Query         gi|254781145|ref|YP_003065558.1| hypothetical protein CLIBASIA_05245 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 350
No_of_seqs    150 out of 629
Neff          8.4 
Searched_HMMs 33803
Date          Wed Jun  1 23:19:40 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781145.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >2jes_A Portal protein; DNA tr  42.8      18 0.00054   15.0   5.2   92  183-278     2-95  (97)
  2 >1oqy_A HHR23A, UV excision re  40.3     9.8 0.00029   16.8   0.8   28   77-104    20-47  (60)
  3 >1vg5_A RSGI RUH-014, rhomboid  38.6     7.2 0.00021   17.6  -0.1   26   78-103    33-58  (73)
  4 >1oqy_A HHR23A, UV excision re  35.6      16 0.00046   15.4   1.2   27   78-104    47-73  (99)
  5 >1ify_A HHR23A, UV excision re  31.9      16 0.00048   15.3   0.8   26   78-103    12-37  (49)
  6 >1dv0_A DNA repair protein HHR  25.9      17 0.00049   15.2   0.0   31   78-108     8-38  (47)
  7 >1wgn_A UBAP1, ubiquitin assoc  25.3      11 0.00032   16.5  -1.0   15   79-93     24-38  (63)
  8 >2g3q_A Protein YBL047C; endoc  25.0      29 0.00084   13.7   1.1   22   77-98      7-28  (43)
  9 >1wiv_A UBP14, ubiquitin-speci  24.3      20  0.0006   14.6   0.2   17   78-94     33-49  (73)
 10 >2vdr_B Integrin beta-3; cell   24.1      36  0.0011   13.0   1.5   42   25-66     36-78  (138)
 11 >2cpw_A CBL-interacting protei  23.3      26 0.00077   14.0   0.6   17   78-94     23-39  (64)
 12 >2dna_A Unnamed protein produc  23.2      22 0.00066   14.4   0.3   17   78-94     23-40  (67)
 13 >1veg_A NEDD8 ultimate buster-  21.8      22 0.00065   14.4  -0.0   26   77-102    32-57  (83)
 14 >2dai_A Ubadc1, ubiquitin asso  21.3      24 0.00072   14.1   0.1   26   77-102    32-57  (83)

No 1  
>>2jes_A Portal protein; DNA translocation, molecular motor, viral portal protein, viral protein; 3.4A {Bacteriophage SPP1} (A:256-352)
Probab=42.76  E-value=18  Score=14.97  Aligned_cols=92  Identities=13%  Similarity=0.095  Sum_probs=63.9

Q ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCC-CCC-CCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             543102899998998848878763036622531343-121-000011225741450466655444444568876567999
Q gi|254781145|r  183 AASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGS-IID-PESVLNPQFGKPIRVAAGMDIRSVLGIHSVPMIEKSFSM  260 (350)
Q Consensus       183 ~d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~-~~~-~~d~~~~~~g~~v~~~~~~~~~~i~~~~~~~~~~~~~~~  260 (350)
                      .+.+.+++.+.+.++....+...-...+.+.+ .|. ..+ .+..-+.+-.+++.+.+++.++-   +.-+-.....-..
T Consensus         2 ~e~v~~LIDayd~~~S~~an~~~df~~a~lvl-~G~~~~~~~e~~~~lk~~~~i~l~~~~~v~~---Ltk~~~~~~~e~~   77 (97)
T 2jes_A            2 LKFYKDLIDNYDSITSSTMDSFSDFQQIVYVL-KNYDGENPKEFTANLRYHSVIKVSGDGGVDT---LRAEIPVDSAAKE   77 (97)
T ss_dssp             GGGTHHHHHHHHHHHHHHHHHHHHTTSCEEEE-EEESCSCHHHHHHHHHHSSEEEEEEEEEEEE---ECCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCCHHHHHHHHHCCCEEEECCCCCCEE---EEECCCHHHHHHH
T ss_conf             56558999999999868889999865368786-0788665155665553054362089998068---8615881899999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999998875246664
Q gi|254781145|r  261 LHYLDQELVDRTGISDIS  278 (350)
Q Consensus       261 l~~~~~~~e~~tGi~~~~  278 (350)
                      ++.+...+-+.|.+++.+
T Consensus        78 ~~~L~~~I~~~s~~pd~~   95 (97)
T 2jes_A           78 LERIQDELYKSAQAVDNS   95 (97)
T ss_dssp             HHHHHHHHHHHTTCCCCS
T ss_pred             HHHHHHHHHHHHCCCCCC
T ss_conf             999999999985888877


No 2  
>>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} (A:309-368)
Probab=40.29  E-value=9.8  Score=16.75  Aligned_cols=28  Identities=11%  Similarity=0.134  Sum_probs=20.0

Q ss_pred             CHHHHHHHCCCCHHHCCCCCCCCCCHHH
Q ss_conf             6899987279804430277787641013
Q gi|254781145|r   77 TRSDLISMGYDRESINNLPIISSQNIEN  104 (350)
Q Consensus        77 t~~eL~~~Gy~~d~v~~~~~~~~~~~~~  104 (350)
                      ....|.+|||+++...+.-.....+.+.
T Consensus        20 ~i~~L~~MGF~~~~a~~AL~~~~~n~e~   47 (60)
T 1oqy_A           20 AIERLKALGFPESLVIQAYFACEKNENL   47 (60)
T ss_dssp             HHHHHHHHTCCSHHHHHHTSSSSSCSSH
T ss_pred             HHHHHHHCCCCHHHHHHHHHHCCCCHHH
T ss_conf             9999998499989999999982998999


No 3  
>>1vg5_A RSGI RUH-014, rhomboid family protein; UBA domain, cDNA, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} (A:)
Probab=38.59  E-value=7.2  Score=17.65  Aligned_cols=26  Identities=19%  Similarity=0.464  Sum_probs=14.4

Q ss_pred             HHHHHHHCCCCHHHCCCCCCCCCCHH
Q ss_conf             89998727980443027778764101
Q gi|254781145|r   78 RSDLISMGYDRESINNLPIISSQNIE  103 (350)
Q Consensus        78 ~~eL~~~Gy~~d~v~~~~~~~~~~~~  103 (350)
                      ..+|.+|||.++.+.+.-.....+.+
T Consensus        33 i~~L~~MGF~~~~a~~AL~~~~~nve   58 (73)
T 1vg5_A           33 IQKLVAMGFDRTQVEVALAAADDDLT   58 (73)
T ss_dssp             HHHHHTTTCCHHHHHHHHHHHTSCHH
T ss_pred             HHHHHHCCCCHHHHHHHHHHHCCCHH
T ss_conf             99999939999999999999589999


No 4  
>>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} (A:126-224)
Probab=35.62  E-value=16  Score=15.43  Aligned_cols=27  Identities=30%  Similarity=0.443  Sum_probs=17.3

Q ss_pred             HHHHHHHCCCCHHHCCCCCCCCCCHHH
Q ss_conf             899987279804430277787641013
Q gi|254781145|r   78 RSDLISMGYDRESINNLPIISSQNIEN  104 (350)
Q Consensus        78 ~~eL~~~Gy~~d~v~~~~~~~~~~~~~  104 (350)
                      ..+|.+|||.++.+.+.-.....+.+.
T Consensus        47 i~~L~eMGF~~~~a~~AL~~~~~nve~   73 (99)
T 1oqy_A           47 LTEIMSMGYERERVVAALRASYNNPHR   73 (99)
T ss_dssp             HHHHHTTTCCSHHHHHHHHHSCSSTTH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCHHH
T ss_conf             999985063779999999987618899


No 5  
>>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} (A:)
Probab=31.86  E-value=16  Score=15.30  Aligned_cols=26  Identities=31%  Similarity=0.456  Sum_probs=17.6

Q ss_pred             HHHHHHHCCCCHHHCCCCCCCCCCHH
Q ss_conf             89998727980443027778764101
Q gi|254781145|r   78 RSDLISMGYDRESINNLPIISSQNIE  103 (350)
Q Consensus        78 ~~eL~~~Gy~~d~v~~~~~~~~~~~~  103 (350)
                      ..+|.+|||+++.+.+.-.....+.+
T Consensus        12 v~~L~~MGF~~~~a~~AL~~~~~n~e   37 (49)
T 1ify_A           12 LTEIMSMGYERERVVAALRASYNNPH   37 (49)
T ss_dssp             HHHHHHTTCCHHHHHHHHHTTTSCSH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             99999800279999999998716817


No 6  
>>1dv0_A DNA repair protein HHR23A; helical bundle, DNA binding protein; HET: DNA; NMR {Homo sapiens} (A:)
Probab=25.90  E-value=17  Score=15.22  Aligned_cols=31  Identities=13%  Similarity=0.166  Sum_probs=21.0

Q ss_pred             HHHHHHHCCCCHHHCCCCCCCCCCHHHHHHC
Q ss_conf             8999872798044302777876410133202
Q gi|254781145|r   78 RSDLISMGYDRESINNLPIISSQNIENTWKF  108 (350)
Q Consensus        78 ~~eL~~~Gy~~d~v~~~~~~~~~~~~~~~~~  108 (350)
                      .++|.+|||.++...+.-.....+.+.-..+
T Consensus         8 i~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~   38 (47)
T 1dv0_A            8 IERLKALGFPESLVIQAYFACEKNENLAANF   38 (47)
T ss_dssp             HTTTTTTTCCHHHHHHHHTTTTSCHHHHHHH
T ss_pred             HHHHHHCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf             9999983998889999999818769999999


No 7  
>>1wgn_A UBAP1, ubiquitin associated protein; ubiquitin associated protein 1 (UBAP1), UBA domain, structural genomics; NMR {Homo sapiens} (A:)
Probab=25.31  E-value=11  Score=16.47  Aligned_cols=15  Identities=27%  Similarity=0.611  Sum_probs=5.9

Q ss_pred             HHHHHHCCCCHHHCC
Q ss_conf             999872798044302
Q gi|254781145|r   79 SDLISMGYDRESINN   93 (350)
Q Consensus        79 ~eL~~~Gy~~d~v~~   93 (350)
                      .+|.+|||+++.+.+
T Consensus        24 ~~L~~MGF~~~~a~~   38 (63)
T 1wgn_A           24 ETVVNMGYSYECVLR   38 (63)
T ss_dssp             HHHHHHHCCHHHHHH
T ss_pred             HHHHHCCCCHHHHHH
T ss_conf             999986998999999


No 8  
>>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} (A:)
Probab=25.00  E-value=29  Score=13.68  Aligned_cols=22  Identities=23%  Similarity=0.309  Sum_probs=14.8

Q ss_pred             CHHHHHHHCCCCHHHCCCCCCC
Q ss_conf             6899987279804430277787
Q gi|254781145|r   77 TRSDLISMGYDRESINNLPIIS   98 (350)
Q Consensus        77 t~~eL~~~Gy~~d~v~~~~~~~   98 (350)
                      ...+|.+|||+++.+.+.-...
T Consensus         7 ~v~~L~~MGF~~~~a~~AL~~~   28 (43)
T 2g3q_A            7 AVEELSGMGFTEEEAHNALEKC   28 (43)
T ss_dssp             HHHHHHTTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCHHHHHHHHHHC
T ss_conf             9999997699999999999992


No 9  
>>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} (A:)
Probab=24.28  E-value=20  Score=14.65  Aligned_cols=17  Identities=18%  Similarity=0.427  Sum_probs=8.5

Q ss_pred             HHHHHHHCCCCHHHCCC
Q ss_conf             89998727980443027
Q gi|254781145|r   78 RSDLISMGYDRESINNL   94 (350)
Q Consensus        78 ~~eL~~~Gy~~d~v~~~   94 (350)
                      ..+|.+|||.++.+.+.
T Consensus        33 i~~L~~MGF~~~~a~~A   49 (73)
T 1wiv_A           33 VDTLLSFGFAEDVARKA   49 (73)
T ss_dssp             HHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHCCCCHHHHHHH
T ss_conf             99999469999999999


No 10 
>>2vdr_B Integrin beta-3; cell adhesion/immune system, alternative splicing, platelet integrin ALPHAIIBBETA3, polymorphism, glycoprotein, cell adhesion, calcium; HET: NAG MAN; 2.40A {Homo sapiens} PDB: 2vc2_B* 2vdk_B* 2vdm_B* 2vdn_B* 2vdl_B* 2vdp_B* 2vdq_B* 2vdo_B* 3fcu_B* 1txv_B* 1ty3_B* 1ty5_B* 1ty6_B* 1ty7_B* 1tye_B* (B:58-109,B:352-437)
Probab=24.14  E-value=36  Score=12.96  Aligned_cols=42  Identities=14%  Similarity=0.275  Sum_probs=33.2

Q ss_pred             CCCCCEEEEEEEEEEEECCEEEEEEE-CHHHEEECCCCCCHHH
Q ss_conf             66761577589999974683689857-6587434679988646
Q gi|254781145|r   25 EDGGEKVHDLRIRRKYSQGKVCVDAV-SPDEFLIHPDSVDIEK   66 (350)
Q Consensus        25 ~~~~~~~~~v~~~r~~~~~~v~ie~V-~pedf~vdp~A~~l~d   66 (350)
                      -++...++.+++|+..++++|.++.= .|+.+-+++.|...+.
T Consensus        36 Rpg~~~~f~~~~rq~eD~S~V~l~~~~~p~~v~isy~s~C~~g   78 (138)
T 2vdr_B           36 RPDDSKNFSIQVRQVEDRSKVELEVRDLPEELSLSFNATCLNN   78 (138)
T ss_dssp             CTTCEEEEEEEEECCSCCEEEEEEEESCCTTEEEEEEEECTTC
T ss_pred             CCCCCEEEEEEEECCCCHEEEEEECCCCCCCEEEEEEEECCCC
T ss_conf             4998289998621377714899852799985799999887999


No 11 
>>2cpw_A CBL-interacting protein STS-1 variant; ubiquitin associated domain, UBA, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=23.26  E-value=26  Score=13.96  Aligned_cols=17  Identities=29%  Similarity=0.466  Sum_probs=9.2

Q ss_pred             HHHHHHHCCCCHHHCCC
Q ss_conf             89998727980443027
Q gi|254781145|r   78 RSDLISMGYDRESINNL   94 (350)
Q Consensus        78 ~~eL~~~Gy~~d~v~~~   94 (350)
                      .++|.+|||.+....+.
T Consensus        23 v~~L~~MGF~~~~a~kA   39 (64)
T 2cpw_A           23 LDVLLSMGFPRARAQKA   39 (64)
T ss_dssp             HHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHCCCCHHHHHHH
T ss_conf             99999969989999999


No 12 
>>2dna_A Unnamed protein product; ubiquitin associated domain, DSK2 protein, proteasome, structural genomics, NPPSFA; NMR {Mus musculus} (A:)
Probab=23.22  E-value=22  Score=14.37  Aligned_cols=17  Identities=18%  Similarity=0.210  Sum_probs=8.6

Q ss_pred             HHHHHHHCC-CCHHHCCC
Q ss_conf             899987279-80443027
Q gi|254781145|r   78 RSDLISMGY-DRESINNL   94 (350)
Q Consensus        78 ~~eL~~~Gy-~~d~v~~~   94 (350)
                      .++|.+||| +++...+.
T Consensus        23 l~~L~~MGF~d~~~~~~A   40 (67)
T 2dna_A           23 MECLQAMGFVNYNANLQA   40 (67)
T ss_dssp             HHHHHHHTCCCHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHH
T ss_conf             999999389969999999


No 13 
>>1veg_A NEDD8 ultimate buster-1; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Mus musculus} (A:)
Probab=21.81  E-value=22  Score=14.41  Aligned_cols=26  Identities=19%  Similarity=0.312  Sum_probs=15.2

Q ss_pred             CHHHHHHHCCCCHHHCCCCCCCCCCH
Q ss_conf             68999872798044302777876410
Q gi|254781145|r   77 TRSDLISMGYDRESINNLPIISSQNI  102 (350)
Q Consensus        77 t~~eL~~~Gy~~d~v~~~~~~~~~~~  102 (350)
                      +..+|.+|||.++...+.-.....+.
T Consensus        32 ~i~~L~~MGF~~~~a~~AL~~~~nnv   57 (83)
T 1veg_A           32 SINQLVYMGFDTVVAEAALRVFGGNV   57 (83)
T ss_dssp             HHHHHHHHSCCHHHHHHHHHHTTTCH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHCCCH
T ss_conf             89999983423888999999964509


No 14 
>>2dai_A Ubadc1, ubiquitin associated domain containing 1; UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=21.26  E-value=24  Score=14.13  Aligned_cols=26  Identities=12%  Similarity=0.267  Sum_probs=14.3

Q ss_pred             CHHHHHHHCCCCHHHCCCCCCCCCCH
Q ss_conf             68999872798044302777876410
Q gi|254781145|r   77 TRSDLISMGYDRESINNLPIISSQNI  102 (350)
Q Consensus        77 t~~eL~~~Gy~~d~v~~~~~~~~~~~  102 (350)
                      ...+|.+|||.++.+.+.-.....+.
T Consensus        32 ~i~~L~~MGF~~~~a~~AL~~~~~nv   57 (83)
T 2dai_A           32 ALRQLTEMGFPENRATKALQLNHMSV   57 (83)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHTTSCH
T ss_pred             HHHHHHHCCCCHHHHHHHHHHCCCCH
T ss_conf             99999996999999999999919999


Done!