Query         gi|255764475|ref|YP_003084341.1| hypothetical protein CLIBASIA_03592 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 59
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 17:11:41 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764475.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01524 ATPase-IIIB_Mg magne  39.8      14 0.00037   18.7   1.3   31   20-51    841-877 (892)
  2 PRK06569 F0F1 ATP synthase sub  33.0      46  0.0012   15.9   3.7   29   30-58      6-34  (157)
  3 TIGR02842 CyoC cytochrome o ub  28.9      49  0.0013   15.7   2.5   17   33-49     71-87  (180)
  4 PRK09174 F0F1 ATP synthase sub  28.0      56  0.0014   15.4   3.8   31   28-58     47-77  (204)
  5 pfam12062 HSNSD heparan sulfat  26.5      33 0.00084   16.7   1.3   12   42-53    129-140 (487)
  6 TIGR02808 short_TIGR02808 cons  26.0      29 0.00075   17.0   1.0   10   30-39     14-23  (42)
  7 TIGR01113 mtrE tetrahydrometha  25.0      29 0.00074   17.0   0.8   10   24-33    157-166 (298)
  8 pfam04206 MtrE Tetrahydrometha  21.7      38 0.00097   16.4   0.8   17   22-42    151-167 (269)
  9 PRK00972 tetrahydromethanopter  20.2      43  0.0011   16.1   0.8   19   20-42    155-173 (293)
 10 pfam10798 YmgB Biofilm develop  16.5      85  0.0022   14.4   1.7   14   31-44     21-34  (60)

No 1  
>TIGR01524 ATPase-IIIB_Mg magnesium-translocating P-type ATPase; InterPro: IPR006415   This group describes the magnesium translocating P-type ATPase found in a limited number of bacterial species and best described in Salmonella typhimurium, which contains two isoforms . These transporters are active in low external Mg2+ concentrations and pump the ion into the cytoplasm. The magnesium ATPases have been classified as type IIIB by a phylogenetic analysis .; GO: 0015444 magnesium-importing ATPase activity, 0015693 magnesium ion transport, 0016021 integral to membrane.
Probab=39.84  E-value=14  Score=18.69  Aligned_cols=31  Identities=42%  Similarity=0.754  Sum_probs=17.4

Q ss_pred             EEEEECCC-----CHHHHHHH-HHHHHHHHHHHHHHHH
Q ss_conf             38970477-----21788769-9999999999988789
Q gi|255764475|r   20 VQISIPFP-----MPIVAMPA-IILWLIITLLRGYCRE   51 (59)
Q Consensus        20 vqisipfp-----mpivampa-iilwliitllrgycre   51 (59)
                      +-|+|||.     .-..+.|. -.-|||.+|+ |||--
T Consensus       841 ~Gi~iPFsplg~~~gl~~LPlSYFPWLiaiLv-gYm~~  877 (892)
T TIGR01524       841 VGIIIPFSPLGASVGLEALPLSYFPWLIAILV-GYMLV  877 (892)
T ss_pred             HHHHCCCCCHHHHHCCCCCCCCHHHHHHHHHH-HHHHH
T ss_conf             44213751002321022588750079999999-99999


No 2  
>PRK06569 F0F1 ATP synthase subunit B'; Validated
Probab=33.02  E-value=46  Score=15.89  Aligned_cols=29  Identities=28%  Similarity=0.420  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             78876999999999999887899987642
Q gi|255764475|r   30 IVAMPAIILWLIITLLRGYCREYIIFLSR   58 (59)
Q Consensus        30 ivampaiilwliitllrgycreyiiflsr   58 (59)
                      ..-.|.-+.||++|+.--|.--.-+++.|
T Consensus         6 ~~~~~sQifWL~itF~~ly~~~sk~~lPr   34 (157)
T PRK06569          6 IATYYSQIFWLIVTFGLLYIFVYKFITPK   34 (157)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             22408999999999999999999998604


No 3  
>TIGR02842 CyoC cytochrome o ubiquinol oxidase, subunit III; InterPro: IPR014206   This entry represents subunit 3 (CyoC) of the cytochrome o terminal oxidase complex, which is a component of the aerobic respiratory chain that reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two heme b cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilise cytochrome c as the reductant and contain heme a cofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant..
Probab=28.85  E-value=49  Score=15.72  Aligned_cols=17  Identities=47%  Similarity=0.804  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             76999999999999887
Q gi|255764475|r   33 MPAIILWLIITLLRGYC   49 (59)
Q Consensus        33 mpaiilwliitllrgyc   49 (59)
                      ...++.||.||.+=|-|
T Consensus        71 ~~~v~~WL~iTF~LG~~   87 (180)
T TIGR02842        71 KKKVILWLAITFLLGLG   87 (180)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             76899999999999999


No 4  
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=28.03  E-value=56  Score=15.41  Aligned_cols=31  Identities=26%  Similarity=0.299  Sum_probs=22.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             2178876999999999999887899987642
Q gi|255764475|r   28 MPIVAMPAIILWLIITLLRGYCREYIIFLSR   58 (59)
Q Consensus        28 mpivampaiilwliitllrgycreyiiflsr   58 (59)
                      +-....|.-|.||+|++.-.|---.-+++.|
T Consensus        47 ld~~t~~sQifWL~I~F~~lY~~~sk~~lPr   77 (204)
T PRK09174         47 FDSTHYASQLLWLAITFGLFYLFLSRVILPR   77 (204)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9834508999999999999999999997603


No 5  
>pfam12062 HSNSD heparan sulfate-N-deacetylase. This family of proteins is are heparan sulfate N-deacetylase enzymes. This protein is found in eukaryotes. This proteinenzyme is often found associated with pfam00685.
Probab=26.48  E-value=33  Score=16.70  Aligned_cols=12  Identities=50%  Similarity=0.916  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999998878999
Q gi|255764475|r   42 ITLLRGYCREYI   53 (59)
Q Consensus        42 itllrgycreyi   53 (59)
                      -.||.-|||||-
T Consensus       129 R~LLDKYC~ey~  140 (487)
T pfam12062       129 RELLDKYCKEYG  140 (487)
T ss_pred             HHHHHHHHHHHC
T ss_conf             999999999728


No 6  
>TIGR02808 short_TIGR02808 conserved hypothetical protein TIGR02808; InterPro: IPR014175   This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC 7966..
Probab=26.02  E-value=29  Score=16.97  Aligned_cols=10  Identities=60%  Similarity=0.750  Sum_probs=7.0

Q ss_pred             HHHHHHHHHH
Q ss_conf             7887699999
Q gi|255764475|r   30 IVAMPAIILW   39 (59)
Q Consensus        30 ivampaiilw   39 (59)
                      --|||.|+|=
T Consensus        14 Y~AMP~I~L~   23 (42)
T TIGR02808        14 YAAMPVIILS   23 (42)
T ss_pred             HHHHHHHHHH
T ss_conf             6655799998


No 7  
>TIGR01113 mtrE tetrahydromethanopterin S-methyltransferase, subunit E; InterPro: IPR005780    This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit E in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump.  5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate.  Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0006814 sodium ion transport, 0005737 cytoplasm, 0012506 vesicle membrane.
Probab=25.03  E-value=29  Score=17.01  Aligned_cols=10  Identities=50%  Similarity=1.338  Sum_probs=8.6

Q ss_pred             ECCCCHHHHH
Q ss_conf             0477217887
Q gi|255764475|r   24 IPFPMPIVAM   33 (59)
Q Consensus        24 ipfpmpivam   33 (59)
                      -|||.|..|+
T Consensus       157 HPFPLPllA~  166 (298)
T TIGR01113       157 HPFPLPLLAL  166 (298)
T ss_pred             CCCCHHHHHH
T ss_conf             9973688999


No 8  
>pfam04206 MtrE Tetrahydromethanopterin S-methyltransferase, subunit E. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump.
Probab=21.74  E-value=38  Score=16.35  Aligned_cols=17  Identities=47%  Similarity=1.187  Sum_probs=12.6

Q ss_pred             EEECCCCHHHHHHHHHHHHHH
Q ss_conf             970477217887699999999
Q gi|255764475|r   22 ISIPFPMPIVAMPAIILWLII   42 (59)
Q Consensus        22 isipfpmpivampaiilwlii   42 (59)
                      +.-|||+|++++    +|=|.
T Consensus       151 l~hPFplPlla~----iwGit  167 (269)
T pfam04206       151 LKHPFPLPLLAM----IWGIT  167 (269)
T ss_pred             HCCCCCHHHHHH----HHHHH
T ss_conf             059975159999----99884


No 9  
>PRK00972 tetrahydromethanopterin S-methyltransferase subunit E; Provisional
Probab=20.20  E-value=43  Score=16.07  Aligned_cols=19  Identities=42%  Similarity=1.097  Sum_probs=13.1

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHH
Q ss_conf             38970477217887699999999
Q gi|255764475|r   20 VQISIPFPMPIVAMPAIILWLII   42 (59)
Q Consensus        20 vqisipfpmpivampaiilwlii   42 (59)
                      +-+.-|||+|++++    +|=|.
T Consensus       155 ~~l~hPFPlPlla~----iwGIt  173 (293)
T PRK00972        155 VALGHPFPLPLLAL----IWGIT  173 (293)
T ss_pred             HHCCCCCCHHHHHH----HHHHH
T ss_conf             86069975259999----99885


No 10 
>pfam10798 YmgB Biofilm development protein YmgB/AriR. YmgB is part of the three gene cluster ymgABC which has a role in biofilm development and stability. YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility and also protects the cell from acid which indicates that YmgB has an important function in acid-resistance. YmgB binds as a dimer to genes which are important for biofilm formation via a ligand. Due to its important function in acid resistance it is also known as AriR (regulator of acid resistance influenced by indole).
Probab=16.46  E-value=85  Score=14.43  Aligned_cols=14  Identities=50%  Similarity=0.472  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             88769999999999
Q gi|255764475|r   31 VAMPAIILWLIITL   44 (59)
Q Consensus        31 vampaiilwliitl   44 (59)
                      |.-.+||+|||-.|
T Consensus        21 vtNK~IIl~LI~~L   34 (60)
T pfam10798        21 VSNKDIILKLIHKL   34 (60)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             66599999999998


Done!