Query gi|254781212|ref|YP_003065625.1| hypothetical protein CLIBASIA_05595 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 109 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 07:01:16 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781212.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PTZ00056 glutathione peroxidas 68.5 4.1 0.00011 22.1 2.4 34 70-103 29-65 (180) 2 TIGR02237 recomb_radB DNA repa 61.8 6.5 0.00017 20.9 2.4 23 84-106 42-64 (223) 3 pfam00255 GSHPx Glutathione pe 61.5 6.8 0.00017 20.8 2.4 33 71-103 12-46 (108) 4 PRK10606 btuE putative glutath 56.5 8.4 0.00021 20.3 2.2 24 72-95 17-40 (183) 5 KOG0475 consensus 55.9 6.2 0.00016 21.0 1.5 31 77-107 196-226 (696) 6 PTZ00256 glutathione peroxidas 54.8 11 0.00028 19.6 2.6 32 72-103 32-67 (183) 7 KOG1502 consensus 43.3 19 0.00048 18.3 2.3 73 7-94 18-91 (327) 8 TIGR02540 gpx7 putative glutat 42.9 15 0.00038 18.8 1.7 23 75-97 17-39 (153) 9 COG0386 BtuE Glutathione perox 37.7 26 0.00067 17.4 2.3 34 72-105 17-55 (162) 10 COG4888 Uncharacterized Zn rib 37.0 15 0.00038 18.8 1.0 22 78-99 38-59 (104) 11 cd00340 GSH_Peroxidase Glutath 29.6 24 0.00061 17.6 1.0 24 72-95 14-37 (152) 12 pfam08423 Rad51 Rad51. Rad51 i 29.6 38 0.00097 16.5 2.0 57 46-103 24-98 (261) 13 KOG1651 consensus 29.6 28 0.00071 17.3 1.3 23 74-96 28-50 (171) 14 pfam03254 XG_FTase Xyloglucan 29.2 54 0.0014 15.6 3.1 50 59-108 331-380 (477) 15 COG1052 LdhA Lactate dehydroge 28.6 22 0.00057 17.8 0.7 85 1-106 217-307 (324) 16 KOG3220 consensus 27.2 20 0.00051 18.1 0.3 39 20-58 27-87 (225) 17 pfam05300 DUF737 Protein of un 26.3 61 0.0016 15.3 2.9 26 21-46 129-154 (187) 18 TIGR01754 flav_RNR ribonucleot 25.8 52 0.0013 15.7 2.2 21 3-23 13-33 (145) 19 TIGR00457 asnS asparaginyl-tRN 20.7 60 0.0015 15.3 1.7 20 88-107 459-478 (495) 20 pfam02826 2-Hacid_dh_C D-isome 20.6 51 0.0013 15.7 1.3 33 1-33 106-141 (176) 21 pfam04316 FlgM Anti-sigma-28 f 20.6 77 0.002 14.7 2.2 25 9-33 31-55 (57) No 1 >PTZ00056 glutathione peroxidase; Provisional Probab=68.46 E-value=4.1 Score=22.07 Aligned_cols=34 Identities=21% Similarity=0.405 Sum_probs=24.7 Q ss_pred CCHHEEEEECCCCEEEEEEECCCCCC---HHHHHHHH Q ss_conf 52000101016632568873146865---99999986 Q gi|254781212|r 70 DSAHQLALLEGKRSLAVHIASNCGLS---FERIVQMY 103 (109) Q Consensus 70 dsahqlallegkrslavhiasncgls---ferivqmy 103 (109) .....|.-..||--|.|..||.||++ ++...++| T Consensus 29 G~~~~l~~ykGkv~LIVNvAS~CG~T~q~y~~L~~L~ 65 (180) T PTZ00056 29 GNPVPMSSLKNKVLMITNSASKCGLTKSHVKQMNRLH 65 (180) T ss_pred CCEECHHHCCCCEEEEEEECCCCCCCHHHHHHHHHHH T ss_conf 8993489949988999981577788666799999999 No 2 >TIGR02237 recomb_radB DNA repair and recombination protein RadB; InterPro: IPR011939 This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO) and DMC1 (IPR011940 from INTERPRO), and archaeal RadA (IPR011938 from INTERPRO) ,, .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination. Probab=61.76 E-value=6.5 Score=20.92 Aligned_cols=23 Identities=39% Similarity=0.408 Sum_probs=21.0 Q ss_pred EEEEEECCCCCCHHHHHHHHCCC Q ss_conf 56887314686599999986268 Q gi|254781212|r 84 LAVHIASNCGLSFERIVQMYSDN 106 (109) Q Consensus 84 lavhiasncglsferivqmysdn 106 (109) .+|-|-+.-|||.||+-||.+++ T Consensus 42 ~v~YiDTEGGLS~ER~~q~~~~~ 64 (223) T TIGR02237 42 KVVYIDTEGGLSPERFKQIAEDR 64 (223) T ss_pred CEEEEECCCCCHHHHHHHHHHCC T ss_conf 58999628983289999986305 No 3 >pfam00255 GSHPx Glutathione peroxidase. Probab=61.55 E-value=6.8 Score=20.81 Aligned_cols=33 Identities=30% Similarity=0.558 Sum_probs=23.8 Q ss_pred CHHEEEEECCCCEEEEEEECCCCCC--HHHHHHHH Q ss_conf 2000101016632568873146865--99999986 Q gi|254781212|r 71 SAHQLALLEGKRSLAVHIASNCGLS--FERIVQMY 103 (109) Q Consensus 71 sahqlallegkrslavhiasncgls--ferivqmy 103 (109) ....|.-..||--|.|..||.||++ ++...++| T Consensus 12 ~~~~l~~ykGkv~LIVNvAS~Cg~t~qy~~L~~L~ 46 (108) T pfam00255 12 EPVPLDQYRGKVLLIVNVASKCGLTPQYTELNELQ 46 (108) T ss_pred CEECHHHCCCCEEEEEEECCCCCCCCCHHHHHHHH T ss_conf 99488993998899999557788970799999999 No 4 >PRK10606 btuE putative glutathione peroxidase; Provisional Probab=56.55 E-value=8.4 Score=20.27 Aligned_cols=24 Identities=38% Similarity=0.624 Sum_probs=19.7 Q ss_pred HHEEEEECCCCEEEEEEECCCCCC Q ss_conf 000101016632568873146865 Q gi|254781212|r 72 AHQLALLEGKRSLAVHIASNCGLS 95 (109) Q Consensus 72 ahqlallegkrslavhiasncgls 95 (109) ...|.-..||--|.|..||.||++ T Consensus 17 ~~~l~~y~GKvvLIVNvAS~CG~T 40 (183) T PRK10606 17 VTTLEKYAGNVLLIVNVASKCGLT 40 (183) T ss_pred EECHHHCCCCEEEEEECCCCCCCC T ss_conf 934899399689999777557880 No 5 >KOG0475 consensus Probab=55.89 E-value=6.2 Score=21.04 Aligned_cols=31 Identities=39% Similarity=0.474 Sum_probs=27.3 Q ss_pred EECCCCEEEEEEECCCCCCHHHHHHHHCCCC Q ss_conf 1016632568873146865999999862689 Q gi|254781212|r 77 LLEGKRSLAVHIASNCGLSFERIVQMYSDNP 107 (109) Q Consensus 77 llegkrslavhiasncglsferivqmysdnp 107 (109) |--||..--||||.+||--|++|..-|++|- T Consensus 196 LSlGKEGP~VHiA~c~g~~~s~~f~~~~~~e 226 (696) T KOG0475 196 LSLGKEGPSVHIATCIGNIFSKIFPKYRLNE 226 (696) T ss_pred CCCCCCCCCEEEEECHHHHHHHHHHHHCCCH T ss_conf 5557778733654101036766420101223 No 6 >PTZ00256 glutathione peroxidase; Provisional Probab=54.83 E-value=11 Score=19.58 Aligned_cols=32 Identities=34% Similarity=0.837 Sum_probs=22.2 Q ss_pred HHEEEEECCCCEEE-EEEECCCCCC---HHHHHHHH Q ss_conf 00010101663256-8873146865---99999986 Q gi|254781212|r 72 AHQLALLEGKRSLA-VHIASNCGLS---FERIVQMY 103 (109) Q Consensus 72 ahqlallegkrsla-vhiasncgls---ferivqmy 103 (109) ...|.-.+||.-|- |..||.||+. ++...++| T Consensus 32 ~~~L~~y~Gk~vlivVNvAS~CG~T~q~Y~~L~~L~ 67 (183) T PTZ00256 32 KTQLSKFQGKKAYICVNVACSCGLTSSNYSELVELY 67 (183) T ss_pred EEEHHHCCCCEEEEEEEECCCCCCCCCCHHHHHHHH T ss_conf 952899599879999981567789836189999999 No 7 >KOG1502 consensus Probab=43.34 E-value=19 Score=18.26 Aligned_cols=73 Identities=27% Similarity=0.423 Sum_probs=44.3 Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC-CCEEEHHHHHCCCCCCCCCCCCHHEEEEECCCCEEE Q ss_conf 9999987664225410448999775688899888777640788-605101123405300012575200010101663256 Q gi|254781212|r 7 LADMIKSKVLSRGYTVDSDALARQLEEDERRIRHYKHVYSTPE-GRFVLTDLMVEGGLLSSVSNDSAHQLALLEGKRSLA 85 (109) Q Consensus 7 ladmikskvlsrgytvdsdalarqleederrirhykhvystpe-grfvltdlmveggllssvsndsahqlallegkrsla 85 (109) +|--|-...|+|||+|- +..|..|+ +..+.|-+..-..+| ....-.||.-++.+...+.. -.-- T Consensus 18 Igswivk~LL~rGY~V~--gtVR~~~~-~k~~~~L~~l~~a~~~l~l~~aDL~d~~sf~~ai~g------------cdgV 82 (327) T KOG1502 18 IGSWIVKLLLSRGYTVR--GTVRDPED-EKKTEHLRKLEGAKERLKLFKADLLDEGSFDKAIDG------------CDGV 82 (327) T ss_pred HHHHHHHHHHHCCCEEE--EEECCCCH-HHHHHHHHHCCCCCCCCEEEECCCCCCCHHHHHHHC------------CCEE T ss_conf 99999999986899899--99708630-565899986515754425885243551359999707------------8789 Q ss_pred EEEECCCCC Q ss_conf 887314686 Q gi|254781212|r 86 VHIASNCGL 94 (109) Q Consensus 86 vhiasncgl 94 (109) .|+||.+-. T Consensus 83 fH~Asp~~~ 91 (327) T KOG1502 83 FHTASPVDF 91 (327) T ss_pred EEECCCCCC T ss_conf 991766787 No 8 >TIGR02540 gpx7 putative glutathione peroxidase Gpx7; InterPro: IPR013376 This model represents one of several families of known and probable glutathione peroxidases. It is restricted to animals and designated GPX7.; GO: 0004602 glutathione peroxidase activity, 0006979 response to oxidative stress. Probab=42.91 E-value=15 Score=18.82 Aligned_cols=23 Identities=39% Similarity=0.595 Sum_probs=18.9 Q ss_pred EEEECCCCEEEEEEECCCCCCHH Q ss_conf 10101663256887314686599 Q gi|254781212|r 75 LALLEGKRSLAVHIASNCGLSFE 97 (109) Q Consensus 75 lallegkrslavhiasncglsfe 97 (109) |.-..||-||.|.+||.|++.=. T Consensus 17 LeKYrG~vsLVVNVAS~c~~td~ 39 (153) T TIGR02540 17 LEKYRGKVSLVVNVASECEFTDQ 39 (153) T ss_pred EEEECCEEEEEEEECCCCCCHHH T ss_conf 11001107899870278810057 No 9 >COG0386 BtuE Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones] Probab=37.73 E-value=26 Score=17.42 Aligned_cols=34 Identities=35% Similarity=0.590 Sum_probs=24.8 Q ss_pred HHEEEEECCCCEEEEEEECCCCCC-----HHHHHHHHCC Q ss_conf 000101016632568873146865-----9999998626 Q gi|254781212|r 72 AHQLALLEGKRSLAVHIASNCGLS-----FERIVQMYSD 105 (109) Q Consensus 72 ahqlallegkrslavhiasncgls-----ferivqmysd 105 (109) .-.|.-..||--|-|..||.||+. +|.+-+-|.| T Consensus 17 ~~~l~~y~GkVlLIVNtASkCGfTpQYegLe~Ly~ky~~ 55 (162) T COG0386 17 PVSLSDYKGKVLLIVNTASKCGFTPQYEGLEALYKKYKD 55 (162) T ss_pred CCCHHHHCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHH T ss_conf 824899299689999745446886758999999999864 No 10 >COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only] Probab=37.00 E-value=15 Score=18.81 Aligned_cols=22 Identities=32% Similarity=0.625 Sum_probs=17.7 Q ss_pred ECCCCEEEEEEECCCCCCHHHH Q ss_conf 0166325688731468659999 Q gi|254781212|r 78 LEGKRSLAVHIASNCGLSFERI 99 (109) Q Consensus 78 legkrslavhiasncglsferi 99 (109) +.-+-..++-+-+|||||||-- T Consensus 38 vkk~~~~g~~~Cg~CGls~e~e 59 (104) T COG4888 38 VKKTVNIGTAVCGNCGLSFECE 59 (104) T ss_pred EEECCCEEEEECCCCCCEEEEE T ss_conf 9742745689714575537882 No 11 >cd00340 GSH_Peroxidase Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection against reactive oxygen species, redox regulation of many metabolic processes, peroxinitrite scavenging, and modulation of inflammatory processes. Probab=29.63 E-value=24 Score=17.64 Aligned_cols=24 Identities=38% Similarity=0.643 Sum_probs=18.3 Q ss_pred HHEEEEECCCCEEEEEEECCCCCC Q ss_conf 000101016632568873146865 Q gi|254781212|r 72 AHQLALLEGKRSLAVHIASNCGLS 95 (109) Q Consensus 72 ahqlallegkrslavhiasncgls 95 (109) ...|.-..||-.|.|..||.||.+ T Consensus 14 ~~~l~~y~GkvvLiVNvAS~Cg~t 37 (152) T cd00340 14 PVSLSKYKGKVLLIVNVASKCGFT 37 (152) T ss_pred EECHHHCCCCEEEEEECCCCCCCC T ss_conf 945899399789999667788887 No 12 >pfam08423 Rad51 Rad51. Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein. Probab=29.56 E-value=38 Score=16.48 Aligned_cols=57 Identities=25% Similarity=0.359 Sum_probs=32.8 Q ss_pred CCCCCCEEEHHHHHCCCCCCCC---------C--CCCHHEEEE-------ECCCCEEEEEEECCCCCCHHHHHHHH Q ss_conf 0788605101123405300012---------5--752000101-------01663256887314686599999986 Q gi|254781212|r 46 STPEGRFVLTDLMVEGGLLSSV---------S--NDSAHQLAL-------LEGKRSLAVHIASNCGLSFERIVQMY 103 (109) Q Consensus 46 stpegrfvltdlmveggllssv---------s--ndsahqlal-------legkrslavhiasncglsferivqmy 103 (109) .-|-|-..|.+++- ||+-... | ..-+|||++ +.|.-.-++-|-+.-+++-||+.||- T Consensus 24 ~isTg~~~LD~lLg-GGi~~g~ITEi~G~~gsGKTQlc~qlav~~qlp~~~gg~~g~vvyIDTEg~f~~eRl~qia 98 (261) T pfam08423 24 RITTGSKELDKLLG-GGIETGSITEVFGEFRTGKTQLCHTLCVTCQLPLEMGGGEGKALYIDTEGTFRPERIVAIA 98 (261) T ss_pred EECCCCHHHHHHHC-CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCHHHHCCCCCEEEEEECCCCCCHHHHHHHH T ss_conf 57789878998737-9866772999989988878999999999940709656999728999368886989999999 No 13 >KOG1651 consensus Probab=29.55 E-value=28 Score=17.27 Aligned_cols=23 Identities=43% Similarity=0.678 Sum_probs=18.9 Q ss_pred EEEEECCCCEEEEEEECCCCCCH Q ss_conf 01010166325688731468659 Q gi|254781212|r 74 QLALLEGKRSLAVHIASNCGLSF 96 (109) Q Consensus 74 qlallegkrslavhiasncglsf 96 (109) .|.-..||-.|-|.+||-||+.- T Consensus 28 ~l~~yrGkV~LiVNVAS~Cg~T~ 50 (171) T KOG1651 28 SLSQYRGKVVLIVNVASQCGLTE 50 (171) T ss_pred CHHHHCCEEEEEEECCCCCCCCH T ss_conf 67891873999997100105651 No 14 >pfam03254 XG_FTase Xyloglucan fucosyltransferase. Plant cell walls are crucial for development, signal transduction, and disease resistance in plants. Cell walls are made of cellulose, hemicelluloses, and pectins. Xyloglucan (XG), the principal load-bearing hemicellulose of dicotyledonous plants, has a terminal fucosyl residue. This fucosyltransferase adds this residue. Probab=29.15 E-value=54 Score=15.58 Aligned_cols=50 Identities=24% Similarity=0.326 Sum_probs=34.4 Q ss_pred HCCCCCCCCCCCCHHEEEEECCCCEEEEEEECCCCCCHHHHHHHHCCCCC Q ss_conf 40530001257520001010166325688731468659999998626899 Q gi|254781212|r 59 VEGGLLSSVSNDSAHQLALLEGKRSLAVHIASNCGLSFERIVQMYSDNPR 108 (109) Q Consensus 59 veggllssvsndsahqlallegkrslavhiasncglsferivqmysdnpr 108 (109) .+-.||..|...+.--..-....++-||-|+|--.--+|+|-.||-.+|. T Consensus 331 ~~e~LLPev~~~~~~~~~~~~~~~~kAVLVtSL~~~Yye~lr~mY~~~pt 380 (477) T pfam03254 331 QKEKLLPEVDTQEPSVASASRNQKSKAVLVTSLYSEYYEKIKNMYWEHPT 380 (477) T ss_pred HHCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHCCCC T ss_conf 64345888666677777767788547999995878999999998850777 No 15 >COG1052 LdhA Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only] Probab=28.56 E-value=22 Score=17.84 Aligned_cols=85 Identities=28% Similarity=0.375 Sum_probs=49.4 Q ss_pred CCCHHHHHHHHHHHHH---HCCCCCCHHHHHHHHHHHHHHHHHHH-HHHCCCCCCEEEHHHHHCCCCCCCCCCCCHHEEE Q ss_conf 9639999999987664---22541044899977568889988877-7640788605101123405300012575200010 Q gi|254781212|r 1 MVNFRKLADMIKSKVL---SRGYTVDSDALARQLEEDERRIRHYK-HVYSTPEGRFVLTDLMVEGGLLSSVSNDSAHQLA 76 (109) Q Consensus 1 mvnfrkladmikskvl---srgytvdsdalarqleederrirhyk-hvystpegrfvltdlmveggllssvsndsahqla 76 (109) |+|-..|+.|-+.-+| +||-.||.+||.+-|++. .|..+- .||..-.-.+ |. .|. T Consensus 217 Lin~~~l~~mk~ga~lVNtaRG~~VDe~ALi~AL~~g--~i~gaglDV~e~Ep~~~-----------------d~--~l~ 275 (324) T COG1052 217 LINAEELAKMKPGAILVNTARGGLVDEQALIDALKSG--KIAGAGLDVFENEPALF-----------------DH--PLL 275 (324) T ss_pred HCCHHHHHHCCCCEEEEECCCCCEECHHHHHHHHHCC--CCCEEEECCCCCCCCCC-----------------CH--HHH T ss_conf 3299999756897699964874216599999999809--74226701167888778-----------------80--676 Q ss_pred EEC--CCCEEEEEEECCCCCCHHHHHHHHCCC Q ss_conf 101--663256887314686599999986268 Q gi|254781212|r 77 LLE--GKRSLAVHIASNCGLSFERIVQMYSDN 106 (109) Q Consensus 77 lle--gkrslavhiasncglsferivqmysdn 106 (109) -+. .+-.+.-||||--.-+.+++++.--+| T Consensus 276 ~l~~~~~vvltPHia~at~ea~~~m~~~~~~n 307 (324) T COG1052 276 RLDNFPNVVLTPHIASATEEARKAMAELALEN 307 (324) T ss_pred HCCCCCCEEEECCCCCCCHHHHHHHHHHHHHH T ss_conf 36689987970441302099999999999999 No 16 >KOG3220 consensus Probab=27.18 E-value=20 Score=18.12 Aligned_cols=39 Identities=33% Similarity=0.470 Sum_probs=26.8 Q ss_pred CCCCHHHHHHHHHH--------------HH--------HHHHHHHHHHCCCCCCEEEHHHH Q ss_conf 41044899977568--------------88--------99888777640788605101123 Q gi|254781212|r 20 YTVDSDALARQLEE--------------DE--------RRIRHYKHVYSTPEGRFVLTDLM 58 (109) Q Consensus 20 ytvdsdalarqlee--------------de--------rrirhykhvystpegrfvltdlm 58 (109) ..+|+|.+||+.-+ +| .|-.--+-|++.|+-|-.|++.| T Consensus 27 ~vIDaD~vaR~vv~PG~p~~~~ive~FG~eiLl~~G~inR~~LG~~vF~~~~~r~~Ln~It 87 (225) T KOG3220 27 PVIDADVVAREVVEPGTPAYRRIVEAFGTEILLEDGEINRKVLGKRVFSDPKKRQALNKIT 87 (225) T ss_pred CEECHHHHHHHHHCCCCHHHHHHHHHHCCEEECCCCCCCHHHHHHHHHCCHHHHHHHHHCC T ss_conf 5762789999985599807899999848400056884168998678708988999987313 No 17 >pfam05300 DUF737 Protein of unknown function (DUF737). This family consists of several uncharacterized mammalian proteins of unknown function. Probab=26.29 E-value=61 Score=15.27 Aligned_cols=26 Identities=35% Similarity=0.543 Sum_probs=20.1 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 10448999775688899888777640 Q gi|254781212|r 21 TVDSDALARQLEEDERRIRHYKHVYS 46 (109) Q Consensus 21 tvdsdalarqleederrirhykhvys 46 (109) -..++.||||||+-|+-+++-.-.|- T Consensus 129 r~ka~~lArqLE~kEaELkr~daFYK 154 (187) T pfam05300 129 RQKAKHLARQLEEKEAELKRLDAFYK 154 (187) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999988999998999999 No 18 >TIGR01754 flav_RNR ribonucleotide reductase-associated flavodoxin, putative; InterPro: IPR010088 This entry represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulphate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation.. Probab=25.84 E-value=52 Score=15.69 Aligned_cols=21 Identities=33% Similarity=0.528 Sum_probs=19.9 Q ss_pred CHHHHHHHHHHHHHHCCCCCC Q ss_conf 399999999876642254104 Q gi|254781212|r 3 NFRKLADMIKSKVLSRGYTVD 23 (109) Q Consensus 3 nfrkladmikskvlsrgytvd 23 (109) |-+..|+||+...-++|..|| T Consensus 13 NT~eVA~~I~~~l~~~G~eVD 33 (145) T TIGR01754 13 NTKEVADIIRDILEKDGHEVD 33 (145) T ss_pred CHHHHHHHHHHHHHHCCCEEE T ss_conf 778999999999984797767 No 19 >TIGR00457 asnS asparaginyl-tRNA synthetase; InterPro: IPR004522 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 . AsparaginyltRNA synthetase (6.1.1.22 from EC) is an alpha2 dimer that belongs to class IIb. There is a striking similarity between asparaginyl-tRNA synthetases and archaeal/eukaryotic type aspartyl-tRNA synthetases (IPR004523 from INTERPRO) and a striking divergence of bacterial type aspartyl-tRNA synthetases (IPR004524 from INTERPRO). This family, AsnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.; GO: 0000166 nucleotide binding, 0004816 asparagine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006421 asparaginyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=20.74 E-value=60 Score=15.31 Aligned_cols=20 Identities=35% Similarity=0.466 Sum_probs=15.6 Q ss_pred EECCCCCCHHHHHHHHCCCC Q ss_conf 73146865999999862689 Q gi|254781212|r 88 IASNCGLSFERIVQMYSDNP 107 (109) Q Consensus 88 iasncglsferivqmysdnp 107 (109) -.|.-||.|||+|+--++.+ T Consensus 459 PH~GFGLGfERl~ay~~G~~ 478 (495) T TIGR00457 459 PHSGFGLGFERLVAYITGLE 478 (495) T ss_pred CCCCCCHHHHHHHHHHHCCC T ss_conf 64664324899999981787 No 20 >pfam02826 2-Hacid_dh_C D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain. This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389. Probab=20.62 E-value=51 Score=15.73 Aligned_cols=33 Identities=36% Similarity=0.472 Sum_probs=20.4 Q ss_pred CCCHHHHHHHHHHHH---HHCCCCCCHHHHHHHHHH Q ss_conf 963999999998766---422541044899977568 Q gi|254781212|r 1 MVNFRKLADMIKSKV---LSRGYTVDSDALARQLEE 33 (109) Q Consensus 1 mvnfrkladmikskv---lsrgytvdsdalarqlee 33 (109) |+|...+.-|-+.-+ .+||-.||.+||...|++ T Consensus 106 li~~~~l~~mk~~a~lIN~sRG~ivde~aL~~aL~~ 141 (176) T pfam02826 106 LINAERLALMKPGAILINTARGGLVDEDALIAALKS 141 (176) T ss_pred CCCHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHH T ss_conf 346999985189988998067551289999999980 No 21 >pfam04316 FlgM Anti-sigma-28 factor, FlgM. FlgM binds and inhibits the activity of the transcription factor sigma 28. Inhibition of sigma 28 prevents the expression of genes from flagellar transcriptional class 3, which include genes for the filament and chemotaxis. Correctly assembled basal body-hook structures export FlgM, relieving inhibition of sigma 28 and allowing expression of class 3 genes. NMR studies show that free FlgM is mostly unfolded, which may facilitate its export. The C terminal half of FlgM adopts a tertiary structure when it binds to sigma 28. All mutations in FlgM that prevent sigma 28 inhibition affect the C-terminal domain and is the region thought to constitute the binding domain. A minimal binding domain has been identified between Glu 64 and Arg 88 in Salmonella typhimurium. The N-terminal portion remains unstructured and may be necessary for recognition by the export machinery. Probab=20.60 E-value=77 Score=14.71 Aligned_cols=25 Identities=24% Similarity=0.501 Sum_probs=20.6 Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHH Q ss_conf 9998766422541044899977568 Q gi|254781212|r 9 DMIKSKVLSRGYTVDSDALARQLEE 33 (109) Q Consensus 9 dmikskvlsrgytvdsdalarqlee 33 (109) .-||..+-+-.|.||++.+|..+-+ T Consensus 31 ~~iK~~I~~G~Y~vd~~~iA~kml~ 55 (57) T pfam04316 31 EEIKAAIANGSYKVDAEKIADKMLN 55 (57) T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHC T ss_conf 9999999869988899999999883 Done!