Query         gi|254780990|ref|YP_003065403.1| hypothetical protein CLIBASIA_04455 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 66
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 02:40:11 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780990.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK06813 homoserine dehydrogen  49.2      24 0.00061   18.1   3.6   63    4-66    241-307 (341)
  2 KOG2130 consensus               36.1      16 0.00042   18.9   1.1   21    6-26    157-177 (407)
  3 pfam07991 IlvN Acetohydroxy ac  33.1      50  0.0013   16.4   3.2   41    1-42     65-105 (165)
  4 PRK06270 homoserine dehydrogen  22.6      82  0.0021   15.4   3.1   62    4-66    244-306 (342)
  5 TIGR01437 selA_rel pyridoxal p  17.6      55  0.0014   16.2   0.9   22   13-34    195-216 (391)
  6 KOG3175 consensus               16.4     9.7 0.00025   20.1  -3.2   51   12-62     64-114 (366)
  7 pfam08304 consensus             12.8      80   0.002   15.4   0.7   23    9-31    180-202 (378)
  8 TIGR01501 MthylAspMutase methy  12.5 1.2E+02   0.003   14.6   1.5   26   23-50     51-76  (134)
  9 TIGR02974 phageshock_pspF psp   11.6      53  0.0013   16.3  -0.5   20   28-47     43-62  (349)
 10 pfam08411 Exonuc_X-T_C Exonucl  11.0 1.4E+02  0.0036   14.1   1.5   33   22-54     13-45  (268)

No 1  
>PRK06813 homoserine dehydrogenase; Validated
Probab=49.20  E-value=24  Score=18.10  Aligned_cols=63  Identities=14%  Similarity=0.300  Sum_probs=48.4

Q ss_pred             CCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCEEE----EEEEEHHHHHCCCCCCCCCCCCEEEEEC
Q ss_conf             45643456777554541389521898650222134----5441052210076520002463465429
Q gi|254780990|r    4 VPDDGIDDLFEEDLFQYDANKSELVLISSLWSIDF----FEINCALLRRRHPINKYEKTDNFFALYT   66 (66)
Q Consensus         4 vpddgiddlfeedlfqydankselvlisslwsidf----feincallrrrhpinkyektdnffalyt   66 (66)
                      |+-.||+.+..+|+-+-.+....+-|+.+..-.+-    ..+.-.++.+-||+..-+-++|.+.++|
T Consensus       241 v~~~GI~~i~~~di~~A~~~g~~iklva~~~~~~~g~~~~~V~p~~v~~~~pla~v~g~~N~v~i~t  307 (341)
T PRK06813        241 IHIKGIEHVTKQQIRNAKEQNKIIKLIASAYKDNEGNVNLNVEPYKIEKNHPLANVNGTEKGITFFT  307 (341)
T ss_pred             CCCCCHHHHCHHHHHHHHHCCCEEEEEEEEEECCCCEEEEEEEEEEECCCCCCEECCCCCEEEEEEE
T ss_conf             0116722309999999997799699999999726974999999999589995520579847999971


No 2  
>KOG2130 consensus
Probab=36.13  E-value=16  Score=18.94  Aligned_cols=21  Identities=33%  Similarity=0.640  Sum_probs=16.2

Q ss_pred             CCCHHHHHHHHHHHHCCCCCE
Q ss_conf             643456777554541389521
Q gi|254780990|r    6 DDGIDDLFEEDLFQYDANKSE   26 (66)
Q Consensus         6 ddgiddlfeedlfqydankse   26 (66)
                      |-.+-.+|++|||||-.+++.
T Consensus       157 dY~VPk~F~dDlF~y~g~e~R  177 (407)
T KOG2130         157 DYSVPKYFRDDLFQYLGEERR  177 (407)
T ss_pred             HCCCCHHHHHHHHHHCCCCCC
T ss_conf             047533456779986074669


No 3  
>pfam07991 IlvN Acetohydroxy acid isomeroreductase, catalytic domain. Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine.
Probab=33.10  E-value=50  Score=16.44  Aligned_cols=41  Identities=22%  Similarity=0.413  Sum_probs=31.2

Q ss_pred             CEECCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEEE
Q ss_conf             933456434567775545413895218986502221345441
Q gi|254780990|r    1 MFLVPDDGIDDLFEEDLFQYDANKSELVLISSLWSIDFFEIN   42 (66)
Q Consensus         1 mflvpddgiddlfeedlfqydankselvlisslwsidffein   42 (66)
                      |+|+||...-++++++...+-...+-| ..+.=.+|.|-.|.
T Consensus        65 m~L~PD~~q~~iy~~~I~p~lk~G~~L-~FaHGFnI~y~~I~  105 (165)
T pfam07991        65 MILLPDEVQAEVYEKEIAPNLKEGAAL-AFAHGFNIHFGQIK  105 (165)
T ss_pred             EEECCCHHHHHHHHHHHHHHCCCCCEE-EECCCCEEEECCEE
T ss_conf             983797778999999898657899779-97157577741076


No 4  
>PRK06270 homoserine dehydrogenase; Provisional
Probab=22.55  E-value=82  Score=15.38  Aligned_cols=62  Identities=21%  Similarity=0.174  Sum_probs=44.0

Q ss_pred             CCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCE-EEEEEEEHHHHHCCCCCCCCCCCCEEEEEC
Q ss_conf             456434567775545413895218986502221-345441052210076520002463465429
Q gi|254780990|r    4 VPDDGIDDLFEEDLFQYDANKSELVLISSLWSI-DFFEINCALLRRRHPINKYEKTDNFFALYT   66 (66)
Q Consensus         4 vpddgiddlfeedlfqydankselvlisslwsi-dffeincallrrrhpinkyektdnffalyt   66 (66)
                      |+-.||+++..+|+-+-.....-+-+|.+.-.- .-.++.-.++...||+. -.-++|.+.++|
T Consensus       244 v~~~gI~~i~~~di~~A~~~G~~iklva~~~~~~~~~~V~p~~v~~~~pla-v~g~~N~i~i~t  306 (342)
T PRK06270        244 VEVTGITRITPEAIRLAAKEGYRIKLIGEVSREADKLSVSPRLVPIGHPLA-VSGTLNAATFET  306 (342)
T ss_pred             CCCCCCCCCCHHHHHHHHHCCCEEEEEEEEECCCCEEEEEEEEECCCCCEE-ECCCCEEEEEEE
T ss_conf             034785659999999999879969999999978988999989988999324-789857999984


No 5  
>TIGR01437 selA_rel pyridoxal phosphate-dependent enzyme, putative; InterPro: IPR006337    Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .   PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic .   This entry represents a group of proteins that are related to a number of pyridoxal phosphate-dependent enzymes, and in particular to selenocysteine synthase (SelA), which converts Ser to selenocysteine on its tRNA. While resembling SelA, this protein is found only in species that have a better candidate SelA or else lack the other genes (selB, selC, and selD) required for selenocysteine incorporation. .
Probab=17.56  E-value=55  Score=16.24  Aligned_cols=22  Identities=36%  Similarity=0.374  Sum_probs=18.8

Q ss_pred             HHHHHHHHCCCCCEEEEEEECC
Q ss_conf             7755454138952189865022
Q gi|254780990|r   13 FEEDLFQYDANKSELVLISSLW   34 (66)
Q Consensus        13 feedlfqydankselvlisslw   34 (66)
                      -||||+.|-+.-+.||+-|.--
T Consensus       195 P~edL~~y~~~GaDlViYSGaK  216 (391)
T TIGR01437       195 PEEDLTRYLKAGADLVIYSGAK  216 (391)
T ss_pred             CHHHHHHHHHHCCCEEEECCHH
T ss_conf             8014689997168755532034


No 6  
>KOG3175 consensus
Probab=16.44  E-value=9.7  Score=20.08  Aligned_cols=51  Identities=22%  Similarity=0.167  Sum_probs=37.4

Q ss_pred             HHHHHHHHHCCCCCEEEEEEECCCEEEEEEEEHHHHHCCCCCCCCCCCCEE
Q ss_conf             777554541389521898650222134544105221007652000246346
Q gi|254780990|r   12 LFEEDLFQYDANKSELVLISSLWSIDFFEINCALLRRRHPINKYEKTDNFF   62 (66)
Q Consensus        12 lfeedlfqydankselvlisslwsidffeincallrrrhpinkyektdnff   62 (66)
                      --.+|.|||+.-|+.+.-|-.+|.+--|-+.--+----||-..|+++|.|.
T Consensus        64 ~pn~d~~~y~~~k~~~~~~~~~~n~~~~t~~~~~e~li~p~~nv~~~dk~~  114 (366)
T KOG3175          64 NPNVDYIPYDEMKERILKIVTGFNGIPFTIQRLCELLIDPRRNVTGTDKFL  114 (366)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHH
T ss_conf             998772127889876622424303788899998787427222657214666


No 7  
>pfam08304 consensus
Probab=12.82  E-value=80  Score=15.42  Aligned_cols=23  Identities=39%  Similarity=0.622  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             45677755454138952189865
Q gi|254780990|r    9 IDDLFEEDLFQYDANKSELVLIS   31 (66)
Q Consensus         9 iddlfeedlfqydankselvlis   31 (66)
                      -||-|||....|+..++-|-|-.
T Consensus       180 CDD~FEEHVL~Y~~~~aGLyLHG  202 (378)
T pfam08304       180 CDDSFEEHILPYPKDKAGLYLHG  202 (378)
T ss_pred             CCCCHHHHHCCCCHHHCCEEEEC
T ss_conf             07517765347890104234301


No 8  
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit; InterPro: IPR006394   These sequences represent the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation. ; GO: 0016866 intramolecular transferase activity, 0019670 anaerobic glutamate catabolic process.
Probab=12.54  E-value=1.2e+02  Score=14.59  Aligned_cols=26  Identities=38%  Similarity=0.621  Sum_probs=20.7

Q ss_pred             CCCEEEEEEECCCEEEEEEEEHHHHHCC
Q ss_conf             9521898650222134544105221007
Q gi|254780990|r   23 NKSELVLISSLWSIDFFEINCALLRRRH   50 (66)
Q Consensus        23 nkselvlisslwsidffeincallrrrh   50 (66)
                      .+..-+|+|||+--  =+|.|+=||.|-
T Consensus        51 t~ADAilvSSlYGh--g~~DC~Glr~~c   76 (134)
T TIGR01501        51 TDADAILVSSLYGH--GEIDCAGLRDKC   76 (134)
T ss_pred             CCCCEEEEECCCCC--CCCCHHHHHHHH
T ss_conf             89988998302078--000124578999


No 9  
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF; InterPro: IPR014317   Members of this protein are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, found in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol and filamentous phage infection..
Probab=11.63  E-value=53  Score=16.35  Aligned_cols=20  Identities=30%  Similarity=0.652  Sum_probs=16.8

Q ss_pred             EEEEECCCEEEEEEEEHHHH
Q ss_conf             98650222134544105221
Q gi|254780990|r   28 VLISSLWSIDFFEINCALLR   47 (66)
Q Consensus        28 vlisslwsidffeincallr   47 (66)
                      -..|+=|.-.|...|||-|-
T Consensus        43 HyLS~RW~~Plv~LNCAALs   62 (349)
T TIGR02974        43 HYLSKRWQQPLVKLNCAALS   62 (349)
T ss_pred             HHHHHHHCCCCEEEECCCCC
T ss_conf             33246554886266101278


No 10 
>pfam08411 Exonuc_X-T_C Exonuclease C-terminal. This bacterial domain is found at the C-terminus of Exodeoxyribonuclease I/Exonuclease I (pfam00929), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in E. coli is associated with DNA deoxyribophosphodiesterase (dRPase).
Probab=11.00  E-value=1.4e+02  Score=14.14  Aligned_cols=33  Identities=24%  Similarity=0.236  Sum_probs=0.0

Q ss_pred             CCCCEEEEEEECCCEEEEEEEEHHHHHCCCCCC
Q ss_conf             895218986502221345441052210076520
Q gi|254780990|r   22 ANKSELVLISSLWSIDFFEINCALLRRRHPINK   54 (66)
Q Consensus        22 ankselvlisslwsidffeincallrrrhpink   54 (66)
                      .+..-+|.||+..+-...-+.+.+---.||.||
T Consensus        13 ~~~~P~vhvSg~~~a~~~~~s~v~Pla~HP~N~   45 (268)
T pfam08411        13 VAMKPLVHVSGMFGAERGCTSWVLPLAWHPTNK   45 (268)
T ss_pred             CCCCCEEEECCCCCCCCCCEEEEEECCCCCCCC
T ss_conf             789966987686641148837887513589998


Done!