Query 017044
Match_columns 378
No_of_seqs 164 out of 1363
Neff 4.0
Searched_HMMs 29240
Date Mon Mar 25 08:00:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017044.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/017044hhsearch_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 99.9 8E-22 2.7E-26 198.9 10.8 127 252-378 91-254 (438)
2 3ugo_A RNA polymerase sigma fa 99.9 7.3E-22 2.5E-26 184.4 9.8 125 253-377 5-166 (245)
3 2a6h_F RNA polymerase sigma fa 99.8 9.8E-22 3.3E-26 196.2 4.0 125 253-377 77-238 (423)
4 1sig_A Sigma70, RNA polymerase 98.8 1.6E-09 5.4E-14 104.0 4.6 59 319-377 252-321 (339)
5 3iyd_F RNA polymerase sigma fa 98.5 3.2E-08 1.1E-12 102.9 2.0 60 318-377 360-430 (613)
6 1l0o_C Sigma factor; bergerat 98.1 2.8E-07 9.7E-12 80.4 0.0 53 326-378 26-85 (243)
7 1rp3_A RNA polymerase sigma fa 98.0 4.2E-06 1.4E-10 73.2 3.8 52 326-377 10-71 (239)
8 2q1z_A RPOE, ECF SIGE; ECF sig 96.0 0.0033 1.1E-07 53.1 3.1 51 326-377 25-82 (184)
9 3iyd_F RNA polymerase sigma fa 95.9 0.0018 6.3E-08 67.3 0.8 34 253-286 94-127 (613)
10 1or7_A Sigma-24, RNA polymeras 95.3 0.012 4.1E-07 49.9 3.7 49 326-377 21-76 (194)
11 2o7g_A Probable RNA polymerase 83.0 0.82 2.8E-05 35.9 3.1 39 326-365 22-60 (112)
12 1h3l_A RNA polymerase sigma fa 79.2 1 3.5E-05 33.7 2.4 40 326-365 10-49 (87)
13 2jt1_A PEFI protein; solution 73.6 2.9 9.8E-05 32.7 3.6 34 291-324 13-46 (77)
14 2k9s_A Arabinose operon regula 60.9 34 0.0012 26.5 7.5 37 289-325 6-43 (107)
15 3mn2_A Probable ARAC family tr 60.5 32 0.0011 26.6 7.3 37 289-325 5-41 (108)
16 3oio_A Transcriptional regulat 59.3 33 0.0011 26.8 7.3 37 289-325 10-46 (113)
17 3lsg_A Two-component response 57.9 42 0.0014 25.7 7.5 36 290-325 6-42 (103)
18 3ugo_A RNA polymerase sigma fa 57.1 2.2 7.6E-05 39.3 0.0 41 287-327 198-240 (245)
19 3oou_A LIN2118 protein; protei 52.3 56 0.0019 25.2 7.5 36 290-325 9-44 (108)
20 2ofy_A Putative XRE-family tra 52.0 35 0.0012 25.0 6.0 49 304-361 29-77 (86)
21 1bl0_A Protein (multiple antib 51.4 43 0.0015 26.9 6.9 37 289-325 14-50 (129)
22 3mkl_A HTH-type transcriptiona 46.1 67 0.0023 25.3 7.2 67 290-360 11-79 (120)
23 3kz3_A Repressor protein CI; f 38.7 63 0.0022 23.4 5.5 39 303-348 26-64 (80)
24 3k2z_A LEXA repressor; winged 36.8 28 0.00097 30.2 3.8 27 298-324 20-46 (196)
25 2zc2_A DNAD-like replication p 36.8 20 0.00069 27.0 2.5 58 296-357 11-75 (78)
26 2kpj_A SOS-response transcript 36.5 63 0.0022 24.3 5.4 48 303-360 23-70 (94)
27 3g5g_A Regulatory protein; tra 36.5 64 0.0022 25.1 5.5 49 303-361 42-90 (99)
28 3b7h_A Prophage LP1 protein 11 35.1 48 0.0017 23.4 4.3 48 303-359 21-68 (78)
29 2k9q_A Uncharacterized protein 35.1 49 0.0017 23.8 4.4 51 303-363 16-66 (77)
30 1lmb_3 Protein (lambda repress 34.8 60 0.0021 23.9 4.9 47 303-359 31-77 (92)
31 2ewt_A BLDD, putative DNA-bind 34.7 57 0.0019 22.7 4.6 46 303-358 22-69 (71)
32 3f6w_A XRE-family like protein 34.7 71 0.0024 23.0 5.2 48 303-360 28-75 (83)
33 2b5a_A C.BCLI; helix-turn-heli 33.8 88 0.003 21.9 5.5 49 303-361 24-72 (77)
34 1jko_C HIN recombinase, DNA-in 33.4 45 0.0015 21.5 3.6 23 303-325 22-44 (52)
35 1tc3_C Protein (TC3 transposas 31.1 93 0.0032 19.5 4.8 22 303-324 22-43 (51)
36 1msk_A Cobalamin-dependent met 31.1 63 0.0022 31.7 5.6 46 327-372 193-243 (331)
37 3hug_A RNA polymerase sigma fa 31.0 1.7E+02 0.0057 22.0 8.3 30 299-328 50-79 (92)
38 3gbg_A TCP pilus virulence reg 31.0 77 0.0026 28.0 5.8 34 291-324 174-207 (276)
39 1y7y_A C.AHDI; helix-turn-heli 30.8 56 0.0019 22.8 3.9 47 303-359 27-73 (74)
40 3vk0_A NHTF, transcriptional r 29.7 60 0.0021 25.4 4.4 48 303-360 35-82 (114)
41 3s8q_A R-M controller protein; 28.7 89 0.0031 22.5 4.9 49 303-361 25-73 (82)
42 3f2g_A Alkylmercury lyase; MER 28.3 40 0.0014 31.3 3.5 27 299-325 33-59 (220)
43 2lnb_A Z-DNA-binding protein 1 27.3 51 0.0017 26.5 3.4 27 299-325 31-57 (80)
44 1sig_A Sigma70, RNA polymerase 27.3 17 0.00056 34.5 0.7 19 269-287 1-19 (339)
45 3t72_q RNA polymerase sigma fa 24.8 2.6E+02 0.0089 22.2 7.4 53 301-360 38-92 (99)
46 2ef8_A C.ECOT38IS, putative tr 23.9 1.1E+02 0.0036 21.9 4.5 52 303-361 24-76 (84)
47 2a6h_F RNA polymerase sigma fa 23.5 91 0.0031 30.8 5.3 34 287-320 270-305 (423)
48 1d5y_A ROB transcription facto 23.5 1.2E+02 0.0041 26.9 5.6 38 288-325 5-42 (292)
49 3mzy_A RNA polymerase sigma-H 23.2 1.9E+02 0.0066 22.6 6.3 30 299-328 121-150 (164)
50 2xi8_A Putative transcription 23.0 75 0.0026 21.5 3.3 47 303-359 15-61 (66)
51 2o2k_A Methionine synthase; C- 21.5 1.1E+02 0.0039 30.2 5.4 45 328-372 205-254 (355)
52 3f52_A CLP gene regulator (CLG 21.4 1.2E+02 0.004 23.5 4.6 52 303-364 42-93 (117)
53 3nxc_A HTH-type protein SLMA; 20.7 2.4E+02 0.0083 22.6 6.6 27 298-324 40-67 (212)
54 2fjr_A Repressor protein CI; g 20.7 1.2E+02 0.0041 25.4 4.8 48 300-359 19-66 (189)
55 3ppb_A Putative TETR family tr 20.6 3.1E+02 0.011 21.5 9.5 63 298-360 24-87 (195)
56 1qgp_A Protein (double strande 20.2 77 0.0026 24.0 3.1 26 300-325 29-54 (77)
57 1rp3_A RNA polymerase sigma fa 20.1 1.2E+02 0.004 25.7 4.6 36 293-328 194-229 (239)
58 3bs3_A Putative DNA-binding pr 20.0 72 0.0025 22.4 2.8 47 303-359 24-70 (76)
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=99.86 E-value=8e-22 Score=198.95 Aligned_cols=127 Identities=30% Similarity=0.466 Sum_probs=107.9
Q ss_pred CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHhhcCCCcchHHHHHH--
Q 017044 252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS------------------KLQSQFGREPTLIEWAKA-- 311 (378)
Q Consensus 252 ~~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~------------------~Le~~lGrePT~~EWA~A-- 311 (378)
...|+++.||++|+++||||++||++|+++|+.++.++.... .....+|+.|+..+|+..
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 122345678888887532
Q ss_pred ----------hccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccc
Q 017044 312 ----------IGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLL 374 (378)
Q Consensus 312 ----------aG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rF 374 (378)
.|++..+|..++..|..|+++||.+|+|+|++||++|.|+|++++||||||+|| |||++|++|
T Consensus 171 ~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rF 250 (438)
T 1l9z_H 171 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 250 (438)
T ss_pred hhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCh
Confidence 355667888888889999999999999999999999999999999999999999 999999999
Q ss_pred cccC
Q 017044 375 FQYH 378 (378)
Q Consensus 375 stY~ 378 (378)
+||.
T Consensus 251 sTYA 254 (438)
T 1l9z_H 251 STYA 254 (438)
T ss_pred HHHH
Confidence 9983
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=99.86 E-value=7.3e-22 Score=184.37 Aligned_cols=125 Identities=30% Similarity=0.468 Sum_probs=106.3
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH-HHHHHHHH--Hh-----------------------hcCCCcchH
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR-LEKEKSKL--QS-----------------------QFGREPTLI 306 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~-LEkik~~L--e~-----------------------~lGrePT~~ 306 (378)
.+|++++||++||++||||++||++|+++|+.++. .+.+.... +. ..+.+|+..
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 58999999999999999999999999999999876 33332210 00 014689999
Q ss_pred HHHHHhccchhh----hhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccc
Q 017044 307 EWAKAIGLSCRD----LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLF 375 (378)
Q Consensus 307 EWA~AaG~s~~e----Lr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFs 375 (378)
+||.+.|++... |.+....|..|+++||..|+++|.++|++|.+++.+.+||+|||++| |||++|++|+
T Consensus 85 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~ 164 (245)
T 3ugo_A 85 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 164 (245)
T ss_dssp HHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHH
T ss_pred HHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHH
Confidence 999999997543 44455678899999999999999999999999999999999999999 9999999999
Q ss_pred cc
Q 017044 376 QY 377 (378)
Q Consensus 376 tY 377 (378)
||
T Consensus 165 ty 166 (245)
T 3ugo_A 165 TY 166 (245)
T ss_dssp HH
T ss_pred HH
Confidence 98
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=99.83 E-value=9.8e-22 Score=196.21 Aligned_cols=125 Identities=31% Similarity=0.484 Sum_probs=102.8
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH------------------HHhhcCCCcchHH-------
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK------------------LQSQFGREPTLIE------- 307 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~------------------Le~~lGrePT~~E------- 307 (378)
..|+++.||++|++.|+||++||++|+++|+.+..++..... .....|+.|+..+
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 568999999999999999999999999999998654332111 1112234555444
Q ss_pred --HHH---HhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccc
Q 017044 308 --WAK---AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLF 375 (378)
Q Consensus 308 --WA~---AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFs 375 (378)
|+. ++|++..+|..++..|..|+++||.+|+|+|++||++|.|+|++++||||||+|| |||++|++|+
T Consensus 157 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~Fs 236 (423)
T 2a6h_F 157 EEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 236 (423)
T ss_dssp HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCHH
T ss_pred hhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHH
Confidence 332 3466778888888889999999999999999999999999999999999999999 9999999999
Q ss_pred cc
Q 017044 376 QY 377 (378)
Q Consensus 376 tY 377 (378)
||
T Consensus 237 tY 238 (423)
T 2a6h_F 237 TY 238 (423)
T ss_dssp HH
T ss_pred HH
Confidence 98
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=98.84 E-value=1.6e-09 Score=103.99 Aligned_cols=59 Identities=29% Similarity=0.622 Sum_probs=52.8
Q ss_pred hhhhccccH----HHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 319 LKSELHSGN----SSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 319 Lr~~L~~G~----~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
|-.++..|. .|.+.|+..|+++|+++|++|.++|..++||+|||+|| |+|.+|++|.||
T Consensus 252 l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~tw 321 (339)
T 1sig_A 252 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 321 (339)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHH
T ss_pred HHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHH
Confidence 334444454 69999999999999999999999999999999999998 999999999998
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=98.48 E-value=3.2e-08 Score=102.86 Aligned_cols=60 Identities=30% Similarity=0.639 Sum_probs=53.0
Q ss_pred hhhhhccccH-HH---HHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 318 DLKSELHSGN-SS---REKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 318 eLr~~L~~G~-~A---RekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+|-.++..|. .| ++.||..|+++|+++|++|.++|..++||+|||+|| |+|.+|++|+||
T Consensus 360 ~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fsty 430 (613)
T 3iyd_F 360 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 430 (613)
T ss_dssp HHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTT
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHH
Confidence 3444555553 34 999999999999999999999999999999999998 999999999999
No 6
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2
Probab=98.14 E-value=2.8e-07 Score=80.39 Aligned_cols=53 Identities=26% Similarity=0.486 Sum_probs=0.0
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
+..+.+.|+..|.++|..+|++|.+.+.+.+||+|||.++ |+|.+|..|.||.
T Consensus 26 d~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l 85 (243)
T 1l0o_C 26 DQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYA 85 (243)
T ss_dssp ------------------------------------------------------------
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHH
Confidence 3578889999999999999999999999999999999998 8999999999984
No 7
>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=97.96 E-value=4.2e-06 Score=73.19 Aligned_cols=52 Identities=21% Similarity=0.224 Sum_probs=48.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhcc---CCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~---grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..+.+.|+..|.++|..+|++|. +.+.+.+||+|||.+| |||++|..|.||
T Consensus 10 ~~~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~ 71 (239)
T 1rp3_A 10 NQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 71 (239)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHH
T ss_pred cchHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHH
Confidence 345899999999999999999998 6789999999999998 999999999998
No 8
>2q1z_A RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc bindin transcription factor; 2.40A {Rhodobacter sphaeroides} PDB: 2z2s_A
Probab=96.04 E-value=0.0033 Score=53.12 Aligned_cols=51 Identities=12% Similarity=-0.000 Sum_probs=45.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..+-+.|+..+.++|..+|.+|.+.....+|++||+.+. |++.+| .|.+|
T Consensus 25 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~~-~~~~w 82 (184)
T 2q1z_A 25 DEAAFAELFQHFAPKVKGFLMKSGSVASQAEECAQDVMATVWQKAHLFDPSRA-SVATW 82 (184)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHSGGGCCTTTC-CHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhhcCcccC-cHHHH
Confidence 5789999999999999999999998888999999999997 777776 66665
No 9
>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=95.85 E-value=0.0018 Score=67.29 Aligned_cols=34 Identities=32% Similarity=0.570 Sum_probs=14.0
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHH
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 286 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~ 286 (378)
.+|||++||++||..+|||+++|++|+++|..|.
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 6899999999999999999999999999999874
No 10
>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A
Probab=95.27 E-value=0.012 Score=49.89 Aligned_cols=49 Identities=12% Similarity=0.148 Sum_probs=42.6
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..|-+.|+..+.++|..+|.+|.+ ....+||+||+.++ |++..+ |.+|
T Consensus 21 d~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~~--~~~~ 76 (194)
T 1or7_A 21 DQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDSA--FYTW 76 (194)
T ss_dssp CHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSSC--HHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCccc--hHHH
Confidence 4679999999999999999999999 99999999999997 676643 5554
No 11
>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}
Probab=82.95 E-value=0.82 Score=35.89 Aligned_cols=39 Identities=21% Similarity=0.055 Sum_probs=35.5
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
...+-+.|+..+.+.|..+|.+| +....-+|++||..+.
T Consensus 22 d~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~ 60 (112)
T 2o7g_A 22 NGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLR 60 (112)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHH
Confidence 46788999999999999999999 8878899999999986
No 12
>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1
Probab=79.16 E-value=1 Score=33.70 Aligned_cols=40 Identities=18% Similarity=0.055 Sum_probs=36.6
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+-+.|+..+.+.+..+|.++.+...+-+||+||..+.
T Consensus 10 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~ 49 (87)
T 1h3l_A 10 RSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAK 49 (87)
T ss_dssp HHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH
Confidence 4568889999999999999999998888999999999986
No 13
>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}
Probab=73.65 E-value=2.9 Score=32.67 Aligned_cols=34 Identities=21% Similarity=0.169 Sum_probs=24.8
Q ss_pred HHHHHHhhcCCCcchHHHHHHhccchhhhhhhcc
Q 017044 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (378)
Q Consensus 291 ik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~ 324 (378)
++..+++..|.+||..|.|+++|++...+++-|.
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 3444445458899999999999998766654443
No 14
>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}
Probab=60.91 E-value=34 Score=26.47 Aligned_cols=37 Identities=11% Similarity=0.104 Sum_probs=29.9
Q ss_pred HHHHHHHHhhcC-CCcchHHHHHHhccchhhhhhhccc
Q 017044 289 EKEKSKLQSQFG-REPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 289 Ekik~~Le~~lG-rePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
.++..-+.+.++ .+++..++|+.+|++...|.+....
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 445555666777 7899999999999999999888864
No 15
>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}
Probab=60.55 E-value=32 Score=26.58 Aligned_cols=37 Identities=14% Similarity=0.253 Sum_probs=29.7
Q ss_pred HHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc
Q 017044 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 289 Ekik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
+++..-+.+.+..+++..++|+.+|++...|.+....
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 3445556667777899999999999999999888774
No 16
>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}
Probab=59.34 E-value=33 Score=26.80 Aligned_cols=37 Identities=16% Similarity=0.192 Sum_probs=29.8
Q ss_pred HHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc
Q 017044 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 289 Ekik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
.++..-+.+.+..+++..++|+.+|++...|.+.+..
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 3444556677778899999999999999999888764
No 17
>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}
Probab=57.85 E-value=42 Score=25.68 Aligned_cols=36 Identities=14% Similarity=0.135 Sum_probs=28.2
Q ss_pred HHHHHHHhhcCC-CcchHHHHHHhccchhhhhhhccc
Q 017044 290 KEKSKLQSQFGR-EPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 290 kik~~Le~~lGr-ePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
++..-+++.+.. +++..++|+.+|++...|.+.+..
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 799999999999999999888764
No 18
>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=57.08 E-value=2.2 Score=39.35 Aligned_cols=41 Identities=29% Similarity=0.562 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhc--cchhhhhhhccccH
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIG--LSCRDLKSELHSGN 327 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG--~s~~eLr~~L~~G~ 327 (378)
+|.+...+|...+|++||..|.|+..| ++.+.++.+|..+.
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 345566678888899999999999999 99999998887653
No 19
>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=52.26 E-value=56 Score=25.23 Aligned_cols=36 Identities=11% Similarity=0.112 Sum_probs=28.8
Q ss_pred HHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc
Q 017044 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 290 kik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
++..-+.+.++.+++..++|+.+|++...|.+.+..
T Consensus 9 ~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 44 (108)
T 3oou_A 9 NVLSYITEHFSEGMSLKTLGNDFHINAVYLGQLFQK 44 (108)
T ss_dssp HHHHHHHHHTTSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344455666777899999999999999999888763
No 20
>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=51.97 E-value=35 Score=25.00 Aligned_cols=49 Identities=22% Similarity=0.310 Sum_probs=34.0
Q ss_pred chHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHH
Q 017044 304 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQV 361 (378)
Q Consensus 304 T~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQE 361 (378)
+..++|+.+|++...+.+... |.. -.-++..+..||+-| |+++.+|+..
T Consensus 29 sq~~lA~~~gis~~~is~~E~-g~~-----~~p~~~~l~~ia~~l---~v~~~~l~~~ 77 (86)
T 2ofy_A 29 SMVTVAFDAGISVETLRKIET-GRI-----ATPAFFTIAAVARVL---DLSLDDVAAV 77 (86)
T ss_dssp CHHHHHHHHTCCHHHHHHHHT-TCC-----SSCBHHHHHHHHHHT---TCCHHHHHTT
T ss_pred CHHHHHHHhCCCHHHHHHHHc-CCC-----CCCCHHHHHHHHHHh---CCCHHHHhcc
Confidence 788999999999887764433 321 023456677788776 7888888754
No 21
>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=51.40 E-value=43 Score=26.89 Aligned_cols=37 Identities=11% Similarity=0.081 Sum_probs=29.6
Q ss_pred HHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc
Q 017044 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 289 Ekik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
+++..-+.+.+..+++..++|+.+|++...|.+.+..
T Consensus 14 ~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 50 (129)
T 1bl0_A 14 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 50 (129)
T ss_dssp HHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHH
T ss_pred HHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3444456667778899999999999999999888864
No 22
>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}
Probab=46.11 E-value=67 Score=25.33 Aligned_cols=67 Identities=22% Similarity=0.202 Sum_probs=41.0
Q ss_pred HHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc-cHHHHHHHHHHhHHHHHHHHHhc-cCCCCChhhHHH
Q 017044 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS-GNSSREKLINANLRLVVHVAKQY-QGRGISLHDLLQ 360 (378)
Q Consensus 290 kik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~-G~~ARekLI~sNLRLVvsIAKkY-~grGls~eDLIQ 360 (378)
++..-+.+.+..+++..++|+.+|++...|.+.+.. |...++-+... || ..|++. ...++++.|+-.
T Consensus 11 ~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~G~s~~~~~~~~--Rl--~~A~~lL~~~~~si~eIA~ 79 (120)
T 3mkl_A 11 RVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTEC--RM--QRALQLIVIHGFSIKRVAV 79 (120)
T ss_dssp HHHHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHHHTTCCHHHHHHHH--HH--HHHHHHHTSTTCCHHHHHH
T ss_pred HHHHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHH--HH--HHHHHHHHcCCCCHHHHHH
Confidence 444455666777899999999999999988877653 33333322222 21 223332 345677776654
No 23
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}
Probab=38.73 E-value=63 Score=23.44 Aligned_cols=39 Identities=15% Similarity=0.077 Sum_probs=27.5
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhc
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQY 348 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY 348 (378)
.|-.+.|+.+|++...+.+...... .-+...+..||+-|
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 5788999999998887765554321 23556777888776
No 24
>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=36.77 E-value=28 Score=30.18 Aligned_cols=27 Identities=22% Similarity=0.252 Sum_probs=22.0
Q ss_pred hcCCCcchHHHHHHhccchhhhhhhcc
Q 017044 298 QFGREPTLIEWAKAIGLSCRDLKSELH 324 (378)
Q Consensus 298 ~lGrePT~~EWA~AaG~s~~eLr~~L~ 324 (378)
+.|.+||..|+|++.|++...+.++|.
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 348999999999999998776665554
No 25
>2zc2_A DNAD-like replication protein; GI 24377835, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Streptococcus mutans UA159}
Probab=36.76 E-value=20 Score=26.99 Aligned_cols=58 Identities=16% Similarity=0.194 Sum_probs=38.0
Q ss_pred HhhcCCCcchH------HHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCC-hhh
Q 017044 296 QSQFGREPTLI------EWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGIS-LHD 357 (378)
Q Consensus 296 e~~lGrePT~~------EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls-~eD 357 (378)
+..+||.|+.. +|-..-|++.+.+...++... .. =+.|++.|-.|++++...|+. ++|
T Consensus 11 e~~~gr~ls~~e~~~i~~w~~~~~~~~elI~~A~~~a~-~~---~~~s~~Yi~~Il~~W~~~gi~T~e~ 75 (78)
T 2zc2_A 11 ERELGRMLSPFELEDLQKTVSDDKTDPDLVRSALREAV-FN---GKTNWNYIQAILRNWRHEGISTLRQ 75 (78)
T ss_dssp HHHHTSCCCHHHHHHHHHHHTTTCCCHHHHHHHHHHHH-HH---TCCCHHHHHHHHHHHHHTTCCSHHH
T ss_pred HHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHH-Hc---CCCCHHHHHHHHHHHHHcCCCCHHH
Confidence 34457766654 355556677776666655542 11 246899999999999999974 444
No 26
>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}
Probab=36.53 E-value=63 Score=24.26 Aligned_cols=48 Identities=27% Similarity=0.359 Sum_probs=33.9
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQ 360 (378)
.|..+.|+.+|++...+.+... |.. .-++..+..||+.| |+++++|+-
T Consensus 23 lsq~~lA~~~gis~~~is~~e~-G~~------~p~~~~l~~ia~~l---~v~~~~l~~ 70 (94)
T 2kpj_A 23 KTQLEIAKSIGVSPQTFNTWCK-GIA------IPRMGKVQALADYF---NINKSDLIE 70 (94)
T ss_dssp SCHHHHHHHHTCCHHHHHHHHT-TSC------CCCHHHHHHHHHHH---TCCTHHHHS
T ss_pred CCHHHHHHHHCcCHHHHHHHHh-CCC------CCCHHHHHHHHHHH---CcCHHHHhc
Confidence 6889999999999887765443 321 12466677788776 688888874
No 27
>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A
Probab=36.51 E-value=64 Score=25.08 Aligned_cols=49 Identities=12% Similarity=0.036 Sum_probs=35.7
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQV 361 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQE 361 (378)
.|..+.|+.+|++...+.+... |. ..-++..+..||+-| |+++++|+..
T Consensus 42 ltq~elA~~~gis~~~is~iE~-G~------~~ps~~~l~~ia~~l---~v~~~~l~~~ 90 (99)
T 3g5g_A 42 MTQEDLAYKSNLDRTYISGIER-NS------RNLTIKSLELIMKGL---EVSDVVFFEM 90 (99)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHT-TC------SCCBHHHHHHHHHHT---TCCHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHC-CC------CCCCHHHHHHHHHHH---CcCHHHHhcc
Confidence 6788999999999888764443 32 134677788888876 6888888753
No 28
>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}
Probab=35.10 E-value=48 Score=23.43 Aligned_cols=48 Identities=21% Similarity=0.320 Sum_probs=32.6
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLI 359 (378)
.|..+.|+.+|++...+.+...... -.-++..+..||+-| |+++++|+
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 6788999999999888765444321 023455666777766 67777776
No 29
>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}
Probab=35.09 E-value=49 Score=23.79 Aligned_cols=51 Identities=16% Similarity=0.163 Sum_probs=35.5
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhh
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQ 363 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~ 363 (378)
.|..+.|+.+|++...+.+... |.. .-++..+..||+-| |+++++|+....
T Consensus 16 lsq~~lA~~~gis~~~i~~~e~-g~~------~p~~~~l~~ia~~l---~v~~~~l~~~~~ 66 (77)
T 2k9q_A 16 LTAKSVAEEMGISRQQLCNIEQ-SET------APVVVKYIAFLRSK---GVDLNALFDRII 66 (77)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHT-CCS------CCHHHHHHHHHHHT---TCCHHHHHHHHS
T ss_pred CCHHHHHHHhCCCHHHHHHHHc-CCC------CCCHHHHHHHHHHh---CcCHHHHhCccc
Confidence 5788899999999887765443 321 13455677788776 789999986543
No 30
>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=34.75 E-value=60 Score=23.93 Aligned_cols=47 Identities=15% Similarity=0.123 Sum_probs=31.4
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLI 359 (378)
.|..++|..+|++...+.+... |. ..-++..+..||+-| |++.++|+
T Consensus 31 lsq~~lA~~~gis~~~is~~e~-g~------~~~~~~~l~~ia~~l---~v~~~~l~ 77 (92)
T 1lmb_3 31 LSQESVADKMGMGQSGVGALFN-GI------NALNAYNAALLAKIL---KVSVEEFS 77 (92)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHT-TS------SCCCHHHHHHHHHHH---TSCGGGTC
T ss_pred CCHHHHHHHHCcCHHHHHHHHc-CC------CCCCHHHHHHHHHHH---CCCHHHHh
Confidence 5788999999999887765443 32 124556677788776 45555554
No 31
>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}
Probab=34.73 E-value=57 Score=22.67 Aligned_cols=46 Identities=15% Similarity=0.208 Sum_probs=28.5
Q ss_pred cchHHHHHHhc--cchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhH
Q 017044 303 PTLIEWAKAIG--LSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDL 358 (378)
Q Consensus 303 PT~~EWA~AaG--~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDL 358 (378)
.|..+.|+.+| ++...+.+... |. ..-++..+..||+-| |+++++|
T Consensus 22 lsq~~lA~~~g~~is~~~i~~~e~-g~------~~~~~~~l~~la~~l---~v~~~~l 69 (71)
T 2ewt_A 22 LSLHGVEEKSQGRWKAVVVGSYER-GD------RAVTVQRLAELADFY---GVPVQEL 69 (71)
T ss_dssp CCHHHHHHHTTTSSCHHHHHHHHH-TC------SCCCHHHHHHHHHHH---TSCGGGG
T ss_pred CCHHHHHHHHCCcCCHHHHHHHHC-CC------CCCCHHHHHHHHHHH---CcCHHHH
Confidence 67888999999 88777643332 32 123455667777766 4555554
No 32
>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=34.71 E-value=71 Score=23.04 Aligned_cols=48 Identities=15% Similarity=0.084 Sum_probs=34.8
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQ 360 (378)
.|..+.|+.+|++...+.+... |. ..-++..+..||+-| |++..+|+.
T Consensus 28 ltq~elA~~~gis~~~is~~e~-g~------~~~~~~~l~~l~~~l---~~~~~~l~~ 75 (83)
T 3f6w_A 28 ITQKELAARLGRPQSFVSKTEN-AE------RRLDVIEFMDFCRGI---GTDPYALLS 75 (83)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHT-TS------SCCCHHHHHHHHHHH---TCCHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHC-CC------CCCCHHHHHHHHHHc---CCCHHHHHH
Confidence 6788999999998887765444 32 124667788888776 788888875
No 33
>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3
Probab=33.81 E-value=88 Score=21.94 Aligned_cols=49 Identities=16% Similarity=0.179 Sum_probs=34.1
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQV 361 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQE 361 (378)
.|..+.|+.+|++...+.+... |.. .-++..+..||+-| |+++.+|+..
T Consensus 24 lsq~~lA~~~gis~~~i~~~e~-g~~------~~~~~~l~~la~~l---~~~~~~l~~~ 72 (77)
T 2b5a_A 24 VSQEELADLAGLHRTYISEVER-GDR------NISLINIHKICAAL---DIPASTFFRK 72 (77)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHT-TCS------CCBHHHHHHHHHHT---TCCHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHC-CCC------CCCHHHHHHHHHHh---CcCHHHHhcc
Confidence 6788999999999887765443 321 23566677788766 6788888754
No 34
>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=33.36 E-value=45 Score=21.55 Aligned_cols=23 Identities=13% Similarity=0.104 Sum_probs=19.6
Q ss_pred cchHHHHHHhccchhhhhhhccc
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
.+..+.|+..|++...+.+.+..
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 57889999999999888877764
No 35
>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=31.13 E-value=93 Score=19.46 Aligned_cols=22 Identities=23% Similarity=0.206 Sum_probs=16.5
Q ss_pred cchHHHHHHhccchhhhhhhcc
Q 017044 303 PTLIEWAKAIGLSCRDLKSELH 324 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~ 324 (378)
.+..+.|+..|++...+.+.+.
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 4788899999988877765543
No 36
>1msk_A Cobalamin-dependent methionine synthase; methyltransferase, transferase, methionine biosynthesis, vitamin B12; HET: SAM; 1.80A {Escherichia coli K12} SCOP: d.173.1.1
Probab=31.09 E-value=63 Score=31.65 Aligned_cols=46 Identities=15% Similarity=0.189 Sum_probs=35.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHh-ccCCC----CChhhHHHHhhcccccCCCc
Q 017044 327 NSSREKLINANLRLVVHVAKQ-YQGRG----ISLHDLLQVNQATFNFGKWL 372 (378)
Q Consensus 327 ~~ARekLI~sNLRLVvsIAKk-Y~grG----ls~eDLIQEG~iGFDpsRG~ 372 (378)
+.+-++|+++-.-.+..-.++ +-|.+ ++.+|||.++..|.-|+=||
T Consensus 193 ~alAdrlAEA~AE~~h~~VR~e~wGya~~e~l~~~~l~~~~Y~GiR~sPGY 243 (331)
T 1msk_A 193 KALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGY 243 (331)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTSCSCTTCCCCHHHHHTTCSSCBCCCTTS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCccccCHHHHHhhccCccCCCCCC
Confidence 345677777777666666677 65654 89999999999998888776
No 37
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}
Probab=31.01 E-value=1.7e+02 Score=21.98 Aligned_cols=30 Identities=23% Similarity=0.275 Sum_probs=24.4
Q ss_pred cCCCcchHHHHHHhccchhhhhhhccccHH
Q 017044 299 FGREPTLIEWAKAIGLSCRDLKSELHSGNS 328 (378)
Q Consensus 299 lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ 328 (378)
.-..-+..|.|+..|++...++.++..+..
T Consensus 50 ~~~g~s~~eIA~~lgis~~tV~~~l~ra~~ 79 (92)
T 3hug_A 50 YYRGWSTAQIATDLGIAEGTVKSRLHYAVR 79 (92)
T ss_dssp HTSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344579999999999999999988876544
No 38
>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=31.00 E-value=77 Score=28.04 Aligned_cols=34 Identities=18% Similarity=0.099 Sum_probs=26.9
Q ss_pred HHHHHHhhcCCCcchHHHHHHhccchhhhhhhcc
Q 017044 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (378)
Q Consensus 291 ik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~ 324 (378)
+..-+.+....+.+.+++|+.+|++...|.+...
T Consensus 174 ~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk 207 (276)
T 3gbg_A 174 ISCLVKSDITRNWRWADICGELRTNRMILKKELE 207 (276)
T ss_dssp HHHHHHHTTTSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3444556677789999999999999988887664
No 39
>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3
Probab=30.77 E-value=56 Score=22.77 Aligned_cols=47 Identities=19% Similarity=0.163 Sum_probs=30.1
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLI 359 (378)
.|..+.|+.+|++...+.+... |. ..-+...+..||+-| |++.++|+
T Consensus 27 ~s~~~lA~~~gis~~~i~~~e~-g~------~~~~~~~l~~l~~~l---~~~~~~l~ 73 (74)
T 1y7y_A 27 LSQETLAFLSGLDRSYVGGVER-GQ------RNVSLVNILKLATAL---DIEPRELF 73 (74)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHT-TC------SCCBHHHHHHHHHHT---TSCGGGGC
T ss_pred CCHHHHHHHHCcCHHHHHHHHC-CC------CCCCHHHHHHHHHHh---CcCHHHHc
Confidence 6788999999998877765443 21 123455566777766 45665553
No 40
>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}
Probab=29.72 E-value=60 Score=25.43 Aligned_cols=48 Identities=21% Similarity=0.162 Sum_probs=33.4
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQ 360 (378)
.|..+.|+.+|++...+.+... |.. .-++..+..||+-| |+++++|+.
T Consensus 35 ltq~elA~~~gis~~~is~~E~-G~~------~p~~~~l~~ia~~l---~v~~~~l~~ 82 (114)
T 3vk0_A 35 WSQEELARQCGLDRTYVSAVER-KRW------NIALSNIEKMAAAL---GVAAYQLLL 82 (114)
T ss_dssp CCHHHHHHHHTCCHHHHHHHTT-TCC------CCCHHHHHHHHHHH---TSCHHHHTS
T ss_pred CCHHHHHHHHCcCHHHHHHHHc-CCC------CCCHHHHHHHHHHh---CCCHHHHhC
Confidence 6788889999998877765443 321 24677788888776 667777763
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=28.66 E-value=89 Score=22.49 Aligned_cols=49 Identities=12% Similarity=0.036 Sum_probs=34.6
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQV 361 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQE 361 (378)
.|..+.|+.+|++...+.+... |. ..-++..+..||+-| |+++++|+-.
T Consensus 25 lsq~~lA~~~gis~~~i~~~e~-g~------~~~~~~~l~~ia~~l---~v~~~~l~~~ 73 (82)
T 3s8q_A 25 MTQEDLAYKSNLDRTYISGIER-NS------RNLTIKSLELIMKGL---EVSDVVFFEM 73 (82)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHT-TC------CCCBHHHHHHHHHHT---TCCHHHHHHH
T ss_pred CCHHHHHHHhCcCHHHHHHHHC-CC------CCCCHHHHHHHHHHH---CcCHHHHhcC
Confidence 6888999999998887764433 32 133667778888766 6788887743
No 42
>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=28.34 E-value=40 Score=31.31 Aligned_cols=27 Identities=15% Similarity=0.156 Sum_probs=24.1
Q ss_pred cCCCcchHHHHHHhccchhhhhhhccc
Q 017044 299 FGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 299 lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
.||+|+..+.|++.|++.+++++.|+.
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 599999999999999999988877764
No 43
>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}
Probab=27.33 E-value=51 Score=26.48 Aligned_cols=27 Identities=22% Similarity=0.197 Sum_probs=23.7
Q ss_pred cCCCcchHHHHHHhccchhhhhhhccc
Q 017044 299 FGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 299 lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
.|.+....+.|+.+|++.+++.++|..
T Consensus 31 aG~PlkageIae~~GvdKKeVdKaik~ 57 (80)
T 2lnb_A 31 AGSPVKLAQLVKECQAPKRELNQVLYR 57 (80)
T ss_dssp HTSCEEHHHHHHHHTSCHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 489999999999999999999877753
No 44
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1
Probab=27.27 E-value=17 Score=34.47 Aligned_cols=19 Identities=21% Similarity=0.267 Sum_probs=15.0
Q ss_pred CCCHHHHHHHHHHHHHHHH
Q 017044 269 LLTADEEFELIAQIQDLIR 287 (378)
Q Consensus 269 LLTaeEE~eL~~~IQ~l~~ 287 (378)
|||+|.|++++++|..|.+
T Consensus 1 LLTREgEI~IAKRIE~G~~ 19 (339)
T 1sig_A 1 GSHMEGEIDIAKRIEDGIN 19 (339)
T ss_dssp ---CCTHHHHHHHHHHHHH
T ss_pred CCChHHHHHHHHHHHHHHH
Confidence 7999999999999999876
No 45
>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=24.80 E-value=2.6e+02 Score=22.15 Aligned_cols=53 Identities=19% Similarity=0.171 Sum_probs=36.8
Q ss_pred CCcchHHHHHHhccchhhhhhhccccHH-HHHHHHHHhHHHHHHHHHhc-cCCCCChhhHHH
Q 017044 301 REPTLIEWAKAIGLSCRDLKSELHSGNS-SREKLINANLRLVVHVAKQY-QGRGISLHDLLQ 360 (378)
Q Consensus 301 rePT~~EWA~AaG~s~~eLr~~L~~G~~-ARekLI~sNLRLVvsIAKkY-~grGls~eDLIQ 360 (378)
.+-|..|+|+..|++...++.++..+.. .|..+-..+| +.| .+.|++-+.|+.
T Consensus 38 e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~~~~~l-------~~~~~~~~~~~~~~~~ 92 (99)
T 3t72_q 38 TDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL-------RSGSSGSGTPEEKLLR 92 (99)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHhcCCCHHHHHH
Confidence 5689999999999999999988876543 3333333322 334 467888777764
No 46
>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}
Probab=23.95 E-value=1.1e+02 Score=21.91 Aligned_cols=52 Identities=17% Similarity=0.115 Sum_probs=30.7
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccC-CCCChhhHHHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQV 361 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~g-rGls~eDLIQE 361 (378)
-|..+.|+.+|++...+.+... |.. ..++..+..+++.+.. -|+++++|+..
T Consensus 24 lsq~~lA~~~gis~~~i~~~e~-g~~------~~~~~~l~~~~~~l~~~~~v~~~~l~~~ 76 (84)
T 2ef8_A 24 LSQSELAIFLGLSQSDISKIES-FER------RLDALELFELLEVVASRLGLPMDILLKD 76 (84)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHT-TSS------CCBHHHHHHHHHHHHHHHTCCHHHHHHH
T ss_pred CCHHHHHHHhCCCHHHHHHHHc-CCC------CCCHHHHHHHHHHHccccCCCHHHHHcc
Confidence 6788999999999887765443 321 1222223333433322 27888888754
No 47
>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=23.51 E-value=91 Score=30.81 Aligned_cols=34 Identities=35% Similarity=0.646 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhc--cchhhhh
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIG--LSCRDLK 320 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG--~s~~eLr 320 (378)
++.+.+.+|...+|++|+..+.|...| ++.+.++
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 445566778888999999999999999 7665554
No 48
>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=23.48 E-value=1.2e+02 Score=26.95 Aligned_cols=38 Identities=16% Similarity=0.122 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc
Q 017044 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 288 LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
+.++..-+++.+..+++..++|+.+|+|...|++....
T Consensus 5 ~~~~~~~i~~~~~~~~~~~~la~~~~~s~~~l~r~f~~ 42 (292)
T 1d5y_A 5 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 42 (292)
T ss_dssp HHHHHHHHHTTSSSSCCCHHHHTTTSSCHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455566677788899999999999999999888763
No 49
>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=23.23 E-value=1.9e+02 Score=22.64 Aligned_cols=30 Identities=10% Similarity=0.096 Sum_probs=24.9
Q ss_pred cCCCcchHHHHHHhccchhhhhhhccccHH
Q 017044 299 FGREPTLIEWAKAIGLSCRDLKSELHSGNS 328 (378)
Q Consensus 299 lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ 328 (378)
.-..-+..|.|+..|++...++.++..+..
T Consensus 121 ~~~g~s~~EIA~~lgis~~tV~~~~~ra~~ 150 (164)
T 3mzy_A 121 LIRGYSYREIATILSKNLKSIDNTIQRIRK 150 (164)
T ss_dssp HTTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344579999999999999999988877654
No 50
>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A
Probab=23.00 E-value=75 Score=21.45 Aligned_cols=47 Identities=19% Similarity=0.249 Sum_probs=31.2
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLI 359 (378)
.|..+.|+.+|++...+.+...... .-+...+..||+-| |+++++|+
T Consensus 15 ~s~~~lA~~~gis~~~i~~~e~g~~-------~~~~~~l~~i~~~l---~~~~~~l~ 61 (66)
T 2xi8_A 15 ISQSELAALLEVSRQTINGIEKNKY-------NPSLQLALKIAYYL---NTPLEDIF 61 (66)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHTTSC-------CCCHHHHHHHHHHT---TSCHHHHE
T ss_pred CCHHHHHHHHCcCHHHHHHHHcCCC-------CCCHHHHHHHHHHH---CcCHHHHh
Confidence 5778899999998877765444221 12455667777766 56777764
No 51
>2o2k_A Methionine synthase; C-shaped, twisted anti-parallel beta sheet, beta-meander region, transferase; 1.60A {Homo sapiens}
Probab=21.50 E-value=1.1e+02 Score=30.24 Aligned_cols=45 Identities=9% Similarity=0.034 Sum_probs=34.4
Q ss_pred HHHHHHHHHhHHHHHHHHHh-ccCCC----CChhhHHHHhhcccccCCCc
Q 017044 328 SSREKLINANLRLVVHVAKQ-YQGRG----ISLHDLLQVNQATFNFGKWL 372 (378)
Q Consensus 328 ~ARekLI~sNLRLVvsIAKk-Y~grG----ls~eDLIQEG~iGFDpsRG~ 372 (378)
.+-++|+++-.-.+..-.++ +-|.+ ++.+|||.++..|.-|+=||
T Consensus 205 aLAdrlAEA~AE~lH~~VR~e~wGya~de~l~~~~l~~e~Y~GiRpSPGY 254 (355)
T 2o2k_A 205 ALGDRLAEAFAEELHERVRRELWAYCGSEQLDVADLRRLRYKGIRPAPGY 254 (355)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTSCTTTTCCCCHHHHHTTCSSSBCCCTTS
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCccccCHHHHHhccCCccCCCCCC
Confidence 45677777777666666666 65653 89999999999998888776
No 52
>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A
Probab=21.37 E-value=1.2e+02 Score=23.54 Aligned_cols=52 Identities=27% Similarity=0.229 Sum_probs=37.0
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhc
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQA 364 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~i 364 (378)
.|..+.|+.+|++...+.+... |. ..-++..+..||+-| |++..+|+-.+.-
T Consensus 42 lsq~~lA~~~gis~~~is~~E~-g~------~~~~~~~l~~la~~l---~v~~~~l~~~~~~ 93 (117)
T 3f52_A 42 VTLRELAEASRVSPGYLSELER-GR------KEVSSELLASVCHAL---GASVADVLIEAAG 93 (117)
T ss_dssp CCHHHHHHHTTSCHHHHHHHHT-TS------SCCCHHHHHHHHHHH---TCCHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHC-CC------CCCCHHHHHHHHHHh---CCCHHHHHhcccc
Confidence 5788899999998887754433 32 134667788888766 6888888876543
No 53
>3nxc_A HTH-type protein SLMA; nucleoid occlusion, cell division, TETR family member, DNA B protein; 2.50A {Escherichia coli}
Probab=20.69 E-value=2.4e+02 Score=22.64 Aligned_cols=27 Identities=22% Similarity=0.229 Sum_probs=17.8
Q ss_pred hcC-CCcchHHHHHHhccchhhhhhhcc
Q 017044 298 QFG-REPTLIEWAKAIGLSCRDLKSELH 324 (378)
Q Consensus 298 ~lG-rePT~~EWA~AaG~s~~eLr~~L~ 324 (378)
+.| ...|..+.|+++|++...|-....
T Consensus 40 ~~G~~~~t~~~Ia~~agvs~~t~Y~~F~ 67 (212)
T 3nxc_A 40 SDGSQRITTAKLAASVGVSEAALYRHFP 67 (212)
T ss_dssp ------CCHHHHHHHTTSCHHHHHTTCS
T ss_pred cCChhhcCHHHHHHHhCCChhHHHHHCC
Confidence 336 569999999999998776654444
No 54
>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A
Probab=20.69 E-value=1.2e+02 Score=25.38 Aligned_cols=48 Identities=23% Similarity=0.331 Sum_probs=31.5
Q ss_pred CCCcchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHH
Q 017044 300 GREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (378)
Q Consensus 300 GrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLI 359 (378)
+.. |..|+|+.+|++...+.+....+.. . ...+..||+.| |++.+.|+
T Consensus 19 ~~~-tq~elA~~~Gis~~~i~~~e~g~~~-------p-~~~l~~ia~~~---~v~~~~l~ 66 (189)
T 2fjr_A 19 GFS-QKIQLANHFDIASSSLSNRYTRGAI-------S-YDFAAHCALET---GANLQWLL 66 (189)
T ss_dssp TCS-SHHHHHHHTTCCHHHHHHHHHSSSC-------C-HHHHHHHHHHH---CCCHHHHH
T ss_pred hhc-CHHHHHHHhCcCHHHHHHHHhCCCC-------C-HHHHHHHHHHH---CCCHHHHh
Confidence 544 8999999999998887765553211 1 23455667655 56666666
No 55
>3ppb_A Putative TETR family transcription regulator; DNA-binding, helix-turn-helix motif, HTH motif, DNA/RNA-BIND helical bundle fold; HET: MSE PG4; 2.10A {Shewanella loihica}
Probab=20.57 E-value=3.1e+02 Score=21.47 Aligned_cols=63 Identities=13% Similarity=0.058 Sum_probs=37.1
Q ss_pred hcC-CCcchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHH
Q 017044 298 QFG-REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (378)
Q Consensus 298 ~lG-rePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQ 360 (378)
+.| ...|..+.|+.+|++...+-.....-...-..++.....-+..........+.+..+-+.
T Consensus 24 ~~G~~~~tv~~Ia~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 87 (195)
T 3ppb_A 24 SQGFHGTSTATIAREAGVATGTLFHHFPSKEQLLEQLFLGVKQEFADAIQASVSSRGDLKQDAE 87 (195)
T ss_dssp HTCSTTSCHHHHHHHHTCCHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHTCCCCSCHHHHHH
T ss_pred hcCcccCCHHHHHHHhCCChhHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHH
Confidence 347 568999999999999888876655444444444444444443333333344445444443
No 56
>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19
Probab=20.17 E-value=77 Score=24.03 Aligned_cols=26 Identities=19% Similarity=0.344 Sum_probs=21.0
Q ss_pred CCCcchHHHHHHhccchhhhhhhccc
Q 017044 300 GREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 300 GrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
|...|..|.|+..|++...++++|..
T Consensus 29 ~~~~t~~eLA~~Lgvs~~tV~~~L~~ 54 (77)
T 1qgp_A 29 GKATTAHDLSGKLGTPKKEINRVLYS 54 (77)
T ss_dssp SSCEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 45679999999999999888766653
No 57
>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=20.12 E-value=1.2e+02 Score=25.67 Aligned_cols=36 Identities=19% Similarity=0.017 Sum_probs=27.5
Q ss_pred HHHHhhcCCCcchHHHHHHhccchhhhhhhccccHH
Q 017044 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 328 (378)
Q Consensus 293 ~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ 328 (378)
.-+.-.....-+..|+|+..|++...++.++..+..
T Consensus 194 ~vl~l~~~~g~s~~EIA~~lgis~~~V~~~~~ra~~ 229 (239)
T 1rp3_A 194 LVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALE 229 (239)
T ss_dssp HHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 334444456789999999999999999888876554
No 58
>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}
Probab=20.02 E-value=72 Score=22.35 Aligned_cols=47 Identities=19% Similarity=0.201 Sum_probs=30.0
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLI 359 (378)
.|..+.|+.+|++...+.+...... ..+...+..||+.| |++.++|+
T Consensus 24 ~s~~~lA~~~gis~~~i~~~e~g~~-------~~~~~~l~~ia~~l---~~~~~~l~ 70 (76)
T 3bs3_A 24 RTNRWLAEQMGKSENTISRWCSNKS-------QPSLDMLVKVAELL---NVDPRQLI 70 (76)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHTTSS-------CCCHHHHHHHHHHH---TSCGGGGB
T ss_pred CCHHHHHHHHCcCHHHHHHHHcCCC-------CCCHHHHHHHHHHH---CcCHHHHh
Confidence 5778888888888877765444221 12455566777766 56666654
Done!