Query gi|254780607|ref|YP_003065020.1| hypothetical protein CLIBASIA_02470 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 131 No_of_seqs 104 out of 574 Neff 7.8 Searched_HMMs 23785 Date Tue May 31 19:49:25 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780607.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3gi7_A Secreted protein of unk 99.9 1E-22 4.4E-27 153.2 13.2 112 16-128 3-121 (122) 2 2a3m_A COG3005: nitrate/TMAO r 19.2 19 0.00081 15.1 0.0 17 1-17 1-17 (130) 3 1xdp_A Polyphosphate kinase; P 10.4 70 0.0029 11.8 2.9 51 26-76 69-124 (687) 4 2zzs_A Cytochrome C554; C-type 9.8 52 0.0022 12.5 0.1 14 104-117 86-99 (103) 5 2rno_A Putative DNA-binding pr 8.9 80 0.0034 11.4 1.7 16 101-116 13-28 (110) 6 1dtl_A Cardiac troponin C; hel 8.2 68 0.0029 11.9 0.1 10 27-36 36-45 (161) 7 2gzd_C RAB11 family-interactin 7.2 96 0.004 11.0 1.4 12 107-118 66-77 (107) 8 2p3y_A Hypothetical protein VP 7.0 79 0.0033 11.5 0.0 21 1-21 1-22 (491) 9 2f2f_C CDT C, cytolethal diste 6.8 1E+02 0.0042 10.9 0.5 14 1-14 1-14 (186) 10 2wrg_I Hemagglutinin HA2 chain 6.6 1E+02 0.0043 10.8 3.4 26 37-62 105-130 (222) No 1 >3gi7_A Secreted protein of unknown function DUF1311; NP_742474.1, structural genomics, joint center for structural genomics, JCSG; 1.85A {Pseudomonas putida KT2440} Probab=99.89 E-value=1e-22 Score=153.21 Aligned_cols=112 Identities=17% Similarity=0.360 Sum_probs=100.6 Q ss_pred HHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 1012202378899899999999999999999999999999732------9356899999999999999997887551246 Q gi|254780607|r 16 FQSMALNCNETLMQADMNQCTGNSFALVKEKLEATYKKVLEKV------EKHQRELFEKSQMAWEIYRGSECAFAASGAE 89 (131) Q Consensus 16 ~~a~a~dC~~a~t~~e~~~C~~~~~~~ad~~Ln~~y~~l~~~l------~~~~~~~L~~sQr~W~~~R~~~C~~~~~~~~ 89 (131) ....++||+++.|+.|+++|+..++..+|++||++|+.+++++ +++.++.|+.+|++|++||+++|.+....+. T Consensus 3 ~~~~~~~C~~~~t~~e~~~C~~~~~~~~d~~Ln~~Y~~~~~~l~~~~~~~~~~~~~L~~aQraW~~~Rd~~C~~~~~~~~ 82 (122) T 3gi7_A 3 DEEESTPCDNVETDQQTFACAAFNKQVAERELQSAYDELIERMRDQFGDEAGLMSRIEAAEKVWSQLRDADCKVETHAEQ 82 (122) T ss_dssp ---------CTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSCTTHHHHHHHHHHHHHHHHHHHHHHHTTTSC T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 65568998888987999999999999999999999999998600223247899999999999999999988778750336 Q ss_pred CCCH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 8835-67999999999999999999997137236758899 Q gi|254780607|r 90 EGTA-QSMIYANCLQGHAIERNEKLESYLTCPEGDLLCPF 128 (131) Q Consensus 90 ~Gs~-~~~~~~~C~~~~t~~R~~eL~~~l~~~eg~~~~~~ 128 (131) +||+ +++.+.+|++++|++|+.+|+.+... .+|.++|. T Consensus 83 ~gs~~~~~~~~~C~~~~t~~R~~~L~~l~~~-~~~~pa~~ 121 (122) T 3gi7_A 83 PGSNAYQIAWNSCIAQRSDERAEYLRSLGSQ-NSDEPAPE 121 (122) T ss_dssp TTSHHHHHHHHHHHHHHHHHHHHHHHHHHTC-C------- T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCCCCC T ss_conf 9976788999999999999999999998752-58999999 No 2 >2a3m_A COG3005: nitrate/TMAO reductases, membrane-bound tetraheme cytochrome C subunit; electron transport; HET: HEM; 1.50A {Desulfovibrio desulfuricans subsp} PDB: 2a3p_A* Probab=19.21 E-value=19 Score=15.14 Aligned_cols=17 Identities=12% Similarity=0.212 Sum_probs=8.9 Q ss_pred CCHHHHHHHHHHHHHHH Q ss_conf 92599999999996310 Q gi|254780607|r 1 MCRKIIFALTIIAIAFQ 17 (131) Q Consensus 1 m~k~il~~~~~~~~s~~ 17 (131) |+|.|+.++.+.++++. T Consensus 1 mkk~l~~~~~~~~~~~~ 17 (130) T 2a3m_A 1 MRKSLFAVMVLALVAAF 17 (130) T ss_dssp ----------------- T ss_pred CHHHHHHHHHHHHHHHH T ss_conf 90499999999999999 No 3 >1xdp_A Polyphosphate kinase; PPK, PPK complex with AMPPNP, AMPPNP, transferase; HET: ATP; 2.50A {Escherichia coli} SCOP: a.7.15.1 d.322.1.2 d.136.1.4 d.136.1.4 PDB: 1xdo_A* Probab=10.45 E-value=70 Score=11.80 Aligned_cols=51 Identities=10% Similarity=0.181 Sum_probs=35.8 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH-----HHHHHHHHHHHHHH Q ss_conf 8998999999999999999999999999997329356-----89999999999999 Q gi|254780607|r 26 TLMQADMNQCTGNSFALVKEKLEATYKKVLEKVEKHQ-----RELFEKSQMAWEIY 76 (131) Q Consensus 26 a~t~~e~~~C~~~~~~~ad~~Ln~~y~~l~~~l~~~~-----~~~L~~sQr~W~~~ 76 (131) ..|..+...-.........++.+.+|..++..|..+. .+.|...|+.|++. T Consensus 69 g~tp~eqL~~I~~~v~~l~~~~~~i~~~llp~L~~~gI~il~~~eL~~~qk~~l~~ 124 (687) T 1xdp_A 69 NSHSRHLLGKIQSRVLKADQEFDGLYNELLLEMARNQIFLINERQLSVNQQNWLRH 124 (687) T ss_dssp CSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCEEECGGGCCTTHHHHHHH T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECHHHCCHHHHHHHHH T ss_conf 99999999999999999999999999999999997897995646599999999999 No 4 >2zzs_A Cytochrome C554; C-type cytochrome, electron transport; HET: HEC; 1.80A {Vibrio parahaemolyticus} Probab=9.83 E-value=52 Score=12.55 Aligned_cols=14 Identities=14% Similarity=0.105 Sum_probs=8.5 Q ss_pred HHHHHHHHHHHHHC Q ss_conf 99999999999971 Q gi|254780607|r 104 GHAIERNEKLESYL 117 (131) Q Consensus 104 ~~t~~R~~eL~~~l 117 (131) .++.+-+..|-.|+ T Consensus 86 ~Lsd~ei~~laaYi 99 (103) T 2zzs_A 86 LLSDDDIANLAAYY 99 (103) T ss_dssp TCCHHHHHHHHHHH T ss_pred CCCHHHHHHHHHHH T ss_conf 29999999999999 No 5 >2rno_A Putative DNA-binding protein; SUMO ligase, sumoylation, metal-BI zinc-finger, ligase; NMR {Oryza sativa subsp} Probab=8.86 E-value=80 Score=11.44 Aligned_cols=16 Identities=25% Similarity=0.301 Sum_probs=5.5 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9999999999999997 Q gi|254780607|r 101 CLQGHAIERNEKLESY 116 (131) Q Consensus 101 C~~~~t~~R~~eL~~~ 116 (131) |...+.-=||.||+.. T Consensus 13 Ck~kL~~FrIkeLKDv 28 (110) T 2rno_A 13 CKDKLAYFRIKELKDI 28 (110) T ss_dssp HHHHHHHSCHHHHHHH T ss_pred HHHHHHHHHHHHHHHH T ss_conf 9999878769999999 No 6 >1dtl_A Cardiac troponin C; helix-turn-helix, structural protein; HET: BEP; 2.15A {Gallus gallus} SCOP: a.39.1.5 PDB: 1j1d_A 1j1e_A 2jt3_A 2jt0_A 1la0_A 2jtz_A* 2jt8_A* 2kfx_T* 1wrk_A* 1wrl_A* 1ap4_A 1lxf_C* 1mxl_C 1spy_A 2krd_C* 2l1r_A* 2ctn_A 2kgb_C 2jxl_A 1r2u_A ... Probab=8.19 E-value=68 Score=11.85 Aligned_cols=10 Identities=0% Similarity=0.262 Sum_probs=4.0 Q ss_pred CCHHHHHHHH Q ss_conf 9989999999 Q gi|254780607|r 27 LMQADMNQCT 36 (131) Q Consensus 27 ~t~~e~~~C~ 36 (131) .+-.|...+. T Consensus 36 I~~~el~~~L 45 (161) T 1dtl_A 36 ISTKELGKVM 45 (161) T ss_dssp BCHHHHHHHH T ss_pred ECHHHHHHHH T ss_conf 9999999999 No 7 >2gzd_C RAB11 family-interacting protein 2; G protein folds, A-helical coiled coil, protein transport; HET: GTP; 2.44A {Homo sapiens} SCOP: h.1.31.1 PDB: 2gzh_B* 2k6s_A Probab=7.16 E-value=96 Score=10.98 Aligned_cols=12 Identities=25% Similarity=0.396 Sum_probs=6.9 Q ss_pred HHHHHHHHHHCC Q ss_conf 999999999713 Q gi|254780607|r 107 IERNEKLESYLT 118 (131) Q Consensus 107 ~~R~~eL~~~l~ 118 (131) .+++.||+.|++ T Consensus 66 ~~~irELEDYID 77 (107) T 2gzd_C 66 DTHIRELEDYID 77 (107) T ss_dssp HHHHHHHHHHHH T ss_pred HHHHHHHHHHHH T ss_conf 889999999999 No 8 >2p3y_A Hypothetical protein VPA0735; structural genomics, PSI-2, protein structure initiative; 1.80A {Vibrio parahaemolyticus rimd 2210633} SCOP: e.65.1.1 Probab=7.04 E-value=79 Score=11.47 Aligned_cols=21 Identities=14% Similarity=0.208 Sum_probs=9.4 Q ss_pred CCHHHHHHHH-HHHHHHHHCCC Q ss_conf 9259999999-99963101220 Q gi|254780607|r 1 MCRKIIFALT-IIAIAFQSMAL 21 (131) Q Consensus 1 m~k~il~~~~-~~~~s~~a~a~ 21 (131) |||+|+..++ .++.+..+.+. T Consensus 1 mkk~~l~~a~~~~~ls~~~~a~ 22 (491) T 2p3y_A 1 MKKRILAVAVTSMLLSASVFAQ 22 (491) T ss_dssp ---------------------C T ss_pred CCHHHHHHHHHHHHHHHHHCCC T ss_conf 9178999999999752230145 No 9 >2f2f_C CDT C, cytolethal distending toxin C; actinobacillus actinomycetemcomitans, oligomerization, stability and toxic activity; 2.40A {Aggregatibacter actinomycetemcomitans} SCOP: b.42.2.1 Probab=6.80 E-value=1e+02 Score=10.87 Aligned_cols=14 Identities=14% Similarity=0.192 Sum_probs=9.6 Q ss_pred CCHHHHHHHHHHHH Q ss_conf 92599999999996 Q gi|254780607|r 1 MCRKIIFALTIIAI 14 (131) Q Consensus 1 m~k~il~~~~~~~~ 14 (131) |||++|+++..+.. T Consensus 1 mkK~~i~f~~~l~~ 14 (186) T 2f2f_C 1 MKKYLLSFLLSMIL 14 (186) T ss_dssp -------------- T ss_pred CCHHHHHHHHHHHH T ss_conf 93248999999997 No 10 >2wrg_I Hemagglutinin HA2 chain; viral protein, envelope protein, glycoprotein, lipoprotein; HET: NAG SIA GAL; 3.00A {Influenza a virus} PDB: 2wrh_I* Probab=6.58 E-value=1e+02 Score=10.80 Aligned_cols=26 Identities=12% Similarity=0.319 Sum_probs=20.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHH Q ss_conf 99999999999999999997329356 Q gi|254780607|r 37 GNSFALVKEKLEATYKKVLEKVEKHQ 62 (131) Q Consensus 37 ~~~~~~ad~~Ln~~y~~l~~~l~~~~ 62 (131) ....+..|..+++.|.+++++|.+.. T Consensus 105 q~Tid~~Ds~~~~L~ekvrrqLr~NA 130 (222) T 2wrg_I 105 ERTLDFHDSNVRNLYEKVKSQLKNNA 130 (222) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHGGGE T ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCH T ss_conf 65442114689999999999984115 Done!