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!