Query gi|254780931|ref|YP_003065344.1| hypothetical protein CLIBASIA_04150 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 56 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 00:59:18 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780931.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam09556 RE_HaeIII HaeIII res 95.3 0.022 5.6E-07 34.5 3.9 52 2-53 132-183 (300) 2 pfam05061 Pox_A11 Poxvirus A11 42.9 6.4 0.00016 21.0 -0.2 12 1-12 21-32 (309) 3 COG4383 Mu-like prophage prote 24.0 28 0.00071 17.5 0.5 20 19-38 51-70 (517) 4 pfam10957 DUF2758 Protein of u 22.0 24 0.00061 17.8 -0.1 16 24-39 17-32 (60) 5 pfam01736 Polyoma_agno Polyoma 17.1 98 0.0025 14.5 2.1 19 22-49 22-40 (62) 6 TIGR00803 nst UDP-galactose tr 15.4 61 0.0015 15.6 0.7 23 24-46 102-125 (235) 7 PHA02105 hypothetical protein 14.8 99 0.0025 14.4 1.7 18 2-19 21-38 (68) 8 TIGR00004 TIGR00004 endoribonu 13.5 40 0.001 16.6 -0.7 17 19-35 68-84 (129) 9 COG5248 TAF19 Transcription in 13.1 66 0.0017 15.4 0.4 13 23-35 5-17 (126) 10 pfam11387 DUF2795 Protein of u 12.1 95 0.0024 14.5 0.9 11 1-11 4-14 (44) No 1 >pfam09556 RE_HaeIII HaeIII restriction endonuclease. This family includes the HaeIII (recognizes and cleaves GG^CC) restriction endonuclease. Probab=95.33 E-value=0.022 Score=34.52 Aligned_cols=52 Identities=25% Similarity=0.590 Sum_probs=47.9 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH Q ss_conf 8765499999999999754202334245532053228999999999999998 Q gi|254780931|r 2 DYPCNKEYFKTISTVFGKLGDMRAQNIFLKDIKDKDIIFYLHILIAFEKVID 53 (56) Q Consensus 2 dypcnkeyfktistvfgklgdmraqniflkdikdkdiifylhiliafekvid 53 (56) .-||.+.||..|..+|..|...++++....+|.+|+--.|.-+|-||-.-|. T Consensus 132 gipcSq~Ywd~I~PiF~~Le~~k~~g~~w~~i~~KEe~vYvPLL~AFi~El~ 183 (300) T pfam09556 132 GIPSSQNYFDEINPLFEELEELKKEGELWRNISNKEERIYVPLLKAFIREIE 183 (300) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCEEHHHHHHHHHHHHH T ss_conf 8975076787777899999999862860111766320151999999999999 No 2 >pfam05061 Pox_A11 Poxvirus A11 Protein. Family of conserved Chordopoxvirinae A11 family proteins. Conserved region spans entire protein in the majority of family members. Probab=42.91 E-value=6.4 Score=21.00 Aligned_cols=12 Identities=50% Similarity=0.689 Sum_probs=9.5 Q ss_pred CCCCCCHHHHHH Q ss_conf 987654999999 Q gi|254780931|r 1 MDYPCNKEYFKT 12 (56) Q Consensus 1 mdypcnkeyfkt 12 (56) ++|||||.|--| T Consensus 21 d~YP~NKnYEIT 32 (309) T pfam05061 21 DGYPSNKNYEIT 32 (309) T ss_pred CCCCCCCCCEEE T ss_conf 788877772321 No 3 >COG4383 Mu-like prophage protein gp29 [Function unknown] Probab=24.00 E-value=28 Score=17.49 Aligned_cols=20 Identities=45% Similarity=0.743 Sum_probs=17.7 Q ss_pred HHHHHHHHHHHHHHCCCCHH Q ss_conf 54202334245532053228 Q gi|254780931|r 19 KLGDMRAQNIFLKDIKDKDI 38 (56) Q Consensus 19 klgdmraqniflkdikdkdi 38 (56) .-|||+||.-...||..||- T Consensus 51 ErGDl~AQseL~aDiEEkDt 70 (517) T COG4383 51 ERGDLRAQSELFADIEEKDT 70 (517) T ss_pred HCCCHHHHHHHHHHHHHHHH T ss_conf 52355667888755665201 No 4 >pfam10957 DUF2758 Protein of unknown function (DUF2758). This family of proteins has no known function. Probab=22.03 E-value=24 Score=17.85 Aligned_cols=16 Identities=44% Similarity=0.775 Sum_probs=13.2 Q ss_pred HHHHHHHHHCCCCHHH Q ss_conf 3342455320532289 Q gi|254780931|r 24 RAQNIFLKDIKDKDII 39 (56) Q Consensus 24 raqniflkdikdkdii 39 (56) ++-|.|||.|.++++| T Consensus 17 ~~vN~FLk~i~e~~li 32 (60) T pfam10957 17 DEVNVFLKKIDDDQLI 32 (60) T ss_pred HHHHHHHHHCCCCCEE T ss_conf 9999999727804479 No 5 >pfam01736 Polyoma_agno Polyomavirus agnoprotein. This family consist of the DNA binding protein or agnoprotein from various polyomaviruses. This protein is highly basic and can bind single stranded and double stranded DNA. Mutations in the agnoprotein produce smaller viral plaques, hence its function is not essential for growth in tissue culture cells but something has slowed in the normal replication cycle. There is also evidence suggesting that the agnogene and agnoprotein act as regulators of structural protein synthesis. Probab=17.05 E-value=98 Score=14.46 Aligned_cols=19 Identities=53% Similarity=0.840 Sum_probs=14.4 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 0233424553205322899999999999 Q gi|254780931|r 22 DMRAQNIFLKDIKDKDIIFYLHILIAFE 49 (56) Q Consensus 22 dmraqniflkdikdkdiifylhiliafe 49 (56) .-|||.|| ||.|..|..|- T Consensus 22 kkraqrif---------if~lelll~fc 40 (62) T pfam01736 22 KKRAQRIF---------IFVLELLLQFC 40 (62) T ss_pred HHHHHHHH---------HHHHHHHHHHH T ss_conf 57778899---------99999999983 No 6 >TIGR00803 nst UDP-galactose transporter; InterPro: IPR004689 Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as Caenorhabditis elegans possess many of these transporters. Humans have at least two closely related isoforms of the UDP-galactose:UMP exchange transporter. NSTs generally appear to function by antiport mechanisms, exchanging a nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid is exchanged for CMP; GDP-mannose is preferentially exchanged for GMP, and UDP-galactose and UDP-N-acetylglucosamine are exchanged for UMP (or possibly UDP). Other nucleotide sugars (e.g., GDP-fucose, UDP-xylose, UDP-glucose, UDP-N-acetylgalactosamine, etc.) may also be transported in exchange for various nucleotides, but their transporters have not been molecularly characterised. Each compound appears to be translocated by its own transport protein. Transport allows the compound, synthesized in the cytoplasm, to be exported to the lumen of the Golgi apparatus or the endoplasmic reticulum where it is used for the synthesis of glycoproteins and glycolipids. ; GO: 0005338 nucleotide-sugar transmembrane transporter activity, 0015780 nucleotide-sugar transport, 0016021 integral to membrane. Probab=15.43 E-value=61 Score=15.61 Aligned_cols=23 Identities=39% Similarity=0.405 Sum_probs=18.8 Q ss_pred HHHHHHHHHCCCCHHH-HHHHHHH Q ss_conf 3342455320532289-9999999 Q gi|254780931|r 24 RAQNIFLKDIKDKDII-FYLHILI 46 (56) Q Consensus 24 raqniflkdikdkdii-fylhili 46 (56) -+.-+|.|-.||+|.. ||.|++- T Consensus 102 ~~~~Yf~~~lk~~~~~Pfw~~~l~ 125 (235) T TIGR00803 102 FAGVYFEKILKDKDTSPFWVRNLQ 125 (235) T ss_pred HHHHHHHHCCCCCCCCCHHHHHHH T ss_conf 631024331677778614357889 No 7 >PHA02105 hypothetical protein Probab=14.84 E-value=99 Score=14.45 Aligned_cols=18 Identities=39% Similarity=0.779 Sum_probs=15.8 Q ss_pred CCCCCHHHHHHHHHHHHH Q ss_conf 876549999999999975 Q gi|254780931|r 2 DYPCNKEYFKTISTVFGK 19 (56) Q Consensus 2 dypcnkeyfktistvfgk 19 (56) .||.|.|-|....+||.- T Consensus 21 eyp~~~e~~~ql~svfsi 38 (68) T PHA02105 21 EYPVELELFDQLKTVFSI 38 (68) T ss_pred CCCCCHHHHHHHHHHCCC T ss_conf 465207889988876135 No 8 >TIGR00004 TIGR00004 endoribonuclease L-PSP, putative; InterPro: IPR006056 This family includes proteins encoded by the yabJ gene from Bacillus subtilis that is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The structure of this protein has been solved and the protein is found to form a homotrimer. The trimer has a deep cleft that is a probably ligand binding site and possibly forms an enzymatic active site. However the ligand and reaction are unknown.. Probab=13.50 E-value=40 Score=16.63 Aligned_cols=17 Identities=35% Similarity=0.702 Sum_probs=11.9 Q ss_pred HHHHHHHHHHHHHHCCC Q ss_conf 54202334245532053 Q gi|254780931|r 19 KLGDMRAQNIFLKDIKD 35 (56) Q Consensus 19 klgdmraqniflkdikd 35 (56) .++|.=--++||+||.| T Consensus 68 ~~~~vVK~TvfL~D~~d 84 (129) T TIGR00004 68 SLDDVVKTTVFLTDLND 84 (129) T ss_pred CCCCEEEEEEEECCHHH T ss_conf 84666888663026566 No 9 >COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription] Probab=13.12 E-value=66 Score=15.41 Aligned_cols=13 Identities=54% Similarity=0.869 Sum_probs=9.2 Q ss_pred HHHHHHHHHHCCC Q ss_conf 2334245532053 Q gi|254780931|r 23 MRAQNIFLKDIKD 35 (56) Q Consensus 23 mraqniflkdikd 35 (56) .|.||.|.||||. T Consensus 5 ~rr~nLF~KDiks 17 (126) T COG5248 5 ARRVNLFMKDIKS 17 (126) T ss_pred HHHHHHHHHHHHH T ss_conf 6788778889999 No 10 >pfam11387 DUF2795 Protein of unknown function (DUF2795). This family of proteins has no known function. Probab=12.11 E-value=95 Score=14.54 Aligned_cols=11 Identities=36% Similarity=0.782 Sum_probs=8.3 Q ss_pred CCCCCCHHHHH Q ss_conf 98765499999 Q gi|254780931|r 1 MDYPCNKEYFK 11 (56) Q Consensus 1 mdypcnkeyfk 11 (56) +|||.+|+-.- T Consensus 4 ~~yPa~K~~Lv 14 (44) T pfam11387 4 VDYPATKDELI 14 (44) T ss_pred CCCCCCHHHHH T ss_conf 99987899999 Done!