Query 022167
Match_columns 301
No_of_seqs 138 out of 1165
Neff 3.8
Searched_HMMs 29240
Date Mon Mar 25 15:01:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022167.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/022167hhsearch_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 99.7 4.1E-18 1.4E-22 153.9 9.1 115 186-300 2-146 (245)
2 1l9z_H Sigma factor SIGA; heli 99.7 1.2E-17 4.3E-22 163.2 8.3 110 191-300 94-233 (438)
3 2a6h_F RNA polymerase sigma fa 99.7 1.1E-17 3.7E-22 161.6 2.4 111 190-300 78-218 (423)
4 1sig_A Sigma70, RNA polymerase 98.1 1.1E-06 3.9E-11 81.3 3.4 56 245-300 239-301 (339)
5 3iyd_F RNA polymerase sigma fa 97.5 3.3E-06 1.1E-10 84.8 -4.3 36 265-300 375-410 (613)
6 1l0o_C Sigma factor; bergerat 97.2 6.3E-05 2.1E-09 63.1 0.0 61 200-300 4-64 (243)
7 3iyd_F RNA polymerase sigma fa 96.6 0.00025 8.7E-09 71.2 -1.2 35 189-223 94-128 (613)
8 2q1z_A RPOE, ECF SIGE; ECF sig 92.1 0.083 2.8E-06 42.8 2.9 38 263-300 26-63 (184)
9 2o7g_A Probable RNA polymerase 89.3 0.21 7.3E-06 37.9 2.7 36 264-300 24-59 (112)
10 2k9s_A Arabinose operon regula 78.1 5.7 0.00019 29.9 6.3 38 224-261 5-43 (107)
11 1h3l_A RNA polymerase sigma fa 76.6 0.94 3.2E-05 32.7 1.5 38 263-300 11-48 (87)
12 3oou_A LIN2118 protein; protei 74.3 6.6 0.00023 29.6 5.8 38 224-261 7-44 (108)
13 2jt1_A PEFI protein; solution 73.6 4.1 0.00014 30.7 4.4 31 231-261 17-47 (77)
14 3oio_A Transcriptional regulat 71.6 5.4 0.00018 30.4 4.7 37 225-261 10-46 (113)
15 1bl0_A Protein (multiple antib 71.4 6.8 0.00023 30.6 5.4 58 225-283 14-85 (129)
16 3lsg_A Two-component response 70.7 9.2 0.00031 28.5 5.8 37 225-261 5-42 (103)
17 3ugo_A RNA polymerase sigma fa 69.6 1.4 4.9E-05 39.3 1.2 41 223-263 198-240 (245)
18 1tc3_C Protein (TC3 transposas 66.9 19 0.00066 22.0 6.0 43 201-260 1-43 (51)
19 3mn2_A Probable ARAC family tr 63.9 12 0.00042 28.0 5.3 38 224-261 4-41 (108)
20 3gbg_A TCP pilus virulence reg 57.7 23 0.00079 30.3 6.6 60 223-283 170-242 (276)
21 1d5y_A ROB transcription facto 55.1 14 0.00049 31.8 4.8 58 225-283 6-77 (292)
22 1jko_C HIN recombinase, DNA-in 50.2 22 0.00075 22.3 4.0 23 239-261 22-44 (52)
23 3mkl_A HTH-type transcriptiona 46.7 23 0.00079 27.1 4.4 38 224-261 9-46 (120)
24 2zc2_A DNAD-like replication p 46.2 34 0.0012 24.8 5.0 58 229-290 8-71 (78)
25 2kkm_A Translation machinery-a 45.6 9.7 0.00033 32.0 2.1 67 204-300 43-111 (144)
26 2o8x_A Probable RNA polymerase 41.6 72 0.0025 21.4 5.9 26 238-263 31-56 (70)
27 3k2z_A LEXA repressor; winged 41.3 47 0.0016 27.8 5.8 29 233-261 19-47 (196)
28 1rp3_A RNA polymerase sigma fa 39.0 63 0.0021 26.4 6.1 34 225-258 102-135 (239)
29 1sig_A Sigma70, RNA polymerase 38.8 9.2 0.00031 35.0 1.0 19 205-223 1-19 (339)
30 3f2g_A Alkylmercury lyase; MER 38.5 29 0.00099 31.2 4.2 28 235-262 33-60 (220)
31 1zx4_A P1 PARB, plasmid partit 37.7 27 0.00093 30.6 3.8 60 238-297 24-92 (192)
32 2a6h_F RNA polymerase sigma fa 36.0 45 0.0015 31.9 5.4 35 224-258 271-307 (423)
33 3hug_A RNA polymerase sigma fa 33.5 1.4E+02 0.0047 21.7 8.9 30 235-264 50-79 (92)
34 1rp3_A RNA polymerase sigma fa 33.3 1.8E+02 0.0061 23.6 8.0 38 228-265 193-230 (239)
35 3tqn_A Transcriptional regulat 32.9 37 0.0013 26.2 3.5 23 239-261 34-56 (113)
36 1ku3_A Sigma factor SIGA; heli 31.2 1.1E+02 0.0039 21.2 5.6 26 237-262 29-54 (73)
37 2p7v_B Sigma-70, RNA polymeras 30.3 1.2E+02 0.0041 20.7 5.6 26 237-262 24-49 (68)
38 1je8_A Nitrate/nitrite respons 30.0 1.1E+02 0.0037 22.1 5.5 41 240-283 38-78 (82)
39 2jpc_A SSRB; DNA binding prote 28.6 1E+02 0.0035 20.3 4.8 42 239-283 14-55 (61)
40 2k9q_A Uncharacterized protein 28.6 1.3E+02 0.0045 20.6 5.6 49 239-297 16-64 (77)
41 1tty_A Sigma-A, RNA polymerase 28.3 1.2E+02 0.0043 21.9 5.6 26 237-262 37-62 (87)
42 2ofy_A Putative XRE-family tra 28.3 1.1E+02 0.0037 21.4 5.1 49 240-297 29-77 (86)
43 4dyq_A Gene 1 protein; GP1, oc 26.9 1.1E+02 0.0038 24.6 5.5 28 199-226 6-33 (140)
44 4fe7_A Xylose operon regulator 26.5 83 0.0028 28.6 5.2 58 225-283 308-379 (412)
45 1qgp_A Protein (double strande 26.4 61 0.0021 23.8 3.6 25 237-261 30-54 (77)
46 1l9z_H Sigma factor SIGA; heli 26.2 71 0.0024 31.1 5.0 33 225-257 287-321 (438)
47 3neu_A LIN1836 protein; struct 26.0 1.8E+02 0.0063 22.6 6.6 24 238-261 37-60 (125)
48 1or7_A Sigma-24, RNA polymeras 25.9 93 0.0032 24.7 4.9 37 210-286 9-45 (194)
49 1u78_A TC3 transposase, transp 25.4 1.6E+02 0.0055 22.1 6.0 44 200-260 1-44 (141)
50 2heo_A Z-DNA binding protein 1 24.9 89 0.0031 22.0 4.1 27 235-261 22-48 (67)
51 1x3u_A Transcriptional regulat 24.5 1.5E+02 0.005 20.4 5.2 43 239-284 32-74 (79)
52 1lmb_3 Protein (lambda repress 23.2 99 0.0034 21.9 4.2 48 239-296 31-78 (92)
53 2v79_A DNA replication protein 22.6 1E+02 0.0036 24.9 4.6 44 206-261 30-74 (135)
54 3u7d_B Protein HEG homolog 1; 22.2 23 0.00077 22.1 0.4 12 120-131 8-19 (26)
55 3mzy_A RNA polymerase sigma-H 21.8 2.6E+02 0.0088 21.0 8.6 32 234-265 120-151 (164)
56 1qbj_A Protein (double-strande 21.8 1.4E+02 0.0046 22.4 4.8 26 236-261 25-50 (81)
57 2xi8_A Putative transcription 21.5 71 0.0024 20.8 2.9 48 239-296 15-62 (66)
58 2glo_A Brinker CG9653-PA; prot 21.5 1.6E+02 0.0055 19.7 4.8 29 241-269 28-56 (59)
59 3bs3_A Putative DNA-binding pr 21.1 75 0.0026 21.4 3.0 48 239-296 24-71 (76)
60 3f6w_A XRE-family like protein 20.9 78 0.0027 22.0 3.1 48 239-296 28-75 (83)
61 2rnj_A Response regulator prot 20.7 1E+02 0.0035 22.4 3.9 42 239-283 45-86 (91)
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=99.74 E-value=4.1e-18 Score=153.90 Aligned_cols=115 Identities=25% Similarity=0.341 Sum_probs=93.1
Q ss_pred chhhcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHH-HHHHH--HHH-----------------------hCCCC
Q 022167 186 PELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDD-HKLRL--KER-----------------------LGCEP 239 (301)
Q Consensus 186 pel~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~-~r~eL--ee~-----------------------LGreP 239 (301)
|...+|+++.||++|+++||||++||++|+++|+.|..... +.... +.. .+.+|
T Consensus 2 ~~~~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~ 81 (245)
T 3ugo_A 2 PHMTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDP 81 (245)
T ss_dssp ---CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCH
T ss_pred CCCCCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccc
Confidence 44567999999999999999999999999999998876332 21100 000 14688
Q ss_pred CHHHHHHHhccChH----HHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 240 SMEQLAASLRISRP----ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 240 t~eEwA~a~g~S~~----eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
+..+||++.+++.. +|.+....+..|+++|+..|+++|.++|++|.+++.+.+||+|||+|
T Consensus 82 ~~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi 146 (245)
T 3ugo_A 82 KTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 146 (245)
T ss_dssp HHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHH
T ss_pred hhHHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence 89999999999764 44556677899999999999999999999999999999999999986
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=99.70 E-value=1.2e-17 Score=163.18 Aligned_cols=110 Identities=25% Similarity=0.351 Sum_probs=92.3
Q ss_pred chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHH------------------HHHHHHhCCCCCHHHHHHH-----
Q 022167 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHK------------------LRLKERLGCEPSMEQLAAS----- 247 (301)
Q Consensus 191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r------------------~eLee~LGrePt~eEwA~a----- 247 (301)
|.++.||++|+++|+||++||++|+++|+.|..++... .+....+++.|+.++|+..
T Consensus 94 d~~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (438)
T 1l9z_H 94 DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEE 173 (438)
T ss_pred ChHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchhhhh
Confidence 78999999999999999999999999999986544322 1222346788888887542
Q ss_pred -------hccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 248 -------LRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 248 -------~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
++++..+|...+..+..|+++||.+|+|||++||++|.|+|++++||||||+|
T Consensus 174 ~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~I 233 (438)
T 1l9z_H 174 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 233 (438)
T ss_pred hhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 34566778888888899999999999999999999999999999999999986
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=99.66 E-value=1.1e-17 Score=161.59 Aligned_cols=111 Identities=27% Similarity=0.351 Sum_probs=88.4
Q ss_pred cchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHH------------------HHHHHhCCCCCHHHHH------
Q 022167 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL------------------RLKERLGCEPSMEQLA------ 245 (301)
Q Consensus 190 ~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~------------------eLee~LGrePt~eEwA------ 245 (301)
.|+++.||++|++.|+||++||++|+++|+.|..+..... +....+++.|+.++|+
T Consensus 78 ~d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (423)
T 2a6h_F 78 SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE 157 (423)
T ss_dssp HHHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHHHH
T ss_pred CcHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhhhh
Confidence 4889999999999999999999999999998754332111 0112334566644432
Q ss_pred ---H---HhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 246 ---A---SLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 246 ---~---a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
. +++++..+|...+..+..|+++||.+|+|||++||++|.|+|++++||||||||
T Consensus 158 ~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~i 218 (423)
T 2a6h_F 158 EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 218 (423)
T ss_dssp HHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHH
T ss_pred hhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 2 235667778888888999999999999999999999999999999999999986
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=98.11 E-value=1.1e-06 Score=81.30 Aligned_cols=56 Identities=27% Similarity=0.381 Sum_probs=43.9
Q ss_pred HHHhccChHHHHH---HhhhHH----HHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 245 AASLRISRPELQS---ILMECS----LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 245 A~a~g~S~~eLrr---~L~eG~----~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
...+|++..+... .+..|. .|.+.|+..|+++|+++|++|.++|.+++||+|||+|
T Consensus 239 e~~~~l~~~~~~~l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i 301 (339)
T 1sig_A 239 EEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 301 (339)
T ss_dssp HHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHH
T ss_pred HHHcCCChHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHH
Confidence 3444555544433 333343 6999999999999999999999999999999999986
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=97.52 E-value=3.3e-06 Score=84.79 Aligned_cols=36 Identities=42% Similarity=0.618 Sum_probs=34.6
Q ss_pred HHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 265 ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
|.+.|+..|+++|+++|++|.++|..++||||||+|
T Consensus 375 A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi 410 (613)
T 3iyd_F 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 410 (613)
T ss_dssp HHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 499999999999999999999999999999999986
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=97.15 E-value=6.3e-05 Score=63.06 Aligned_cols=61 Identities=28% Similarity=0.419 Sum_probs=0.0
Q ss_pred cCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHH
Q 022167 200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS 279 (301)
Q Consensus 200 i~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVS 279 (301)
|...+.++.+++.+|...++.|.. .|.+.|+..|.++|..
T Consensus 4 ~~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~ 43 (243)
T 1l0o_C 4 MQGQSPIKDQEMKELIRRSQEGDQ----------------------------------------EARDEIIEKNMRLVWS 43 (243)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHH
Confidence 345566788888888888877665 7888999999999999
Q ss_pred HHhhccCCCCChhhHhhhccC
Q 022167 280 IAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 280 IAKRY~grGLsfeDLIQEGnI 300 (301)
+|.+|.+...+.+||+|||.+
T Consensus 44 ~~~~~~~~~~~aeDl~Qe~~l 64 (243)
T 1l0o_C 44 VVQRFLNRGYEADDLFQIGCI 64 (243)
T ss_dssp ---------------------
T ss_pred HHHHHhccCCCHHHHHHHHHH
Confidence 999999999999999999976
No 7
>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=96.55 E-value=0.00025 Score=71.20 Aligned_cols=35 Identities=23% Similarity=0.487 Sum_probs=14.6
Q ss_pred hcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCc
Q 022167 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (301)
Q Consensus 189 ~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~ 223 (301)
++||+++||++||.+||||+++|++|+++|..|..
T Consensus 94 ~~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~~ 128 (613)
T 3iyd_F 94 TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGIN 128 (613)
T ss_dssp -----------C--------CSSSTTTHHHHHHHH
T ss_pred CCCcHHHHHHHhcccccCCchhHHHHHHHHHHhHH
Confidence 56999999999999999999999999999998764
No 8
>2q1z_A RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc bindin transcription factor; 2.40A {Rhodobacter sphaeroides} PDB: 2z2s_A
Probab=92.12 E-value=0.083 Score=42.77 Aligned_cols=38 Identities=11% Similarity=0.058 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|-+.|+..+.++|..+|.+|.+...+.+|++||+.+
T Consensus 26 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l 63 (184)
T 2q1z_A 26 EAAFAELFQHFAPKVKGFLMKSGSVASQAEECAQDVMA 63 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHH
Confidence 47889999999999999999999988899999999864
No 9
>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}
Probab=89.29 E-value=0.21 Score=37.91 Aligned_cols=36 Identities=19% Similarity=0.134 Sum_probs=31.9
Q ss_pred HHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 264 ~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.|-+.|+..+.+.|..+|.+| +....-+|++||..+
T Consensus 24 ~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl 59 (112)
T 2o7g_A 24 RALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFL 59 (112)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHH
Confidence 677889999999999999999 877889999999753
No 10
>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}
Probab=78.08 E-value=5.7 Score=29.93 Aligned_cols=38 Identities=11% Similarity=0.225 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhC-CCCCHHHHHHHhccChHHHHHHhhh
Q 022167 224 LDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 224 Le~~r~eLee~LG-rePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.++..-+.+.+. .+++.+++|+.+|+|...|.+.+..
T Consensus 5 i~~~~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 43 (107)
T 2k9s_A 5 VREACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQ 43 (107)
T ss_dssp HHHHHHHHHHTSSCSSCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred HHHHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3445556677777 7899999999999999999888776
No 11
>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1
Probab=76.63 E-value=0.94 Score=32.72 Aligned_cols=38 Identities=29% Similarity=0.226 Sum_probs=33.9
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|=+.|+..+.+.+..+|.++.+...+-+|++||..+
T Consensus 11 ~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl 48 (87)
T 1h3l_A 11 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYA 48 (87)
T ss_dssp HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 57778899999999999999999888899999999753
No 12
>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}
Probab=74.26 E-value=6.6 Score=29.60 Aligned_cols=38 Identities=13% Similarity=0.201 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+..+..-+.+.++.+++.+++|+.+|+|...|.+.+..
T Consensus 7 i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 44 (108)
T 3oou_A 7 IQNVLSYITEHFSEGMSLKTLGNDFHINAVYLGQLFQK 44 (108)
T ss_dssp HHHHHHHHHHHTTSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 45566667778888999999999999999998887766
No 13
>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}
Probab=73.61 E-value=4.1 Score=30.74 Aligned_cols=31 Identities=13% Similarity=0.085 Sum_probs=24.0
Q ss_pred HHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 231 LKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 231 Lee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
.++..|.+||..|+|+++|+|...+++-|..
T Consensus 17 i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~ 47 (77)
T 2jt1_A 17 QNMDDGAPVKTRDIADAAGLSIYQVRLYLEQ 47 (77)
T ss_dssp HHHHTTSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred HhhccCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 3333588999999999999998777765554
No 14
>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}
Probab=71.63 E-value=5.4 Score=30.35 Aligned_cols=37 Identities=14% Similarity=0.226 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
.++..-+.+.+..+++.+++|+.+|++...|.+.+..
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 4445556666777899999999999999988887766
No 15
>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=71.45 E-value=6.8 Score=30.64 Aligned_cols=58 Identities=21% Similarity=0.226 Sum_probs=40.5
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh--------------HHHHHHHHHHHhHHHHHHHHhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME--------------CSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e--------------G~~ARekLV~aNLRLVVSIAKR 283 (301)
.++..-+.+.+..+++.+++|+.+|+|...|.+.+.. ...|++.|...++. |..||..
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 3444556667777899999999999999998887766 24566666555542 5556654
No 16
>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}
Probab=70.70 E-value=9.2 Score=28.45 Aligned_cols=37 Identities=14% Similarity=0.117 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhCC-CCCHHHHHHHhccChHHHHHHhhh
Q 022167 225 DDHKLRLKERLGC-EPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 225 e~~r~eLee~LGr-ePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.+..-+.+.+.. +++.+++|+.+|++...|.+.+..
T Consensus 5 ~~i~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 42 (103)
T 3lsg_A 5 ELIQNIIEESYTDSQFTLSVLSEKLDLSSGYLSIMFKK 42 (103)
T ss_dssp HHHHHHHHHHTTCTTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred HHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3445556667776 889999999999999999888766
No 17
>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=69.64 E-value=1.4 Score=39.29 Aligned_cols=41 Identities=24% Similarity=0.384 Sum_probs=0.0
Q ss_pred cHHHHHHHHHHHhCCCCCHHHHHHHhc--cChHHHHHHhhhHH
Q 022167 223 SLDDHKLRLKERLGCEPSMEQLAASLR--ISRPELQSILMECS 263 (301)
Q Consensus 223 ~Le~~r~eLee~LGrePt~eEwA~a~g--~S~~eLrr~L~eG~ 263 (301)
.+.....+|...+|+.||.+|+|+.+| ++...++..+..++
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 344555668888999999999999999 99999988876543
No 18
>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=66.86 E-value=19 Score=22.04 Aligned_cols=43 Identities=16% Similarity=0.178 Sum_probs=27.2
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 201 ~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
|+.+.|+.++-..+...+..|. +..++|+.+|++...+.+.+.
T Consensus 1 GR~~~l~~~~~~~i~~~~~~g~-----------------s~~~IA~~lgis~~Tv~~~~~ 43 (51)
T 1tc3_C 1 PRGSALSDTERAQLDVMKLLNV-----------------SLHEMSRKISRSRHCIRVYLK 43 (51)
T ss_dssp CCSCCCCHHHHHHHHHHHHTTC-----------------CHHHHHHHHTCCHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHcCC-----------------CHHHHHHHHCcCHHHHHHHHh
Confidence 3455677665444444443333 567889999999887776654
No 19
>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}
Probab=63.85 E-value=12 Score=27.99 Aligned_cols=38 Identities=13% Similarity=0.079 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.++..-+.+.+..+++.+++|+.+|++...|.+.+..
T Consensus 4 i~~~~~~i~~~~~~~~~~~~lA~~~~~s~~~l~r~fk~ 41 (108)
T 3mn2_A 4 VRQVEEYIEANWMRPITIEKLTALTGISSRGIFKAFQR 41 (108)
T ss_dssp HHHHHHHHHHHTTSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred HHHHHHHHHHcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34555667778888899999999999999999888776
No 20
>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=57.67 E-value=23 Score=30.32 Aligned_cols=60 Identities=15% Similarity=0.166 Sum_probs=44.8
Q ss_pred cHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh-------------HHHHHHHHHHHhHHHHHHHHhh
Q 022167 223 SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME-------------CSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 223 ~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e-------------G~~ARekLV~aNLRLVVSIAKR 283 (301)
.+.++..-+.+.+..+++.+++|+.+|+|..-|.+...+ ...|++.|...++. |..||..
T Consensus 170 ~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~G~t~~~~l~~~Rl~~A~~lL~~~~~s-i~eIA~~ 242 (276)
T 3gbg_A 170 AMEKISCLVKSDITRNWRWADICGELRTNRMILKKELESRGVKFRELINSIRISYSISLMKTGEFK-IKQIAYQ 242 (276)
T ss_dssp HHHHHHHHHHHTTTSCCCHHHHHHHHTCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCCC-HHHHHHH
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhCCCCC-HHHHHHH
Confidence 355666777788888999999999999999998887654 45677777666554 5566654
No 21
>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=55.13 E-value=14 Score=31.85 Aligned_cols=58 Identities=22% Similarity=0.248 Sum_probs=41.0
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh--------------HHHHHHHHHHHhHHHHHHHHhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME--------------CSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e--------------G~~ARekLV~aNLRLVVSIAKR 283 (301)
.++..-+++.+...++.+++|+.+|+|..-|++.+.. ...|+..|...++. |..||..
T Consensus 6 ~~~~~~i~~~~~~~~~~~~la~~~~~s~~~l~r~f~~~~g~s~~~~~~~~Rl~~a~~~L~~~~~~-i~~ia~~ 77 (292)
T 1d5y_A 6 RDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKSAVALRLTARP-ILDIALQ 77 (292)
T ss_dssp HHHHHHHHTTSSSSCCCHHHHTTTSSCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHH
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhcCCCC-HHHHHHH
Confidence 4455566677788999999999999999999888766 24555555544443 4556654
No 22
>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=50.19 E-value=22 Score=22.29 Aligned_cols=23 Identities=22% Similarity=0.154 Sum_probs=18.7
Q ss_pred CCHHHHHHHhccChHHHHHHhhh
Q 022167 239 PSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~e 261 (301)
-+..++|..+|++...+.+.+..
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 46788999999999888877654
No 23
>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}
Probab=46.68 E-value=23 Score=27.08 Aligned_cols=38 Identities=18% Similarity=0.175 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.++..-+.+.+..+++.+++|+.+|++...|.+.+..
T Consensus 9 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 46 (120)
T 3mkl_A 9 RTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLRE 46 (120)
T ss_dssp HHHHHHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455556666777889999999999999998887655
No 24
>2zc2_A DNAD-like replication protein; GI 24377835, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Streptococcus mutans UA159}
Probab=46.16 E-value=34 Score=24.79 Aligned_cols=58 Identities=16% Similarity=0.134 Sum_probs=40.0
Q ss_pred HHHHHHhCCCCCHH------HHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCC
Q 022167 229 LRLKERLGCEPSME------QLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGAD 290 (301)
Q Consensus 229 ~eLee~LGrePt~e------EwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLs 290 (301)
...++..||.|+.- +|....|++.+-+..++..+. ..+ +.|++-|-.|++.+...|+.
T Consensus 8 ~~~e~~~gr~ls~~e~~~i~~w~~~~~~~~elI~~A~~~a~-~~~---~~s~~Yi~~Il~~W~~~gi~ 71 (78)
T 2zc2_A 8 EDFERELGRMLSPFELEDLQKTVSDDKTDPDLVRSALREAV-FNG---KTNWNYIQAILRNWRHEGIS 71 (78)
T ss_dssp HHHHHHHTSCCCHHHHHHHHHHHTTTCCCHHHHHHHHHHHH-HHT---CCCHHHHHHHHHHHHHTTCC
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHH-HcC---CCCHHHHHHHHHHHHHcCCC
Confidence 34455567776643 455566677777776776663 222 56899999999999999875
No 25
>2kkm_A Translation machinery-associated protein 16; nucleus, structural genomics, PSI-2, protein structure initiative; NMR {Saccharomyces cerevisiae}
Probab=45.64 E-value=9.7 Score=31.98 Aligned_cols=67 Identities=19% Similarity=0.227 Sum_probs=40.9
Q ss_pred CCCCHHHHHHHHHHH--HcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHH
Q 022167 204 ELLTHAEVVRLSKKI--KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIA 281 (301)
Q Consensus 204 ~LLT~EEEveLs~kI--q~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIA 281 (301)
+.+|.+|-.+|...+ +....|++++ ++.+-||+|+.. +.+++.- ...-.
T Consensus 43 ~~~t~~e~~~lI~~yl~R~d~ELeql~--~~rR~gRp~s~R------------------------e~~L~~~---~~~E~ 93 (144)
T 2kkm_A 43 PIFDHAHTREFIQSFIERDDTELDELK--KKRRSNRPPSNR------------------------QVLLQQR---RDQEL 93 (144)
T ss_dssp CCCCHHHHHHHHHHHHHHHHHHHHHHH--HHGGGTCCCTTH------------------------HHHHHHH---HHHHH
T ss_pred CCCCHHHHHHHHHHHHhcCcHHHHHHH--HhhCCCCCCchH------------------------HHHHHHH---HHHHH
Confidence 579999999998875 2333344443 244668888643 3333221 12334
Q ss_pred hhccCCCCChhhHhhhccC
Q 022167 282 QRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 282 KRY~grGLsfeDLIQEGnI 300 (301)
+-|.+ |+.+-||..+.|+
T Consensus 94 ~ey~t-G~~iPDLtd~~nv 111 (144)
T 2kkm_A 94 KEFKA-GFLCPDLSDAKNM 111 (144)
T ss_dssp HHHHT-TEEEECSCCHHHH
T ss_pred HHHcc-CccCCCCCCHHHH
Confidence 56876 9999898876653
No 26
>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}
Probab=41.55 E-value=72 Score=21.39 Aligned_cols=26 Identities=15% Similarity=0.020 Sum_probs=21.0
Q ss_pred CCCHHHHHHHhccChHHHHHHhhhHH
Q 022167 238 EPSMEQLAASLRISRPELQSILMECS 263 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~eG~ 263 (301)
.-+.+|+|+.+|++...++..+..+.
T Consensus 31 g~s~~eIA~~lgis~~tv~~~~~ra~ 56 (70)
T 2o8x_A 31 GLSYADAAAVCGCPVGTIRSRVARAR 56 (70)
T ss_dssp CCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45788999999999998887776644
No 27
>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=41.31 E-value=47 Score=27.77 Aligned_cols=29 Identities=28% Similarity=0.413 Sum_probs=23.2
Q ss_pred HHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 233 ERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 233 e~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+..|.+||..|+|+++|++...+.+.|..
T Consensus 19 ~~~g~~~s~~eia~~lgl~~~tv~~~l~~ 47 (196)
T 3k2z_A 19 EKNGYPPSVREIARRFRITPRGALLHLIA 47 (196)
T ss_dssp HHHSSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHhCCCCCHHHHHHHcCCCcHHHHHHHHH
Confidence 45688999999999999997776665544
No 28
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A
Probab=39.01 E-value=63 Score=26.37 Aligned_cols=34 Identities=41% Similarity=0.523 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHH
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~ 258 (301)
......+...+|+.|+.+++|..+|++.+++...
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 135 (239)
T 1rp3_A 102 KEVVEKLKEKLGREPTDEEVAKELGISTEELFKT 135 (239)
T ss_dssp HHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHH
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 4456677788999999999999999988776544
No 29
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1
Probab=38.85 E-value=9.2 Score=34.97 Aligned_cols=19 Identities=16% Similarity=0.305 Sum_probs=14.7
Q ss_pred CCCHHHHHHHHHHHHcCCc
Q 022167 205 LLTHAEVVRLSKKIKTGLS 223 (301)
Q Consensus 205 LLT~EEEveLs~kIq~g~~ 223 (301)
|||+|.|++++++|..|..
T Consensus 1 LLTREgEI~IAKRIE~G~~ 19 (339)
T 1sig_A 1 GSHMEGEIDIAKRIEDGIN 19 (339)
T ss_dssp ---CCTHHHHHHHHHHHHH
T ss_pred CCChHHHHHHHHHHHHHHH
Confidence 7999999999999988765
No 30
>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=38.47 E-value=29 Score=31.24 Aligned_cols=28 Identities=21% Similarity=0.205 Sum_probs=25.3
Q ss_pred hCCCCCHHHHHHHhccChHHHHHHhhhH
Q 022167 235 LGCEPSMEQLAASLRISRPELQSILMEC 262 (301)
Q Consensus 235 LGrePt~eEwA~a~g~S~~eLrr~L~eG 262 (301)
.|++|+.+++|..+|.+.++++++|...
T Consensus 33 ~Grpv~~~~LA~~~g~~~~~v~~~L~~l 60 (220)
T 3f2g_A 33 KGRPVSRTTLAGILDWPAERVAAVLEQA 60 (220)
T ss_dssp TTSCBCHHHHHHHHTCCHHHHHHHHHHC
T ss_pred cCCCCCHHHHHHHhCcCHHHHHHHHHhC
Confidence 6999999999999999999998887663
No 31
>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A
Probab=37.68 E-value=27 Score=30.63 Aligned_cols=60 Identities=18% Similarity=0.288 Sum_probs=43.6
Q ss_pred CCCHHHHHHHhccChHHHHHHhhhHHH---------HHHHHHHHhHHHHHHHHhhccCCCCChhhHhhh
Q 022167 238 EPSMEQLAASLRISRPELQSILMECSL---------AREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~eG~~---------ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQE 297 (301)
-.|-+|+|+.+|+|...+-+.+..++- .-+.+-....-+...+|+.+...++++.|||+.
T Consensus 24 g~tQ~eIA~~lGiSr~~VSR~L~~A~~~~~lv~lfp~~~~ls~p~~~~L~k~~~~l~~~~~~l~eLi~~ 92 (192)
T 1zx4_A 24 GMSQKDIAAKEGLSQAKVTRALQAASAPEELVALFPVQSELTFSDYKTLCAVGDEMGNKNLEFDQLIQN 92 (192)
T ss_dssp TCCHHHHHHHHTCCHHHHHHHHHHHTSCHHHHTTCSCGGGCCHHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHhccchhhHHHcCCcccCccchHHHHHHHHHHhhhcCCCHHHHHHH
Confidence 378899999999999998887765420 013344456677788888888888888888853
No 32
>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=36.01 E-value=45 Score=31.87 Aligned_cols=35 Identities=23% Similarity=0.436 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhc--cChHHHHHH
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLR--ISRPELQSI 258 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g--~S~~eLrr~ 258 (301)
+.+.+.++.+.+|++|+.+++|..+| ++.++++..
T Consensus 271 lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~ 307 (423)
T 2a6h_F 271 LSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEET 307 (423)
T ss_dssp HHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHH
Confidence 34455677788999999999999999 887776554
No 33
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}
Probab=33.55 E-value=1.4e+02 Score=21.70 Aligned_cols=30 Identities=23% Similarity=0.067 Sum_probs=23.9
Q ss_pred hCCCCCHHHHHHHhccChHHHHHHhhhHHH
Q 022167 235 LGCEPSMEQLAASLRISRPELQSILMECSL 264 (301)
Q Consensus 235 LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ 264 (301)
+-..-+..|+|+.+|++...++..+..+..
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 344568899999999999999888876544
No 34
>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=33.25 E-value=1.8e+02 Score=23.56 Aligned_cols=38 Identities=16% Similarity=0.076 Sum_probs=28.8
Q ss_pred HHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHH
Q 022167 228 KLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLA 265 (301)
Q Consensus 228 r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~A 265 (301)
+.-+.-.....-+.+|+|+.+|++...++..+..+...
T Consensus 193 r~vl~l~~~~g~s~~EIA~~lgis~~~V~~~~~ra~~~ 230 (239)
T 1rp3_A 193 KLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALER 230 (239)
T ss_dssp HHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 34444455667899999999999999998888765543
No 35
>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}
Probab=32.85 E-value=37 Score=26.17 Aligned_cols=23 Identities=13% Similarity=0.327 Sum_probs=20.2
Q ss_pred CCHHHHHHHhccChHHHHHHhhh
Q 022167 239 PSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~e 261 (301)
|+..++|+.+|+|..-+++++..
T Consensus 34 Ps~~~La~~~~vSr~tvr~al~~ 56 (113)
T 3tqn_A 34 PSIRKISTEYQINPLTVSKAYQS 56 (113)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHH
Confidence 79999999999999888877665
No 36
>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*
Probab=31.22 E-value=1.1e+02 Score=21.17 Aligned_cols=26 Identities=19% Similarity=0.362 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhhH
Q 022167 237 CEPSMEQLAASLRISRPELQSILMEC 262 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~eG 262 (301)
..-+.+|+|+.+|++...++..+..+
T Consensus 29 ~~~s~~eIA~~l~is~~tV~~~~~ra 54 (73)
T 1ku3_A 29 REHTLEEVGAYFGVTRERIRQIENKA 54 (73)
T ss_dssp SCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45688999999999999988776654
No 37
>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2
Probab=30.29 E-value=1.2e+02 Score=20.71 Aligned_cols=26 Identities=12% Similarity=0.365 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhhH
Q 022167 237 CEPSMEQLAASLRISRPELQSILMEC 262 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~eG 262 (301)
..-+.+|+|+.+|++...++..+..+
T Consensus 24 ~g~s~~eIA~~lgis~~tV~~~~~ra 49 (68)
T 2p7v_B 24 TDYTLEEVGKQFDVTRERIRQIEAKA 49 (68)
T ss_dssp SCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 35688999999999999888776653
No 38
>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A
Probab=30.00 E-value=1.1e+02 Score=22.08 Aligned_cols=41 Identities=10% Similarity=0.086 Sum_probs=28.3
Q ss_pred CHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhh
Q 022167 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 240 t~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKR 283 (301)
+..|+|+.+|++...++..+. +++.+|-..|..=.+..|.+
T Consensus 38 s~~eIA~~l~is~~tV~~~l~---r~~~kL~~~~~~~l~~~a~~ 78 (82)
T 1je8_A 38 PNKMIARRLDITESTVKVHVK---HMLKKMKLKSRVEAAVWVHQ 78 (82)
T ss_dssp CHHHHHHHHTSCHHHHHHHHH---HHHHHTTCSSHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHH---HHHHHHcCCCHHHHHHHHHH
Confidence 578999999999988877665 55666655555545554443
No 39
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}
Probab=28.60 E-value=1e+02 Score=20.29 Aligned_cols=42 Identities=21% Similarity=0.228 Sum_probs=30.7
Q ss_pred CCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhh
Q 022167 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKR 283 (301)
-+..|+|+.+|++...++..+. .++.+|=..|..=.+..|.+
T Consensus 14 ~s~~eIA~~l~is~~tV~~~~~---~~~~kl~~~~~~~l~~~~~~ 55 (61)
T 2jpc_A 14 YTNHGISEKLHISIKTVETHRM---NMMRKLQVHKVTELLNCARR 55 (61)
T ss_dssp CCSHHHHHHTCSCHHHHHHHHH---HHHHHHTCSSHHHHHHHHHC
T ss_pred CCHHHHHHHhCCCHHHHHHHHH---HHHHHHCCCCHHHHHHHHHH
Confidence 3568999999999988876655 56677777776666666654
No 40
>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}
Probab=28.56 E-value=1.3e+02 Score=20.63 Aligned_cols=49 Identities=20% Similarity=0.241 Sum_probs=33.7
Q ss_pred CCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhh
Q 022167 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQE 297 (301)
-|.+++|+.+|++...+.+.... .. .-++..+..||+.| |+++.+|+..
T Consensus 16 lsq~~lA~~~gis~~~i~~~e~g-~~------~p~~~~l~~ia~~l---~v~~~~l~~~ 64 (77)
T 2k9q_A 16 LTAKSVAEEMGISRQQLCNIEQS-ET------APVVVKYIAFLRSK---GVDLNALFDR 64 (77)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHTC-CS------CCHHHHHHHHHHHT---TCCHHHHHHH
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC-CC------CCCHHHHHHHHHHh---CcCHHHHhCc
Confidence 57788999999998887665433 11 12455667777766 6888888754
No 41
>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2
Probab=28.33 E-value=1.2e+02 Score=21.87 Aligned_cols=26 Identities=12% Similarity=0.340 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhhH
Q 022167 237 CEPSMEQLAASLRISRPELQSILMEC 262 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~eG 262 (301)
..-|.+|+|+.+|++...++..+..+
T Consensus 37 ~~~s~~EIA~~lgis~~tV~~~~~ra 62 (87)
T 1tty_A 37 KPKTLEEVGQYFNVTRERIRQIEVKA 62 (87)
T ss_dssp SCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56789999999999999988877654
No 42
>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=28.26 E-value=1.1e+02 Score=21.43 Aligned_cols=49 Identities=20% Similarity=0.218 Sum_probs=34.1
Q ss_pred CHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhh
Q 022167 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297 (301)
Q Consensus 240 t~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQE 297 (301)
+.+++|+.+|++...+.+.... .. -.-++..+..||+-| |++..+|+.+
T Consensus 29 sq~~lA~~~gis~~~is~~E~g-~~-----~~p~~~~l~~ia~~l---~v~~~~l~~~ 77 (86)
T 2ofy_A 29 SMVTVAFDAGISVETLRKIETG-RI-----ATPAFFTIAAVARVL---DLSLDDVAAV 77 (86)
T ss_dssp CHHHHHHHHTCCHHHHHHHHTT-CC-----SSCBHHHHHHHHHHT---TCCHHHHHTT
T ss_pred CHHHHHHHhCCCHHHHHHHHcC-CC-----CCCCHHHHHHHHHHh---CCCHHHHhcc
Confidence 8889999999998887765443 11 013456677788766 7888888754
No 43
>4dyq_A Gene 1 protein; GP1, octamer, DNA-binding, viral protein; 1.50A {Shigella phage SF6} PDB: 4dyc_A 4dyr_A 3hef_A 4dzj_A 4dzp_A
Probab=26.86 E-value=1.1e+02 Score=24.56 Aligned_cols=28 Identities=11% Similarity=-0.041 Sum_probs=20.0
Q ss_pred hcCCCCCCCHHHHHHHHHHHHcCCcHHH
Q 022167 199 GVVSEELLTHAEVVRLSKKIKTGLSLDD 226 (301)
Q Consensus 199 ei~~~~LLT~EEEveLs~kIq~g~~Le~ 226 (301)
..|+...+|++-.-+++..|..|..+.+
T Consensus 6 k~GRPtk~t~e~~e~I~~~i~~G~sl~~ 33 (140)
T 4dyq_A 6 KAGRPSDYMPEVADDICSLLSSGESLLK 33 (140)
T ss_dssp ----CCSCCTTHHHHHHHHHHTTCCHHH
T ss_pred CCCCCCCCCHHHHHHHHHHHHCCCcHHH
Confidence 4577788898888889999999988543
No 44
>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=26.46 E-value=83 Score=28.58 Aligned_cols=58 Identities=19% Similarity=0.201 Sum_probs=40.1
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhH--------------HHHHHHHHHHhHHHHHHHHhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC--------------SLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG--------------~~ARekLV~aNLRLVVSIAKR 283 (301)
.++..-+.+.+....+.++||+.+|+|...|.+.+... ..|++.|...++. |..||..
T Consensus 308 ~~~~~~i~~~~~~~~~~~~~a~~~~~s~~~l~r~f~~~~g~s~~~~~~~~r~~~a~~~L~~~~~~-i~~ia~~ 379 (412)
T 4fe7_A 308 IQAMHYIRNHACKGIKVDQVLDAVGISRSNLEKRFKEEVGETIHAMIHAEKLEKARSLLISTTLS-INEISQM 379 (412)
T ss_dssp HHHHHHHHHHGGGTCCHHHHHHHTTCCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHH
T ss_pred HHHHHHHHhhccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhcCCCC-HHHHHHH
Confidence 34445556667778999999999999999998887763 4566655554443 4555554
No 45
>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=26.42 E-value=61 Score=23.78 Aligned_cols=25 Identities=16% Similarity=0.321 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhh
Q 022167 237 CEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
..-+..|+|+.+|++...+++.|..
T Consensus 30 ~~~t~~eLA~~Lgvs~~tV~~~L~~ 54 (77)
T 1qgp_A 30 KATTAHDLSGKLGTPKKEINRVLYS 54 (77)
T ss_dssp SCEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3567899999999999988877765
No 46
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1
Probab=26.18 E-value=71 Score=31.11 Aligned_cols=33 Identities=24% Similarity=0.435 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhc--cChHHHHH
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLR--ISRPELQS 257 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g--~S~~eLrr 257 (301)
.+.+.++.+.+|++|+.+++|..+| ++..++..
T Consensus 287 rr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~ 321 (438)
T 1l9z_H 287 SRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEE 321 (438)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHH
Confidence 3455667788999999999999999 77666544
No 47
>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}
Probab=26.04 E-value=1.8e+02 Score=22.58 Aligned_cols=24 Identities=17% Similarity=0.325 Sum_probs=20.6
Q ss_pred CCCHHHHHHHhccChHHHHHHhhh
Q 022167 238 EPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
-|+..++|+.+|+|+.-+++++..
T Consensus 37 Lps~~~La~~~~vSr~tvr~Al~~ 60 (125)
T 3neu_A 37 LPSVREMGVKLAVNPNTVSRAYQE 60 (125)
T ss_dssp CCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 478999999999999888887665
No 48
>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=25.88 E-value=93 Score=24.66 Aligned_cols=37 Identities=24% Similarity=0.226 Sum_probs=0.0
Q ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccC
Q 022167 210 EVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDN 286 (301)
Q Consensus 210 EEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~g 286 (301)
.+.+|...++.|+. .|-+.|+..+.++|..+|.+|.+
T Consensus 9 ~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~l~~~~~~~~~ 45 (194)
T 1or7_A 9 TDQVLVERVQKGDQ----------------------------------------KAFNLLVVRYQHKVASLVSRYVP 45 (194)
T ss_dssp HHHHHHHHHHTTCH----------------------------------------HHHHHHHHHHHHHHHHHHTTTSC
T ss_pred ChHHHHHHHHccCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHcC
No 49
>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2
Probab=25.36 E-value=1.6e+02 Score=22.12 Aligned_cols=44 Identities=16% Similarity=0.186 Sum_probs=25.5
Q ss_pred cCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 200 i~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
|++.+.||.++-..+...+..|.. ..++|..+|++...+.+.+.
T Consensus 1 Mgr~~~~s~~~r~~i~~~~~~G~s-----------------~~~ia~~lgis~~Tv~r~~~ 44 (141)
T 1u78_A 1 MPRGSALSDTERAQLDVMKLLNVS-----------------LHEMSRKISRSRHCIRVYLK 44 (141)
T ss_dssp -CCSCCCCHHHHHHHHHHHHTTCC-----------------HHHHHHHHTCCHHHHHHHHH
T ss_pred CCCcccCCHHHHHHHHHHHHcCCC-----------------HHHHHHHHCcCHHHHHHHHH
Confidence 456677887776666655555554 44555556665555554443
No 50
>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A
Probab=24.88 E-value=89 Score=22.02 Aligned_cols=27 Identities=19% Similarity=0.276 Sum_probs=21.8
Q ss_pred hCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 235 LGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 235 LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
-+.+.+..|+|+.+|++...+.+.+..
T Consensus 22 ~~~~~s~~eLA~~lglsr~tv~~~l~~ 48 (67)
T 2heo_A 22 DGGPVAIFQLVKKCQVPKKTLNQVLYR 48 (67)
T ss_dssp HCSCEEHHHHHHHHCSCHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 355678999999999999888766654
No 51
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}
Probab=24.50 E-value=1.5e+02 Score=20.40 Aligned_cols=43 Identities=14% Similarity=0.057 Sum_probs=32.1
Q ss_pred CCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhc
Q 022167 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRY 284 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY 284 (301)
-+..|+|+.+|++...++..+. +++.+|-..|..-.+..|.++
T Consensus 32 ~s~~eIA~~l~is~~tV~~~~~---r~~~kl~~~~~~~l~~~~~~~ 74 (79)
T 1x3u_A 32 LPNKSIAYDLDISPRTVEVHRA---NVMAKMKAKSLPHLVRMALAG 74 (79)
T ss_dssp CCHHHHHHHTTSCHHHHHHHHH---HHHHHTTCCSHHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHH---HHHHHHcCCCHHHHHHHHHHh
Confidence 4678999999999988876654 577777777777666666554
No 52
>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=23.20 E-value=99 Score=21.85 Aligned_cols=48 Identities=10% Similarity=0.104 Sum_probs=31.6
Q ss_pred CCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhh
Q 022167 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQ 296 (301)
-|.+++|..+|++...+.+.... . ..-++..+..||+-| |++..+|+-
T Consensus 31 lsq~~lA~~~gis~~~is~~e~g-~------~~~~~~~l~~ia~~l---~v~~~~l~~ 78 (92)
T 1lmb_3 31 LSQESVADKMGMGQSGVGALFNG-I------NALNAYNAALLAKIL---KVSVEEFSP 78 (92)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHTT-S------SCCCHHHHHHHHHHH---TSCGGGTCH
T ss_pred CCHHHHHHHHCcCHHHHHHHHcC-C------CCCCHHHHHHHHHHH---CCCHHHHhh
Confidence 57889999999998877665443 2 123455677777766 456666553
No 53
>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}
Probab=22.58 E-value=1e+02 Score=24.92 Aligned_cols=44 Identities=27% Similarity=0.232 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHHcCCcHHHHHHHHHHHhC-CCCCHHHHHHHhccChHHHHHHhhh
Q 022167 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 206 LT~EEEveLs~kIq~g~~Le~~r~eLee~LG-rePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
||..|-.-|...... ...| ..||.+++|+.+|++..++.+.+..
T Consensus 30 Ls~~E~~lLl~L~~~------------~~~g~~~ps~~~LA~~~~~s~~~v~~~L~~ 74 (135)
T 2v79_A 30 LNETELILLLKIKMH------------LEKGSYFPTPNQLQEGMSISVEECTNRLRM 74 (135)
T ss_dssp CCHHHHHHHHHHHHH------------HTTTCCSCCHHHHHTTSSSCHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH------------HhcCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 566665555544432 1234 3599999999999999998766554
No 54
>3u7d_B Protein HEG homolog 1; FERM domain, RAP1 effector, membrane protein cytoplasmic TAI protein binding; 2.49A {Homo sapiens}
Probab=22.17 E-value=23 Score=22.13 Aligned_cols=12 Identities=33% Similarity=0.310 Sum_probs=8.8
Q ss_pred Hhhhcccccccc
Q 022167 120 EKQWNLSFERTV 131 (301)
Q Consensus 120 ekqw~l~~e~~~ 131 (301)
--|||+||--++
T Consensus 8 pgqynpsfisdd 19 (26)
T 3u7d_B 8 PGQYNPSFISDE 19 (26)
T ss_pred cCccCcccccCc
Confidence 359999997443
No 55
>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=21.78 E-value=2.6e+02 Score=21.01 Aligned_cols=32 Identities=13% Similarity=0.024 Sum_probs=25.7
Q ss_pred HhCCCCCHHHHHHHhccChHHHHHHhhhHHHH
Q 022167 234 RLGCEPSMEQLAASLRISRPELQSILMECSLA 265 (301)
Q Consensus 234 ~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~A 265 (301)
..-..-+.+|+|+.+|++...++..+..+...
T Consensus 120 ~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~ 151 (164)
T 3mzy_A 120 YLIRGYSYREIATILSKNLKSIDNTIQRIRKK 151 (164)
T ss_dssp HHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 44456789999999999999998888776543
No 56
>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A
Probab=21.76 E-value=1.4e+02 Score=22.36 Aligned_cols=26 Identities=19% Similarity=0.394 Sum_probs=21.7
Q ss_pred CCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 236 GCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 236 GrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
|..-+..|+|+.+|++...+++.|..
T Consensus 25 g~~~t~~eLA~~Lgvsr~tV~~~L~~ 50 (81)
T 1qbj_A 25 GKATTAHDLSGKLGTPKKEINRVLYS 50 (81)
T ss_dssp TCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 45678999999999999998877665
No 57
>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=21.48 E-value=71 Score=20.76 Aligned_cols=48 Identities=27% Similarity=0.327 Sum_probs=32.4
Q ss_pred CCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhh
Q 022167 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQ 296 (301)
-|.+++|+.+|++...+.+...... .-+...+..||+-| |++..+|+.
T Consensus 15 ~s~~~lA~~~gis~~~i~~~e~g~~-------~~~~~~l~~i~~~l---~~~~~~l~~ 62 (66)
T 2xi8_A 15 ISQSELAALLEVSRQTINGIEKNKY-------NPSLQLALKIAYYL---NTPLEDIFQ 62 (66)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHTTSC-------CCCHHHHHHHHHHT---TSCHHHHEE
T ss_pred CCHHHHHHHHCcCHHHHHHHHcCCC-------CCCHHHHHHHHHHH---CcCHHHHhC
Confidence 5678889999998888776554311 12455667777766 677777764
No 58
>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}
Probab=21.48 E-value=1.6e+02 Score=19.75 Aligned_cols=29 Identities=24% Similarity=0.174 Sum_probs=24.0
Q ss_pred HHHHHHHhccChHHHHHHhhhHHHHHHHH
Q 022167 241 MEQLAASLRISRPELQSILMECSLAREKL 269 (301)
Q Consensus 241 ~eEwA~a~g~S~~eLrr~L~eG~~ARekL 269 (301)
..++|..+|++...|.+.+......+..+
T Consensus 28 ~~~vA~~~gIs~~tl~~W~~~~~~~~~~~ 56 (59)
T 2glo_A 28 QRATARKYNIHRRQIQKWLQCESNLRSSV 56 (59)
T ss_dssp HHHHHHHTTSCHHHHHHHHTTHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 88999999999999998888776666544
No 59
>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}
Probab=21.10 E-value=75 Score=21.43 Aligned_cols=48 Identities=15% Similarity=0.185 Sum_probs=33.3
Q ss_pred CCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhh
Q 022167 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQ 296 (301)
-+.+++|+.+|++...+.+...... .-+...+..||+.| |++..+|+.
T Consensus 24 ~s~~~lA~~~gis~~~i~~~e~g~~-------~~~~~~l~~ia~~l---~~~~~~l~~ 71 (76)
T 3bs3_A 24 RTNRWLAEQMGKSENTISRWCSNKS-------QPSLDMLVKVAELL---NVDPRQLIN 71 (76)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHTTSS-------CCCHHHHHHHHHHH---TSCGGGGBC
T ss_pred CCHHHHHHHHCcCHHHHHHHHcCCC-------CCCHHHHHHHHHHH---CcCHHHHhc
Confidence 5778899999999888776554311 13456677788776 678877764
No 60
>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=20.91 E-value=78 Score=21.95 Aligned_cols=48 Identities=19% Similarity=0.133 Sum_probs=32.9
Q ss_pred CCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhh
Q 022167 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQ 296 (301)
-|.+|+|+.+|++...+.+.... . ..-++..+..||+-| |++..+|+.
T Consensus 28 ltq~elA~~~gis~~~is~~e~g-~------~~~~~~~l~~l~~~l---~~~~~~l~~ 75 (83)
T 3f6w_A 28 ITQKELAARLGRPQSFVSKTENA-E------RRLDVIEFMDFCRGI---GTDPYALLS 75 (83)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHTT-S------SCCCHHHHHHHHHHH---TCCHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHCC-C------CCCCHHHHHHHHHHc---CCCHHHHHH
Confidence 57788888888888777655543 2 123566777777776 677777764
No 61
>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}
Probab=20.73 E-value=1e+02 Score=22.41 Aligned_cols=42 Identities=14% Similarity=0.096 Sum_probs=30.1
Q ss_pred CCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhh
Q 022167 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKR 283 (301)
-+..|+|+.+|++...++..+. +++.+|-..|..-.+..|.+
T Consensus 45 ~s~~eIA~~l~is~~tV~~~l~---r~~~kL~~~~~~~l~~~a~~ 86 (91)
T 2rnj_A 45 YSNQEIASASHITIKTVKTHVS---NILSKLEVQDRTQAVIYAFQ 86 (91)
T ss_dssp CCTTHHHHHHTCCHHHHHHHHH---HHHHHTTCCSSHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHH---HHHHHHCCCCHHHHHHHHHH
Confidence 3577999999999988877665 56667766666655555544
Done!