Query 016077
Match_columns 395
No_of_seqs 171 out of 1302
Neff 4.1
Searched_HMMs 29240
Date Mon Mar 25 07:29:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016077.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/016077hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1l9z_H Sigma factor SIGA; heli 99.5 2.6E-14 9.1E-19 145.3 9.2 106 289-395 91-227 (438)
2 3ugo_A RNA polymerase sigma fa 99.5 4E-14 1.4E-18 133.1 8.0 105 290-395 5-140 (245)
3 2a6h_F RNA polymerase sigma fa 99.4 5.4E-14 1.9E-18 141.5 3.1 106 289-395 76-212 (423)
4 1sig_A Sigma70, RNA polymerase 95.7 0.0041 1.4E-07 59.9 2.7 31 365-395 265-295 (339)
5 3iyd_F RNA polymerase sigma fa 94.9 0.0025 8.5E-08 66.8 -2.1 35 289-324 93-128 (613)
6 3iyd_F RNA polymerase sigma fa 93.5 0.011 3.6E-07 62.1 -0.7 42 354-395 359-404 (613)
7 2k9s_A Arabinose operon regula 75.3 6.4 0.00022 30.9 6.2 38 325-362 5-43 (107)
8 2jt1_A PEFI protein; solution 73.5 3.7 0.00013 32.3 4.2 35 327-361 12-46 (77)
9 1bl0_A Protein (multiple antib 67.4 8.5 0.00029 31.4 5.4 59 325-384 13-85 (129)
10 3mn2_A Probable ARAC family tr 63.2 12 0.00039 29.4 5.2 38 325-362 4-41 (108)
11 3lsg_A Two-component response 58.7 16 0.00054 28.3 5.3 36 326-361 5-41 (103)
12 3oou_A LIN2118 protein; protei 58.0 16 0.00056 28.6 5.3 59 325-384 7-79 (108)
13 3oio_A Transcriptional regulat 56.9 14 0.00046 29.3 4.6 37 325-361 9-45 (113)
14 3ugo_A RNA polymerase sigma fa 53.8 2.7 9.3E-05 39.0 0.0 41 324-364 198-240 (245)
15 2zc2_A DNAD-like replication p 53.4 13 0.00044 28.3 3.8 58 330-391 8-71 (78)
16 3k2z_A LEXA repressor; winged 52.8 26 0.00089 30.7 6.2 28 334-361 19-46 (196)
17 3mkl_A HTH-type transcriptiona 50.1 19 0.00065 28.8 4.5 37 325-361 9-45 (120)
18 1d5y_A ROB transcription facto 44.7 24 0.00082 31.8 4.8 60 325-385 5-78 (292)
19 3gbg_A TCP pilus virulence reg 42.1 46 0.0016 29.7 6.2 57 327-384 173-242 (276)
20 1tc3_C Protein (TC3 transposas 42.0 64 0.0022 20.4 5.7 23 340-362 22-44 (51)
21 1jko_C HIN recombinase, DNA-in 36.4 46 0.0016 21.7 4.1 24 340-363 22-45 (52)
22 4fe7_A Xylose operon regulator 32.4 48 0.0016 31.6 4.9 57 327-384 309-379 (412)
23 3mzy_A RNA polymerase sigma-H 29.0 2.1E+02 0.0071 22.6 7.6 37 335-371 120-156 (164)
24 2o8x_A Probable RNA polymerase 27.6 1.1E+02 0.0037 21.4 5.1 29 337-365 29-57 (70)
25 2a6h_F RNA polymerase sigma fa 26.7 1E+02 0.0035 30.7 6.4 36 324-359 270-307 (423)
26 1rp3_A RNA polymerase sigma fa 26.4 1.2E+02 0.0041 25.8 6.1 41 332-372 196-236 (239)
27 3f2g_A Alkylmercury lyase; MER 26.0 59 0.002 30.4 4.2 27 336-362 33-59 (220)
28 1rp3_A RNA polymerase sigma fa 25.9 93 0.0032 26.5 5.2 36 324-359 100-135 (239)
29 3kz3_A Repressor protein CI; f 24.2 2.1E+02 0.007 20.7 6.6 39 340-385 26-64 (80)
30 2p7v_B Sigma-70, RNA polymeras 23.9 1.4E+02 0.0049 21.2 5.2 27 338-364 24-50 (68)
31 1ku3_A Sigma factor SIGA; heli 23.3 1.4E+02 0.0048 21.6 5.1 27 338-364 29-55 (73)
32 1tty_A Sigma-A, RNA polymerase 22.5 1.4E+02 0.0048 22.6 5.1 28 338-365 37-64 (87)
33 3hug_A RNA polymerase sigma fa 22.2 2.5E+02 0.0087 21.1 9.6 36 335-370 49-84 (92)
34 1x3u_A Transcriptional regulat 21.3 2.3E+02 0.0079 20.3 6.7 46 337-385 29-74 (79)
35 1qbj_A Protein (double-strande 21.3 1.3E+02 0.0046 23.3 4.8 26 337-362 25-50 (81)
36 1jhf_A LEXA repressor; LEXA SO 21.1 1.6E+02 0.0056 25.3 5.9 28 334-361 20-48 (202)
37 1sig_A Sigma70, RNA polymerase 20.8 31 0.0011 32.8 1.2 19 306-324 1-19 (339)
38 1l9z_H Sigma factor SIGA; heli 20.6 1.5E+02 0.005 30.1 6.2 35 324-358 285-321 (438)
39 1u8b_A ADA polyprotein; protei 20.4 1.2E+02 0.0041 24.4 4.6 34 326-361 82-115 (133)
40 3t72_q RNA polymerase sigma fa 20.3 3.3E+02 0.011 21.7 8.3 39 338-376 38-77 (99)
No 1
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1
Probab=99.50 E-value=2.6e-14 Score=145.28 Aligned_cols=106 Identities=25% Similarity=0.346 Sum_probs=88.3
Q ss_pred CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHHHcCCCCChHHHHH--
Q 016077 289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE------------------VLSERCGGSPTFAQWAA-- 347 (395)
Q Consensus 289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~------------------~L~e~lGrePT~~EWAe-- 347 (395)
...|+++ ||++| +++||||++||++|+++|+.++.++.... +....+++.|+..+|+.
T Consensus 91 ~~~d~~~~Yl~ei-~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 169 (438)
T 1l9z_H 91 STSDPVRQYLHEI-GQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPK 169 (438)
T ss_pred CCCChHHHHHHHh-ccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccch
Confidence 4568999 99999 99999999999999999999866543321 22234678899888753
Q ss_pred ----------HhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 348 ----------AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 348 ----------A~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
+++++..+|.+++..|..|+++||.+|+|||++||++|.|+|++++|+
T Consensus 170 ~~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDL 227 (438)
T 1l9z_H 170 TVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL 227 (438)
T ss_pred hhhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence 235667888888889999999999999999999999999999999885
No 2
>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*
Probab=99.48 E-value=4e-14 Score=133.08 Aligned_cols=105 Identities=29% Similarity=0.363 Sum_probs=85.5
Q ss_pred CCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHH-HHHHH------H-HHH------------------cCCCCCh
Q 016077 290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLE-GLREV------L-SER------------------CGGSPTF 342 (395)
Q Consensus 290 ~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE-~ir~~------L-~e~------------------lGrePT~ 342 (395)
.+||++ ||++| |++||||++||++|+++|+.|+... .+... + .+. .+.+|+.
T Consensus 5 ~~d~~~~yl~~i-~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~ 83 (245)
T 3ugo_A 5 TSDPVRQYLHEI-GQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT 83 (245)
T ss_dssp CCHHHHHHHHHH-TTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHH
T ss_pred CCCcHHHHHHHc-ccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchh
Confidence 589999 99999 9999999999999999999987633 22211 0 000 1478999
Q ss_pred HHHHHHhcCcH----HHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 343 AQWAAAAGVDQ----RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 343 ~EWAeA~Gms~----~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
.+||++.|++. ..|.+....|..|+++|+..|+++|.+||++|.+.+.+++|+
T Consensus 84 ~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDL 140 (245)
T 3ugo_A 84 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL 140 (245)
T ss_dssp HHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHH
T ss_pred HHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHH
Confidence 99999999865 344555678899999999999999999999999999988774
No 3
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H
Probab=99.40 E-value=5.4e-14 Score=141.47 Aligned_cols=106 Identities=26% Similarity=0.343 Sum_probs=84.7
Q ss_pred CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH------------------HHHHcCCCCChHHHHH--
Q 016077 289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREV------------------LSERCGGSPTFAQWAA-- 347 (395)
Q Consensus 289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~------------------L~e~lGrePT~~EWAe-- 347 (395)
...|+++ ||++| +++||||++||++|+++|+.+..++..... .....++.|+..+|+.
T Consensus 76 ~~~d~~~~Yl~ei-~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 154 (423)
T 2a6h_F 76 STSDPVRQYLHEI-GQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPK 154 (423)
T ss_dssp TTHHHHHHHHHHH-HHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTH
T ss_pred CCCcHHHHHHHHh-cccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhh
Confidence 3468999 99999 999999999999999999998654432211 1123356777665442
Q ss_pred ----------HhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 348 ----------AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 348 ----------A~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
+++++..+|..++..|..|+++||.+|+|||++||++|.|+|++++|+
T Consensus 155 ~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDL 212 (423)
T 2a6h_F 155 TVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL 212 (423)
T ss_dssp HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHH
T ss_pred hhhhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence 346677888888888999999999999999999999999999998884
No 4
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1
Probab=95.73 E-value=0.0041 Score=59.92 Aligned_cols=31 Identities=42% Similarity=0.546 Sum_probs=29.0
Q ss_pred HHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 365 LCKDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 365 ~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
.|++.|+..|+++|+++|++|.+.|..++|+
T Consensus 265 ~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDl 295 (339)
T 1sig_A 265 RAKKEMVEANLRLVISIAKKYTNRGLQFLDL 295 (339)
T ss_dssp HHHHHHHHHTHHHHHHHHTTSTTSSSCHHHH
T ss_pred hhhHHHHHHHHHHHHHHHHHHhcCCCCHhHH
Confidence 6999999999999999999999999988774
No 5
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}
Probab=94.87 E-value=0.0025 Score=66.78 Aligned_cols=35 Identities=31% Similarity=0.602 Sum_probs=14.7
Q ss_pred CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHH
Q 016077 289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK 324 (395)
Q Consensus 289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~ 324 (395)
..+||++ ||++| |+.+|||.++|++|+++|..|..
T Consensus 93 ~~~dpvrmyl~em-g~~~ll~~~~e~~~ak~ie~g~~ 128 (613)
T 3iyd_F 93 RTTDPVRMYMREM-GTVELLTREGEIDIAKRIEDGIN 128 (613)
T ss_dssp ------------C---------CSSSTTTHHHHHHHH
T ss_pred CCCCcHHHHHHHh-cccccCCchhHHHHHHHHHHhHH
Confidence 4699999 99999 99999999999999999998864
No 6
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}
Probab=93.53 E-value=0.011 Score=62.07 Aligned_cols=42 Identities=38% Similarity=0.608 Sum_probs=34.5
Q ss_pred HHHHHhhhhcHH-H---HHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 354 RELRRRLNYGIL-C---KDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 354 ~eLr~~L~~G~~-A---RerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
..|-.++..|.. | ++.|+..|+++|++||++|.++|..+.||
T Consensus 359 ~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDl 404 (613)
T 3iyd_F 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 404 (613)
T ss_dssp HHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTT
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence 344455555543 4 99999999999999999999999999996
No 7
>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}
Probab=75.29 E-value=6.4 Score=30.93 Aligned_cols=38 Identities=11% Similarity=0.081 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHcC-CCCChHHHHHHhcCcHHHHHHhhhh
Q 016077 325 LEGLREVLSERCG-GSPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 325 LE~ir~~L~e~lG-rePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
+.++..-+.+.+. ..++..++|+.+||+...|.+....
T Consensus 5 i~~~~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 43 (107)
T 2k9s_A 5 VREACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQ 43 (107)
T ss_dssp HHHHHHHHHHTSSCSSCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred HHHHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4556666777888 8999999999999999999887753
No 8
>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}
Probab=73.45 E-value=3.7 Score=32.25 Aligned_cols=35 Identities=23% Similarity=0.169 Sum_probs=27.6
Q ss_pred HHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 327 ~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
-++..+.+..|.+||..|.|+++|++...+++-|.
T Consensus 12 ~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~ 46 (77)
T 2jt1_A 12 IVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLE 46 (77)
T ss_dssp HHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred HHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 34555555569999999999999999888777664
No 9
>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=67.38 E-value=8.5 Score=31.39 Aligned_cols=59 Identities=12% Similarity=0.202 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh--------------cHHHHHHHHHHhHHHHHHHHHh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY--------------GILCKDKMITSNIRLVISIAKN 384 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~--------------G~~ARerLVkSNLRLVVSIAKr 384 (395)
+.++..-+.+.+...++..++|+.+||+...|.+.... -..|++.|...++. |..||..
T Consensus 13 i~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~G~s~~~~l~~~Rl~~A~~lL~~~~~s-i~~IA~~ 85 (129)
T 1bl0_A 13 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEP-ILYLAER 85 (129)
T ss_dssp HHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHH
T ss_pred HHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 44556667778888899999999999999999887753 24566666655553 5556654
No 10
>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}
Probab=63.23 E-value=12 Score=29.41 Aligned_cols=38 Identities=13% Similarity=0.222 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
++++..-+.+.+...+|..++|+.+||+...|.+....
T Consensus 4 i~~~~~~i~~~~~~~~~~~~lA~~~~~s~~~l~r~fk~ 41 (108)
T 3mn2_A 4 VRQVEEYIEANWMRPITIEKLTALTGISSRGIFKAFQR 41 (108)
T ss_dssp HHHHHHHHHHHTTSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred HHHHHHHHHHcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44566667788888999999999999999999887753
No 11
>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}
Probab=58.75 E-value=16 Score=28.34 Aligned_cols=36 Identities=11% Similarity=0.123 Sum_probs=29.3
Q ss_pred HHHHHHHHHHcCC-CCChHHHHHHhcCcHHHHHHhhh
Q 016077 326 EGLREVLSERCGG-SPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 326 E~ir~~L~e~lGr-ePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
+++..-+.+.+.. .++..++|+.+||+...|.+.+.
T Consensus 5 ~~i~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk 41 (103)
T 3lsg_A 5 ELIQNIIEESYTDSQFTLSVLSEKLDLSSGYLSIMFK 41 (103)
T ss_dssp HHHHHHHHHHTTCTTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred HHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4455556677776 89999999999999999988774
No 12
>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=57.99 E-value=16 Score=28.60 Aligned_cols=59 Identities=8% Similarity=0.128 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh--------------cHHHHHHHHHHhHHHHHHHHHh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY--------------GILCKDKMITSNIRLVISIAKN 384 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~--------------G~~ARerLVkSNLRLVVSIAKr 384 (395)
+.++..-+.+.++..++..++|+.+||+...|.+.... -..|++.|...++. |-.||..
T Consensus 7 i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~~~~~~~Rl~~A~~lL~~~~~s-i~~IA~~ 79 (108)
T 3oou_A 7 IQNVLSYITEHFSEGMSLKTLGNDFHINAVYLGQLFQKEMGEHFTDYLNRYRVNYAKEELLQTKDN-LTIIAGK 79 (108)
T ss_dssp HHHHHHHHHHHTTSCCCHHHHHHHHTSCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHH
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 34555667778888999999999999999998887742 24455555555543 3455554
No 13
>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}
Probab=56.86 E-value=14 Score=29.31 Aligned_cols=37 Identities=19% Similarity=0.226 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
+.++..-+.+.+...++..++|+.+||+...|.+.+.
T Consensus 9 i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk 45 (113)
T 3oio_A 9 LTEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFK 45 (113)
T ss_dssp HHHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4555666777888889999999999999999988774
No 14
>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*
Probab=53.76 E-value=2.7 Score=39.04 Aligned_cols=41 Identities=24% Similarity=0.399 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhc--CcHHHHHHhhhhcH
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAG--VDQRELRRRLNYGI 364 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~G--ms~~eLr~~L~~G~ 364 (395)
++.+...+|...+|+.||..|.|+.+| +++.+++.+|..++
T Consensus 198 ~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar 240 (245)
T 3ugo_A 198 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQ 240 (245)
T ss_dssp -------------------------------------------
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHHh
Confidence 345566678888999999999999999 99999999887654
No 15
>2zc2_A DNAD-like replication protein; GI 24377835, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Streptococcus mutans UA159}
Probab=53.38 E-value=13 Score=28.28 Aligned_cols=58 Identities=16% Similarity=0.121 Sum_probs=42.2
Q ss_pred HHHHHHcCCCCChH------HHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCCC
Q 016077 330 EVLSERCGGSPTFA------QWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRM 391 (395)
Q Consensus 330 ~~L~e~lGrePT~~------EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGLs 391 (395)
..++..+||.||.. +|-...|++.+.+...++... . -=+.|++.|-.|+++....|+.
T Consensus 8 ~~~e~~~gr~ls~~e~~~i~~w~~~~~~~~elI~~A~~~a~---~-~~~~s~~Yi~~Il~~W~~~gi~ 71 (78)
T 2zc2_A 8 EDFERELGRMLSPFELEDLQKTVSDDKTDPDLVRSALREAV---F-NGKTNWNYIQAILRNWRHEGIS 71 (78)
T ss_dssp HHHHHHHTSCCCHHHHHHHHHHHTTTCCCHHHHHHHHHHHH---H-HTCCCHHHHHHHHHHHHHTTCC
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHH---H-cCCCCHHHHHHHHHHHHHcCCC
Confidence 44555678888775 477778888888777666543 1 1256899999999999998863
No 16
>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}
Probab=52.82 E-value=26 Score=30.68 Aligned_cols=28 Identities=21% Similarity=0.203 Sum_probs=24.2
Q ss_pred HHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 334 ERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 334 e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
+..|.+||..|.|+++|++...+.++|.
T Consensus 19 ~~~g~~~s~~eia~~lgl~~~tv~~~l~ 46 (196)
T 3k2z_A 19 EKNGYPPSVREIARRFRITPRGALLHLI 46 (196)
T ss_dssp HHHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred HHhCCCCCHHHHHHHcCCCcHHHHHHHH
Confidence 4679999999999999999888777664
No 17
>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}
Probab=50.12 E-value=19 Score=28.82 Aligned_cols=37 Identities=16% Similarity=0.160 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
+.++..-+.+.+...++..++|+.+||+...|.+.+.
T Consensus 9 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk 45 (120)
T 3mkl_A 9 RTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLR 45 (120)
T ss_dssp HHHHHHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3455566777788899999999999999999988764
No 18
>1d5y_A ROB transcription factor; protein-DNA complex, DNA, transcription/DNA complex; HET: DNA; 2.70A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 d.60.1.2
Probab=44.69 E-value=24 Score=31.84 Aligned_cols=60 Identities=18% Similarity=0.150 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh--------------cHHHHHHHHHHhHHHHHHHHHhc
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY--------------GILCKDKMITSNIRLVISIAKNY 385 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~--------------G~~ARerLVkSNLRLVVSIAKrY 385 (395)
+.++..-+.+.+...+|..++|+.+||+...|++.... -..|+..|...++. |..||..+
T Consensus 5 ~~~~~~~i~~~~~~~~~~~~la~~~~~s~~~l~r~f~~~~g~s~~~~~~~~Rl~~a~~~L~~~~~~-i~~ia~~~ 78 (292)
T 1d5y_A 5 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKSAVALRLTARP-ILDIALQY 78 (292)
T ss_dssp HHHHHHHHHTTSSSSCCCHHHHTTTSSCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHT
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhcCCCC-HHHHHHHc
Confidence 45566677888899999999999999999999887743 23455555544443 45666554
No 19
>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=42.06 E-value=46 Score=29.74 Aligned_cols=57 Identities=12% Similarity=0.100 Sum_probs=39.7
Q ss_pred HHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh-------------hcHHHHHHHHHHhHHHHHHHHHh
Q 016077 327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN-------------YGILCKDKMITSNIRLVISIAKN 384 (395)
Q Consensus 327 ~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~-------------~G~~ARerLVkSNLRLVVSIAKr 384 (395)
++..-+.+.+....|..++|+.+||+...|.+..+ +-..|+..|...++. |-.||..
T Consensus 173 ~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~G~t~~~~l~~~Rl~~A~~lL~~~~~s-i~eIA~~ 242 (276)
T 3gbg_A 173 KISCLVKSDITRNWRWADICGELRTNRMILKKELESRGVKFRELINSIRISYSISLMKTGEFK-IKQIAYQ 242 (276)
T ss_dssp HHHHHHHHTTTSCCCHHHHHHHHTCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCCC-HHHHHHH
T ss_pred HHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhCCCCC-HHHHHHH
Confidence 33445566778889999999999999988877653 244577777666653 5566654
No 20
>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=42.04 E-value=64 Score=20.42 Aligned_cols=23 Identities=9% Similarity=0.069 Sum_probs=18.4
Q ss_pred CChHHHHHHhcCcHHHHHHhhhh
Q 016077 340 PTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 340 PT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
-|..+.|+.+|++...+.+.+..
T Consensus 22 ~s~~~IA~~lgis~~Tv~~~~~~ 44 (51)
T 1tc3_C 22 VSLHEMSRKISRSRHCIRVYLKD 44 (51)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHHC
T ss_pred CCHHHHHHHHCcCHHHHHHHHhh
Confidence 47889999999998888776643
No 21
>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=36.43 E-value=46 Score=21.68 Aligned_cols=24 Identities=21% Similarity=0.120 Sum_probs=20.6
Q ss_pred CChHHHHHHhcCcHHHHHHhhhhc
Q 016077 340 PTFAQWAAAAGVDQRELRRRLNYG 363 (395)
Q Consensus 340 PT~~EWAeA~Gms~~eLr~~L~~G 363 (395)
-|..+.|+.+|++...+.+.+...
T Consensus 22 ~s~~~ia~~lgvs~~Tv~r~l~~~ 45 (52)
T 1jko_C 22 HPRQQLAIIFGIGVSTLYRYFPAS 45 (52)
T ss_dssp CCHHHHHHTTSCCHHHHHHHSCTT
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHc
Confidence 688999999999999998887643
No 22
>4fe7_A Xylose operon regulatory protein; HTH_ARAC, helix-turn-helix, PBP, periplasmic binding protein binding transcription regulator, DNA xylose; HET: XYS; 2.90A {Escherichia coli} PDB: 4fe4_A
Probab=32.42 E-value=48 Score=31.61 Aligned_cols=57 Identities=12% Similarity=0.179 Sum_probs=39.6
Q ss_pred HHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh--------------cHHHHHHHHHHhHHHHHHHHHh
Q 016077 327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY--------------GILCKDKMITSNIRLVISIAKN 384 (395)
Q Consensus 327 ~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~--------------G~~ARerLVkSNLRLVVSIAKr 384 (395)
++...+.+.+....+..+||+.+|++...|.+.++. -..|++.|...++. |-.||..
T Consensus 309 ~~~~~i~~~~~~~~~~~~~a~~~~~s~~~l~r~f~~~~g~s~~~~~~~~r~~~a~~~L~~~~~~-i~~ia~~ 379 (412)
T 4fe7_A 309 QAMHYIRNHACKGIKVDQVLDAVGISRSNLEKRFKEEVGETIHAMIHAEKLEKARSLLISTTLS-INEISQM 379 (412)
T ss_dssp HHHHHHHHHGGGTCCHHHHHHHTTCCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHH
T ss_pred HHHHHHHhhccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhcCCCC-HHHHHHH
Confidence 334445566778899999999999999999888753 24466666555543 4555554
No 23
>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}
Probab=29.03 E-value=2.1e+02 Score=22.63 Aligned_cols=37 Identities=5% Similarity=-0.023 Sum_probs=29.3
Q ss_pred HcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHH
Q 016077 335 RCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 371 (395)
Q Consensus 335 ~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLV 371 (395)
..-..-|..|.|+.+|++...++.+++.+..--.+.+
T Consensus 120 ~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 156 (164)
T 3mzy_A 120 YLIRGYSYREIATILSKNLKSIDNTIQRIRKKSEEWI 156 (164)
T ss_dssp HHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4556679999999999999999999988766444443
No 24
>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}
Probab=27.65 E-value=1.1e+02 Score=21.42 Aligned_cols=29 Identities=21% Similarity=0.118 Sum_probs=24.1
Q ss_pred CCCCChHHHHHHhcCcHHHHHHhhhhcHH
Q 016077 337 GGSPTFAQWAAAAGVDQRELRRRLNYGIL 365 (395)
Q Consensus 337 GrePT~~EWAeA~Gms~~eLr~~L~~G~~ 365 (395)
...-|..|.|+.+|++...++.+++.+..
T Consensus 29 ~~g~s~~eIA~~lgis~~tv~~~~~ra~~ 57 (70)
T 2o8x_A 29 LLGLSYADAAAVCGCPVGTIRSRVARARD 57 (70)
T ss_dssp TSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34568999999999999999998877654
No 25
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H
Probab=26.74 E-value=1e+02 Score=30.66 Aligned_cols=36 Identities=28% Similarity=0.438 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhc--CcHHHHHHh
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAG--VDQRELRRR 359 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~G--ms~~eLr~~ 359 (395)
++.+.+.+|...+|++|+..+.|+.+| ++.+.++..
T Consensus 270 ~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~ 307 (423)
T 2a6h_F 270 KLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEET 307 (423)
T ss_dssp HHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHH
Confidence 345566778888999999999999999 988887764
No 26
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A
Probab=26.40 E-value=1.2e+02 Score=25.79 Aligned_cols=41 Identities=5% Similarity=-0.102 Sum_probs=31.3
Q ss_pred HHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHH
Q 016077 332 LSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT 372 (395)
Q Consensus 332 L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVk 372 (395)
|.-.....-|..|.|+.+|++...++++++.+..--.+.++
T Consensus 196 l~l~~~~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l~ 236 (239)
T 1rp3_A 196 IQLIFYEELPAKEVAKILETSVSRVSQLKAKALERLREMLS 236 (239)
T ss_dssp HHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 33344667899999999999999999999877665444443
No 27
>3f2g_A Alkylmercury lyase; MERB, organomercurial lyase, mercury resistance, mercuric resistance, plasmid; 1.78A {Escherichia coli} PDB: 3f2h_A 3fn8_A 1s6l_A 3f0o_A 3f0p_A 3f2f_A
Probab=25.97 E-value=59 Score=30.37 Aligned_cols=27 Identities=11% Similarity=-0.001 Sum_probs=25.1
Q ss_pred cCCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077 336 CGGSPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 336 lGrePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
.|++|+..+.|..+|++.+++++.|+.
T Consensus 33 ~Grpv~~~~LA~~~g~~~~~v~~~L~~ 59 (220)
T 3f2g_A 33 KGRPVSRTTLAGILDWPAERVAAVLEQ 59 (220)
T ss_dssp TTSCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHhCcCHHHHHHHHHh
Confidence 799999999999999999999988864
No 28
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A
Probab=25.90 E-value=93 Score=26.54 Aligned_cols=36 Identities=28% Similarity=0.421 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHh
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR 359 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~ 359 (395)
++.+....+....|+.|+..+.|+..|++.+.++..
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 135 (239)
T 1rp3_A 100 RIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKT 135 (239)
T ss_dssp HHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 456677788888999999999999999988776543
No 29
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}
Probab=24.17 E-value=2.1e+02 Score=20.72 Aligned_cols=39 Identities=18% Similarity=0.054 Sum_probs=27.6
Q ss_pred CChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhc
Q 016077 340 PTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNY 385 (395)
Q Consensus 340 PT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY 385 (395)
-|..+.|+.+|++...+.+...... .-+...+..||+-|
T Consensus 26 ltq~~lA~~~gvs~~~is~~e~g~~-------~~~~~~~~~ia~~l 64 (80)
T 3kz3_A 26 LSYESVADKMGMGQSAVAALFNGIN-------ALNAYNAALLAKIL 64 (80)
T ss_dssp CCHHHHHHHTTSCHHHHHHHHTTSS-------CCCHHHHHHHHHHH
T ss_pred CCHHHHHHHhCcCHHHHHHHHcCCC-------CCCHHHHHHHHHHh
Confidence 4788899999999888876665432 23556677777765
No 30
>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2
Probab=23.93 E-value=1.4e+02 Score=21.22 Aligned_cols=27 Identities=11% Similarity=0.101 Sum_probs=23.2
Q ss_pred CCCChHHHHHHhcCcHHHHHHhhhhcH
Q 016077 338 GSPTFAQWAAAAGVDQRELRRRLNYGI 364 (395)
Q Consensus 338 rePT~~EWAeA~Gms~~eLr~~L~~G~ 364 (395)
..-|..|.|+..|++...++.+++.+.
T Consensus 24 ~g~s~~eIA~~lgis~~tV~~~~~ra~ 50 (68)
T 2p7v_B 24 TDYTLEEVGKQFDVTRERIRQIEAKAL 50 (68)
T ss_dssp SCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 578999999999999999998876644
No 31
>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*
Probab=23.34 E-value=1.4e+02 Score=21.58 Aligned_cols=27 Identities=22% Similarity=0.263 Sum_probs=23.4
Q ss_pred CCCChHHHHHHhcCcHHHHHHhhhhcH
Q 016077 338 GSPTFAQWAAAAGVDQRELRRRLNYGI 364 (395)
Q Consensus 338 rePT~~EWAeA~Gms~~eLr~~L~~G~ 364 (395)
..-|..|.|+..|++...++.++..+.
T Consensus 29 ~~~s~~eIA~~l~is~~tV~~~~~ra~ 55 (73)
T 1ku3_A 29 REHTLEEVGAYFGVTRERIRQIENKAL 55 (73)
T ss_dssp SCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 678999999999999999998876654
No 32
>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2
Probab=22.46 E-value=1.4e+02 Score=22.55 Aligned_cols=28 Identities=11% Similarity=0.060 Sum_probs=24.2
Q ss_pred CCCChHHHHHHhcCcHHHHHHhhhhcHH
Q 016077 338 GSPTFAQWAAAAGVDQRELRRRLNYGIL 365 (395)
Q Consensus 338 rePT~~EWAeA~Gms~~eLr~~L~~G~~ 365 (395)
..-|..|.|+..|++...++.++..+..
T Consensus 37 ~~~s~~EIA~~lgis~~tV~~~~~ra~~ 64 (87)
T 1tty_A 37 KPKTLEEVGQYFNVTRERIRQIEVKALR 64 (87)
T ss_dssp SCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6789999999999999999998876543
No 33
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}
Probab=22.16 E-value=2.5e+02 Score=21.08 Aligned_cols=36 Identities=19% Similarity=0.211 Sum_probs=28.3
Q ss_pred HcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHH
Q 016077 335 RCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM 370 (395)
Q Consensus 335 ~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerL 370 (395)
.+-..-|..|.|+.+|++...++.+++.+..--.+.
T Consensus 49 ~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 84 (92)
T 3hug_A 49 SYYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLT 84 (92)
T ss_dssp HHTSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 345667999999999999999999998766544333
No 34
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}
Probab=21.31 E-value=2.3e+02 Score=20.25 Aligned_cols=46 Identities=11% Similarity=0.009 Sum_probs=36.4
Q ss_pred CCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhc
Q 016077 337 GGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNY 385 (395)
Q Consensus 337 GrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY 385 (395)
...-|..|.|+.+|++...++..+. .++.+|-..|..-.+..|.++
T Consensus 29 ~~g~s~~eIA~~l~is~~tV~~~~~---r~~~kl~~~~~~~l~~~~~~~ 74 (79)
T 1x3u_A 29 VAGLPNKSIAYDLDISPRTVEVHRA---NVMAKMKAKSLPHLVRMALAG 74 (79)
T ss_dssp TTTCCHHHHHHHTTSCHHHHHHHHH---HHHHHTTCCSHHHHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHH---HHHHHHcCCCHHHHHHHHHHh
Confidence 4556899999999999999988775 577788878877777777664
No 35
>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A
Probab=21.30 E-value=1.3e+02 Score=23.31 Aligned_cols=26 Identities=23% Similarity=0.341 Sum_probs=22.7
Q ss_pred CCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077 337 GGSPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 337 GrePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
|..-|..+.|+.+|++...++++|..
T Consensus 25 g~~~t~~eLA~~Lgvsr~tV~~~L~~ 50 (81)
T 1qbj_A 25 GKATTAHDLSGKLGTPKKEINRVLYS 50 (81)
T ss_dssp TCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 56789999999999999998888754
No 36
>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A
Probab=21.08 E-value=1.6e+02 Score=25.28 Aligned_cols=28 Identities=25% Similarity=0.309 Sum_probs=22.7
Q ss_pred HHcCCCCChHHHHHHhcCc-HHHHHHhhh
Q 016077 334 ERCGGSPTFAQWAAAAGVD-QRELRRRLN 361 (395)
Q Consensus 334 e~lGrePT~~EWAeA~Gms-~~eLr~~L~ 361 (395)
++.|-.||..|.|+++|++ ...+.+.+.
T Consensus 20 ~~~g~~ps~~elA~~lgiss~~tv~~~~~ 48 (202)
T 1jhf_A 20 SQTGMPPTRAEIAQRLGFRSPNAAEEHLK 48 (202)
T ss_dssp HHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred HHhCCCccHHHHHHHhCCCChHHHHHHHH
Confidence 4568889999999999998 887776543
No 37
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1
Probab=20.81 E-value=31 Score=32.85 Aligned_cols=19 Identities=16% Similarity=0.207 Sum_probs=15.0
Q ss_pred CCCHHHHHHHHHHHHHHHH
Q 016077 306 LLTANEEMQLSAGIQDLLK 324 (395)
Q Consensus 306 LLTaeEEveLa~~IQ~~~~ 324 (395)
|||.|.|++++++|..|.+
T Consensus 1 LLTREgEI~IAKRIE~G~~ 19 (339)
T 1sig_A 1 GSHMEGEIDIAKRIEDGIN 19 (339)
T ss_dssp ---CCTHHHHHHHHHHHHH
T ss_pred CCChHHHHHHHHHHHHHHH
Confidence 7999999999999999865
No 38
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1
Probab=20.60 E-value=1.5e+02 Score=30.07 Aligned_cols=35 Identities=26% Similarity=0.443 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhc--CcHHHHHH
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAG--VDQRELRR 358 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~G--ms~~eLr~ 358 (395)
++.+.+.+|...+|++|+..+.|+.+| ++.++++.
T Consensus 285 ~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~ 321 (438)
T 1l9z_H 285 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEE 321 (438)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHH
Confidence 345566778889999999999999999 88776654
No 39
>1u8b_A ADA polyprotein; protein-DNA complex, methylation, zinc, helix-turn-helix, metal binding protein/DNA complex; 2.10A {Escherichia coli} PDB: 1zgw_A* 1wpk_A* 1adn_A 1eyf_A
Probab=20.43 E-value=1.2e+02 Score=24.45 Aligned_cols=34 Identities=15% Similarity=0.149 Sum_probs=24.9
Q ss_pred HHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 326 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 326 E~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
+++...|.+ ....+..+||..+|++..-|.+..+
T Consensus 82 ~~a~~~i~~--~~~~sl~~lA~~~g~S~~~f~r~Fk 115 (133)
T 1u8b_A 82 THACRLLEQ--ETPVTLEALADQVAMSPFHLHRLFK 115 (133)
T ss_dssp HHHHHHTCS--SSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHHHHHh--cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334444433 6788999999999999888877653
No 40
>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B
Probab=20.32 E-value=3.3e+02 Score=21.68 Aligned_cols=39 Identities=10% Similarity=0.088 Sum_probs=29.8
Q ss_pred CCCChHHHHHHhcCcHHHHHHhhhhcHH-HHHHHHHHhHH
Q 016077 338 GSPTFAQWAAAAGVDQRELRRRLNYGIL-CKDKMITSNIR 376 (395)
Q Consensus 338 rePT~~EWAeA~Gms~~eLr~~L~~G~~-ARerLVkSNLR 376 (395)
..-|..|+|+.+|++...++.++..+.. -|+.+-..+|+
T Consensus 38 e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~~~~~l~ 77 (99)
T 3t72_q 38 TDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 77 (99)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6789999999999999999999987655 34444444443
Done!