Query gi|254780211|ref|YP_003064624.1| hypothetical protein CLIBASIA_00480 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 56
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 23 14:59:32 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780211.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02088 LEU3_arch isopropylm 57.8 4.5 0.00011 21.5 1.0 25 5-29 112-139 (350)
2 TIGR01338 phycocy_alpha phycoc 14.7 47 0.0012 16.6 -0.0 22 34-55 67-88 (161)
3 PRK12495 hypothetical protein; 13.3 65 0.0017 15.9 0.4 27 5-31 28-56 (221)
4 TIGR00175 mito_nad_idh isocitr 11.6 1E+02 0.0026 15.0 1.0 11 15-25 120-130 (348)
5 TIGR02034 CysN sulfate adenyly 11.3 68 0.0017 15.9 -0.0 14 38-51 91-105 (411)
6 TIGR00452 TIGR00452 methyltran 10.9 97 0.0025 15.1 0.7 30 5-34 218-248 (316)
7 COG4029 Uncharacterized protei 10.3 1E+02 0.0027 15.0 0.6 30 26-55 57-86 (142)
8 TIGR02089 TTC tartrate dehydro 9.7 1.3E+02 0.0034 14.5 1.0 12 15-26 128-139 (355)
9 COG0473 LeuB Isocitrate/isopro 9.4 1.5E+02 0.0039 14.1 1.2 24 3-26 109-132 (348)
10 TIGR02852 spore_dpaB dipicolin 9.1 99 0.0025 15.1 0.1 11 39-49 40-50 (188)
No 1
>TIGR02088 LEU3_arch isopropylmalate/isohomocitrate dehydrogenases; InterPro: IPR011828 This entry represents a group of archaeal decarboxylating dehydrogenases which include the leucine biosynthesis enzyme 3-isopropylmalate dehydrogenase (LeuB, LEU3) and the methanogenic cofactor CoB biosynthesis enzyme isohomocitrate dehydrogenase (AksF). Both of these have been characterised in Methanococcus janaschii . Sequences from the non-methanogenic archaea are also represented in this entry, presumably LeuB, although phylogenetic trees cannot establish which gene is which in the methanogens.; GO: 0003862 3-isopropylmalate dehydrogenase activity, 0051287 NAD binding, 0009098 leucine biosynthetic process.
Probab=57.83 E-value=4.5 Score=21.53 Aligned_cols=25 Identities=36% Similarity=0.329 Sum_probs=17.2
Q ss_pred CCCCHHHE---EEEEEEEEECCCCCHHH
Q ss_conf 01301121---12112001125685345
Q gi|254780211|r 5 QIEGELFL---KTALVVVRERTECPIHR 29 (56)
Q Consensus 5 qiegelfl---ktalvvvrertecpihr 29 (56)
.|++--++ .--+|+|||-|||--.+
T Consensus 112 ~I~~~~~~na~~~DiVIVRENTE~LY~G 139 (350)
T TIGR02088 112 GIEDLYNLNAKNLDIVIVRENTEGLYAG 139 (350)
T ss_pred CCCCCCCCCCCCCEEEEEEECCCCCCCC
T ss_conf 2245566678882179986256543247
No 2
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit; InterPro: IPR006246 These sequences in this family represent the phycocyanin alpha subunit. Other, homologous phyobiliproteins of the phycobilisome include phycocyanin alpha chain and the allophycocyanin and phycoerythrin alpha and beta chains. Not included are the closely related phycoerythrocyanin alpha subunit sequences.; GO: 0006118 electron transport, 0015979 photosynthesis, 0030089 phycobilisome.
Probab=14.74 E-value=47 Score=16.63 Aligned_cols=22 Identities=41% Similarity=0.516 Sum_probs=16.8
Q ss_pred HHHHHHHHCCHHHHHHHHHCCC
Q ss_conf 1124013112010334530358
Q gi|254780211|r 34 AVFIKQYTNTAFGKSKCKRGRG 55 (56)
Q Consensus 34 avfikqytntafgkskckrgrg 55 (56)
..+-.+|..++.||.||.|.-|
T Consensus 67 ~~~GP~~as~~~Gk~kC~rdiG 88 (161)
T TIGR01338 67 QQNGPNYASTAEGKAKCVRDIG 88 (161)
T ss_pred CCCCCCHHHHHHHHHHHHHHHH
T ss_conf 4577313556545665567778
No 3
>PRK12495 hypothetical protein; Provisional
Probab=13.29 E-value=65 Score=15.93 Aligned_cols=27 Identities=33% Similarity=0.426 Sum_probs=19.9
Q ss_pred CCCCHHHEEEEEEEEEECCCC--CHHHHE
Q ss_conf 013011211211200112568--534520
Q gi|254780211|r 5 QIEGELFLKTALVVVRERTEC--PIHRYF 31 (56)
Q Consensus 5 qiegelflktalvvvrertec--pihryf 31 (56)
|--.||.||-|-..-+.-.+| ||.||=
T Consensus 28 qrMSeLLLqGATMTN~HC~~CGdPIFR~d 56 (221)
T PRK12495 28 ERMSELLLQGATMTNAHCDECGSPIFRHD 56 (221)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCCHHHHCC
T ss_conf 99999997332102120022367234047
No 4
>TIGR00175 mito_nad_idh isocitrate dehydrogenase, NAD-dependent; InterPro: IPR004434 Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the multimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologs. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; the latter carbon, now adjacent to a carbonyl group, readily decarboxylates. Mitochondrial NAD-dependent isocitrate dehydrogenases (IDH) resemble prokaryotic NADP-dependent IDH and 3-isopropylmalate dehydrogenase (an NAD-dependent enzyme) more closely than they resemble eukaryotic NADP-dependent IDH. The mitochondrial NAD-dependent isocitrate dehydrogenase is believed to be an alpha(2)-beta-gamma heterotetramer. All subunits are homologous and belog to this group. The NADP-dependent IDH of Thermus thermophilus strain HB8 resembles these NAD-dependent IDH, except for the residues involved in cofactor specificity, much more closely than it resembles other prokaryotic NADP-dependent IDH, including that of Thermus aquaticus. ; GO: 0004449 isocitrate dehydrogenase (NAD+) activity, 0006099 tricarboxylic acid cycle, 0005739 mitochondrion.
Probab=11.61 E-value=1e+02 Score=15.00 Aligned_cols=11 Identities=45% Similarity=0.752 Sum_probs=8.4
Q ss_pred EEEEEEECCCC
Q ss_conf 11200112568
Q gi|254780211|r 15 ALVVVRERTEC 25 (56)
Q Consensus 15 alvvvrertec 25 (56)
-+|++||-||-
T Consensus 120 D~v~IRENTEG 130 (348)
T TIGR00175 120 DIVIIRENTEG 130 (348)
T ss_pred CEEEEEECCCC
T ss_conf 36899634772
No 5
>TIGR02034 CysN sulfate adenylyltransferase, large subunit; InterPro: IPR011779 Metabolic assimilation of sulphur from inorganic sulphate, requires sulphate activation by coupling to a nucleoside, for the production of high-energy nucleoside phosphosulphates. This pathway appears to be similar in all prokaryotic organisms. Activation is first achieved through sulphation of sulphate with ATP by sulphate adenylyltransferase (ATP sulphurylase) to produce 5'-phosphosulphate (APS), coupled by GTP hydrolysis. Subsequently, APS is phosphorylated by an APS kinase to produce 3'-phosphoadenosine-5'-phosphosulphate (PAPS) . In Escherichia coli, ATP sulphurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulphur-containing amino acids . Homologous to this E. coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulphurase and APS kinase activity, yet are involved in Nod factor sulphation, and sulphation of other macromolecules . With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulphurase) and cysC (APS kinase) , .; GO: 0016772 transferase activity transferring phosphorus-containing groups.
Probab=11.35 E-value=68 Score=15.86 Aligned_cols=14 Identities=50% Similarity=0.646 Sum_probs=10.9
Q ss_pred HHHH-CCHHHHHHHH
Q ss_conf 0131-1201033453
Q gi|254780211|r 38 KQYT-NTAFGKSKCK 51 (56)
Q Consensus 38 kqyt-ntafgkskck 51 (56)
.||| |.|-|-|-|.
T Consensus 91 EQYTRNMATGAST~d 105 (411)
T TIGR02034 91 EQYTRNMATGASTAD 105 (411)
T ss_pred CCCCCCCCHHCCCCC
T ss_conf 415443000013112
No 6
>TIGR00452 TIGR00452 methyltransferase, putative; InterPro: IPR010017 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order . Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI ), shared by other AdoMet-Mtases , is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments , although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases , , , . The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences . This is a set of proteobacterial proteins, which have homology in their central region to a large number of methyltransferases active on a variety of substrates. .
Probab=10.89 E-value=97 Score=15.11 Aligned_cols=30 Identities=30% Similarity=0.367 Sum_probs=21.6
Q ss_pred CCCCHHHEEEEEEEEEEC-CCCCHHHHEEEH
Q ss_conf 013011211211200112-568534520001
Q gi|254780211|r 5 QIEGELFLKTALVVVRER-TECPIHRYFKIA 34 (56)
Q Consensus 5 qiegelflktalvvvrer-tecpihryfkia 34 (56)
.++|||.|.|-.+--.+. .-||-.||-|.-
T Consensus 218 ~~~GELVL~TLviD~d~~~~LvP~~~YAkMk 248 (316)
T TIGR00452 218 VKKGELVLETLVIDGDLNTVLVPKDRYAKMK 248 (316)
T ss_pred HHCCCEEEEEEEECCCCCEEECCCCCCCCEE
T ss_conf 7579358653466077675864754442200
No 7
>COG4029 Uncharacterized protein conserved in archaea [Function unknown]
Probab=10.29 E-value=1e+02 Score=14.96 Aligned_cols=30 Identities=27% Similarity=0.308 Sum_probs=25.5
Q ss_pred CHHHHEEEHHHHHHHHCCHHHHHHHHHCCC
Q ss_conf 534520001124013112010334530358
Q gi|254780211|r 26 PIHRYFKIAVFIKQYTNTAFGKSKCKRGRG 55 (56)
Q Consensus 26 pihryfkiavfikqytntafgkskckrgrg 55 (56)
-|..|++-++|+|.---.+-.+..|.+-||
T Consensus 57 riR~~d~~~IF~KdRGfp~gD~RrCR~~RG 86 (142)
T COG4029 57 RIRELDGNAIFSKDRGFPAGDPRRCRATRG 86 (142)
T ss_pred HHHHHCCCCEEECCCCCCCCCHHHHHHCCC
T ss_conf 998755675343135889998046553369
No 8
>TIGR02089 TTC tartrate dehydrogenase; InterPro: IPR011829 Tartrate dehydrogenase catalyzes the oxidation of both meso- and (+)-tartrate as well as a D-malate . These enzymes are closely related to the 3-isopropylmalate and isohomocitrate dehydrogenases found in IPR004429 from INTERPRO and IPR011828 from INTERPRO, respectively.; GO: 0009027 tartrate dehydrogenase activity, 0051287 NAD binding.
Probab=9.72 E-value=1.3e+02 Score=14.46 Aligned_cols=12 Identities=50% Similarity=0.642 Sum_probs=9.3
Q ss_pred EEEEEEECCCCC
Q ss_conf 112001125685
Q gi|254780211|r 15 ALVVVRERTECP 26 (56)
Q Consensus 15 alvvvrertecp 26 (56)
-++||||.||--
T Consensus 128 D~~vvRENsEGE 139 (355)
T TIGR02089 128 DFVVVRENSEGE 139 (355)
T ss_pred EEEEEEECCCCC
T ss_conf 589986458752
No 9
>COG0473 LeuB Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]
Probab=9.39 E-value=1.5e+02 Score=14.14 Aligned_cols=24 Identities=29% Similarity=0.404 Sum_probs=15.5
Q ss_pred CCCCCCHHHEEEEEEEEEECCCCC
Q ss_conf 000130112112112001125685
Q gi|254780211|r 3 FSQIEGELFLKTALVVVRERTECP 26 (56)
Q Consensus 3 fsqiegelflktalvvvrertecp 26 (56)
+|-+..++--..-+|+|||-||..
T Consensus 109 ~~~~k~~~~~~~D~viVREnTeG~ 132 (348)
T COG0473 109 LPGLKSPLVKGVDIVIVRENTEGL 132 (348)
T ss_pred CCCCCCCCCCCCCEEEEEECCCCC
T ss_conf 799987666895089996388760
No 10
>TIGR02852 spore_dpaB dipicolinic acid synthetase, B subunit; InterPro: IPR014214 Members of this entry represent the B subunit of dipicolinic acid synthetase, an enzyme that synthesizes a small molecule that appears to confer heat stability to bacterial endospores such as those of Bacillus subtilis. The A and B subunits are together in what was originally designated the spoVF locus for stage V of endospore formation..
Probab=9.10 E-value=99 Score=15.06 Aligned_cols=11 Identities=45% Similarity=0.652 Sum_probs=0.0
Q ss_pred HHHCCHHHHHH
Q ss_conf 13112010334
Q gi|254780211|r 39 QYTNTAFGKSK 49 (56)
Q Consensus 39 qytntafgksk 49 (56)
|.|+|-||+++
T Consensus 40 ~~T~TrFG~~~ 50 (188)
T TIGR02852 40 QTTDTRFGDGA 50 (188)
T ss_pred CCCCCCCCCHH
T ss_conf 43565568618
Done!