Query         gi|254780906|ref|YP_003065319.1| hypothetical protein CLIBASIA_04025 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 96
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 33803
Date          Wed Jun  1 18:24:18 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780906.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1c0m_A Protein (integrase); H  27.0      16 0.00048   18.3   0.1   16   64-86      4-19  (67)
  2 >3cai_A Possible aminotransfer  12.7      84  0.0025   14.5   1.1   13   73-85     50-62  (118)
  3 >1ifw_A Polyadenylate-binding    9.6      91  0.0027   14.3   0.4   10   11-20     43-52  (92)
  4 >1zq7_A Hypothetical protein M   8.0 1.4E+02   0.004   13.4   0.8   75   19-93     81-159 (207)
  5 >1yfn_E Sigma-E factor negativ   6.8 1.4E+02   0.004   13.4   0.3   11   73-83      1-11  (32)
  6 >1q16_B Respiratory nitrate re   6.1 1.3E+02  0.0039   13.5  -0.1   16   70-85     25-49  (89)
  7 >3fz3_A Prunin; TREE NUT aller   6.0 1.8E+02  0.0052   12.8   0.5   48   13-60     80-219 (365)
  8 >1b3t_A Protein (nuclear prote   5.9 1.9E+02  0.0057   12.6   0.7    7   74-80     89-95  (147)
  9 >2jpj_A Bacteriocin lactococci   5.9 1.4E+02   0.004   13.4  -0.1   16   25-40     24-39  (39)
 10 >3g7u_A Cytosine-specific meth   5.7      69   0.002   15.0  -1.7   20   53-72     23-42  (44)

No 1  
>>1c0m_A Protein (integrase); HIV, X-RAY crystallography, protein structure, transferase; 2.53A {Rous sarcoma virus} (A:172-238)
Probab=27.01  E-value=16  Score=18.29  Aligned_cols=16  Identities=44%  Similarity=1.103  Sum_probs=11.6

Q ss_pred             EEEECCCCCCCCCCCCCCCCCCC
Q ss_conf             17840230078998322357767
Q gi|254780906|r   64 SIKIKNNIIEPQPGPSRWEGGWN   86 (96)
Q Consensus        64 sikiknniiepqpgpsrweggwn   86 (96)
                      .++|||++       ..||+||+
T Consensus         4 ~V~vk~el-------g~WE~GW~   19 (67)
T 1c0m_A            4 PVKIRIET-------GEWEKGWN   19 (67)
T ss_dssp             EEEEECTT-------SCEEEEEE
T ss_pred             EEEEECCC-------CCCCCCCE
T ss_conf             07850687-------76558711


No 2  
>>3cai_A Possible aminotransferase; RV3778C; 1.80A {Mycobacterium tuberculosis H37RV} (A:36-85,A:255-322)
Probab=12.72  E-value=84  Score=14.51  Aligned_cols=13  Identities=38%  Similarity=0.562  Sum_probs=10.5

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             7899832235776
Q gi|254780906|r   73 EPQPGPSRWEGGW   85 (96)
Q Consensus        73 epqpgpsrweggw   85 (96)
                      ++.+.|.|||.|-
T Consensus        50 ~~~~~P~rfEaGT   62 (118)
T 3cai_A           50 DYATGPARLEIGV   62 (118)
T ss_dssp             CTCCGGGGGCCSC
T ss_pred             CCCCCCCCCCCCC
T ss_conf             9256400001023


No 3  
>>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} (A:)
Probab=9.55  E-value=91  Score=14.32  Aligned_cols=10  Identities=60%  Similarity=0.511  Sum_probs=6.9

Q ss_pred             EEHHHHHHHH
Q ss_conf             1226589853
Q gi|254780906|r   11 FFITGMILSS   20 (96)
Q Consensus        11 ffitgmilss   20 (96)
                      --||||+|--
T Consensus        43 ~KITGMLLE~   52 (92)
T 1ifw_A           43 GKITGMILDL   52 (92)
T ss_dssp             HHHHHHHTTS
T ss_pred             CCEEEEEECC
T ss_conf             5400112348


No 4  
>>1zq7_A Hypothetical protein MM0484; X-RAY, NESG, MAR9, Q8PZK8, structural genomics, PSI, protein structure initiative; 2.11A {Methanosarcina mazei} (A:)
Probab=7.95  E-value=1.4e+02  Score=13.39  Aligned_cols=75  Identities=12%  Similarity=0.158  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCEEEEE---EEECCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCC-CCCCCHHHHHHH
Q ss_conf             53100110012210124543215888---7405555668621289844178402300789983223-577675567675
Q gi|254780906|r   19 SSCGDTLSDSKQHNKINNTKNHLDLL---FPIDDSHNQKPTEKKPNTSSIKIKNNIIEPQPGPSRW-EGGWNGERYVRE   93 (96)
Q Consensus        19 sscgdtlsdskqhnkinntknhldll---fpiddshnqkptekkpntssikiknniiepqpgpsrw-eggwngeryvre   93 (96)
                      +.+.|.---.-+.....+..-...+|   -||+++...-+-.-.|..-.+-|+-+------=|.-| |.+|+.+.+++.
T Consensus        81 AA~~DpRF~Pl~~~EL~~l~ieVsvLs~~e~i~~~~~~~~~~~~~G~~Glii~~g~~~g~~LPqV~~E~~w~~~~fl~~  159 (207)
T 1zq7_A           81 AATRDPRFPTVEQDEXKNILVEVTILTQPEKINASPKELPDKVEIGKHGLIVKQGYCQGLLLPQVAPENDXDSIDFLSH  159 (207)
T ss_dssp             HHHSCTTSCCCCGGGGGGCEEEEEEECCCEECCSCTTTHHHHCCTTTCEEEEEETTEEEEECTTHHHHTTCCHHHHHHH
T ss_pred             HHHCCCCCCCCCHHHHCCCEEEEEECCCCEECCCCHHHHHHHHCCCCCEEEEEECCCCEEECCCCHHHCCCCHHHHHHH
T ss_conf             9848999899996795378899997788578368745639970456635999848834688987310129999999999


No 5  
>>1yfn_E Sigma-E factor negative regulatory protein; protein-peptide complex, SSPB, RSEA, protein binding; 1.80A {Escherichia coli} (E:)
Probab=6.84  E-value=1.4e+02  Score=13.41  Aligned_cols=11  Identities=45%  Similarity=1.162  Sum_probs=8.9

Q ss_pred             CCCCCCCCCCC
Q ss_conf             78998322357
Q gi|254780906|r   73 EPQPGPSRWEG   83 (96)
Q Consensus        73 epqpgpsrweg   83 (96)
                      |.||-|+.|..
T Consensus         1 EsQP~P~~W~~   11 (32)
T 1yfn_E            1 EAQPAPHQWQK   11 (32)
T ss_pred             CCCCCHHHHHH
T ss_conf             99887167763


No 6  
>>1q16_B Respiratory nitrate reductase 1 beta chain; membrane protein, electron-transfer, oxidoreductase; HET: FME MD1 HEM AGA 3PH; 1.90A {Escherichia coli} (B:18-78,B:157-184)
Probab=6.08  E-value=1.3e+02  Score=13.47  Aligned_cols=16  Identities=56%  Similarity=1.562  Sum_probs=0.0

Q ss_pred             CCCCCCCC---CCCC------CCCC
Q ss_conf             30078998---3223------5776
Q gi|254780906|r   70 NIIEPQPG---PSRW------EGGW   85 (96)
Q Consensus        70 niiepqpg---psrw------eggw   85 (96)
                      |-+|..||   |.+|      .|||
T Consensus        25 NNVETkPG~GYPr~WEdqe~~~GGW   49 (89)
T 1q16_B           25 NNVETKPGQGFPTDWENQEKYKGGW   49 (89)
T ss_dssp             SEEEEESSCTTTTTTTCHHHHCCSE
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCE
T ss_conf             2545778778874401344457864


No 7  
>>3fz3_A Prunin; TREE NUT allergen, allergy, amandin, almond, 11S SEED storage protein; 2.40A {Prunus dulcis} PDB: 3ehk_A (A:1-365)
Probab=5.97  E-value=1.8e+02  Score=12.78  Aligned_cols=48  Identities=17%  Similarity=0.302  Sum_probs=0.0

Q ss_pred             HHHHHHH--------------------HHHHHHHHH--------------------------------------------
Q ss_conf             2658985--------------------310011001--------------------------------------------
Q gi|254780906|r   13 ITGMILS--------------------SCGDTLSDS--------------------------------------------   28 (96)
Q Consensus        13 itgmils--------------------scgdtlsds--------------------------------------------   28 (96)
                      |.||++.                    .|++|.-+.                                            
T Consensus        80 i~G~v~P~~~e~~~~~~~~~~~~~~~~gc~eT~~~~~~~~~~~~~~~g~~g~~~g~s~e~~~~~~~~~~~~~~~~~~~q~  159 (365)
T 3fz3_A           80 VLGAVFSGCPETFEESQQSSQQGRQQEQEQERQQQQQGEQGRQQGQQEQQQERQGRQQGRQQQEEGRQQEQQQGQQGRPQ  159 (365)
T ss_dssp             EEEECCTTCCCCEECCCC--------------------------------------------------------------
T ss_pred             EEEEECCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             67646689910210631123444445443333322233332222210000023222222332222333333211123343


Q ss_pred             --------HHHCCC--------------------CCCCCEEEEEEEECCCCCCCCCCCCC
Q ss_conf             --------221012--------------------45432158887405555668621289
Q gi|254780906|r   29 --------KQHNKI--------------------NNTKNHLDLLFPIDDSHNQKPTEKKP   60 (96)
Q Consensus        29 --------kqhnki--------------------nntknhldllfpiddshnqkptekkp   60 (96)
                              .+|-||                    |+...-|.+++-+|-|.++..-+..|
T Consensus       160 ~~~~~~~~D~hQKV~~~r~GDViAiPaGva~W~YNdGd~pLV~V~l~DtsN~~NQLD~~~  219 (365)
T 3fz3_A          160 QQQQFRQLDRHQKTRRIREGDVVAIPAGVAYWSYNDGDQELVAVNLFHVSSDHNQLDQNP  219 (365)
T ss_dssp             -----CCSCEESCCEEEETTEEEEECTTCCEEEECCSSSCEEEEEEEETTCTTCCSCSSC
T ss_pred             CCCCCCCCCHHHEEEECCCCCEEEECCCCEEEEEECCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf             323445676102356425578898789875998858998479999963667444477762


No 8  
>>1b3t_A Protein (nuclear protein EBNA1); nuclear protein, protein-DNA complex, DNA-binding, activator; HET: DNA; 2.20A {Epstein-barr virus} (A:)
Probab=5.89  E-value=1.9e+02  Score=12.59  Aligned_cols=7  Identities=86%  Similarity=1.649  Sum_probs=0.0

Q ss_pred             CCCCCCC
Q ss_conf             8998322
Q gi|254780906|r   74 PQPGPSR   80 (96)
Q Consensus        74 pqpgpsr   80 (96)
                      |||||-|
T Consensus        89 PqPgPl~   95 (147)
T 1b3t_A           89 PQPGPLR   95 (147)
T ss_dssp             CCCCTTC
T ss_pred             CCCCCCH
T ss_conf             9897620


No 9  
>>2jpj_A Bacteriocin lactococcin-G subunit alpha; peptide, anti-microbial, membrane bound, antimicrobial protein; NMR {Lactococcus lactis} PDB: 2jpl_A (A:)
Probab=5.85  E-value=1.4e+02  Score=13.41  Aligned_cols=16  Identities=50%  Similarity=0.717  Sum_probs=0.0

Q ss_pred             HHHHHHHCCCCCCCCE
Q ss_conf             1001221012454321
Q gi|254780906|r   25 LSDSKQHNKINNTKNH   40 (96)
Q Consensus        25 lsdskqhnkinntknh   40 (96)
                      +||-.|...||..|.|
T Consensus        24 msdvnqasrinrkkkh   39 (39)
T 2jpj_A           24 LSDVNQASRINRKKKH   39 (39)
T ss_dssp             CSHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHHHHCCC
T ss_conf             5343378874130059


No 10 
>>3g7u_A Cytosine-specific methyltransferase; DNA-binding, NAD-binding, structural genomics, protein structure initiative, PSI; 1.75A {Escherichia coli O157} (A:211-254)
Probab=5.73  E-value=69  Score=14.98  Aligned_cols=20  Identities=45%  Similarity=0.504  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCEEEECCCCC
Q ss_conf             68621289844178402300
Q gi|254780906|r   53 QKPTEKKPNTSSIKIKNNII   72 (96)
Q Consensus        53 qkptekkpntssikiknnii   72 (96)
                      |-|..--...|-.|+|||||
T Consensus        23 qiprnvgdtesiaklknnii   42 (44)
T 3g7u_A           23 QIPRNVGDTESIAKLKNNII   42 (44)
T ss_dssp             CCCTTCSCHHHHHHHHTTEE
T ss_pred             CCCCCCCCHHHHHHHHHCCC
T ss_conf             26656540788987640235


Done!