Query 018065
Match_columns 361
No_of_seqs 166 out of 1294
Neff 3.9
Searched_HMMs 29240
Date Mon Mar 25 09:23:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018065.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/018065hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3ugo_A RNA polymerase sigma fa 99.6 1.3E-15 4.3E-20 141.3 8.7 108 253-360 5-142 (245)
2 1l9z_H Sigma factor SIGA; heli 99.6 1.9E-15 6.6E-20 151.6 8.6 109 252-360 91-229 (438)
3 2a6h_F RNA polymerase sigma fa 99.5 3.9E-15 1.3E-19 147.6 2.5 108 253-360 77-214 (423)
4 1sig_A Sigma70, RNA polymerase 97.0 0.00024 8.1E-09 67.6 2.3 33 328-360 265-297 (339)
5 3iyd_F RNA polymerase sigma fa 95.7 0.0014 5E-08 67.6 -0.6 34 253-286 94-127 (613)
6 3iyd_F RNA polymerase sigma fa 95.5 0.0045 1.5E-07 63.9 2.2 42 319-360 361-406 (613)
7 1l0o_C Sigma factor; bergerat 94.4 0.0073 2.5E-07 51.9 0.0 36 326-361 26-61 (243)
8 2jt1_A PEFI protein; solution 70.4 3.6 0.00012 31.9 3.5 34 291-324 13-46 (77)
9 2k9s_A Arabinose operon regula 67.6 8.7 0.0003 29.7 5.2 37 289-325 6-43 (107)
10 1bl0_A Protein (multiple antib 63.1 8.3 0.00028 31.0 4.4 58 289-347 14-85 (129)
11 2q1z_A RPOE, ECF SIGE; ECF sig 60.8 4.5 0.00015 33.4 2.5 35 326-360 25-59 (184)
12 3kz3_A Repressor protein CI; f 52.6 36 0.0012 24.6 6.1 52 295-358 20-71 (80)
13 3ugo_A RNA polymerase sigma fa 50.2 3.4 0.00012 37.9 0.0 40 287-326 198-239 (245)
14 2zc2_A DNAD-like replication p 49.7 9.1 0.00031 28.8 2.4 56 295-354 10-71 (78)
15 1lmb_3 Protein (lambda repress 49.7 38 0.0013 24.9 5.9 54 294-359 24-77 (92)
16 3oio_A Transcriptional regulat 49.7 27 0.00091 27.1 5.2 37 289-325 10-46 (113)
17 3lsg_A Two-component response 49.5 35 0.0012 25.9 5.8 36 290-325 6-42 (103)
18 3mn2_A Probable ARAC family tr 47.2 37 0.0013 26.0 5.7 37 289-325 5-41 (108)
19 2ofy_A Putative XRE-family tra 43.8 25 0.00085 25.6 4.0 47 304-359 29-75 (86)
20 2o7g_A Probable RNA polymerase 43.2 6.3 0.00021 30.5 0.6 34 326-360 22-55 (112)
21 2ewt_A BLDD, putative DNA-bind 42.6 52 0.0018 22.7 5.4 47 303-359 22-70 (71)
22 3oou_A LIN2118 protein; protei 42.4 25 0.00084 27.1 3.9 35 290-324 9-43 (108)
23 1y7y_A C.AHDI; helix-turn-heli 39.1 78 0.0027 21.8 5.9 47 303-359 27-73 (74)
24 1d5y_A ROB transcription facto 36.7 26 0.0009 31.1 3.7 36 289-324 6-41 (292)
25 3mkl_A HTH-type transcriptiona 35.2 29 0.001 27.3 3.4 35 290-324 11-45 (120)
26 1jko_C HIN recombinase, DNA-in 35.1 35 0.0012 21.9 3.3 23 303-325 22-44 (52)
27 3gbg_A TCP pilus virulence reg 32.9 65 0.0022 28.3 5.6 56 291-347 174-242 (276)
28 2k9q_A Uncharacterized protein 31.3 27 0.00093 25.0 2.4 47 303-359 16-62 (77)
29 3f6w_A XRE-family like protein 29.7 59 0.002 23.3 4.0 47 303-359 28-74 (83)
30 3omt_A Uncharacterized protein 28.3 95 0.0032 21.7 4.8 47 303-359 22-68 (73)
31 3k2z_A LEXA repressor; winged 27.8 57 0.002 28.0 4.2 27 298-324 20-46 (196)
32 3g5g_A Regulatory protein; tra 27.6 44 0.0015 25.8 3.2 47 303-359 42-88 (99)
33 2kpj_A SOS-response transcript 27.5 58 0.002 24.3 3.7 47 303-359 23-69 (94)
34 1h3l_A RNA polymerase sigma fa 27.3 11 0.00039 27.6 -0.4 35 326-360 10-44 (87)
35 3vk0_A NHTF, transcriptional r 26.8 46 0.0016 25.9 3.2 20 303-322 35-54 (114)
36 3hug_A RNA polymerase sigma fa 26.7 1.5E+02 0.0052 22.1 6.0 35 294-328 45-79 (92)
37 1tc3_C Protein (TC3 transposas 26.7 1.2E+02 0.004 18.8 4.7 22 303-324 22-43 (51)
38 3f2g_A Alkylmercury lyase; MER 26.6 39 0.0013 31.1 3.1 27 299-325 33-59 (220)
39 4fe7_A Xylose operon regulator 26.6 72 0.0024 29.9 5.0 52 295-347 314-379 (412)
40 3t72_q RNA polymerase sigma fa 24.7 2.2E+02 0.0075 22.5 6.8 38 301-338 38-76 (99)
41 3s8q_A R-M controller protein; 24.6 57 0.0019 23.4 3.1 47 303-359 25-71 (82)
42 3b7h_A Prophage LP1 protein 11 24.3 78 0.0027 22.1 3.7 48 303-359 21-68 (78)
43 1sig_A Sigma70, RNA polymerase 23.3 22 0.00074 33.4 0.7 19 269-287 1-19 (339)
44 2a6h_F RNA polymerase sigma fa 21.8 1.1E+02 0.0037 30.1 5.4 34 287-320 270-305 (423)
45 4ghj_A Probable transcriptiona 21.8 1.9E+02 0.0066 22.7 5.9 69 269-359 27-96 (101)
46 1rp3_A RNA polymerase sigma fa 20.6 1.3E+02 0.0044 25.2 5.0 41 283-323 96-136 (239)
No 1
>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=99.60 E-value=1.3e-15 Score=141.30 Aligned_cols=108 Identities=33% Similarity=0.475 Sum_probs=89.7
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHH-HHHHH------H--HH-----------------hhCCCCcHH
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE-KEKSK------L--QS-----------------QFGREPTLI 306 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LE-kir~~------L--e~-----------------~lGrePT~~ 306 (361)
.+|+++.||++|+++||||++||++|+++|+.++... .+... + +. ..+.+|+..
T Consensus 5 ~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~ 84 (245)
T 3ugo_A 5 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTV 84 (245)
T ss_dssp CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHHH
T ss_pred CCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchhH
Confidence 5899999999999999999999999999999987633 33221 0 00 014689999
Q ss_pred HHHHHhccchh----hhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 307 EWAKAIGLSCR----DLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 307 EWA~AaG~d~~----~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
+||.+.|++.. .|.+....|..|+++||..|+++|.++|++|.+.|.+++||+|
T Consensus 85 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQ 142 (245)
T 3ugo_A 85 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 142 (245)
T ss_dssp HHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHH
T ss_pred HHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHH
Confidence 99999999654 3444566788999999999999999999999999999999998
No 2
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1
Probab=99.58 E-value=1.9e-15 Score=151.57 Aligned_cols=109 Identities=33% Similarity=0.494 Sum_probs=90.4
Q ss_pred CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHHhhCCCCcHHHHHH---
Q 018065 252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS------------------KLQSQFGREPTLIEWAK--- 310 (361)
Q Consensus 252 ~~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~------------------~Le~~lGrePT~~EWA~--- 310 (361)
...|+++.||++|+++||||++||++|+++|+.++.++.... .....+|+.|+..+|+.
T Consensus 91 ~~~d~~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 170 (438)
T 1l9z_H 91 STSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT 170 (438)
T ss_pred CCCChHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchh
Confidence 467899999999999999999999999999999865443221 12234567898888753
Q ss_pred ---------HhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 311 ---------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 311 ---------AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
++|++...|..++..|..|+++||.+|+|||++||++|.|+|++++||||
T Consensus 171 ~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQ 229 (438)
T 1l9z_H 171 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 229 (438)
T ss_pred hhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence 23556677888888899999999999999999999999999999999998
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=99.50 E-value=3.9e-15 Score=147.63 Aligned_cols=108 Identities=34% Similarity=0.527 Sum_probs=85.7
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH------------------HHhhCCCCcHHH-------
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKL------------------QSQFGREPTLIE------- 307 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~L------------------e~~lGrePT~~E------- 307 (361)
..|+++.||++|+++|+||++||++|+++|+.+..++...... ....|+.|+..+
T Consensus 77 ~~d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 (423)
T 2a6h_F 77 TSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTV 156 (423)
T ss_dssp THHHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHHH
T ss_pred CCcHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhhh
Confidence 5689999999999999999999999999999975443321110 112235565444
Q ss_pred --HHH---HhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 308 --WAK---AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 308 --WA~---AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
|+. ++|++...|..++..|..|+++||.+|+|||++||++|.|+|++++||||
T Consensus 157 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQ 214 (423)
T 2a6h_F 157 EEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 214 (423)
T ss_dssp HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHH
T ss_pred hhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence 332 34667778888888899999999999999999999999999999999998
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=96.99 E-value=0.00024 Score=67.59 Aligned_cols=33 Identities=42% Similarity=0.858 Sum_probs=32.2
Q ss_pred HHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 328 ~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
.|.+.|+..|+++|+++|++|.+.|..++||+|
T Consensus 265 ~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQ 297 (339)
T 1sig_A 265 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 297 (339)
T ss_dssp HHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHH
T ss_pred hhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHH
Confidence 699999999999999999999999999999998
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=95.71 E-value=0.0014 Score=67.58 Aligned_cols=34 Identities=32% Similarity=0.570 Sum_probs=13.8
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHH
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 286 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~ 286 (361)
.+||+++||++||..+|||+++|++|++.|..+.
T Consensus 94 ~~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~ 127 (613)
T 3iyd_F 94 TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127 (613)
T ss_dssp -----------C--------CSSSTTTHHHHHHH
T ss_pred CCCcHHHHHHHhcccccCCchhHHHHHHHHHHhH
Confidence 6899999999999999999999999999999864
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=95.51 E-value=0.0045 Score=63.92 Aligned_cols=42 Identities=36% Similarity=0.773 Sum_probs=35.3
Q ss_pred hhhhccccH-HH---HHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 319 LKSELHSGN-SS---REKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 319 Lr~~L~~G~-~A---RekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
|-.++..|. .| ++.||..|+++|++||++|.++|..++||||
T Consensus 361 Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQ 406 (613)
T 3iyd_F 361 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 406 (613)
T ss_dssp HHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTH
T ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence 333444443 34 9999999999999999999999999999998
No 7
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2
Probab=94.36 E-value=0.0073 Score=51.93 Aligned_cols=36 Identities=36% Similarity=0.664 Sum_probs=0.0
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 326 G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
+..|.+.|+..|.++|..+|++|.+.+.+.+||+|.
T Consensus 26 d~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe 61 (243)
T 1l0o_C 26 DQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQI 61 (243)
T ss_dssp ------------------------------------
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHH
Confidence 467889999999999999999999999999999983
No 8
>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}
Probab=70.36 E-value=3.6 Score=31.87 Aligned_cols=34 Identities=21% Similarity=0.169 Sum_probs=25.0
Q ss_pred HHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 291 ir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
++..+++..|.+||..|.|++.|++...+++-|.
T Consensus 13 I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~ 46 (77)
T 2jt1_A 13 VQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLE 46 (77)
T ss_dssp HHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred HHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 3344444468999999999999998777665443
No 9
>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}
Probab=67.61 E-value=8.7 Score=29.71 Aligned_cols=37 Identities=11% Similarity=0.104 Sum_probs=29.5
Q ss_pred HHHHHHHHHhhC-CCCcHHHHHHHhccchhhhhhhccc
Q 018065 289 EKEKSKLQSQFG-REPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 289 Ekir~~Le~~lG-rePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
.++..-+...++ .+++..++|+.+|++...|.+.+..
T Consensus 6 ~~~~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 43 (107)
T 2k9s_A 6 REACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQ 43 (107)
T ss_dssp HHHHHHHHHTSSCSSCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 345555666777 7899999999999999999887764
No 10
>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=63.05 E-value=8.3 Score=31.02 Aligned_cols=58 Identities=16% Similarity=0.186 Sum_probs=39.9
Q ss_pred HHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc--c------------HHHHHHHHHHhHHHHHHHHHh
Q 018065 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS--G------------NSSREKLINANLRLVVHVAKQ 347 (361)
Q Consensus 289 Ekir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~--G------------~~ARekLI~sNLRLVVSIAKr 347 (361)
+++..-+...++.+++..++|+.+|++...|.+.+.. | ..|++.|...++. |..||..
T Consensus 14 ~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~G~s~~~~l~~~Rl~~A~~lL~~~~~s-i~~IA~~ 85 (129)
T 1bl0_A 14 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEP-ILYLAER 85 (129)
T ss_dssp HHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHH
T ss_pred HHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 3444556667778899999999999999999887763 2 3455555555543 5556654
No 11
>2q1z_A RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc bindin transcription factor; 2.40A {Rhodobacter sphaeroides} PDB: 2z2s_A
Probab=60.75 E-value=4.5 Score=33.37 Aligned_cols=35 Identities=9% Similarity=-0.051 Sum_probs=31.8
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 326 G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
+..|-+.|+..+.++|..+|++|.|..-..+|++|
T Consensus 25 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Q 59 (184)
T 2q1z_A 25 DEAAFAELFQHFAPKVKGFLMKSGSVASQAEECAQ 59 (184)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHH
Confidence 57789999999999999999999988888889887
No 12
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}
Probab=52.63 E-value=36 Score=24.59 Aligned_cols=52 Identities=15% Similarity=0.197 Sum_probs=34.2
Q ss_pred HHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCc
Q 018065 295 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDL 358 (361)
Q Consensus 295 Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDL 358 (361)
+.+..| -|..+.|+.+|++...+.+...... .-+...+..||+-| |++..||
T Consensus 20 ~r~~~g--ltq~~lA~~~gvs~~~is~~e~g~~-------~~~~~~~~~ia~~l---~v~~~~l 71 (80)
T 3kz3_A 20 KKNELG--LSYESVADKMGMGQSAVAALFNGIN-------ALNAYNAALLAKIL---KVSVEEF 71 (80)
T ss_dssp HHHHHT--CCHHHHHHHTTSCHHHHHHHHTTSS-------CCCHHHHHHHHHHH---TSCGGGT
T ss_pred HHHHcC--CCHHHHHHHhCcCHHHHHHHHcCCC-------CCCHHHHHHHHHHh---CCCHHHH
Confidence 333445 5788999999998888876655431 23556777888776 4555554
No 13
>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=50.16 E-value=3.4 Score=37.88 Aligned_cols=40 Identities=30% Similarity=0.570 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhc--cchhhhhhhcccc
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIG--LSCRDLKSELHSG 326 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG--~d~~~Lr~~L~~G 326 (361)
+|.+....|...+|+.||..|.|+..| ++..+++.+|..+
T Consensus 198 ~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~a 239 (245)
T 3ugo_A 198 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIA 239 (245)
T ss_dssp ------------------------------------------
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Confidence 344556678888899999999999999 9999999888764
No 14
>2zc2_A DNAD-like replication protein; GI 24377835, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Streptococcus mutans UA159}
Probab=49.73 E-value=9.1 Score=28.76 Aligned_cols=56 Identities=14% Similarity=0.163 Sum_probs=37.7
Q ss_pred HHHhhCCCCcH------HHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCC
Q 018065 295 LQSQFGREPTL------IEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGIS 354 (361)
Q Consensus 295 Le~~lGrePT~------~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLs 354 (361)
++..+||.||. .+|...-|++.+.+...++... .. =+.|++.|-.|++++...|+.
T Consensus 10 ~e~~~gr~ls~~e~~~i~~w~~~~~~~~elI~~A~~~a~-~~---~~~s~~Yi~~Il~~W~~~gi~ 71 (78)
T 2zc2_A 10 FERELGRMLSPFELEDLQKTVSDDKTDPDLVRSALREAV-FN---GKTNWNYIQAILRNWRHEGIS 71 (78)
T ss_dssp HHHHHTSCCCHHHHHHHHHHHTTTCCCHHHHHHHHHHHH-HH---TCCCHHHHHHHHHHHHHTTCC
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHH-Hc---CCCCHHHHHHHHHHHHHcCCC
Confidence 44456777664 4566666777766665555432 11 256899999999999999974
No 15
>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A*
Probab=49.73 E-value=38 Score=24.88 Aligned_cols=54 Identities=17% Similarity=0.185 Sum_probs=34.4
Q ss_pred HHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 294 KLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 294 ~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
.+....| -|..+.|..+|++...+.+...... .-++..+..||+-| |++..+|+
T Consensus 24 ~~R~~~g--lsq~~lA~~~gis~~~is~~e~g~~-------~~~~~~l~~ia~~l---~v~~~~l~ 77 (92)
T 1lmb_3 24 KKKNELG--LSQESVADKMGMGQSGVGALFNGIN-------ALNAYNAALLAKIL---KVSVEEFS 77 (92)
T ss_dssp HHHHHHT--CCHHHHHHHHTSCHHHHHHHHTTSS-------CCCHHHHHHHHHHH---TSCGGGTC
T ss_pred HHHHHcC--CCHHHHHHHHCcCHHHHHHHHcCCC-------CCCHHHHHHHHHHH---CCCHHHHh
Confidence 3344446 5888999999998887765554321 23455677777766 45655554
No 16
>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}
Probab=49.66 E-value=27 Score=27.14 Aligned_cols=37 Identities=16% Similarity=0.192 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 289 Ekir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
.++..-+...+..+++..++|+.+|++...|.+.+..
T Consensus 10 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 46 (113)
T 3oio_A 10 TEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQ 46 (113)
T ss_dssp HHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3444556666777899999999999999988887663
No 17
>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}
Probab=49.48 E-value=35 Score=25.93 Aligned_cols=36 Identities=14% Similarity=0.135 Sum_probs=27.7
Q ss_pred HHHHHHHHhhCC-CCcHHHHHHHhccchhhhhhhccc
Q 018065 290 KEKSKLQSQFGR-EPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 290 kir~~Le~~lGr-ePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
++..-+++.+.. .++..++|+.+|++...|.+.+..
T Consensus 6 ~i~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 42 (103)
T 3lsg_A 6 LIQNIIEESYTDSQFTLSVLSEKLDLSSGYLSIMFKK 42 (103)
T ss_dssp HHHHHHHHHTTCTTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred HHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344445566666 799999999999999999887763
No 18
>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}
Probab=47.16 E-value=37 Score=25.98 Aligned_cols=37 Identities=14% Similarity=0.253 Sum_probs=29.5
Q ss_pred HHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 289 Ekir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
+++..-+...++.+++..++|+.+|++...|.+.+..
T Consensus 5 ~~~~~~i~~~~~~~~~~~~lA~~~~~s~~~l~r~fk~ 41 (108)
T 3mn2_A 5 RQVEEYIEANWMRPITIEKLTALTGISSRGIFKAFQR 41 (108)
T ss_dssp HHHHHHHHHHTTSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred HHHHHHHHHcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3445556667777899999999999999999887764
No 19
>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PS protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3
Probab=43.77 E-value=25 Score=25.65 Aligned_cols=47 Identities=19% Similarity=0.241 Sum_probs=30.3
Q ss_pred cHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 304 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 304 T~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
|..++|+.+|++...+.+...... -.-++..+..||+-| |+++.+|+
T Consensus 29 sq~~lA~~~gis~~~is~~E~g~~------~~p~~~~l~~ia~~l---~v~~~~l~ 75 (86)
T 2ofy_A 29 SMVTVAFDAGISVETLRKIETGRI------ATPAFFTIAAVARVL---DLSLDDVA 75 (86)
T ss_dssp CHHHHHHHHTCCHHHHHHHHTTCC------SSCBHHHHHHHHHHT---TCCHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC------CCCCHHHHHHHHHHh---CCCHHHHh
Confidence 788999999999888765544321 012455567777766 55555554
No 20
>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}
Probab=43.21 E-value=6.3 Score=30.47 Aligned_cols=34 Identities=24% Similarity=0.116 Sum_probs=29.0
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 326 G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
+..+-+.|+..+.+.|..+|.+| |..-.-+|++|
T Consensus 22 d~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQ 55 (112)
T 2o7g_A 22 NGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQ 55 (112)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHH
Confidence 46788899999999999999999 77677788887
No 21
>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}
Probab=42.62 E-value=52 Score=22.74 Aligned_cols=47 Identities=15% Similarity=0.192 Sum_probs=31.3
Q ss_pred CcHHHHHHHhc--cchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 303 PTLIEWAKAIG--LSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 303 PT~~EWA~AaG--~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
-|..+.|+.+| ++...+.+...... .-++..+..||+-| |+++.+|+
T Consensus 22 lsq~~lA~~~g~~is~~~i~~~e~g~~-------~~~~~~l~~la~~l---~v~~~~l~ 70 (71)
T 2ewt_A 22 LSLHGVEEKSQGRWKAVVVGSYERGDR-------AVTVQRLAELADFY---GVPVQELL 70 (71)
T ss_dssp CCHHHHHHHTTTSSCHHHHHHHHHTCS-------CCCHHHHHHHHHHH---TSCGGGGC
T ss_pred CCHHHHHHHHCCcCCHHHHHHHHCCCC-------CCCHHHHHHHHHHH---CcCHHHHc
Confidence 67888999999 88777754433211 23556677788766 56777765
No 22
>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=42.36 E-value=25 Score=27.13 Aligned_cols=35 Identities=11% Similarity=0.114 Sum_probs=27.8
Q ss_pred HHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 290 kir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
++..-+...++...+..++|+.+|++...|.+.+.
T Consensus 9 ~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk 43 (108)
T 3oou_A 9 NVLSYITEHFSEGMSLKTLGNDFHINAVYLGQLFQ 43 (108)
T ss_dssp HHHHHHHHHTTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34445566677789999999999999988888765
No 23
>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3
Probab=39.05 E-value=78 Score=21.80 Aligned_cols=47 Identities=17% Similarity=0.126 Sum_probs=32.6
Q ss_pred CcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
-|..+.|+.+|++...+.+...... .-+...+..||+-| |++..+|+
T Consensus 27 ~s~~~lA~~~gis~~~i~~~e~g~~-------~~~~~~l~~l~~~l---~~~~~~l~ 73 (74)
T 1y7y_A 27 LSQETLAFLSGLDRSYVGGVERGQR-------NVSLVNILKLATAL---DIEPRELF 73 (74)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHTTCS-------CCBHHHHHHHHHHT---TSCGGGGC
T ss_pred CCHHHHHHHHCcCHHHHHHHHCCCC-------CCCHHHHHHHHHHh---CcCHHHHc
Confidence 6888999999998887766544321 23455677788766 67777775
No 24
>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=36.70 E-value=26 Score=31.05 Aligned_cols=36 Identities=17% Similarity=0.098 Sum_probs=29.4
Q ss_pred HHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 289 Ekir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
.++..-+++.+...++..++|+.+|++...|++.+.
T Consensus 6 ~~~~~~i~~~~~~~~~~~~la~~~~~s~~~l~r~f~ 41 (292)
T 1d5y_A 6 RDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFK 41 (292)
T ss_dssp HHHHHHHHTTSSSSCCCHHHHTTTSSCHHHHHHHHH
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345555667778889999999999999999988766
No 25
>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}
Probab=35.20 E-value=29 Score=27.27 Aligned_cols=35 Identities=23% Similarity=0.189 Sum_probs=27.4
Q ss_pred HHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 290 kir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
++..-+...+..+++..++|+.+|++...|.+.+.
T Consensus 11 ~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk 45 (120)
T 3mkl_A 11 RVCTVINNNIAHEWTLARIASELLMSPSLLKKKLR 45 (120)
T ss_dssp HHHHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred HHHHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34445556667789999999999999988887764
No 26
>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=35.07 E-value=35 Score=21.92 Aligned_cols=23 Identities=13% Similarity=0.104 Sum_probs=19.5
Q ss_pred CcHHHHHHHhccchhhhhhhccc
Q 018065 303 PTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
-+..+.|+..|++...+.+.+..
T Consensus 22 ~s~~~ia~~lgvs~~Tv~r~l~~ 44 (52)
T 1jko_C 22 HPRQQLAIIFGIGVSTLYRYFPA 44 (52)
T ss_dssp CCHHHHHHTTSCCHHHHHHHSCT
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 67889999999999888887764
No 27
>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=32.93 E-value=65 Score=28.30 Aligned_cols=56 Identities=20% Similarity=0.190 Sum_probs=38.5
Q ss_pred HHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc-c------------HHHHHHHHHHhHHHHHHHHHh
Q 018065 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS-G------------NSSREKLINANLRLVVHVAKQ 347 (361)
Q Consensus 291 ir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~-G------------~~ARekLI~sNLRLVVSIAKr 347 (361)
+..-+.+.+....+..++|+.+|++...|.+.... | ..|+..|...++. |-.||..
T Consensus 174 ~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~G~t~~~~l~~~Rl~~A~~lL~~~~~s-i~eIA~~ 242 (276)
T 3gbg_A 174 ISCLVKSDITRNWRWADICGELRTNRMILKKELESRGVKFRELINSIRISYSISLMKTGEFK-IKQIAYQ 242 (276)
T ss_dssp HHHHHHHTTTSCCCHHHHHHHHTCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCCC-HHHHHHH
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhCCCCC-HHHHHHH
Confidence 34445566777899999999999998888776542 2 3466666666554 5566655
No 28
>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}
Probab=31.27 E-value=27 Score=25.03 Aligned_cols=47 Identities=19% Similarity=0.212 Sum_probs=30.1
Q ss_pred CcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
-|..+.|+.+|++...+.+...... .-++..+..||+-| |+++.+|+
T Consensus 16 lsq~~lA~~~gis~~~i~~~e~g~~-------~p~~~~l~~ia~~l---~v~~~~l~ 62 (77)
T 2k9q_A 16 LTAKSVAEEMGISRQQLCNIEQSET-------APVVVKYIAFLRSK---GVDLNALF 62 (77)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHTCCS-------CCHHHHHHHHHHHT---TCCHHHHH
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC-------CCCHHHHHHHHHHh---CcCHHHHh
Confidence 5778899999998877765544321 12455566777766 55555554
No 29
>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}
Probab=29.75 E-value=59 Score=23.32 Aligned_cols=47 Identities=15% Similarity=0.096 Sum_probs=31.0
Q ss_pred CcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
-|..+.|+.+|++...+.+...... .-++..+..||+-| |++..+|+
T Consensus 28 ltq~elA~~~gis~~~is~~e~g~~-------~~~~~~l~~l~~~l---~~~~~~l~ 74 (83)
T 3f6w_A 28 ITQKELAARLGRPQSFVSKTENAER-------RLDVIEFMDFCRGI---GTDPYALL 74 (83)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHTTSS-------CCCHHHHHHHHHHH---TCCHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHCCCC-------CCCHHHHHHHHHHc---CCCHHHHH
Confidence 6788899999998877765554321 23566777777766 55555543
No 30
>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}
Probab=28.26 E-value=95 Score=21.73 Aligned_cols=47 Identities=9% Similarity=0.197 Sum_probs=33.6
Q ss_pred CcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
-|..+.|+.+|++...+.+..... ..-++..+..||+-| |+++++|+
T Consensus 22 lsq~~lA~~~gis~~~is~~e~g~-------~~~~~~~l~~ia~~l---~v~~~~l~ 68 (73)
T 3omt_A 22 KTNLWLTETLDKNKTTVSKWCTND-------VQPSLETLFDIAEAL---NVDVRELI 68 (73)
T ss_dssp CCHHHHHHHTTCCHHHHHHHHTTS-------SCCCHHHHHHHHHHH---TSCGGGGB
T ss_pred CCHHHHHHHHCcCHHHHHHHHcCC-------CCCCHHHHHHHHHHH---CcCHHHHh
Confidence 577888888888887776655432 124667788888877 67777776
No 31
>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=27.79 E-value=57 Score=28.02 Aligned_cols=27 Identities=22% Similarity=0.252 Sum_probs=21.8
Q ss_pred hhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065 298 QFGREPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 298 ~lGrePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
..|.+||..|.|++.|++...+.+.|.
T Consensus 20 ~~g~~~s~~eia~~lgl~~~tv~~~l~ 46 (196)
T 3k2z_A 20 KNGYPPSVREIARRFRITPRGALLHLI 46 (196)
T ss_dssp HHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred HhCCCCCHHHHHHHcCCCcHHHHHHHH
Confidence 459999999999999998766665544
No 32
>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A
Probab=27.64 E-value=44 Score=25.83 Aligned_cols=47 Identities=13% Similarity=0.014 Sum_probs=30.9
Q ss_pred CcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
-|..+.|+.+|++...+.+..... ..-++..+..||+-| |+++.+|+
T Consensus 42 ltq~elA~~~gis~~~is~iE~G~-------~~ps~~~l~~ia~~l---~v~~~~l~ 88 (99)
T 3g5g_A 42 MTQEDLAYKSNLDRTYISGIERNS-------RNLTIKSLELIMKGL---EVSDVVFF 88 (99)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHTTC-------SCCBHHHHHHHHHHT---TCCHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHCCC-------CCCCHHHHHHHHHHH---CcCHHHHh
Confidence 577888888888887776554432 123666777777766 55655554
No 33
>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}
Probab=27.50 E-value=58 Score=24.30 Aligned_cols=47 Identities=26% Similarity=0.289 Sum_probs=29.7
Q ss_pred CcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
-|..+.|+.+|++...+.+...... .-++..+..||+.| |+++.+|+
T Consensus 23 lsq~~lA~~~gis~~~is~~e~G~~-------~p~~~~l~~ia~~l---~v~~~~l~ 69 (94)
T 2kpj_A 23 KTQLEIAKSIGVSPQTFNTWCKGIA-------IPRMGKVQALADYF---NINKSDLI 69 (94)
T ss_dssp SCHHHHHHHHTCCHHHHHHHHTTSC-------CCCHHHHHHHHHHH---TCCTHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHhCCC-------CCCHHHHHHHHHHH---CcCHHHHh
Confidence 6788889999998877765544321 12455667777765 44544443
No 34
>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1
Probab=27.31 E-value=11 Score=27.63 Aligned_cols=35 Identities=17% Similarity=0.068 Sum_probs=29.5
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 326 G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
+..+-+.|+..+.+.+..+|.+|.+..-+-+||+|
T Consensus 10 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQ 44 (87)
T 1h3l_A 10 RSARFERDALEFLDQMYSAALRMTRNPADAEDLVQ 44 (87)
T ss_dssp HHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Confidence 45678889999999999999999887777888877
No 35
>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}
Probab=26.78 E-value=46 Score=25.91 Aligned_cols=20 Identities=20% Similarity=0.101 Sum_probs=11.3
Q ss_pred CcHHHHHHHhccchhhhhhh
Q 018065 303 PTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~ 322 (361)
-|..+.|+.+|++...+.+.
T Consensus 35 ltq~elA~~~gis~~~is~~ 54 (114)
T 3vk0_A 35 WSQEELARQCGLDRTYVSAV 54 (114)
T ss_dssp CCHHHHHHHHTCCHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 45556666666665555443
No 36
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}
Probab=26.75 E-value=1.5e+02 Score=22.05 Aligned_cols=35 Identities=23% Similarity=0.272 Sum_probs=26.1
Q ss_pred HHHHhhCCCCcHHHHHHHhccchhhhhhhccccHH
Q 018065 294 KLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 328 (361)
Q Consensus 294 ~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ 328 (361)
.+.-..-..-+..|.|+..|++...++.+++.+..
T Consensus 45 vl~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~ 79 (92)
T 3hug_A 45 VIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVR 79 (92)
T ss_dssp HHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33333344579999999999999999988877544
No 37
>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=26.70 E-value=1.2e+02 Score=18.80 Aligned_cols=22 Identities=23% Similarity=0.206 Sum_probs=15.8
Q ss_pred CcHHHHHHHhccchhhhhhhcc
Q 018065 303 PTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
-+..+.|+..|++...+.+.+.
T Consensus 22 ~s~~~IA~~lgis~~Tv~~~~~ 43 (51)
T 1tc3_C 22 VSLHEMSRKISRSRHCIRVYLK 43 (51)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHh
Confidence 4678888888888766665543
No 38
>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=26.63 E-value=39 Score=31.15 Aligned_cols=27 Identities=15% Similarity=0.156 Sum_probs=24.2
Q ss_pred hCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 299 FGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 299 lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
.|++|+..+.|+++|++.+++++.|+.
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 699999999999999999888887764
No 39
>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=26.56 E-value=72 Score=29.89 Aligned_cols=52 Identities=15% Similarity=0.304 Sum_probs=35.0
Q ss_pred HHHhhCCCCcHHHHHHHhccchhhhhhhcccc--------------HHHHHHHHHHhHHHHHHHHHh
Q 018065 295 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSG--------------NSSREKLINANLRLVVHVAKQ 347 (361)
Q Consensus 295 Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G--------------~~ARekLI~sNLRLVVSIAKr 347 (361)
+...+....+..+||+.+|++...|.+.+..- ..|+..|...++. |..||..
T Consensus 314 i~~~~~~~~~~~~~a~~~~~s~~~l~r~f~~~~g~s~~~~~~~~r~~~a~~~L~~~~~~-i~~ia~~ 379 (412)
T 4fe7_A 314 IRNHACKGIKVDQVLDAVGISRSNLEKRFKEEVGETIHAMIHAEKLEKARSLLISTTLS-INEISQM 379 (412)
T ss_dssp HHHHGGGTCCHHHHHHHTTCCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHH
T ss_pred HHhhccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhcCCCC-HHHHHHH
Confidence 33445667899999999999999998877632 3455555554443 4555554
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=24.70 E-value=2.2e+02 Score=22.46 Aligned_cols=38 Identities=16% Similarity=0.067 Sum_probs=28.1
Q ss_pred CCCcHHHHHHHhccchhhhhhhccccHH-HHHHHHHHhH
Q 018065 301 REPTLIEWAKAIGLSCRDLKSELHSGNS-SREKLINANL 338 (361)
Q Consensus 301 rePT~~EWA~AaG~d~~~Lr~~L~~G~~-ARekLI~sNL 338 (361)
..-|..|+|+..|++...++.++..+.. .|..+-..+|
T Consensus 38 e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~~~~~l 76 (99)
T 3t72_q 38 TDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 76 (99)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999988876543 3444443333
No 41
>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*
Probab=24.61 E-value=57 Score=23.41 Aligned_cols=47 Identities=13% Similarity=0.033 Sum_probs=29.6
Q ss_pred CcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
-|..+.|+.+|++...+.+...... .-++..+..||+-| |+++.+|+
T Consensus 25 lsq~~lA~~~gis~~~i~~~e~g~~-------~~~~~~l~~ia~~l---~v~~~~l~ 71 (82)
T 3s8q_A 25 MTQEDLAYKSNLDRTYISGIERNSR-------NLTIKSLELIMKGL---EVSDVVFF 71 (82)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHTTCC-------CCBHHHHHHHHHHT---TCCHHHHH
T ss_pred CCHHHHHHHhCcCHHHHHHHHCCCC-------CCCHHHHHHHHHHH---CcCHHHHh
Confidence 6788888888888777765544221 23566677777665 45555443
No 42
>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}
Probab=24.25 E-value=78 Score=22.14 Aligned_cols=48 Identities=21% Similarity=0.320 Sum_probs=30.6
Q ss_pred CcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCcc
Q 018065 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (361)
Q Consensus 303 PT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLI 359 (361)
-|..+.|+.+|++...+.+...... -.-++..+..||+-| |+++.+|+
T Consensus 21 ~sq~~lA~~~gis~~~i~~~e~g~~------~~~~~~~l~~ia~~l---~~~~~~l~ 68 (78)
T 3b7h_A 21 LTINRVATLAGLNQSTVNAMFEGRS------KRPTITTIRKVCGTL---GISVHDFF 68 (78)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHCTTC------CCCCHHHHHHHHHHH---TCCHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHcCCC------CCCCHHHHHHHHHHc---CCCHHHHh
Confidence 6788899999998888876555321 012445566677765 55555554
No 43
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1
Probab=23.28 E-value=22 Score=33.41 Aligned_cols=19 Identities=21% Similarity=0.267 Sum_probs=14.7
Q ss_pred CCCHHHHHHHHHHHHHHHH
Q 018065 269 LLTADEEFELIAQIQDLIR 287 (361)
Q Consensus 269 LLTaEEE~eL~~~IQ~l~~ 287 (361)
|||+|.|++++++|.++.+
T Consensus 1 LLTREgEI~IAKRIE~G~~ 19 (339)
T 1sig_A 1 GSHMEGEIDIAKRIEDGIN 19 (339)
T ss_dssp ---CCTHHHHHHHHHHHHH
T ss_pred CCChHHHHHHHHHHHHHHH
Confidence 7999999999999998765
No 44
>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=21.85 E-value=1.1e+02 Score=30.06 Aligned_cols=34 Identities=35% Similarity=0.646 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhc--cchhhhh
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIG--LSCRDLK 320 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG--~d~~~Lr 320 (361)
++.+.+.+|...+|++|+..+.|...| ++.+.++
T Consensus 270 ~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~ 305 (423)
T 2a6h_F 270 KLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVE 305 (423)
T ss_dssp HHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHH
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHH
Confidence 345566778888999999999999999 7655544
No 45
>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}
Probab=21.79 E-value=1.9e+02 Score=22.73 Aligned_cols=69 Identities=13% Similarity=0.165 Sum_probs=40.2
Q ss_pred CCCHHH-HHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHh
Q 018065 269 LLTADE-EFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 347 (361)
Q Consensus 269 LLTaEE-E~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKr 347 (361)
-++... -.+|+..|+.+ ++..| -|..+.|+.+|++...+.+. ..|. .++...+.||+-
T Consensus 27 ~~~~~~l~~~lG~~ir~~----------R~~~g--lTQ~eLA~~~gvs~~~is~~-E~G~--------~~~~~l~~i~~a 85 (101)
T 4ghj_A 27 HVTAAALAEEIGDRLKQA----------RLNRD--LTQSEVAEIAGIARKTVLNA-EKGK--------VQLDIMIAILMA 85 (101)
T ss_dssp CCCHHHHHHHHHHHHHHH----------HHHTT--CCHHHHHHHHTSCHHHHHHH-HTTC--------CBHHHHHHHHHH
T ss_pred hccHHHHHHHHHHHHHHH----------HHHcC--CCHHHHHHHcCCCHHHHHHH-HCCC--------CCHHHHHHHHHH
Confidence 344433 33466666653 33345 78899999999998887643 4453 344556666654
Q ss_pred cCCCCCCccCcc
Q 018065 348 YQGRGISLHDLL 359 (361)
Q Consensus 348 Y~grGLsfqDLI 359 (361)
+ |...+++.|+
T Consensus 86 L-~~~~~ld~ll 96 (101)
T 4ghj_A 86 L-DLTEQIDLFI 96 (101)
T ss_dssp T-TCCGGGGGSS
T ss_pred c-CCCccHHHcC
Confidence 3 4444454443
No 46
>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=20.59 E-value=1.3e+02 Score=25.21 Aligned_cols=41 Identities=37% Similarity=0.509 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhc
Q 018065 283 QDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (361)
Q Consensus 283 Q~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L 323 (361)
....++.+....+....|+.|+..+.|+..|++.+.+...+
T Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 136 (239)
T 1rp3_A 96 EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTL 136 (239)
T ss_dssp HHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Done!