Query gi|254781145|ref|YP_003065558.1| hypothetical protein CLIBASIA_05245 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 350 No_of_seqs 150 out of 629 Neff 8.4 Searched_HMMs 33803 Date Wed Jun 1 23:19:40 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781145.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >2jes_A Portal protein; DNA tr 42.8 18 0.00054 15.0 5.2 92 183-278 2-95 (97) 2 >1oqy_A HHR23A, UV excision re 40.3 9.8 0.00029 16.8 0.8 28 77-104 20-47 (60) 3 >1vg5_A RSGI RUH-014, rhomboid 38.6 7.2 0.00021 17.6 -0.1 26 78-103 33-58 (73) 4 >1oqy_A HHR23A, UV excision re 35.6 16 0.00046 15.4 1.2 27 78-104 47-73 (99) 5 >1ify_A HHR23A, UV excision re 31.9 16 0.00048 15.3 0.8 26 78-103 12-37 (49) 6 >1dv0_A DNA repair protein HHR 25.9 17 0.00049 15.2 0.0 31 78-108 8-38 (47) 7 >1wgn_A UBAP1, ubiquitin assoc 25.3 11 0.00032 16.5 -1.0 15 79-93 24-38 (63) 8 >2g3q_A Protein YBL047C; endoc 25.0 29 0.00084 13.7 1.1 22 77-98 7-28 (43) 9 >1wiv_A UBP14, ubiquitin-speci 24.3 20 0.0006 14.6 0.2 17 78-94 33-49 (73) 10 >2vdr_B Integrin beta-3; cell 24.1 36 0.0011 13.0 1.5 42 25-66 36-78 (138) 11 >2cpw_A CBL-interacting protei 23.3 26 0.00077 14.0 0.6 17 78-94 23-39 (64) 12 >2dna_A Unnamed protein produc 23.2 22 0.00066 14.4 0.3 17 78-94 23-40 (67) 13 >1veg_A NEDD8 ultimate buster- 21.8 22 0.00065 14.4 -0.0 26 77-102 32-57 (83) 14 >2dai_A Ubadc1, ubiquitin asso 21.3 24 0.00072 14.1 0.1 26 77-102 32-57 (83) No 1 >>2jes_A Portal protein; DNA translocation, molecular motor, viral portal protein, viral protein; 3.4A {Bacteriophage SPP1} (A:256-352) Probab=42.76 E-value=18 Score=14.97 Aligned_cols=92 Identities=13% Similarity=0.095 Sum_probs=63.9 Q ss_pred HHHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCC-CCC-CCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCHHHHHH Q ss_conf 543102899998998848878763036622531343-121-000011225741450466655444444568876567999 Q gi|254781145|r 183 AASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGS-IID-PESVLNPQFGKPIRVAAGMDIRSVLGIHSVPMIEKSFSM 260 (350) Q Consensus 183 ~d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~-~~~-~~d~~~~~~g~~v~~~~~~~~~~i~~~~~~~~~~~~~~~ 260 (350) .+.+.+++.+.+.++....+...-...+.+.+ .|. ..+ .+..-+.+-.+++.+.+++.++- +.-+-.....-.. T Consensus 2 ~e~v~~LIDayd~~~S~~an~~~df~~a~lvl-~G~~~~~~~e~~~~lk~~~~i~l~~~~~v~~---Ltk~~~~~~~e~~ 77 (97) T 2jes_A 2 LKFYKDLIDNYDSITSSTMDSFSDFQQIVYVL-KNYDGENPKEFTANLRYHSVIKVSGDGGVDT---LRAEIPVDSAAKE 77 (97) T ss_dssp GGGTHHHHHHHHHHHHHHHHHHHHTTSCEEEE-EEESCSCHHHHHHHHHHSSEEEEEEEEEEEE---ECCCCCHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCCHHHHHHHHHCCCEEEECCCCCCEE---EEECCCHHHHHHH T ss_conf 56558999999999868889999865368786-0788665155665553054362089998068---8615881899999 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 999999998875246664 Q gi|254781145|r 261 LHYLDQELVDRTGISDIS 278 (350) Q Consensus 261 l~~~~~~~e~~tGi~~~~ 278 (350) ++.+...+-+.|.+++.+ T Consensus 78 ~~~L~~~I~~~s~~pd~~ 95 (97) T 2jes_A 78 LERIQDELYKSAQAVDNS 95 (97) T ss_dssp HHHHHHHHHHHTTCCCCS T ss_pred HHHHHHHHHHHHCCCCCC T ss_conf 999999999985888877 No 2 >>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} (A:309-368) Probab=40.29 E-value=9.8 Score=16.75 Aligned_cols=28 Identities=11% Similarity=0.134 Sum_probs=20.0 Q ss_pred CHHHHHHHCCCCHHHCCCCCCCCCCHHH Q ss_conf 6899987279804430277787641013 Q gi|254781145|r 77 TRSDLISMGYDRESINNLPIISSQNIEN 104 (350) Q Consensus 77 t~~eL~~~Gy~~d~v~~~~~~~~~~~~~ 104 (350) ....|.+|||+++...+.-.....+.+. T Consensus 20 ~i~~L~~MGF~~~~a~~AL~~~~~n~e~ 47 (60) T 1oqy_A 20 AIERLKALGFPESLVIQAYFACEKNENL 47 (60) T ss_dssp HHHHHHHHTCCSHHHHHHTSSSSSCSSH T ss_pred HHHHHHHCCCCHHHHHHHHHHCCCCHHH T ss_conf 9999998499989999999982998999 No 3 >>1vg5_A RSGI RUH-014, rhomboid family protein; UBA domain, cDNA, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} (A:) Probab=38.59 E-value=7.2 Score=17.65 Aligned_cols=26 Identities=19% Similarity=0.464 Sum_probs=14.4 Q ss_pred HHHHHHHCCCCHHHCCCCCCCCCCHH Q ss_conf 89998727980443027778764101 Q gi|254781145|r 78 RSDLISMGYDRESINNLPIISSQNIE 103 (350) Q Consensus 78 ~~eL~~~Gy~~d~v~~~~~~~~~~~~ 103 (350) ..+|.+|||.++.+.+.-.....+.+ T Consensus 33 i~~L~~MGF~~~~a~~AL~~~~~nve 58 (73) T 1vg5_A 33 IQKLVAMGFDRTQVEVALAAADDDLT 58 (73) T ss_dssp HHHHHTTTCCHHHHHHHHHHHTSCHH T ss_pred HHHHHHCCCCHHHHHHHHHHHCCCHH T ss_conf 99999939999999999999589999 No 4 >>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} (A:126-224) Probab=35.62 E-value=16 Score=15.43 Aligned_cols=27 Identities=30% Similarity=0.443 Sum_probs=17.3 Q ss_pred HHHHHHHCCCCHHHCCCCCCCCCCHHH Q ss_conf 899987279804430277787641013 Q gi|254781145|r 78 RSDLISMGYDRESINNLPIISSQNIEN 104 (350) Q Consensus 78 ~~eL~~~Gy~~d~v~~~~~~~~~~~~~ 104 (350) ..+|.+|||.++.+.+.-.....+.+. T Consensus 47 i~~L~eMGF~~~~a~~AL~~~~~nve~ 73 (99) T 1oqy_A 47 LTEIMSMGYERERVVAALRASYNNPHR 73 (99) T ss_dssp HHHHHTTTCCSHHHHHHHHHSCSSTTH T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCHHH T ss_conf 999985063779999999987618899 No 5 >>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} (A:) Probab=31.86 E-value=16 Score=15.30 Aligned_cols=26 Identities=31% Similarity=0.456 Sum_probs=17.6 Q ss_pred HHHHHHHCCCCHHHCCCCCCCCCCHH Q ss_conf 89998727980443027778764101 Q gi|254781145|r 78 RSDLISMGYDRESINNLPIISSQNIE 103 (350) Q Consensus 78 ~~eL~~~Gy~~d~v~~~~~~~~~~~~ 103 (350) ..+|.+|||+++.+.+.-.....+.+ T Consensus 12 v~~L~~MGF~~~~a~~AL~~~~~n~e 37 (49) T 1ify_A 12 LTEIMSMGYERERVVAALRASYNNPH 37 (49) T ss_dssp HHHHHHTTCCHHHHHHHHHTTTSCSH T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHH T ss_conf 99999800279999999998716817 No 6 >>1dv0_A DNA repair protein HHR23A; helical bundle, DNA binding protein; HET: DNA; NMR {Homo sapiens} (A:) Probab=25.90 E-value=17 Score=15.22 Aligned_cols=31 Identities=13% Similarity=0.166 Sum_probs=21.0 Q ss_pred HHHHHHHCCCCHHHCCCCCCCCCCHHHHHHC Q ss_conf 8999872798044302777876410133202 Q gi|254781145|r 78 RSDLISMGYDRESINNLPIISSQNIENTWKF 108 (350) Q Consensus 78 ~~eL~~~Gy~~d~v~~~~~~~~~~~~~~~~~ 108 (350) .++|.+|||.++...+.-.....+.+.-..+ T Consensus 8 i~~L~~MGF~~~~a~~AL~~~~~n~e~A~~~ 38 (47) T 1dv0_A 8 IERLKALGFPESLVIQAYFACEKNENLAANF 38 (47) T ss_dssp HTTTTTTTCCHHHHHHHHTTTTSCHHHHHHH T ss_pred HHHHHHCCCCHHHHHHHHHHHCCCHHHHHHH T ss_conf 9999983998889999999818769999999 No 7 >>1wgn_A UBAP1, ubiquitin associated protein; ubiquitin associated protein 1 (UBAP1), UBA domain, structural genomics; NMR {Homo sapiens} (A:) Probab=25.31 E-value=11 Score=16.47 Aligned_cols=15 Identities=27% Similarity=0.611 Sum_probs=5.9 Q ss_pred HHHHHHCCCCHHHCC Q ss_conf 999872798044302 Q gi|254781145|r 79 SDLISMGYDRESINN 93 (350) Q Consensus 79 ~eL~~~Gy~~d~v~~ 93 (350) .+|.+|||+++.+.+ T Consensus 24 ~~L~~MGF~~~~a~~ 38 (63) T 1wgn_A 24 ETVVNMGYSYECVLR 38 (63) T ss_dssp HHHHHHHCCHHHHHH T ss_pred HHHHHCCCCHHHHHH T ss_conf 999986998999999 No 8 >>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} (A:) Probab=25.00 E-value=29 Score=13.68 Aligned_cols=22 Identities=23% Similarity=0.309 Sum_probs=14.8 Q ss_pred CHHHHHHHCCCCHHHCCCCCCC Q ss_conf 6899987279804430277787 Q gi|254781145|r 77 TRSDLISMGYDRESINNLPIIS 98 (350) Q Consensus 77 t~~eL~~~Gy~~d~v~~~~~~~ 98 (350) ...+|.+|||+++.+.+.-... T Consensus 7 ~v~~L~~MGF~~~~a~~AL~~~ 28 (43) T 2g3q_A 7 AVEELSGMGFTEEEAHNALEKC 28 (43) T ss_dssp HHHHHHTTTSCHHHHHHHHHHH T ss_pred HHHHHHHCCCCHHHHHHHHHHC T ss_conf 9999997699999999999992 No 9 >>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} (A:) Probab=24.28 E-value=20 Score=14.65 Aligned_cols=17 Identities=18% Similarity=0.427 Sum_probs=8.5 Q ss_pred HHHHHHHCCCCHHHCCC Q ss_conf 89998727980443027 Q gi|254781145|r 78 RSDLISMGYDRESINNL 94 (350) Q Consensus 78 ~~eL~~~Gy~~d~v~~~ 94 (350) ..+|.+|||.++.+.+. T Consensus 33 i~~L~~MGF~~~~a~~A 49 (73) T 1wiv_A 33 VDTLLSFGFAEDVARKA 49 (73) T ss_dssp HHHHHHHTCCHHHHHHH T ss_pred HHHHHHCCCCHHHHHHH T ss_conf 99999469999999999 No 10 >>2vdr_B Integrin beta-3; cell adhesion/immune system, alternative splicing, platelet integrin ALPHAIIBBETA3, polymorphism, glycoprotein, cell adhesion, calcium; HET: NAG MAN; 2.40A {Homo sapiens} PDB: 2vc2_B* 2vdk_B* 2vdm_B* 2vdn_B* 2vdl_B* 2vdp_B* 2vdq_B* 2vdo_B* 3fcu_B* 1txv_B* 1ty3_B* 1ty5_B* 1ty6_B* 1ty7_B* 1tye_B* (B:58-109,B:352-437) Probab=24.14 E-value=36 Score=12.96 Aligned_cols=42 Identities=14% Similarity=0.275 Sum_probs=33.2 Q ss_pred CCCCCEEEEEEEEEEEECCEEEEEEE-CHHHEEECCCCCCHHH Q ss_conf 66761577589999974683689857-6587434679988646 Q gi|254781145|r 25 EDGGEKVHDLRIRRKYSQGKVCVDAV-SPDEFLIHPDSVDIEK 66 (350) Q Consensus 25 ~~~~~~~~~v~~~r~~~~~~v~ie~V-~pedf~vdp~A~~l~d 66 (350) -++...++.+++|+..++++|.++.= .|+.+-+++.|...+. T Consensus 36 Rpg~~~~f~~~~rq~eD~S~V~l~~~~~p~~v~isy~s~C~~g 78 (138) T 2vdr_B 36 RPDDSKNFSIQVRQVEDRSKVELEVRDLPEELSLSFNATCLNN 78 (138) T ss_dssp CTTCEEEEEEEEECCSCCEEEEEEEESCCTTEEEEEEEECTTC T ss_pred CCCCCEEEEEEEECCCCHEEEEEECCCCCCCEEEEEEEECCCC T ss_conf 4998289998621377714899852799985799999887999 No 11 >>2cpw_A CBL-interacting protein STS-1 variant; ubiquitin associated domain, UBA, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=23.26 E-value=26 Score=13.96 Aligned_cols=17 Identities=29% Similarity=0.466 Sum_probs=9.2 Q ss_pred HHHHHHHCCCCHHHCCC Q ss_conf 89998727980443027 Q gi|254781145|r 78 RSDLISMGYDRESINNL 94 (350) Q Consensus 78 ~~eL~~~Gy~~d~v~~~ 94 (350) .++|.+|||.+....+. T Consensus 23 v~~L~~MGF~~~~a~kA 39 (64) T 2cpw_A 23 LDVLLSMGFPRARAQKA 39 (64) T ss_dssp HHHHHHHTCCHHHHHHH T ss_pred HHHHHHCCCCHHHHHHH T ss_conf 99999969989999999 No 12 >>2dna_A Unnamed protein product; ubiquitin associated domain, DSK2 protein, proteasome, structural genomics, NPPSFA; NMR {Mus musculus} (A:) Probab=23.22 E-value=22 Score=14.37 Aligned_cols=17 Identities=18% Similarity=0.210 Sum_probs=8.6 Q ss_pred HHHHHHHCC-CCHHHCCC Q ss_conf 899987279-80443027 Q gi|254781145|r 78 RSDLISMGY-DRESINNL 94 (350) Q Consensus 78 ~~eL~~~Gy-~~d~v~~~ 94 (350) .++|.+||| +++...+. T Consensus 23 l~~L~~MGF~d~~~~~~A 40 (67) T 2dna_A 23 MECLQAMGFVNYNANLQA 40 (67) T ss_dssp HHHHHHHTCCCHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHH T ss_conf 999999389969999999 No 13 >>1veg_A NEDD8 ultimate buster-1; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Mus musculus} (A:) Probab=21.81 E-value=22 Score=14.41 Aligned_cols=26 Identities=19% Similarity=0.312 Sum_probs=15.2 Q ss_pred CHHHHHHHCCCCHHHCCCCCCCCCCH Q ss_conf 68999872798044302777876410 Q gi|254781145|r 77 TRSDLISMGYDRESINNLPIISSQNI 102 (350) Q Consensus 77 t~~eL~~~Gy~~d~v~~~~~~~~~~~ 102 (350) +..+|.+|||.++...+.-.....+. T Consensus 32 ~i~~L~~MGF~~~~a~~AL~~~~nnv 57 (83) T 1veg_A 32 SINQLVYMGFDTVVAEAALRVFGGNV 57 (83) T ss_dssp HHHHHHHHSCCHHHHHHHHHHTTTCH T ss_pred HHHHHHHHCCCHHHHHHHHHHHCCCH T ss_conf 89999983423888999999964509 No 14 >>2dai_A Ubadc1, ubiquitin associated domain containing 1; UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=21.26 E-value=24 Score=14.13 Aligned_cols=26 Identities=12% Similarity=0.267 Sum_probs=14.3 Q ss_pred CHHHHHHHCCCCHHHCCCCCCCCCCH Q ss_conf 68999872798044302777876410 Q gi|254781145|r 77 TRSDLISMGYDRESINNLPIISSQNI 102 (350) Q Consensus 77 t~~eL~~~Gy~~d~v~~~~~~~~~~~ 102 (350) ...+|.+|||.++.+.+.-.....+. T Consensus 32 ~i~~L~~MGF~~~~a~~AL~~~~~nv 57 (83) T 2dai_A 32 ALRQLTEMGFPENRATKALQLNHMSV 57 (83) T ss_dssp HHHHHHHHTCCHHHHHHHHHHTTSCH T ss_pred HHHHHHHCCCCHHHHHHHHHHCCCCH T ss_conf 99999996999999999999919999 Done!