Query         gi|254780354|ref|YP_003064767.1| hypothetical protein CLIBASIA_01195 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 38
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 14:54:08 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780354.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam01445 SH Viral small hydro  56.1     9.3 0.00024   19.1   2.4   19   18-36     15-33  (57)
  2 COG4467 Regulator of replicati  48.9       9 0.00023   19.2   1.4   20    4-23     75-94  (114)
  3 PRK13169 DNA replication intia  47.8     7.5 0.00019   19.6   0.8   20    4-23     69-88  (107)
  4 pfam06156 DUF972 Protein of un  46.8       7 0.00018   19.7   0.6   19    4-22     72-90  (106)
  5 PRK13716 leader peptide RepL;   45.3      12  0.0003   18.6   1.5   17   14-30      6-22  (26)
  6 pfam06388 DUF1075 Protein of u  32.7      44  0.0011   15.8   2.8   18   17-34     97-114 (146)
  7 KOG4491 consensus               27.7      53  0.0013   15.4   2.5   19   16-34      7-25  (323)
  8 KOG2736 consensus               26.3      40   0.001   16.0   1.7   19   18-36    340-358 (406)
  9 TIGR01773 GABAperm GABA permea  26.1      28 0.00071   16.8   0.9   20   14-33    255-274 (462)
 10 COG5505 Predicted integral mem  25.0      63  0.0016   15.0   3.5   28    3-30     74-107 (384)
 11 TIGR00844 c_cpa1 sodium/hydrog  24.4      59  0.0015   15.2   2.3   15   18-32    111-125 (923)
 12 pfam08320 PIG-X PIG-X / PBN1.   23.3      69  0.0018   14.8   2.6   18   19-36    187-204 (206)
 13 KOG2082 consensus               21.5      71  0.0018   14.8   2.2   20   11-30    572-591 (1075)
 14 smart00780 PIG-X PIG-X / PBN1.  21.4      76  0.0019   14.6   2.6   18   19-36    184-201 (203)

No 1  
>pfam01445 SH Viral small hydrophobic protein. The SH (small hydrophobic) protein is a membrane protein of uncertain function.
Probab=56.05  E-value=9.3  Score=19.11  Aligned_cols=19  Identities=42%  Similarity=0.938  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999973
Q gi|254780354|r   18 ICSLFVVIACFVWIISEIV   36 (38)
Q Consensus        18 icslfvviacfvwiiseiv   36 (38)
                      .--|...|.-+||||+.|.
T Consensus        15 lilL~liitlyvwi~~tit   33 (57)
T pfam01445        15 LILLYLIITLYVWIISTIT   33 (57)
T ss_pred             HHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999998755


No 2  
>COG4467 Regulator of replication initiation timing [Replication,    recombination, and repair]
Probab=48.94  E-value=9  Score=19.20  Aligned_cols=20  Identities=30%  Similarity=0.741  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             37889999999999999999
Q gi|254780354|r    4 SFCDLRVIFQEAFFICSLFV   23 (38)
Q Consensus         4 sfcdlrvifqeafficslfv   23 (38)
                      +.-.|+-||||.|.||..+-
T Consensus        75 ~~dnL~~lY~EGFHICn~hy   94 (114)
T COG4467          75 GYDNLARLYQEGFHICNVHY   94 (114)
T ss_pred             CCHHHHHHHHCCCHHHHHHH
T ss_conf             85059999865403688874


No 3  
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=47.77  E-value=7.5  Score=19.57  Aligned_cols=20  Identities=35%  Similarity=0.638  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             37889999999999999999
Q gi|254780354|r    4 SFCDLRVIFQEAFFICSLFV   23 (38)
Q Consensus         4 sfcdlrvifqeafficslfv   23 (38)
                      |.-.|.-++||.|-||..+-
T Consensus        69 g~~NL~~LY~EGFHICn~~y   88 (107)
T PRK13169         69 GKDNLARLYQEGFHICNLHY   88 (107)
T ss_pred             HHHHHHHHHHCCCCCCHHHH
T ss_conf             68999999875730056763


No 4  
>pfam06156 DUF972 Protein of unknown function (DUF972). This family consists of several hypothetical bacterial sequences. The function of this family is unknown.
Probab=46.83  E-value=7  Score=19.72  Aligned_cols=19  Identities=37%  Similarity=0.838  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             3788999999999999999
Q gi|254780354|r    4 SFCDLRVIFQEAFFICSLF   22 (38)
Q Consensus         4 sfcdlrvifqeafficslf   22 (38)
                      |.-.|.-++||.|-||..+
T Consensus        72 g~~NL~~LY~EGFHICn~~   90 (106)
T pfam06156        72 GYDNLARLYQEGFHICNLH   90 (106)
T ss_pred             HHHHHHHHHHCCCEECHHH
T ss_conf             6999999987573105687


No 5  
>PRK13716 leader peptide RepL; Provisional
Probab=45.30  E-value=12  Score=18.59  Aligned_cols=17  Identities=41%  Similarity=0.989  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999
Q gi|254780354|r   14 EAFFICSLFVVIACFVW   30 (38)
Q Consensus        14 eafficslfvviacfvw   30 (38)
                      ..||.|||..-|..--|
T Consensus         6 qdfflcslllrivsagw   22 (26)
T PRK13716          6 QDFFLCSLLLRIVSAGW   22 (26)
T ss_pred             HHHHHHHHHHHHHHCCC
T ss_conf             68899999999982455


No 6  
>pfam06388 DUF1075 Protein of unknown function (DUF1075). This family consists of several eukaryotic proteins of unknown function.
Probab=32.71  E-value=44  Score=15.79  Aligned_cols=18  Identities=28%  Similarity=0.691  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999
Q gi|254780354|r   17 FICSLFVVIACFVWIISE   34 (38)
Q Consensus        17 ficslfvviacfvwiise   34 (38)
                      ++--.+.+++|++|+|+.
T Consensus        97 y~Mi~lT~igC~~mvi~G  114 (146)
T pfam06388        97 YIMIALTVVGCIIMVISG  114 (146)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             899999999999999983


No 7  
>KOG4491 consensus
Probab=27.74  E-value=53  Score=15.42  Aligned_cols=19  Identities=42%  Similarity=0.662  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999
Q gi|254780354|r   16 FFICSLFVVIACFVWIISE   34 (38)
Q Consensus        16 fficslfvviacfvwiise   34 (38)
                      ..||||-+-|.-+.||||-
T Consensus         7 i~~~~l~i~isl~~w~~~~   25 (323)
T KOG4491           7 IVILSLIICISLAFWIISM   25 (323)
T ss_pred             HHHHHHHHHHHHHHHHHHH
T ss_conf             3666859999999999998


No 8  
>KOG2736 consensus
Probab=26.28  E-value=40  Score=16.00  Aligned_cols=19  Identities=42%  Similarity=0.593  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999973
Q gi|254780354|r   18 ICSLFVVIACFVWIISEIV   36 (38)
Q Consensus        18 icslfvviacfvwiiseiv   36 (38)
                      -|.++.||||||-|+....
T Consensus       340 ~~d~~TviAC~vaIL~GL~  358 (406)
T KOG2736         340 YGDLNTVIACFVAILIGLC  358 (406)
T ss_pred             CCCHHHHHHHHHHHHHHHH
T ss_conf             0774879999999999999


No 9  
>TIGR01773 GABAperm GABA permease; InterPro: IPR011265   GABA permease (gabP) catalyzes the translocation of 4-aminobutyrate (GABA) across the plasma membrane, with homologues expressed in Gram-negative and Gram-positive organisms. This permease is a highly hydrophobic transmembrane protein consisting of 12 transmembrane domains with hydrophilic N- and C-terminal ends . Induced by nitrogen-limited culture conditions in both Escherichia coli and Bacillus subtilis, gabP is an energy dependent transport system stimulated by membrane potential and has been observed adjacent and distant from other GABA degradation proteins , .    GabP is highly homologous to amino acid permeases from B. subtilis, E. coli, as well as to other members of the amino acid permease family (IPR004841 from INTERPRO). A member of the APC (amine-polyamine-choline) transporter superfamily, GABA permease possesses a "consensus amphiphatic region" (CAR) found to be evolutionarily conserved within this transport family . This amphiphatic region is located between helix 8 and cytoplasmic loop 8-9, forming a potential channel domain and suggested to play a significant role in ligand recognition and translocation . Unique to GABA permeases, a conserved cysteine residue (CYS-300, E. coli) located at the beginning of the amphiphatic domain, has been determined to be critical for catalytic specificity . ; GO: 0015185 L-gamma-aminobutyric acid transmembrane transporter activity, 0015812 gamma-aminobutyric acid transport, 0016021 integral to membrane.
Probab=26.13  E-value=28  Score=16.78  Aligned_cols=20  Identities=30%  Similarity=0.750  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999
Q gi|254780354|r   14 EAFFICSLFVVIACFVWIIS   33 (38)
Q Consensus        14 eafficslfvviacfvwiis   33 (38)
                      .-|++||.|+|+|-.-|--.
T Consensus       255 ~~FYl~SI~iVval~PWN~~  274 (462)
T TIGR01773       255 IVFYLVSIFIVVALLPWNSP  274 (462)
T ss_pred             HHHHHHHHHHHHHHCCCCCC
T ss_conf             99999888887421358872


No 10 
>COG5505 Predicted integral membrane protein [Function unknown]
Probab=25.00  E-value=63  Score=15.02  Aligned_cols=28  Identities=36%  Similarity=0.551  Sum_probs=20.7

Q ss_pred             CHHHHHHHHHHH------HHHHHHHHHHHHHHHH
Q ss_conf             037889999999------9999999999999999
Q gi|254780354|r    3 LSFCDLRVIFQE------AFFICSLFVVIACFVW   30 (38)
Q Consensus         3 lsfcdlrvifqe------afficslfvviacfvw   30 (38)
                      |--||+|-||.+      -|++||.-.++.--+|
T Consensus        74 Llqcd~Rki~Klg~rll~ifli~sv~~vlGfIl~  107 (384)
T COG5505          74 LLQCDVRKIFKLGRRLLFIFLISSVGTVLGFILA  107 (384)
T ss_pred             HHHCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9980499998636146578999999999999988


No 11 
>TIGR00844 c_cpa1 sodium/hydrogen antiporter; InterPro: IPR004712   Na^+/H^+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na^+/H^+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na^+ for H^+ in an electroneutral manner, and this activity is carried out by a family of Na^+/H^+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. In mammalian cells, Na^+/H^+ exchange activity is found in both the plasma membrane and inner mitochondrial membrane. To date, six mammalian isoforms have been identified (designated NHE1-NHE6) , . These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region has little similarity throughout the family. There is some evidence that the exchangers may exist in the cell membrane as homodimers, but little is currently known about the mechanism of their antiport .   This group is specific for the fungal members of this family. ; GO: 0015385 sodium:hydrogen antiporter activity, 0006814 sodium ion transport, 0016021 integral to membrane.
Probab=24.40  E-value=59  Score=15.17  Aligned_cols=15  Identities=53%  Similarity=0.997  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999999
Q gi|254780354|r   18 ICSLFVVIACFVWII   32 (38)
Q Consensus        18 icslfvviacfvwii   32 (38)
                      ..|=..|||-||||.
T Consensus       111 MT~GWLvIaLFVWIL  125 (923)
T TIGR00844       111 MTSGWLVIALFVWIL  125 (923)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             666799999998887


No 12 
>pfam08320 PIG-X PIG-X / PBN1. Mammalian PIG-X and yeast PBN1 are essential components of glycosylphosphatidylinositol-mannosyltransferase I. These enzymes are involved in the transfer of sugar molecules.
Probab=23.26  E-value=69  Score=14.85  Aligned_cols=18  Identities=33%  Similarity=0.829  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999973
Q gi|254780354|r   19 CSLFVVIACFVWIISEIV   36 (38)
Q Consensus        19 cslfvviacfvwiiseiv   36 (38)
                      -.+.+++.||+||+..+.
T Consensus       187 ~T~lv~~lg~~~il~~l~  204 (206)
T pfam08320       187 VTLLVVVLGFLWILWKLF  204 (206)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             499999999999989972


No 13 
>KOG2082 consensus
Probab=21.51  E-value=71  Score=14.78  Aligned_cols=20  Identities=45%  Similarity=0.838  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999
Q gi|254780354|r   11 IFQEAFFICSLFVVIACFVW   30 (38)
Q Consensus        11 ifqeafficslfvviacfvw   30 (38)
                      +..--|..|-+||-+||+|-
T Consensus       572 ilsmFFLMCY~fVNLaCavq  591 (1075)
T KOG2082         572 ILSMFFLMCYLFVNLACAVQ  591 (1075)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999997776999999


No 14 
>smart00780 PIG-X PIG-X / PBN1. Mammalian PIG-X and yeast PBN1 are essential components of glycosylphosphatidylinositol-mannosyltransferase I. These enzymes are involved in the transfer of sugar molecules.
Probab=21.39  E-value=76  Score=14.65  Aligned_cols=18  Identities=28%  Similarity=0.670  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999973
Q gi|254780354|r   19 CSLFVVIACFVWIISEIV   36 (38)
Q Consensus        19 cslfvviacfvwiiseiv   36 (38)
                      -.+.+++.||+||+..+.
T Consensus       184 ~T~lvv~lg~~~il~~l~  201 (203)
T smart00780      184 VTLLVVLIGFLYILYKLF  201 (203)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             599999999999999984


Done!