Query         gi|254780667|ref|YP_003065080.1| hypothetical protein CLIBASIA_02770 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 43
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 20:22:20 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780667.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00315 potassium-transportin  13.8 1.4E+02  0.0035   14.3   2.5   34    1-38      1-34  (195)
  2 pfam07436 Curto_V3 Curtovirus   12.6   1E+02  0.0026   14.9   1.2   17   13-29     46-62  (87)
  3 TIGR00717 rpsA ribosomal prote  12.3      67  0.0017   15.8   0.2   12    2-13    398-409 (534)
  4 pfam09272 Hepsin-SRCR Hepsin,   12.2      61  0.0015   16.0  -0.1   28   14-43     75-102 (110)
  5 TIGR02174 CXXU_selWTH selT/sel  12.0   1E+02  0.0027   14.9   1.1   20   24-43     86-105 (144)
  6 PRK13592 ubiA prenyltransferas  11.4 1.3E+02  0.0032   14.4   1.4   20   21-40    180-199 (299)
  7 TIGR00630 uvra excinuclease AB  11.3 1.2E+02  0.0031   14.6   1.2   18    6-23    894-911 (956)
  8 PRK02487 hypothetical protein;   8.8 1.6E+02  0.0042   13.9   1.1   33    8-40      5-37  (163)
  9 COG3124 Uncharacterized protei   7.4 2.4E+02  0.0062   13.1   1.7   23    8-30    163-185 (193)
 10 TIGR02247 HAD-1A3-hyp Epoxide    7.1      51  0.0013   16.4  -2.1   11   29-39      4-14  (228)

No 1  
>PRK00315 potassium-transporting ATPase subunit C; Reviewed
Probab=13.78  E-value=1.4e+02  Score=14.29  Aligned_cols=34  Identities=24%  Similarity=0.155  Sum_probs=23.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             93000110220225899999999981137897443233
Q gi|254780667|r    1 MMKGLLHADDIEFRFTAVQRLVFAFYPSAVVWEFGRIL   38 (43)
Q Consensus         1 mmkgllhaddiefrftavqrlvfafypsavvwefgril   38 (43)
                      |||-+..+    +|++.+--+++.+--..++|-+++++
T Consensus         1 M~k~l~~a----l~~~l~~~vl~G~~YPl~vtgiaq~~   34 (195)
T PRK00315          1 MMKGLRPA----LVLFLFLLLITGGAYPLLTTGLGQWW   34 (195)
T ss_pred             CHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             95889999----99999999999999999999999986


No 2  
>pfam07436 Curto_V3 Curtovirus V3 protein. This family consists of several Curtovirus V3 proteins of around 90 residues in length. The function of this family is unknown.
Probab=12.57  E-value=1e+02  Score=14.93  Aligned_cols=17  Identities=35%  Similarity=0.612  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHCCHH
Q ss_conf             25899999999981137
Q gi|254780667|r   13 FRFTAVQRLVFAFYPSA   29 (43)
Q Consensus        13 frftavqrlvfafypsa   29 (43)
                      --|-++|..||+-|||.
T Consensus        46 elf~k~qqvvy~r~~sr   62 (87)
T pfam07436        46 ELFVKLQQVVYTRYPSR   62 (87)
T ss_pred             HHHHHHHHHHHCCCCCC
T ss_conf             99999999874147642


No 3  
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110   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 , .   Ribosomal protein S1  contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities .    Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=12.27  E-value=67  Score=15.81  Aligned_cols=12  Identities=33%  Similarity=0.916  Sum_probs=7.9

Q ss_pred             CCCCCCCCCHHH
Q ss_conf             300011022022
Q gi|254780667|r    2 MKGLLHADDIEF   13 (43)
Q Consensus         2 mkgllhaddief   13 (43)
                      |+||+|.+||-.
T Consensus       398 idGliH~~D~SW  409 (534)
T TIGR00717       398 IDGLIHLSDLSW  409 (534)
T ss_pred             CCEEEECCCCCC
T ss_conf             223895640153


No 4  
>pfam09272 Hepsin-SRCR Hepsin, SRCR. Members of this family form an extracellular domain of the serine protease hepsin. They are formed primarily by three elements of regular secondary structure: a 12-residue alpha helix, a twisted five-stranded antiparallel beta sheet, and a second, two-stranded, antiparallel sheet. The two beta-sheets lie at roughly right angles to each other, with the helix nestled between the two, adopting an SRCR fold. The exact function of this domain has not been identified, though it probably may serve to orient the protease domain or place it in the vicinity of its substrate.
Probab=12.16  E-value=61  Score=16.01  Aligned_cols=28  Identities=32%  Similarity=0.390  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHCC
Q ss_conf             589999999998113789744323331029
Q gi|254780667|r   14 RFTAVQRLVFAFYPSAVVWEFGRILTATCQ   43 (43)
Q Consensus        14 rftavqrlvfafypsavvwefgriltatcq   43 (43)
                      +.+--|||.-..+|-.  -+-||+|++.||
T Consensus        75 ~L~y~krl~dvlsvCd--Cp~G~fL~~~CQ  102 (110)
T pfam09272        75 ELPYGQRLLTVISVCD--CPRGRFLEAICQ  102 (110)
T ss_pred             CCCHHHHHHHEEEEEC--CCCCCHHHHHHH
T ss_conf             2845561553220303--897512778777


No 5  
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain; InterPro: IPR011893    This is a family found in both bacteria and animals, including the animal proteins SelT, SelW, and SelH, all of which are selenoproteins. These proteins contain a domain with a CXXC motif near the N-terminus, where selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. ; GO: 0008430 selenium binding, 0045454 cell redox homeostasis.
Probab=12.01  E-value=1e+02  Score=14.86  Aligned_cols=20  Identities=30%  Similarity=0.645  Sum_probs=17.3

Q ss_pred             HHCCHHHHHHHHHHHHHHCC
Q ss_conf             98113789744323331029
Q gi|254780667|r   24 AFYPSAVVWEFGRILTATCQ   43 (43)
Q Consensus        24 afypsavvwefgriltatcq   43 (43)
                      -||-++.||=||..+.++|+
T Consensus        86 r~~~~~~vF~~GN~~e~~L~  105 (144)
T TIGR02174        86 RFYACMMVFFFGNMLESQLS  105 (144)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999999999998741


No 6  
>PRK13592 ubiA prenyltransferase; Provisional
Probab=11.38  E-value=1.3e+02  Score=14.45  Aligned_cols=20  Identities=35%  Similarity=0.787  Sum_probs=14.2

Q ss_pred             HHHHHCCHHHHHHHHHHHHH
Q ss_conf             99998113789744323331
Q gi|254780667|r   21 LVFAFYPSAVVWEFGRILTA   40 (43)
Q Consensus        21 lvfafypsavvwefgrilta   40 (43)
                      +.+..|-++.+||+||-..|
T Consensus       180 ~~~t~yf~gli~EI~RKira  199 (299)
T PRK13592        180 LAFTMYFPSLIWEVCRKIRA  199 (299)
T ss_pred             HHHHHHCCHHHHHHHHHCCC
T ss_conf             99999705444987622279


No 7  
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).  During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=11.34  E-value=1.2e+02  Score=14.56  Aligned_cols=18  Identities=50%  Similarity=0.573  Sum_probs=15.1

Q ss_pred             CCCCCHHHHHHHHHHHHH
Q ss_conf             110220225899999999
Q gi|254780667|r    6 LHADDIEFRFTAVQRLVF   23 (43)
Q Consensus         6 lhaddiefrftavqrlvf   23 (43)
                      ||-|||.--..-+||||-
T Consensus       894 LHf~Di~kLL~VlqrLv~  911 (956)
T TIGR00630       894 LHFDDIKKLLEVLQRLVD  911 (956)
T ss_pred             CHHHHHHHHHHHHHHHHH
T ss_conf             418999999999999985


No 8  
>PRK02487 hypothetical protein; Provisional
Probab=8.75  E-value=1.6e+02  Score=13.90  Aligned_cols=33  Identities=24%  Similarity=0.516  Sum_probs=24.7

Q ss_pred             CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
Q ss_conf             022022589999999998113789744323331
Q gi|254780667|r    8 ADDIEFRFTAVQRLVFAFYPSAVVWEFGRILTA   40 (43)
Q Consensus         8 addiefrftavqrlvfafypsavvwefgrilta   40 (43)
                      ++|++------+.|+|..+-....|+.|.++..
T Consensus         5 ~~~l~~l~~qE~~l~f~~F~~~~A~~LG~~l~~   37 (163)
T PRK02487          5 AQDLAQIIAQEQALQFPHFDNDDAWQLGEIIVE   37 (163)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             889999999999745788998899999999999


No 9  
>COG3124 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=7.36  E-value=2.4e+02  Score=13.05  Aligned_cols=23  Identities=22%  Similarity=0.535  Sum_probs=18.6

Q ss_pred             CCCHHHHHHHHHHHHHHHCCHHH
Q ss_conf             02202258999999999811378
Q gi|254780667|r    8 ADDIEFRFTAVQRLVFAFYPSAV   30 (43)
Q Consensus         8 addiefrftavqrlvfafypsav   30 (43)
                      ..|+|-++++.+.+..+|||.-.
T Consensus       163 w~~l~~~Y~~Lea~F~~fYP~mm  185 (193)
T COG3124         163 WYDLDAHYDALEARFWQFYPRMM  185 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98999887899999999859999


No 10 
>TIGR02247 HAD-1A3-hyp Epoxide hydrolase N-terminal domain-like phosphatase; InterPro: IPR011945    This entry represents a small clade of sequences from the metazoa and bacteria. In eukaryotes, this domain exists as an N-terminal fusion to the soluble epoxide hydrolase enzyme and has recently been shown to be an active phosphatase, although the nature of the biological substrate is unclear . These appear to be members of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases by general homology and the conservation of all of the recognized catalytic motifs  (although the first motif is unusual in the replacement of the more common aspartate with glycine). The variable domain is found in between motifs 1 and 2, indicating membership in subfamily I and phylogeny and prediction of the alpha helical nature of the variable domain indicate membership in subfamily IA..
Probab=7.12  E-value=51  Score=16.40  Aligned_cols=11  Identities=45%  Similarity=1.017  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHH
Q ss_conf             78974432333
Q gi|254780667|r   29 AVVWEFGRILT   39 (43)
Q Consensus        29 avvwefgrilt   39 (43)
                      ||+|.||-+|+
T Consensus         4 AVifD~GGVl~   14 (228)
T TIGR02247         4 AVIFDFGGVLL   14 (228)
T ss_pred             EEEEECCCEEC
T ss_conf             89984386564


Done!