Query gi|254780543|ref|YP_003064956.1| NADH dehydrogenase [Candidatus Liberibacter asiaticus str. psy62] Match_columns 131 No_of_seqs 109 out of 570 Neff 5.1 Searched_HMMs 33803 Date Wed Jun 1 16:23:17 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780543.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >3gqh_A Preneck appendage prot 31.1 34 0.001 15.7 2.3 20 39-58 5-24 (109) 2 >3gqn_A Preneck appendage prot 29.9 38 0.0011 15.4 2.5 40 32-71 66-111 (168) 3 >3bgv_A MRNA CAP guanine-N7 me 25.3 22 0.00064 16.7 0.5 27 14-40 13-39 (53) 4 >2r51_A Vacuolar protein sorti 16.3 38 0.0011 15.4 0.2 42 2-43 92-133 (181) 5 >2k0q_A Putative uncharacteriz 14.0 70 0.0021 14.0 1.0 26 18-43 15-40 (74) 6 >1d3b_B Protein (small nuclear 13.5 58 0.0017 14.4 0.5 20 24-43 26-45 (91) 7 >2fau_A Vacuolar protein sorti 12.6 42 0.0012 15.2 -0.4 41 3-43 93-133 (182) 8 >1m5q_A SMAP3, small nuclear r 12.0 78 0.0023 13.7 0.8 23 24-46 22-44 (67) 9 >1b34_B Protein (small nuclear 11.2 85 0.0025 13.5 0.8 20 24-43 51-70 (118) 10 >3bw1_A SMX4 protein, U6 snRNA 11.2 86 0.0025 13.5 0.8 21 23-43 31-51 (96) No 1 >>3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A {Bacillus phage PHI29} PDB: 3gqk_A* (A:1-109) Probab=31.12 E-value=34 Score=15.70 Aligned_cols=20 Identities=20% Similarity=0.135 Sum_probs=8.3 Q ss_pred EEEECCCCCCCCCEEEEECC Q ss_conf 65505777777620899478 Q gi|254780543|r 39 YYESRKNINGSSRRWVIYNG 58 (131) Q Consensus 39 Yye~~~~~~~~~rRwV~Y~~ 58 (131) |||+.+......-..|-..+ T Consensus 5 ~FEs~dg~pi~~G~~VTl~g 24 (109) T 3gqh_A 5 YFESLGGQVIETGYLVTLEK 24 (109) T ss_dssp EEEBTTSSCCCTTCEEEEET T ss_pred HEECCCCCCCCCCEEEEEEC T ss_conf 22306899765646999609 No 2 >>3gqn_A Preneck appendage protein; coiled coil, beta helix, beta barrel, ATP binding, viral protein; HET: ATP; 2.15A {Bacillus phage PHI29} (A:605-772) Probab=29.94 E-value=38 Score=15.39 Aligned_cols=40 Identities=33% Similarity=0.464 Sum_probs=25.8 Q ss_pred EECCCCEEEEECCCCCCCCCEEEEECCCCCC------CCCCCCCCC Q ss_conf 6665878655057777776208994786675------536865320 Q gi|254780543|r 32 KDEFGNTYYESRKNINGSSRRWVIYNGYTDP------SSIPPMWHG 71 (131) Q Consensus 32 ~D~~GNkYye~~~~~~~~~rRwV~Y~~~~d~------s~IppeWh~ 71 (131) .|+||..-||......+...+-.+-+.++|| ..--||||. T Consensus 66 ~defG~~~y~~~~~~~g~~~~~P~~NP~~dp~~~Y~sR~eR~EW~~ 111 (168) T 3gqn_A 66 KNEFGGIIYEEVTTEDGVKFKRPLPNPDFDPNKNYIPRSQRREWHV 111 (168) T ss_dssp BCTTSCBCEEEEECSSSCEEEEECBCTTCCTTSCCCCTTTCSSEEE T ss_pred ECCCCCEEEEEEECCCCCEEECCCCCCCCCCCCCCCCCCCCCCEEE T ss_conf 6136878999831377967602454889897666505023866223 No 3 >>3bgv_A MRNA CAP guanine-N7 methyltransferase; alternative splicing, mRNA capping, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: SAH; 2.30A {Homo sapiens} PDB: 3epp_A* (A:158-210) Probab=25.27 E-value=22 Score=16.72 Aligned_cols=27 Identities=22% Similarity=0.407 Sum_probs=12.9 Q ss_pred CCEEHHHHHHHHHCEEEEEECCCCEEE Q ss_conf 966102143313070436666587865 Q gi|254780543|r 14 GQTLGTRFFTWRFGHIVGKDEFGNTYY 40 (131) Q Consensus 14 ~~TlgT~l~t~~~g~~VG~D~~GNkYy 40 (131) +.++|..+|..+|...--.-.||++|. T Consensus 13 ~~~fGN~vY~V~F~~~~~~p~FG~kY~ 39 (53) T 3bgv_A 13 TESFGNEIYTVKFQKKGDYPLFGCKYD 39 (53) T ss_dssp SSEEECSSEEEEESCSSCCCSSCCEEE T ss_pred HHHHCCCEEEEEECCCCCCCCCCCCCE T ss_conf 132088027998424456677775412 No 4 >>2r51_A Vacuolar protein sorting-associated protein 26B; retromer, fibronectin III, arrestin domain, alternative splicing, cytoplasm, membrane; 2.10A {Mus musculus} (A:160-340) Probab=16.30 E-value=38 Score=15.40 Aligned_cols=42 Identities=17% Similarity=0.192 Sum_probs=29.1 Q ss_pred HHHHHHHHHCCCCCEEHHHHHHHHHCEEEEEECCCCEEEEEC Q ss_conf 667786733147966102143313070436666587865505 Q gi|254780543|r 2 KNFLLQIFTWWNGQTLGTRFFTWRFGHIVGKDEFGNTYYESR 43 (131) Q Consensus 2 ~~~l~~iftWwn~~TlgT~l~t~~~g~~VG~D~~GNkYye~~ 43 (131) ..+|..+|+.=.-.++.-.+-..++=.+|=.|+.|.+||++- T Consensus 92 rl~L~~l~ltPT~~~v~~~FsV~y~Lnlviided~~ryfk~~ 133 (181) T 2r51_A 92 RLFLAGYELTPTXRDINKKFSVRYYLNLVLIDEEERRYFKQQ 133 (181) T ss_dssp EEEGGGSCCCCCEEEETTTEEEEEEEEEEEEETTCCEEEEEE T ss_pred EEECCCCCCCCCCCCCCCCEEEEEEEEEEEECCCCCEEEEEE T ss_conf 997788999995202698499999999999928995799961 No 5 >>2k0q_A Putative uncharacterized protein COPK; copper, heavy metal resistance, open barrel, plasmid- encoded, metal binding protein; NMR {Cupriavidus metallidurans} PDB: 3dso_A 3dsp_A (A:) Probab=13.95 E-value=70 Score=13.99 Aligned_cols=26 Identities=15% Similarity=0.427 Sum_probs=22.5 Q ss_pred HHHHHHHHHCEEEEEECCCCEEEEEC Q ss_conf 02143313070436666587865505 Q gi|254780543|r 18 GTRFFTWRFGHIVGKDEFGNTYYESR 43 (131) Q Consensus 18 gT~l~t~~~g~~VG~D~~GNkYye~~ 43 (131) |..+|.|.-|+.-=+|.+|+-++... T Consensus 15 GstvyiFKDGKM~mEdk~Gra~~m~~ 40 (74) T 2k0q_A 15 GSKVHVFKDGKMGMENKFGKSMNMPE 40 (74) T ss_dssp SCEEEEETTSCEEEECTTSCEECCCB T ss_pred CCEEEEEECCCCCCHHHCCCEEECCC T ss_conf 97899971673100010584277468 No 6 >>1d3b_B Protein (small nuclear ribonucleoprotein associated protein B); snRNP, splicing, core snRNP domain, systemic lupus erythematosus, SLE; HET: CIT; 2.00A {Homo sapiens} (B:) Probab=13.53 E-value=58 Score=14.44 Aligned_cols=20 Identities=15% Similarity=-0.027 Sum_probs=16.1 Q ss_pred HHHCEEEEEECCCCEEEEEC Q ss_conf 13070436666587865505 Q gi|254780543|r 24 WRFGHIVGKDEFGNTYYESR 43 (131) Q Consensus 24 ~~~g~~VG~D~~GNkYye~~ 43 (131) .+.|+|+|-|.++|-=-++- T Consensus 26 ~~~G~L~~~D~~~NlvL~d~ 45 (91) T 1d3b_B 26 IFIGTFKAFDKHMNLILCDC 45 (91) T ss_dssp EEEEEEEECCTTCCEEEEEE T ss_pred EEEEEEEEECCCCCEEEECE T ss_conf 99999999867578797167 No 7 >>2fau_A Vacuolar protein sorting 26; arrestin, retromer, protein transport; HET: CAF; 2.10A {Homo sapiens} (A:160-341) Probab=12.57 E-value=42 Score=15.19 Aligned_cols=41 Identities=20% Similarity=0.171 Sum_probs=29.7 Q ss_pred HHHHHHHHCCCCCEEHHHHHHHHHCEEEEEECCCCEEEEEC Q ss_conf 67786733147966102143313070436666587865505 Q gi|254780543|r 3 NFLLQIFTWWNGQTLGTRFFTWRFGHIVGKDEFGNTYYESR 43 (131) Q Consensus 3 ~~l~~iftWwn~~TlgT~l~t~~~g~~VG~D~~GNkYye~~ 43 (131) .+|..+|++=.-.+..-.+-.-++=.+|=.|+.|.+||++- T Consensus 93 l~L~~l~l~Pt~~~~~~~FsV~y~lnlviided~~~yfk~~ 133 (182) T 2fau_A 93 LFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQ 133 (182) T ss_dssp EESTTTCCCCCEEEEETTEEEEEEEEEEEEETTCCEEEEEE T ss_pred EECCCCCCCCCCCCCCCEEEEEEEEEEEEECCCCCEEEECC T ss_conf 97789999997535797499999999999988886898827 No 8 >>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} (A:1-67) Probab=11.99 E-value=78 Score=13.74 Aligned_cols=23 Identities=17% Similarity=-0.008 Sum_probs=17.9 Q ss_pred HHHCEEEEEECCCCEEEEECCCC Q ss_conf 13070436666587865505777 Q gi|254780543|r 24 WRFGHIVGKDEFGNTYYESRKNI 46 (131) Q Consensus 24 ~~~g~~VG~D~~GNkYye~~~~~ 46 (131) .+.|+|+|-|.+.|---++-... T Consensus 22 ~~~G~L~~~D~~~NlvL~da~E~ 44 (67) T 1m5q_A 22 VYKGVLHAVDNQLNIVLANASNK 44 (67) T ss_dssp EEEEEEEEECTTCCEEEEEEECT T ss_pred EEEEEEEEECCCCEEEEEEEEEC T ss_conf 99999999879965699157987 No 9 >>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemic lupus erythematosus, SLE; 2.50A {Homo sapiens} (B:) Probab=11.24 E-value=85 Score=13.53 Aligned_cols=20 Identities=20% Similarity=0.164 Sum_probs=16.3 Q ss_pred HHHCEEEEEECCCCEEEEEC Q ss_conf 13070436666587865505 Q gi|254780543|r 24 WRFGHIVGKDEFGNTYYESR 43 (131) Q Consensus 24 ~~~g~~VG~D~~GNkYye~~ 43 (131) .+.|.|+|-|++.|---++- T Consensus 51 ~~~G~L~~fD~~mNlvL~d~ 70 (118) T 1b34_B 51 KLLGRVKAFDRHCNMVLENV 70 (118) T ss_dssp EEEEEEEEECTTCCEEEEEE T ss_pred EEEEEEEEECCCCEEEEECE T ss_conf 99999999710002673030 No 10 >>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, homomeric, octamer, cytoplasm; 2.50A {Saccharomyces cerevisiae} (A:) Probab=11.20 E-value=86 Score=13.52 Aligned_cols=21 Identities=14% Similarity=0.066 Sum_probs=16.6 Q ss_pred HHHHCEEEEEECCCCEEEEEC Q ss_conf 313070436666587865505 Q gi|254780543|r 23 TWRFGHIVGKDEFGNTYYESR 43 (131) Q Consensus 23 t~~~g~~VG~D~~GNkYye~~ 43 (131) ..+.|++.|.|.+.|---++- T Consensus 31 ~~~~G~L~~~D~~mNlvL~d~ 51 (96) T 3bw1_A 31 RTLVGTLQAFDSHCNIVLSDA 51 (96) T ss_dssp CEEEEEEEEECTTCCEEEEEE T ss_pred CEEEEEEEEECCCCCEEECCE T ss_conf 199999999889997298848 Done!