Query gi|254780581|ref|YP_003064994.1| hypothetical protein CLIBASIA_02340 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 33
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Sun May 29 21:37:04 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780581.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0313 Predicted methyltransf 38.6 13 0.00034 19.7 0.9 14 3-16 131-144 (275)
2 TIGR01124 ilvA_2Cterm threonin 20.4 12 0.00029 20.1 -2.0 28 2-33 431-458 (508)
3 TIGR01960 ndhF3_CO2 NAD(P)H de 19.6 20 0.00051 18.9 -1.0 11 8-18 176-186 (613)
4 TIGR01179 galE UDP-glucose 4-e 18.1 52 0.0013 16.8 0.9 17 8-24 291-307 (341)
5 TIGR02956 TMAO_torS TMAO reduc 18.0 39 0.00099 17.5 0.2 10 5-14 864-873 (1052)
6 pfam06290 PsiB Plasmid SOS inh 12.7 55 0.0014 16.7 -0.2 11 2-12 52-62 (143)
7 pfam09105 SelB-wing_1 Elongati 12.7 1.2E+02 0.003 15.1 1.6 14 13-26 43-56 (61)
8 PRK13701 psiB plasmid SOS inhi 12.5 55 0.0014 16.7 -0.2 11 2-12 52-62 (144)
9 pfam12503 CMV_1a_C Cucumber mo 12.2 74 0.0019 16.1 0.4 17 1-17 48-64 (84)
10 KOG4359 consensus 9.6 2.1E+02 0.0053 13.9 2.0 23 3-25 32-54 (166)
No 1
>COG0313 Predicted methyltransferases [General function prediction only]
Probab=38.58 E-value=13 Score=19.75 Aligned_cols=14 Identities=43% Similarity=0.959 Sum_probs=11.4
Q ss_pred CEEEEECCCCCCCC
Q ss_conf 30221105544574
Q gi|254780581|r 3 GFNFCGFLPKRAGD 16 (33)
Q Consensus 3 gfnfcgflpkragd 16 (33)
-|-|.||||+..+.
T Consensus 131 ~F~F~GFLP~k~~~ 144 (275)
T COG0313 131 RFLFEGFLPRKSKE 144 (275)
T ss_pred CEEEECCCCCCCCH
T ss_conf 72684117998327
No 2
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic; InterPro: IPR005787 Serine and threonine dehydratases , are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue. This family describes a form of threonine dehydratase, with two copies of the threonine dehydratase C-terminal domain IPR001721 from INTERPRO. Members with known function participate in isoleucine biosynthesis and are inhibited by isoleucine.; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process.
Probab=20.41 E-value=12 Score=20.06 Aligned_cols=28 Identities=43% Similarity=0.846 Sum_probs=19.1
Q ss_pred CCEEEEECCCCCCCCEEEEEEECCCEEEEEEC
Q ss_conf 33022110554457436899806740457859
Q gi|254780581|r 2 YGFNFCGFLPKRAGDLSMLAVENDFEWNLMLF 33 (33)
Q Consensus 2 ygfnfcgflpkragdlsmlavendfewnlmlf 33 (33)
|-|.| |.|.|-|.-.--.=+-+||.-||
T Consensus 431 y~FeF----PErPGAL~~FL~~lq~~WNISLF 458 (508)
T TIGR01124 431 YSFEF----PERPGALLKFLTTLQGEWNISLF 458 (508)
T ss_pred EEEEC----CCCCCHHHHHHHHCCCCCCCCHH
T ss_conf 67646----88844699988530665474155
No 3
>TIGR01960 ndhF3_CO2 NAD(P)H dehydrogenase, subunit NdhF3 family; InterPro: IPR010217 This family represents NAD(P)H dehydrogenase subunit 5, or ndhF. It is restricted to two paralogs in each completed cyanobacterial genome, in which several subtypes of ndhF are found. Included in this family is NdhF3, shown to play a role in high-affinity CO2 uptake in Synechococcus sp. PCC7002. In all cases, neighbouring genes include a paralog of ndhD but do include other NAD(P)H dehydrogenase subunits. Instead, genes related to C02 uptake tend to be found nearby.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport.
Probab=19.56 E-value=20 Score=18.88 Aligned_cols=11 Identities=64% Similarity=0.993 Sum_probs=8.9
Q ss_pred ECCCCCCCCEE
Q ss_conf 10554457436
Q gi|254780581|r 8 GFLPKRAGDLS 18 (33)
Q Consensus 8 gflpkragdls 18 (33)
-||.||-||+-
T Consensus 176 AFLTKRVGDl~ 186 (613)
T TIGR01960 176 AFLTKRVGDLL 186 (613)
T ss_pred CHHHHHHHHHH
T ss_conf 10234788999
No 4
>TIGR01179 galE UDP-glucose 4-epimerase; InterPro: IPR005886 Synonym: UDP-galactose 4-epimerase UDP-glucose 4-epimerase (5.1.3.2 from EC) interconverts UDP-glucose and UDP-galactose which are precursors of glucose- and galactose-containing exopolysaccharides (EPS). A set of related proteins, some of which are tentatively identified as UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus halodurans, and several archaea, but deeply branched from this set and lacking experimental evidence, are excluded and described by a separate model. ; GO: 0003978 UDP-glucose 4-epimerase activity, 0006012 galactose metabolic process.
Probab=18.15 E-value=52 Score=16.83 Aligned_cols=17 Identities=29% Similarity=0.601 Sum_probs=12.9
Q ss_pred ECCCCCCCCEEEEEEEC
Q ss_conf 10554457436899806
Q gi|254780581|r 8 GFLPKRAGDLSMLAVEN 24 (33)
Q Consensus 8 gflpkragdlsmlaven 24 (33)
-+.|+|+||++-|--.+
T Consensus 291 ~~~~RR~GDpa~l~Ada 307 (341)
T TIGR01179 291 ELAPRRPGDPASLVADA 307 (341)
T ss_pred EECCCCCCCCCEEECCH
T ss_conf 87687798845487386
No 5
>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS; InterPro: IPR014302 This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (IPR003594 from INTERPRO), HAMP (IPR003660 from INTERPRO), phosphoacceptor (IPR003661 from INTERPRO), and phosphotransfer (IPR008207 from INTERPRO) domains and a response regulator receiver domain (IPR001789 from INTERPRO)..
Probab=18.04 E-value=39 Score=17.45 Aligned_cols=10 Identities=50% Similarity=0.773 Sum_probs=7.3
Q ss_pred EEEECCCCCC
Q ss_conf 2211055445
Q gi|254780581|r 5 NFCGFLPKRA 14 (33)
Q Consensus 5 nfcgflpkra 14 (33)
-|||||||--
T Consensus 864 GF~G~laKPl 873 (1052)
T TIGR02956 864 GFDGFLAKPL 873 (1052)
T ss_pred HCCCCCCCCC
T ss_conf 0266347998
No 6
>pfam06290 PsiB Plasmid SOS inhibition protein (PsiB). This family consists of several plasmid SOS inhibition protein (PsiB) sequences.
Probab=12.70 E-value=55 Score=16.72 Aligned_cols=11 Identities=45% Similarity=0.951 Sum_probs=8.5
Q ss_pred CCEEEEECCCC
Q ss_conf 33022110554
Q gi|254780581|r 2 YGFNFCGFLPK 12 (33)
Q Consensus 2 ygfnfcgflpk 12 (33)
|+-.||||.|-
T Consensus 52 y~sEFgGffPV 62 (143)
T pfam06290 52 YRSEFGGFFPV 62 (143)
T ss_pred HHHHCCCEEEE
T ss_conf 34321671016
No 7
>pfam09105 SelB-wing_1 Elongation factor SelB, winged helix. Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding.
Probab=12.67 E-value=1.2e+02 Score=15.06 Aligned_cols=14 Identities=50% Similarity=0.864 Sum_probs=12.3
Q ss_pred CCCCEEEEEEECCC
Q ss_conf 45743689980674
Q gi|254780581|r 13 RAGDLSMLAVENDF 26 (33)
Q Consensus 13 ragdlsmlavendf 26 (33)
.||....|.||||.
T Consensus 43 aagqvtllrvendl 56 (61)
T pfam09105 43 AAGQVTLLRVENDL 56 (61)
T ss_pred HCCCEEEEEECCCC
T ss_conf 55753788860540
No 8
>PRK13701 psiB plasmid SOS inhibition protein B; Provisional
Probab=12.47 E-value=55 Score=16.69 Aligned_cols=11 Identities=55% Similarity=1.180 Sum_probs=8.7
Q ss_pred CCEEEEECCCC
Q ss_conf 33022110554
Q gi|254780581|r 2 YGFNFCGFLPK 12 (33)
Q Consensus 2 ygfnfcgflpk 12 (33)
|+-.||||.|-
T Consensus 52 y~sEFgGffPV 62 (144)
T PRK13701 52 YGSEFGGFFPV 62 (144)
T ss_pred HHHHCCCEEEE
T ss_conf 45321670016
No 9
>pfam12503 CMV_1a_C Cucumber mosaic virus 1a protein C terminal. This domain family is found in viruses, and is approximately 90 amino acids in length. The family is found in association with pfam01443, pfam01660. There is a conserved GLG sequence motif. 1a protein is the major virulence factor of the cucumber mosaic virus (CMV). The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein.
Probab=12.21 E-value=74 Score=16.08 Aligned_cols=17 Identities=41% Similarity=0.667 Sum_probs=0.0
Q ss_pred CCCEEEEECCCCCCCCE
Q ss_conf 93302211055445743
Q gi|254780581|r 1 MYGFNFCGFLPKRAGDL 17 (33)
Q Consensus 1 mygfnfcgflpkragdl 17 (33)
|-|||--|.-||.++.|
T Consensus 48 ~VGyNe~GLGpK~~~El 64 (84)
T pfam12503 48 SVGYNESGLGPKFDGEL 64 (84)
T ss_pred EEEECCCCCCCCCCCEE
T ss_conf 97636888786868807
No 10
>KOG4359 consensus
Probab=9.56 E-value=2.1e+02 Score=13.86 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=0.0
Q ss_pred CEEEEECCCCCCCCEEEEEEECC
Q ss_conf 30221105544574368998067
Q gi|254780581|r 3 GFNFCGFLPKRAGDLSMLAVEND 25 (33)
Q Consensus 3 gfnfcgflpkragdlsmlavend 25 (33)
+--||.|.-.|.+.-..+-+|||
T Consensus 32 ~C~FCDia~r~~~~~ell~~En~ 54 (166)
T KOG4359 32 TCVFCDIAGRQDPGTELLHCENE 54 (166)
T ss_pred CEEEEEEECCCCCCCCEEEECCC
T ss_conf 70787601256899850676277
Done!