Query         gi|254781072|ref|YP_003065485.1| hypothetical protein CLIBASIA_04870 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 190
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 33803
Date          Wed Jun  1 21:57:34 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781072.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >2gsv_A Hypothetical protein Y  80.8       3 8.9E-05   22.4   4.7   48   89-140    26-73  (80)
  2 >1qop_B Tryptophan synthase be  30.8      37  0.0011   14.9   2.9   32  116-147    17-54  (101)
  3 >2gai_A DNA topoisomerase I; z  30.3      37  0.0011   14.9   3.0   49   22-87     26-74  (77)
  4 >2ra1_A Surface layer protein;  25.0      34   0.001   15.1   1.5   23   33-55     31-53  (84)
  5 >1wlq_A Geminin; coiled-coil;   24.4      47  0.0014   14.2   4.2   49   97-145    21-69  (83)
  6 >2gb7_A R.ECL18KI; ECL18KI-DNA  24.0      48  0.0014   14.1   3.1   17   55-71     25-41  (137)
  7 >1e8o_B SRP14, signal recognit  18.8      52  0.0015   13.9   1.4   19   33-51      4-22  (106)
  8 >1tte_A Ubiquitin-conjugating   17.9      60  0.0018   13.4   1.5   14  138-151    11-24  (56)
  9 >3cue_D Transport protein part  17.0      67   0.002   13.1   7.7   68   93-175    30-98  (193)
 10 >2aee_A OPRT, oprtase, orotate  15.4      69   0.002   13.0   1.3   43   64-112    28-71  (104)

No 1  
>>2gsv_A Hypothetical protein YVFG; alpha-helical protein, structural genomics, PSI, protein structure initiative; 1.90A {Bacillus subtilis} (A:)
Probab=80.82  E-value=3  Score=22.42  Aligned_cols=48  Identities=33%  Similarity=0.512  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHEEHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999951567102019999999999999888999999999
Q gi|254781072|r   89 YFKALTKYYKSVVAELREFGLGKSAIEIEEITKAVDTLTRAYNEYKKEIREL  140 (190)
Q Consensus        89 yfkaltkyyksvvaelrefglgksaieieeitkavdtltrayneykkeirel  140 (190)
                      -..|+..||+|||..|-.-.|.|.|.-|..    ...|..|||.-++|-..|
T Consensus        26 kIhAmNaYYrsVvstlvqDqltKNavvlkR----iqHLdEAY~KVk~ee~k~   73 (80)
T 2gsv_A           26 KIHAXNSYYRSVVSTLVQDQLTKNAVVLKR----IQHLDEAYNKVKRGESKL   73 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSSCHHHHHHH----HHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999730799999----999999999998777654


No 2  
>>1qop_B Tryptophan synthase beta chain; lyase, carbon-oxygen lyase, tryptophan biosynthesis, pyridoxal phosphate; HET: IPL PLP; 1.4A {Salmonella typhimurium} (B:1-52,B:271-319)
Probab=30.76  E-value=37  Score=14.92  Aligned_cols=32  Identities=13%  Similarity=0.318  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHH
Q ss_conf             999999999999988899------99999999999971
Q gi|254781072|r  116 IEEITKAVDTLTRAYNEY------KKEIRELIEEFIEL  147 (190)
Q Consensus       116 ieeitkavdtltrayney------kkeirelieefiel  147 (190)
                      -|.+..+++-|++||+++      .+|.+.|..+|+..
T Consensus        17 PE~L~~aL~ELe~ay~~~~~Dp~F~~El~~ll~~Yv~~   54 (101)
T 1qop_B           17 PQILMPALNQLEEAFVSAQKDPEFQAQFADLLKNYAKH   54 (101)
T ss_dssp             CGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTHH
T ss_pred             CHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCC
T ss_conf             78889999999999999972989999999998624814


No 3  
>>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga maritima MSB8} PDB: 2gaj_A* (A:128-162,A:505-546)
Probab=30.30  E-value=37  Score=14.87  Aligned_cols=49  Identities=27%  Similarity=0.394  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf             234222044444399999999999999998776666554455533113697863465546568788
Q gi|254781072|r   22 SFLQIRSKESVINKEFVTKVEELYEKAQKAHKKRDKVYGAYDKVSSHKKSPKELSKAFYIDFRTEL   87 (190)
Q Consensus        22 sflqirskesvinkefvtkveelyekaqkahkkrdkvygaydkvsshkkspkelskafyidfrtel   87 (190)
                      ..|+-.-+..++|-+|..++|+-                 .|.+++.+..-+++-+.||-+|...+
T Consensus        26 ~~lw~k~~~~iid~~FTA~ME~~-----------------LD~Ia~G~~~W~~vL~~Fy~~F~~~i   74 (77)
T 2gai_A           26 PVLWRNFKSNVVSVSFTAEMEKD-----------------LDEVEQGKKTDKIVLREFYESFSSVF   74 (77)
T ss_dssp             HHHHHHHSCCTTSHHHHHHHHHH-----------------HHHHHTTSSCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHH-----------------HHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf             77765200340899999999999-----------------99998599989999999999999999


No 4  
>>2ra1_A Surface layer protein; triple coiled-coil, S-layer protein, protein binding, sugar binding protein; 2.41A {Bacillus stearothermophilus} (A:84-167)
Probab=24.98  E-value=34  Score=15.14  Aligned_cols=23  Identities=35%  Similarity=0.476  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             43999999999999999987766
Q gi|254781072|r   33 INKEFVTKVEELYEKAQKAHKKR   55 (190)
Q Consensus        33 inkefvtkveelyekaqkahkkr   55 (190)
                      ++-+-+.+++++|.+-+---+|+
T Consensus        31 ~~a~dl~k~~e~YhklsyEIrk~   53 (84)
T 2ra1_A           31 VDAKDLKKAEELYHKISYELKTR   53 (84)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHS
T ss_pred             HHHCCHHHHHHHHHHHHHHHHHH
T ss_conf             55111167888666665743320


No 5  
>>1wlq_A Geminin; coiled-coil; 2.80A {Mus musculus} (A:)
Probab=24.43  E-value=47  Score=14.17  Aligned_cols=49  Identities=27%  Similarity=0.259  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHCCCCCHHEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999995156710201999999999999988899999999999999
Q gi|254781072|r   97 YKSVVAELREFGLGKSAIEIEEITKAVDTLTRAYNEYKKEIRELIEEFI  145 (190)
Q Consensus        97 yksvvaelrefglgksaieieeitkavdtltrayneykkeirelieefi  145 (190)
                      |--+|||-|.-.|+.+--|.+...+.+..+.---...+.+.+.|.|-.-
T Consensus        21 YWk~lAE~Rr~AL~eaL~EN~~Lh~~ie~l~eEi~~L~~en~~L~Ev~~   69 (83)
T 1wlq_A           21 YWKEVAEQRRKALYEALKENEKLHKEIEQKDSEIARLRKENKDLAEVAE   69 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999888999999999999999999


No 6  
>>2gb7_A R.ECL18KI; ECL18KI-DNA complex, type II restriction endonuclease, nucleotide flipping, base extrusion, hydrolase/DNA complex; HET: DNA; 1.70A {Enterobacter cloacae} PDB: 2fqz_A* (A:1-137)
Probab=24.01  E-value=48  Score=14.12  Aligned_cols=17  Identities=18%  Similarity=0.272  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHHCCCC
Q ss_conf             66655445553311369
Q gi|254781072|r   55 RDKVYGAYDKVSSHKKS   71 (190)
Q Consensus        55 rdkvygaydkvsshkks   71 (190)
                      -|-||-++-+..-|++.
T Consensus        25 f~ivy~~f~~lgy~kqn   41 (137)
T 2gb7_A           25 FALVYKTFCDLGYDQKN   41 (137)
T ss_dssp             HHHHHHHHHHTTGGGSC
T ss_pred             HHHHHHHHHHCCHHHHH
T ss_conf             89999999851411213


No 7  
>>1e8o_B SRP14, signal recognition particle 14 kDa protein; ALU ribonucleoprotein particle, protein recognition of AN RNA U-turn, translational control; HET: GDP; 3.20A {Homo sapiens} (B:)
Probab=18.84  E-value=52  Score=13.87  Aligned_cols=19  Identities=21%  Similarity=0.578  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             4399999999999999998
Q gi|254781072|r   33 INKEFVTKVEELYEKAQKA   51 (190)
Q Consensus        33 inkefvtkveelyekaqka   51 (190)
                      -|.+|.+++.+||++++..
T Consensus         4 ~nd~FL~~Lt~Lf~~~~~~   22 (106)
T 1e8o_B            4 ESEQFLTELTRLFQKCRTS   22 (106)
T ss_dssp             CHHHHHHHHHHHHHHHTTT
T ss_pred             CHHHHHHHHHHHHHHCCCC
T ss_conf             6589999999999856778


No 8  
>>1tte_A Ubiquitin-conjugating enzyme E2-24 kDa; UBC1, ubiquitin-dependent degradation, ligase; NMR {Saccharomyces cerevisiae} (A:160-215)
Probab=17.91  E-value=60  Score=13.41  Aligned_cols=14  Identities=43%  Similarity=0.911  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHCHHC
Q ss_conf             99999999712102
Q gi|254781072|r  138 RELIEEFIELGFDQ  151 (190)
Q Consensus       138 relieefielgfdq  151 (190)
                      ++|+++|..+||+.
T Consensus        11 k~lVd~F~~mGF~~   24 (56)
T 1tte_A           11 HDLIDEFESQGFEK   24 (56)
T ss_dssp             HHHHHHHHHHTCCH
T ss_pred             HHHHHHHHHCCCCH
T ss_conf             89999998638334


No 9  
>>3cue_D Transport protein particle 22 kDa subunit; membrane traffic, GEF, tethering complex, RAB activation, guanine nucleotide exchange factor; HET: PLM; 3.70A {Saccharomyces cerevisiae} (D:)
Probab=16.95  E-value=67  Score=13.12  Aligned_cols=68  Identities=25%  Similarity=0.487  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHHH-CCCCCHHEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99999999999995-15671020199999999999998889999999999999971210233010124678888877789
Q gi|254781072|r   93 LTKYYKSVVAELRE-FGLGKSAIEIEEITKAVDTLTRAYNEYKKEIRELIEEFIELGFDQCDECDLCSEKADVIQKKRIA  171 (190)
Q Consensus        93 ltkyyksvvaelre-fglgksaieieeitkavdtltrayneykkeirelieefielgfdqcdecdlcsekadviqkkria  171 (190)
                      +|--|-+.|+.|-. +.     -.++++.+..|..-  ||   --+ .|||||.-  -..+..|.--.|.||||.|  .+
T Consensus        30 ftLTYGalV~QL~kD~E-----~d~~~VN~qLdkMG--yn---IG~-RLiedFLA--ks~~~rC~~f~etaevIak--vg   94 (193)
T 3cue_D           30 FTLTYGSIVAQLCQDYE-----RDFNKVNDHLYSMG--YN---IGC-RLIEDFLA--RTALPRCENLVKTSEVLSK--CA   94 (193)
T ss_dssp             HHHHHHHHHHHHHHHTT-----TCHHHHHHHHHHHH--HH---HHH-HHHHHHHH--HTCCCCCSSHHHHHHHHHH--HH
T ss_pred             HHHHHHHHHHHHHHHHH-----CCHHHHHHHHHHHC--CC---CCC-HHHHHHHH--HCCCCCCCCHHHHHHHHHH--HH
T ss_conf             99999999999998753-----27999999999823--11---583-05667653--0488643569999999999--99


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|254781072|r  172 FEMV  175 (190)
Q Consensus       172 femv  175 (190)
                      |.|-
T Consensus        95 fKmf   98 (193)
T 3cue_D           95 FKIF   98 (193)
T ss_dssp             HHHH
T ss_pred             HHHH
T ss_conf             9998


No 10 
>>2aee_A OPRT, oprtase, orotate phosphoribosyltransferase; structural genomics, PSI, protein structure initiative; 1.95A {Streptococcus pyogenes} (A:1-67,A:175-211)
Probab=15.44  E-value=69  Score=13.03  Aligned_cols=43  Identities=30%  Similarity=0.349  Sum_probs=27.6

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCCCH
Q ss_conf             53311369786346554656878899999999999999999-95156710
Q gi|254781072|r   64 KVSSHKKSPKELSKAFYIDFRTELKYFKALTKYYKSVVAEL-REFGLGKS  112 (190)
Q Consensus        64 kvsshkkspkelskafyidfrtelkyfkaltkyyksvvael-refglgks  112 (190)
                      ..+|-++||      ||+|.|.-+-|-+.+..--.-....+ +++||-.-
T Consensus        28 tLaSG~~SP------~YvD~R~~~s~P~~~~~i~~~~~~~I~~~~gl~~y   71 (104)
T 2aee_A           28 TWASGIKSP------IYTDNRVTLSYPKTRDLIENGFVETIKAHFPLSNY   71 (104)
T ss_dssp             ECGGGCEES------EEECGGGGGGCHHHHHHHHHHHHHHHHHHCTSCCH
T ss_pred             EECCCCCCH------HHEECHHHHCCHHHHHHHHHHHHHHHHHCCCECCH
T ss_conf             947347761------66149223229589999999999999855655739


Done!