Query 013236
Match_columns 447
No_of_seqs 153 out of 224
Neff 6.7
Searched_HMMs 29240
Date Mon Mar 25 06:46:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013236.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/013236hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3nfi_A DNA-directed RNA polyme 100.0 1.5E-46 5E-51 361.8 12.6 188 246-438 17-237 (237)
2 3nff_A RNA polymerase I subuni 99.8 2.8E-19 9.6E-24 152.5 8.8 101 55-175 10-113 (122)
3 3nfg_A DNA-directed RNA polyme 99.8 3.5E-19 1.2E-23 148.0 9.1 82 55-156 10-91 (102)
4 1nd9_A Translation initiation 59.5 7 0.00024 26.6 3.0 25 395-419 4-28 (49)
5 3mkl_A HTH-type transcriptiona 55.9 10 0.00034 31.0 3.9 30 393-422 23-52 (120)
6 3oio_A Transcriptional regulat 51.6 16 0.00055 29.3 4.4 29 394-422 24-53 (113)
7 2jt1_A PEFI protein; solution 49.0 31 0.0011 26.4 5.4 48 370-417 1-48 (77)
8 3lsg_A Two-component response 48.4 27 0.00093 27.3 5.3 34 389-422 15-49 (103)
9 2k9s_A Arabinose operon regula 48.2 13 0.00046 29.5 3.4 35 388-422 15-50 (107)
10 3mn2_A Probable ARAC family tr 47.2 25 0.00087 27.7 4.9 29 394-422 19-48 (108)
11 3oou_A LIN2118 protein; protei 43.7 23 0.00078 28.1 4.1 30 393-422 21-51 (108)
12 1bl0_A Protein (multiple antib 39.6 45 0.0015 27.3 5.5 29 394-422 28-57 (129)
13 2o3f_A Putative HTH-type trans 34.2 28 0.00096 28.4 3.2 59 354-420 8-66 (111)
14 3iwf_A Transcription regulator 33.4 30 0.001 28.1 3.3 59 354-420 4-62 (107)
15 1fse_A GERE; helix-turn-helix 33.2 51 0.0018 23.7 4.3 27 389-417 24-50 (74)
16 2jpc_A SSRB; DNA binding prote 30.7 63 0.0021 22.4 4.3 32 384-417 6-37 (61)
17 1jko_C HIN recombinase, DNA-in 29.0 38 0.0013 22.2 2.7 32 386-419 16-47 (52)
18 3gbg_A TCP pilus virulence reg 28.5 31 0.0011 31.9 2.9 30 393-422 185-214 (276)
19 2k9l_A RNA polymerase sigma fa 27.1 76 0.0026 23.9 4.4 43 375-417 29-72 (76)
20 2htj_A P fimbrial regulatory p 26.9 57 0.0019 24.4 3.7 32 390-421 11-45 (81)
21 1tc3_C Protein (TC3 transposas 26.2 98 0.0034 19.6 4.5 28 387-416 17-44 (51)
22 2vn2_A DNAD, chromosome replic 22.3 2.3E+02 0.0078 23.2 6.9 25 393-417 51-75 (128)
23 2x48_A CAG38821; archeal virus 21.8 1E+02 0.0035 20.8 4.0 31 383-415 23-53 (55)
24 1xn7_A Hypothetical protein YH 20.5 94 0.0032 23.7 3.8 31 387-417 10-40 (78)
No 1
>3nfi_A DNA-directed RNA polymerase I subunit RPA49; winged helix, transcription, DNA binding, DN protein; HET: MSE PE4; 1.90A {Saccharomyces cerevisiae} PDB: 3nfh_A
Probab=100.00 E-value=1.5e-46 Score=361.76 Aligned_cols=188 Identities=21% Similarity=0.375 Sum_probs=158.7
Q ss_pred ccCCCCCCCCCCCCCCCCCccCCCCCChhHHHHHHHHHHHhhcCc-----ccccC-CCChhHHHHHhHhhccCchHHHHH
Q 013236 246 DTVLNVPPYDANATTPQQAYPLDKIILKGEWDFVQDIFNHVSAGS-----EVISD-AYPSFVCNRIHKLREIQDDVEKQT 319 (447)
Q Consensus 246 ~~~r~iPp~N~dAt~pedVY~le~IIp~~e~~~L~e~~~~l~~~~-----e~~~~-~~s~fV~~rL~~l~~~~~~~~k~~ 319 (447)
+.+|||||||.||++|+||||+++|||+.||++|+ +...+.+.+ +.... .+|.||.+||..|.+ + ++.+
T Consensus 17 ~~~r~iPp~n~dAt~pedVY~le~iIp~~e~~~L~-~~~~~~~~d~~~~~~~~~~~~~s~~V~~rL~~l~~-~---~~~~ 91 (237)
T 3nfi_A 17 SNDRPTPLANIDATDVEQIYPIESIIPKKELQFIR-VSSILKEADKEKKLELFPYQNNSKYVAKKLDSLTQ-P---SQMT 91 (237)
T ss_dssp --CCSSCCCCTTCSSGGGTSCHHHHSCHHHHTTCC-CHHHHHCCCHHHHHHTSSCCCSCCHHHHHHTTCCS-G---GGHH
T ss_pred hccCCCCCCCCCCCCHHhCCchHhcCCHHHHHHhh-hhhhhccccHHHHHhhcccCccChHHHHHHHHhcc-h---hHHH
Confidence 57999999999999999999999999999999998 455555543 11122 579999999999965 2 2233
Q ss_pred HHHHHHHHHHHHHhhhccCcCcc-c-ccccCCCCHHHHHHHHhhcccC--C--------CCccCHHHHHHHHHHHHHHHH
Q 013236 320 LASIFSYITHLVKFKDQHSMDGG-A-SAKQHRIPKILHQKFLTSFSDA--E--------SKRLSDDKIHLLISYVLVLTL 387 (447)
Q Consensus 320 ~~~iL~Yls~Ll~f~~~~~~~k~-~-~~~l~~~p~~v~~~il~~Ft~~--~--------~~~~s~~~~dkLl~yilvLaL 387 (447)
.+|+|+||++|++|++.+++..+ . ..+++++|++|+++|+++||+. | ++.||++++|||+||||||||
T Consensus 92 k~~~L~Yl~~Li~f~~~~~~~~k~~L~~~L~~~P~~v~~~ll~~Ft~~~~g~~~~s~~~~~~is~~~~dkLl~yilvLaL 171 (237)
T 3nfi_A 92 KLQMLYYLSLLLGVYENRRVNNKTKLLERLNSPPEILVDGILSRFTVIKPGQFGRSKDRSYFIDPQNEDKILCYILAIIM 171 (237)
T ss_dssp HHHHHHHHHHHHHHHHTTTCCBHHHHHTTSSCCCHHHHHHHHHHHSEECCCHHHHHHCCBEECCHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcCCCcHHHHHHhccCCCHHHHHHHHHHccCCcCCccccccccccccCHHHHHHHHHHHHHHHH
Confidence 47899999999999977654333 2 4567899999999999999974 2 248999999999999999999
Q ss_pred hcCCCccCcHhHHHHhCCCHHHHHHHHHHhCCEEeecC---------------CeEEEEEcCCCCC
Q 013236 388 HADDFRTNPTDIAKDLRMSEFKLRDHFEKLGCKLLREK---------------NMLYATLPVPLQF 438 (447)
Q Consensus 388 ~ldnf~vd~~~La~dLkl~~~kl~~~fr~LGc~v~k~~---------------~~kia~LkvPl~f 438 (447)
|+|||+||+++||+||+|++++|++|||+|||+|++.+ .+++|+|++||+|
T Consensus 172 ~idnf~vd~~~La~DLkl~~~~l~~~fr~lGckv~~~~~~~~~~~g~~k~~a~~~k~a~L~vPl~~ 237 (237)
T 3nfi_A 172 HLDNFIVEITPLAHELNLKPSKVVSLFRVLGAIVKGATVAQAEAFGIPKSTAASYKIATMKVPFKL 237 (237)
T ss_dssp HHTTTEEEHHHHHHHHTCCHHHHHHHHHHTTCEEEECCHHHHHHHTCCGGGGGGSEEEECCSSCCC
T ss_pred HHcCCccCHHHHHHHhCCCHHHHHHHHHHhCCEeCCCchhHHHHhCCchhhhhcceeEEEecCCCC
Confidence 99999999999999999999999999999999998843 4799999999986
No 2
>3nff_A RNA polymerase I subunit A49; tripple barrel, transcription, dimerization; 3.24A {Candida glabrata}
Probab=99.78 E-value=2.8e-19 Score=152.50 Aligned_cols=101 Identities=15% Similarity=0.321 Sum_probs=78.3
Q ss_pred EEEEEecCCCCCCCCEEEEcCCCCCCCCCCCCCCCCCcEEEEeccccccCCCCcccEEEecCCCCeeEEeccCCCCCCCc
Q 013236 55 AKVQFIPEQPNKAPPLVGYFPSIYKPDVDHPDEEMRPKVRVYRNMNEKKNRTGRMELVVSPRDSSVDYVGTSYSGEAMAP 134 (447)
Q Consensus 55 v~v~~~~~~~~~~~P~v~~F~~G~~p~~~~~~~~~~~~F~ly~~~~~~~~~~~r~~~vv~~e~~~l~YvG~~~~~~~~~~ 134 (447)
|+|+++.++|+.. |++|++|+.++ +++.|++|+++ +. .+++|+|||++|+|+|+|++. ++
T Consensus 10 ~~v~~~~~~p~~~---v~~ffpGl~~P-------~~t~F~lY~kk----~~---~e~LLhgEt~rLdY~g~e~~~---~~ 69 (122)
T 3nff_A 10 IAIDSYQEDPSVV---VSNFFKGVRVP-------KDTEFQLYKKR----KQ---DQFVLHGENERLEYDGETDEL---TT 69 (122)
T ss_dssp CEEEECCCSSCCC---EEECCTTCCCC-------SSCEEEEEEEC----CC---CCCEEEEECSSCEEEEECCTT---HH
T ss_pred EEEEeeccCCCEE---EEeccCCccCC-------CCCceeeeccC----Cc---cceEEEccCCceeEEeccccc---cc
Confidence 8999999999954 99999998764 88999999993 21 168999999999999999872 56
Q ss_pred cCCceEEEEEeCCCCcEEEEec--cccceeee-cccccCccccc
Q 013236 135 QFCHYAVGVLDRSTQTLKIVPI--AANKIFRL-EPRVRGSDVAD 175 (447)
Q Consensus 135 ~~~~Y~VgV~dk~T~~l~l~Pv--~~~ki~~l-~p~vk~~~~~~ 175 (447)
..|+||||||||+||+|+|+|+ ...+++.. ...++|+.+++
T Consensus 70 ~~~~YyVgVyDP~T~~leL~~Apl~~~rv~sk~~~~~~gp~ik~ 113 (122)
T 3nff_A 70 KTNQYMVGLYDKQSGKINLYRAPVVTSKIVSKFSKNLKGPEIKS 113 (122)
T ss_dssp HHEEEEEEEEETTTTEEEEEECCEEEEEEECSSTTTC-C-----
T ss_pred ccccEEEEEEcCCCCeEEEEEcceEEEEEEecccccccCCcccc
Confidence 6799999999999999999975 33445555 34678887763
No 3
>3nfg_A DNA-directed RNA polymerase I subunit RPA49; triple barrel, transcription, dimerization; 2.51A {Candida glabrata}
Probab=99.78 E-value=3.5e-19 Score=148.02 Aligned_cols=82 Identities=15% Similarity=0.304 Sum_probs=72.0
Q ss_pred EEEEEecCCCCCCCCEEEEcCCCCCCCCCCCCCCCCCcEEEEeccccccCCCCcccEEEecCCCCeeEEeccCCCCCCCc
Q 013236 55 AKVQFIPEQPNKAPPLVGYFPSIYKPDVDHPDEEMRPKVRVYRNMNEKKNRTGRMELVVSPRDSSVDYVGTSYSGEAMAP 134 (447)
Q Consensus 55 v~v~~~~~~~~~~~P~v~~F~~G~~p~~~~~~~~~~~~F~ly~~~~~~~~~~~r~~~vv~~e~~~l~YvG~~~~~~~~~~ 134 (447)
|+|+++.++|+ .+|++|++|+.++ +++.|++|+++ +. .+++|+|||++|+|+|+|++. ++
T Consensus 10 ~~v~~~~~~p~---~~v~~f~pGl~~P-------~~t~F~lY~kk----~~---~e~lLhgEt~rLdY~g~e~~~---~~ 69 (102)
T 3nfg_A 10 IAIDSYQEDPS---VVVSNFFKGVRVP-------KDTEFQLYKKR----KQ---DQFVLHGENERLEYDGETDEL---TT 69 (102)
T ss_dssp EEEEEEECSCC---CEEEECCTTCCCC-------TTCEEEEEEEC----CC---CCEEEEEECSSEEEEEECCHH---HH
T ss_pred EEEEEeccCCC---EEEEeccCCccCC-------CCceeEeeecC----CC---cceEEEeCCCceEEEeccccc---Cc
Confidence 99999999998 5699999998764 88999999993 21 169999999999999999863 66
Q ss_pred cCCceEEEEEeCCCCcEEEEec
Q 013236 135 QFCHYAVGVLDRSTQTLKIVPI 156 (447)
Q Consensus 135 ~~~~Y~VgV~dk~T~~l~l~Pv 156 (447)
..|+||||||||+||+|+|+|+
T Consensus 70 ~~~~y~VgVyDp~t~~lel~~A 91 (102)
T 3nfg_A 70 KTNQYMVGLYDKQSGKINLYRA 91 (102)
T ss_dssp HHEEEEEEEEETTTTEEEEEEE
T ss_pred ccccEEEEEEcCCCCeEEEEEe
Confidence 7899999999999999999976
No 4
>1nd9_A Translation initiation factor IF-2; NMR {Escherichia coli} SCOP: a.6.1.6
Probab=59.55 E-value=7 Score=26.63 Aligned_cols=25 Identities=20% Similarity=0.258 Sum_probs=23.4
Q ss_pred CcHhHHHHhCCCHHHHHHHHHHhCC
Q 013236 395 NPTDIAKDLRMSEFKLRDHFEKLGC 419 (447)
Q Consensus 395 d~~~La~dLkl~~~kl~~~fr~LGc 419 (447)
-+..||.+|+++++++.+.++.+|-
T Consensus 4 rv~~lAkel~~~~k~l~~~l~~~g~ 28 (49)
T 1nd9_A 4 TIKTLAAERQTSVERLVQQFADAGI 28 (49)
T ss_dssp CTTHHHHHHSSSHHHHHHHHHHHTS
T ss_pred cHHHHHHHHCcCHHHHHHHHHHcCC
Confidence 4678999999999999999999998
No 5
>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}
Probab=55.95 E-value=10 Score=30.98 Aligned_cols=30 Identities=20% Similarity=0.144 Sum_probs=27.2
Q ss_pred ccCcHhHHHHhCCCHHHHHHHHHHhCCEEe
Q 013236 393 RTNPTDIAKDLRMSEFKLRDHFEKLGCKLL 422 (447)
Q Consensus 393 ~vd~~~La~dLkl~~~kl~~~fr~LGc~v~ 422 (447)
.+.+.+||..++|++..|..+|+..|+.+.
T Consensus 23 ~~~~~~lA~~~~~S~~~l~r~fk~~G~s~~ 52 (120)
T 3mkl_A 23 EWTLARIASELLMSPSLLKKKLREEETSYS 52 (120)
T ss_dssp CCCHHHHHHHTTCCHHHHHHHHHHTTCCHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCCCHH
Confidence 478999999999999999999999998763
No 6
>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}
Probab=51.59 E-value=16 Score=29.29 Aligned_cols=29 Identities=24% Similarity=0.244 Sum_probs=26.7
Q ss_pred cCcHhHHHHhCCCHHHHHHHHHHh-CCEEe
Q 013236 394 TNPTDIAKDLRMSEFKLRDHFEKL-GCKLL 422 (447)
Q Consensus 394 vd~~~La~dLkl~~~kl~~~fr~L-Gc~v~ 422 (447)
+.+..||..++|++..|..+|+.. |+.+.
T Consensus 24 ~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~ 53 (113)
T 3oio_A 24 LSTDDIAYYVGVSRRQLERLFKQYLGTVPS 53 (113)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHHHHTSSCHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcCHH
Confidence 788999999999999999999998 98764
No 7
>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}
Probab=48.98 E-value=31 Score=26.45 Aligned_cols=48 Identities=25% Similarity=0.279 Sum_probs=34.0
Q ss_pred cCHHHHHHHHHHHHHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 370 LSDDKIHLLISYVLVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 370 ~s~~~~dkLl~yilvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
|+......+|.||---.---+++.+.+..||+.|++++..+..+..+|
T Consensus 1 ~~~~r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~L 48 (77)
T 2jt1_A 1 MSESIVTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQL 48 (77)
T ss_dssp CCCTHHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344455555555543222223688999999999999999999988877
No 8
>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}
Probab=48.43 E-value=27 Score=27.32 Aligned_cols=34 Identities=21% Similarity=0.153 Sum_probs=28.9
Q ss_pred cCCCccCcHhHHHHhCCCHHHHHHHHHHh-CCEEe
Q 013236 389 ADDFRTNPTDIAKDLRMSEFKLRDHFEKL-GCKLL 422 (447)
Q Consensus 389 ldnf~vd~~~La~dLkl~~~kl~~~fr~L-Gc~v~ 422 (447)
+.+-.+.+..||..++|++..|..+|+.. |+.+.
T Consensus 15 ~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~g~s~~ 49 (103)
T 3lsg_A 15 YTDSQFTLSVLSEKLDLSSGYLSIMFKKNFGIPFQ 49 (103)
T ss_dssp TTCTTCCHHHHHHHTTCCHHHHHHHHHHHHSSCHH
T ss_pred ccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH
Confidence 34445789999999999999999999998 98764
No 9
>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}
Probab=48.23 E-value=13 Score=29.48 Aligned_cols=35 Identities=23% Similarity=0.359 Sum_probs=29.0
Q ss_pred hcCCCccCcHhHHHHhCCCHHHHHHHHHHh-CCEEe
Q 013236 388 HADDFRTNPTDIAKDLRMSEFKLRDHFEKL-GCKLL 422 (447)
Q Consensus 388 ~ldnf~vd~~~La~dLkl~~~kl~~~fr~L-Gc~v~ 422 (447)
++.+-.+.++.||..++|++..|..+|+.. |+.+.
T Consensus 15 ~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~ 50 (107)
T 2k9s_A 15 HLADSNFDIASVAQHVCLSPSRLSHLFRQQLGISVL 50 (107)
T ss_dssp TSSCSSCCHHHHHHHTTSCHHHHHHHHHHHHSSCHH
T ss_pred HhccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH
Confidence 344345789999999999999999999985 98764
No 10
>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}
Probab=47.15 E-value=25 Score=27.75 Aligned_cols=29 Identities=10% Similarity=0.121 Sum_probs=26.5
Q ss_pred cCcHhHHHHhCCCHHHHHHHHHHh-CCEEe
Q 013236 394 TNPTDIAKDLRMSEFKLRDHFEKL-GCKLL 422 (447)
Q Consensus 394 vd~~~La~dLkl~~~kl~~~fr~L-Gc~v~ 422 (447)
+.+++||..++|++..|..+|+.. |+.+.
T Consensus 19 ~~~~~lA~~~~~s~~~l~r~fk~~~G~s~~ 48 (108)
T 3mn2_A 19 ITIEKLTALTGISSRGIFKAFQRSRGYSPM 48 (108)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHHHHTSSCHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHhCcCHH
Confidence 788999999999999999999987 98764
No 11
>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}
Probab=43.70 E-value=23 Score=28.10 Aligned_cols=30 Identities=17% Similarity=0.289 Sum_probs=27.1
Q ss_pred ccCcHhHHHHhCCCHHHHHHHHHHh-CCEEe
Q 013236 393 RTNPTDIAKDLRMSEFKLRDHFEKL-GCKLL 422 (447)
Q Consensus 393 ~vd~~~La~dLkl~~~kl~~~fr~L-Gc~v~ 422 (447)
.+.+.+||..++|++..|..+|+.. |+.+.
T Consensus 21 ~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~ 51 (108)
T 3oou_A 21 GMSLKTLGNDFHINAVYLGQLFQKEMGEHFT 51 (108)
T ss_dssp CCCHHHHHHHHTSCHHHHHHHHHHHHSSCHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH
Confidence 5789999999999999999999887 98764
No 12
>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_A
Probab=39.61 E-value=45 Score=27.30 Aligned_cols=29 Identities=21% Similarity=0.284 Sum_probs=26.6
Q ss_pred cCcHhHHHHhCCCHHHHHHHHHHh-CCEEe
Q 013236 394 TNPTDIAKDLRMSEFKLRDHFEKL-GCKLL 422 (447)
Q Consensus 394 vd~~~La~dLkl~~~kl~~~fr~L-Gc~v~ 422 (447)
+.+++||..++|++..|..+|+.. |+.+.
T Consensus 28 ~sl~~lA~~~~~S~~~l~r~fk~~~G~s~~ 57 (129)
T 1bl0_A 28 LSLEKVSERSGYSKWHLQRMFKKETGHSLG 57 (129)
T ss_dssp CCCHHHHHHSSSCHHHHHHHHHHHHSSCHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcCHH
Confidence 789999999999999999999986 98764
No 13
>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20
Probab=34.16 E-value=28 Score=28.36 Aligned_cols=59 Identities=17% Similarity=0.104 Sum_probs=38.8
Q ss_pred HHHHHHhhcccCCCCccCHHHHHHHHHHHHHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHhCCE
Q 013236 354 LHQKFLTSFSDAESKRLSDDKIHLLISYVLVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKLGCK 420 (447)
Q Consensus 354 v~~~il~~Ft~~~~~~~s~~~~dkLl~yilvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~LGc~ 420 (447)
++..|...+.. +|+. .-++.-||+-=--.+- ...+..||+..+.++..+..++|.|||.
T Consensus 8 i~~~i~~~~~~-----ls~~-e~~ia~yil~~~~~~~--~~si~elA~~~~vS~aTv~Rf~kklG~~ 66 (111)
T 2o3f_A 8 GLAIIQSMXHX-----LPPS-ERKLADYILAHPHXAI--ESTVNEISALANSSDAAVIRLCXSLGLK 66 (111)
T ss_dssp HHHHHHHHGGG-----SCHH-HHHHHHHHHHCHHHHH--TCCHHHHHHHTTCCHHHHHHHHHHTTCS
T ss_pred HHHHHHHHhcc-----CCHH-HHHHHHHHHHChHHHH--hcCHHHHHHHHCCCHHHHHHHHHHcCCC
Confidence 44555554432 4443 3456666653211111 2467999999999999999999999996
No 14
>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}
Probab=33.41 E-value=30 Score=28.07 Aligned_cols=59 Identities=12% Similarity=0.142 Sum_probs=39.4
Q ss_pred HHHHHHhhcccCCCCccCHHHHHHHHHHHHHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHhCCE
Q 013236 354 LHQKFLTSFSDAESKRLSDDKIHLLISYVLVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKLGCK 420 (447)
Q Consensus 354 v~~~il~~Ft~~~~~~~s~~~~dkLl~yilvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~LGc~ 420 (447)
|+..|...+.. +|+. .-++.-||+.=--.+- ...+..||+..+.++..+..++|.|||.
T Consensus 4 i~~~I~~~~~~-----lt~~-e~~ia~yil~~~~~~~--~~si~elA~~~~vS~aTv~Rf~kkLGf~ 62 (107)
T 3iwf_A 4 ILYKIDNQYPY-----FTKN-EKKIAQFILNYPHKVV--NMTSQEIANQLETSSTSIIRLSKKVTPG 62 (107)
T ss_dssp HHHHHHHHGGG-----SCHH-HHHHHHHHHHCHHHHT--TCCHHHHHHHHTSCHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHh-----cCHH-HHHHHHHHHhCHHHHH--HCCHHHHHHHHCCCHHHHHHHHHHhCCC
Confidence 34445554432 4443 4456666654322222 2467999999999999999999999995
No 15
>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2
Probab=33.16 E-value=51 Score=23.65 Aligned_cols=27 Identities=30% Similarity=0.450 Sum_probs=22.0
Q ss_pred cCCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 389 ADDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 389 ldnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
.+++ ....+|+.|++++..+..+.+.+
T Consensus 24 ~~g~--s~~eIA~~l~is~~tV~~~~~~~ 50 (74)
T 1fse_A 24 VQDK--TTKEIASELFISEKTVRNHISNA 50 (74)
T ss_dssp TTTC--CHHHHHHHHTSCHHHHHHHHHHH
T ss_pred HcCC--CHHHHHHHHCCCHHHHHHHHHHH
Confidence 5666 67999999999999888877654
No 16
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}
Probab=30.68 E-value=63 Score=22.36 Aligned_cols=32 Identities=22% Similarity=0.346 Sum_probs=23.9
Q ss_pred HHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 384 VLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 384 vLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
+|.|+.+++ ....+|..|++++..+..+.+.+
T Consensus 6 vl~l~~~g~--s~~eIA~~l~is~~tV~~~~~~~ 37 (61)
T 2jpc_A 6 VLKLIDEGY--TNHGISEKLHISIKTVETHRMNM 37 (61)
T ss_dssp HHHHHHTSC--CSHHHHHHTCSCHHHHHHHHHHH
T ss_pred HHHHHHcCC--CHHHHHHHhCCCHHHHHHHHHHH
Confidence 344456776 45899999999999988776543
No 17
>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C
Probab=28.97 E-value=38 Score=22.25 Aligned_cols=32 Identities=13% Similarity=0.033 Sum_probs=24.9
Q ss_pred HHhcCCCccCcHhHHHHhCCCHHHHHHHHHHhCC
Q 013236 386 TLHADDFRTNPTDIAKDLRMSEFKLRDHFEKLGC 419 (447)
Q Consensus 386 aL~ldnf~vd~~~La~dLkl~~~kl~~~fr~LGc 419 (447)
.|+.++ ..+..||..|+++...+-.+++..|-
T Consensus 16 ~l~~~g--~s~~~ia~~lgvs~~Tv~r~l~~~~~ 47 (52)
T 1jko_C 16 RLLEKG--HPRQQLAIIFGIGVSTLYRYFPASSI 47 (52)
T ss_dssp HHHHTT--CCHHHHHHTTSCCHHHHHHHSCTTC-
T ss_pred HHHHcC--CCHHHHHHHHCCCHHHHHHHHHHccc
Confidence 344455 56789999999999999998887764
No 18
>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix, ARAC family, activator, DNA-binding transcription, transcription regulation; HET: PAM; 1.90A {Vibrio cholerae}
Probab=28.47 E-value=31 Score=31.89 Aligned_cols=30 Identities=27% Similarity=0.369 Sum_probs=27.2
Q ss_pred ccCcHhHHHHhCCCHHHHHHHHHHhCCEEe
Q 013236 393 RTNPTDIAKDLRMSEFKLRDHFEKLGCKLL 422 (447)
Q Consensus 393 ~vd~~~La~dLkl~~~kl~~~fr~LGc~v~ 422 (447)
...++.||+.++|++..+..+|++.|..+.
T Consensus 185 ~~sl~~lA~~~~~S~~~l~r~fk~~G~t~~ 214 (276)
T 3gbg_A 185 NWRWADICGELRTNRMILKKELESRGVKFR 214 (276)
T ss_dssp CCCHHHHHHHHTCCHHHHHHHHHTTTCCHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCCCHH
Confidence 467899999999999999999999998764
No 19
>2k9l_A RNA polymerase sigma factor RPON; protein, transcription; NMR {Aquifex aeolicus}
Probab=27.14 E-value=76 Score=23.94 Aligned_cols=43 Identities=21% Similarity=0.186 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHhcCCCc-cCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 375 IHLLISYVLVLTLHADDFR-TNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 375 ~dkLl~yilvLaL~ldnf~-vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
+++.++..|+=+|==++|- .++..||..|+++...+....+.|
T Consensus 29 ~~~~Ia~~iI~~LD~~GYL~~~l~eia~~l~~~~~eve~vL~~l 72 (76)
T 2k9l_A 29 KEQELALELLNYLNEKGFLSKSVEEISDVLRCSVEELEKVRQKV 72 (76)
T ss_dssp TSHHHHHHHHHHCTTSSTTCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCCCCCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 4577888888888778885 799999999999999988776543
No 20
>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73
Probab=26.89 E-value=57 Score=24.38 Aligned_cols=32 Identities=16% Similarity=0.200 Sum_probs=24.8
Q ss_pred CCCccCcHhHHHHhCCCHHHHHHHHHH---hCCEE
Q 013236 390 DDFRTNPTDIAKDLRMSEFKLRDHFEK---LGCKL 421 (447)
Q Consensus 390 dnf~vd~~~La~dLkl~~~kl~~~fr~---LGc~v 421 (447)
.+-.+...+||+.|+++...+..+.+. .|...
T Consensus 11 ~~~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~ 45 (81)
T 2htj_A 11 RHNGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQ 45 (81)
T ss_dssp HSCCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 334578899999999999988877655 57654
No 21
>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2
Probab=26.23 E-value=98 Score=19.62 Aligned_cols=28 Identities=7% Similarity=0.180 Sum_probs=22.4
Q ss_pred HhcCCCccCcHhHHHHhCCCHHHHHHHHHH
Q 013236 387 LHADDFRTNPTDIAKDLRMSEFKLRDHFEK 416 (447)
Q Consensus 387 L~ldnf~vd~~~La~dLkl~~~kl~~~fr~ 416 (447)
|+.+++ ....+|+.|+++...+..+.+.
T Consensus 17 ~~~~g~--s~~~IA~~lgis~~Tv~~~~~~ 44 (51)
T 1tc3_C 17 MKLLNV--SLHEMSRKISRSRHCIRVYLKD 44 (51)
T ss_dssp HHHTTC--CHHHHHHHHTCCHHHHHHHHHC
T ss_pred HHHcCC--CHHHHHHHHCcCHHHHHHHHhh
Confidence 345665 4789999999999999888764
No 22
>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}
Probab=22.28 E-value=2.3e+02 Score=23.16 Aligned_cols=25 Identities=16% Similarity=0.336 Sum_probs=22.1
Q ss_pred ccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 393 RTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 393 ~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
-..+..||+.|++++..+..+.+.|
T Consensus 51 ~ps~~~LA~~l~~s~~~V~~~l~~L 75 (128)
T 2vn2_A 51 FPTPAELAERMTVSAAECMEMVRRL 75 (128)
T ss_dssp SCCHHHHHHTSSSCHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3789999999999999999888765
No 23
>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}
Probab=21.76 E-value=1e+02 Score=20.79 Aligned_cols=31 Identities=29% Similarity=0.339 Sum_probs=23.7
Q ss_pred HHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHH
Q 013236 383 LVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFE 415 (447)
Q Consensus 383 lvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr 415 (447)
.++.|+.+++ ....+|+.|++++..+..+.+
T Consensus 23 ~i~~l~~~g~--s~~eIA~~lgis~~TV~~~l~ 53 (55)
T 2x48_A 23 VAHELAKMGY--TVQQIANALGVSERKVRRYLE 53 (55)
T ss_dssp HHHHHHHTTC--CHHHHHHHHTSCHHHHHHHHT
T ss_pred HHHHHHHcCC--CHHHHHHHHCcCHHHHHHHHH
Confidence 3334455666 578999999999999988764
No 24
>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62
Probab=20.55 E-value=94 Score=23.68 Aligned_cols=31 Identities=19% Similarity=0.214 Sum_probs=25.2
Q ss_pred HhcCCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 387 LHADDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 387 L~ldnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
+.-.+-.+.+++||+.|++++..|......|
T Consensus 10 ~L~~~g~vsv~eLa~~l~VS~~TIRrdL~~L 40 (78)
T 1xn7_A 10 LLALRGRMEAAQISQTLNTPQPMINAMLQQL 40 (78)
T ss_dssp HHHHSCSBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred HHHHcCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 3345677999999999999999998776654
Done!