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 23785 Date Tue May 31 20:38:48 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780543.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3gqh_A Preneck appendage prote 24.7 37 0.0015 14.7 2.4 12 32-43 61-72 (163) 2 2c4b_A Barnase mcoeeti fusion; 23.2 39 0.0016 14.5 3.4 37 21-58 41-91 (143) 3 3gqn_A Preneck appendage prote 16.8 55 0.0023 13.7 2.5 16 32-47 670-685 (772) 4 2k0q_A Putative uncharacterize 14.0 49 0.0021 14.0 1.0 26 18-43 15-40 (74) 5 2kxq_A E3 ubiquitin-protein li 13.8 66 0.0028 13.3 2.3 28 26-56 12-39 (90) 6 3cw1_G Small nuclear ribonucle 12.6 48 0.002 14.0 0.7 20 24-43 26-45 (76) 7 1d3b_B Protein (small nuclear 11.1 53 0.0022 13.8 0.5 20 24-43 26-45 (91) 8 2fwk_A U6 snRNA-associated SM- 10.7 75 0.0032 13.0 1.1 21 24-44 50-70 (121) 9 3da7_A Barnase circular permut 9.9 75 0.0031 13.0 0.9 21 36-56 2-25 (111) 10 1p6r_A Penicillinase repressor 9.7 64 0.0027 13.4 0.5 29 12-40 39-67 (82) No 1 >3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A {Bacillus phage PHI29} PDB: 3gqk_A* Probab=24.65 E-value=37 Score=14.69 Aligned_cols=12 Identities=50% Similarity=0.869 Sum_probs=5.8 Q ss_pred EECCCCEEEEEC Q ss_conf 666587865505 Q gi|254780543|r 32 KDEFGNTYYESR 43 (131) Q Consensus 32 ~D~~GNkYye~~ 43 (131) .|+||+.=||.- T Consensus 61 ~DefG~~iye~~ 72 (163) T 3gqh_A 61 KNEFGGIIYEEV 72 (163) T ss_dssp BCTTSCBCEEEE T ss_pred ECCCCCEEEEEC T ss_conf 745799998970 No 2 >2c4b_A Barnase mcoeeti fusion; squash inhibitor, hybrid microprotein, fusion protein, ribonuclease, endonuclease, hydrolase, nuclease; HET: 2PE MES; 1.3A {Bacillus amyloliquefaciens} SCOP: d.1.1.2 g.3.2.1 PDB: 1b3s_A 2kf3_A 2kf4_A 2kf5_A 2kf6_A 1a2p_A 1b27_A 1b2x_A 1bgs_A 1bni_A 1bnj_A 1bnr_A 1brn_L* 1brs_A 1fw7_A 1x1u_A 1x1w_A 1x1x_A 1yvs_A 3kch_A ... Probab=23.16 E-value=39 Score=14.53 Aligned_cols=37 Identities=27% Similarity=0.401 Sum_probs=22.9 Q ss_pred HHHHHHCEEEEEECCCCE-----------EEEECCCCCCC---CCEEEEECC Q ss_conf 433130704366665878-----------65505777777---620899478 Q gi|254780543|r 21 FFTWRFGHIVGKDEFGNT-----------YYESRKNINGS---SRRWVIYNG 58 (131) Q Consensus 21 l~t~~~g~~VG~D~~GNk-----------Yye~~~~~~~~---~rRwV~Y~~ 58 (131) |--...|+-+|-|.|+|+ |+|--.+..+. .+|.| |.+ T Consensus 41 L~~v~pGk~IGGd~F~NrE~~LP~~~g~~Y~E~DV~~~gg~RGa~RIV-~s~ 91 (143) T 2c4b_A 41 LADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRIL-YSS 91 (143) T ss_dssp HHHHSTTCEEEEEEECCTTCCSCCCTTCCEEEEECSCCSSSCCSCEEE-EET T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEE-ECC T ss_conf 100488752067533478576888889838887648999888987699-869 No 3 >3gqn_A Preneck appendage protein; coiled coil, beta helix, beta barrel, ATP binding, viral protein; HET: ATP; 2.15A {Bacillus phage PHI29} Probab=16.79 E-value=55 Score=13.75 Aligned_cols=16 Identities=38% Similarity=0.654 Sum_probs=7.5 Q ss_pred EECCCCEEEEECCCCC Q ss_conf 6665878655057777 Q gi|254780543|r 32 KDEFGNTYYESRKNIN 47 (131) Q Consensus 32 ~D~~GNkYye~~~~~~ 47 (131) +|+||..-||....+. T Consensus 670 ~~~~g~~~~~~~~~~~ 685 (772) T 3gqn_A 670 KNEFGGIIYEEVTTED 685 (772) T ss_dssp BCTTSCBCEEEEECSS T ss_pred ECCCCCEEEEEEECCC T ss_conf 4247878988863167 No 4 >2k0q_A Putative uncharacterized protein COPK; copper, heavy metal resistance, open barrel, plasmid- encoded, metal binding protein; NMR {Cupriavidus metallidurans} PDB: 2km0_A 3dso_A 3dsp_A Probab=13.99 E-value=49 Score=14.00 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 CCEEEEECCCCEEHHHHCCCEEECCC T ss_conf 96899972782110010485077579 No 5 >2kxq_A E3 ubiquitin-protein ligase smurf2; WW, smurf2, TGF-beta, modular binding, protein BIN; NMR {Homo sapiens} Probab=13.82 E-value=66 Score=13.31 Aligned_cols=28 Identities=14% Similarity=0.156 Sum_probs=18.2 Q ss_pred HCEEEEEECCCCEEEEECCCCCCCCCEEEEE Q ss_conf 0704366665878655057777776208994 Q gi|254780543|r 26 FGHIVGKDEFGNTYYESRKNINGSSRRWVIY 56 (131) Q Consensus 26 ~g~~VG~D~~GNkYye~~~~~~~~~rRwV~Y 56 (131) -|--+-.|..|..||-+.... .--|+.. T Consensus 12 ~GWe~~~d~~Gr~YY~n~~T~---~TtW~~P 39 (90) T 2kxq_A 12 EGYEQRTTQQGQVYFLHTQTG---VSTWHDP 39 (90) T ss_dssp SSCEEEEETTTEEEEEETTTT---EEESSCS T ss_pred CCCEEEECCCCCEEEEECCCC---EEECCCC T ss_conf 996898989999998978998---0763589 No 6 >3cw1_G Small nuclear ribonucleoprotein G; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, zinc finger, RNA recognition motif; 5.49A {Homo sapiens} Probab=12.63 E-value=48 Score=14.04 Aligned_cols=20 Identities=25% Similarity=0.205 Sum_probs=16.4 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~~mNlvL~~~ 45 (76) T 3cw1_G 26 HVQGILRGFDPFMNLVIDEC 45 (76) T ss_pred EEEEEEEEECCCCCEEECCE T ss_conf 99999999977235898047 No 7 >1d3b_B Protein (small nuclear ribonucleoprotein associated protein B); snRNP, splicing, core snRNP domain, systemic lupus erythematosus, SLE; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Probab=11.15 E-value=53 Score=13.81 Aligned_cols=20 Identities=15% Similarity=-0.027 Sum_probs=15.6 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~~~ 45 (91) T 1d3b_B 26 IFIGTFKAFDKHMNLILCDC 45 (91) T ss_dssp EEEEEEEECCTTCCEEEEEE T ss_pred EEEEEEEEECCCCCEEEECE T ss_conf 99999999987568885065 No 8 >2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 Probab=10.74 E-value=75 Score=13.01 Aligned_cols=21 Identities=24% Similarity=0.213 Sum_probs=17.2 Q ss_pred HHHCEEEEEECCCCEEEEECC Q ss_conf 130704366665878655057 Q gi|254780543|r 24 WRFGHIVGKDEFGNTYYESRK 44 (131) Q Consensus 24 ~~~g~~VG~D~~GNkYye~~~ 44 (131) .+.|+|+|-|.+.|---++-. T Consensus 50 ~~~G~L~~fD~~mNLvL~d~~ 70 (121) T 2fwk_A 50 EFSGVLRGFDEYVNMVLDDVQ 70 (121) T ss_dssp EECCEEEEECTTCCEEEESCC T ss_pred EEEEEEEEECCCCCEEEEEEE T ss_conf 999999999776885785279 No 9 >3da7_A Barnase circular permutant; circular permutant, protein-protein complex, endonuclease, cytoplasm, protein binding; 2.25A {Bacillus amyloliquefaciens} Probab=9.94 E-value=75 Score=13.03 Aligned_cols=21 Identities=29% Similarity=0.357 Sum_probs=9.0 Q ss_pred CCEEEEECCCCCCC---CCEEEEE Q ss_conf 87865505777777---6208994 Q gi|254780543|r 36 GNTYYESRKNINGS---SRRWVIY 56 (131) Q Consensus 36 GNkYye~~~~~~~~---~rRwV~Y 56 (131) |..|||.-.+..++ ..|.|.= T Consensus 2 Gr~w~EaDiny~~g~Rga~Rivys 25 (111) T 3da7_A 2 GRTWREADINYTSGFRNSDRILYS 25 (111) T ss_dssp -CCEEEEECSCCSBSCCSCEEEEE T ss_pred CCEEEECCCCCCCCCCCCCEEEEE T ss_conf 857788101666788886368995 No 10 >1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B Probab=9.67 E-value=64 Score=13.38 Aligned_cols=29 Identities=14% Similarity=0.296 Sum_probs=0.0 Q ss_pred CCCCEEHHHHHHHHHCEEEEEECCCCEEE Q ss_conf 47966102143313070436666587865 Q gi|254780543|r 12 WNGQTLGTRFFTWRFGHIVGKDEFGNTYY 40 (131) Q Consensus 12 wn~~TlgT~l~t~~~g~~VG~D~~GNkYy 40 (131) |.-.|+-|.|.-...-.+|..+..|+.|+ T Consensus 39 ~~~sTv~T~L~RL~~Kg~l~~~~~gr~~~ 67 (82) T 1p6r_A 39 WSPKTIQTMLLRLIKKGALNHHKEGRVFV 67 (82) T ss_dssp CCHHHHHHHHHHHHHTTSEEEEEETTEEE T ss_pred CCHHHHHHHHHHHHHCCCEEEEECCCEEE T ss_conf 72857999999999889868872598389 Done!