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!