Query gi|254780887|ref|YP_003065300.1| hypothetical protein CLIBASIA_03920 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 86
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 00:05:51 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780887.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam08540 HMG_CoA_synt_C Hydro 28.3 16 0.00041 18.6 -0.0 35 22-56 239-273 (282)
2 COG3814 Uncharacterized protei 24.1 51 0.0013 16.0 1.9 62 14-75 74-135 (157)
3 pfam09189 DUF1952 Domain of un 22.0 38 0.00098 16.7 0.9 20 5-24 42-61 (78)
4 KOG2990 consensus 20.7 51 0.0013 16.0 1.3 13 13-25 39-51 (317)
5 KOG2145 consensus 17.2 63 0.0016 15.5 1.2 25 62-86 80-105 (397)
6 pfam06997 consensus 12.9 1.3E+02 0.0034 13.8 1.9 56 19-74 58-121 (246)
7 pfam00513 Late_protein_L2 Late 12.7 92 0.0024 14.7 1.0 13 4-16 36-48 (466)
8 TIGR01833 HMG-CoA-S_euk hydrox 11.3 73 0.0018 15.2 0.1 36 22-57 416-453 (461)
9 TIGR01050 rpsS_bact ribosomal 10.5 1.1E+02 0.0027 14.4 0.7 23 31-53 27-49 (92)
10 KOG4119 consensus 10.4 1.4E+02 0.0035 13.8 1.3 39 3-41 32-70 (71)
No 1
>pfam08540 HMG_CoA_synt_C Hydroxymethylglutaryl-coenzyme A synthase C terminal.
Probab=28.33 E-value=16 Score=18.60 Aligned_cols=35 Identities=26% Similarity=0.508 Sum_probs=28.8
Q ss_pred EECCCCCCCCHHHCCCCCCCCEECCCCEEEEEECC
Q ss_conf 52143355811003744642000344044454304
Q gi|254780887|r 22 EMGLRHKNHPKKALKPSCNLSTIIPQTVSFELINN 56 (86)
Q Consensus 22 emglrhknhpkkalkpscnlstiipqtvsfelinn 56 (86)
.|-||.++|-++...|+++.+++-|-|--.+-|..
T Consensus 239 ~~~lre~~~~~~~~~p~~s~~~l~pGtyYL~~VD~ 273 (282)
T pfam08540 239 TMELREQAHHKKNFTPQGSIDSLFPGTYYLTNVDS 273 (282)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCHH
T ss_conf 99999997078998778970227998864011024
No 2
>COG3814 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.09 E-value=51 Score=16.01 Aligned_cols=62 Identities=24% Similarity=0.355 Sum_probs=42.4
Q ss_pred CCCEEEEEEECCCCCCCCHHHCCCCCCCCEECCCCEEEEEECCCCEEEECCCCCCCCCCCCC
Q ss_conf 54047875521433558110037446420003440444543043101422787610466787
Q gi|254780887|r 14 MGITRIRFEMGLRHKNHPKKALKPSCNLSTIIPQTVSFELINNLNYSVSTNDKPFTYPSRGA 75 (86)
Q Consensus 14 mgitrirfemglrhknhpkkalkpscnlstiipqtvsfelinnlnysvstndkpftypsrga 75 (86)
|-.|.--|+.||....-|++-.-|--.|....--.|.|||--|..-....+..|-.+|+.++
T Consensus 74 l~v~dtgFsv~lsF~~vpe~l~iPf~Al~~FyDpsvnf~LeF~~~~~~~e~~e~~~~p~~~~ 135 (157)
T COG3814 74 LKVTDTGFSVTLSFSGVPEKLYIPFDALRGFYDPSVNFELEFDVSLNIEEEAEPEAEPSNKA 135 (157)
T ss_pred CEECCCCEEEEEEECCCCEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf 21024624899885796307996258855014887657999744225544567655544422
No 3
>pfam09189 DUF1952 Domain of unknown function (DUF1952). Members of this family are found in various Thermus thermophilus proteins. Their exact function has not, as yet, been determined.
Probab=21.99 E-value=38 Score=16.65 Aligned_cols=20 Identities=40% Similarity=0.564 Sum_probs=14.9
Q ss_pred HHHHHHHCCCCCEEEEEEEC
Q ss_conf 88887640354047875521
Q gi|254780887|r 5 EKKILKVGSMGITRIRFEMG 24 (86)
Q Consensus 5 ekkilkvgsmgitrirfemg 24 (86)
|-.-|+|||..|.|.+.|..
T Consensus 42 e~~pl~vgsl~ip~l~veve 61 (78)
T pfam09189 42 EVEPLKVGSLSIPQLLVEVE 61 (78)
T ss_pred CCCCCEECCCCCCEEEEEEC
T ss_conf 26971004220541788863
No 4
>KOG2990 consensus
Probab=20.72 E-value=51 Score=16.03 Aligned_cols=13 Identities=54% Similarity=0.738 Sum_probs=10.7
Q ss_pred CCCCEEEEEEECC
Q ss_conf 3540478755214
Q gi|254780887|r 13 SMGITRIRFEMGL 25 (86)
Q Consensus 13 smgitrirfemgl 25 (86)
+-||--|||||-.
T Consensus 39 ~~gilvIRFEMPy 51 (317)
T KOG2990 39 DQGILVIRFEMPY 51 (317)
T ss_pred CCCEEEEEEECCC
T ss_conf 6661799973565
No 5
>KOG2145 consensus
Probab=17.22 E-value=63 Score=15.53 Aligned_cols=25 Identities=40% Similarity=0.671 Sum_probs=17.1
Q ss_pred ECCCCCC-CCCCCCCCCCCCCCCCCC
Q ss_conf 2278761-046678776677400249
Q gi|254780887|r 62 STNDKPF-TYPSRGASSSDLPIKGLI 86 (86)
Q Consensus 62 stndkpf-typsrgasssdlpikgli 86 (86)
-.+.||| -|..||.||..+-+--+|
T Consensus 80 ~eq~kpFyLYTGRGpSS~smHlGHli 105 (397)
T KOG2145 80 YEQGKPFYLYTGRGPSSESMHLGHLI 105 (397)
T ss_pred HHCCCCEEEEECCCCCCCCCCCCCCH
T ss_conf 97299659984789985540023301
No 6
>pfam06997 consensus
Probab=12.93 E-value=1.3e+02 Score=13.84 Aligned_cols=56 Identities=21% Similarity=0.140 Sum_probs=35.7
Q ss_pred EEEEECCCCCCCCHHHCCCCCCCC--------EECCCCEEEEEECCCCEEEECCCCCCCCCCCC
Q ss_conf 875521433558110037446420--------00344044454304310142278761046678
Q gi|254780887|r 19 IRFEMGLRHKNHPKKALKPSCNLS--------TIIPQTVSFELINNLNYSVSTNDKPFTYPSRG 74 (86)
Q Consensus 19 irfemglrhknhpkkalkpscnls--------tiipqtvsfelinnlnysvstndkpftypsrg 74 (86)
-|.++-+|+...|.|-.+-.|... ...--+|.|+-+.-+-+|+.|-+.+|++.+.+
T Consensus 58 ~~~~fyI~~~~~p~kry~V~~~~~~~p~~~~~~~~~f~v~F~~~~g~aeSi~ts~~~~~~~~~~ 121 (246)
T pfam06997 58 SRKEYYIRTDREPGKRYYVKPKSEIAPDRKGAKYGTFTVEFENPSGYAESIGTSLDDFDFDEDV 121 (246)
T ss_pred CCCCEEEEECCCCCEEEEEEECCCCCCCCCCCCEEEEEEEEECCCCCEEEEECCCCCCCCCCCC
T ss_conf 6877899980789869999958876866467725899999813875045520268700035555
No 7
>pfam00513 Late_protein_L2 Late Protein L2.
Probab=12.71 E-value=92 Score=14.68 Aligned_cols=13 Identities=46% Similarity=0.935 Sum_probs=8.2
Q ss_pred HHHHHHHHCCCCC
Q ss_conf 7888876403540
Q gi|254780887|r 4 VEKKILKVGSMGI 16 (86)
Q Consensus 4 vekkilkvgsmgi 16 (86)
+..||||.||||+
T Consensus 36 iADkILk~gS~gV 48 (466)
T pfam00513 36 IADKILQYGSLGV 48 (466)
T ss_pred HHHHHHHHCCCEE
T ss_conf 6898875410217
No 8
>TIGR01833 HMG-CoA-S_euk hydroxymethylglutaryl-CoA synthase; InterPro: IPR010122 Synonym(s): 3-hydroxy-3-methylglutaryl-coenzyme A synthase, HMG-CoA synthase. Hydroxymethylglutaryl-CoA synthase (2.3.3.10 from EC) catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA . HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria . In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi . In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes , . This entry is specific for eukaryotic HMG-CoA synthase enzymes.; GO: 0004421 hydroxymethylglutaryl-CoA synthase activity, 0008299 isoprenoid biosynthetic process.
Probab=11.33 E-value=73 Score=15.22 Aligned_cols=36 Identities=31% Similarity=0.572 Sum_probs=30.0
Q ss_pred EECCCCCCCCHHHCCC--CCCCCEECCCCEEEEEECCC
Q ss_conf 5214335581100374--46420003440444543043
Q gi|254780887|r 22 EMGLRHKNHPKKALKP--SCNLSTIIPQTVSFELINNL 57 (86)
Q Consensus 22 emglrhknhpkkalkp--scnlstiipqtvsfelinnl 57 (86)
.|-+|+.+|-|+...| .|......|-|--.+-|..+
T Consensus 416 ~m~~Re~~h~k~nf~P~k~gsi~~L~~GTyYL~~vD~~ 453 (461)
T TIGR01833 416 AMELREQAHHKKNFTPTKEGSIESLFPGTYYLESVDSL 453 (461)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCEECCCCCHH
T ss_conf 99999873035788547677704378960320211232
No 9
>TIGR01050 rpsS_bact ribosomal protein S19; InterPro: IPR005732 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The small ribosomal subunit protein S19 contains 88-144 amino acid residues. In Escherichia coli, S19 is known to form a complex with S13 that binds strongly to 16S ribosomal RNA. Experimental evidence has revealed that S19 is moderately exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=10.47 E-value=1.1e+02 Score=14.37 Aligned_cols=23 Identities=39% Similarity=0.504 Sum_probs=16.8
Q ss_pred CHHHCCCCCCCCEECCCCEEEEE
Q ss_conf 11003744642000344044454
Q gi|254780887|r 31 PKKALKPSCNLSTIIPQTVSFEL 53 (86)
Q Consensus 31 pkkalkpscnlstiipqtvsfel 53 (86)
-++..|-----|||+|+-|.+..
T Consensus 27 ~~~~iKtwSRrS~I~P~mvG~t~ 49 (92)
T TIGR01050 27 KKKVIKTWSRRSTIIPEMVGHTI 49 (92)
T ss_pred CCCEEEEEECCEEECCCCCCCEE
T ss_conf 76236886111032563123067
No 10
>KOG4119 consensus
Probab=10.36 E-value=1.4e+02 Score=13.77 Aligned_cols=39 Identities=21% Similarity=0.324 Sum_probs=27.6
Q ss_pred HHHHHHHHHCCCCCEEEEEEECCCCCCCCHHHCCCCCCC
Q ss_conf 578888764035404787552143355811003744642
Q gi|254780887|r 3 KVEKKILKVGSMGITRIRFEMGLRHKNHPKKALKPSCNL 41 (86)
Q Consensus 3 kvekkilkvgsmgitrirfemglrhknhpkkalkpscnl 41 (86)
+.-+.+++----..++--+.-|.+.+..|.+-.|+.|-+
T Consensus 32 ~a~~el~~y~E~~~~~DpLl~gv~~~~NPf~e~K~~Csi 70 (71)
T KOG4119 32 KAAAELLEYCETHATEDPLLEGVPEKENPFREKKSVCSI 70 (71)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 999999999996475576456871002877556777545
Done!