Query         gi|254781190|ref|YP_003065603.1| hypothetical protein CLIBASIA_05485 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 233
No_of_seqs    140 out of 347
Neff          7.7 
Searched_HMMs 33803
Date          Wed Jun  1 23:33:53 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781190.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1ro2_A Hypothetical protein O  99.8 9.5E-20 2.8E-24  132.5   4.8  135    2-141    46-193 (216)
  2 >3h20_A Replication protein B;  82.7     2.9 8.5E-05   20.2   5.4   65    3-71     48-114 (212)
  3 >3kya_A Putative phosphatase;   34.5      22 0.00065   15.1   1.8   28   84-111    57-84  (128)
  4 >2yhx_A Hexokinase B; transfer  29.1      14  0.0004   16.3   0.0   31    1-31     46-76  (284)
  5 >1dt9_A ERF1, protein (eukaryo  25.3      40  0.0012   13.7   2.0   26    8-33     58-88  (102)
  6 >1wgx_A KIAA1903 protein; MYB   19.6      52  0.0015   13.0   4.3   40  156-199     5-44  (73)
  7 >2i9z_A Putative septation pro  15.1      67   0.002   12.4   2.2   32   85-116    36-68  (105)
  8 >2iru_A Putative DNA ligase-li  14.8      68   0.002   12.3   6.0   43   25-68      3-53  (132)
  9 >2i9x_A Putative septation pro  14.7      68   0.002   12.3   2.2   31   85-115    36-67  (87)
 10 >2fao_A Probable ATP-dependent  14.1      71  0.0021   12.2   6.0   44   24-68      6-57  (182)

No 1  
>>1ro2_A Hypothetical protein ORF904; DNA polymerase, primase, replication, polymerization, evolution of nucleic acid polymerizing enzymes; 1.60A {Sulfolobus islandicus} (A:)
Probab=99.78  E-value=9.5e-20  Score=132.51  Aligned_cols=135  Identities=11%  Similarity=0.132  Sum_probs=89.9

Q ss_pred             CHHHHHCCCCC-CEEEEECCCCCCEEEEEEECCCHHHHHHHHHH---HHHHCCCCEEEECCCCCEEEEEECCCCCCCCCC
Q ss_conf             23787518616-88997078848889999548984678999997---764089862986788953999844743124335
Q gi|254781190|r    2 VATDVDHYVYN-GFGILCGIGTHPVYAFDVDVLDEQVVDRFNNE---FQSCCGKPISRVGQAPKTLMLFRMQETNLKKQK   77 (233)
Q Consensus         2 va~~~~~~p~~-giGi~~G~~s~~l~~iDiD~~d~~~~~~~~~~---~~~~~~~~~~~~g~~~~~~~lfr~~~~~~~~~~   77 (233)
                      |..++..+|.+ ||||.||.  .++++||+|.  ......+..+   ...+..++.++++ ++++|+|||+|+....+..
T Consensus        46 i~~w~~~~p~~~nigi~~G~--~~~vviD~D~--~~g~~~~~~l~~~~~~l~~t~~~~T~-~gG~h~~f~~p~~~~~~~~  120 (216)
T 1ro2_A           46 KQRFLKMIEEGYNYAIPGGQ--KGMVIMDFES--KEKLKAWIGESALEELCRKTLCTNTV-HGGIHIYVLSNDIPPHKIN  120 (216)
T ss_dssp             HHHHHHHHHHTCEEEEESSG--GGEEEEEESC--HHHHHHHHCHHHHHHHHHHSCEEECT-TSCEEEEEECSCCCSSCCC
T ss_pred             HHHHHHHCCCCCEEEEECCC--CCEEEEECCC--CCHHHHHHHHHHHHHCCCCCEEEECC-CCCEEEEEECCCCCCCCCC
T ss_conf             99999849975659996487--7789998888--52034442224566238886489858-9917999976888865315


Q ss_pred             C--CCCCCCCEEEEECCCEEEECCC----CCCCCCCEEEECCCCC---CCHHHCCCCCHHHHHHHHHHHHHHC
Q ss_conf             7--7767663589845832895366----8888884574216776---8822367689999999997544201
Q gi|254781190|r   78 S--EEKIQGHLEFLAYGQQFVAYNI----HPKTQRAYTWSIAPHA---LKVEELPLLTPDEVEYFFEFFDTIT  141 (233)
Q Consensus        78 ~--~~~~~~~iEi~~~g~q~V~~g~----hp~Tg~~Y~W~~~~~~---~~~~~lP~~~~~~l~~~~~~~~~~~  141 (233)
                      .  ......+||||+.|+|+|+|||    ||.||+.|+|..++..   .+...++.+....+..+........
T Consensus       121 ~~~~~~~~~gvdir~~g~~vV~ppS~~~~~~~~g~~Y~w~~~~~~~~~~p~~~~~~l~~~~~~~~~~~~~~~~  193 (216)
T 1ro2_A          121 PLFEENGKGIIDLQSYNSYVLGLGSCVNHLHCTTDKCPWKEQNYTTCYTLYNELKEISKVDLKSLLRFLAEKG  193 (216)
T ss_dssp             CSEESSSSEEEEEECTTCEEECTTCEEEGGGCCSTTCTTTTCSCEEECEESSSCCCCEECCHHHHHHHHHHHH
T ss_pred             CCEECCCCCEEEEEECCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             5443278842889836988996361046646787766524566556676743335554255367899999877


No 2  
>>3h20_A Replication protein B; primase, nucleotidyltransferase, helix-bundle-domain; 1.99A {Plasmid RSF1010} PDB: 3h25_A (A:1-212)
Probab=82.71  E-value=2.9  Score=20.24  Aligned_cols=65  Identities=11%  Similarity=-0.007  Sum_probs=34.7

Q ss_pred             HHHHHCCCCCCEEE--EECCCCCCEEEEEEECCCHHHHHHHHHHHHHHCCCCEEEECCCCCEEEEEECCCC
Q ss_conf             37875186168899--7078848889999548984678999997764089862986788953999844743
Q gi|254781190|r    3 ATDVDHYVYNGFGI--LCGIGTHPVYAFDVDVLDEQVVDRFNNEFQSCCGKPISRVGQAPKTLMLFRMQET   71 (233)
Q Consensus         3 a~~~~~~p~~giGi--~~G~~s~~l~~iDiD~~d~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~lfr~~~~   71 (233)
                      ..++.+++..|.||  .... ....+.||||.........+.++  .+.++..+-||+ |..|.+++...+
T Consensus        48 ~~~l~~~~~~g~~i~~~~~~-~~~~~~vdiD~~~~~~~~~~~~~--~~~Ps~iv~SG~-G~~h~~~~~~~p  114 (212)
T 3h20_A           48 TPWLKRMNAQGNDVYIRPAE-QERHGLVLVDDLSEFDLDDMKAE--GREPALVVETSP-KNYQAWVKVADA  114 (212)
T ss_dssp             HHHHHHHHHTTEEEEEEECT-TCCCCEEEEEEECHHHHHHHHHT--TCCCSEEEEEET-TEEEEEEECCSC
T ss_pred             CHHHHHHCCCCCCEEECCCC-CCCCCEEEECCCCHHHHHHHHHC--CCCCCEEEEECC-CCEEEEEEECCC
T ss_conf             77877623356745876456-78842588447877789999864--567625888379-974789981788


No 3  
>>3kya_A Putative phosphatase; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: MSE; 1.77A {Bacteroides thetaiotaomicron} (A:182-309)
Probab=34.50  E-value=22  Score=15.13  Aligned_cols=28  Identities=25%  Similarity=0.296  Sum_probs=20.8

Q ss_pred             CCEEEEECCCEEEECCCCCCCCCCEEEE
Q ss_conf             6358984583289536688888845742
Q gi|254781190|r   84 GHLEFLAYGQQFVAYNIHPKTQRAYTWS  111 (233)
Q Consensus        84 ~~iEi~~~g~q~V~~g~hp~Tg~~Y~W~  111 (233)
                      ....+++++.++...-.||.||.-|.=.
T Consensus        57 ~~~~~l~~~k~c~g~aVHP~tGeLYfn~   84 (128)
T 3kya_A           57 SDIQLIAAYKQCNGATIHPINGELYFNS   84 (128)
T ss_dssp             SCEEEEEEESCCCCEEECTTTCCEEEEE
T ss_pred             CCCCEEECCCCCCEEEEECCCCEEEEEE
T ss_conf             8740231268972599978999399998


No 4  
>>2yhx_A Hexokinase B; transferase(phosphoryl,alcohol acceptr); HET: OTG; 2.10A {Saccharomyces cerevisiae} (A:1-54,A:201-430)
Probab=29.05  E-value=14  Score=16.34  Aligned_cols=31  Identities=29%  Similarity=0.329  Sum_probs=23.9

Q ss_pred             CCHHHHHCCCCCCEEEEECCCCCCEEEEEEE
Q ss_conf             9237875186168899707884888999954
Q gi|254781190|r    1 MVATDVDHYVYNGFGILCGIGTHPVYAFDVD   31 (233)
Q Consensus         1 ~va~~~~~~p~~giGi~~G~~s~~l~~iDiD   31 (233)
                      ||-.|+-+.|..-||++.|-.+|.-++-+++
T Consensus        46 ~~~~~~~~~p~t~iGlIlGTGtNaaY~E~~~   76 (284)
T 2yhx_A           46 MVPGWVLKQAXIKMGIIFGSGVNAAYWCDST   76 (284)
T ss_dssp             CEECCCCCCTTEEEEEEESSSEEEEEEECGG
T ss_pred             CCCCCCCCCCCCEEEEEECCEEEEEEEEECC
T ss_conf             1666568898616899975658889984445


No 5  
>>1dt9_A ERF1, protein (eukaryotic peptide chain release factor subunit 1); tRNA mimicry, protein sythesis, STOP codon recognition, peptidyl-tRNA hydrolysis; 2.70A {Homo sapiens} (A:30-131)
Probab=25.28  E-value=40  Score=13.67  Aligned_cols=26  Identities=19%  Similarity=0.315  Sum_probs=12.5

Q ss_pred             CCCCCCEEEEECCCCC-----CEEEEEEECC
Q ss_conf             1861688997078848-----8899995489
Q gi|254781190|r    8 HYVYNGFGILCGIGTH-----PVYAFDVDVL   33 (233)
Q Consensus         8 ~~p~~giGi~~G~~s~-----~l~~iDiD~~   33 (233)
                      +-|.+|+.|.||....     ..+.+||+.+
T Consensus        58 k~P~NGLvifcG~v~~~~g~ek~~~~~~ePp   88 (102)
T 1dt9_A           58 KVPPNGLVVYCGTIVTEEGKEKKVNIDFEPF   88 (102)
T ss_dssp             SCCTTCEEEEEEEEECGGGCEEEEEEEECCS
T ss_pred             CCCCCEEEEEEEEEECCCCCEEEEEEEECCC
T ss_conf             8899848999613315898167899960586


No 6  
>>1wgx_A KIAA1903 protein; MYB DNA-binding domain, human cDNA, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} (A:)
Probab=19.61  E-value=52  Score=13.00  Aligned_cols=40  Identities=8%  Similarity=0.055  Sum_probs=29.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHC
Q ss_conf             66765301456999999997358001356745799999876302
Q gi|254781190|r  156 IWKSHNNRRYTNIEIRAFLSCFGEEFYNGSHDEWIPVVMAIHYE  199 (233)
Q Consensus       156 ~~~~~~~~~~~~~~a~~~L~~i~~~~~~~dyd~W~~vg~AL~~~  199 (233)
                      ..++..-.+.++.....++..++++    ++.-|.+|.|+...-
T Consensus         5 ~~~d~~W~e~EL~klh~a~~slpkh----~~~fW~~Va~~VgtR   44 (73)
T 1wgx_A            5 SSGDKEWNEKELQKLHCAFASLPKH----KPGFWSEVAAAVGSR   44 (73)
T ss_dssp             CCSSSCCCHHHHHHHHHHHHHSCSS----SSSHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCC----CCCCHHHHHHHHCCC
T ss_conf             6766532899999999999835887----775099999998358


No 7  
>>2i9z_A Putative septation protein spovg; APC86317, structural genomics, PSI-2, protein structure initiative; 2.30A {Staphylococcus epidermidis atcc 12228} (A:)
Probab=15.07  E-value=67  Score=12.36  Aligned_cols=32  Identities=16%  Similarity=0.168  Sum_probs=21.3

Q ss_pred             CEEEE-ECCCEEEECCCCCCCCCCEEEECCCCC
Q ss_conf             35898-458328953668888884574216776
Q gi|254781190|r   85 HLEFL-AYGQQFVAYNIHPKTQRAYTWSIAPHA  116 (233)
Q Consensus        85 ~iEi~-~~g~q~V~~g~hp~Tg~~Y~W~~~~~~  116 (233)
                      +|-|. +..|-+|+|||.....+.|+=..-|..
T Consensus        36 dikVieg~~GLFVaMPs~k~~~g~ykDi~~Pit   68 (105)
T 2i9z_A           36 DLRVIEGNSGLFVAXPSKRTPDGEFRDIAHPIN   68 (105)
T ss_dssp             EEEEEEETTEEEEECCEEECTTSCEEECEEESS
T ss_pred             EEEEEECCCCCEEECCCCCCCCCCEEEEEEECC
T ss_conf             679998899749989875889997878999899


No 8  
>>2iru_A Putative DNA ligase-like protein RV0938/MT0965; polymerase, primase, NHEJ, transferase; 1.65A {Mycobacterium tuberculosis H37RV} PDB: 2irx_A* 2iry_A* 2r9l_A* (A:134-265)
Probab=14.82  E-value=68  Score=12.32  Aligned_cols=43  Identities=12%  Similarity=0.065  Sum_probs=25.4

Q ss_pred             EEEEEEECCCH-------HHHHHHHHHHHHHC-CCCEEEECCCCCEEEEEEC
Q ss_conf             89999548984-------67899999776408-9862986788953999844
Q gi|254781190|r   25 VYAFDVDVLDE-------QVVDRFNNEFQSCC-GKPISRVGQAPKTLMLFRM   68 (233)
Q Consensus        25 l~~iDiD~~d~-------~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~lfr~   68 (233)
                      .+++|+|..+.       .++..+.+++.++. ...+.|||.. |.|.+--+
T Consensus         3 ~lV~DLDP~~~~~f~~v~~~A~~~r~~L~~~gL~~~~KTSG~k-GlHv~vPl   53 (132)
T 2iru_A            3 RLVFDLDPGEGVMMAQLAEVARAVRDLLADIGLVTFPVTSGSK-GLHLYTPL   53 (132)
T ss_dssp             EEEEEEEECTTCCHHHHHHHHHHHHHHHHTTTCCCEEEECSSS-CEEEEEEE
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEECCCCC-EEEEEEEC
T ss_conf             5998489886899999999999999999976996330536998-36999968


No 9  
>>2i9x_A Putative septation protein spovg; APC86317.1, structural genomics, PSI-2, protein structure initiative; 1.80A {Staphylococcus epidermidis atcc 12228} (A:)
Probab=14.74  E-value=68  Score=12.30  Aligned_cols=31  Identities=16%  Similarity=0.176  Sum_probs=21.1

Q ss_pred             CEEEE-ECCCEEEECCCCCCCCCCEEEECCCC
Q ss_conf             35898-45832895366888888457421677
Q gi|254781190|r   85 HLEFL-AYGQQFVAYNIHPKTQRAYTWSIAPH  115 (233)
Q Consensus        85 ~iEi~-~~g~q~V~~g~hp~Tg~~Y~W~~~~~  115 (233)
                      +|-|. +..|-+|+|||.....+.|+=..-|.
T Consensus        36 ~ikVieg~~GLFVaMPsrk~~~g~ykDi~~Pi   67 (87)
T 2i9x_A           36 DLRVIEGNSGLFVAXPSKRTPDGEFRDIAHPI   67 (87)
T ss_dssp             EEEEEEETTEEEEECCEEECTTSCEEECEEEC
T ss_pred             EEEEEECCCCCEEECCCCCCCCCCEEEEEEEC
T ss_conf             57999889974998877599999899999989


No 10 
>>2fao_A Probable ATP-dependent DNA ligase; polymerase, primase, NHEJ, hydrolase/transferase complex; 1.50A {Pseudomonas aeruginosa} PDB: 2faq_A* 2far_A* (A:128-309)
Probab=14.15  E-value=71  Score=12.21  Aligned_cols=44  Identities=9%  Similarity=0.064  Sum_probs=27.4

Q ss_pred             CEEEEEEECCCH-------HHHHHHHHHHHHHC-CCCEEEECCCCCEEEEEEC
Q ss_conf             889999548984-------67899999776408-9862986788953999844
Q gi|254781190|r   24 PVYAFDVDVLDE-------QVVDRFNNEFQSCC-GKPISRVGQAPKTLMLFRM   68 (233)
Q Consensus        24 ~l~~iDiD~~d~-------~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~lfr~   68 (233)
                      ..++||.|..+.       +++..+.+++.++. ...+.|||.. |.|.+--+
T Consensus         6 D~lVfDLDP~~~~~f~~v~~~A~~vr~~L~~lgL~sf~KTSG~k-GlHv~vPl   57 (182)
T 2fao_A            6 DRFVLDLDPDPALPWKRMLEATQLSLTLLDELGLRAFLKTSGGK-GMHLLVPL   57 (182)
T ss_dssp             SEEEEEEEECTTSCHHHHHHHHHHHHHHHHHHTCCCEEEECSSS-SEEEEEEC
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-EEEEEEEC
T ss_conf             86999579998988899999999999999976997430415898-57999957


Done!