Query         gi|254780205|ref|YP_003064618.1| prenyltransferase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 310
No_of_seqs    167 out of 2519
Neff          7.3 
Searched_HMMs 23785
Date          Mon May 23 13:38:57 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780205.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 2an6_E Peptide from phyllopod;  20.1      19  0.0008   14.5   0.1   17   95-111     2-18  (26)
  2 2fho_A Spliceosomal protein SF  13.8      44  0.0019   12.3   0.8   17   88-109    11-27  (47)
  3 1v74_A Colicin D; colicin D -    9.8      65  0.0027   11.3   0.6   13  101-113     2-14  (107)
  4 2w6b_A RHO guanine nucleotide    9.7      67  0.0028   11.2   1.2   26  201-226     9-34  (56)
  5 3l4f_A RHO guanine nucleotide    8.4      76  0.0032   10.9   1.2   26  201-226     6-31  (61)
  6 2odx_A Cytochrome C oxidase po   7.7      72   0.003   11.0   0.1   22   84-105     2-24  (80)
  7 2ihi_A Pyrophosphate synthase;   7.0      88  0.0037   10.4   4.1   40   75-119   115-154 (395)
  8 1t95_A Hypothetical protein AF   6.6      73  0.0031   11.0  -0.4   16   95-111   118-133 (240)
  9 2kdo_A Ribosome maturation pro   6.5      77  0.0032   10.8  -0.3   16   95-111   122-137 (252)
 10 2wbm_A MTHSBDS, ribosome matur   6.5      72   0.003   11.0  -0.5   14   95-109   133-146 (252)

No 1  
>2an6_E Peptide from phyllopod; protein-peptide complex, ligase; 3.00A {Mus musculus}
Probab=20.08  E-value=19  Score=14.51  Aligned_cols=17  Identities=35%  Similarity=0.292  Sum_probs=11.6

Q ss_pred             CCCCCCCHHHHCCCCCH
Q ss_conf             34234310100123321
Q gi|254780205|r   95 QVLRTRSRPLPSGQCTR  111 (310)
Q Consensus        95 ~~~RT~~RPl~sG~is~  111 (310)
                      +-+|||-||.+.-+-++
T Consensus         2 qqertklrpvamvrptv   18 (26)
T 2an6_E            2 QQERTKLRPVAMVRPTV   18 (26)
T ss_pred             CCCCCCCCCEEEECCCE
T ss_conf             43202345125653624


No 2  
>2fho_A Spliceosomal protein SF3B155; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=13.76  E-value=44  Score=12.27  Aligned_cols=17  Identities=35%  Similarity=0.677  Sum_probs=10.8

Q ss_pred             CCCCCCCCCCCCCCHHHHCCCC
Q ss_conf             3887784342343101001233
Q gi|254780205|r   88 VDHDIDSQVLRTRSRPLPSGQC  109 (310)
Q Consensus        88 ~D~diD~~~~RT~~RPl~sG~i  109 (310)
                      +++|||.     +|||+....+
T Consensus        11 ~e~eid~-----RNRpltDeeL   27 (47)
T 2fho_A           11 WEREIDE-----RNRPLSDEEL   27 (47)
T ss_dssp             CCCCCCC-----CCCCSCTTHH
T ss_pred             HHHHHHH-----HCCCCCHHHH
T ss_conf             9998997-----3488858899


No 3  
>1v74_A Colicin D; colicin D - IMMD complex, cytotoxicity, transfer RNAse, protein-protein inhibition; HET: 1PE; 2.00A {Escherichia coli} SCOP: d.243.1.1 PDB: 1tfo_A 1tfk_A*
Probab=9.84  E-value=65  Score=11.26  Aligned_cols=13  Identities=46%  Similarity=0.682  Sum_probs=8.6

Q ss_pred             CHHHHCCCCCHHH
Q ss_conf             1010012332101
Q gi|254780205|r  101 SRPLPSGQCTRFQ  113 (310)
Q Consensus       101 ~RPl~sG~is~~~  113 (310)
                      +-||+||+.|.++
T Consensus         2 ~~plds~~ft~kq   14 (107)
T 1v74_A            2 NDPLDSGRFSRKQ   14 (107)
T ss_dssp             CCTTCBTTBCHHH
T ss_pred             CCCCCCCCCCHHH
T ss_conf             9876465130998


No 4  
>2w6b_A RHO guanine nucleotide exchange factor 7; X-RAY crystallography, phosphoprotein, guanine-nucleotide releasing factor, GIT, PAK, PIX, COOL; 2.80A {Rattus norvegicus}
Probab=9.71  E-value=67  Score=11.18  Aligned_cols=26  Identities=23%  Similarity=0.284  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             57998887531000257203466542
Q gi|254780205|r  201 FDTVYAHQDKKDDELIGVNSTARLFS  226 (310)
Q Consensus       201 ~dtiYa~~D~edD~k~GikSlav~~G  226 (310)
                      -||+||..|--.+.+.--|.+.-.+.
T Consensus         9 VDtVYaLkDqV~eL~~e~k~lkk~le   34 (56)
T 2w6b_A            9 VDTVYALKDEVQELRQDNKKMKKSLE   34 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999998888


No 5  
>3l4f_A RHO guanine nucleotide exchange factor 7; coiled-coil, PDZ, guanine-nucleotide releasing factor, phosphoprotein, SH3 domain; 2.80A {Rattus norvegicus}
Probab=8.42  E-value=76  Score=10.86  Aligned_cols=26  Identities=23%  Similarity=0.284  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             57998887531000257203466542
Q gi|254780205|r  201 FDTVYAHQDKKDDELIGVNSTARLFS  226 (310)
Q Consensus       201 ~dtiYa~~D~edD~k~GikSlav~~G  226 (310)
                      -||+||..|--...+.--|.+.-.+.
T Consensus         6 VDtVYaLkDqV~eL~~e~krlkk~le   31 (61)
T 3l4f_A            6 VDTVYALKDEVQELRQDNKKMKKSLE   31 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999998888


No 6  
>2odx_A Cytochrome C oxidase polypeptide IV; all beta-protein, metallo-protein, oxidoreductase; NMR {Saccharomyces cerevisiae}
Probab=7.67  E-value=72  Score=10.99  Aligned_cols=22  Identities=27%  Similarity=0.356  Sum_probs=15.3

Q ss_pred             HHHHCCCC-CCCCCCCCCCHHHH
Q ss_conf             96413887-78434234310100
Q gi|254780205|r   84 WNDLVDHD-IDSQVLRTRSRPLP  105 (310)
Q Consensus        84 ~Nd~~D~d-iD~~~~RT~~RPl~  105 (310)
                      +-|++|.+ +|+-..-|++.|+.
T Consensus         2 ~~D~Fdm~pl~~s~~GT~e~P~l   24 (80)
T 2odx_A            2 MADVFDTKPLDSSRKGTMKDPII   24 (80)
T ss_dssp             -----------------CCSCSE
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEE
T ss_conf             64652576544588986639858


No 7  
>2ihi_A Pyrophosphate synthase; PV092040, structural genomics, structural genomics consortium, SGC, transferase; 2.00A {Plasmodium vivax sai-1} PDB: 3mav_A 3cc9_A* 3ez3_A* 3mys_A*
Probab=6.96  E-value=88  Score=10.45  Aligned_cols=40  Identities=8%  Similarity=-0.234  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHCCCCCHHHCCCHHH
Q ss_conf             999899999964138877843423431010012332101100134
Q gi|254780205|r   75 IVTRGAACTWNDLVDHDIDSQVLRTRSRPLPSGQCTRFQALVFAV  119 (310)
Q Consensus        75 ~~~r~ag~~~Nd~~D~diD~~~~RT~~RPl~sG~is~~~A~~~~~  119 (310)
                      =+...+..+-.|+.|.+-=|+.+     |-.-.+-....|...+-
T Consensus       115 EllH~asLIHDDI~D~s~~RRG~-----pt~h~~~g~~~Ail~GD  154 (395)
T 2ihi_A          115 EILQAAFLVADDIMDKGEMRRNK-----YCWYLLKDVETKNAVND  154 (395)
T ss_dssp             HHHHHHHHHHHHHHTTCSEETTE-----ECGGGSTTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCC-----CCHHCCCCCHHHHHHCH
T ss_conf             99999999985741488988997-----11411678158888351


No 8  
>1t95_A Hypothetical protein AF0491; shwachman-bodian-diamond syndrome protein orthologue, unknown function; 1.90A {Archaeoglobus fulgidus} SCOP: a.5.8.1 d.235.1.2 d.58.11.3 PDB: 1p9q_C
Probab=6.59  E-value=73  Score=10.97  Aligned_cols=16  Identities=31%  Similarity=0.407  Sum_probs=11.6

Q ss_pred             CCCCCCCHHHHCCCCCH
Q ss_conf             34234310100123321
Q gi|254780205|r   95 QVLRTRSRPLPSGQCTR  111 (310)
Q Consensus        95 ~~~RT~~RPl~sG~is~  111 (310)
                      .++|| +||.|..+|-.
T Consensus       118 VnP~T-~~P~p~~rIE~  133 (240)
T 1t95_A          118 IDPRT-NAPHPPSRIER  133 (240)
T ss_dssp             EBTTT-TBCCCHHHHHH
T ss_pred             CCCCC-CCCCCHHHHHH
T ss_conf             29888-99898899999


No 9  
>2kdo_A Ribosome maturation protein SBDS; SBDS protein, protein structure, RNA-interacting protein, acetylation, cytoplasm, disease mutation; NMR {Homo sapiens}
Probab=6.53  E-value=77  Score=10.81  Aligned_cols=16  Identities=25%  Similarity=0.123  Sum_probs=11.6

Q ss_pred             CCCCCCCHHHHCCCCCH
Q ss_conf             34234310100123321
Q gi|254780205|r   95 QVLRTRSRPLPSGQCTR  111 (310)
Q Consensus        95 ~~~RT~~RPl~sG~is~  111 (310)
                      .++|| +||.|..+|-.
T Consensus       122 VnP~T-~~P~p~~rIE~  137 (252)
T 2kdo_A          122 VNPET-KRPYTVILIER  137 (252)
T ss_dssp             ECCTT-SCTTCHHHHHH
T ss_pred             CCCCC-CCCCCHHHHHH
T ss_conf             59888-99899999999


No 10 
>2wbm_A MTHSBDS, ribosome maturation protein SDO1 homolog; shwachman-bodian-diamond syndrome protein, ribosome binding; 1.75A {Methanothermobacterthermautotrophicus}
Probab=6.46  E-value=72  Score=11.00  Aligned_cols=14  Identities=14%  Similarity=0.164  Sum_probs=0.0

Q ss_pred             CCCCCCCHHHHCCCC
Q ss_conf             342343101001233
Q gi|254780205|r   95 QVLRTRSRPLPSGQC  109 (310)
Q Consensus        95 ~~~RT~~RPl~sG~i  109 (310)
                      .++|| +||.|..+|
T Consensus       133 VnP~T-~~P~p~~rI  146 (252)
T 2wbm_A          133 INPQN-GLPHPPKRI  146 (252)
T ss_dssp             ECTTT-CCCCCHHHH
T ss_pred             CCCCC-CCCCCHHHH
T ss_conf             28888-998998999


Done!