Query T0602 3NKZ, Yersinia enterocolitica, 123 residues Match_columns 123 No_of_seqs 89 out of 91 Neff 5.6 Searched_HMMs 22458 Date Mon Jul 5 08:57:38 2010 Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0602.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pdb70_15May10_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pdb70search/T0602.hhr No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3a7m_A Flagellar protein FLIT; 100.0 1.2E-40 5.6E-45 267.6 14.9 120 4-123 1-120 (122) 2 3h3m_A Flagellar protein FLIT; 100.0 2.8E-35 1.2E-39 234.9 11.7 113 2-114 12-124 (126) 3 2fup_A Hypothetical protein PA 68.4 6.2 0.00028 19.1 7.3 102 9-111 14-141 (157) 4 2f86_B Hypothetical protein K1 47.1 14 0.00064 16.8 3.8 28 12-39 9-36 (143) 5 2ux0_A Calcium-calmodulin depe 42.6 17 0.00075 16.4 4.9 37 3-39 1-37 (143) 6 3blz_A NTF2-like protein of un 35.3 22 0.00098 15.7 4.0 35 4-39 2-36 (128) 7 2hz8_A De novo designed DIIRON 32.8 24 0.0011 15.5 4.9 80 4-88 1-84 (115) 8 3h51_A Putative calcium/calmod 30.3 27 0.0012 15.2 2.8 29 12-40 17-45 (156) 9 3bc1_B Synaptotagmin-like prot 29.4 28 0.0012 15.1 2.8 38 69-106 9-46 (59) 10 2r4i_A Uncharacterized protein 26.2 31 0.0014 14.8 3.3 28 14-41 5-32 (123) 11 3e4x_A APC36150; structural ge 21.6 39 0.0017 14.2 2.7 50 1-50 1-65 (157) 12 2rfr_A Uncharacterized protein 21.5 39 0.0017 14.2 3.0 35 6-40 10-44 (155) No 1 >3a7m_A Flagellar protein FLIT; UP-DOWN helix bundle, bacterial flagellum biogenesis, chaper cytoplasm, repressor, transcription; 3.20A {Salmonella typhimurium} Probab=100.00 E-value=1.2e-40 Score=267.60 Aligned_cols=120 Identities=35% Similarity=0.584 Sum_probs=118.4 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 66417899999999999999999886238189999999999999998730588999988899999999999864899999 Q T0602 4 MERHQHLLSEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKAVESTANITISSCSSLMLQDLLREKLRAILDNEIEIKR 83 (123) Q Consensus 4 M~~~~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~ndaeIr~ 83 (123) |+++.++|+.|++|+++|++||++|++||||+|+++|.+|+.+|+.+++.+++++++++++++++++|++||+||++||+ T Consensus 1 M~~~~~ll~~Yq~il~lS~~ML~aA~~gdWd~L~~lE~~y~~~ve~l~~~~~~~~l~~~~~~~~~~lL~~IL~ndaeIr~ 80 (122) T 3a7m_A 1 MTSTVEFINRWQRIALLSQSLLELAQRGEWDLLLQQEVSYLQSIETVMEKQTPPGITRSIQDMVAGYIKQTLDNEQLLKG 80 (122) T ss_dssp -CTTHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSCCCSCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99679999999999999999999988788888999999999999999847899999999999999999999976999999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 9999999999999853556789876642479844789899 Q T0602 84 LLQLRLDRLSDLVGQSTKQQAVNNTYGQFPDHALLLGETQ 123 (123) Q Consensus 84 Llq~rldeL~~li~q~~~q~~l~~aYgqf~~~~l~~~~~~ 123 (123) |++||||+|+.+|+++++||++|+|||||+|++||||+|- T Consensus 81 Ll~~rmdeL~~l~~~~~~q~~l~~aYgqf~g~~l~p~~~~ 120 (122) T 3a7m_A 81 LLQQRLDELSSLIGQSTRQKSLNNAYGRLSGMLLVPDAPG 120 (122) T ss_dssp HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCCCCC---- T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC T ss_conf 9999999999999988887999999875888746899988 No 2 >3h3m_A Flagellar protein FLIT; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.50A {Bordetella bronchiseptica} Probab=100.00 E-value=2.8e-35 Score=234.93 Aligned_cols=113 Identities=28% Similarity=0.431 Sum_probs=110.4 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 75664178999999999999999998862381899999999999999987305889999888999999999998648999 Q T0602 2 NAMERHQHLLSEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKAVESTANITISSCSSLMLQDLLREKLRAILDNEIEI 81 (123) Q Consensus 2 ~~M~~~~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~ndaeI 81 (123) .+|+++.++|++||+|+++|++||++|++||||+|+++|.+|+.+||.|++.+++++++++++++|+++|++||+||++| T Consensus 12 ~~m~~~~~ll~~Yq~I~~lS~~ML~aA~~gdWD~Lv~lE~~y~~lVe~L~~~~~~~~l~~~~~~~k~~lL~~IL~nDaeI 91 (126) T 3h3m_A 12 TALTQHAPVLEIYQDIANLTSRMLAAANASNWDLVLNHGQEYVCLVERLRELEPGEPLDEAARGMKFDLLVRILENDAAV 91 (126) T ss_dssp ------CCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHCSCSCCCSHHHHHHHHHHHHHHHHHHHH T ss_pred HHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 40302439999999999999999999888877889998999999999998558899999999999999999999879999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 999999999999999853556789876642479 Q T0602 82 KRLLQLRLDRLSDLVGQSTKQQAVNNTYGQFPD 114 (123) Q Consensus 82 r~Llq~rldeL~~li~q~~~q~~l~~aYgqf~~ 114 (123) |+|++|||++|+.+|+++++++++|+|||.|++ T Consensus 92 R~Ll~prld~L~~l~~~~~rq~~l~~aYg~~a~ 124 (126) T 3h3m_A 92 RDLALPQLARLSDLLGRMKRQQSLLATYSGKAN 124 (126) T ss_dssp HHHHHHHHHHHHHHC------------------ T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999999999876787799998702037 No 3 >2fup_A Hypothetical protein PA3352; structural genomics, PSI, protein structure initiative, joint center for structural genomics, JCSG; 1.48A {Pseudomonas aeruginosa} SCOP: a.47.5.1 Probab=68.35 E-value=6.2 Score=19.07 Aligned_cols=102 Identities=13% Similarity=0.083 Sum_probs=61.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCC-----------------------CCCCCHH--- Q ss_conf 89999999999999999988623818999999999999999873058-----------------------8999988--- Q T0602 9 HLLSEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKAVESTANITI-----------------------SSCSSLM--- 62 (123) Q Consensus 9 ~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~-----------------------~~~l~~~--- 62 (123) +-+..|+.+..+-++=..+-..+|.|.|..+-..=..+++.+...+. ..+..+. T Consensus 14 ~e~~~~~~L~~lL~~e~~aL~~~d~~~L~~l~~~k~~l~~~l~~l~~~R~~~l~~~g~~~~~~~~~~~~~~~~~~~~l~~ 93 (157) T 2fup_A 14 EDIGHANQLLQLVDEEFQALERRELPVLQQLLGAKQPLMQQLERNGRARAEILREAGVSLDREGLARYARERADGAELLA 93 (157) T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSHHHHHHHHTTCTTHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHHHHH T ss_conf 99999999999999999999808999999999999999999999999999999982899882059998734774599999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8999999999998648999999999999999999853556789876642 Q T0602 63 LQDLLREKLRAILDNEIEIKRLLQLRLDRLSDLVGQSTKQQAVNNTYGQ 111 (123) Q Consensus 63 ~q~~~~~lL~~IL~ndaeIr~Llq~rldeL~~li~q~~~q~~l~~aYgq 111 (123) ..+.+..+++++-+-...=..|++..+......+.-.+.+ .-..+||. T Consensus 94 ~~~~L~~~~~~~~~~N~~N~~Li~~~l~~~~~~l~iL~~~-~~~~~Y~~ 141 (157) T 2fup_A 94 RGDELGELLERCQQANLRNGRIIRANQASTGSLLNILRGQ-DAPSLYDS 141 (157) T ss_dssp HHHHHHHHHHHHHHHHHHHHHC--CTTHHHHHHHHHHC----------- T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCC T ss_conf 9999999999999999999999999999999999985769-88889798 No 4 >2f86_B Hypothetical protein K11E8.1D; UNC-43, oligomerization domain, transferase; 2.64A {Caenorhabditis elegans} SCOP: d.17.4.7 Probab=47.15 E-value=14 Score=16.84 Aligned_cols=28 Identities=14% Similarity=0.323 Sum_probs=24.1 Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHH Q ss_conf 9999999999999998862381899999 Q T0602 12 SEYQQILTLSEQMLVLATEGNWDALVDL 39 (123) Q Consensus 12 ~~Yq~il~lS~~ML~lA~~gdWD~Lv~l 39 (123) +.=|+|..+.++|..+...||||.+..+ T Consensus 9 a~~qeI~~l~~~~~~A~~~~D~d~~~~~ 36 (143) T 2f86_B 9 AQKQDIVRVTQTLLDAISCKDFETYTRL 36 (143) T ss_dssp HHHHHHHHHHHHHHHHHHHTCHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHH T ss_conf 4899999999999999985899999876 No 5 >2ux0_A Calcium-calmodulin dependent protein kinase (CAM kinase) II gamma; transferase, oligomerisation domain, serine- threonine kinase, ATP-binding; 2.46A {Homo sapiens} SCOP: d.17.4.7 PDB: 2w2c_A 1hkx_A* Probab=42.56 E-value=17 Score=16.40 Aligned_cols=37 Identities=22% Similarity=0.480 Sum_probs=32.7 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH Q ss_conf 5664178999999999999999998862381899999 Q T0602 3 AMERHQHLLSEYQQILTLSEQMLVLATEGNWDALVDL 39 (123) Q Consensus 3 ~M~~~~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~l 39 (123) +|....+.-+.-+.|..+.+++..+-..||++.+..+ T Consensus 1 ~~~~~~~~~~~~~eI~~~~~~~~~A~~~~D~~~~~~~ 37 (143) T 2ux0_A 1 SMTEDEDLKVRKQEIIKITEQLIEAINNGDFEAYTKI 37 (143) T ss_dssp CCCHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHH T ss_conf 9653544024899999999999999985899899874 No 6 >3blz_A NTF2-like protein of unknown function; YP_001049020.1, structural genomics, joint center for structural genomics, JCSG; 1.75A {Shewanella baltica OS155} SCOP: d.17.4.14 Probab=35.33 E-value=22 Score=15.71 Aligned_cols=35 Identities=11% Similarity=0.147 Sum_probs=29.2 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH Q ss_conf 664178999999999999999998862381899999 Q T0602 4 MERHQHLLSEYQQILTLSEQMLVLATEGNWDALVDL 39 (123) Q Consensus 4 M~~~~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~l 39 (123) |++. ..++.+++|..+-..-..+-..+|||.|-.+ T Consensus 2 m~~~-~~~~D~~aI~~~~~~Y~~a~d~~D~~~l~~~ 36 (128) T 3blz_A 2 MTNT-TYVQEYHAIVEVLSKYNEGGKKADSTIMRPA 36 (128) T ss_dssp --CC-CHHHHHHHHHHHHHHHHHHHHHTCHHHHGGG T ss_pred CCCC-CCHHHHHHHHHHHHHHHHHHHCCCHHHHHHH T ss_conf 8984-5077999999999999999984899899875 No 7 >2hz8_A De novo designed DIIRON protein; four-helix bundle, de novo protein; NMR {Escherichia coli} Probab=32.81 E-value=24 Score=15.46 Aligned_cols=80 Identities=24% Similarity=0.267 Sum_probs=51.9 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH----HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 664178999999999999999998862381899999999999----9999873058899998889999999999986489 Q T0602 4 MERHQHLLSEYQQILTLSEQMLVLATEGNWDALVDLEMTYLK----AVESTANITISSCSSLMLQDLLREKLRAILDNEI 79 (123) Q Consensus 4 M~~~~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~----~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~nda 79 (123) |+....++..-++...+-.+.|--|+.||=.+|..+-.+-.. ++..-+.+..-...+ .++..|.+||++|. T Consensus 1 mdelrellkaeqqaikiykevlkkakegdeqelarllrEl~K~E~Qa~K~YrEA~E~~~nP-----ek~~Vl~KILEDEE 75 (115) T 2hz8_A 1 MDELRELLKAEQQAIKIYKEVLKKAKEGDEQELARLIQEIVKAEKQAVKVYKEAAEKARNP-----EKRQVIDKILEDEE 75 (115) T ss_dssp CCTHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHTTTHHHHHHHHHHHHHHHHHHHHSCCCT-----TTTTTHHHHHHHHH T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-----HHHHHHHHHHHHHH T ss_conf 9588999998999999999999885026599999999999999999999999999883696-----48789999988489 Q ss_pred HHHHHHHHH Q ss_conf 999999999 Q T0602 80 EIKRLLQLR 88 (123) Q Consensus 80 eIr~Llq~r 88 (123) .--.++++- T Consensus 76 KHIEWLeaa 84 (115) T 2hz8_A 76 KHIEWLKAA 84 (115) T ss_dssp HHHHHHHHH T ss_pred HHHHHHHHH T ss_conf 999999998 No 8 >3h51_A Putative calcium/calmodulin dependent protein kinase II association domain; NP_636218.1, structural genomics; HET: MSE PG4; 1.70A {Xanthomonas campestris PV} Probab=30.30 E-value=27 Score=15.20 Aligned_cols=29 Identities=21% Similarity=0.219 Sum_probs=24.3 Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 99999999999999988623818999999 Q T0602 12 SEYQQILTLSEQMLVLATEGNWDALVDLE 40 (123) Q Consensus 12 ~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE 40 (123) +.-++|..+-+++..+-.++|||.+..+= T Consensus 17 ~de~eI~al~~~~~~A~~~~D~d~~~~~~ 45 (156) T 3h51_A 17 GEAREVAALFDTWNAALATGNPHKVADLY 45 (156) T ss_dssp SHHHHHHHHHHHHHHHHHHTCHHHHHTTE T ss_pred CCHHHHHHHHHHHHHHHHCCCHHHHHHHH T ss_conf 76999999999999999859999999750 No 9 >3bc1_B Synaptotagmin-like protein 2; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophilin-4, GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Homo sapiens} Probab=29.43 E-value=28 Score=15.11 Aligned_cols=38 Identities=16% Similarity=0.339 Sum_probs=29.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999986489999999999999999998535567898 Q T0602 69 EKLRAILDNEIEIKRLLQLRLDRLSDLVGQSTKQQAVN 106 (123) Q Consensus 69 ~lL~~IL~ndaeIr~Llq~rldeL~~li~q~~~q~~l~ 106 (123) ..|-++|.-|+++|..=+-|.-.|.+-+..-.+-+.++ T Consensus 9 ~aI~~VL~RDaeLk~~Ee~RV~kL~~t~~D~~~lk~lt 46 (59) T 3bc1_B 9 EAIMKVLQRDAALKRAEEERVRHLPEKIKDDQQLKNMS 46 (59) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHGGGTCCCHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH T ss_conf 99999998629998848778999987117899996123 No 10 >2r4i_A Uncharacterized protein; YP_678039.1, NTF2-like protein of unknown function, structural genomics; HET: MSE CIT; 1.60A {Cytophaga hutchinsonii atcc 33406} SCOP: d.17.4.15 Probab=26.17 E-value=31 Score=14.75 Aligned_cols=28 Identities=18% Similarity=0.188 Sum_probs=23.2 Q ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHH Q ss_conf 9999999999999886238189999999 Q T0602 14 YQQILTLSEQMLVLATEGNWDALVDLEM 41 (123) Q Consensus 14 Yq~il~lS~~ML~lA~~gdWD~Lv~lE~ 41 (123) =+.|..+..++.+|...+|++.+.++=. T Consensus 5 ~~~I~~~~~~~~~A~~~~D~~~l~~l~~ 32 (123) T 2r4i_A 5 RDVILDCEKKLLTAIQNNDVESLEVLLH 32 (123) T ss_dssp HHHHTHHHHHHHHHHHHTCHHHHHHHEE T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHC T ss_conf 9999999999999998699999997504 No 11 >3e4x_A APC36150; structural genomics, DINB superfamily, PSI-2, protein structure initiative; 2.51A {Geobacillus stearothermophilus} PDB: 3gor_A Probab=21.57 E-value=39 Score=14.21 Aligned_cols=50 Identities=14% Similarity=0.223 Sum_probs=36.3 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHH---------------HHHHHHHHHHHHHHHH Q ss_conf 9756641789999999999999999988623818---------------9999999999999998 Q T0602 1 SNAMERHQHLLSEYQQILTLSEQMLVLATEGNWD---------------ALVDLEMTYLKAVEST 50 (123) Q Consensus 1 ~~~M~~~~~ll~~Yq~il~lS~~ML~lA~~gdWD---------------~Lv~lE~~y~~~Ve~l 50 (123) ||+|+....++..|+..-..+.+.++.--..+|+ .++..+..+...+..- T Consensus 1 ~~~m~~~~~~i~~~~~~r~~~~~~l~~l~~e~l~~~p~~~~~Si~~ll~Hi~~~~~~~~~~~~~~ 65 (157) T 3e4x_A 1 SNAMSRAKKWVQYFLSHRHVTMELIHKIDEAHYDYKPTPTSMTAKQLATHMLFSFYNFANTAKHG 65 (157) T ss_dssp CCTTCHHHHHHHHHHHHHHHHHHHHHTCCGGGTTCCSSTTSCCHHHHHHHHHHHHHHHHHHHHHT T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC T ss_conf 99787999999999999999999998199999378889988779999999998888999987276 No 12 >2rfr_A Uncharacterized protein; YP_001166107.1, structural genomics, joint center for structural genomics, JCSG; 1.16A {Novosphingobium aromaticivorans DSM12444} SCOP: d.17.4.28 Probab=21.47 E-value=39 Score=14.20 Aligned_cols=35 Identities=29% Similarity=0.314 Sum_probs=28.9 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 41789999999999999999988623818999999 Q T0602 6 RHQHLLSEYQQILTLSEQMLVLATEGNWDALVDLE 40 (123) Q Consensus 6 ~~~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE 40 (123) ..-.-|..-++|..+......+...+|||.+.++= T Consensus 10 ~rl~~led~~aI~~l~~~y~~~~D~~d~~~~~~lF 44 (155) T 2rfr_A 10 ARLRLLEDREEIRELIARYGPLADSGDAEALSELW 44 (155) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHTTE T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC T ss_conf 99999999999999999999998289999998744 Done!