Query 016321
Match_columns 391
No_of_seqs 256 out of 1874
Neff 4.3
Searched_HMMs 29240
Date Mon Mar 25 11:37:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016321.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/016321hhsearch_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 100.0 1.3E-28 4.4E-33 232.0 15.0 194 189-385 5-239 (245)
2 1l9z_H Sigma factor SIGA; heli 99.9 1.7E-27 5.6E-32 242.2 14.9 151 191-341 94-274 (438)
3 2a6h_F RNA polymerase sigma fa 99.9 1.7E-27 5.7E-32 240.0 10.6 152 191-342 79-260 (423)
4 1sig_A Sigma70, RNA polymerase 99.6 2.7E-16 9.1E-21 152.6 9.9 75 264-338 265-339 (339)
5 3iyd_F RNA polymerase sigma fa 99.6 7.8E-17 2.7E-21 168.8 0.4 119 265-383 375-499 (613)
6 1rp3_A RNA polymerase sigma fa 99.4 2.7E-12 9.2E-17 114.1 10.6 76 263-338 11-89 (239)
7 1l0o_C Sigma factor; bergerat 99.3 1.5E-13 5E-18 122.0 -0.2 98 200-337 4-101 (243)
8 1or7_A Sigma-24, RNA polymeras 98.8 1.4E-08 4.9E-13 87.9 9.9 74 263-339 22-95 (194)
9 2q1z_A RPOE, ECF SIGE; ECF sig 98.6 8E-09 2.8E-13 89.0 2.6 75 263-338 26-100 (184)
10 3mzy_A RNA polymerase sigma-H 98.5 1.6E-07 5.4E-12 78.4 7.6 51 288-339 1-51 (164)
11 2o7g_A Probable RNA polymerase 98.4 4.9E-07 1.7E-11 73.1 7.4 72 264-338 24-95 (112)
12 1h3l_A RNA polymerase sigma fa 98.2 1E-06 3.5E-11 68.2 5.2 75 261-337 9-83 (87)
13 2lfw_A PHYR sigma-like domain; 97.0 3.2E-05 1.1E-09 66.3 -3.3 68 267-336 4-71 (157)
14 3n0r_A Response regulator; sig 95.5 0.0018 6.2E-08 61.0 -0.8 70 263-334 20-89 (286)
15 3iyd_F RNA polymerase sigma fa 93.5 0.012 4.2E-07 61.6 -0.3 35 189-223 94-128 (613)
16 1tc3_C Protein (TC3 transposas 52.6 42 0.0014 21.3 6.1 40 204-260 4-43 (51)
17 2jt1_A PEFI protein; solution 52.2 16 0.00055 28.4 4.2 26 232-257 18-43 (77)
18 2kkm_A Translation machinery-a 47.5 13 0.00044 32.5 3.3 91 191-314 25-122 (144)
19 3ugo_A RNA polymerase sigma fa 47.0 6.9 0.00024 36.3 1.6 39 224-262 199-239 (245)
20 3mn2_A Probable ARAC family tr 42.7 35 0.0012 26.5 4.9 36 226-261 6-41 (108)
21 3oou_A LIN2118 protein; protei 38.3 45 0.0015 26.0 5.0 36 226-261 9-44 (108)
22 3oio_A Transcriptional regulat 37.9 35 0.0012 26.9 4.2 34 228-261 13-46 (113)
23 3lsg_A Two-component response 36.6 51 0.0018 25.3 5.0 34 228-261 8-42 (103)
24 2k9s_A Arabinose operon regula 35.8 48 0.0016 25.8 4.7 35 227-261 8-43 (107)
25 2zc2_A DNAD-like replication p 31.9 65 0.0022 24.2 4.7 46 244-293 29-75 (78)
26 3f2g_A Alkylmercury lyase; MER 31.1 41 0.0014 31.4 4.1 27 235-261 33-59 (220)
27 1bl0_A Protein (multiple antib 29.1 53 0.0018 26.5 4.1 33 229-261 18-50 (129)
28 3mkl_A HTH-type transcriptiona 27.7 65 0.0022 25.6 4.3 34 228-261 13-46 (120)
29 1jko_C HIN recombinase, DNA-in 27.3 83 0.0028 20.3 4.1 22 240-261 23-44 (52)
30 1sig_A Sigma70, RNA polymerase 25.0 25 0.00086 33.5 1.5 19 205-223 1-19 (339)
31 3knw_A Putative transcriptiona 24.5 2.8E+02 0.0097 22.4 11.7 72 234-305 29-101 (212)
32 1p4w_A RCSB; solution structur 24.2 2.6E+02 0.0091 22.0 7.9 57 186-260 15-71 (99)
33 3pru_C Phycobilisome 32.1 kDa 24.1 2.7E+02 0.0093 24.7 7.9 57 250-306 55-121 (154)
34 3s8q_A R-M controller protein; 23.8 1.6E+02 0.0055 21.2 5.6 49 239-297 25-73 (82)
35 1rp3_A RNA polymerase sigma fa 23.1 3.4E+02 0.012 22.9 8.4 40 231-270 196-235 (239)
36 3g5g_A Regulatory protein; tra 23.0 1.8E+02 0.0061 22.6 6.0 48 240-297 43-90 (99)
37 1zx4_A P1 PARB, plasmid partit 23.0 68 0.0023 29.1 3.9 90 239-337 25-123 (192)
38 3f6w_A XRE-family like protein 22.8 1.9E+02 0.0064 20.8 5.8 48 239-296 28-75 (83)
39 3eup_A Transcriptional regulat 22.7 1.6E+02 0.0056 23.7 6.0 70 239-308 32-101 (204)
40 3k2z_A LEXA repressor; winged 22.4 1.1E+02 0.0037 26.7 5.0 26 233-258 19-44 (196)
41 3qbm_A TETR transcriptional re 22.2 3E+02 0.01 21.9 9.0 70 234-303 22-92 (199)
42 2o8x_A Probable RNA polymerase 22.1 2E+02 0.0067 20.0 5.6 26 239-264 32-57 (70)
43 3nph_B Phycobilisome 32.1 kDa 22.0 3.4E+02 0.011 23.9 8.0 100 180-306 6-116 (148)
44 2ofy_A Putative XRE-family tra 21.8 2E+02 0.0069 20.9 5.8 47 240-295 29-75 (86)
45 3mzy_A RNA polymerase sigma-H 21.8 2.4E+02 0.0084 22.2 6.8 36 237-272 123-158 (164)
46 2a6h_F RNA polymerase sigma fa 20.4 1E+02 0.0035 30.7 4.9 33 226-258 273-307 (423)
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=99.96 E-value=1.3e-28 Score=232.05 Aligned_cols=194 Identities=29% Similarity=0.379 Sum_probs=130.7
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHh-----------------------------hCCCC
Q 016321 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKER-----------------------------LGCEP 239 (391)
Q Consensus 189 ~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~-----------------------------~g~eP 239 (391)
..|.++.||++|+++|+||++||++|+++|+.|..+... +... .+.+|
T Consensus 5 ~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~ 81 (245)
T 3ugo_A 5 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKK---LSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDP 81 (245)
T ss_dssp CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHH---HHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCH
T ss_pred CCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHH---HHhccCCcHHHHHHhhhhhhhccchhcccccccccccc
Confidence 347999999999999999999999999999998753221 2111 14678
Q ss_pred chHHHHHHhcCCh----HHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCC
Q 016321 240 SMEQLAASLRISR----PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGF 315 (391)
Q Consensus 240 s~~e~A~a~~~s~----~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~ 315 (391)
+..+||.+.+++. .+|.+.++.|..|+++|++.|.|+|+++|.+|.+.+.+.+||+|+|+|||++|+++|||++|+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~ 161 (245)
T 3ugo_A 82 KTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRF 161 (245)
T ss_dssp HHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCC
T ss_pred hhHHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCC
Confidence 8999999999974 456667788999999999999999999999999999999999999999999999999999999
Q ss_pred chhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhhhhc---cccc---ccCCCCCChhHHhh--HHHHHHHHHHHHH
Q 016321 316 KISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLK---FDLS---SSLPKKGSKFEQIG--VLLSSICKLLMYL 385 (391)
Q Consensus 316 rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~~~l~---~dl~---~~~~k~ge~~e~ig--~~ls~v~~~L~~~ 385 (391)
+|+||+.||||++|.++|+++.+.++....-......+. ..+. ...++..++++.+| +..+.|.+.|...
T Consensus 162 ~F~tya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~a 239 (245)
T 3ugo_A 162 KFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIA 239 (245)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHTC-------------------------------------------------------
T ss_pred cHHHHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Confidence 999999999999999999999887663221111111111 1111 13457778999999 9999988877643
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=99.95 E-value=1.7e-27 Score=242.18 Aligned_cols=151 Identities=32% Similarity=0.492 Sum_probs=131.7
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHH------------------HHHhhCCCCchHHHHH------
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLR------------------LKERLGCEPSMEQLAA------ 246 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~------------------l~~~~g~ePs~~e~A~------ 246 (391)
+.++.||++|+++|+||++||++|+++++.|+.+.+.... ....+++.|+..+|+.
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 5788999999999999999999999999999654432211 1234567788777632
Q ss_pred ------HhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhh
Q 016321 247 ------SLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320 (391)
Q Consensus 247 ------a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTY 320 (391)
+++++..+|...+..|..|+++||..|+++|+++|++|.++|.+.+||||||+|||++|+++|||++|++|+||
T Consensus 174 ~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rFsTY 253 (438)
T 1l9z_H 174 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY 253 (438)
T ss_pred hhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHH
Confidence 23556788888998999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhhhh
Q 016321 321 VYWWIRQVRLLLICTFKQFIA 341 (391)
Q Consensus 321 A~~~IR~aI~~aIre~~R~ir 341 (391)
|+||||+.|.++|+++.|.++
T Consensus 254 A~~wIR~~I~~~i~~~~R~ir 274 (438)
T 1l9z_H 254 ATWWIRQAINRAIADQARTIR 274 (438)
T ss_pred HHHHHHHHHHHHHHHhcchhc
Confidence 999999999999999988776
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=99.94 E-value=1.7e-27 Score=239.96 Aligned_cols=152 Identities=32% Similarity=0.504 Sum_probs=129.0
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHH------------------HHHhhCCCCchHH---------
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLR------------------LKERLGCEPSMEQ--------- 243 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~------------------l~~~~g~ePs~~e--------- 243 (391)
+.++.||++|+++|+||++||++|+++++.|+.+...... ....+++.|+.++
T Consensus 79 d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (423)
T 2a6h_F 79 DPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEE 158 (423)
T ss_dssp HHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHHHHH
T ss_pred cHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhhhhh
Confidence 6899999999999999999999999999998643322111 1112345565333
Q ss_pred HHH---HhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhh
Q 016321 244 LAA---SLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320 (391)
Q Consensus 244 ~A~---a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTY 320 (391)
|+. +++++..+|...+..|..|+++||..|+++|+++|++|.++|.+.+||||||+|||++|+++|||++|++|+||
T Consensus 159 ~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~FstY 238 (423)
T 2a6h_F 159 IDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY 238 (423)
T ss_dssp HHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCHHHH
T ss_pred hhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHH
Confidence 322 34667788999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhhhhh
Q 016321 321 VYWWIRQVRLLLICTFKQFIAW 342 (391)
Q Consensus 321 A~~~IR~aI~~aIre~~R~ir~ 342 (391)
|+||||++|.++|+++.|.++.
T Consensus 239 a~~wIr~~i~~~i~~~~r~ir~ 260 (423)
T 2a6h_F 239 ATWWIRQAINRAIADQARTIRI 260 (423)
T ss_dssp HHHHHHHHHHHHHHHHSSSSCC
T ss_pred HHHHHHHHHHHHHHHccceeec
Confidence 9999999999999999887763
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=99.65 E-value=2.7e-16 Score=152.60 Aligned_cols=75 Identities=43% Similarity=0.795 Sum_probs=71.1
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.|++.|+..|.|+|+++|.+|.+.+.+.+||+|+|+|||++|+++||+.+|.+|+||+++||++.|.++++++.|
T Consensus 265 ~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn~~~~~lr~~~r 339 (339)
T 1sig_A 265 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 339 (339)
T ss_dssp HHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC--
T ss_pred hhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 799999999999999999999999999999999999999999999999999999999999999999999987653
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=99.60 E-value=7.8e-17 Score=168.75 Aligned_cols=119 Identities=34% Similarity=0.527 Sum_probs=93.6
Q ss_pred HHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhh
Q 016321 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLK 344 (391)
Q Consensus 265 Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~ 344 (391)
|++.|+..|.++|+++|.+|.+++.+.+||+|+|+|||++|+++||+.+|++|+||++||||++|.++|+++.|.++...
T Consensus 375 A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~irn~i~~~lr~~~r~~rip~ 454 (613)
T 3iyd_F 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 454 (613)
T ss_dssp HHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHHHHHHHHTTTSCSSSCCCS
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHHHHHHHHHHhcCcceeCcH
Confidence 39999999999999999999999999999999999999999999999999999999999999999999999887666332
Q ss_pred hHHHhhhhhcc---ccc---ccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 345 TDVLLKNQLKF---DLS---SSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 345 r~v~l~~~l~~---dl~---~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
.-....+.+.. .+. ...|+..+.++.+|+.+..+.+++.
T Consensus 455 ~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~ 499 (613)
T 3iyd_F 455 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLK 499 (613)
T ss_dssp HHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 22211122111 111 1335556677777777777766654
No 6
>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=99.36 E-value=2.7e-12 Score=114.11 Aligned_cols=76 Identities=21% Similarity=0.413 Sum_probs=71.4
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcc---cCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~---~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..++++|+..|.|+|..+|.+|. +.+.+.+||+|+|+++|++++++||+.+|.+|.||+.+||++.+.++++...+
T Consensus 11 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~~ 89 (239)
T 1rp3_A 11 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLDF 89 (239)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSST
T ss_pred chHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcCc
Confidence 35899999999999999999998 56789999999999999999999999999999999999999999999988765
No 7
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2
Probab=99.32 E-value=1.5e-13 Score=121.97 Aligned_cols=98 Identities=32% Similarity=0.409 Sum_probs=1.3
Q ss_pred cCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHH
Q 016321 200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS 279 (391)
Q Consensus 200 i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~ 279 (391)
+.+.+.++++++.+|+.+++.|+. .+.+.|+..|.++|..
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 445677788888899988888865 7899999999999999
Q ss_pred HHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 280 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 280 IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+|.+|.+...+.+||+|+|+++|++++++||+.+|.+|.||+..+|++.+.++++...
T Consensus 44 ~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~~d~~r~~~ 101 (243)
T 1l0o_C 44 VVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG 101 (243)
T ss_dssp --------------------------------------------------------CC
T ss_pred HHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 9999998889999999999999999999999999999999999999999999998765
No 8
>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=98.83 E-value=1.4e-08 Score=87.93 Aligned_cols=74 Identities=22% Similarity=0.276 Sum_probs=68.5
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQF 339 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ 339 (391)
..|.+.|+..|.|.|..+|.+|.+ ..+.+|++|++++.+++++++|++.. .|.+|+...+++.+.++++..++.
T Consensus 22 ~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~~d~~R~~~~~ 95 (194)
T 1or7_A 22 QKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTAKNYLVAQGRR 95 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHHHHhcc
Confidence 379999999999999999999999 88999999999999999999999875 599999999999999999877653
No 9
>2q1z_A RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc bindin transcription factor; 2.40A {Rhodobacter sphaeroides} PDB: 2z2s_A
Probab=98.65 E-value=8e-09 Score=88.99 Aligned_cols=75 Identities=15% Similarity=0.171 Sum_probs=67.8
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..+.+.|+..|.|.|..++.++.+...+.+|++|++++.+++++++|++..| .|.+|+...+++.+.++++..++
T Consensus 26 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~ 100 (184)
T 2q1z_A 26 EAAFAELFQHFAPKVKGFLMKSGSVASQAEECAQDVMATVWQKAHLFDPSRA-SVATWIFTIARNRRIDGLRKDRQ 100 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHSGGGCCTTTC-CHHHHHHHHHHTSCCTTTCSSSC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhhcCcccC-cHHHHHHHHHHHHHHHHHHhhcc
Confidence 4899999999999999999999887788999999999999999999999876 89999999999988887765543
No 10
>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=98.54 E-value=1.6e-07 Score=78.40 Aligned_cols=51 Identities=33% Similarity=0.559 Sum_probs=44.2
Q ss_pred CCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhh
Q 016321 288 GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQF 339 (391)
Q Consensus 288 Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ 339 (391)
|.+.+|++|+|+++|++++.+||+.+ .+|.+|+..++++.+.++++...+.
T Consensus 1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~ 51 (164)
T 3mzy_A 1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQ 51 (164)
T ss_dssp ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcc
Confidence 67899999999999999999999988 7999999999999999999987653
No 11
>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}
Probab=98.42 E-value=4.9e-07 Score=73.14 Aligned_cols=72 Identities=17% Similarity=0.144 Sum_probs=62.2
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+.+.|+..|.+.+..+|.++ +...+.+|++|+..+.+++.+.+|++. ..|.+|+...+++.+.++++..++
T Consensus 24 ~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~ 95 (112)
T 2o7g_A 24 RALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIRHVRS 95 (112)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCS--SCHHHHHHHHHHHHHHHHTC----
T ss_pred HHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHHHHHHhhc
Confidence 789999999999999999999 776789999999999999999999974 379999999999999888765543
No 12
>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1
Probab=98.25 E-value=1e-06 Score=68.19 Aligned_cols=75 Identities=19% Similarity=0.167 Sum_probs=65.2
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 261 eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
.+..+.+.|+..|.+.+..+|.++.+...+-+|++|+..+.+++.+..|++. ..|.+|+...+++.+.+.++..+
T Consensus 9 g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~ 83 (87)
T 1h3l_A 9 ERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQ 83 (87)
T ss_dssp HHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC---
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhc
Confidence 4568999999999999999999998877889999999999999999999975 47999999999999888765543
No 13
>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}
Probab=96.99 E-value=3.2e-05 Score=66.34 Aligned_cols=68 Identities=6% Similarity=0.042 Sum_probs=60.6
Q ss_pred HHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHh
Q 016321 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTF 336 (391)
Q Consensus 267 e~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~ 336 (391)
+.|+..|.+.|..+|.++.+...+.+|++|++.+.+++++.+|++.. .|.+|++..+++.+.+.++..
T Consensus 4 ~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~ 71 (157)
T 2lfw_A 4 GQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADG 71 (157)
T ss_dssp GGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTT
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhcc
Confidence 46788899999999999988777899999999999999999999864 699999999999999987653
No 14
>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A
Probab=95.47 E-value=0.0018 Score=61.02 Aligned_cols=70 Identities=13% Similarity=0.063 Sum_probs=61.9
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHH
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLIC 334 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIr 334 (391)
..+.++|+..|.+.++.+|.+|.+..-+-+|++||..+-+++...+|++. ..|.+|.+.-.++...+.++
T Consensus 20 ~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r 89 (286)
T 3n0r_A 20 EMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGA 89 (286)
T ss_dssp CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC
T ss_pred cCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhcc
Confidence 35789999999999999999998877788999999999999999999875 36999999999888877655
No 15
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}
Probab=93.49 E-value=0.012 Score=61.64 Aligned_cols=35 Identities=23% Similarity=0.487 Sum_probs=14.9
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCc
Q 016321 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (391)
Q Consensus 189 ~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~ 223 (391)
+.|+++.||+++++.|+||.++|++|+++|..|..
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 34899999999999999999999999999999964
No 16
>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=52.60 E-value=42 Score=21.35 Aligned_cols=40 Identities=18% Similarity=0.214 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhh
Q 016321 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (391)
Q Consensus 204 ~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~ 260 (391)
+.|++++-.++...+..|. +..++|+.+|++...+.+++.
T Consensus 4 ~~l~~~~~~~i~~~~~~g~-----------------s~~~IA~~lgis~~Tv~~~~~ 43 (51)
T 1tc3_C 4 SALSDTERAQLDVMKLLNV-----------------SLHEMSRKISRSRHCIRVYLK 43 (51)
T ss_dssp CCCCHHHHHHHHHHHHTTC-----------------CHHHHHHHHTCCHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHcCC-----------------CHHHHHHHHCcCHHHHHHHHh
Confidence 4567666555665555553 467889999999776665554
No 17
>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}
Probab=52.20 E-value=16 Score=28.45 Aligned_cols=26 Identities=12% Similarity=0.083 Sum_probs=19.9
Q ss_pred HHhhCCCCchHHHHHHhcCChHHHHH
Q 016321 232 KERLGCEPSMEQLAASLRISRPELQS 257 (391)
Q Consensus 232 ~~~~g~ePs~~e~A~a~~~s~~eL~~ 257 (391)
.+..|.+||..|+|+++|+|....++
T Consensus 18 ~~~~g~~psv~EIa~~lgvS~~TVrr 43 (77)
T 2jt1_A 18 NMDDGAPVKTRDIADAAGLSIYQVRL 43 (77)
T ss_dssp HHHTTSCEEHHHHHHHHTCCHHHHHH
T ss_pred hhccCCCcCHHHHHHHHCCCHHHHHH
Confidence 33358899999999999999654433
No 18
>2kkm_A Translation machinery-associated protein 16; nucleus, structural genomics, PSI-2, protein structure initiative; NMR {Saccharomyces cerevisiae}
Probab=47.52 E-value=13 Score=32.45 Aligned_cols=91 Identities=23% Similarity=0.260 Sum_probs=56.6
Q ss_pred hhHHHHHHhcCCC-----CCCCHHHHHHHHHHHHc--CCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhH
Q 016321 191 NRLKGYVKGVVSE-----ELLTHAEVVRLSKKIKT--GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECS 263 (391)
Q Consensus 191 ~~l~~YL~~i~~~-----~lLT~eEE~eL~~kiq~--G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~ 263 (391)
+.+.-|...|... +.+|.+|-.+|+..+-. ...|++++ ++..-||+|+..+
T Consensus 25 ~rl~wFq~~i~e~~~~~~~~~t~~e~~~lI~~yl~R~d~ELeql~--~~rR~gRp~s~Re-------------------- 82 (144)
T 2kkm_A 25 ARVKFMQDVVNSDTFKGQPIFDHAHTREFIQSFIERDDTELDELK--KKRRSNRPPSNRQ-------------------- 82 (144)
T ss_dssp HHHHHHHHHHHSTTTTTCCCCCHHHHHHHHHHHHHHHHHHHHHHH--HHGGGTCCCTTHH--------------------
T ss_pred HHHHHHHHHcccccccccCCCCHHHHHHHHHHHHhcCcHHHHHHH--HhhCCCCCCchHH--------------------
Confidence 3555555555432 57999999999887543 33344333 3456788887443
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCC
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKG 314 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG 314 (391)
.+++. .+..-...|.+ |+++-||....++-+++ .+|.+-+
T Consensus 83 ----~~L~~---~~~~E~~ey~t-G~~iPDLtd~~nvk~Lr---~W~G~~~ 122 (144)
T 2kkm_A 83 ----VLLQQ---RRDQELKEFKA-GFLCPDLSDAKNMEFLR---NWNGTFG 122 (144)
T ss_dssp ----HHHHH---HHHHHHHHHHT-TEEEECSCCHHHHHHHH---TCSSCST
T ss_pred ----HHHHH---HHHHHHHHHcc-CccCCCCCCHHHHHHHH---HcCCChh
Confidence 22211 22334456766 99999999999988865 6776543
No 19
>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=46.97 E-value=6.9 Score=36.29 Aligned_cols=39 Identities=26% Similarity=0.401 Sum_probs=0.0
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhc--CChHHHHHHhhhh
Q 016321 224 LDDHKLRLKERLGCEPSMEQLAASLR--ISRPELQSILMEC 262 (391)
Q Consensus 224 L~~~~~~l~~~~g~ePs~~e~A~a~~--~s~~eL~~~l~eg 262 (391)
+......+...+|+.||++|+|+.+| ++..++...+..+
T Consensus 199 l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~a 239 (245)
T 3ugo_A 199 LSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIA 239 (245)
T ss_dssp -----------------------------------------
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Confidence 33445567788999999999999999 9988887776553
No 20
>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}
Probab=42.68 E-value=35 Score=26.54 Aligned_cols=36 Identities=14% Similarity=0.069 Sum_probs=28.3
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 226 ~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
.+..-+...+..+++.+++|+.+|+|...|.+..+.
T Consensus 6 ~~~~~i~~~~~~~~~~~~lA~~~~~s~~~l~r~fk~ 41 (108)
T 3mn2_A 6 QVEEYIEANWMRPITIEKLTALTGISSRGIFKAFQR 41 (108)
T ss_dssp HHHHHHHHHTTSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred HHHHHHHHcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344455666777899999999999999888777765
No 21
>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=38.35 E-value=45 Score=25.95 Aligned_cols=36 Identities=14% Similarity=0.178 Sum_probs=28.6
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 226 ~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
.+..-+...+..+++.+++|+.+|+|...|.+..+.
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 344455666777899999999999999888887776
No 22
>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}
Probab=37.90 E-value=35 Score=26.85 Aligned_cols=34 Identities=15% Similarity=0.227 Sum_probs=26.6
Q ss_pred HHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 228 KLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 228 ~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
..-+.+.+..+++.+++|+.+|+|...|.+.++.
T Consensus 13 ~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 46 (113)
T 3oio_A 13 VSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQ 46 (113)
T ss_dssp HHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3344555667789999999999999888887776
No 23
>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}
Probab=36.55 E-value=51 Score=25.34 Aligned_cols=34 Identities=15% Similarity=0.161 Sum_probs=26.6
Q ss_pred HHHHHHhhCC-CCchHHHHHHhcCChHHHHHHhhh
Q 016321 228 KLRLKERLGC-EPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 228 ~~~l~~~~g~-ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
..-+.+.+.. +++.+++|+.+|+|...|.+..+.
T Consensus 8 ~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 42 (103)
T 3lsg_A 8 QNIIEESYTDSQFTLSVLSEKLDLSSGYLSIMFKK 42 (103)
T ss_dssp HHHHHHHTTCTTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred HHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3445555666 789999999999999888887776
No 24
>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}
Probab=35.77 E-value=48 Score=25.78 Aligned_cols=35 Identities=11% Similarity=0.204 Sum_probs=27.5
Q ss_pred HHHHHHHhhC-CCCchHHHHHHhcCChHHHHHHhhh
Q 016321 227 HKLRLKERLG-CEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 227 ~~~~l~~~~g-~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
+..-+.+.+. .+++.+++|+.+|+|...|.+..+.
T Consensus 8 ~~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 43 (107)
T 2k9s_A 8 ACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQ 43 (107)
T ss_dssp HHHHHHHTSSCSSCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred HHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444556666 7889999999999999888887775
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=31.90 E-value=65 Score=24.24 Aligned_cols=46 Identities=13% Similarity=0.174 Sum_probs=29.2
Q ss_pred HHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCC-hhH
Q 016321 244 LAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGAD-MAD 293 (391)
Q Consensus 244 ~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd-~eD 293 (391)
|-...|++.+-+..+++.+. ... ..+.++|.+|+..+...|+. .+|
T Consensus 29 w~~~~~~~~elI~~A~~~a~-~~~---~~s~~Yi~~Il~~W~~~gi~T~e~ 75 (78)
T 2zc2_A 29 TVSDDKTDPDLVRSALREAV-FNG---KTNWNYIQAILRNWRHEGISTLRQ 75 (78)
T ss_dssp HHTTTCCCHHHHHHHHHHHH-HHT---CCCHHHHHHHHHHHHHTTCCSHHH
T ss_pred HHHHhCCCHHHHHHHHHHHH-HcC---CCCHHHHHHHHHHHHHcCCCCHHH
Confidence 33445566666655555542 111 24789999999999988875 444
No 26
>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=31.14 E-value=41 Score=31.40 Aligned_cols=27 Identities=22% Similarity=0.207 Sum_probs=23.9
Q ss_pred hCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 235 LGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 235 ~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
.|++|+.+++|..+|++.++.+..|.+
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 799999999999999999888776655
No 27
>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=29.14 E-value=53 Score=26.53 Aligned_cols=33 Identities=18% Similarity=0.224 Sum_probs=26.3
Q ss_pred HHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 229 LRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 229 ~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
.-+...+..+++.+++|+.+|+|...|.+..+.
T Consensus 18 ~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 50 (129)
T 1bl0_A 18 DWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 50 (129)
T ss_dssp HHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHH
T ss_pred HHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344555677799999999999999888877765
No 28
>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}
Probab=27.69 E-value=65 Score=25.57 Aligned_cols=34 Identities=21% Similarity=0.239 Sum_probs=25.7
Q ss_pred HHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 228 KLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 228 ~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
..-+.+.+..+++.+++|+.+|+|...|.+.++.
T Consensus 13 ~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 46 (120)
T 3mkl_A 13 CTVINNNIAHEWTLARIASELLMSPSLLKKKLRE 46 (120)
T ss_dssp HHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred HHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3344455566789999999999998887776654
No 29
>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=27.34 E-value=83 Score=20.33 Aligned_cols=22 Identities=23% Similarity=0.178 Sum_probs=17.5
Q ss_pred chHHHHHHhcCChHHHHHHhhh
Q 016321 240 SMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 240 s~~e~A~a~~~s~~eL~~~l~e 261 (391)
+..++|+.+|+|...+.+.+..
T Consensus 23 s~~~ia~~lgvs~~Tv~r~l~~ 44 (52)
T 1jko_C 23 PRQQLAIIFGIGVSTLYRYFPA 44 (52)
T ss_dssp CHHHHHHTTSCCHHHHHHHSCT
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 5678899999998887776654
No 30
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1
Probab=24.95 E-value=25 Score=33.46 Aligned_cols=19 Identities=16% Similarity=0.305 Sum_probs=14.8
Q ss_pred CCCHHHHHHHHHHHHcCCc
Q 016321 205 LLTHAEVVRLSKKIKTGLS 223 (391)
Q Consensus 205 lLT~eEE~eL~~kiq~G~~ 223 (391)
|||.++|++++++|..|..
T Consensus 1 LLTREgEI~IAKRIE~G~~ 19 (339)
T 1sig_A 1 GSHMEGEIDIAKRIEDGIN 19 (339)
T ss_dssp ---CCTHHHHHHHHHHHHH
T ss_pred CCChHHHHHHHHHHHHHHH
Confidence 6999999999999999964
No 31
>3knw_A Putative transcriptional regulator (TETR/ACRR FAM; TETR-like protein, MCSG, PSI, structural genomics, protein S initiative; 2.45A {Acinetobacter SP}
Probab=24.48 E-value=2.8e+02 Score=22.44 Aligned_cols=72 Identities=7% Similarity=0.009 Sum_probs=44.2
Q ss_pred hhCC-CCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHH
Q 016321 234 RLGC-EPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG 305 (391)
Q Consensus 234 ~~g~-ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikA 305 (391)
..|- ..|..++|+++|++...+-.--..-.+....++..+..-+..........+.+..+.+..-...++..
T Consensus 29 ~~G~~~~ti~~IA~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 101 (212)
T 3knw_A 29 RKGFVGVGLQEILKTSGVPKGSFYHYFESKEAFGCELLKHYISDYQIRLNQLWTTETSARDKLMNYLQCWVKD 101 (212)
T ss_dssp HHCSTTCCHHHHHHHHTCCHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHC
T ss_pred HcCCccCCHHHHHHHhCCChHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHH
Confidence 3453 58899999999999877766655555555556665555544444444333556666655555555444
No 32
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2
Probab=24.21 E-value=2.6e+02 Score=22.02 Aligned_cols=57 Identities=19% Similarity=0.236 Sum_probs=36.6
Q ss_pred hhhhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhh
Q 016321 186 PELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (391)
Q Consensus 186 pe~~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~ 260 (391)
|..-+-.+..+...-.....||+.| .+.+..+..|. +.+|+|+.+|++...+...+.
T Consensus 15 ~~~~~~~l~~l~~~~~~~~~Lt~re-~~Vl~l~~~G~-----------------s~~EIA~~L~iS~~TV~~~l~ 71 (99)
T 1p4w_A 15 PESVAKLLEKISAGGYGDKRLSPKE-SEVLRLFAEGF-----------------LVTEIAKKLNRSIKTISSQKK 71 (99)
T ss_dssp CSHHHHHHHHHHCCCCSSSSCCHHH-HHHHHHHHHTC-----------------CHHHHHHHHTSCHHHHHHHHH
T ss_pred cchhHHHHHHHccCCcccCCCCHHH-HHHHHHHHcCC-----------------CHHHHHHHHCcCHHHHHHHHH
Confidence 3333344455555555567788765 56666666665 468999999999766655444
No 33
>3pru_C Phycobilisome 32.1 kDa linker polypeptide, phycoc associated, ROD 1; structural genomics, PSI-biology; 2.68A {Synechocystis SP} PDB: 2l8v_A
Probab=24.09 E-value=2.7e+02 Score=24.68 Aligned_cols=57 Identities=16% Similarity=0.145 Sum_probs=42.0
Q ss_pred CChHHHHHHhhhhHHHHHHHHHH--cHHHHHHHHHhcccCCCC-h------hHHH-HHHHHHHHHHH
Q 016321 250 ISRPELQSILMECSLAREKLVMS--NVRLVMSIAQRYDNMGAD-M------ADLV-QGGLIGLLRGI 306 (391)
Q Consensus 250 ~s~~eL~~~l~eg~~Are~LIe~--nlpLV~~IAkkY~~~Gvd-~------eDLI-QEG~IGLikAI 306 (391)
++..++.+.|-....-++..+.. |.++|--.-+++.||... . -+++ ..|.-|++.|+
T Consensus 55 ItVReFVR~LakSe~Yr~~f~~~~~n~R~IEl~~khlLGR~p~~~~E~~~~~~i~a~~G~~a~IDsl 121 (154)
T 3pru_C 55 ISVREFVRTVAKSELYKKKFLYNNFQTRVIELNYKHLLGRAPFSEDEVIFHLDLYENQGFDADIDSY 121 (154)
T ss_dssp SCHHHHHHHHHTSHHHHHHHTTTSCHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred cCHHHHHHHHHcCHHHHHHhccCCCchHHHHHHHHHhhCCCCCCHHHHHHHHHHHHccCchhhhhHh
Confidence 57888888888888888888854 678888888999998643 2 2333 36777777775
No 34
>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=23.76 E-value=1.6e+02 Score=21.19 Aligned_cols=49 Identities=12% Similarity=0.070 Sum_probs=29.0
Q ss_pred CchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHH
Q 016321 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 297 (391)
Q Consensus 239 Ps~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQE 297 (391)
-|-+++|+.+|++...+.++.+... .-....+.+||.-| |++.++|+..
T Consensus 25 lsq~~lA~~~gis~~~i~~~e~g~~-------~~~~~~l~~ia~~l---~v~~~~l~~~ 73 (82)
T 3s8q_A 25 MTQEDLAYKSNLDRTYISGIERNSR-------NLTIKSLELIMKGL---EVSDVVFFEM 73 (82)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHTTCC-------CCBHHHHHHHHHHT---TCCHHHHHHH
T ss_pred CCHHHHHHHhCcCHHHHHHHHCCCC-------CCCHHHHHHHHHHH---CcCHHHHhcC
Confidence 3566777777777766655544321 11445556666655 5777777654
No 35
>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=23.13 E-value=3.4e+02 Score=22.90 Aligned_cols=40 Identities=10% Similarity=0.062 Sum_probs=28.2
Q ss_pred HHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 016321 231 LKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (391)
Q Consensus 231 l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LI 270 (391)
+.-.+...-+.+|+|+.+|+|...+...+..+.....+.+
T Consensus 196 l~l~~~~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l 235 (239)
T 1rp3_A 196 IQLIFYEELPAKEVAKILETSVSRVSQLKAKALERLREML 235 (239)
T ss_dssp HHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3334455678899999999999888887776555444443
No 36
>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A
Probab=23.01 E-value=1.8e+02 Score=22.57 Aligned_cols=48 Identities=13% Similarity=0.088 Sum_probs=28.5
Q ss_pred chHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHH
Q 016321 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 297 (391)
Q Consensus 240 s~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQE 297 (391)
|-+++|+.+|++...+.++.+... .-....+.+||.-| |++.++|+..
T Consensus 43 tq~elA~~~gis~~~is~iE~G~~-------~ps~~~l~~ia~~l---~v~~~~l~~~ 90 (99)
T 3g5g_A 43 TQEDLAYKSNLDRTYISGIERNSR-------NLTIKSLELIMKGL---EVSDVVFFEM 90 (99)
T ss_dssp CHHHHHHHHTCCHHHHHHHHTTCS-------CCBHHHHHHHHHHT---TCCHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCC-------CCCHHHHHHHHHHH---CcCHHHHhcc
Confidence 456777777777766655544321 11445566666665 6777777654
No 37
>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A
Probab=22.97 E-value=68 Score=29.15 Aligned_cols=90 Identities=18% Similarity=0.197 Sum_probs=53.1
Q ss_pred CchHHHHHHhcCChHHHHHHhhhhHH---------HHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhc
Q 016321 239 PSMEQLAASLRISRPELQSILMECSL---------AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKF 309 (391)
Q Consensus 239 Ps~~e~A~a~~~s~~eL~~~l~eg~~---------Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekF 309 (391)
-|-+++|+.+|+|+..+-+++..+.- .-+.+-........+++..+...+++++||++. +-..+...
T Consensus 25 ~tQ~eIA~~lGiSr~~VSR~L~~A~~~~~lv~lfp~~~~ls~p~~~~L~k~~~~l~~~~~~l~eLi~~----~~~~i~~~ 100 (192)
T 1zx4_A 25 MSQKDIAAKEGLSQAKVTRALQAASAPEELVALFPVQSELTFSDYKTLCAVGDEMGNKNLEFDQLIQN----ISPEINDI 100 (192)
T ss_dssp CCHHHHHHHHTCCHHHHHHHHHHHTSCHHHHTTCSCGGGCCHHHHHHHHHHHHHTTTCHHHHHHHHHH----HHHHHHHH
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHhccchhhHHHcCCcccCccchHHHHHHHHHHhhhcCCCHHHHHHH----HHHHHHHH
Confidence 56789999999999888777665310 002222334555667777776777888999975 33333332
Q ss_pred CCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 310 DSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 310 Dp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
.... .+...-++..|...|....
T Consensus 101 ~~~~-----~~~~~e~k~~I~~~i~~~~ 123 (192)
T 1zx4_A 101 LSIN-----EMAEDEVKNKILRLITKEA 123 (192)
T ss_dssp HHC------CCCHHHHHHHHHHHHHHHH
T ss_pred hhcc-----ccCCHHHHHHHHHHHHHHH
Confidence 1110 1224455666776665554
No 38
>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=22.84 E-value=1.9e+02 Score=20.82 Aligned_cols=48 Identities=19% Similarity=0.120 Sum_probs=30.4
Q ss_pred CchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHH
Q 016321 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296 (391)
Q Consensus 239 Ps~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQ 296 (391)
-|-+++|+.+|++...+.++.+.... -....+..+|.-| |++.++|+.
T Consensus 28 ltq~elA~~~gis~~~is~~e~g~~~-------~~~~~l~~l~~~l---~~~~~~l~~ 75 (83)
T 3f6w_A 28 ITQKELAARLGRPQSFVSKTENAERR-------LDVIEFMDFCRGI---GTDPYALLS 75 (83)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHTTSSC-------CCHHHHHHHHHHH---TCCHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHCCCCC-------CCHHHHHHHHHHc---CCCHHHHHH
Confidence 35678888888887776666554211 1344566666666 677777764
No 39
>3eup_A Transcriptional regulator, TETR family; structural genomics, MCSG, protein structure initiative, midwest center for STRU genomics; 1.99A {Cytophaga hutchinsonii}
Probab=22.74 E-value=1.6e+02 Score=23.68 Aligned_cols=70 Identities=7% Similarity=-0.083 Sum_probs=36.8
Q ss_pred CchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHh
Q 016321 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308 (391)
Q Consensus 239 Ps~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIek 308 (391)
.|..++|+++|++..-+-.--..-.+....++..+..-+..........+.+..+.+..-...++..+..
T Consensus 32 ~ti~~IA~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 101 (204)
T 3eup_A 32 TSLTDLTEATNLTKGSIYGNFENKEAVAIAAFDYNWGHVKSVLTAKVQACNTYKEMLLVYSSMYNDADGS 101 (204)
T ss_dssp CCHHHHHHHHTCCHHHHTTTSSSHHHHHHHHHHHHHHHHHHHHHHHHTTCSSHHHHHTCHHHHHHGGGGT
T ss_pred CCHHHHHHHhCCCcHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhc
Confidence 6789999999997655544333333444444444444333333333333445555555444444443333
No 40
>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=22.35 E-value=1.1e+02 Score=26.65 Aligned_cols=26 Identities=27% Similarity=0.377 Sum_probs=20.5
Q ss_pred HhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 233 ERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 233 ~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
+..|.+||..|+|+++|++...+.+.
T Consensus 19 ~~~g~~~s~~eia~~lgl~~~tv~~~ 44 (196)
T 3k2z_A 19 EKNGYPPSVREIARRFRITPRGALLH 44 (196)
T ss_dssp HHHSSCCCHHHHHHHHTSCHHHHHHH
T ss_pred HHhCCCCCHHHHHHHcCCCcHHHHHH
Confidence 35789999999999999996554443
No 41
>3qbm_A TETR transcriptional regulator; DNA/RNA-binding three-helical bundle, structural genomics, J center for structural genomics, JCSG; HET: MSE PGE; 1.80A {Chloroflexus aurantiacus}
Probab=22.23 E-value=3e+02 Score=21.93 Aligned_cols=70 Identities=7% Similarity=-0.129 Sum_probs=39.3
Q ss_pred hhCC-CCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHH
Q 016321 234 RLGC-EPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL 303 (391)
Q Consensus 234 ~~g~-ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLi 303 (391)
..|- ..|..++|+++|+|...+-.--..-.+....++..+..-+............+..+-+....-.++
T Consensus 22 ~~G~~~~t~~~IA~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ 92 (199)
T 3qbm_A 22 VSGYAGTAISDIMAATGLEKGGIYRHFESKEQLALAAFDYAAEKVRERFAVGLAGHKHTVDTIIAFLDVFR 92 (199)
T ss_dssp HHCSTTCCHHHHHHHHTCCHHHHHTTCSSHHHHHHHHHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHH
T ss_pred HhCcCcCCHHHHHHHhCCCccHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHccCccHHHHHHHHHHHHH
Confidence 4454 478999999999987665554444444555555555444444333333334455555544444433
No 42
>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}
Probab=22.12 E-value=2e+02 Score=19.98 Aligned_cols=26 Identities=15% Similarity=-0.020 Sum_probs=19.6
Q ss_pred CchHHHHHHhcCChHHHHHHhhhhHH
Q 016321 239 PSMEQLAASLRISRPELQSILMECSL 264 (391)
Q Consensus 239 Ps~~e~A~a~~~s~~eL~~~l~eg~~ 264 (391)
-+.+++|+.+|+|...+...+..+..
T Consensus 32 ~s~~eIA~~lgis~~tv~~~~~ra~~ 57 (70)
T 2o8x_A 32 LSYADAAAVCGCPVGTIRSRVARARD 57 (70)
T ss_dssp CCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35789999999998877776665433
No 43
>3nph_B Phycobilisome 32.1 kDa linker polypeptide, phycoc associated, ROD 2; PFAM00427 domain, linker protein, phycobiliprotein, photosyn; 1.85A {Synechocystis SP} PDB: 2l3w_A
Probab=21.95 E-value=3.4e+02 Score=23.94 Aligned_cols=100 Identities=18% Similarity=0.212 Sum_probs=62.6
Q ss_pred ccccCChhhhhhhHH-HHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 180 LRSMISPELIQNRLK-GYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 180 ~~~~~~pe~~~~~l~-~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
+++..+++.++..++ .|.+=+++...+..+....|-.++++|. ++..++.+.
T Consensus 6 l~~~~s~~~~~~vI~AaYrQVfgn~~~~~seR~~~lESqLrnG~---------------------------ItVReFVR~ 58 (148)
T 3nph_B 6 LRSRSTEEEVDAVILAVYRQVLGNDHLMSQERLTSAESLLRGRE---------------------------ISVRDFVRA 58 (148)
T ss_dssp BCSSSCSHHHHHHHHHHHHHHHSCSCCCTTTSCHHHHHHHHTTS---------------------------SCHHHHHHH
T ss_pred ccCCCCHHHHHHHHHHHHHHHhCCcccccccccccHHHHHhcCC---------------------------ccHHHHHHH
Confidence 444455554444443 3444444444444444455555666664 577788888
Q ss_pred hhhhHHHHHHHHHH--cHHHHHHHHHhcccCCC-Chh------HHH-HHHHHHHHHHH
Q 016321 259 LMECSLAREKLVMS--NVRLVMSIAQRYDNMGA-DMA------DLV-QGGLIGLLRGI 306 (391)
Q Consensus 259 l~eg~~Are~LIe~--nlpLV~~IAkkY~~~Gv-d~e------DLI-QEG~IGLikAI 306 (391)
|-....-++..+.. |.++|--.-+++.||.. +.. +++ ..|.-|++.|+
T Consensus 59 LakSe~Yr~~f~~~~~n~R~IEl~~khlLGRap~~q~Ei~~~~~i~a~~G~~a~IDsl 116 (148)
T 3nph_B 59 VALSEVYRQKFFHSNPQNRFIELNYKHLLGRAPYDQSEIAFHTDLYHQGGYEAEINSY 116 (148)
T ss_dssp HHTSHHHHHHHTTTSCHHHHHHHHHHHHTSSCCSSHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred HHccHHHHHHhccCCCcchHHHHHhhhhcCCCCCCHHHHHHHHHHHHhcCcHHHHHHH
Confidence 88887888888844 67888888899999854 222 333 36788887775
No 44
>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=21.81 E-value=2e+02 Score=20.87 Aligned_cols=47 Identities=19% Similarity=0.149 Sum_probs=32.0
Q ss_pred chHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHH
Q 016321 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLV 295 (391)
Q Consensus 240 s~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLI 295 (391)
+.+++|+.+|++...+.++.+.... .-....+.+||.-| |++.++|+
T Consensus 29 sq~~lA~~~gis~~~is~~E~g~~~------~p~~~~l~~ia~~l---~v~~~~l~ 75 (86)
T 2ofy_A 29 SMVTVAFDAGISVETLRKIETGRIA------TPAFFTIAAVARVL---DLSLDDVA 75 (86)
T ss_dssp CHHHHHHHHTCCHHHHHHHHTTCCS------SCBHHHHHHHHHHT---TCCHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC------CCCHHHHHHHHHHh---CCCHHHHh
Confidence 7889999999998777666554210 01344566777766 67888875
No 45
>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=21.81 E-value=2.4e+02 Score=22.20 Aligned_cols=36 Identities=11% Similarity=0.097 Sum_probs=26.4
Q ss_pred CCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHH
Q 016321 237 CEPSMEQLAASLRISRPELQSILMECSLAREKLVMS 272 (391)
Q Consensus 237 ~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~ 272 (391)
..-+.+|+|+.+|+|...+...+..+.....+.+..
T Consensus 123 ~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 158 (164)
T 3mzy_A 123 RGYSYREIATILSKNLKSIDNTIQRIRKKSEEWIKE 158 (164)
T ss_dssp TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 345789999999999988888877765555554443
No 46
>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=20.36 E-value=1e+02 Score=30.68 Aligned_cols=33 Identities=21% Similarity=0.417 Sum_probs=26.0
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhc--CChHHHHHH
Q 016321 226 DHKLRLKERLGCEPSMEQLAASLR--ISRPELQSI 258 (391)
Q Consensus 226 ~~~~~l~~~~g~ePs~~e~A~a~~--~s~~eL~~~ 258 (391)
..+.++...+|++|+.+++|..+| ++.+++..+
T Consensus 273 r~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~ 307 (423)
T 2a6h_F 273 RTARQLQQELGREPTYEEIAEAMGPGWDAKRVEET 307 (423)
T ss_dssp HHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHH
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHH
Confidence 344566678999999999999999 998776443
Done!