Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N or C termini being less important . Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins . This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring , .; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009425 flagellin-based flagellum basal body.
Probab=98.08 E-value=1.1e-05 Score=52.23 Aligned_cols=73 Identities=18% Similarity=0.357 Sum_probs=66.4
Q ss_pred HHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECC-CCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEE
Q ss_conf 2343055138999992134429999457978899847-778880699999989999999995688870558999731
Q gi|254780688|r 69 FDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLD-KRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEIL 144 (147)
Q Consensus 69 ~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld-~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~ii 144 (147)
...+..+++.+...+|...+++++++++.+|++++++ ....+++.+.++|++.+.+... ..++++++++++.+
T Consensus 254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gd~~~~~~~~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~~~~~~ 327 (328)
T TIGR01397 254 KRELSTVPLDLVAVLGEVELSLRELLNLQPGDVLPLGNTDLPDELSLRVGGLPKFLAQPG---VKGGKLAVRITEEI 327 (328)
T ss_pred HHHHHHCCEEEEEECCCCCCCHHHHHCCCCCCEEEECCCCCCCCEEEEECCCCEEEECCC---CCCCCEEEEEECCC
T ss_conf 987751540144420221000577641577753541666666412676545300000045---44660246530013
No 24
>PRK05933 type III secretion system protein; Validated
Probab=96.81 E-value=0.0072 Score=36.27 Aligned_cols=67 Identities=15% Similarity=0.351 Sum_probs=55.1
Q ss_pred HHHC-CCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCC------EEEEECCEEEEEEEEEEECCCCCEEEE
Q ss_conf 3430-55138999992134429999457978899847778880------699999989999999995688870558
Q gi|254780688|r 70 DLIM-NIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGES------VDITINNQKIAKGEITIMEEDDTHFGV 138 (147)
Q Consensus 70 ~~l~-dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~ep------V~i~vng~~ia~GElv~v~e~~~~~gv 138 (147)
.-+. .+|+.+++|.|.+.++-+|--++..||.|-||-..-+| +-+.|||+++++|.+. |...|+|-|
T Consensus 207 ~~ld~~~~i~lsvEvG~tqLsqeEW~qv~~GdFi~LDSCsyDP~~~~~~~lLti~g~~ff~gr~~--d~~~g~fki 280 (371)
T PRK05933 207 HKLDKQTPITLSVEVGYCQLSQEEWHQVVPGSFILLDSCLYDPDTEESGALLTVQGHQFFGGRFL--DPQSGEFKI 280 (371)
T ss_pred HHHCCCCCEEEEEEEEEEEECHHHHHHCCCCCEEEEECCCCCCCCCCCCEEEEECCEECCCCEEC--CCCCCCEEE
T ss_conf 33056652599998613897499985106785798721344898765535899856862265635--777770576
No 25
>PRK06933 type III secretion system protein; Validated
Probab=96.06 E-value=0.018 Score=34.00 Aligned_cols=54 Identities=15% Similarity=0.291 Sum_probs=47.3
Q ss_pred CCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCC--CCCCCEEEEECCEEEEEEEE
Q ss_conf 0551389999921344299994579788998477--78880699999989999999
Q gi|254780688|r 73 MNIPVKMQIILGSCCMQISNLVNLSKGDVITLDK--RVGESVDITINNQKIAKGEI 126 (147)
Q Consensus 73 ~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~--~~~epV~i~vng~~ia~GEl 126 (147)
.-+|+.+++..|++.+++.++..|..|||+-++. .++.++-++|.|++.||..+
T Consensus 153 l~LPl~LSlqwg~~~Ltl~e~~tLe~GDVll~p~~~~~~~q~L~~ve~~p~a~cql 208 (307)
T PRK06933 153 IPLPLLLSLQWGKVYLTLDEFDSLELGDVLLAPEGSGPNSPVLAYVEGRPWAYCQL 208 (307)
T ss_pred CCCEEEEEEEEEEEEEEHHHHHCCCCCCEEECCCCCCCCCEEEEEECCCCCEEECC
T ss_conf 14206999874026987878410022558802875677871489983886556504
No 26
>PRK08158 surface presentation of antigens protein SpaO; Validated
Probab=95.91 E-value=0.024 Score=33.31 Aligned_cols=50 Identities=20% Similarity=0.226 Sum_probs=44.1
Q ss_pred HCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEE
Q ss_conf 30551389999921344299994579788998477788806999999899999
Q gi|254780688|r 72 IMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKG 124 (147)
Q Consensus 72 l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~G 124 (147)
...+|+.+.|+||...++.+-|.++..|||+-..... ..+.|+|+.|++=
T Consensus 145 ~~~lp~~l~fvLG~S~ls~~lL~~I~~GDvLlI~~~~---~~v~i~gr~ig~f 194 (303)
T PRK08158 145 PKMLRWPLRFVIGSSDTQRSLLGRIGIGDVLLISTSR---AEVYCYAKKIGHF 194 (303)
T ss_pred CCCCCEEEEEEEEECCCCHHHHHCCCCCCEEEEEECC---CEEEECCEEEEEE
T ss_conf 5656268999975340789887205667589995055---1379957998888
No 27
>TIGR02551 SpaO_YscQ type III secretion apparatus protein, YscQ/HrcQ family; InterPro: IPR013385 Proteins in this entry are encoded within type III secretion operons and are involved in many different functions. For example, YscQ in Yersinia is essential for YOPs secretion , while SpaO in Shigella is involved in the Surface Presentation of Antigens apparatus found on the virulence plasmid , and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae .; GO: 0030254 protein secretion by the type III secretion system.
Probab=93.03 E-value=0.15 Score=28.77 Aligned_cols=44 Identities=23% Similarity=0.435 Sum_probs=38.9
Q ss_pred HHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCE
Q ss_conf 23430551389999921344299994579788998477788806
Q gi|254780688|r 69 FDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESV 112 (147)
Q Consensus 69 ~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV 112 (147)
-..+..||+.+.+++|.+.+++++|.+|.+|||+-++.....+.
T Consensus 136 ~~~~~~~~~~~~l~~G~~~l~~~~L~~l~~GDvLL~~~~~~~~~ 179 (326)
T TIGR02551 136 TVRLKALPLPVRLEIGSSRLALAELRSLEPGDVLLLDNPAAARA 179 (326)
T ss_pred CCCCCCCEEEEEEEEEEEEECHHHHHHHCCCCEEECCCCCCCCC
T ss_conf 44345530688899853563467762320585663265311220
No 28
>TIGR02305 HpaG-N-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal subunit; InterPro: IPR012686 This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related C-terminal domain (IPR012684 from INTERPRO). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity.
Probab=55.32 E-value=13 Score=17.68 Aligned_cols=32 Identities=25% Similarity=0.434 Sum_probs=23.8
Q ss_pred CHHHHHCCCCCCEEECCCCCCCCEEEEECCEEE
Q ss_conf 299994579788998477788806999999899
Q gi|254780688|r 89 QISNLVNLSKGDVITLDKRVGESVDITINNQKI 121 (147)
Q Consensus 89 ~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~i 121 (147)
.|.|++.|.+||||-+.. .++.+.+.-|++..
T Consensus 162 ~~s~FmTL~~GDvll~Gt-~~~~~~v~~Gd~V~ 193 (206)
T TIGR02305 162 EVSDFMTLEAGDVLLLGT-PEERVKVGPGDRVR 193 (206)
T ss_pred HHHHHHHCCCCCEEEECC-CCCCEECCCCCEEE
T ss_conf 975886027698899706-78862427887888
No 29
>TIGR01439 lp_hng_hel_AbrB transcriptional regulator, AbrB family; InterPro: IPR006339 This DNA-binding domain is found in proteins like AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. .
Probab=49.52 E-value=15 Score=17.36 Aligned_cols=27 Identities=15% Similarity=0.277 Sum_probs=21.6
Q ss_pred CHHHHHCCCCCCEEECCCCCCCCEEEE
Q ss_conf 299994579788998477788806999
Q gi|254780688|r 89 QISNLVNLSKGDVITLDKRVGESVDIT 115 (147)
Q Consensus 89 ~i~dll~L~~G~Vi~Ld~~~~epV~i~ 115 (147)
.+++-|+|++||-+++...-++.+.|.
T Consensus 15 ~iR~~lgl~eGd~l~~~~~~d~~i~l~ 41 (44)
T TIGR01439 15 EIREKLGLKEGDKLEVIRVEDGEIILR 41 (44)
T ss_pred HHHHHCCCCCCCEEEEEEECCCEEEEE
T ss_conf 896406999998788988279879898
No 30
>pfam06622 SepQ SepQ protein. This family consists of several enterobacterial SepQ proteins from Escherichia coli and Citrobacter rodentium. The function of this family is unclear.
Probab=42.39 E-value=27 Score=15.92 Aligned_cols=63 Identities=24% Similarity=0.308 Sum_probs=49.4
Q ss_pred EEEEEEEEEEECHHHHHCCCCCCEEECCCC-CCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEE
Q ss_conf 899999213442999945797889984777-888069999998999999999568887055899973
Q gi|254780688|r 78 KMQIILGSCCMQISNLVNLSKGDVITLDKR-VGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEI 143 (147)
Q Consensus 78 ~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~-~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~i 143 (147)
.+...+|...+.+..|.+++..++|.-..- .=....+.-|+..||+|-++.++| .|-..|.-+
T Consensus 240 riycaigtihidih~lrn~kkddii~s~gyhlfggc~lirnnt~iaygsiikine---dfyf~is~v 303 (305)
T pfam06622 240 RIYCAIGTIHVDIHKLRNAKKDDIIDSTGYHLFGGCRLIRNNTIIAYGSIIKINE---DFYFNISLV 303 (305)
T ss_pred EEEEEEEEEEEEHHHHHCCCCCCCCCCCCEEEECCEEEEECCCEEEEEEEEEECC---CEEEEEEEE
T ss_conf 1688632589874875354523433674427753448984584798754899636---469999996
No 31
>TIGR01570 A_thal_3588 uncharacterized plant-specific domain TIGR01570; InterPro: IPR006460 This family of hypothetical plant proteins are defined by a region of about 170 amino acids found at the C terminus. These proteins have highly divergent N-terminal regions rich in low complexity sequence. PSI-BLAST reveals no clear similarity to any characterised protein. At least 12 distinct members are found in Arabidopsis thaliana..
Probab=41.86 E-value=14 Score=17.54 Aligned_cols=13 Identities=15% Similarity=0.202 Sum_probs=11.4
Q ss_pred EEEEECCEEEEEE
Q ss_conf 6999999899999
Q gi|254780688|r 112 VDITINNQKIAKG 124 (147)
Q Consensus 112 V~i~vng~~ia~G 124 (147)
=.+|||||.++++
T Consensus 71 WtmyCNGrK~GYa 83 (172)
T TIGR01570 71 WTMYCNGRKVGYA 83 (172)
T ss_pred CCCEECCEEEEEE
T ss_conf 1400478261023
No 32
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=41.69 E-value=27 Score=15.86 Aligned_cols=30 Identities=10% Similarity=0.323 Sum_probs=24.5
Q ss_pred HCCCCCCEEECCC--CCCCCEEEEECCEEEEE
Q ss_conf 4579788998477--78880699999989999
Q gi|254780688|r 94 VNLSKGDVITLDK--RVGESVDITINNQKIAK 123 (147)
Q Consensus 94 l~L~~G~Vi~Ld~--~~~epV~i~vng~~ia~ 123 (147)
+.+-+|+.+.+-+ +.|+|+.+.++|..++-
T Consensus 29 mGl~pG~~v~v~r~APLGDPiei~vrg~~LsL 60 (75)
T PRK09555 29 LGMLPGSSFNVVRVAPLGDPIHIETRRVSLVL 60 (75)
T ss_pred CCCCCCCEEEEEEECCCCCCEEEEECCEEEEE
T ss_conf 68988979999995789998899987879997
No 33
>TIGR01196 edd phosphogluconate dehydratase; InterPro: IPR004786 Two dehydratases, dihydroxy-acid dehydratase (gene ilvD or ILV3) and 6-phosphogluconate dehydratase (gene edd) have been shown to be evolutionary related . Dihydroxy-acid dehydratase catalyzes the fourth step in the biosynthesis of isoleucine and valine, the dehydratation of 2,3-dihydroxy-isovaleic acid into alpha-ketoisovaleric acid. 6-Phosphogluconate dehydratase catalyzes the first step in the Entner-Doudoroff pathway, the dehydratation of 6-phospho-D-gluconate into 6-phospho-2-dehydro-3-deoxy-D-gluconate. Another protein containing this signature is the Escherichia coli hypothetical protein yjhG. The N-terminal part of the proteins contains a cysteine that could be involved in the binding of a 2Fe-2S iron-sulphur cluster . This family defines the 6-phosphogluconate dehydratases.; GO: 0004456 phosphogluconate dehydratase activity, 0009255 Entner-Doudoroff pathway.
Probab=40.64 E-value=7.6 Score=19.03 Aligned_cols=46 Identities=22% Similarity=0.515 Sum_probs=32.4
Q ss_pred HHHHCCCCCCEEECCCCCCCCEEEEECCEE---EEEEEEEEEC-CCCCEEE
Q ss_conf 999457978899847778880699999989---9999999956-8887055
Q gi|254780688|r 91 SNLVNLSKGDVITLDKRVGESVDITINNQK---IAKGEITIME-EDDTHFG 137 (147)
Q Consensus 91 ~dll~L~~G~Vi~Ld~~~~epV~i~vng~~---ia~GElv~v~-e~~~~~g 137 (147)
+-|.+++.||+|++|..-|+ +.|+|++.. +.-=++-.++ =++++||
T Consensus 541 G~iAkirdGD~iR~D~~nG~-L~VLv~d~EkrG~~aR~~~~~dnL~~~~~G 590 (614)
T TIGR01196 541 GPIAKIRDGDLIRVDAVNGE-LNVLVDDAEKRGLNAREPEEIDNLSDNEFG 590 (614)
T ss_pred CCEEEEECCCEEEECCCCCE-EEEEHHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf 97478623878898077880-442147785146565663553457887866
No 34
>TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; InterPro: IPR012684 This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species, this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (IPR012686 from INTERPRO). In other species such as Pasteurella multocida, these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity.
Probab=40.37 E-value=26 Score=16.00 Aligned_cols=47 Identities=21% Similarity=0.347 Sum_probs=36.2
Q ss_pred HHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEE
Q ss_conf 00234305513899999213442999945797889984777888069999998999
Q gi|254780688|r 67 DNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIA 122 (147)
Q Consensus 67 ~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia 122 (147)
+.-+||-|||-=|.+ |+.|+.|+|||+|-...+-|- .++..++....
T Consensus 188 ~T~dMiF~va~LiEy--------lS~~mTL~PgD~ilTGTPKG~-~dv~pGD~v~~ 234 (249)
T TIGR02303 188 NTSDMIFSVAYLIEY--------LSEFMTLEPGDVILTGTPKGL-SDVKPGDVVRL 234 (249)
T ss_pred CCCHHHHCHHHHHHH--------HHHCCCCCCCCEEEECCCCCC-CCCCCCCEEEE
T ss_conf 742112046789998--------631024785648870588875-22355878999
No 35
>TIGR00409 proS_fam_II prolyl-tRNA synthetase; InterPro: IPR004500 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Prolyl-tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form, is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This family includes the enzyme from Escherichia coli that contains all three of the conserved consensus motifs characteristic of class II aminoacyl-tRNA synthetases and the enzyme from the spirochete Borrelia burgdorferi.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=33.32 E-value=2.7 Score=21.61 Aligned_cols=56 Identities=14% Similarity=0.279 Sum_probs=46.8
Q ss_pred EEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEE-EEEECCCCCEEEEEEEEEECC
Q ss_conf 3442999945797889984777888069999998999999-999568887055899973167
Q gi|254780688|r 86 CCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGE-ITIMEEDDTHFGVRVIEILNA 146 (147)
Q Consensus 86 ~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GE-lv~v~e~~~~~gvrIt~iis~ 146 (147)
.+=+|+-...+.+|.||.|.....+++...+-|+- ++-+ ++.+| =|||-|++++++
T Consensus 442 g~G~L~~~~gIEVGHIF~LG~kYS~al~A~f~de~-Gk~~t~~~MG----CYGIGVSRl~~A 498 (620)
T TIGR00409 442 GKGTLKIAKGIEVGHIFKLGTKYSKALKATFLDEN-GKEQTFLTMG----CYGIGVSRLVSA 498 (620)
T ss_pred CCCEEEECCCCEEEEEECCCHHHHHHHCCEEECCC-CCCCCEEECC----CCCCHHHHHHHH
T ss_conf 87405640562341133022033333065564668-8502525605----557138999999
No 36
>pfam10071 DUF2310 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310). Members of this family of proteobacterial zinc ribbon proteins are thought to bind to nucleic acids, however their exact function has not as yet been defined.
Probab=32.07 E-value=39 Score=14.96 Aligned_cols=24 Identities=29% Similarity=0.317 Sum_probs=11.3
Q ss_pred EECCEEEEEEEEEEECCCCCEEEEEE
Q ss_conf 99998999999999568887055899
Q gi|254780688|r 115 TINNQKIAKGEITIMEEDDTHFGVRV 140 (147)
Q Consensus 115 ~vng~~ia~GElv~v~e~~~~~gvrI 140 (147)
+-||+.++|...+.+.+ +.|.+|+
T Consensus 32 ryNGQIlgREfp~~~~~--~~f~~rv 55 (259)
T pfam10071 32 RYNGQILGREFPVAMHQ--GEFVVRV 55 (259)
T ss_pred HHCCEEECCCCCEEEEC--CCEEEEE
T ss_conf 96495545542047734--8079999
No 37
>cd00982 gltB_C gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the transfer of ammonia and electrons among three distinct active centers that carry out L-Gln hydrolysis, conversion of 2-oxoglutarate into L-Glu, and electron uptake from a donor. These catalytic sites appear to occur in other domains within the protein, and not the domain in this CD. This particular domain has no known function, but it likely has a structural role as it interacts with the amidotransferase and FMN-binding domains of gltS.
Probab=26.93 E-value=44 Score=14.67 Aligned_cols=19 Identities=26% Similarity=0.422 Sum_probs=10.8
Q ss_pred CCEEEEEEEEEEECCCCCEEEEEEE
Q ss_conf 9989999999995688870558999
Q gi|254780688|r 117 NNQKIAKGEITIMEEDDTHFGVRVI 141 (147)
Q Consensus 117 ng~~ia~GElv~v~e~~~~~gvrIt 141 (147)
.|++++.| ..|| ||+||-.
T Consensus 124 ~G~lf~~G---~aGE---RF~VRNS 142 (251)
T cd00982 124 SGEAFIRG---RAGE---RFAVRNS 142 (251)
T ss_pred CCEEEEEC---CCCC---EEEEECC
T ss_conf 64499963---5442---2467236
No 38
>COG1838 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]
Probab=26.10 E-value=45 Score=14.62 Aligned_cols=15 Identities=33% Similarity=0.614 Sum_probs=7.0
Q ss_pred HHHHCCCCCCEEECC
Q ss_conf 999457978899847
Q gi|254780688|r 91 SNLVNLSKGDVITLD 105 (147)
Q Consensus 91 ~dll~L~~G~Vi~Ld 105 (147)
.++..|++||++-|.
T Consensus 11 e~i~~LkvGd~v~ls 25 (184)
T COG1838 11 EEIAKLKVGDVVYLS 25 (184)
T ss_pred HHHHHCCCCCEEEEE
T ss_conf 888736678889994
No 39
>pfam09956 DUF2190 Uncharacterized conserved protein (DUF2190). This domain, found in various hypothetical prokaryotic proteins, as well as in some putative RecA/RadA recombinases, has no known function.
Probab=25.18 E-value=53 Score=14.25 Aligned_cols=20 Identities=25% Similarity=0.466 Sum_probs=9.1
Q ss_pred EEEEEEEEECCCCCEEEEEEEEE
Q ss_conf 99999999568887055899973
Q gi|254780688|r 121 IAKGEITIMEEDDTHFGVRVIEI 143 (147)
Q Consensus 121 ia~GElv~v~e~~~~~gvrIt~i 143 (147)
+..|++|++|. -|||-++++
T Consensus 19 V~SG~~V~vG~---l~gVA~~d~ 38 (106)
T pfam09956 19 VASGDGVLVGS---LFGVALGDA 38 (106)
T ss_pred EECCCEEEECC---EEEEEECCC
T ss_conf 53188799898---999984454
No 40
>pfam11399 DUF3192 Protein of unknown function (DUF3192). Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Probab=23.98 E-value=52 Score=14.27 Aligned_cols=16 Identities=31% Similarity=0.169 Sum_probs=12.5
Q ss_pred EEEEECCEEEEEEEEE
Q ss_conf 6999999899999999
Q gi|254780688|r 112 VDITINNQKIAKGEIT 127 (147)
Q Consensus 112 V~i~vng~~ia~GElv 127 (147)
--++-||++||+|+-.
T Consensus 83 plvfkn~~LigWG~~a 98 (102)
T pfam11399 83 PLVFKNNKLIGWGEDA 98 (102)
T ss_pred EEEEECCEEEEECCCH
T ss_conf 6899889788956211
No 41
>COG0070 GltB Glutamate synthase domain 3 [Amino acid transport and metabolism]
Probab=23.53 E-value=55 Score=14.15 Aligned_cols=19 Identities=37% Similarity=0.534 Sum_probs=12.0
Q ss_pred EEEEEECCCCCEEEEEEEE
Q ss_conf 9999956888705589997
Q gi|254780688|r 124 GEITIMEEDDTHFGVRVIE 142 (147)
Q Consensus 124 GElv~v~e~~~~~gvrIt~ 142 (147)
|++.+-|..+.|||||-..
T Consensus 151 G~~fi~G~AGeRfaVrnsG 169 (301)
T COG0070 151 GELFIRGNAGERFGVRNSG 169 (301)
T ss_pred CEEEEECCCEEEEEEECCC
T ss_conf 5899965751047897468
No 42
>COG0469 PykF Pyruvate kinase [Carbohydrate transport and metabolism]
Probab=23.50 E-value=53 Score=14.24 Aligned_cols=77 Identities=16% Similarity=0.312 Sum_probs=51.0
Q ss_pred HHHHHHCCCCEEEEEEEEEEEECHHHHHC----CCCCCEEECCCCCC----CCEEEEECC----EEEEEEEEEEECCCCC
Q ss_conf 00234305513899999213442999945----79788998477788----806999999----8999999999568887
Q gi|254780688|r 67 DNFDLIMNIPVKMQIILGSCCMQISNLVN----LSKGDVITLDKRVG----ESVDITINN----QKIAKGEITIMEEDDT 134 (147)
Q Consensus 67 ~~~~~l~dipv~i~veLG~~~i~i~dll~----L~~G~Vi~Ld~~~~----epV~i~vng----~~ia~GElv~v~e~~~ 134 (147)
+.....++.|+-+-.-+--.++.+..+.. |+.|+.+.|..... .+=.+.++. .-+..|..+.++| |
T Consensus 54 R~~~~~~~~~vaIl~DlkGPkIR~g~~~~~~~~l~~G~~~~~~~~~~~~~~~~~~v~v~y~~l~~dV~~G~~iLlDD--G 131 (477)
T COG0469 54 REAAEKLGRPVAILLDLKGPKIRTGKFKGGAVELEKGEKFTLTTDDKVGEGDEERVSVDYKDLAKDVKPGDRILLDD--G 131 (477)
T ss_pred HHHHHHHCCCEEEEECCCCCCCEEEECCCCCEEEECCCEEEEECCCCCCCCCCCEEECCHHHHHHHCCCCCEEEEEC--C
T ss_conf 99999839916999759898430475378848962698899963444568877578425788786538898899968--9
Q ss_pred EEEEEEEEEEC
Q ss_conf 05589997316
Q gi|254780688|r 135 HFGVRVIEILN 145 (147)
Q Consensus 135 ~~gvrIt~iis 145 (147)
++..+++++-.
T Consensus 132 ~i~l~V~~v~~ 142 (477)
T COG0469 132 KIELRVVEVDG 142 (477)
T ss_pred EEEEEEEEEEC
T ss_conf 04899999608
No 43
>pfam04023 FeoA FeoA domain. This family includes FeoA a small protein, probably involved in Fe2+ transport. This presumed short domain is also found at the C-terminus of a variety of metal dependent transcriptional regulators. This suggests that this domain may be metal-binding. In most cases this is likely to be either iron or manganese.
Probab=23.32 E-value=57 Score=14.04 Aligned_cols=31 Identities=19% Similarity=0.401 Sum_probs=24.2
Q ss_pred HCCCCCCEEECCCCC--CCCEEEEECCEEEEEE
Q ss_conf 457978899847778--8806999999899999
Q gi|254780688|r 94 VNLSKGDVITLDKRV--GESVDITINNQKIAKG 124 (147)
Q Consensus 94 l~L~~G~Vi~Ld~~~--~epV~i~vng~~ia~G 124 (147)
+.+.+|..|.+-... +.|+.+.+++..++-+
T Consensus 30 ~Gi~~G~~i~vi~~~~~~g~i~i~i~~~~~al~ 62 (73)
T pfam04023 30 LGLVPGTEVTVVRKAPFGGPLVVRVGGTRIALR 62 (73)
T ss_pred CCCCCCCEEEEEEECCCCCCEEEEECCEEEEEC
T ss_conf 899999899999978899979999999999969
No 44
>TIGR01021 rpsE_bact ribosomal protein S5; InterPro: IPR005712 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 , . This family includes chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=22.92 E-value=58 Score=13.99 Aligned_cols=29 Identities=3% Similarity=0.237 Sum_probs=23.7
Q ss_pred EEEEECCEEEEEEEEEEECCCCCEEEEEE
Q ss_conf 69999998999999999568887055899
Q gi|254780688|r 112 VDITINNQKIAKGEITIMEEDDTHFGVRV 140 (147)
Q Consensus 112 V~i~vng~~ia~GElv~v~e~~~~~gvrI 140 (147)
-.+.=+||.+.--=||+|||.+||.|+=+
T Consensus 15 sKVVKGGRrfsF~ALvVVGd~~G~VG~G~ 43 (157)
T TIGR01021 15 SKVVKGGRRFSFSALVVVGDKKGRVGFGF 43 (157)
T ss_pred EEEEECCCCEEEEEEEEEECCCCEEEEEE
T ss_conf 87642894036899999717874378865
No 45
>pfam00577 Usher Fimbrial Usher protein. This protein is involved in biogenesis of gram negative bacterial pili.
Probab=22.66 E-value=59 Score=13.96 Aligned_cols=10 Identities=10% Similarity=0.242 Sum_probs=3.5
Q ss_pred CCEEEEEEEE
Q ss_conf 9989999999
Q gi|254780688|r 117 NNQKIAKGEI 126 (147)
Q Consensus 117 ng~~ia~GEl 126 (147)
+|+++-.|-.
T Consensus 729 ~G~~lP~Ga~ 738 (784)
T pfam00577 729 DGKPLPFGAE 738 (784)
T ss_pred CCCCCCCCCE
T ss_conf 9885898549
No 46
>cd00288 Pyruvate_Kinase Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state. PK exists as several different isozymes, depending on organism and tissue type. In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung. PK forms a homotetramer, with each subunit containing three domains. The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer.
Probab=22.13 E-value=60 Score=13.90 Aligned_cols=70 Identities=13% Similarity=0.282 Sum_probs=38.7
Q ss_pred CCCCEEEEEEEEEEEECHHHH-----HCCCCCCEEECCC----CCCCCEEEEECCE----EEEEEEEEEECCCCCEEEEE
Q ss_conf 055138999992134429999-----4579788998477----7888069999998----99999999956888705589
Q gi|254780688|r 73 MNIPVKMQIILGSCCMQISNL-----VNLSKGDVITLDK----RVGESVDITINNQ----KIAKGEITIMEEDDTHFGVR 139 (147)
Q Consensus 73 ~dipv~i~veLG~~~i~i~dl-----l~L~~G~Vi~Ld~----~~~epV~i~vng~----~ia~GElv~v~e~~~~~gvr 139 (147)
.+.|+.+-+-|.-.++.++++ ..|+.|+.+.|.. ..+.+-.++++-. .+-.|..+.+++ |++-.+
T Consensus 57 ~~~~i~Il~Dl~GpkiR~g~~~~~~~i~l~~G~~v~l~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~I~idD--G~i~l~ 134 (480)
T cd00288 57 TGGPVAIALDTKGPEIRTGLFKGGKDISLKAGDKFLVTTDPAAKKGTKEKIYVDYKNLTKDVSPGNTILVDD--GLLSLK 134 (480)
T ss_pred CCCCEEEEEECCCCEEEEEECCCCCEEEECCCCEEEEEECCCCCCCCCCEEECCHHHHHHHCCCCCEEEEEC--CEEEEE
T ss_conf 199807999788983589854899637954899999985687678988889657288897658998899947--838999
Q ss_pred EEEEE
Q ss_conf 99731
Q gi|254780688|r 140 VIEIL 144 (147)
Q Consensus 140 It~ii 144 (147)
++++-
T Consensus 135 V~~~~ 139 (480)
T cd00288 135 VLSKD 139 (480)
T ss_pred EEEEC
T ss_conf 99985
No 47
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=20.50 E-value=65 Score=13.70 Aligned_cols=57 Identities=21% Similarity=0.173 Sum_probs=42.3
Q ss_pred HHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEE-ECCEEEEEE
Q ss_conf 023430551389999921344299994579788998477788806999-999899999
Q gi|254780688|r 68 NFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDIT-INNQKIAKG 124 (147)
Q Consensus 68 ~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~-vng~~ia~G 124 (147)
....-.++|++|++=+|.-.-++.++-++.+-..=---.+-|+.|-|. -||++.++|
T Consensus 252 E~s~~~~ipLTLSiGvg~g~~~~~elg~vA~~~L~lAlgRGGDQVvIke~~~k~~fyG 309 (655)
T COG3887 252 EESSQKNIPLTLSIGVGYGENNLIELGEVAQSNLDLALGRGGDQVVIKENNGKVRFYG 309 (655)
T ss_pred HHHHCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEC
T ss_conf 8740347646999985367665778999998757887426886699973799555647
No 48
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=20.18 E-value=67 Score=13.66 Aligned_cols=28 Identities=18% Similarity=0.372 Sum_probs=13.3
Q ss_pred EEECCEEEEEEEEEEECCCCCEEEEEEEEE
Q ss_conf 999998999999999568887055899973
Q gi|254780688|r 114 ITINNQKIAKGEITIMEEDDTHFGVRVIEI 143 (147)
Q Consensus 114 i~vng~~ia~GElv~v~e~~~~~gvrIt~i 143 (147)
+++|++++|+++++.... +++=|++.--
T Consensus 139 V~~Gd~vvAkA~V~~~~g--nk~~V~V~s~ 166 (185)
T PRK04424 139 VKLGERVVAKAEVVRVTD--NKYIVEVKSY 166 (185)
T ss_pred CCCCCEEEEEEEEEEECC--CEEEEEEEEE
T ss_conf 566989999999999729--9999999999
No 49
>pfam02837 Glyco_hydro_2_N Glycosyl hydrolases family 2, sugar binding domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold.
Probab=20.09 E-value=67 Score=13.65 Aligned_cols=42 Identities=7% Similarity=0.016 Sum_probs=26.2
Q ss_pred EEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEE
Q ss_conf 99213442999945797889984777888069999998999999
Q gi|254780688|r 82 ILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGE 125 (147)
Q Consensus 82 eLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GE 125 (147)
--=|+.+.+..-.. ...-.|.|+ .+....+|++||+.++.-+
T Consensus 62 ~wYr~~f~ip~~~~-~~~~~L~f~-gv~~~~~V~lNG~~vG~~~ 103 (159)
T pfam02837 62 GWYRRTFTVPADWK-GKRVFLRFE-GVDSAAYVWVNGEFVGYHK 103 (159)
T ss_pred EEEEEEEEECCCCC-CCEEEEEEC-CEEEEEEEEECCEEEEEEC
T ss_conf 99999989285018-998999989-8818989999999987507
Done!