Query gi|254780188|ref|YP_003064601.1| hypothetical protein CLIBASIA_00355 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 36
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 23 06:35:02 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780188.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02190 GlrX-dom Glutaredoxi 28.1 23 0.0006 18.2 0.8 10 24-33 59-68 (79)
2 PRK05291 trmE tRNA modificatio 20.5 14 0.00035 19.3 -1.6 11 22-32 111-121 (445)
3 pfam05590 DUF769 Xylella fasti 18.0 49 0.0013 16.6 0.8 14 20-33 57-70 (279)
4 TIGR02888 spore_YlmC_YmxH spor 17.9 84 0.0022 15.5 1.9 20 9-28 37-57 (76)
5 COG0486 ThdF Predicted GTPase 17.1 20 0.00051 18.6 -1.4 11 22-32 112-122 (454)
6 KOG2293 consensus 9.9 1.3E+02 0.0033 14.6 1.0 17 17-33 485-506 (547)
7 TIGR01836 PHA_synth_III_C poly 9.4 78 0.002 15.7 -0.3 17 19-35 276-292 (367)
8 pfam11730 DUF3297 Protein of u 8.5 1.7E+02 0.0044 14.0 1.2 12 11-22 60-71 (71)
9 TIGR00450 thdF tRNA modificati 7.7 79 0.002 15.7 -0.9 12 22-33 112-123 (473)
10 COG3157 Hcp Type VI protein se 7.5 2.5E+02 0.0063 13.2 2.8 22 5-28 89-113 (162)
No 1
>TIGR02190 GlrX-dom Glutaredoxin-family domain; InterPro: IPR011906 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain..
Probab=28.11 E-value=23 Score=18.23 Aligned_cols=10 Identities=60% Similarity=1.052 Sum_probs=7.5
Q ss_pred EEEEEEEEEE
Q ss_conf 4233410676
Q gi|254780188|r 24 KNAFINGKMI 33 (36)
Q Consensus 24 knafingkmi 33 (36)
-.-|||||.|
T Consensus 59 PQVFI~G~lI 68 (79)
T TIGR02190 59 PQVFINGKLI 68 (79)
T ss_pred CEEEECCEEE
T ss_conf 8376498563
No 2
>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed
Probab=20.52 E-value=14 Score=19.35 Aligned_cols=11 Identities=64% Similarity=1.165 Sum_probs=7.8
Q ss_pred EEEEEEEEEEE
Q ss_conf 86423341067
Q gi|254780188|r 22 FIKNAFINGKM 32 (36)
Q Consensus 22 fiknafingkm 32 (36)
|-+.||+||||
T Consensus 111 FT~RAflNgK~ 121 (445)
T PRK05291 111 FTKRAFLNGKL 121 (445)
T ss_pred HHHHHHHCCCC
T ss_conf 16889865886
No 3
>pfam05590 DUF769 Xylella fastidiosa protein of unknown function (DUF769). This family consists of several uncharacterized hypothetical proteins of unknown function from Xylella fastidiosa, the organism that causes Pierce's disease in plants.
Probab=18.03 E-value=49 Score=16.65 Aligned_cols=14 Identities=50% Similarity=0.812 Sum_probs=10.5
Q ss_pred EEEEEEEEEEEEEE
Q ss_conf 69864233410676
Q gi|254780188|r 20 SFFIKNAFINGKMI 33 (36)
Q Consensus 20 sffiknafingkmi 33 (36)
.+-+|.|||||--|
T Consensus 57 QYTVKHAFINgini 70 (279)
T pfam05590 57 QYTVKHAFINGINI 70 (279)
T ss_pred CEEEEEEEECCCCC
T ss_conf 00000000146461
No 4
>TIGR02888 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family; InterPro: IPR014238 Proteins in this entry belong to the broader family of PRC-barrel domain proteins, but are found only in endospore-forming bacteria within the Firmicutes (low-GC, Gram-positive bacteria). Most species encode two of these proteins, though their function is unknown. In Bacillus subtilis, which encodes YlmC and YmxH, YmxH is strongly induced by the mother cell-specific sigma-E factor ..
Probab=17.92 E-value=84 Score=15.52 Aligned_cols=20 Identities=35% Similarity=0.529 Sum_probs=16.2
Q ss_pred EEEEEE-CCCEEEEEEEEEEE
Q ss_conf 589973-55044698642334
Q gi|254780188|r 9 KTIIVS-KGKVESFFIKNAFI 28 (36)
Q Consensus 9 ktiivs-kgkvesffiknafi 28 (36)
.++|++ +|+.-+||-|+..+
T Consensus 37 ~~lIip~~g~~~glf~~~~~~ 57 (76)
T TIGR02888 37 ESLIIPGKGKKFGLFSKGEEI 57 (76)
T ss_pred EEEEECCCCEEEECEECCCCE
T ss_conf 898871897052210068754
No 5
>COG0486 ThdF Predicted GTPase [General function prediction only]
Probab=17.06 E-value=20 Score=18.57 Aligned_cols=11 Identities=64% Similarity=1.129 Sum_probs=7.3
Q ss_pred EEEEEEEEEEE
Q ss_conf 86423341067
Q gi|254780188|r 22 FIKNAFINGKM 32 (36)
Q Consensus 22 fiknafingkm 32 (36)
|-+.||.||||
T Consensus 112 Fs~RAFLNgK~ 122 (454)
T COG0486 112 FSKRAFLNGKL 122 (454)
T ss_pred CHHHHHHCCCC
T ss_conf 36888865884
No 6
>KOG2293 consensus
Probab=9.92 E-value=1.3e+02 Score=14.58 Aligned_cols=17 Identities=47% Similarity=0.751 Sum_probs=11.5
Q ss_pred CEEEEEEEEE-----EEEEEEE
Q ss_conf 0446986423-----3410676
Q gi|254780188|r 17 KVESFFIKNA-----FINGKMI 33 (36)
Q Consensus 17 kvesffikna-----fingkmi 33 (36)
.--||||||- ++||+-+
T Consensus 485 n~GsF~IkNlGK~~I~vng~~l 506 (547)
T KOG2293 485 NDGSFFIKNLGKRSILVNGGEL 506 (547)
T ss_pred CCCCEEECCCCCEEEEECCCCC
T ss_conf 6785775147632488678134
No 7
>TIGR01836 PHA_synth_III_C poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit; InterPro: IPR010125 This entry represents the PhaC subunit of a heterodimeric form of polyhydroxyalkanoic acid (PHA) synthase. Excepting the PhaC of Bacillus megaterium (which needs PhaR), all members require PhaE (IPR010123 from INTERPRO) for activity and are designated class III. This enzyme builds ester polymers for carbon and energy storage that accumulate in inclusions, and both this enzyme and the depolymerase associate with the inclusions. Class III enzymes polymerise short-chain-length hydroxyalkanoates.; GO: 0008415 acyltransferase activity, 0042619 poly-hydroxybutyrate biosynthetic process.
Probab=9.42 E-value=78 Score=15.68 Aligned_cols=17 Identities=29% Similarity=0.675 Sum_probs=12.5
Q ss_pred EEEEEEEEEEEEEEEEE
Q ss_conf 46986423341067660
Q gi|254780188|r 19 ESFFIKNAFINGKMIFE 35 (36)
Q Consensus 19 esffiknafingkmife 35 (36)
..|+-+|.||||+|..-
T Consensus 276 kdFYQ~N~li~G~~~iG 292 (367)
T TIGR01836 276 KDFYQQNGLINGEVEIG 292 (367)
T ss_pred HHHHHHCCCEECEEEEC
T ss_conf 99987166142407986
No 8
>pfam11730 DUF3297 Protein of unknown function (DUF3297). This family is expressed in Proteobacteria and Actinobacteria. The function is not known.
Probab=8.46 E-value=1.7e+02 Score=13.99 Aligned_cols=12 Identities=42% Similarity=0.772 Sum_probs=7.3
Q ss_pred EEEECCCEEEEE
Q ss_conf 997355044698
Q gi|254780188|r 11 IIVSKGKVESFF 22 (36)
Q Consensus 11 iivskgkvesff 22 (36)
.|--||+||.||
T Consensus 60 ~iklkG~VEa~y 71 (71)
T pfam11730 60 TIKLKGTVEAYY 71 (71)
T ss_pred EEEECCEEEECC
T ss_conf 999743266339
No 9
>TIGR00450 thdF tRNA modification GTPase TrmE; InterPro: IPR004520 The GTP-binding domain of all TrmE/ThdF orthologues is found in the C-terminal portion of the molecule. The N-terminal half can be removed without affecting the GTP-binding/hydrolysis function of the GTP-binding domain. The last four amino acids of all orthologues of ThdF/TrmE are highly conserved, being either CIGK or CLGK. This matches the Caax (where 'a' represents an aliphatic amino acid, and 'x' represents any amino acid) motif for isoprenylation that anchors small GTP-binding proteins to cell membranes in eukaryotic cells. However, protein isoprenylation has never been shown to occur in bacteria. Interestingly, biochemical experiments have shown that the Escherichia coli TrmE protein peripherally associates with the membrane fraction . Although the biochemical properties of TrmE have been investigated for the E. coli and Thermotoga maritima proteins, nothing is known about the relationship of this protein to tRNA modification. Orthologues of TrmE are present in eukaryotes and bacteria, but are not present in archaea. In Saccharomyces cerevisiae, Mss1p is a nuclear-encoded mitochondrial protein that is the yeast orthologue of TrmE. Mss1p interacts with the 15S rRNA of the yeast mitochondria, which is equivalent to the 16S rRNA of bacteria. Subsequent analysis of the S. cerevisiae MTO1 gene suggests that MSS1 and MTO1 act together in a pathway involved in optimizing mitochondrial protein synthesis. TrmE may play a role in tRNA processing and may be directly or indirectly involved in regulating ribosome function.; GO: 0003924 GTPase activity, 0005525 GTP binding, 0006400 tRNA modification, 0005622 intracellular.
Probab=7.67 E-value=79 Score=15.66 Aligned_cols=12 Identities=58% Similarity=0.958 Sum_probs=8.4
Q ss_pred EEEEEEEEEEEE
Q ss_conf 864233410676
Q gi|254780188|r 22 FIKNAFINGKMI 33 (36)
Q Consensus 22 fiknafingkmi 33 (36)
|-+.||.||||=
T Consensus 112 Ft~raFLn~k~d 123 (473)
T TIGR00450 112 FTQRAFLNGKMD 123 (473)
T ss_pred CHHHHHHHCCCC
T ss_conf 204666412447
No 10
>COG3157 Hcp Type VI protein secretion system component Hcp (secreted cytotoxin) [Intracellular trafficking, secretion, and vesicular transport]
Probab=7.53 E-value=2.5e+02 Score=13.24 Aligned_cols=22 Identities=41% Similarity=0.848 Sum_probs=0.0
Q ss_pred EEEEEEEEEECCCEEEEEE---EEEEE
Q ss_conf 5666589973550446986---42334
Q gi|254780188|r 5 LDWYKTIIVSKGKVESFFI---KNAFI 28 (36)
Q Consensus 5 ldwyktiivskgkvesffi---knafi 28 (36)
+.||++. +.|+.|.|++ +||.|
T Consensus 89 ~~~~R~~--~~G~~~~y~~~~Ltna~I 113 (162)
T COG3157 89 LTWYRTG--DAGQQEEYLTIKLTNALI 113 (162)
T ss_pred EEEEEEC--CCCCCEEEEEEEEEEEEE
T ss_conf 9999907--899724899999821599
Done!