Query gi|254781125|ref|YP_003065538.1| hypothetical protein CLIBASIA_05135 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 59
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 05:10:56 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781125.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam05418 Apo-VLDL-II Apovitel 21.8 43 0.0011 16.7 1.1 25 22-46 6-30 (82)
2 KOG0676 consensus 18.7 54 0.0014 16.1 1.1 47 2-48 82-132 (372)
3 pfam07982 Herpes_UL74 Herpes U 18.7 14 0.00035 19.4 -2.0 36 10-45 344-379 (457)
4 COG1096 Predicted RNA-binding 18.2 76 0.0019 15.3 1.8 17 15-31 134-150 (188)
5 pfam10876 DUF2669 Protein of u 16.1 41 0.0011 16.8 0.0 25 4-28 67-94 (133)
6 CHL00004 psbD photosystem II p 14.1 27 0.00069 17.8 -1.4 24 12-35 323-347 (353)
7 TIGR01793 cit_synth_euk citrat 12.5 1E+02 0.0027 14.6 1.2 24 30-53 114-138 (430)
8 cd01730 LSm3 The eukaryotic Sm 11.4 1.4E+02 0.0035 13.9 1.5 18 17-34 26-43 (82)
9 COG1973 HypE Hydrogenase matur 11.1 1.5E+02 0.0039 13.6 1.8 26 34-59 261-286 (449)
10 PRK10141 DNA-binding transcrip 11.1 62 0.0016 15.8 -0.3 18 1-19 2-19 (106)
No 1
>pfam05418 Apo-VLDL-II Apovitellenin I (Apo-VLDL-II). This family consists of several avian apovitellenin I sequences. As part of the avian reproductive effort, large quantities of triglyceride-rich very-low-density lipoprotein (VLDL) particles are transported by receptor-mediated endocytosis into the female germ cells. Although the oocytes are surrounded by a layer of granulosa cells harbouring high levels of active lipoprotein lipase, non-lipolysed VLDL is transported into the yolk. This is because VLDL particles from laying chickens are protected from lipolysis by apolipoprotein (apo)-VLDL-II, a potent dimeric lipoprotein lipase inhibitor. Apo-VLDL-II is produced in the liver and secreted into the blood stream when induced by estrogen production in female birds.
Probab=21.81 E-value=43 Score=16.68 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=16.9
Q ss_pred CCCCEEEEEECCCHHHHHHHHCCCH
Q ss_conf 5875037871114377898616871
Q gi|254781125|r 22 KDPHYNVIFRDEVPSFIYETLNIPA 46 (59)
Q Consensus 22 kdphynvifrdevpsfiyetlnipa 46 (59)
+|-.--...-|.+.++|||+.|--.
T Consensus 6 rdRRdwlviPda~AaYiYEaVNk~s 30 (82)
T pfam05418 6 RDRRDWLVIPDAVAAYIYEAVNKMS 30 (82)
T ss_pred CCCCCEEECHHHHHHHHHHHHHHCC
T ss_conf 3543313340899999999987028
No 2
>KOG0676 consensus
Probab=18.67 E-value=54 Score=16.14 Aligned_cols=47 Identities=23% Similarity=0.360 Sum_probs=30.9
Q ss_pred CHHHHHHH---HCCCCCEEEEECCCCCEEE-EEECCCHHHHHHHHCCCHHH
Q ss_conf 24899998---5078641473025875037-87111437789861687113
Q gi|254781125|r 2 SPILEYIR---CLNDPNRYRLSAKDPHYNV-IFRDEVPSFIYETLNIPADK 48 (59)
Q Consensus 2 spileyir---clndpnryrlsakdphynv-ifrdevpsfiyetlnipadk 48 (59)
..|..|+. -..+|+-..+..-+|.+|- -.|...-.+.+||+|+||=-
T Consensus 82 e~iw~~if~~~L~~~Pee~pvllte~pl~p~~nREk~tqi~FE~fnvpa~y 132 (372)
T KOG0676 82 EKIWHHLFYSELLVAPEEHPVLLTEPPLNPKANREKLTQIMFETFNVPALY 132 (372)
T ss_pred HHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCHHH
T ss_conf 999999998764238664864754378883576888887755436863658
No 3
>pfam07982 Herpes_UL74 Herpes UL74 glycoproteins. Members of this family are viral glycoproteins that form part of an envelope complex.
Probab=18.66 E-value=14 Score=19.40 Aligned_cols=36 Identities=36% Similarity=0.553 Sum_probs=26.8
Q ss_pred HCCCCCEEEEECCCCCEEEEEECCCHHHHHHHHCCC
Q ss_conf 507864147302587503787111437789861687
Q gi|254781125|r 10 CLNDPNRYRLSAKDPHYNVIFRDEVPSFIYETLNIP 45 (59)
Q Consensus 10 clndpnryrlsakdphynvifrdevpsfiyetlnip 45 (59)
|-.+-||-..|.---+-.|..|.|.|.-||.||+..
T Consensus 344 C~~~RNrTAvSefmknThvlirNeTPyTIYGTLdms 379 (457)
T pfam07982 344 CKPDRNRTAVSEFMKNTHVLIRNETPYTIYGTLDMS 379 (457)
T ss_pred CCCCCCHHHHHHHHHCCEEEEECCCCEEEEEEECCH
T ss_conf 686544478999863236887358870478751010
No 4
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=18.24 E-value=76 Score=15.34 Aligned_cols=17 Identities=29% Similarity=0.471 Sum_probs=15.0
Q ss_pred CEEEEECCCCCEEEEEE
Q ss_conf 41473025875037871
Q gi|254781125|r 15 NRYRLSAKDPHYNVIFR 31 (59)
Q Consensus 15 nryrlsakdphynvifr 31 (59)
..++||.+.++|.|||-
T Consensus 134 ~~~~Lst~~~dlGVI~A 150 (188)
T COG1096 134 DPIQLSTKGNDLGVIYA 150 (188)
T ss_pred CCEEEEECCCCCEEEEE
T ss_conf 87189852786169999
No 5
>pfam10876 DUF2669 Protein of unknown function (DUF2669). This family of proteins has no known function.
Probab=16.13 E-value=41 Score=16.76 Aligned_cols=25 Identities=36% Similarity=0.680 Sum_probs=19.4
Q ss_pred HHHHHHHC-CCCCEEEEEC--CCCCEEE
Q ss_conf 89999850-7864147302--5875037
Q gi|254781125|r 4 ILEYIRCL-NDPNRYRLSA--KDPHYNV 28 (59)
Q Consensus 4 ileyircl-ndpnryrlsa--kdphynv 28 (59)
||++.-|- +|-|.||||. -+.|+|.
T Consensus 67 Vlk~t~~~~~dG~~yrLs~d~Fn~HFNt 94 (133)
T pfam10876 67 VLKHTSCEGQDGKTYRLSPDRFNQHFNT 94 (133)
T ss_pred HHHHHEEECCCCCEEEECHHHHHHHHHH
T ss_conf 9887316658995798378898889888
No 6
>CHL00004 psbD photosystem II protein D2
Probab=14.09 E-value=27 Score=17.77 Aligned_cols=24 Identities=42% Similarity=0.635 Sum_probs=15.4
Q ss_pred CCCCEEEEECC-CCCEEEEEECCCH
Q ss_conf 78641473025-8750378711143
Q gi|254781125|r 12 NDPNRYRLSAK-DPHYNVIFRDEVP 35 (59)
Q Consensus 12 ndpnryrlsak-dphynvifrdevp 35 (59)
|+--|-..++. .||-|.+|..||-
T Consensus 323 neg~r~wm~~~dqphen~~f~eevl 347 (353)
T CHL00004 323 NEGIRAWMAAQDQPHENLIFPEEVL 347 (353)
T ss_pred HHHHHHHHCCCCCCCCCCCCCHHHC
T ss_conf 7778887402358753456726646
No 7
>TIGR01793 cit_synth_euk citrate (Si)-synthase, eukaryotic; InterPro: IPR010109 Citrate synthase 2.3.3.1 from EC is a member of a small family of enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors. It catalyses the first reaction in the Krebs' cycle, namely the conversion of oxaloacetate and acetyl-coenzyme A into citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The reaction proceeds via a non-covalently bound citryl-coenzyme A intermediate in a 2-step process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA). Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a conformational change upon binding of the oxaloacetate ligand, whereby the active site cleft closes over in order to form the acetyl-CoA binding site . The energy required for domain closure comes from the interaction of the enzyme with the substrate. Type II enzymes possess an extra N-terminal beta-sheet domain, and some type II enzymes are allosterically inhibited by NADH . This entry includes both mitochondrial and peroxisomal forms of citrate synthase. Peroxisomal forms of the enzyme, recognized by the C-terminal targeting motif SKL, act in the glyoxylate cycle. Eukaryotic homologs include a Tetrahymena thermophila citrate synthase that doubles as a filament protein, a putative citrate synthase from Plasmodium falciparum (no TCA cycle), and a methylcitrate synthase from Aspergillus nidulans (Emericella nidulans).; GO: 0004108 citrate (Si)-synthase activity, 0044262 cellular carbohydrate metabolic process.
Probab=12.54 E-value=1e+02 Score=14.58 Aligned_cols=24 Identities=21% Similarity=0.462 Sum_probs=17.8
Q ss_pred EECCCHHHHHHHH-CCCHHHHHHHH
Q ss_conf 7111437789861-68711346888
Q gi|254781125|r 30 FRDEVPSFIYETL-NIPADKRKMAV 53 (59)
Q Consensus 30 frdevpsfiyetl-nipadkrkmav 53 (59)
-|-.+|.||++++ ++|..-.-||-
T Consensus 114 aRadlP~hv~~~iD~~P~tlHPMaQ 138 (430)
T TIGR01793 114 ARADLPKHVVKLIDALPSTLHPMAQ 138 (430)
T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf 5500278999998505743572789
No 8
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=11.41 E-value=1.4e+02 Score=13.94 Aligned_cols=18 Identities=44% Similarity=0.493 Sum_probs=14.4
Q ss_pred EEEECCCCCEEEEEECCC
Q ss_conf 473025875037871114
Q gi|254781125|r 17 YRLSAKDPHYNVIFRDEV 34 (59)
Q Consensus 17 yrlsakdphynvifrdev 34 (59)
-+|-|-|.|+|.+..|-.
T Consensus 26 G~L~afD~h~NlVL~d~e 43 (82)
T cd01730 26 GRLHAYDQHLNMILGDVE 43 (82)
T ss_pred EEEEEECCEEEEEEECCE
T ss_conf 999973402268851639
No 9
>COG1973 HypE Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=11.14 E-value=1.5e+02 Score=13.64 Aligned_cols=26 Identities=31% Similarity=0.351 Sum_probs=18.2
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf 43778986168711346888887519
Q gi|254781125|r 34 VPSFIYETLNIPADKRKMAVIRSYML 59 (59)
Q Consensus 34 vpsfiyetlnipadkrkmavirsyml 59 (59)
.+..++||||+---+.--|.+||+.+
T Consensus 261 m~DVv~ETlnv~fi~a~eai~~s~L~ 286 (449)
T COG1973 261 MHDVVEETLNVDFIRACEAIVRSGLL 286 (449)
T ss_pred CHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf 27888876274899999999985056
No 10
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=11.13 E-value=62 Score=15.80 Aligned_cols=18 Identities=22% Similarity=0.650 Sum_probs=13.7
Q ss_pred CCHHHHHHHHCCCCCEEEE
Q ss_conf 9248999985078641473
Q gi|254781125|r 1 MSPILEYIRCLNDPNRYRL 19 (59)
Q Consensus 1 mspileyirclndpnryrl 19 (59)
|+|+ +..++|.||+|.+.
T Consensus 2 ~~~v-~lFkaLaD~tRl~I 19 (106)
T PRK10141 2 LTPL-QLFKILSDETRLGI 19 (106)
T ss_pred CCHH-HHHHHHCCHHHHHH
T ss_conf 9889-99999088999999
Done!