Query gi|254781113|ref|YP_003065526.1| amino acid ABC transporter (permease) [Candidatus Liberibacter asiaticus str. psy62] Match_columns 226 No_of_seqs 117 out of 6342 Neff 7.4 Searched_HMMs 23785 Date Wed Jun 1 01:03:44 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781113.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3dhw_A D-methionine transport 100.0 5.1E-33 2.1E-37 198.9 9.9 207 13-220 5-217 (217) 2 3d31_C Sulfate/molybdate ABC t 100.0 4.1E-28 1.7E-32 171.9 14.0 205 15-223 78-295 (295) 3 2onk_C Molybdate/tungstate ABC 99.9 6.1E-26 2.6E-30 160.0 11.8 203 15-221 68-281 (284) 4 2r6g_F Maltose transport syste 99.9 3.1E-21 1.3E-25 134.1 14.2 201 15-216 275-511 (514) 5 2r6g_G Maltose transport syste 99.8 1.2E-18 5.2E-23 119.8 13.0 153 17-170 81-237 (296) 6 3dhw_A D-methionine transport 88.9 0.17 7.3E-06 25.7 2.2 47 170-216 171-217 (217) 7 1umq_A Photosynthetic apparatu 73.1 3.5 0.00015 18.6 4.0 35 106-140 42-76 (81) 8 1eto_A FIS, factor for inversi 72.8 3.5 0.00015 18.5 4.0 33 107-139 60-92 (98) 9 1ntc_A Protein (nitrogen regul 72.2 3 0.00013 18.9 3.5 34 106-139 52-85 (91) 10 3e7l_A Transcriptional regulat 63.1 6.2 0.00026 17.2 4.0 35 105-139 19-53 (63) 11 1g2h_A Transcriptional regulat 52.6 9.5 0.0004 16.1 3.8 35 104-139 20-54 (61) 12 1ojl_A Transcriptional regulat 45.5 12 0.00052 15.5 3.6 31 109-139 272-302 (304) 13 2cw1_A SN4M; lambda CRO fold, 37.2 12 0.0005 15.6 1.6 16 118-133 13-28 (65) 14 1i3j_A I-TEVI, intron-associat 28.6 24 0.001 14.0 2.4 24 119-142 84-107 (116) No 1 >3dhw_A D-methionine transport system permease protein METI; ABC-transporter, methionine uptake transporter, membrane protein, amino-acid transport; 3.70A {Escherichia coli K12} SCOP: f.58.1.1 Probab=100.00 E-value=5.1e-33 Score=198.85 Aligned_cols=207 Identities=19% Similarity=0.288 Sum_probs=166.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 999999999999999999999999999999999970------67637999999999998555322222211122333210 Q gi|254781113|r 13 FPQLLYAAIVVTLPIACISFVISLIIGFFIAVIRIF------FSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIGI 86 (226) Q Consensus 13 ~~~~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~------~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g~ 86 (226) .-.++++++++|+.+++.+++++.++|+++|+.... ..+++.......++.+++++|.+++++......+.... T Consensus 5 ~~~l~l~~~~~Tl~~a~~~~~~~~~ig~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ip~~~~~~~~~~~~~~~~~ 84 (217) T 3dhw_A 5 MMWLLVRGVWETLAMTFVSGFFGFVIGLPVGVLLYVTRPGQIIANAKLYRTVSAIVNIFRSIPFIILLVWMIPFTRVIVG 84 (217) T ss_dssp -CHHHHHHHHHHHHHHHHHHHHHHHTTGGGGGGGGGGTTCSSSCCSSHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTC T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999999999999999986444320089999999999999999999999999999999986 Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 14433333310011000001578999887528336899865174635657787522357644567787889875267999 Q gi|254781113|r 87 VFDSFVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTSVA 166 (226) Q Consensus 87 ~~~~~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~tsl~ 166 (226) ...++..+++++++...||+.+.++++++++|++++||||++|+|+||++|||++||++|.+++++.+.++..++++++. T Consensus 85 ~~~~~~~~ii~~~~~~~~~~~~~~~~~l~~i~~~~~eAA~~lGas~~q~f~~vilP~~~p~ii~~~~~~~~~~i~~~~i~ 164 (217) T 3dhw_A 85 TSIGLQAAIVPLTVGAAPFIARMVENALLEIPTGLIEASRAMGATPMQIVRKVLLPEALPGLVNAATITLITLVGYSAMG 164 (217) T ss_dssp CSSSHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTTTTHHHHHTCCTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 12369999999999867999999999998589899999871898989996974199789999999999999999999999 Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 997699999999999832357799999999999999999999999999986213 Q gi|254781113|r 167 STITIPEIFQTAQRIVSTTYQPLIIYCELAFVYLILTSFCYIIQIKIESSVTQH 220 (226) Q Consensus 167 s~ig~~el~~~a~~i~~~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr~~~~ 220 (226) +.+|.+++.....+.....++. +......+++.+++.....+.++++||++|| T Consensus 165 ~~ig~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~rR 217 (217) T 3dhw_A 165 GAVGAGGLGQIGYQYGYIGYNA-TVMNTVLVLLVILVYLIQFAGDRIVRAVTRK 217 (217) T ss_dssp CSTTCCHHHHHHHHHHHSSCCT-THHHHHHHHHHHHHHHHHHHCC--------- T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 9998879999999999986008-9999999999999999999999999975699 No 2 >3d31_C Sulfate/molybdate ABC transporter, permease protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: f.58.1.1 Probab=99.96 E-value=4.1e-28 Score=171.89 Aligned_cols=205 Identities=11% Similarity=0.121 Sum_probs=154.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------- Q ss_conf 99999999999999999999999999999999706763799999999999855532222221112233321--------- Q gi|254781113|r 15 QLLYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIG--------- 85 (226) Q Consensus 15 ~~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g--------- 85 (226) ..+++++++|+.+++++++++.++|+++|....+.+.+. ++.......+...+|..+..+..+......| T Consensus 78 ~~~~~~i~~Tl~~a~~s~~i~~ilg~~~a~~l~~~~~~~-~~~~~~l~~~p~~~p~~v~~~~~~~~~~~~g~~~~~~~~~ 156 (295) T 3d31_C 78 RSVISSIFLSLYAGFLATLLALLLGAPTGYILARFDFPG-KRLVESIIDVPVVVPHTVAGIALLTVFGSRGLIGEPLESY 156 (295) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCTT-HHHHHHHHHGGGTSCHHHHHHHHHHHHSTTSTTTGGGTTT T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHCC T ss_conf 899999999999999999999999999999999645435-8999999999999998889999999861246533210102 Q ss_pred -CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf -0144333333100110000015789998875283368998651746356577875223576445677878898752679 Q gi|254781113|r 86 -IVFDSFVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTS 164 (226) Q Consensus 86 -~~~~~~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~ts 164 (226) ....++.+.+++.++...||..+.++++++++|++++|||+++|+|+||++|||++|++.|.++++....++..+++.. T Consensus 157 ~~~~~~~~~iii~~~~~~~p~~~~~~~~~l~~i~~~~~eAA~~~Gas~~~~~~~IiLP~~~p~i~~~~~l~f~~~~~~f~ 236 (295) T 3d31_C 157 IQFRDALPGIVVAMLFVSMPYLANSAREGFKSVDPRLENAARSLGAPLWKAFFFVTLPLSARYLLIGSVMTWARAISEFG 236 (295) T ss_dssp CCCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTTCCHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTCCH T ss_pred CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHCCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 67125789999999998074432015788873152699999984999366323533998999999999999999999999 Q ss_pred HHHHHHHHHHHHH---HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 9999769999999---9999832357799999999999999999999999999986213747 Q gi|254781113|r 165 VASTITIPEIFQT---AQRIVSTTYQPLIIYCELAFVYLILTSFCYIIQIKIESSVTQHTYS 223 (226) Q Consensus 165 l~s~ig~~el~~~---a~~i~~~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr~~~~~~~ 223 (226) ....+|..+.... -+...+.++ +...+.+++.++++..+..+.+++|||+++|||+ T Consensus 237 ~~~~l~~~~~~~~~~i~~~~~~~~~---~~a~a~a~il~ii~l~i~~~~~~L~~~~~~~~r~ 295 (295) T 3d31_C 237 AVVILAYYPMVGPTLIYDRFISYGL---SASRPIAVLLILVTLSIFLVIRTLSAGWSIYDRD 295 (295) T ss_dssp HHHHHHCTTCCHHHHHHHHHHHSTT---TTTHHHHHHHHHHHHHHHHHHC------------ T ss_pred HHHHHHCCCCHHHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHCCC T ss_conf 9998848973499999999993489---9999999999999999999999999745033579 No 3 >2onk_C Molybdate/tungstate ABC transporter, permease protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: f.58.1.1 Probab=99.93 E-value=6.1e-26 Score=159.99 Aligned_cols=203 Identities=13% Similarity=0.098 Sum_probs=144.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-------- Q ss_conf 999999999999999999999999999999997067637999999999998555322222211122333210-------- Q gi|254781113|r 15 QLLYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIGI-------- 86 (226) Q Consensus 15 ~~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g~-------- 86 (226) ..+++++++|+.++++++++++++|+++|....+++.+ .+...+....+...+|.++..+...+.....+. T Consensus 68 ~~~~~~~~~Sl~~a~~s~~l~~~ig~~~a~~l~~~~~~-~~~~~~~l~~~p~~iP~~v~~~~~~~~~~~~~~~~~~~~~~ 146 (284) T 2onk_C 68 PAVWKVVLTTYYAALISTLIAVIFGTPLAYILARKSFP-GKSVVEGIVDLPVVIPHTVAGIALLVVFGSSGLIGSFSPLK 146 (284) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCCS-SHHHHHHHHHHHHHSCHHHHHHHHHHHHSTTSTTTTTCSSC T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCH T ss_conf 79999999999999999999999999999999982644-89999999997874451445666655331225567621000 Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 14433333310011000001578999887528336899865174635657787522357644567787889875267999 Q gi|254781113|r 87 VFDSFVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTSVA 166 (226) Q Consensus 87 ~~~~~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~tsl~ 166 (226) ....+.+.+++.++...||..++.+++++++|+++.|||+++|+|+||++|||++|++.|.++++....+...+++.... T Consensus 147 ~~~~~~~iil~~~~~~~p~~~~~~~~~l~~i~~~l~eaA~~lGas~~~~~~~IilP~~~p~i~~~~il~f~~~~~~~~~~ 226 (284) T 2onk_C 147 FVDALPGIVVAMLFVSVPIYINQAKEGFASVDVRLEHVARTLGSSPLRVFFTVSLPLSVRHIVAGAIMSWARGISEFGAV 226 (284) T ss_dssp CTTSHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTTCCHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCCHHH T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCCEEEHEEEHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 32106999999886146502223435531588568999997598935301102499999999999999999999999999 Q ss_pred HHHHHHHHH---HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 997699999---9999998323577999999999999999999999999999862137 Q gi|254781113|r 167 STITIPEIF---QTAQRIVSTTYQPLIIYCELAFVYLILTSFCYIIQIKIESSVTQHT 221 (226) Q Consensus 167 s~ig~~el~---~~a~~i~~~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr~~~~~ 221 (226) ..++..... ...+...+.++.. ....+.+.++++..+..+.+++++|-+.+| T Consensus 227 ~~l~~~~~~~~~~i~~~~~~~~~~~---~~a~a~il~~i~l~~~~~~~~l~~r~~~~~ 281 (284) T 2onk_C 227 VVIAYYPMIAPTLIYERYLSEGLSA---AMPVAAILILLSLAVFVALRIIVGREDVSE 281 (284) T ss_dssp HTTCCSSCCHHHHHHHHHHHHCGGG---THHHHHHHHHHHHHHHHHHHHTTC------ T ss_pred HHHHCCCCHHHHHHHHHHHCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 9882898529999999998058999---999999999999999999999997137743 No 4 >2r6g_F Maltose transport system permease protein MALF; ABC transporter, catalytic intermediate, E. coli maltose transporter, MBP; HET: MAL ATP; 2.80A {Escherichia coli K12} SCOP: e.70.1.1 f.58.1.1 PDB: 3fh6_F Probab=99.87 E-value=3.1e-21 Score=134.11 Aligned_cols=201 Identities=16% Similarity=0.173 Sum_probs=136.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH--------- Q ss_conf 9999999999999999999999999999999970676379999999999985553222222111223-332--------- Q gi|254781113|r 15 QLLYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGL-PHI--------- 84 (226) Q Consensus 15 ~~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~-~~~--------- 84 (226) +.+++.+.+|+..+++++++++++|++++....+. +...+...+....+...+|.++..+.+.+.+ +.. T Consensus 275 ~~~~~sl~~t~~~a~~s~~l~~~~gl~la~~~~~~-~~r~~~~~~~l~~lP~~iP~iv~~l~~~~lf~~~~G~i~~~l~~ 353 (514) T 2r6g_F 275 KPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWE-ALRGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSA 353 (514) T ss_dssp TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCS-SSTTHHHHHHHTTHHHHSCHHHHHHHHHHHTCSSSSHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHEEHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH T ss_conf 89999999999998788999999999999998641-23511130251269999999999999999871244235556664 Q ss_pred --HCCC----C---CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf --1014----4---333333100110000015789998875283368998651746356577875223576445677878 Q gi|254781113|r 85 --GIVF----D---SFVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSE 155 (226) Q Consensus 85 --g~~~----~---~~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~ 155 (226) |... + ...+.+++..+...||+..+++++++++|++++|||+.+|+|+||++|||++|++.|.+++..... T Consensus 354 l~g~~~~~l~~~~~~~~~vil~~~~~~~P~~~~i~~~al~sIp~~l~EAA~idGAs~~q~f~~I~lPll~p~i~~~~il~ 433 (514) T 2r6g_F 354 LFGVKPAWFSDPTTARTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIAS 433 (514) T ss_dssp TSSCCCCTTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSCTHHHHHHHHTCCCSHHHHHHTTGGGTHHHHHHHHHHH T ss_pred CCCCCCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHEEEHHHHHHHHHHHHHHH T ss_conf 04888503137687799999999988887877765544316985899999975988622301130364699999999999 Q ss_pred HHHHHHHHHHHHHHHH--------------HH-HHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8987526799999769--------------99-9999999983--235779999999999999999999999999998 Q gi|254781113|r 156 FISILKSTSVASTITI--------------PE-IFQTAQRIVS--TTYQPLIIYCELAFVYLILTSFCYIIQIKIESS 216 (226) Q Consensus 156 ~i~lik~tsl~s~ig~--------------~e-l~~~a~~i~~--~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr 216 (226) ++..+++..+...+.- .| +.....+... .....+....+.+++.++++..+..+..+..|| T Consensus 434 f~~~~~~F~~~~lLt~Ggp~~~~~~~~~~~t~~l~~~~y~~af~~~~~~~~g~AaAiavil~liv~~l~~i~~r~~r~ 511 (514) T 2r6g_F 434 FAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIAFEGGGGQDFGLAAAIATLIFLLVGALAIVNLKATRM 511 (514) T ss_dssp HHHHHTCHHHHHHHCSSCSBCSSCSSCCBSSCCHHHHHHHHHTSSSSCCCHHHHHHHHHHHHHHHHHHHHC------- T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999888999994799875555565406889999999999851545678999999999999999999999999811 No 5 >2r6g_G Maltose transport system permease protein MALG; ABC transporter, catalytic intermediate, E. coli maltose transporter, MBP; HET: MAL ATP; 2.80A {Escherichia coli K12} SCOP: f.58.1.1 PDB: 3fh6_G Probab=99.79 E-value=1.2e-18 Score=119.85 Aligned_cols=153 Identities=18% Similarity=0.107 Sum_probs=108.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCCC Q ss_conf 99999999999999999999999999999970676379999999999985553222222111223332101----44333 Q gi|254781113|r 17 LYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIGIV----FDSFV 92 (226) Q Consensus 17 l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g~~----~~~~~ 92 (226) ++.++.||+.+++.++++++++|.+.|..-.+.+.+..+..... ....-.+|..+.....+......|.. ..... T Consensus 81 ~~~~l~nSl~~a~~~~~~~~~i~~~~a~~l~r~~~~~~~~~~~~-~~~~~~~~~~~~~i~~~~~~~~~g~~~~~~~~~~~ 159 (296) T 2r6g_G 81 VLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKG-MLIFQMFPAVLSLVALYALFDRLGEYIPFIGLNTH 159 (296) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCTTSHHHHHH-HHHTTSSCSSSHHHHHHHHHHHHHHHSTTSSTTSH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH-HHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHCCCH T ss_conf 99999999999999999999999999999983478517999999-98622476779899999999861421344302336 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 333100110000015789998875283368998651746356577875223576445677878898752679999976 Q gi|254781113|r 93 AIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTSVASTIT 170 (226) Q Consensus 93 ~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~tsl~s~ig 170 (226) .+++...+...|+...+++++++++|++++|||+.+|+|+||++|||++|+..|.++.+..-.++..+++-......+ T Consensus 160 ~~vi~~~~~~~pf~~~~~~~~l~~ip~~l~EAA~~dGAs~~~~f~~I~lPll~p~i~~~~~l~fi~~~~~f~~~~~~~ 237 (296) T 2r6g_G 160 GGVIFAYLGGIALHVWTIKGYFETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLL 237 (296) T ss_dssp HHHHHHHTTTTHHHHHHHHHHHTTSCTHHHHHHHHTTCCHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTCCHHHHHHC T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHCEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 999999999999899999999973407778889875993033243899847568999999999999999768888135 No 6 >3dhw_A D-methionine transport system permease protein METI; ABC-transporter, methionine uptake transporter, membrane protein, amino-acid transport; 3.70A {Escherichia coli K12} SCOP: f.58.1.1 Probab=88.88 E-value=0.17 Score=25.70 Aligned_cols=47 Identities=9% Similarity=-0.094 Sum_probs=30.6 Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 69999999999983235779999999999999999999999999998 Q gi|254781113|r 170 TIPEIFQTAQRIVSTTYQPLIIYCELAFVYLILTSFCYIIQIKIESS 216 (226) Q Consensus 170 g~~el~~~a~~i~~~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr 216 (226) |.++.....+....+............+++++++...+.+.+++||| T Consensus 171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~rR 217 (217) T 3dhw_A 171 GLGQIGYQYGYIGYNATVMNTVLVLLVILVYLIQFAGDRIVRAVTRK 217 (217) T ss_dssp HHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHCC--------- T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 99999999999860089999999999999999999999999975699 No 7 >1umq_A Photosynthetic apparatus regulatory protein; DNA-binding protein, response regulator, DNA binding domain, helix-turn-helix; NMR {Rhodobacter sphaeroides} SCOP: a.4.1.12 Probab=73.07 E-value=3.5 Score=18.56 Aligned_cols=35 Identities=11% Similarity=0.072 Sum_probs=29.1 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 15789998875283368998651746356577875 Q gi|254781113|r 106 ISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHII 140 (226) Q Consensus 106 ~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~ii 140 (226) =-+.++.+++.-+-.+-+||+.||.|+...++|+- T Consensus 42 Er~~I~~aL~~~~GN~s~AAr~LGIsR~TLyrklk 76 (81) T 1umq_A 42 RWEHIQRIYEMCDRNVSETARRLNMHRRTLQRILA 76 (81) T ss_dssp HHHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHHH T ss_pred HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH T ss_conf 99999999999727799999997989999999999 No 8 >1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} SCOP: a.4.1.12 PDB: 1etq_A 1ety_A 1fia_A 3fis_A 3iv5_A* 3jr9_A* 3jra_A* 3jrb_A* 3jrc_A* 3jrd_A* 3jre_A* 3jrf_A* 3jrg_A* 3jrh_A* 3jri_A* 1f36_A 1etv_A 1etk_A 1etx_A 1fip_A ... Probab=72.82 E-value=3.5 Score=18.52 Aligned_cols=33 Identities=12% Similarity=0.182 Sum_probs=28.2 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 578999887528336899865174635657787 Q gi|254781113|r 107 SEIIRSSIISIPKGQWDASYAIGLTRKQTIRHI 139 (226) Q Consensus 107 ~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i 139 (226) -+.++.+++.-.-.+.+||+.+|.|+...++|+ T Consensus 60 ~~~I~~aL~~~~gn~~~aA~~LGisR~tL~~kl 92 (98) T 1eto_A 60 QPLLDMVMQYTLGNQTRAALMMGINRGTLRKKL 92 (98) T ss_dssp HHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHH T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH T ss_conf 999999999919988999999798999999999 No 9 >1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12 Probab=72.16 E-value=3 Score=18.88 Aligned_cols=34 Identities=6% Similarity=0.114 Sum_probs=28.2 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 1578999887528336899865174635657787 Q gi|254781113|r 106 ISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHI 139 (226) Q Consensus 106 ~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i 139 (226) =.++++.+++...-.+.+||+.+|.|+-...+|+ T Consensus 52 Er~lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~Kl 85 (91) T 1ntc_A 52 ERTLLTTALRHTQGHKQEAARLLGWGAATLTAKL 85 (91) T ss_dssp HHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHH T ss_pred HHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH T ss_conf 9999999999968959999999798999999999 No 10 >3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} Probab=63.09 E-value=6.2 Score=17.17 Aligned_cols=35 Identities=14% Similarity=0.151 Sum_probs=28.8 Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 01578999887528336899865174635657787 Q gi|254781113|r 105 YISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHI 139 (226) Q Consensus 105 ~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i 139 (226) +=.+.++.+++.-+-.+-+||+.+|.++...++++ T Consensus 19 ~E~~~I~~aL~~~~gn~s~aA~~Lgi~r~tL~~kl 53 (63) T 3e7l_A 19 FEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKI 53 (63) T ss_dssp HHHHHHHHHHHHTTTCHHHHHHHHTCCHHHHHHHH T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH T ss_conf 99999999999919989999999897999999999 No 11 >1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} SCOP: a.4.1.12 Probab=52.55 E-value=9.5 Score=16.15 Aligned_cols=35 Identities=6% Similarity=0.184 Sum_probs=27.8 Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 001578999887528336899865174635657787 Q gi|254781113|r 104 AYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHI 139 (226) Q Consensus 104 ~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i 139 (226) .|=-++++.+++.- .+..+||+.+|.|+...++++ T Consensus 20 ~~Ek~~I~~aL~~~-g~~~~aA~~Lgisr~tL~rKl 54 (61) T 1g2h_A 20 FYEAQVLKLFYAEY-PSTRKLAQRLGVSHTAIANKL 54 (61) T ss_dssp HHHHHHHHHHHHHS-CSHHHHHHHTTSCTHHHHHHH T ss_pred HHHHHHHHHHHHHC-CCHHHHHHHHCCCHHHHHHHH T ss_conf 99999999999996-899999999797899999999 No 12 >1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium} Probab=45.47 E-value=12 Score=15.51 Aligned_cols=31 Identities=19% Similarity=0.362 Sum_probs=16.4 Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 8999887528336899865174635657787 Q gi|254781113|r 109 IIRSSIISIPKGQWDASYAIGLTRKQTIRHI 139 (226) Q Consensus 109 i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i 139 (226) .+..+++.-...+.+||+.+|+|+...+||+ T Consensus 272 ~I~~aL~~~~gn~~~aA~~LGisR~tLyrkl 302 (304) T 1ojl_A 272 VILAALEKTGGNKTEAARQLGITRKTLLAKL 302 (304) T ss_dssp HHHHHHHTTTTCHHHHHHHHTSCHHHHHHHT T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH T ss_conf 9999999929989999999888999999986 No 13 >2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1 Probab=37.18 E-value=12 Score=15.59 Aligned_cols=16 Identities=44% Similarity=0.464 Sum_probs=14.3 Q ss_pred CCCHHHHHHHHCCCHH Q ss_conf 8336899865174635 Q gi|254781113|r 118 PKGQWDASYAIGLTRK 133 (226) Q Consensus 118 ~~~~~EAA~alG~s~~ 133 (226) |+.|.-|||++|.|.. T Consensus 13 dknqeyaaralglsqk 28 (65) T 2cw1_A 13 DKNQEYAARALGLSQK 28 (65) T ss_dssp TSCHHHHHHHSSSCHH T ss_pred HHHHHHHHHHHCCHHH T ss_conf 0028899998411699 No 14 >1i3j_A I-TEVI, intron-associated endonuclease 1; protein-DNA complex, extended structure, Zn-finger, minor groove helix, helix-turn-helix; 2.20A {Enterobacteria phage T4} SCOP: d.285.1.1 PDB: 1t2t_A Probab=28.59 E-value=24 Score=13.96 Aligned_cols=24 Identities=8% Similarity=-0.025 Sum_probs=19.9 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 336899865174635657787522 Q gi|254781113|r 119 KGQWDASYAIGLTRKQTIRHIILP 142 (226) Q Consensus 119 ~~~~EAA~alG~s~~q~~~~iilP 142 (226) .+..|||+.+|.+.-.+.+|+-=| T Consensus 84 ~S~~EAAr~Lgis~~TI~~RiKs~ 107 (116) T 1i3j_A 84 DCAADAARHFKISSGLVTYRVKSD 107 (116) T ss_dssp SSHHHHHHHHTCCHHHHHHHHHCT T ss_pred CCHHHHHHHHCCCHHHHHHHHHCC T ss_conf 289999999689837789987088 Done!