Query         gi|254780389|ref|YP_003064802.1| hypothetical protein CLIBASIA_01370 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 45
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 15:31:06 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780389.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam08854 DUF1824 Domain of un  54.6     8.4 0.00022   20.8   2.0   25   13-37     77-107 (125)
  2 KOG0905 consensus               17.1      32 0.00082   17.8  -0.4   25   20-44   1173-1197(1639)
  3 KOG0064 consensus               14.3      48  0.0012   17.0  -0.1   15    6-20    680-694 (728)
  4 TIGR00042 TIGR00042 non-canoni  14.1      94  0.0024   15.5   1.4   28    3-31     66-94  (205)
  5 KOG2666 consensus               14.0      74  0.0019   16.0   0.8   10    1-10    438-448 (481)
  6 cd06636 STKc_MAP4K4_6 Serine/t  11.6 1.2E+02  0.0031   14.9   1.3   26    6-31     11-36  (282)
  7 cd05173 PI3Kc_IA_beta Phosphoi  11.5      13 0.00033   19.9  -3.7   27   18-44    183-209 (362)
  8 pfam04478 Mid2 Mid2 like cell   10.8 1.1E+02  0.0029   15.0   1.0   19   19-37     39-57  (155)
  9 TIGR01179 galE UDP-glucose 4-e  10.2      35  0.0009   17.6  -1.8   21   25-45     97-124 (341)
 10 cd06637 STKc_TNIK Serine/threo  10.2 1.5E+02  0.0038   14.5   1.4   27    7-33      2-28  (272)

No 1  
>pfam08854 DUF1824 Domain of unknown function (DUF1824). This uncharacterized family of proteins are principally found in cyanobacteria.
Probab=54.58  E-value=8.4  Score=20.82  Aligned_cols=25  Identities=36%  Similarity=0.523  Sum_probs=20.4

Q ss_pred             EEEEEEECCCC------HHHHHHEEEEEEEE
Q ss_conf             78999818875------22441111223212
Q gi|254780389|r   13 IRFLKFNGEGG------YSKYYRNFIISCRT   37 (45)
Q Consensus        13 irflkfngegg------yskyyrnfiiscrt   37 (45)
                      --|||+|...|      |.--+|...|||..
T Consensus        77 pVfLK~Nqktg~~~ir~e~Glg~GvLiscq~  107 (125)
T pfam08854        77 PVFLKANQKTGSIYIRIETGLGRGVLISCQS  107 (125)
T ss_pred             CEEEEECCCCCCEEEECCCCCCEEEEEEEEC
T ss_conf             7699841777868996258852169998546


No 2  
>KOG0905 consensus
Probab=17.05  E-value=32  Score=17.85  Aligned_cols=25  Identities=40%  Similarity=0.518  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHEEEEEEEEEEEEEEC
Q ss_conf             8875224411112232124655320
Q gi|254780389|r   20 GEGGYSKYYRNFIISCRTYRVFTAI   44 (45)
Q Consensus        20 geggyskyyrnfiiscrtyrvftai   44 (45)
                      +|-.|.|--||||.||.-+-|-|-+
T Consensus      1173 ~e~eYekA~eNFiySCAG~cVaTYV 1197 (1639)
T KOG0905        1173 SEFEYEKAVENFIYSCAGWCVATYV 1197 (1639)
T ss_pred             CHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             8899999999888743340254575


No 3  
>KOG0064 consensus
Probab=14.33  E-value=48  Score=16.98  Aligned_cols=15  Identities=40%  Similarity=0.654  Sum_probs=7.6

Q ss_pred             EECCCCCEEEEEEEC
Q ss_conf             542668478999818
Q gi|254780389|r    6 IFDGMGNIRFLKFNG   20 (45)
Q Consensus         6 ifdgmgnirflkfng   20 (45)
                      -|||-|+-+|-++|-
T Consensus       680 ~fDg~Ggwqf~~~n~  694 (728)
T KOG0064         680 EFDGEGGWQFRALNT  694 (728)
T ss_pred             HCCCCCCEEEECCCH
T ss_conf             126888703202784


No 4  
>TIGR00042 TIGR00042 non-canonical purine NTP pyrophosphatase, rdgB/HAM1 family; InterPro: IPR002637   This family contains the Saccharomyces cerevisiae HAM1 protein P47119 from SWISSPROT and other hypothetical archaeal, bacterial and Caenorhabditis elegans proteins. Saccharomyces cerevisiae HAM1 protects against the mutagenic effects of the base analog 6-N-hydroxylaminopurine (HAP) which can be a natural product of monooxygenase activity on adenine. HAM1 protein protects the cell from HAP, either on the level of deoxynucleoside triphosphate or the DNA level by a yet unidentified set of reactions .; GO: 0016787 hydrolase activity.
Probab=14.08  E-value=94  Score=15.47  Aligned_cols=28  Identities=32%  Similarity=0.469  Sum_probs=19.0

Q ss_pred             CCEEECCCCCEEEEEEECC-CCHHHHHHEE
Q ss_conf             6435426684789998188-7522441111
Q gi|254780389|r    3 HPFIFDGMGNIRFLKFNGE-GGYSKYYRNF   31 (45)
Q Consensus         3 hpfifdgmgnirflkfnge-ggyskyyrnf   31 (45)
                      .|+|-|--| ..+=.+||. |-||+||.+.
T Consensus        66 ~~vi~eDSG-L~v~aL~G~PG~YSary~~e   94 (205)
T TIGR00042        66 KPVIAEDSG-LFVDALNGAPGIYSARYAGE   94 (205)
T ss_pred             CEEEEECCC-EEEEECCCCCCCEEEEECCC
T ss_conf             809998452-00000279989635000461


No 5  
>KOG2666 consensus
Probab=14.03  E-value=74  Score=16.01  Aligned_cols=10  Identities=70%  Similarity=1.301  Sum_probs=6.5

Q ss_pred             CCCC-EEECCC
Q ss_conf             9864-354266
Q gi|254780389|r    1 MMHP-FIFDGM   10 (45)
Q Consensus         1 mmhp-fifdgm   10 (45)
                      |++| |||||-
T Consensus       438 MqkPAfiFDGR  448 (481)
T KOG2666         438 MQKPAFIFDGR  448 (481)
T ss_pred             CCCCEEEECCH
T ss_conf             03871786544


No 6  
>cd06636 STKc_MAP4K4_6 Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase kinase 4 (MAPKKKK4 or MAP4K4) and MAPKKKK6 (or MAP4K6) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAP4K4/MAP4K6 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. MAP4Ks (or MAPKKKKs) are involved in MAPK signaling pathways that are important in mediating cellular responses to extracellular signals by activating a MAPK kinase kinase (MAPKKK or MAP3K or MKKK). Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal e
Probab=11.58  E-value=1.2e+02  Score=14.90  Aligned_cols=26  Identities=23%  Similarity=0.506  Sum_probs=21.1

Q ss_pred             EECCCCCEEEEEEECCCCHHHHHHEE
Q ss_conf             54266847899981887522441111
Q gi|254780389|r    6 IFDGMGNIRFLKFNGEGGYSKYYRNF   31 (45)
Q Consensus         6 ifdgmgnirflkfngeggyskyyrnf   31 (45)
                      +-|-.|.-++++.-|+|+|++-|+-.
T Consensus        11 ~~~p~~~Y~~~~~IG~G~fg~Vy~a~   36 (282)
T cd06636          11 LRDPAGIFELVEVVGNGTYGQVYKGR   36 (282)
T ss_pred             CCCCCCCEEEEEEEECCCCEEEEEEE
T ss_conf             56998884888898328582999999


No 7  
>cd05173 PI3Kc_IA_beta Phosphoinositide 3-kinase (PI3K), class IA, beta isoform, catalytic domain; The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. They are further classified into class IA (alpha, beta and de
Probab=11.50  E-value=13  Score=19.88  Aligned_cols=27  Identities=26%  Similarity=0.511  Sum_probs=19.2

Q ss_pred             EECCCCHHHHHHEEEEEEEEEEEEEEC
Q ss_conf             818875224411112232124655320
Q gi|254780389|r   18 FNGEGGYSKYYRNFIISCRTYRVFTAI   44 (45)
Q Consensus        18 fngeggyskyyrnfiiscrtyrvftai   44 (45)
                      .|....|.+--+||+-||-.|-|.|-+
T Consensus       183 ~n~~~~~~~A~~nFv~ScAgYcV~TYv  209 (362)
T cd05173         183 YNSGDDLERAIEEFTLSCAGYCVATYV  209 (362)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             098377999999999988889999986


No 8  
>pfam04478 Mid2 Mid2 like cell wall stress sensor. This family represents a region near the C terminus of Mid2, which contains a transmembrane region. The remainder of the protein sequence is serine-rich and of low complexity, and is therefore impossible to align accurately. Mid2 is thought to act as a mechanosensor of cell wall stress. The C-terminal cytoplasmic region of Mid2 is known to interact with Rom2, a guanine nucleotide exchange factor (GEF) for Rho1, which is part of the cell wall integrity signalling pathway.
Probab=10.82  E-value=1.1e+02  Score=15.04  Aligned_cols=19  Identities=37%  Similarity=0.693  Sum_probs=15.5

Q ss_pred             ECCCCHHHHHHEEEEEEEE
Q ss_conf             1887522441111223212
Q gi|254780389|r   19 NGEGGYSKYYRNFIISCRT   37 (45)
Q Consensus        19 ngeggyskyyrnfiiscrt   37 (45)
                      +|.-|.||--||.||.|-.
T Consensus        39 ~g~~GLS~KNrnIvIGCVV   57 (155)
T pfam04478        39 SGHHGLSKKNKNIVIGCVV   57 (155)
T ss_pred             CCCCCCCCCCCCEEEEEEE
T ss_conf             6766656478867999886


No 9  
>TIGR01179 galE UDP-glucose 4-epimerase; InterPro: IPR005886    Synonym: UDP-galactose 4-epimerase UDP-glucose 4-epimerase (5.1.3.2 from EC) interconverts UDP-glucose and UDP-galactose which are precursors of glucose- and galactose-containing exopolysaccharides (EPS). A set of related proteins, some of which are tentatively identified as UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus halodurans, and several archaea, but deeply branched from this set and lacking experimental evidence, are excluded and described by a separate model. ; GO: 0003978 UDP-glucose 4-epimerase activity, 0006012 galactose metabolic process.
Probab=10.21  E-value=35  Score=17.64  Aligned_cols=21  Identities=38%  Similarity=0.554  Sum_probs=14.0

Q ss_pred             HHHHHE-------EEEEEEEEEEEEECC
Q ss_conf             244111-------122321246553209
Q gi|254780389|r   25 SKYYRN-------FIISCRTYRVFTAIF   45 (45)
Q Consensus        25 skyyrn-------fiiscrtyrvftaif   45 (45)
                      -|||+|       .|-+|+.+.|+.-||
T Consensus        97 l~YY~NNv~nTl~L~~~m~~~GV~~~iF  124 (341)
T TIGR01179        97 LKYYRNNVVNTLNLLEAMQETGVKKFIF  124 (341)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCEEE
T ss_conf             5440004689999999999818974153


No 10 
>cd06637 STKc_TNIK Serine/threonine kinases (STKs),Traf2- and Nck-interacting kinase (TNIK) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The TNIK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain, similar to mitogen-activated protein kinase (MAPK), kinase kinase kinase 4 (MAP4K4), and MAP4K6. MAP4Ks participate in some MAPK signaling pathways by activating a MAPK kinase kinase (MAPKKK or MAP3K or MKKK). TNIK is an effector of Rap2, a small GTP-binding protein from the Ras family. TNIK specifically activates the c-Jun N-terminal kinase (JNK) pathway and plays a role in regulating the actin cytos
Probab=10.20  E-value=1.5e+02  Score=14.47  Aligned_cols=27  Identities=22%  Similarity=0.487  Sum_probs=21.9

Q ss_pred             ECCCCCEEEEEEECCCCHHHHHHEEEE
Q ss_conf             426684789998188752244111122
Q gi|254780389|r    7 FDGMGNIRFLKFNGEGGYSKYYRNFII   33 (45)
Q Consensus         7 fdgmgnirflkfngeggyskyyrnfii   33 (45)
                      -|--|+-++++.=|+|++++-|+-.-.
T Consensus         2 ~dp~g~y~~~~~IG~G~fg~Vy~a~~~   28 (272)
T cd06637           2 RDPAGIFELVELVGNGTYGQVYKGRHV   28 (272)
T ss_pred             CCCCCCEEEEEEEECCCCEEEEEEEEC
T ss_conf             599888698779922878299999998


Done!