Query         gi|254780519|ref|YP_003064932.1| flagellar biosynthesis protein FliQ [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 88
No_of_seqs    112 out of 591
Neff          4.8 
Searched_HMMs 23785
Date          Tue May 31 21:22:50 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780519.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3dhw_A D-methionine transport   14.6      50  0.0021   13.5   1.2   37    5-41      4-40  (217)
  2 1v54_M VIIIB, IX, cytochrome C   6.7 1.2E+02  0.0051   11.7   3.3   25   55-79     19-43  (46)
  3 3kpe_B Fusion glycoprotein F0;   6.3 1.3E+02  0.0054   11.5   2.2   15   41-55     11-28  (39)
  4 1g2c_B Fusion protein (F); mem   5.8 1.4E+02  0.0058   11.4   2.2   15   41-55     16-33  (43)
  5 1vf5_E Protein PET L; photosyn   5.8 1.4E+02  0.0058   11.4   1.1   21   24-44      9-29  (32)
  6 1brv_A Protein G, BRSV-G regio   5.1      73  0.0031   12.7  -1.1   10   45-54      7-16  (32)
  7 2dam_A ETEA protein; KIAA0887,   4.5 1.7E+02  0.0072   10.9   0.5   16   35-50     22-37  (67)
  8 2nqb_D Histone H2B; nucleosome   4.5 1.7E+02  0.0073   10.9   2.7   17   70-86     57-73  (123)
  9 2wj9_A ARDB, intergenic-region   4.4 1.7E+02  0.0073   10.9   1.3   32   45-76     53-88  (181)
 10 3fjv_A Uncharacterized novel p   3.5 2.1E+02  0.0088   10.5   0.5    5   43-47     54-58  (194)

No 1  
>3dhw_A D-methionine transport system permease protein METI; ABC-transporter, methionine uptake transporter, membrane protein, amino-acid transport; 3.70A {Escherichia coli K12} SCOP: f.58.1.1
Probab=14.56  E-value=50  Score=13.54  Aligned_cols=37  Identities=14%  Similarity=0.287  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999999999
Q gi|254780519|r    5 DVLEIARAAMWTILSSSAPVLFSAMFLGILIAFLQAL   41 (88)
Q Consensus         5 ~vi~l~~~al~~~l~ls~P~Ll~alvvGl~Isi~QA~   41 (88)
                      ...++..+++|..+.++.-....+.+.|+.+|++=+.
T Consensus         4 ~~~~l~l~~~~~Tl~~a~~~~~~~~~ig~~lg~~~~~   40 (217)
T 3dhw_A            4 PMMWLLVRGVWETLAMTFVSGFFGFVIGLPVGVLLYV   40 (217)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHTTGGGGGGGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999999999999999999999999


No 2  
>1v54_M VIIIB, IX, cytochrome C oxidase polypeptide VIII-heart; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: f.23.7.1 PDB: 1oco_M* 1occ_M* 1ocz_M* 1ocr_M* 1v55_M* 2dyr_M* 2dys_M* 2eij_M* 2eik_M* 2eil_M* 2eim_M* 2ein_M* 2occ_M* 2zxw_M* 3abk_M* 3abl_M* 3abm_M* 3ag1_M* 3ag2_M* 3ag3_M* ...
Probab=6.73  E-value=1.2e+02  Score=11.66  Aligned_cols=25  Identities=8%  Similarity=0.352  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999
Q gi|254780519|r   55 IIAVFITLIISAPFIGGQISSFVTL   79 (88)
Q Consensus        55 liav~~~l~~~~pwm~~~l~~f~~~   79 (88)
                      +-..+++++.-.+|.++.+-+|-++
T Consensus        19 lt~~f~~fL~PaGWVLshLe~YKk~   43 (46)
T 1v54_M           19 LSVTFLSFLLPAGWVLYHLDNYKKS   43 (46)
T ss_dssp             HHHHHHHHHHHHHHHHHTHHHHHTC
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHC
T ss_conf             9999999980099999869987214


No 3  
>3kpe_B Fusion glycoprotein F0; peptide/small-molecule complex, alpha helix, coiled-coil, envelope protein, fusion protein; HET: TM3 PG4; 1.47A {Human respiratory syncytial virus A2}
Probab=6.25  E-value=1.3e+02  Score=11.52  Aligned_cols=15  Identities=33%  Similarity=0.658  Sum_probs=9.3

Q ss_pred             HHHHHH---HHHHHHHHH
Q ss_conf             988465---369889999
Q gi|254780519|r   41 LTQIQE---VTLTFVPKI   55 (88)
Q Consensus        41 ~TQIQE---qTLsFvPKl   55 (88)
                      ..|++|   |.|.|+-|-
T Consensus        11 isqvnekinqslafirks   28 (39)
T 3kpe_B           11 ISQVNEKINQSLAFIRKS   28 (39)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             999999997889999843


No 4  
>1g2c_B Fusion protein (F); membrane fusion, pneumovirus, HRSV, viral protein; 2.30A {Human respiratory syncytial virusstrain rss-2} SCOP: h.3.2.1
Probab=5.82  E-value=1.4e+02  Score=11.39  Aligned_cols=15  Identities=33%  Similarity=0.658  Sum_probs=9.4

Q ss_pred             HHHHHH---HHHHHHHHH
Q ss_conf             988465---369889999
Q gi|254780519|r   41 LTQIQE---VTLTFVPKI   55 (88)
Q Consensus        41 ~TQIQE---qTLsFvPKl   55 (88)
                      ..|++|   |+|.|+-|-
T Consensus        16 isqvnekinqslafirks   33 (43)
T 1g2c_B           16 ISQVNEKINQSLAFIRKS   33 (43)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             999999997889999843


No 5  
>1vf5_E Protein PET L; photosynthesis, membrane protein complex, electron transfer complex; HET: HEM TDS PL9 OPC CLA BCR; 3.00A {Mastigocladus laminosus} SCOP: f.23.24.1 PDB: 2d2c_E* 2e74_E* 2e75_E* 2e76_E*
Probab=5.82  E-value=1.4e+02  Score=11.39  Aligned_cols=21  Identities=33%  Similarity=0.762  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999884
Q gi|254780519|r   24 VLFSAMFLGILIAFLQALTQI   44 (88)
Q Consensus        24 ~Ll~alvvGl~Isi~QA~TQI   44 (88)
                      +...|+.-|..+++.-|..+|
T Consensus         9 ivfialffgiavgiifaiksi   29 (32)
T 1vf5_E            9 IVFIALFFGIAVGIIFAIKSI   29 (32)
T ss_dssp             HHHHHHHHHHHHHHHTTTTTS
T ss_pred             HHHHHHHHHHHHHHEEEEEEE
T ss_conf             999999997886321457877


No 6  
>1brv_A Protein G, BRSV-G region; attachment protein G of bovine respiratory syncytial virus, immunoglobulin-binding protein; NMR {Bovine respiratory syncytial virus} SCOP: j.33.1.1
Probab=5.13  E-value=73  Score=12.73  Aligned_cols=10  Identities=40%  Similarity=0.507  Sum_probs=6.5

Q ss_pred             HHHHHHHHHH
Q ss_conf             6536988999
Q gi|254780519|r   45 QEVTLTFVPK   54 (88)
Q Consensus        45 QEqTLsFvPK   54 (88)
                      +-|||+++|-
T Consensus         7 n~qtlpyvpc   16 (32)
T 1brv_A            7 NFQTLPYVPC   16 (32)
T ss_pred             CCCCCCCCCC
T ss_conf             5430465454


No 7  
>2dam_A ETEA protein; KIAA0887, UBA-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=4.52  E-value=1.7e+02  Score=10.93  Aligned_cols=16  Identities=25%  Similarity=0.300  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999884653698
Q gi|254780519|r   35 IAFLQALTQIQEVTLT   50 (88)
Q Consensus        35 Isi~QA~TQIQEqTLs   50 (88)
                      +.-||.+|-|.++.+.
T Consensus        22 llqFQdiTGied~~~C   37 (67)
T 2dam_A           22 LLQFQDLTGIESMDQC   37 (67)
T ss_dssp             HHHHHHHHCCSCHHHH
T ss_pred             HHHHHHHHCCCCHHHH
T ss_conf             9999871076759999


No 8  
>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D*
Probab=4.45  E-value=1.7e+02  Score=10.91  Aligned_cols=17  Identities=29%  Similarity=0.440  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999344
Q gi|254780519|r   70 GGQISSFVTLVLSRIQS   86 (88)
Q Consensus        70 ~~~l~~f~~~if~~ip~   86 (88)
                      .+.|.+|..++|++|..
T Consensus        57 m~imnSfv~diferIa~   73 (123)
T 2nqb_D           57 MSIMNSFVNDIFERIAA   73 (123)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999


No 9  
>2wj9_A ARDB, intergenic-region protein; antirestriction, hydrolase inhibitor; 1.62A {Escherichia coli}
Probab=4.40  E-value=1.7e+02  Score=10.88  Aligned_cols=32  Identities=9%  Similarity=0.168  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
Q ss_conf             65369889999999----999999999999999999
Q gi|254780519|r   45 QEVTLTFVPKIIAV----FITLIISAPFIGGQISSF   76 (88)
Q Consensus        45 QEqTLsFvPKliav----~~~l~~~~pwm~~~l~~f   76 (88)
                      .||-++|.||....    ...=-....||-+...+|
T Consensus        53 d~~Rl~FlP~~FG~~~~~~~~E~~Vy~~m~rlc~dY   88 (181)
T 2wj9_A           53 DEQRISFWPQHFGLIPQWVTLEPRVFGWMDRLCENY   88 (181)
T ss_dssp             HHHHTTHHHHHHTTSTTGGGHHHHHHHHHHHHC---
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             778876589885757888988999999999764367


No 10 
>3fjv_A Uncharacterized novel protein; YP_111841.1, novel protein of unknown function, structural genomics; HET: MSE; 1.90A {Burkholderia pseudomallei K96243}
Probab=3.54  E-value=2.1e+02  Score=10.50  Aligned_cols=5  Identities=60%  Similarity=0.873  Sum_probs=0.0

Q ss_pred             HHHHH
Q ss_conf             84653
Q gi|254780519|r   43 QIQEV   47 (88)
Q Consensus        43 QIQEq   47 (88)
                      |||||
T Consensus        54 QIqEM   58 (194)
T 3fjv_A           54 QIHEM   58 (194)
T ss_dssp             HHHHH
T ss_pred             HHHHH
T ss_conf             99999


Done!