Query gi|254780179|ref|YP_003064592.1| hypothetical protein CLIBASIA_00310 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 75 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 23785 Date Mon May 23 02:36:30 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780179.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 2caz_B Vacuolar protein sortin 12.9 76 0.0032 13.5 3.1 41 27-75 74-114 (155) 2 2f6m_B Vacuolar protein sortin 10.7 91 0.0038 13.1 2.3 40 27-74 57-96 (109) 3 2p22_B Vacuolar protein sortin 7.7 92 0.0039 13.1 0.6 40 27-74 66-105 (118) 4 2hma_A Probable tRNA (5-methyl 6.0 72 0.003 13.6 -0.7 15 57-71 165-179 (376) 5 2der_A TRNA-specific 2-thiouri 5.0 1.2E+02 0.0049 12.5 -0.1 14 58-71 174-187 (380) 6 3b8e_G Na+/K+ ATPase gamma sub 4.5 78 0.0033 13.5 -1.3 10 39-48 1-10 (29) 7 2jo1_A Phospholemman; FXYD1, N 4.2 1.9E+02 0.008 11.4 0.5 12 38-49 12-23 (72) 8 2vvp_A Ribose-5-phosphate isom 3.5 1.4E+02 0.0058 12.2 -0.7 38 11-48 29-68 (162) 9 2jp3_A FXYD domain-containing 3.4 2.4E+02 0.01 10.9 2.7 24 39-62 14-38 (67) 10 3bz1_M PSII-M, photosystem II 3.4 2.4E+02 0.01 10.9 2.1 17 46-62 15-31 (36) No 1 >2caz_B Vacuolar protein sorting-associated protein VPS28; protein transport, ESCRT, MVB, multivesicular bodies, endosome, lysosome, PH domain, protein sorting; 3.6A {Saccharomyces cerevisiae} SCOP: a.2.17.2 Probab=12.93 E-value=76 Score=13.52 Aligned_cols=41 Identities=20% Similarity=0.259 Sum_probs=25.9 Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCHHHHHHHHCC Q ss_conf 3544323445788987520149999999999974000337888873179 Q gi|254780179|r 27 SYCHYGKRLSTQYKTLRKGILIPVVFSILYFTISKSIFPLSHFKKHYRF 75 (75) Q Consensus 27 sychygkrlstqyktlrkgilipvvfsilyftisksifplshfkkhyrf 75 (75) .|-.--.||-.|||++.+.+.-.. +++.+..+..|.+.|+. T Consensus 74 eYt~tC~rLL~QYKt~l~~~~~~~--------v~~~f~~le~F~~~Y~l 114 (155) T 2caz_B 74 QYTNTVDKLLKQFKVYLNSQNKEE--------INKHFQSIEAFCDTYNI 114 (155) T ss_dssp HHHHHHHHHHHHHHHHHTSSSCHH--------HHHHTCSHHHHHHHTTC T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--------HHCCCCCHHHHHHHHCC T ss_conf 999999999999999998610365--------53137999999999788 No 2 >2f6m_B Vacuolar protein sorting-associated protein VPS28; endosomes, trafficking complex, vacuole protein sorting, ESCRT protein complexes; HET: DDQ; 2.10A {Saccharomyces cerevisiae} SCOP: a.2.17.2 PDB: 2f66_B Probab=10.71 E-value=91 Score=13.12 Aligned_cols=40 Identities=18% Similarity=0.237 Sum_probs=23.2 Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCHHHHHHHHC Q ss_conf 354432344578898752014999999999997400033788887317 Q gi|254780179|r 27 SYCHYGKRLSTQYKTLRKGILIPVVFSILYFTISKSIFPLSHFKKHYR 74 (75) Q Consensus 27 sychygkrlstqyktlrkgilipvvfsilyftisksifplshfkkhyr 74 (75) .|-.--.||-.|||++.+.+.-+.|- +..-.+..|.+.|+ T Consensus 57 eYt~~c~rLl~QYK~~~~~~~~~~v~--------~~~~~le~F~~~y~ 96 (109) T 2f6m_B 57 QYTNTVDKLLKQFKVYLNSQNKEEIN--------KHFQSIEAFADTYN 96 (109) T ss_dssp HHHHHHHHHHHHHHHHHTCTTTTHHH--------HHHHHHHHHHHHTT T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--------CCCCCHHHHHHHHC T ss_conf 89999999999999999870006652--------03688999999978 No 3 >2p22_B Vacuolar protein sorting-associated protein 28; endosome, trafficking complex, VPS23, VPS28, VPS37, MVB12; 2.70A {Saccharomyces cerevisiae} Probab=7.73 E-value=92 Score=13.09 Aligned_cols=40 Identities=18% Similarity=0.270 Sum_probs=22.1 Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCHHHHHHHHC Q ss_conf 354432344578898752014999999999997400033788887317 Q gi|254780179|r 27 SYCHYGKRLSTQYKTLRKGILIPVVFSILYFTISKSIFPLSHFKKHYR 74 (75) Q Consensus 27 sychygkrlstqyktlrkgilipvvfsilyftisksifplshfkkhyr 74 (75) .|-.--.||-.|||++.+...-+.| ++....+..|.+.|+ T Consensus 66 eYt~~c~rLl~QYK~~~~~~~~~~v--------~~~~~~le~F~~~y~ 105 (118) T 2p22_B 66 QYTNTVDKLLKQFKVYLNSQNKEEI--------NKHFQSIEAFADTYN 105 (118) T ss_dssp HHHHHHHHHHHHHHHHHHTTTTTC------------------------ T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH--------HCCCCCHHHHHHHHC T ss_conf 8999999999999999987201665--------203798999999878 No 4 >2hma_A Probable tRNA (5-methylaminomethyl-2- thiouridylate)-methyltransferase; alpha-beta, beta barrel, structural genomics, PSI-2; HET: MSE SAM; 2.41A {Streptococcus pneumoniae} Probab=5.98 E-value=72 Score=13.64 Aligned_cols=15 Identities=40% Similarity=0.837 Sum_probs=9.5 Q ss_pred HHHHHCCCCHHHHHH Q ss_conf 997400033788887 Q gi|254780179|r 57 FTISKSIFPLSHFKK 71 (75) Q Consensus 57 ftisksifplshfkk 71 (75) -.+++.+|||.++.| T Consensus 165 ~~L~~~iFPLG~~~K 179 (376) T 2hma_A 165 EQLQKTMFPLGHLEK 179 (376) T ss_dssp HHHTTEECTTTTCCH T ss_pred HHHHCCCCCCCCCCH T ss_conf 788366688899977 No 5 >2der_A TRNA-specific 2-thiouridylase MNMA; protein-RNA complex, transferase/RNA complex; 3.10A {Escherichia coli} PDB: 2det_A 2deu_A* Probab=5.03 E-value=1.2e+02 Score=12.53 Aligned_cols=14 Identities=36% Similarity=0.838 Sum_probs=7.9 Q ss_pred HHHHCCCCHHHHHH Q ss_conf 97400033788887 Q gi|254780179|r 58 TISKSIFPLSHFKK 71 (75) Q Consensus 58 tisksifplshfkk 71 (75) .+++.+|||.++.| T Consensus 174 ~L~~~~FPLG~~~K 187 (380) T 2der_A 174 QIAQSLFPVGELEK 187 (380) T ss_dssp HHHHEECCGGGSCH T ss_pred HHCCEEECCCCCCH T ss_conf 50554768978855 No 6 >3b8e_G Na+/K+ ATPase gamma subunit transcript variant A; P-type ATPase, cation pump, membrane protein, hydrolase, ATP-binding, calcium transport; HET: PC1; 3.50A {Sus scrofa} PDB: 3kdp_G* Probab=4.48 E-value=78 Score=13.49 Aligned_cols=10 Identities=60% Similarity=0.963 Sum_probs=6.1 Q ss_pred HHHHHHCCHH Q ss_conf 8987520149 Q gi|254780179|r 39 YKTLRKGILI 48 (75) Q Consensus 39 yktlrkgili 48 (75) |.|.|+|-|| T Consensus 1 yetvr~ggli 10 (29) T 3b8e_G 1 YETVRNGGLI 10 (29) T ss_dssp CTTTSTTSSG T ss_pred CCCEECCCEE T ss_conf 9442338675 No 7 >2jo1_A Phospholemman; FXYD1, Na,K-ATPase, micelle, hydrolase regulator; NMR {Homo sapiens} Probab=4.21 E-value=1.9e+02 Score=11.42 Aligned_cols=12 Identities=33% Similarity=0.603 Sum_probs=9.4 Q ss_pred HHHHHHHCCHHH Q ss_conf 889875201499 Q gi|254780179|r 38 QYKTLRKGILIP 49 (75) Q Consensus 38 qyktlrkgilip 49 (75) .|.|||.|=||- T Consensus 12 DY~tLRiGGLi~ 23 (72) T 2jo1_A 12 DYQSLQIGGLVI 23 (72) T ss_dssp STHHHHHHHHHH T ss_pred CHHHHEECCCHH T ss_conf 417850544245 No 8 >2vvp_A Ribose-5-phosphate isomerase B; RPIB, RV2465C, RARE sugar, carbohydrate metabolism, pentose phosphate pathway; HET: R52 5RP; 1.65A {Mycobacterium tuberculosis} SCOP: c.121.1.1 PDB: 2vvo_A* 2vvq_A* 2bes_A* 2bet_A* 1usl_A Probab=3.53 E-value=1.4e+02 Score=12.17 Aligned_cols=38 Identities=18% Similarity=0.141 Sum_probs=23.7 Q ss_pred CHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH--HHCCHH Q ss_conf 01201115025666433544323445788987--520149 Q gi|254780179|r 11 EEEIIDFNSNHLLSSLSYCHYGKRLSTQYKTL--RKGILI 48 (75) Q Consensus 11 eeeiidfnsnhllsslsychygkrlstqyktl--rkgili 48 (75) .-|++|+...-.-++..|-.|+++++.....- ..||++ T Consensus 29 g~ev~D~G~~~~~~~~dYpd~a~~va~~v~~~~~~~GIli 68 (162) T 2vvp_A 29 GHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVL 68 (162) T ss_dssp TCEEEECSCCSCCTTCCHHHHHHHHHHHHHHSTTCEEEEE T ss_pred CCEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEE T ss_conf 9989967998666778725899998887436877779998 No 9 >2jp3_A FXYD domain-containing ION transport regulator 4; protein, transcription; NMR {Rattus norvegicus} Probab=3.42 E-value=2.4e+02 Score=10.91 Aligned_cols=24 Identities=21% Similarity=0.289 Sum_probs=0.0 Q ss_pred HHHHHHCCH-HHHHHHHHHHHHHHC Q ss_conf 898752014-999999999997400 Q gi|254780179|r 39 YKTLRKGIL-IPVVFSILYFTISKS 62 (75) Q Consensus 39 yktlrkgil-ipvvfsilyftisks 62 (75) |.+||.|=| +.+|.-++-..|--| T Consensus 14 y~tLRigGLi~a~vlf~~GiliilS 38 (67) T 2jp3_A 14 WESLQLGGLIFGGLLCIAGIALALS 38 (67) T ss_dssp GHHHHHHHHHHHHHHHHHHHHHHHT T ss_pred HHHHEECCCHHHHHHHHHHHHHHHC T ss_conf 1784143415799999999999986 No 10 >3bz1_M PSII-M, photosystem II reaction center protein M; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 1s5l_M* 2axt_M* 3bz2_M* 3kzi_M* 3a0b_M* 3a0h_M* Probab=3.35 E-value=2.4e+02 Score=10.87 Aligned_cols=17 Identities=35% Similarity=0.784 Sum_probs=0.0 Q ss_pred CHHHHHHHHHHHHHHHC Q ss_conf 14999999999997400 Q gi|254780179|r 46 ILIPVVFSILYFTISKS 62 (75) Q Consensus 46 ilipvvfsilyftisks 62 (75) |++|.+|-+..+.-..| T Consensus 15 ilvPt~FLlILyvqT~s 31 (36) T 3bz1_M 15 VLVPSVFLIILYVQTES 31 (36) T ss_dssp HHHHHHHHHHHHHHHHT T ss_pred HHHHHHHHHHHEEEECC T ss_conf 99988887653144133 Done!