Query gi|254780692|ref|YP_003065105.1| hypothetical protein CLIBASIA_02895 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 72 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Sun May 29 20:01:25 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780692.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG4591 LolE ABC-type transpor 55.9 10 0.00025 19.2 2.5 21 6-26 36-56 (408) 2 TIGR00263 trpB tryptophan synt 46.1 5.6 0.00014 20.5 -0.0 43 24-66 136-180 (412) 3 pfam06388 DUF1075 Protein of u 41.5 32 0.00083 16.5 3.4 39 7-45 100-140 (146) 4 KOG1469 consensus 35.4 22 0.00055 17.4 1.6 43 23-65 282-324 (392) 5 pfam04111 APG6 Autophagy prote 23.0 52 0.0013 15.5 1.7 18 47-64 326-343 (356) 6 TIGR02002 PTS-II-BC-glcB PTS s 16.7 93 0.0024 14.2 1.9 19 3-21 147-165 (518) 7 pfam12297 EVC2_like Ellis van 15.9 1E+02 0.0026 14.0 2.2 22 2-23 73-94 (429) 8 COG4220 Phage DNA packaging pr 13.7 1.2E+02 0.003 13.6 2.2 29 24-52 67-95 (174) 9 COG1398 OLE1 Fatty-acid desatu 13.5 1.2E+02 0.0031 13.6 2.2 20 3-22 167-186 (289) 10 COG5438 Predicted multitransme 11.7 1.4E+02 0.0035 13.3 2.3 21 3-23 183-203 (385) No 1 >COG4591 LolE ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane] Probab=55.93 E-value=10 Score=19.19 Aligned_cols=21 Identities=43% Similarity=0.779 Sum_probs=17.3 Q ss_pred HHHHHHHHHHHHCCHHHHHHH Q ss_conf 899999999983132567877 Q gi|254780692|r 6 GIIFTIICLYMMNGYQKEKKD 26 (72) Q Consensus 6 giiftiiclymmngyqkekkd 26 (72) |+..-|+-+.+|||.|+|-.+ T Consensus 36 gV~~LIv~lsvmnGf~~el~~ 56 (408) T COG4591 36 GVAVLIVVLSVMNGFQKELEN 56 (408) T ss_pred HHHHHHHHHHHHHHHHHHHHH T ss_conf 899999999988567999984 No 2 >TIGR00263 trpB tryptophan synthase, beta subunit; InterPro: IPR006654 Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan , :L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H_2O It has two functional domains, each found in bacteria and plants on a separate subunit: alpha chain (IPR002028 from INTERPRO) is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and beta chain is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together on a single multifunctional protein . The beta chain of the enzyme, represented here, requires pyridoxal-phosphate as a cofactor. The pyridoxal-phosphate group is attached to a lysine residue. The region around this lysine residue also contains two histidine residues which are part of the pyridoxal-phosphate binding site.; GO: 0004834 tryptophan synthase activity, 0006568 tryptophan metabolic process. Probab=46.08 E-value=5.6 Score=20.47 Aligned_cols=43 Identities=21% Similarity=0.339 Sum_probs=25.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH--HCCHHHHHHHHHHHHHHHHCC Q ss_conf 8778887733688773389873--032455669999998751028 Q gi|254780692|r 24 KKDIERTRLNIERTRLTCEEAR--HTQDENLTKACKDELKNIKSN 66 (72) Q Consensus 24 kkdiertrlniertrltceear--htqdenltkackdelkniksn 66 (72) .+|+||-+||+.|-||---+-- +.-...|-.||.+-|..--|| T Consensus 136 a~DV~RQ~pNVFRMellGA~V~pV~sGs~TLKDA~N~AlrDWv~~ 180 (412) T TIGR00263 136 AEDVERQKPNVFRMELLGAKVVPVTSGSGTLKDAVNEALRDWVTS 180 (412) T ss_pred CCCHHHCCCCHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHCC T ss_conf 613514577523451377868330157870378999999874136 No 3 >pfam06388 DUF1075 Protein of unknown function (DUF1075). This family consists of several eukaryotic proteins of unknown function. Probab=41.47 E-value=32 Score=16.54 Aligned_cols=39 Identities=28% Similarity=0.502 Sum_probs=25.8 Q ss_pred HHHHHH-HHHHH-CCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999-99983-1325678778887733688773389873 Q gi|254780692|r 7 IIFTII-CLYMM-NGYQKEKKDIERTRLNIERTRLTCEEAR 45 (72) Q Consensus 7 iiftii-clymm-ngyqkekkdiertrlniertrltceear 45 (72) |.+||| |++|+ .|-|--|..---|.+|+|+-.---|||. T Consensus 100 i~lT~igC~~mvi~GKkA~kr~es~t~~Nlekka~~reeaa 140 (146) T pfam06388 100 IALTVVGCIIMVISGKKAAERHESLTSMNLEKKAKWNEEAA 140 (146) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf 99999999999998336664445287753899987717876 No 4 >KOG1469 consensus Probab=35.44 E-value=22 Score=17.45 Aligned_cols=43 Identities=35% Similarity=0.433 Sum_probs=37.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHC Q ss_conf 7877888773368877338987303245566999999875102 Q gi|254780692|r 23 EKKDIERTRLNIERTRLTCEEARHTQDENLTKACKDELKNIKS 65 (72) Q Consensus 23 ekkdiertrlniertrltceearhtqdenltkackdelkniks 65 (72) -.+||...|..||.+||-.-+|-|.-|.--.|+.|.|+.-||- T Consensus 282 ~~~diA~sRveiEqaRLLvLkAAh~mD~~G~k~Ak~~iAMiKv 324 (392) T KOG1469 282 VAHDIAESRVEIEQARLLVLKAAHSMDTLGNKGAKKEIAMIKV 324 (392) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHEEEEEE T ss_conf 9999998776766524434236666652064234212002331 No 5 >pfam04111 APG6 Autophagy protein Apg6. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway. Probab=23.00 E-value=52 Score=15.50 Aligned_cols=18 Identities=50% Similarity=0.486 Sum_probs=12.8 Q ss_pred CCHHHHHHHHHHHHHHHH Q ss_conf 324556699999987510 Q gi|254780692|r 47 TQDENLTKACKDELKNIK 64 (72) Q Consensus 47 tqdenltkackdelknik 64 (72) .+||+-|+|||--|-|.| T Consensus 326 N~de~WTkAlK~mLtnlK 343 (356) T pfam04111 326 NSDEQWTKALKFMLTNLK 343 (356) T ss_pred CCCCHHHHHHHHHHHHHH T ss_conf 775379999999999899 No 6 >TIGR02002 PTS-II-BC-glcB PTS system, glucose-specific IIBC component; InterPro: IPR011299 This entry represents the combined B and C domains of the PTS transport system enzyme II specific for glucose transport . Many of the genes in this family also include an A domain as part of the same polypeptide and thus should be given the name 'PTS system, glucose-specific IIABC component' while the Bacillus subtilus enzyme also contains an enzyme III domain which appears to act independently of the enzyme II domains . This group is most closely related to the N-acetylglucosamine-specific PTS enzymes (IPR010974 from INTERPRO).; GO: 0005355 glucose transmembrane transporter activity, 0015758 glucose transport, 0016021 integral to membrane. Probab=16.68 E-value=93 Score=14.17 Aligned_cols=19 Identities=32% Similarity=0.646 Sum_probs=16.1 Q ss_pred HHHHHHHHHHHHHHHCCHH Q ss_conf 5778999999999831325 Q gi|254780692|r 3 FLGGIIFTIICLYMMNGYQ 21 (72) Q Consensus 3 flggiiftiiclymmngyq 21 (72) -+||||--+|.-||-|-|- T Consensus 147 VFGGII~Ga~AA~cYNrFy 165 (518) T TIGR02002 147 VFGGIIVGAVAAYCYNRFY 165 (518) T ss_pred CCHHHHHHHHHHHHHCCCC T ss_conf 5037999999999837532 No 7 >pfam12297 EVC2_like Ellis van Creveld protein 2 like protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 571 and 1310 amino acids in length. There are two conserved sequence motifs: LPA and ELH. EVC2 is implicated in Ellis van Creveld chondrodysplastic dwarfism in humans. Mutations in this protein can give rise to this congenital condition. LIMBIN is a protein which shares around 80% sequence homology with EVC2 and it is implicated in a similar condition in bovine chondrodysplastic dwarfism. Probab=15.94 E-value=1e+02 Score=13.96 Aligned_cols=22 Identities=18% Similarity=0.484 Sum_probs=16.1 Q ss_pred HHHHHHHHHHHHHHHHCCHHHH Q ss_conf 2577899999999983132567 Q gi|254780692|r 2 EFLGGIIFTIICLYMMNGYQKE 23 (72) Q Consensus 2 eflggiiftiiclymmngyqke 23 (72) -|+.+|+.|..|++.|+-+|-- T Consensus 73 af~vsiVlt~~~~f~l~rt~~~ 94 (429) T pfam12297 73 AFLVSIVLTLLAFFLLGRTRCL 94 (429) T ss_pred HHHHHHHHHHHHHHHHHHHHHC T ss_conf 9999999999999999874110 No 8 >COG4220 Phage DNA packaging protein, Nu1 subunit of terminase [DNA replication, recombination, and repair] Probab=13.75 E-value=1.2e+02 Score=13.63 Aligned_cols=29 Identities=34% Similarity=0.397 Sum_probs=21.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHH Q ss_conf 87788877336887733898730324556 Q gi|254780692|r 24 KKDIERTRLNIERTRLTCEEARHTQDENL 52 (72) Q Consensus 24 kkdiertrlniertrltceearhtqdenl 52 (72) .+|+|--+.-+||+|||-+.|-.++-+|- T Consensus 67 ~~dvee~~~~~er~rLt~aQad~q~Lkna 95 (174) T COG4220 67 RDDVEELREARERHRLTRAQADAQELKNA 95 (174) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 22189999999999988998778999879 No 9 >COG1398 OLE1 Fatty-acid desaturase [Lipid metabolism] Probab=13.52 E-value=1.2e+02 Score=13.60 Aligned_cols=20 Identities=20% Similarity=0.456 Sum_probs=16.7 Q ss_pred HHHHHHHHHHHHHHHCCHHH Q ss_conf 57789999999998313256 Q gi|254780692|r 3 FLGGIIFTIICLYMMNGYQK 22 (72) Q Consensus 3 flggiiftiiclymmngyqk 22 (72) .+++|++..+|+|.++||-. T Consensus 167 ~l~~i~~~l~~~~~~gg~~g 186 (289) T COG1398 167 LLMQIVLPLFIGYALGGWLG 186 (289) T ss_pred HHHHHHHHHHHHHHHCCHHH T ss_conf 99988899999999633577 No 10 >COG5438 Predicted multitransmembrane protein [Function unknown] Probab=11.71 E-value=1.4e+02 Score=13.30 Aligned_cols=21 Identities=38% Similarity=0.643 Sum_probs=17.0 Q ss_pred HHHHHHHHHHHHHHHCCHHHH Q ss_conf 577899999999983132567 Q gi|254780692|r 3 FLGGIIFTIICLYMMNGYQKE 23 (72) Q Consensus 3 flggiiftiiclymmngyqke 23 (72) +...++++++-|+|.+|+.+. T Consensus 183 ii~~viit~~tL~~v~g~n~K 203 (385) T COG5438 183 IILCVIITAITLFMVNGINKK 203 (385) T ss_pred HHHHHHHHHHHHHHHCCCCHH T ss_conf 999999999999861585299 Done!