Query         gi|255764479|ref|YP_003084342.1| hypothetical protein CLIBASIA_03362 [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 18:20:38 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764479.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR02037 degP_htrA_DO proteas  44.9      13 0.00033   19.6   1.7   21   21-41     87-111 (484)
  2 KOG2494 consensus               33.1      27 0.00068   17.9   1.7   22    4-25     60-86  (331)
  3 cd01989 STK_N The N-terminal d  28.5      18 0.00045   18.9   0.2   11    1-11    131-141 (146)
  4 TIGR02038 protease_degS peripl  26.3      19 0.00049   18.7   0.0   18   24-41     84-102 (358)
  5 cd01805 RAD23_N RAD23 belongs   21.1      48  0.0012   16.6   1.2   15    6-20     59-73  (77)
  6 PRK05766 rps14P 30S ribosomal   17.7      60  0.0015   16.0   1.1   16   15-30     14-29  (52)
  7 PRK10942 serine endoprotease;   17.6      35 0.00089   17.3  -0.1   20   22-41    112-133 (474)
  8 TIGR00365 TIGR00365 glutaredox  17.4      52  0.0013   16.4   0.8   11    1-11     18-30  (103)
  9 PRK10139 serine endoprotease;   16.0      38 0.00096   17.1  -0.2   20   22-41     90-111 (455)
 10 KOG1540 consensus               15.7      13 0.00033   19.7  -2.7   14   28-41     68-81  (296)

No 1  
>TIGR02037 degP_htrA_DO protease Do; InterPro: IPR011782   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family consists serine peptidases belonging to MEROPS peptidase family S1, subfamily S1C (protease Do, clan PA(S)). They are variously designated DegP, DegQ, heat shock protein HtrA, MucD and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in Escherichia coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens . The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures .; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis.
Probab=44.88  E-value=13  Score=19.63  Aligned_cols=21  Identities=38%  Similarity=0.597  Sum_probs=16.5

Q ss_pred             ECCCCCEEEEE--E--EECCCCEEE
Q ss_conf             22446638876--5--521146378
Q gi|255764479|r   21 CSRQSGVIVAK--R--FDIMNNHVI   41 (43)
Q Consensus        21 csrqsgvivak--r--fdimnnhvi   41 (43)
                      -+.-|||||-+  -  +=+-|||||
T Consensus        87 ~~LGSGvIi~~d~Gk~YilTNnHVv  111 (484)
T TIGR02037        87 RGLGSGVIISADKGKFYILTNNHVV  111 (484)
T ss_pred             EECCCCEEEECCCCEEEEEECCEEE
T ss_conf             6414418984789869998754363


No 2  
>KOG2494 consensus
Probab=33.05  E-value=27  Score=17.95  Aligned_cols=22  Identities=45%  Similarity=1.124  Sum_probs=19.0

Q ss_pred             CCCCCCCCCCCEEEEE-----EECCCC
Q ss_conf             8886655455146557-----522446
Q gi|255764479|r    4 APPSCGVTEGHFINCM-----RCSRQS   25 (43)
Q Consensus         4 appscgvteghfincm-----rcsrqs   25 (43)
                      -|.+|+|..|.||-|.     ||||..
T Consensus        60 P~~~~~V~~g~v~aC~Ds~kgrCsR~n   86 (331)
T KOG2494          60 PPKNCQVSNGRVIACFDSQKGRCSREN   86 (331)
T ss_pred             CCCCCCCCCCEEEEEECCCCCCCCCCC
T ss_conf             998887457807987500147667435


No 3  
>cd01989 STK_N The N-terminal domain of Eukaryotic Serine Threonine  kinases. The Serine Threonine  kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The N-terminal domain is homologous to the USP family which has a ATP binding fold. The N-terminal domain  is predicted to be involved in ATP binding.
Probab=28.53  E-value=18  Score=18.91  Aligned_cols=11  Identities=45%  Similarity=0.767  Sum_probs=7.2

Q ss_pred             CCCCCCCCCCC
Q ss_conf             98788866554
Q gi|255764479|r    1 MKNAPPSCGVT   11 (43)
Q Consensus         1 mknappscgvt   11 (43)
                      +++||++|-|+
T Consensus       131 ~~~ap~~C~V~  141 (146)
T cd01989         131 LKEAPDFCTVY  141 (146)
T ss_pred             HHCCCCCCEEE
T ss_conf             83799998599


No 4  
>TIGR02038 protease_degS periplasmic serine peptidase DegS; InterPro: IPR011783   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family consists of the periplasmic serine protease DegS (HhoB). They belong to MEROPS peptidase family S1, subfamily S1C (protease Do, clan PA(S)). They are a shorter paralogs of protease Do (HtrA, DegP) and DegQ (HhoA). They are found in Escherichia coli and several of the gammaproteobacteria. DegS contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress by detecting misfolded proteins in the periplasm. DegS then cleaves the periplasmic domain of RseA, a transmembrane protein and inhibitor of sigmaE, activating the sigmaE-driven expression of periplasmic proteases/chaperones , , .; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis.
Probab=26.26  E-value=19  Score=18.71  Aligned_cols=18  Identities=50%  Similarity=0.624  Sum_probs=13.3

Q ss_pred             CCCEEEEEEEE-CCCCEEE
Q ss_conf             46638876552-1146378
Q gi|255764479|r   24 QSGVIVAKRFD-IMNNHVI   41 (43)
Q Consensus        24 qsgvivakrfd-imnnhvi   41 (43)
                      -||||+.|+=- |-|.|||
T Consensus        84 GSGVIms~~GYIlTN~Hvi  102 (358)
T TIGR02038        84 GSGVIMSKEGYILTNKHVI  102 (358)
T ss_pred             CCEEEECCCCCEEECHHHH
T ss_conf             6557972887451335754


No 5  
>cd01805 RAD23_N RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=21.06  E-value=48  Score=16.58  Aligned_cols=15  Identities=20%  Similarity=0.319  Sum_probs=12.5

Q ss_pred             CCCCCCCCCEEEEEE
Q ss_conf             866554551465575
Q gi|255764479|r    6 PSCGVTEGHFINCMR   20 (43)
Q Consensus         6 pscgvteghfincmr   20 (43)
                      -+||+.+|.+|.+|-
T Consensus        59 ~~y~I~~~~~i~~vv   73 (77)
T cd01805          59 EEYKIDEKDFVVVMV   73 (77)
T ss_pred             HHCCCCCCCEEEEEE
T ss_conf             992998899999999


No 6  
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=17.67  E-value=60  Score=16.04  Aligned_cols=16  Identities=38%  Similarity=0.804  Sum_probs=12.9

Q ss_pred             EEEEEEECCCCCEEEE
Q ss_conf             4655752244663887
Q gi|255764479|r   15 FINCMRCSRQSGVIVA   30 (43)
Q Consensus        15 fincmrcsrqsgviva   30 (43)
                      .-.|-+|+++.|+|--
T Consensus        14 sr~Cr~Cg~~~glIrK   29 (52)
T PRK05766         14 ARRCRRCGRKGGLIRK   29 (52)
T ss_pred             CCEEEECCCCCCEEEE
T ss_conf             7812526997667887


No 7  
>PRK10942 serine endoprotease; Provisional
Probab=17.61  E-value=35  Score=17.30  Aligned_cols=20  Identities=40%  Similarity=0.687  Sum_probs=15.5

Q ss_pred             CCCCCEEEE-E-EEECCCCEEE
Q ss_conf             244663887-6-5521146378
Q gi|255764479|r   22 SRQSGVIVA-K-RFDIMNNHVI   41 (43)
Q Consensus        22 srqsgviva-k-rfdimnnhvi   41 (43)
                      |--||+|+. . -+=+-|||||
T Consensus       112 ~lGSG~ii~~d~GyIvTN~HVV  133 (474)
T PRK10942        112 ALGSGVIIDADKGYVVTNNHVV  133 (474)
T ss_pred             CCCCEEEEECCCCEEEECHHHH
T ss_conf             6767799979988898076884


No 8  
>TIGR00365 TIGR00365 glutaredoxin homolog; InterPro: IPR004480   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This family groups a number of hypothetical proteins from different organisms which are related to glutaredoxin proteins..
Probab=17.42  E-value=52  Score=16.38  Aligned_cols=11  Identities=55%  Similarity=1.331  Sum_probs=7.1

Q ss_pred             CCCCC--CCCCCC
Q ss_conf             98788--866554
Q gi|255764479|r    1 MKNAP--PSCGVT   11 (43)
Q Consensus         1 mknap--pscgvt   11 (43)
                      ||-.|  |+||-.
T Consensus        18 MKGsP~~P~CGFS   30 (103)
T TIGR00365        18 MKGSPKLPKCGFS   30 (103)
T ss_pred             ECCCCCCCCCCCH
T ss_conf             3688998899881


No 9  
>PRK10139 serine endoprotease; Provisional
Probab=15.96  E-value=38  Score=17.13  Aligned_cols=20  Identities=55%  Similarity=0.775  Sum_probs=15.2

Q ss_pred             CCCCCEEE-E-EEEECCCCEEE
Q ss_conf             24466388-7-65521146378
Q gi|255764479|r   22 SRQSGVIV-A-KRFDIMNNHVI   41 (43)
Q Consensus        22 srqsgviv-a-krfdimnnhvi   41 (43)
                      +--||+|+ . .-+=+-|||||
T Consensus        90 ~~GSG~iids~dG~IvTN~HVV  111 (455)
T PRK10139         90 GLGSGVIIDAAKGYVLTNNHVI  111 (455)
T ss_pred             CCCCEEEEECCCCEEECCHHHH
T ss_conf             5767799989998898287994


No 10 
>KOG1540 consensus
Probab=15.69  E-value=13  Score=19.66  Aligned_cols=14  Identities=50%  Similarity=0.786  Sum_probs=11.1

Q ss_pred             EEEEEEECCCCEEE
Q ss_conf             88765521146378
Q gi|255764479|r   28 IVAKRFDIMNNHVI   41 (43)
Q Consensus        28 ivakrfdimnnhvi   41 (43)
                      -||+++||||.+++
T Consensus        68 ~vA~~YD~mND~mS   81 (296)
T KOG1540          68 SVAKKYDIMNDAMS   81 (296)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             88888877888762


Done!