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!