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 13730
Date          Mon May 23 13:42:14 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780205.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 d1v74a_ d.243.1.1 (A:) Colicin  10.5      34  0.0025   11.5   0.6   13  101-113     2-14  (107)
  2 d1rtra_ a.128.1.1 (A:) Farnesy   8.7      42  0.0031   10.9   1.4   57   74-133    70-126 (290)
  3 d1t95a1 a.5.8.1 (A:87-161) Hyp   7.9      33  0.0024   11.6  -0.4   15   95-110    32-46  (75)
  4 d1r5ba2 b.44.1.1 (A:555-622) E   7.1      50  0.0037   10.5   1.1   15   89-103    42-56  (68)
  5 d1x1na1 c.1.8.1 (A:2-524) Amyl   6.8      45  0.0033   10.8  -0.1   11   22-32    313-323 (523)
  6 d1p94a_ a.43.1.3 (A:) Plasmid    6.6      53  0.0039   10.3   0.6   20   89-112    18-37  (76)
  7 d1eswa_ c.1.8.1 (A:) Amylomalt   6.5      50  0.0036   10.5  -0.0   27    6-34    272-298 (500)
  8 d1rqja_ a.128.1.1 (A:) Farnesy   6.1      57  0.0041   10.2   1.8   56   74-132    73-128 (299)
  9 d2d9qb1 b.1.1.3 (B:3-96) Granu   4.9      22  0.0016   12.7  -2.7   29   80-108    19-49  (94)
 10 d1co4a_ g.47.1.1 (A:) Zinc dom   4.7      77  0.0056    9.4   0.2    9   98-106    34-42  (42)

No 1  
>d1v74a_ d.243.1.1 (A:) Colicin D nuclease domain {Escherichia coli [TaxId: 562]}
Probab=10.50  E-value=34  Score=11.49  Aligned_cols=13  Identities=46%  Similarity=0.682  Sum_probs=9.6

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~~ftrkq   14 (107)
T d1v74a_           2 NDPLDSGRFSRKQ   14 (107)
T ss_dssp             CCTTCBTTBCHHH
T ss_pred             CCCCCCCCCHHHH
T ss_conf             9876576250998


No 2  
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]}
Probab=8.72  E-value=42  Score=10.94  Aligned_cols=57  Identities=16%  Similarity=0.129  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHCCCCCHHHCCCHHHHHHHHHCCCCCCCC
Q ss_conf             999989999996413887784342343101001233210110013443100034555444
Q gi|254780205|r   74 AIVTRGAACTWNDLVDHDIDSQVLRTRSRPLPSGQCTRFQALVFAVLQFLISFVLLLQFN  133 (310)
Q Consensus        74 ~~~~r~ag~~~Nd~~D~diD~~~~RT~~RPl~sG~is~~~A~~~~~~l~~l~~~~~~~ln  133 (310)
                      .=+..+|.-+..|+.|.|-|.  .| ++||-...+-....|...+-.+...++.++...+
T Consensus        70 vEllH~asLIHDDI~d~D~~~--~R-Rg~pt~~~~~g~~~Ail~Gd~l~~~a~~l~~~~~  126 (290)
T d1rtra_          70 LEMIHTYSLIHDDLPAMDNDD--YR-RGKLTNHKVYGEWTAILAGDALLTKAFELISSDD  126 (290)
T ss_dssp             HHHHHHHHHHHHHSTTTTCCS--EE-TTEECHHHHHCHHHHHHHHHHHHHHHHHHHHTCT
T ss_pred             HHHHHHHHHHHCCHHHHHHHH--HH-HCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCC
T ss_conf             999999999852313210011--21-0130368885101788707610679999998478


No 3  
>d1t95a1 a.5.8.1 (A:87-161) Hypothetical protein AF0491, middle domain {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}
Probab=7.88  E-value=33  Score=11.62  Aligned_cols=15  Identities=27%  Similarity=0.330  Sum_probs=10.5

Q ss_pred             CCCCCCCHHHHCCCCC
Q ss_conf             3423431010012332
Q gi|254780205|r   95 QVLRTRSRPLPSGQCT  110 (310)
Q Consensus        95 ~~~RT~~RPl~sG~is  110 (310)
                      .+++| +||.|.++|-
T Consensus        32 VnP~T-~~P~p~~rIE   46 (75)
T d1t95a1          32 IDPRT-NAPHPPSRIE   46 (75)
T ss_dssp             EBTTT-TBCCCHHHHH
T ss_pred             CCCCC-CCCCCHHHHH
T ss_conf             69988-9989899999


No 4  
>d1r5ba2 b.44.1.1 (A:555-622) Eukaryotic peptide chain release factor ERF2, C-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}
Probab=7.06  E-value=50  Score=10.48  Aligned_cols=15  Identities=20%  Similarity=0.432  Sum_probs=8.1

Q ss_pred             CCCCCCCCCCCCCHH
Q ss_conf             887784342343101
Q gi|254780205|r   89 DHDIDSQVLRTRSRP  103 (310)
Q Consensus        89 D~diD~~~~RT~~RP  103 (310)
                      +.++||..++++.||
T Consensus        42 ~~~~~ktg~~~k~~P   56 (68)
T d1r5ba2          42 LHKLDKTNRKSKKPP   56 (68)
T ss_dssp             CCCCCSSCCCCSSCC
T ss_pred             HHHHHCCCCEECCCC
T ss_conf             777732798704497


No 5  
>d1x1na1 c.1.8.1 (A:2-524) Amylomaltase MalQ {Potato (Solanum tuberosum) [TaxId: 4113]}
Probab=6.80  E-value=45  Score=10.77  Aligned_cols=11  Identities=9%  Similarity=-0.230  Sum_probs=3.8

Q ss_pred             HHHHHHCCCCH
Q ss_conf             99986304853
Q gi|254780205|r   22 YVYLARWHSST   32 (310)
Q Consensus        22 Y~~L~R~~kp~   32 (310)
                      +....|+||..
T Consensus       313 ~~d~lRIDH~~  323 (523)
T d1x1na1         313 LFDEFRIDHFR  323 (523)
T ss_dssp             HCSEEEEETGG
T ss_pred             HCCEEEEHHHH
T ss_conf             57841205278


No 6  
>d1p94a_ a.43.1.3 (A:) Plasmid partition protein ParG {Salmonella enterica [TaxId: 28901]}
Probab=6.61  E-value=53  Score=10.34  Aligned_cols=20  Identities=30%  Similarity=0.612  Sum_probs=10.6

Q ss_pred             CCCCCCCCCCCCCHHHHCCCCCHH
Q ss_conf             887784342343101001233210
Q gi|254780205|r   89 DHDIDSQVLRTRSRPLPSGQCTRF  112 (310)
Q Consensus        89 D~diD~~~~RT~~RPl~sG~is~~  112 (310)
                      .||+|+.|.    .|.|+|+...-
T Consensus        18 hRdLekvv~----~p~psgk~Krv   37 (76)
T d1p94a_          18 NRDLERVVT----APVSSGKIKRV   37 (76)
T ss_dssp             TTTTCGGGS----CCSSTTCEEEC
T ss_pred             CCHHHHHHC----CCCCCCCCEEE
T ss_conf             011889864----88987642335


No 7  
>d1eswa_ c.1.8.1 (A:) Amylomaltase MalQ {Thermus aquaticus [TaxId: 271]}
Probab=6.47  E-value=50  Score=10.51  Aligned_cols=27  Identities=15%  Similarity=0.199  Sum_probs=12.1

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHCCCCHHH
Q ss_conf             01355541054677899998630485315
Q gi|254780205|r    6 NFKWVRDCIMGSAIAPYVYLARWHSSTGW   34 (310)
Q Consensus         6 ~~~~~~~~~~~~~i~~Y~~L~R~~kp~g~   34 (310)
                      +++|-++|.  .+.-.+....|+||.+|.
T Consensus       272 gy~ww~~rl--~~~~~~~~~lRIDH~~Gf  298 (500)
T d1eswa_         272 GFSFWIRRL--EKALELFHLVRIDHFRGF  298 (500)
T ss_dssp             TTHHHHHHH--HHHHHHCSEEEEETGGGG
T ss_pred             CCHHHHHHH--HHHHHHCCHHHHHHHHHH
T ss_conf             839999999--999975461425758998


No 8  
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]}
Probab=6.08  E-value=57  Score=10.16  Aligned_cols=56  Identities=20%  Similarity=0.157  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHCCCCCHHHCCCHHHHHHHHHCCCCCCC
Q ss_conf             99998999999641388778434234310100123321011001344310003455544
Q gi|254780205|r   74 AIVTRGAACTWNDLVDHDIDSQVLRTRSRPLPSGQCTRFQALVFAVLQFLISFVLLLQF  132 (310)
Q Consensus        74 ~~~~r~ag~~~Nd~~D~diD~~~~RT~~RPl~sG~is~~~A~~~~~~l~~l~~~~~~~l  132 (310)
                      .=+..+|.-+..|+.|.|-|.  .| +++|-.-.+-....|...+-.+...++-.+...
T Consensus        73 iEllH~asLiHDDI~d~d~~~--~R-RG~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~  128 (299)
T d1rqja_          73 VECIHAYSLIHDDLPAMDDDD--LR-RGLPTCHVKFGEANAILAGDALQTLAFSILSDA  128 (299)
T ss_dssp             HHHHHHHHHHHHTSTTTTCCC--EE-TTEECHHHHHCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHCCCHHHHHHH--CC-CCCCCCEEEECCCHHHHHCCHHHHHHHHHHHHC
T ss_conf             999999999972541345421--12-455431034075433552104788999999867


No 9  
>d2d9qb1 b.1.1.3 (B:3-96) Granulocyte colony-stimulating factor (GC-SF) receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}
Probab=4.95  E-value=22  Score=12.73  Aligned_cols=29  Identities=21%  Similarity=0.353  Sum_probs=0.0

Q ss_pred             HHHHHHH-HCCCCCC-CCCCCCCCHHHHCCC
Q ss_conf             9999964-1388778-434234310100123
Q gi|254780205|r   80 AACTWND-LVDHDID-SQVLRTRSRPLPSGQ  108 (310)
Q Consensus        80 ag~~~Nd-~~D~diD-~~~~RT~~RPl~sG~  108 (310)
                      |.|++|+ .-|-|=+ ...-|+++.++|.++
T Consensus        19 AsC~I~e~C~~~~~a~~I~Wkl~~~~vP~~r   49 (94)
T d2d9qb1          19 ASCIIKQNCSHLDPEPQILWRLGAELQPGGR   49 (94)
T ss_dssp             EEECCCTTSCSSCSCSCCEEESSSCBCTTCE
T ss_pred             EEEEECCCCCCCCCCCEEEEEECCEECCCCC
T ss_conf             9999874146867861699998998878841


No 10 
>d1co4a_ g.47.1.1 (A:) Zinc domain conserved in yeast copper-regulated transcription factors {Synthetic}
Probab=4.67  E-value=77  Score=9.37  Aligned_cols=9  Identities=33%  Similarity=0.722  Sum_probs=0.0

Q ss_pred             CCCCHHHHC
Q ss_conf             343101001
Q gi|254780205|r   98 RTRSRPLPS  106 (310)
Q Consensus        98 RT~~RPl~s  106 (310)
                      |+|.||..+
T Consensus        34 ~~kGRP~st   42 (42)
T d1co4a_          34 KPRGRPPTT   42 (42)
T ss_dssp             CSCCCCSCC
T ss_pred             CCCCCCCCC
T ss_conf             689988989


Done!