Query         gi|254780339|ref|YP_003064752.1| hypothetical protein CLIBASIA_01120 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 88
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 33803
Date          Wed Jun  1 12:05:04 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780339.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1qmh_A RNA 3'-terminal phosph  11.3      64  0.0019   14.8   0.2   25   12-36     27-51  (254)
  2 >2qx5_A Nucleoporin NIC96; mRN  10.2      86  0.0025   14.0   0.5   12   42-53     24-35  (85)
  3 >3dw8_B Serine/threonine-prote   9.6 1.2E+02  0.0036   13.2   1.1   23   59-85     69-91  (151)
  4 >1avy_A Fibritin, gpwac M; coi   9.5      99  0.0029   13.7   0.6   12   76-87     62-73  (74)
  5 >1wq6_A AML1-ETO; NHR2, oncopr   9.3 1.1E+02  0.0034   13.4   0.9   18   43-60     22-39  (72)
  6 >2k9j_B Integrin beta-3; trans   8.9 1.1E+02  0.0034   13.4   0.7   10   42-51     29-38  (43)
  7 >2waq_C DNA-directed RNA polym   8.0      50  0.0015   15.3  -1.4   16    7-22     29-44  (63)
  8 >1df6_A Cycloviolacin O1; cycl   4.9   2E+02  0.0059   12.0   0.3   10   47-56      9-18  (30)
  9 >1f32_A Major pepsin inhibitor   4.7 1.9E+02  0.0056   12.2   0.0    9   62-70      8-16  (50)
 10 >2qp2_A Unknown protein; toxin   4.3 2.5E+02  0.0073   11.5   0.4    9    2-10     25-33  (154)

No 1  
>>1qmh_A RNA 3'-terminal phosphate cyclase; 2'3'cyclic phosphate RNA; HET: CIT; 2.1A {Escherichia coli} (A:1-186,A:280-347)
Probab=11.33  E-value=64  Score=14.77  Aligned_cols=25  Identities=28%  Similarity=0.304  Sum_probs=19.9

Q ss_pred             HHHCCCCEEEEEEEECCCCCEEEEE
Q ss_conf             6520481377444312667616730
Q gi|254780339|r   12 EAITNNRVEIANIRADMSGTSMKIQ   36 (88)
Q Consensus        12 eaitnnrveianiradmsgtsmkiq   36 (88)
                      -++++..|+|.|||+.-+....+-|
T Consensus        27 S~ltgkpv~I~nIRa~R~~PGL~~q   51 (254)
T 1qmh_A           27 SMITGQPFTITSIRAGRAKPGLLRQ   51 (254)
T ss_dssp             HHHHCCCEEEESTTTTBSSCSCCHH
T ss_pred             HHHHCCCEEEEEECCCCCCCCCHHH
T ss_conf             9975897799984689989885699


No 2  
>>2qx5_A Nucleoporin NIC96; mRNA transport, nuclear pore complex, nucleus, protein transport, translocation, transport, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2rfo_A (A:54-88,A:296-345)
Probab=10.25  E-value=86  Score=14.04  Aligned_cols=12  Identities=50%  Similarity=0.745  Sum_probs=8.9

Q ss_pred             CHHHHHHHHHCC
Q ss_conf             125456666402
Q gi|254780339|r   42 MSWKILTTMIGC   53 (88)
Q Consensus        42 mswkilttmigc   53 (88)
                      -|||||..|-.-
T Consensus        24 ~~~~~~~~~~~~   35 (85)
T 2qx5_A           24 ESWKILESMKSK   35 (85)
T ss_dssp             HHHHHHHTTTTS
T ss_pred             HHHHHHHHHHCC
T ss_conf             999999998704


No 3  
>>3dw8_B Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform...; PP2A, holoenzyme, PR55, acetylation, polymorphism, WD repeat, cytoplasm, hydrolase, iron, manganese, metal- binding, methylation; HET: ADD; 2.85A {Homo sapiens} (B:26-176)
Probab=9.58  E-value=1.2e+02  Score=13.21  Aligned_cols=23  Identities=43%  Similarity=0.522  Sum_probs=13.5

Q ss_pred             CCCCEEEEEECCCCCCCCEEEEEECCC
Q ss_conf             030036898505655410057871133
Q gi|254780339|r   59 GTINQVLVLNVPTANSLQNWFLLSTNL   85 (88)
Q Consensus        59 gtinqvlvlnvptanslqnwfllstnl   85 (88)
                      ..||++--  +|++|  .+.||||||-
T Consensus        69 EKINkIkW--l~~~n--~a~fLLSTND   91 (151)
T 3dw8_B           69 EKINKIRW--LPQKN--AAQFLLSTND   91 (151)
T ss_dssp             CCCCEEEE--CCCCS--SSEEEEEECS
T ss_pred             CCEEEEEE--ECCCC--CCEEEEEECC
T ss_conf             98889998--35899--8789999289


No 4  
>>1avy_A Fibritin, gpwac M; coiled coil, structural protein, chaperone, bacteriophage assembly, protein folding; 1.85A {Bacteriophage T4} (A:)
Probab=9.50  E-value=99  Score=13.72  Aligned_cols=12  Identities=58%  Similarity=0.819  Sum_probs=10.1

Q ss_pred             CEEEEEECCCCC
Q ss_conf             005787113344
Q gi|254780339|r   76 QNWFLLSTNLSE   87 (88)
Q Consensus        76 qnwfllstnlse   87 (88)
                      -.|.||||-||.
T Consensus        62 GeWVlLsTflsp   73 (74)
T 1avy_A           62 GEWVLLSTFLSP   73 (74)
T ss_dssp             TEEEEGGGGSSC
T ss_pred             CCEEEEEECCCC
T ss_conf             838986612468


No 5  
>>1wq6_A AML1-ETO; NHR2, oncoprotein; 2.00A {Homo sapiens} (A:)
Probab=9.31  E-value=1.1e+02  Score=13.38  Aligned_cols=18  Identities=22%  Similarity=0.659  Sum_probs=15.5

Q ss_pred             HHHHHHHHHCCCHHHHCC
Q ss_conf             254566664020233303
Q gi|254780339|r   43 SWKILTTMIGCSSAMLGT   60 (88)
Q Consensus        43 swkilttmigcssamlgt   60 (88)
                      .||-+.+|..|-..|...
T Consensus        22 eWkhl~~~LnCI~~MveK   39 (72)
T 1wq6_A           22 EWKHLDHLLNCIXDXVEK   39 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             999899999999999999


No 6  
>>2k9j_B Integrin beta-3; transmembrane complex, alternative splicing, calcium, cell adhesion, cleavage on PAIR of basic residues, disease mutation; NMR {Homo sapiens} PDB: 2rmz_A 2rn0_A (B:)
Probab=8.86  E-value=1.1e+02  Score=13.35  Aligned_cols=10  Identities=40%  Similarity=0.913  Sum_probs=7.1

Q ss_pred             CHHHHHHHHH
Q ss_conf             1254566664
Q gi|254780339|r   42 MSWKILTTMI   51 (88)
Q Consensus        42 mswkilttmi   51 (88)
                      +.||+++|+-
T Consensus        29 ~iWKll~tih   38 (43)
T 2k9j_B           29 LIWKLLITIH   38 (43)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
T ss_conf             9999998875


No 7  
>>2waq_C DNA-directed RNA polymerase RPO1C subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_C 3hkz_C 2pmz_C (C:1-63)
Probab=8.01  E-value=50  Score=15.35  Aligned_cols=16  Identities=31%  Similarity=0.443  Sum_probs=12.5

Q ss_pred             CCHHHHHHCCCCEEEE
Q ss_conf             3105665204813774
Q gi|254780339|r    7 DSNLKEAITNNRVEIA   22 (88)
Q Consensus         7 dsnlkeaitnnrveia   22 (88)
                      -+.|+++|+|+.+++.
T Consensus        29 i~dLr~~i~n~~i~~T   44 (63)
T 2waq_C           29 VEDLKNLISNKEVLVT   44 (63)
T ss_dssp             CTHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHCCCCEECC
T ss_conf             9999987435525428


No 8  
>>1df6_A Cycloviolacin O1; cyclic cystine knot, backbone cyclic, 3-10 helix, double- stranded anti- parallel beta-sheet, hairpin bends, loops; NMR {Viola odorata} (A:)
Probab=4.86  E-value=2e+02  Score=12.01  Aligned_cols=10  Identities=40%  Similarity=1.065  Sum_probs=6.5

Q ss_pred             HHHHHCCCHH
Q ss_conf             6666402023
Q gi|254780339|r   47 LTTMIGCSSA   56 (88)
Q Consensus        47 lttmigcssa   56 (88)
                      .|.++|||-.
T Consensus         9 vtallgcsc~   18 (30)
T 1df6_A            9 VTALLGCSCS   18 (30)
T ss_dssp             SSGGGTCEEE
T ss_pred             EEEEECCCCC
T ss_conf             1035536646


No 9  
>>1f32_A Major pepsin inhibitor PI-3; proteinase inhibitor, hydrolase inhibitor; 1.75A {Ascaris suum} (A:11-60)
Probab=4.73  E-value=1.9e+02  Score=12.16  Aligned_cols=9  Identities=67%  Similarity=1.010  Sum_probs=0.0

Q ss_pred             CEEEEEECC
Q ss_conf             036898505
Q gi|254780339|r   62 NQVLVLNVP   70 (88)
Q Consensus        62 nqvlvlnvp   70 (88)
                      |||.|-|.|
T Consensus         8 nqvfvanlp   16 (50)
T 1f32_A            8 NQVFVANLP   16 (50)
T ss_dssp             TEEEETTEE
T ss_pred             CEEEECCCE
T ss_conf             898855744


No 10 
>>2qp2_A Unknown protein; toxin, unknown function; 2.00A {Photorhabdus luminescens subsp} (A:358-511)
Probab=4.34  E-value=2.5e+02  Score=11.50  Aligned_cols=9  Identities=78%  Similarity=0.984  Sum_probs=0.0

Q ss_pred             CCCCCCCHH
Q ss_conf             544433105
Q gi|254780339|r    2 IKSTKDSNL   10 (88)
Q Consensus         2 ikstkdsnl   10 (88)
                      .|||||.||
T Consensus        25 lkstkdenl   33 (154)
T 2qp2_A           25 LKSTKDENL   33 (154)
T ss_dssp             CBSSSBCCS
T ss_pred             CCCCHHHCC
T ss_conf             657033212


Done!