Query         gi|254781222|ref|YP_003065635.1| hypothetical protein CLIBASIA_05645 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 70
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 07:43:36 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781222.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam07051 OCIA Ovarian carcino  63.3     5.8 0.00015   21.0   2.3   23   29-51     19-41  (111)
  2 KOG3811 consensus               36.9      15 0.00038   18.9   0.9   27   30-56    218-247 (434)
  3 KOG1517 consensus               35.3      23 0.00059   17.9   1.7   14   42-55    480-493 (1387)
  4 pfam03299 TF_AP-2 Transcriptio  26.1      25 0.00063   17.7   0.6   27   30-56     15-44  (207)
  5 COG5119 Uncharacterized protei  21.6      25 0.00064   17.7  -0.1   12   43-54     77-88  (119)
  6 KOG3388 consensus               19.0      26 0.00067   17.6  -0.4   47    7-54     50-104 (136)
  7 COG3074 Uncharacterized protei  13.7 1.3E+02  0.0033   14.0   2.2   31   24-56     45-75  (79)
  8 COG0350 Ada Methylated DNA-pro  12.5      29 0.00074   17.4  -1.6   16   45-67    137-152 (168)
  9 TIGR03490 Mycoplas_LppA mycoid  11.2      53  0.0014   16.0  -0.6   17    1-17    239-255 (541)
 10 TIGR00589 ogt methylated-DNA-[  10.5      43  0.0011   16.5  -1.3   16   45-67     51-66  (80)

No 1  
>pfam07051 OCIA Ovarian carcinoma immunoreactive antigen (OCIA). This family consists of several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of this family is unknown.
Probab=63.25  E-value=5.8  Score=20.99  Aligned_cols=23  Identities=35%  Similarity=0.634  Sum_probs=19.9

Q ss_pred             CCHHHHHHCHHHHHHHHHHHHHH
Q ss_conf             20144210489999999988888
Q gi|254781222|r   29 PMTKKYKITKEEHRVFSECHRIR   51 (70)
Q Consensus        29 pmtkkykitkeehrvfsechrir   51 (70)
                      |-..-|..|.||-+|+-||.+.-
T Consensus        19 ~~~~~y~~t~EE~~vlrEC~~ES   41 (111)
T pfam07051        19 PPAMPYIFTEEERKVLRECNEES   41 (111)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             99667645999999999998766


No 2  
>KOG3811 consensus
Probab=36.92  E-value=15  Score=18.88  Aligned_cols=27  Identities=37%  Similarity=0.541  Sum_probs=15.8

Q ss_pred             CHHHHHHCHHHHHH-H--HHHHHHHHHHHH
Q ss_conf             01442104899999-9--998888876332
Q gi|254781222|r   30 MTKKYKITKEEHRV-F--SECHRIRALRGF   56 (70)
Q Consensus        30 mtkkykitkeehrv-f--sechriralrgf   56 (70)
                      -|-|||+|-+|-|- .  -||-.--+|-||
T Consensus       218 stSKYkVTVaEvqRRlspPEcLNaSlLggv  247 (434)
T KOG3811         218 STSKYKVTVAEVQRRLSPPECLNASLLGGV  247 (434)
T ss_pred             CCCCEEEEHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             655135679999750398655125766555


No 3  
>KOG1517 consensus
Probab=35.30  E-value=23  Score=17.86  Aligned_cols=14  Identities=43%  Similarity=0.570  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999888887633
Q gi|254781222|r   42 RVFSECHRIRALRG   55 (70)
Q Consensus        42 rvfsechriralrg   55 (70)
                      -..|.|||+|||+=
T Consensus       480 VLLSQvHRlRAL~L  493 (1387)
T KOG1517         480 VLLSQVHRLRALVL  493 (1387)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999899999999


No 4  
>pfam03299 TF_AP-2 Transcription factor AP-2.
Probab=26.13  E-value=25  Score=17.73  Aligned_cols=27  Identities=37%  Similarity=0.529  Sum_probs=13.0

Q ss_pred             CHHHHHHCHHHHH--HH-HHHHHHHHHHHH
Q ss_conf             0144210489999--99-998888876332
Q gi|254781222|r   30 MTKKYKITKEEHR--VF-SECHRIRALRGF   56 (70)
Q Consensus        30 mtkkykitkeehr--vf-sechriralrgf   56 (70)
                      -|.|||+|-+|-|  ++ .||-..-+|-|+
T Consensus        15 stsKYkVTV~Ev~RRls~PE~LNaSlLgg~   44 (207)
T pfam03299        15 STSKYKVTVAEVQRRLSPPECLNASLLGGV   44 (207)
T ss_pred             CCCEEEEEHHHHHHCCCCHHHCCHHHHHHH
T ss_conf             875056559999870188112038888888


No 5  
>COG5119 Uncharacterized protein, contains ParB-like nuclease domain [General function prediction only]
Probab=21.60  E-value=25  Score=17.70  Aligned_cols=12  Identities=42%  Similarity=0.908  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999988888763
Q gi|254781222|r   43 VFSECHRIRALR   54 (70)
Q Consensus        43 vfsechriralr   54 (70)
                      .|+-|||.+|-.
T Consensus        77 aFgGCHRl~A~d   88 (119)
T COG5119          77 AFGGCHRLEACD   88 (119)
T ss_pred             EECCCHHHHHHH
T ss_conf             617407769998


No 6  
>KOG3388 consensus
Probab=19.02  E-value=26  Score=17.58  Aligned_cols=47  Identities=28%  Similarity=0.462  Sum_probs=25.2

Q ss_pred             HHHHHHHH-----HHHCCCCCCCCCCCCCHHHHHHCHH---HHHHHHHHHHHHHHH
Q ss_conf             59999999-----9720023201344520144210489---999999988888763
Q gi|254781222|r    7 PLEQTIKG-----LFQQSSTDRYGRIEPMTKKYKITKE---EHRVFSECHRIRALR   54 (70)
Q Consensus         7 pleqtikg-----lfqqsstdrygriepmtkkykitke---ehrvfsechriralr   54 (70)
                      +|-.|+||     +-+..+...-|..-|..-- .+.+|   ----|+-|||.+|-.
T Consensus        50 slm~Tmkn~~~c~les~d~~~~aGelpPiDvl-~v~~~G~~~YyaFgGCHRleAhd  104 (136)
T KOG3388          50 SLMETMKNDQNCVLESEDSIRQAGELPPIDVL-EVDSEGGDYYYAFGGCHRLEAHD  104 (136)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHCCCCCCCEEE-EEECCCCEEEEEECCCHHHHHHH
T ss_conf             99998508976331357788743778981289-99517966788617642447888


No 7  
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=13.65  E-value=1.3e+02  Score=14.01  Aligned_cols=31  Identities=32%  Similarity=0.418  Sum_probs=21.5

Q ss_pred             CCCCCCCHHHHHHCHHHHHHHHHHHHHHHHHHH
Q ss_conf             134452014421048999999998888876332
Q gi|254781222|r   24 YGRIEPMTKKYKITKEEHRVFSECHRIRALRGF   56 (70)
Q Consensus        24 ygriepmtkkykitkeehrvfsechriralrgf   56 (70)
                      -+..|.....-.--|+||+.+.|  |||+|-|-
T Consensus        45 q~~reaL~~eneqlk~e~~~WQe--rlrsLLGk   75 (79)
T COG3074          45 QHQREALERENEQLKEEQNGWQE--RLRALLGK   75 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHH
T ss_conf             98799999888999989977999--99998710


No 8  
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=12.52  E-value=29  Score=17.37  Aligned_cols=16  Identities=44%  Similarity=1.037  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99888887633214332110011
Q gi|254781222|r   45 SECHRIRALRGFNDVKKGALGGF   67 (70)
Q Consensus        45 sechriralrgfndvkkgalggf   67 (70)
                      -.|||+..       +.|.||||
T Consensus       137 IPCHRVig-------~~G~L~Gy  152 (168)
T COG0350         137 IPCHRVIG-------ADGDLGGY  152 (168)
T ss_pred             ECCEEEEC-------CCCCCCCC
T ss_conf             54736876-------79973675


No 9  
>TIGR03490 Mycoplas_LppA mycoides cluster lipoprotein, LppA/P72 family. Members of this protein family occur in Mycoplasma mycoides, Mycoplasma hyopneumoniae, and related Mycoplasmas in small paralogous families that may also include truncated forms and/or pseudogenes. Members are predicted lipoproteins with a conserved signal peptidase II processing and lipid attachment site. Note that the name for certain characterized members, p72, reflects an anomalous apparent molecular weight, given a theoretical MW of about 61 kDa.
Probab=11.22  E-value=53  Score=16.02  Aligned_cols=17  Identities=59%  Similarity=0.931  Sum_probs=14.9

Q ss_pred             CCCCHHHHHHHHHHHHH
Q ss_conf             97523459999999972
Q gi|254781222|r    1 MIKAKEPLEQTIKGLFQ   17 (70)
Q Consensus         1 mikakepleqtikglfq   17 (70)
                      .||+||++...++|||.
T Consensus       239 YIK~K~~id~~l~GLfP  255 (541)
T TIGR03490       239 YIKAKEKLDEKLKGLFP  255 (541)
T ss_pred             CCCCCCCCCHHHCCCCH
T ss_conf             14556664633302158


No 10 
>TIGR00589 ogt methylated-DNA-[protein]-cysteine S-methyltransferase; InterPro: IPR014048   Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase   This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases.   The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme . This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources .; GO: 0003824 catalytic activity, 0006281 DNA repair.
Probab=10.52  E-value=43  Score=16.47  Aligned_cols=16  Identities=44%  Similarity=0.993  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99888887633214332110011
Q gi|254781222|r   45 SECHRIRALRGFNDVKKGALGGF   67 (70)
Q Consensus        45 sechriralrgfndvkkgalggf   67 (70)
                      --|||+-.       +.|+||||
T Consensus        51 vPCHRVig-------~~G~ltGY   66 (80)
T TIGR00589        51 VPCHRVIG-------KNGTLTGY   66 (80)
T ss_pred             ECCEEEEC-------CCCCCCCC
T ss_conf             07802542-------78873410


Done!