Query gi|254781090|ref|YP_003065503.1| hypothetical protein CLIBASIA_04960 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 71
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 05:38:16 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781090.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02795 tol_pal_ybgF tol-pal 52.9 18 0.00047 19.1 3.5 28 33-60 10-37 (119)
2 PRK10803 hypothetical protein; 52.8 21 0.00053 18.8 3.7 31 31-61 144-178 (262)
3 COG1729 Uncharacterized protei 48.3 14 0.00036 19.7 2.3 48 13-60 199-250 (262)
4 KOG2433 consensus 48.0 7.2 0.00018 21.4 0.8 34 9-42 406-449 (577)
5 PRK11263 cardiolipin synthase 34.1 40 0.001 17.3 2.8 30 10-39 60-89 (406)
6 TIGR01852 lipid_A_lpxA acyl-[a 30.9 51 0.0013 16.7 2.9 33 22-54 217-250 (257)
7 TIGR00169 leuB 3-isopropylmala 25.0 40 0.001 17.2 1.5 21 46-68 207-228 (370)
8 COG3028 Uncharacterized protei 23.5 38 0.00098 17.4 1.2 22 46-67 132-154 (187)
9 PRK06646 DNA polymerase III su 23.5 30 0.00075 18.0 0.6 52 9-60 81-137 (154)
10 TIGR02493 PFLA pyruvate format 22.4 61 0.0016 16.2 2.0 21 39-59 177-198 (243)
11 KOG1297 consensus 20.1 33 0.00085 17.7 0.3 16 7-22 123-138 (249)
No 1
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF; InterPro: IPR014162 Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, and a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction..
Probab=52.95 E-value=18 Score=19.12 Aligned_cols=28 Identities=32% Similarity=0.667 Sum_probs=17.7
Q ss_pred HHHHHHCCHHHHHHHHHHHHHHCCCCCE
Q ss_conf 9898620116679999999631888740
Q gi|254781090|r 33 QKIVKIGDHAESIKTLADFIKDYPDCDL 60 (71)
Q Consensus 33 qkivkigdhaesiktladfikdypdcdl 60 (71)
..+.|-||.+..|.....|++.||+-.+
T Consensus 10 ~~~lk~gdY~~A~~~F~~F~~~YP~S~y 37 (119)
T TIGR02795 10 LLVLKAGDYADAIQAFQAFLKKYPKSTY 37 (119)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf 9998538878999999999886879876
No 2
>PRK10803 hypothetical protein; Provisional
Probab=52.77 E-value=21 Score=18.81 Aligned_cols=31 Identities=26% Similarity=0.610 Sum_probs=23.6
Q ss_pred HHHHHHH----HCCHHHHHHHHHHHHHHCCCCCEE
Q ss_conf 8998986----201166799999996318887400
Q gi|254781090|r 31 KYQKIVK----IGDHAESIKTLADFIKDYPDCDLE 61 (71)
Q Consensus 31 kyqkivk----igdhaesiktladfikdypdcdle 61 (71)
-|+..+. -++..+.|+-+.+||++||+-.+.
T Consensus 144 ~Y~~A~~Lvl~~k~y~~Ai~aF~~Fi~~yP~s~y~ 178 (262)
T PRK10803 144 DYNAAIALVQDKSRQDDAIVAFQNFIKKYPDSTYQ 178 (262)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf 89999999997356999999999999878799877
No 3
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.32 E-value=14 Score=19.74 Aligned_cols=48 Identities=27% Similarity=0.459 Sum_probs=31.7
Q ss_pred CEEEEEEEHHHCCCCCHHHHHHHH----HHCCHHHHHHHHHHHHHHCCCCCE
Q ss_conf 012112311233864378899898----620116679999999631888740
Q gi|254781090|r 13 VNFRFLLDGYRSGKTSKDKYQKIV----KIGDHAESIKTLADFIKDYPDCDL 60 (71)
Q Consensus 13 vnfrflldgyrsgktskdkyqkiv----kigdhaesiktladfikdypdcdl 60 (71)
.+|.-....|-+.+.+-|-+-|+. ..|.+.+.-+||..+|+.||+.+-
T Consensus 199 ~~f~~~~k~~P~s~KApdallKlg~~~~~l~~~d~A~atl~qv~k~YP~t~a 250 (262)
T COG1729 199 YIFARVVKDYPKSPKAPDALLKLGVSLGRLGNTDEACATLQQVIKRYPGTDA 250 (262)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHH
T ss_conf 9999999838999988289999999999821779999999999987899779
No 4
>KOG2433 consensus
Probab=48.04 E-value=7.2 Score=21.36 Aligned_cols=34 Identities=38% Similarity=0.818 Sum_probs=27.4
Q ss_pred HCCCCEEE--------EEEEHHH--CCCCCHHHHHHHHHHCCHH
Q ss_conf 13460121--------1231123--3864378899898620116
Q gi|254781090|r 9 NGWGVNFR--------FLLDGYR--SGKTSKDKYQKIVKIGDHA 42 (71)
Q Consensus 9 ngwgvnfr--------flldgyr--sgktskdkyqkivkigdha 42 (71)
+|||..+| |.|.||. +-.|...--|-.|+|+|..
T Consensus 406 ~GWGCAYRSlQTIcSWFilqGYT~~pIPtHrEiQqaLvdi~DKp 449 (577)
T KOG2433 406 SGWGCAYRSLQTICSWFILQGYTDKPIPTHREIQQALVDIQDKP 449 (577)
T ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCC
T ss_conf 77532257689999999873866898973799999997505766
No 5
>PRK11263 cardiolipin synthase 2; Provisional
Probab=34.06 E-value=40 Score=17.25 Aligned_cols=30 Identities=30% Similarity=0.467 Sum_probs=22.2
Q ss_pred CCCCEEEEEEEHHHCCCCCHHHHHHHHHHC
Q ss_conf 346012112311233864378899898620
Q gi|254781090|r 10 GWGVNFRFLLDGYRSGKTSKDKYQKIVKIG 39 (71)
Q Consensus 10 gwgvnfrflldgyrsgktskdkyqkivkig 39 (71)
--||..|+|+||+-|.+.++.-.......|
T Consensus 60 ~rGV~VrlL~D~~GS~~~~~~~~~~l~~aG 89 (406)
T PRK11263 60 QRGVKVEVLVDGYGSPDLSDEFVGELTAAG 89 (406)
T ss_pred HCCCEEEEEEECCCCCCCCHHHHHHHHHCC
T ss_conf 879979999988999898999999998299
No 6
>TIGR01852 lipid_A_lpxA acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase; InterPro: IPR010137 This entry describes LpxA, an enzyme for the biosynthesis of lipid A, a component of lipopolysaccharide (LPS) in the outer membrane outer leaflet of most Gram-negative bacteria. Some differences are found between lipid A of different species, but this protein represents the first step (from UDP-N-acetyl-D-glucosamine) and appears to be conserved in function. Proteins from this family contain many copies of the bacterial transferase hexapeptide repeat.; GO: 0008780 acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity, 0008610 lipid biosynthetic process.
Probab=30.95 E-value=51 Score=16.67 Aligned_cols=33 Identities=24% Similarity=0.535 Sum_probs=30.3
Q ss_pred HHCCCCCHHHHHHHHHH-CCHHHHHHHHHHHHHH
Q ss_conf 23386437889989862-0116679999999631
Q gi|254781090|r 22 YRSGKTSKDKYQKIVKI-GDHAESIKTLADFIKD 54 (71)
Q Consensus 22 yrsgktskdkyqkivki-gdhaesiktladfikd 54 (71)
|||+++-++.-|.+... -.+.+.+|.+-|||+.
T Consensus 217 fr~~~~~~~~~~~v~e~P~~~~~~v~~~~~FI~~ 250 (257)
T TIGR01852 217 FRSGLPLQEALQQVAEEPYEDNPEVKEIVDFIRE 250 (257)
T ss_pred HCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHCC
T ss_conf 1799898999999983513377579999998607
No 7
>TIGR00169 leuB 3-isopropylmalate dehydrogenase; InterPro: IPR004429 Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the dimeric 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. Among these decarboxylating dehydrogenases of hydroxyacids, overall sequence homology indicates evolutionary history rather than actual substrate or cofactor specifity, which may be toggled experimentally by replacement of just a few amino acids. 3-isopropylmalate dehydrogenase is an NAD-dependent enzyme and should have a sequence resembling HGSAPDI around residue 340. The subtrate binding loop should include a sequence resembling E[KQR]X(0,1)LLXXR around residue 115.; GO: 0003862 3-isopropylmalate dehydrogenase activity, 0009098 leucine biosynthetic process, 0005737 cytoplasm.
Probab=25.00 E-value=40 Score=17.23 Aligned_cols=21 Identities=48% Similarity=0.825 Sum_probs=15.9
Q ss_pred HHHHHHHH-HCCCCCEEHHHHHHH
Q ss_conf 99999963-188874007754332
Q gi|254781090|r 46 KTLADFIK-DYPDCDLELENLVTD 68 (71)
Q Consensus 46 ktladfik-dypdcdlelenlvtd 68 (71)
||..+.+| +||| ++|+++.-|
T Consensus 207 ~~V~e~~~~eYPd--v~L~H~yiD 228 (370)
T TIGR00169 207 KTVEEIAKEEYPD--VELEHQYID 228 (370)
T ss_pred HHHHHHHHCCCCC--EEECCCHHH
T ss_conf 9999998468880--573021587
No 8
>COG3028 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.51 E-value=38 Score=17.35 Aligned_cols=22 Identities=36% Similarity=0.831 Sum_probs=16.1
Q ss_pred HHHHHHHHHCCCCCEE-HHHHHH
Q ss_conf 9999996318887400-775433
Q gi|254781090|r 46 KTLADFIKDYPDCDLE-LENLVT 67 (71)
Q Consensus 46 ktladfikdypdcdle-lenlvt 67 (71)
..+..|+.+||+||-. |.+||-
T Consensus 132 ~Alt~~l~~~P~aDrq~LR~LvR 154 (187)
T COG3028 132 GALTEFLNQYPDADRQQLRTLIR 154 (187)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 68999998787110999999999
No 9
>PRK06646 DNA polymerase III subunit chi; Provisional
Probab=23.48 E-value=30 Score=17.98 Aligned_cols=52 Identities=19% Similarity=0.264 Sum_probs=38.4
Q ss_pred HCCCCEEEEEEEHHHCCCC-----CHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCE
Q ss_conf 1346012112311233864-----378899898620116679999999631888740
Q gi|254781090|r 9 NGWGVNFRFLLDGYRSGKT-----SKDKYQKIVKIGDHAESIKTLADFIKDYPDCDL 60 (71)
Q Consensus 9 ngwgvnfrflldgyrsgkt-----skdkyqkivkigdhaesiktladfikdypdcdl 60 (71)
|--+.+++||+||-..++. ..+-|+.+|-+.|-.+....+..-.|.+-+..-
T Consensus 81 NPN~A~vlflvdgad~~~~~~~~~~~~~f~R~v~~fD~~dd~~~ar~r~~~~k~~~~ 137 (154)
T PRK06646 81 NPNNASVLVIISPTDIGKILQAKEYIRVFKRIIIITDLPEDLKELTVKINKFTEQEN 137 (154)
T ss_pred CCCCCCEEEEECCCCCCCCCCCCCHHHHEEEEEEECCCHHHHHHHHHHHHHHHHCCC
T ss_conf 998882899975887432222220220002799954877789999999999860899
No 10
>TIGR02493 PFLA pyruvate formate-lyase 1-activating enzyme; InterPro: IPR012838 Members of this family are iron-sulphur proteins with a radical-SAM domain. A single glycine residue in 2.3.1.54 from EC, formate C-acetyltransferase (formate-pyruvate lyase), is oxidized to the corresponding radical by transfer of a proton from its CH2 to AdoMet with concomitant cleavage of the latter. The reaction requires Fe2+. The first stage is reduction of the AdoMet to give methionine and the 5'-deoxyadenosin-5-yl radical, which then abstracts a hydrogen radical from the glycine residue .; GO: 0043365 [formate-C-acetyltransferase]-activating enzyme activity.
Probab=22.39 E-value=61 Score=16.24 Aligned_cols=21 Identities=38% Similarity=0.765 Sum_probs=18.5
Q ss_pred CCHHHHHHHHHHHHHHCCC-CC
Q ss_conf 0116679999999631888-74
Q gi|254781090|r 39 GDHAESIKTLADFIKDYPD-CD 59 (71)
Q Consensus 39 gdhaesiktladfikdypd-cd 59 (71)
-|..|.|..||+|++.+|. |.
T Consensus 177 TD~~eDi~~l~~fv~~~~~ave 198 (243)
T TIGR02493 177 TDSEEDIEALAEFVKTLPNAVE 198 (243)
T ss_pred CCCHHHHHHHHHHHHHCCCCEE
T ss_conf 7998999999999974699279
No 11
>KOG1297 consensus
Probab=20.08 E-value=33 Score=17.68 Aligned_cols=16 Identities=44% Similarity=0.927 Sum_probs=13.0
Q ss_pred HHHCCCCEEEEEEEHH
Q ss_conf 1113460121123112
Q gi|254781090|r 7 LLNGWGVNFRFLLDGY 22 (71)
Q Consensus 7 llngwgvnfrflldgy 22 (71)
-|..|-|||++.-+|-
T Consensus 123 ~L~SWEVNF~YiE~ge 138 (249)
T KOG1297 123 HLSSWEVNFTYIEDGE 138 (249)
T ss_pred CCCCEEEECEECCCCC
T ss_conf 5541232000103684
Done!