Query gi|254780727|ref|YP_003065140.1| putative pilus assembly protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 474 No_of_seqs 232 out of 2174 Neff 7.2 Searched_HMMs 23785 Date Tue May 31 17:33:25 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780727.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1f1s_A Hyaluronate lyase; the 92.0 0.45 1.9E-05 23.2 7.8 65 47-118 12-76 (814) 2 2kgs_A Uncharacterized protein 87.2 1.1 4.7E-05 20.9 6.4 67 116-193 59-125 (132) 3 2l04_A Major tail protein V; b 86.1 1.3 5.3E-05 20.6 6.0 69 48-117 14-89 (91) 4 1b35_D CRPV, protein (cricket 49.4 4.1 0.00017 17.6 0.8 23 381-403 21-43 (57) 5 3ec1_A YQEH GTPase; atnos1, at 24.8 18 0.00076 13.9 0.8 23 358-380 249-271 (369) 6 1ghh_A DINI, DNA-damage-induci 21.7 29 0.0012 12.7 6.4 46 120-167 22-70 (81) 7 3cdi_A Polynucleotide phosphor 21.2 25 0.0011 13.1 1.0 62 355-416 588-649 (723) 8 3h2y_A GTPase family protein; 21.1 24 0.001 13.2 0.8 22 359-380 249-270 (368) 9 2ftc_C L3MT, MRP-L3, mitochond 17.5 36 0.0015 12.2 3.8 28 87-116 2-29 (211) 10 3gme_A Polyribonucleotide nucl 16.6 35 0.0015 12.2 0.9 52 354-407 25-87 (549) No 1 >1f1s_A Hyaluronate lyase; the structure consists of three distinct structural domains: two beta domains at two terminals and one alpha domain in the middle of the sequence.; 2.10A {Streptococcus agalactiae} SCOP: a.102.3.2 b.1.18.2 b.24.1.1 b.30.5.2 PDB: 1i8q_A* 1lxm_A* Probab=92.04 E-value=0.45 Score=23.23 Aligned_cols=65 Identities=17% Similarity=0.311 Sum_probs=54.2 Q ss_pred CCEEEEEECCEEEEECCCCHHHEEECCCCEEEEEECCCCEEEEEECCCCEEEEEEECCCCCEEEEEEEECCC Q ss_conf 402799507259995377633078537343799971698799995267227999988999778999873045 Q gi|254780727|r 47 GKKISIGLNKVIILQVPVDVQDVLVSDPTKADVVVHSPRTMYLFGKNVGQANVILIGHDGKQMLNLDILIER 118 (474) Q Consensus 47 ~~~l~l~~g~s~~l~~~~~~~rV~V~dp~Vadv~v~s~~~i~i~gk~~G~T~l~v~~~~g~~~~~~~v~v~~ 118 (474) -+.+.+++++-.+++.++ ..--+.||+|+.+. .-++++.++|.|++.+.+++|+.+..+.+.+.. T Consensus 12 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~-----~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 76 (814) T 1f1s_A 12 EKSVNTALNKNYVFNKAD--YQYTLTNPSLGKIV-----GGILYPNATGSTTVKISDKSGKIIKEVPLSVTA 76 (814) T ss_dssp CSCEEEETTSCEECSSTT--SEEEESSGGGEEEE-----TTEEEECSCEEEEEEEECTTCCEEEEEEEEEEC T ss_pred HHHEECCCCCEEEECCCC--EEEEECCCCHHEEE-----CCEEEECCCCEEEEEEECCCCCEEEEEEEEECC T ss_conf 340423447656532664--26776386260121-----645871258807999985899789997636437 No 2 >2kgs_A Uncharacterized protein RV0899/MT0922; outer membrane protein A, BON domain, cell membrane, membrane, transmembrane; NMR {Mycobacterium tuberculosis} PDB: 2ksm_A Probab=87.15 E-value=1.1 Score=20.94 Aligned_cols=67 Identities=15% Similarity=0.243 Sum_probs=51.7 Q ss_pred CCCCHHHHHHHHHHHCCCCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCC Q ss_conf 045414789999985787716999838949999971999999999999998612234555556654430355432777 Q gi|254780727|r 116 IERDIAHLEMTLRRFIADSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIAGE 193 (474) Q Consensus 116 v~~d~~~l~~~l~~~~p~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~~~ 193 (474) ..-|.+..+-...+-.|-.+.......+++.|+|++.++.+.+.+.+-|...-++ -+++|++.|.++ T Consensus 59 raldfsnaepvfta~~~ipdf~lkverdtvtltgta~s~dqkdav~~aats~w~~-----------vki~nnievkg~ 125 (132) T 2kgs_A 59 RSLDFSSAEPVFTASVPIPDFGLKVERDTVTLTGTAPSSEHKDAVKRAATSTWPD-----------MKIVNNIEVTGQ 125 (132) T ss_dssp CCCCGGGCHHHHHHHTTCTTCEEEEEETEEEEECEESSHHHHHHHHHHHHHHCTT-----------SEEEECCEECCC T ss_pred EEECCCCCCCEEECCCCCCCCEEEEEEEEEEEECCCCCCCHHHHHHHHHHCCCCC-----------CEEEEEEEEECC T ss_conf 5401466771244477578845688740588851568930567887765246888-----------457776687268 No 3 >2l04_A Major tail protein V; bacteriophage lambda, phage tail, GPV, IG-like domain, viral; NMR {Enterobacteria phage lambda} Probab=86.10 E-value=1.3 Score=20.61 Aligned_cols=69 Identities=25% Similarity=0.301 Sum_probs=49.4 Q ss_pred CEEEEEECCEEEEEC---CCCHH----HEEECCCCEEEEEECCCCEEEEEECCCCEEEEEEECCCCCEEEEEEEECC Q ss_conf 027995072599953---77633----07853734379997169879999526722799998899977899987304 Q gi|254780727|r 48 KKISIGLNKVIILQV---PVDVQ----DVLVSDPTKADVVVHSPRTMYLFGKNVGQANVILIGHDGKQMLNLDILIE 117 (474) Q Consensus 48 ~~l~l~~g~s~~l~~---~~~~~----rV~V~dp~Vadv~v~s~~~i~i~gk~~G~T~l~v~~~~g~~~~~~~v~v~ 117 (474) ..+.|.+|+...|.. |.... ....+||+|+.+. -+.+...+.|+++|.+.+.+...+|..-....|.|. T Consensus 14 ~~~~l~vG~t~~l~~~v~P~~a~~~~~~w~Ssd~~VatV~-~~G~~~~Vta~~~G~a~Itat~~dg~~~a~~~VtV~ 89 (91) T 2l04_A 14 ASTSVVKGQSTTLTVAFQPEGVTDKSFRAVSADKTKATVS-VSGMTITVNGVAAGKVNIPVVSGNGEFAAVAEITVT 89 (91) T ss_dssp CCEEEETTCEEEEEEEECCSSCCCCCEEECCSCCSSCEEE-EETTEEEEECSSSEEEECCEEETTTTEEECCEEEEE T ss_pred CCEEEECCCEEEEEEEEEECCCCCCEEEEEECCCCEEEEE-CCCCEEEEEEEEEEEEEEEEEECCCCEEEEEEEEEE T ss_conf 8479987988999999986877865899998999889998-889899999984569999999999988999999997 No 4 >1b35_D CRPV, protein (cricket paralysis virus, VP4); insect picorna-like virus, icosahedral virus; 2.40A {Cricket paralysis virus} SCOP: b.121.4.1 Probab=49.44 E-value=4.1 Score=17.63 Aligned_cols=23 Identities=39% Similarity=0.869 Sum_probs=16.7 Q ss_pred CCCCCCCEECCCCEEECCCCCCC Q ss_conf 21257112017612000165645 Q gi|254780727|r 381 LKEGIPLLSKIPILGALFRNSRF 403 (474) Q Consensus 381 ~~~~vP~LgdIPilG~LF~s~~~ 403 (474) -..|+--++.||+||+.|..-.. T Consensus 21 iseglst~s~ipilgn~fs~paw 43 (57) T 1b35_D 21 ISEGLTTLSHIPVLGNIFSTPAW 43 (57) T ss_dssp CGGGCCCTTCCCCSCCSSSSCTT T ss_pred HHHHHHHHHCCCCCCCCCCCHHH T ss_conf 64413332236400121365499 No 5 >3ec1_A YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase, signaling protein; HET: GDP; 2.36A {Geobacillus stearothermophilus} Probab=24.83 E-value=18 Score=13.91 Aligned_cols=23 Identities=26% Similarity=0.420 Sum_probs=18.6 Q ss_pred EEEEECCCCEEEEEEEEEEEECC Q ss_conf 99998589989999766531013 Q gi|254780727|r 358 TTVELPSGGTIVLAGLLKDDIQQ 380 (474) Q Consensus 358 T~V~l~~Get~vIgGL~~~~~~~ 380 (474) .+..+++||++.||||.+-+..+ T Consensus 249 ~~~~l~~gqsl~igGL~rid~~~ 271 (369) T 3ec1_A 249 RVYQLNEGQTLFFGGLARLDYIK 271 (369) T ss_dssp EEEEECTTEEEEETTTEEEEEEE T ss_pred EEEEECCCCEEEEEEEEEEECCC T ss_conf 18996899789980279887167 No 6 >1ghh_A DINI, DNA-damage-inducible protein I; bicelle, dipolar coupling, liquid crystal, PF1, RECA, protein binding; NMR {Escherichia coli} SCOP: d.57.1.1 Probab=21.73 E-value=29 Score=12.73 Aligned_cols=46 Identities=20% Similarity=0.317 Sum_probs=35.0 Q ss_pred HHHHHHHHHHHCCCC--CEEEEEEC-CEEEEEEEECCHHHHHHHHHHHHHH Q ss_conf 147899999857877--16999838-9499999719999999999999986 Q gi|254780727|r 120 IAHLEMTLRRFIADS--NIRVEMVS-DTVVLHGMVRTIQDSQRAVELSETF 167 (474) Q Consensus 120 ~~~l~~~l~~~~p~~--~i~v~~~~-~~vvl~G~v~~~~~~~~~~~ia~~~ 167 (474) ..+|.+.|+..||+. .|+|.... +.+-+.|. +..+.+++.++.+.- T Consensus 22 ~~EL~kRl~~~fPD~~~~V~Vr~~s~n~lsv~g~--~k~dKe~i~eiLqE~ 70 (81) T 1ghh_A 22 AGELSRRIQYAFPDNEGHVSVRYAAANNLSVIGA--TKEDKQRISEILQET 70 (81) T ss_dssp HHHHHHHHHHHCSSSCCEEEEEEESSCEEEEESC--CHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHCCCCCCEEEEEECCCCCEEECCC--CHHHHHHHHHHHHHH T ss_conf 9999998660489986318986658896052598--851499999999999 No 7 >3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Probab=21.21 E-value=25 Score=13.09 Aligned_cols=62 Identities=16% Similarity=0.210 Sum_probs=44.5 Q ss_pred EEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCEEEEEEEEEC Q ss_conf 99999998589989999766531013212571120176120001656455211599999905 Q gi|254780727|r 355 KADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREETEIFIAATP 416 (474) Q Consensus 355 ~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP 416 (474) +...++.+.|..++-|.|--++........|=.+-.-|-+|..|..+=..-.+-=.+|-+-| T Consensus 588 ~tg~~idi~d~g~v~i~~~~~~~~~~A~~~I~~~~~~~e~G~iy~g~V~~i~~fGafve~~p 649 (723) T 3cdi_A 588 ETGTTIEIEDDGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGG 649 (723) T ss_dssp -------------------------------------------------------------- T ss_pred HHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECEEEEEECC T ss_conf 88988998388389999899999999999999835877559889999999995429999669 No 8 >3h2y_A GTPase family protein; GTP-binding protein YQEH, possibly involved in replication initiation, csgid, IDP90222; HET: DGI; 1.80A {Bacillus anthracis str} Probab=21.05 E-value=24 Score=13.22 Aligned_cols=22 Identities=23% Similarity=0.336 Sum_probs=17.9 Q ss_pred EEEECCCCEEEEEEEEEEEECC Q ss_conf 9998589989999766531013 Q gi|254780727|r 359 TVELPSGGTIVLAGLLKDDIQQ 380 (474) Q Consensus 359 ~V~l~~Get~vIgGL~~~~~~~ 380 (474) +..++.||++.||||.+-+..+ T Consensus 249 t~~l~~gqsl~igGL~rid~~~ 270 (368) T 3h2y_A 249 VFQLNEEQTLFFSGLARFDYVS 270 (368) T ss_dssp EEEECTTEEEEETTTEEEEEEE T ss_pred EEEECCCCEEEECCEEEEEECC T ss_conf 9996799679973279998115 No 9 >2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Probab=17.53 E-value=36 Score=12.18 Aligned_cols=28 Identities=14% Similarity=0.224 Sum_probs=20.2 Q ss_pred EEEEECCCCEEEEEEECCCCCEEEEEEEEC Q ss_conf 999952672279999889997789998730 Q gi|254780727|r 87 MYLFGKNVGQANVILIGHDGKQMLNLDILI 116 (474) Q Consensus 87 i~i~gk~~G~T~l~v~~~~g~~~~~~~v~v 116 (474) +=|+|++.|-|.+ |+++|..+-...+.+ T Consensus 2 ~Glig~KiGMT~i--f~~~G~~vpVTVlev 29 (211) T 2ftc_C 2 VGLIALKLGMMPL--WTKDGQKHVVTLLQV 29 (211) T ss_pred EEEEEEECCCCEE--ECCCCCEEEEEEEEE T ss_conf 1899996587077--889996988899996 No 10 >3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex, cytoplasm, nucleotidyltransferase, RNA- binding, transferase, hydrolase; 2.40A {Escherichia coli E24377A} PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A Probab=16.60 E-value=35 Score=12.23 Aligned_cols=52 Identities=25% Similarity=0.395 Sum_probs=0.0 Q ss_pred EEEEEEEEECCCCEEEEEEEEEEEECC-CCCCCCC----------EECCCCEEECCCCCCCCCCE Q ss_conf 999999998589989999766531013-2125711----------20176120001656455211 Q gi|254780727|r 354 RKADTTVELPSGGTIVLAGLLKDDIQQ-LKEGIPL----------LSKIPILGALFRNSRFNREE 407 (474) Q Consensus 354 R~~~T~V~l~~Get~vIgGL~~~~~~~-~~~~vP~----------LgdIPilG~LF~s~~~~~~~ 407 (474) |.++-.|.+..|+|.||.=........ ..+=+|+ -|+|| |.+||...+-.++ T Consensus 25 kqA~Gsv~~~~G~T~vL~T~~~~~~~~~~~dFfPLtVdY~Ek~yAaGkIP--Ggf~kREgrpse~ 87 (549) T 3gme_A 25 RQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVNYQERTYAAGRIP--GSFFRREGRPSEG 87 (549) T ss_dssp TTSSEEEEEEETTEEEEEEEEECSSCCTTCCSCCEEEEEEECGGGTTCCC--SCC-----CCCHH T ss_pred HHCCCEEEEEECCEEEEEEEEECCCCCCCCCCCCCEEEEEEHHHHCCCCC--CCCCCCCCCCCCC T ss_conf 31783399998997999999705888899887675576788323378688--8665678898700 Done!