Query 016894
Match_columns 381
No_of_seqs 262 out of 1516
Neff 4.5
Searched_HMMs 29240
Date Mon Mar 25 05:33:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016894.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/016894hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1l9z_H Sigma factor SIGA; heli 100.0 7.9E-29 2.7E-33 251.7 14.3 158 223-380 94-282 (438)
2 3ugo_A RNA polymerase sigma fa 100.0 1.4E-28 4.7E-33 231.8 14.7 160 221-380 5-195 (245)
3 2a6h_F RNA polymerase sigma fa 100.0 1E-28 3.5E-33 248.9 11.6 159 222-380 78-267 (423)
4 3iyd_F RNA polymerase sigma fa 99.7 2E-18 6.7E-23 180.9 6.0 98 283-380 358-459 (613)
5 1sig_A Sigma70, RNA polymerase 99.7 1.4E-16 4.7E-21 154.8 12.2 87 283-369 249-339 (339)
6 1l0o_C Sigma factor; bergerat 99.4 2E-14 6.8E-19 127.9 -1.1 94 282-376 14-108 (243)
7 1rp3_A RNA polymerase sigma fa 99.4 1.4E-12 4.8E-17 116.3 9.3 75 295-369 12-89 (239)
8 1or7_A Sigma-24, RNA polymeras 99.0 4.1E-10 1.4E-14 97.9 8.2 86 283-371 10-96 (194)
9 2q1z_A RPOE, ECF SIGE; ECF sig 99.0 1.5E-10 5.3E-15 100.0 4.1 93 281-374 11-105 (184)
10 2o7g_A Probable RNA polymerase 98.7 2E-08 6.8E-13 81.4 6.9 88 284-374 12-100 (112)
11 3mzy_A RNA polymerase sigma-H 98.6 1.2E-08 4.3E-13 85.3 3.7 54 319-373 1-54 (164)
12 1h3l_A RNA polymerase sigma fa 98.5 6.1E-08 2.1E-12 75.2 4.8 76 291-368 7-83 (87)
13 2lfw_A PHYR sigma-like domain; 97.7 2E-06 6.8E-11 74.0 -2.5 69 297-367 3-71 (157)
14 3n0r_A Response regulator; sig 97.2 5.6E-05 1.9E-09 71.4 0.1 73 293-367 18-91 (286)
15 3iyd_F RNA polymerase sigma fa 49.9 6.4 0.00022 41.1 2.0 31 223-253 96-127 (613)
16 2jt1_A PEFI protein; solution 42.5 35 0.0012 26.3 4.8 35 255-289 10-44 (77)
17 3mn2_A Probable ARAC family tr 35.3 66 0.0023 24.8 5.5 38 255-292 4-41 (108)
18 3knw_A Putative transcriptiona 31.4 2.1E+02 0.0072 23.2 11.0 78 265-342 29-108 (212)
19 3lsg_A Two-component response 30.8 91 0.0031 23.8 5.5 37 256-292 5-42 (103)
20 2zc2_A DNAD-like replication p 30.4 1.1E+02 0.0036 22.9 5.7 60 261-324 9-75 (78)
21 3oou_A LIN2118 protein; protei 29.3 94 0.0032 24.0 5.4 38 255-292 7-44 (108)
22 2k9s_A Arabinose operon regula 29.2 86 0.0029 24.2 5.2 38 255-292 5-43 (107)
23 3qbm_A TETR transcriptional re 27.4 2.4E+02 0.0081 22.6 8.6 76 264-339 21-97 (199)
24 3oio_A Transcriptional regulat 27.3 67 0.0023 25.1 4.3 38 255-292 9-46 (113)
25 3nxc_A HTH-type protein SLMA; 23.9 2.2E+02 0.0076 23.1 7.1 74 262-335 37-111 (212)
26 3ppb_A Putative TETR family tr 22.1 3E+02 0.01 21.8 10.7 73 264-336 23-96 (195)
27 1bl0_A Protein (multiple antib 22.0 1.1E+02 0.0036 24.6 4.6 38 255-292 13-50 (129)
28 3mkl_A HTH-type transcriptiona 21.8 1.1E+02 0.0036 24.2 4.5 37 256-292 10-46 (120)
29 3dcf_A Transcriptional regulat 21.5 3.3E+02 0.011 22.1 10.2 76 264-339 45-121 (218)
30 3eup_A Transcriptional regulat 21.4 1.8E+02 0.006 23.5 5.9 73 268-340 30-102 (204)
31 1sgm_A Putative HTH-type trans 21.3 3.1E+02 0.01 21.7 7.7 76 265-340 21-98 (191)
32 3pas_A TETR family transcripti 20.2 3.2E+02 0.011 21.5 8.1 70 266-335 24-94 (195)
33 1sig_A Sigma70, RNA polymerase 20.1 36 0.0012 32.3 1.5 19 236-254 1-19 (339)
No 1
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1
Probab=99.96 E-value=7.9e-29 Score=251.68 Aligned_cols=158 Identities=27% Similarity=0.430 Sum_probs=135.0
Q ss_pred hHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHHHHHHH------------------HHHHhCCcCchhHHHHH-----
Q 016894 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTT------------------LEKESGKAASLNCWAQA----- 278 (381)
Q Consensus 223 ~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le~~r~~------------------L~~~~gr~ps~~ewA~a----- 278 (381)
+.++.|++.+++ ||||++||++|+++|+.+..++....+ .....++.|+..+|+..
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 446678888775 999999999999999998655433211 12235678888877432
Q ss_pred -------cCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchH
Q 016894 279 -------AGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY 351 (381)
Q Consensus 279 -------agl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTY 351 (381)
.+++..+|+..++.|..|+++||..|+++|+++|++|.++|.+++||||||+||||+|+++|||++|++|+||
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 2456688899998888899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016894 352 VQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 352 A~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
|+||||+.|.++|+++.+++|+|.|+.+.
T Consensus 254 A~~wIR~~I~~~i~~~~R~irlp~~~~~~ 282 (438)
T 1l9z_H 254 ATWWIRQAINRAIADQARTIRIPVHMVET 282 (438)
T ss_pred HHHHHHHHHHHHHHHhcchhccchHHHHH
Confidence 99999999999999999999999998653
No 2
>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*
Probab=99.96 E-value=1.4e-28 Score=231.83 Aligned_cols=160 Identities=28% Similarity=0.423 Sum_probs=127.7
Q ss_pred hhhHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHH-HHHHHH--------HHH-----------------hCCcCchh
Q 016894 221 TIFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLE-RIKTTL--------EKE-----------------SGKAASLN 273 (381)
Q Consensus 221 ~~~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le-~~r~~L--------~~~-----------------~gr~ps~~ 273 (381)
+.+.|+-|++..++ ||||++||++|+++|+.+..+. .+.... +.. .+.+|+..
T Consensus 5 ~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~ 84 (245)
T 3ugo_A 5 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTV 84 (245)
T ss_dssp CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHHH
T ss_pred CCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchhH
Confidence 45778889988886 8999999999999999987633 332110 000 13678889
Q ss_pred HHHHHcCCC----HHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccc
Q 016894 274 CWAQAAGVS----ERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFS 349 (381)
Q Consensus 274 ewA~aagl~----~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFS 349 (381)
+||.+.|++ ...|.+.++.|+.|+++|++.|.|+|+++|++|.+.+.+.+||+|||++|||+|+++|||++|++|+
T Consensus 85 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~ 164 (245)
T 3ugo_A 85 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 164 (245)
T ss_dssp HHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHH
T ss_pred HHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHH
Confidence 999998875 3456667777788999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016894 350 TYVQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 350 TYA~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
||++||||++|.++++++.+.+++|.++.+.
T Consensus 165 tya~~~ir~~i~~~ir~~~r~~r~p~~l~e~ 195 (245)
T 3ugo_A 165 TYATWWIRQAINRAIADQARTIRIPVHMVET 195 (245)
T ss_dssp HHHHHHHHHHHHHHHHHHTC-----------
T ss_pred HHHHHHHHHHHHHHHHHhcccccccHHHHHH
Confidence 9999999999999999999999999998765
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=99.95 E-value=1e-28 Score=248.86 Aligned_cols=159 Identities=28% Similarity=0.448 Sum_probs=132.5
Q ss_pred hhHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHHHHHHHH------------------HHHhCCcCchhHHH------
Q 016894 222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTL------------------EKESGKAASLNCWA------ 276 (381)
Q Consensus 222 ~~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le~~r~~L------------------~~~~gr~ps~~ewA------ 276 (381)
.+.++.|++..++ |+||++||++|++.|+.+..+....... ....++.|+..+|+
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 4567778877774 9999999999999999986544322111 11223566654432
Q ss_pred ---H---HcCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccch
Q 016894 277 ---Q---AAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFST 350 (381)
Q Consensus 277 ---~---aagl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFST 350 (381)
. +.+++..+|+..++.|..|+++||..|+++|+++|++|.++|.+++||||||++|||+|+++|||.+|++|+|
T Consensus 158 ~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~Fst 237 (423)
T 2a6h_F 158 EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST 237 (423)
T ss_dssp HHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCHHH
T ss_pred hhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHH
Confidence 1 2456778899999988889999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016894 351 YVQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 351 YA~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
||+||||++|.++|+++.++||+|.|+++.
T Consensus 238 Ya~~wIr~~i~~~i~~~~r~ir~p~~~~~~ 267 (423)
T 2a6h_F 238 YATWWIRQAINRAIADQARTIRIPVHMVET 267 (423)
T ss_dssp HHHHHHHHHHHHHHHHHSSSSCCCHHHHHH
T ss_pred HHHHHHHHHHHHHHHHccceeeccHHHHHH
Confidence 999999999999999999999999998653
No 4
>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=99.72 E-value=2e-18 Score=180.87 Aligned_cols=98 Identities=35% Similarity=0.761 Sum_probs=93.0
Q ss_pred HHHHHHHHHhcHH-H---HHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHH
Q 016894 283 ERVLKQHLAFGWY-C---REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (381)
Q Consensus 283 ~eeL~~~l~~G~~-A---re~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~ 358 (381)
..+|+.+++.|+. | +++|++.|.++|+++|++|.+++.+++||+|||++|||+|+++||+.+|++|+||++|||++
T Consensus 358 ~~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~irn 437 (613)
T 3iyd_F 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437 (613)
T ss_dssp HHHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHHH
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHHH
Confidence 5678888999986 5 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCCccCCCccccc
Q 016894 359 SISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 359 aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
+|.++++++.+.+|+|.|+++.
T Consensus 438 ~i~~~lr~~~r~~rip~~~~~~ 459 (613)
T 3iyd_F 438 AITRSIADQARTIRIPVHMIET 459 (613)
T ss_dssp HHHHHTTTSCSSSCCCSHHHHT
T ss_pred HHHHHHHhcCcceeCcHHHHHH
Confidence 9999999999999999998654
No 5
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1
Probab=99.68 E-value=1.4e-16 Score=154.77 Aligned_cols=87 Identities=34% Similarity=0.782 Sum_probs=80.1
Q ss_pred HHHHHHHHHhcH----HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHH
Q 016894 283 ERVLKQHLAFGW----YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (381)
Q Consensus 283 ~eeL~~~l~~G~----~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~ 358 (381)
...|+.+++.|+ .|+++|+..|.|+|+++|++|.+++.+++||+|||++|||+|+++||+.+|++|+||++|||++
T Consensus 249 ~~~l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn 328 (339)
T 1sig_A 249 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 328 (339)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHH
T ss_pred HHHHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHH
Confidence 356788888887 4899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCC
Q 016894 359 SISKMVARHAR 369 (381)
Q Consensus 359 aI~~~Ir~qsr 369 (381)
.|.++++++.+
T Consensus 329 ~~~~~lr~~~r 339 (339)
T 1sig_A 329 AITRSIADQAR 339 (339)
T ss_dssp HHHHHHHHC--
T ss_pred HHHHHHHHhcC
Confidence 99999998753
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=99.39 E-value=2e-14 Score=127.94 Aligned_cols=94 Identities=26% Similarity=0.393 Sum_probs=5.8
Q ss_pred CHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016894 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 282 ~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+..+|+..++.|+. |++.|+..|.++|..+|.+|.+...+.+|++|||+++||+++++||+.+|.+|.||++++|++.+
T Consensus 14 ~~~~l~~~~~~gd~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~ 93 (243)
T 1l0o_C 14 EMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEI 93 (243)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHH
Confidence 35678888888876 99999999999999999999988899999999999999999999999998999999999999999
Q ss_pred HHHHHHcCCCccCCCc
Q 016894 361 SKMVARHARGIKIPVP 376 (381)
Q Consensus 361 ~~~Ir~qsr~IRlP~~ 376 (381)
.++++++. .+++|.+
T Consensus 94 ~d~~r~~~-~~~~~~~ 108 (243)
T 1l0o_C 94 QRFLRDDG-TVKVSRS 108 (243)
T ss_dssp ------CC-CCTTHHH
T ss_pred HHHHHhcC-CccCcHH
Confidence 99999876 6677653
No 7
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A
Probab=99.37 E-value=1.4e-12 Score=116.27 Aligned_cols=75 Identities=23% Similarity=0.353 Sum_probs=71.1
Q ss_pred HHHHHHHHHhhHHHHHHHHHcc---CCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016894 295 YCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~---~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
.++++|+..|.++|..+|++|. +.+.+.+|++|+|+++||+++++||+.+|.+|.||+++||++.|.++++++.+
T Consensus 12 ~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~~ 89 (239)
T 1rp3_A 12 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLDF 89 (239)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSST
T ss_pred hHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcCc
Confidence 4899999999999999999998 56899999999999999999999999999999999999999999999998754
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=99.04 E-value=4.1e-10 Score=97.90 Aligned_cols=86 Identities=15% Similarity=0.161 Sum_probs=78.7
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH
Q 016894 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~ 361 (381)
+.+|+..++.|+. |.+.|+..|.+.|..+|.+|.+ ..+.+|++|++++.+|+++++|++.. .|.+|++..+++.+.
T Consensus 10 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~~ 86 (194)
T 1or7_A 10 DQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTAK 86 (194)
T ss_dssp HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHH
Confidence 5678888888876 9999999999999999999999 89999999999999999999999864 499999999999999
Q ss_pred HHHHHcCCCc
Q 016894 362 KMVARHARGI 371 (381)
Q Consensus 362 ~~Ir~qsr~I 371 (381)
+.++++.+..
T Consensus 87 d~~R~~~~~~ 96 (194)
T 1or7_A 87 NYLVAQGRRP 96 (194)
T ss_dssp HHHHHHTTCC
T ss_pred HHHHHHhccC
Confidence 9999876543
No 9
>2q1z_A RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc bindin transcription factor; 2.40A {Rhodobacter sphaeroides} PDB: 2z2s_A
Probab=99.00 E-value=1.5e-10 Score=99.99 Aligned_cols=93 Identities=15% Similarity=0.019 Sum_probs=83.4
Q ss_pred CCHHHHHHH-HHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHH
Q 016894 281 VSERVLKQH-LAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (381)
Q Consensus 281 l~~eeL~~~-l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~ 358 (381)
++.++|+.. ++.|+. |.+.|+..|.+.|..+|.++.+...+.+|++||+++.+|+++++|++..| .|.+|++..+++
T Consensus 11 ~~~~~li~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~~-~~~~wl~~i~~n 89 (184)
T 2q1z_A 11 TDWVALMRAIRDHRDEAAFAELFQHFAPKVKGFLMKSGSVASQAEECAQDVMATVWQKAHLFDPSRA-SVATWIFTIARN 89 (184)
T ss_dssp TCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHSGGGCCTTTC-CHHHHHHHHHHT
T ss_pred ccHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhhcCcccC-cHHHHHHHHHHH
Confidence 567888888 888876 99999999999999999999988889999999999999999999999876 799999999999
Q ss_pred HHHHHHHHcCCCccCC
Q 016894 359 SISKMVARHARGIKIP 374 (381)
Q Consensus 359 aI~~~Ir~qsr~IRlP 374 (381)
.+.+.++++.+...++
T Consensus 90 ~~~d~~R~~~~~~~~~ 105 (184)
T 2q1z_A 90 RRIDGLRKDRQPEPED 105 (184)
T ss_dssp SCCTTTCSSSCCCCCC
T ss_pred HHHHHHHhhccccccc
Confidence 9999999876554443
No 10
>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}
Probab=98.72 E-value=2e-08 Score=81.43 Aligned_cols=88 Identities=17% Similarity=0.081 Sum_probs=71.9
Q ss_pred HHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHH
Q 016894 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (381)
Q Consensus 284 eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~ 362 (381)
.+|+..++.|+. +.+.|+..|.+.|..+|.++ +...+.+|++||.++.+|+.+.+|++. ..|.+|++..+++.+.+
T Consensus 12 ~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d 88 (112)
T 2o7g_A 12 TALALSAAKGNGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVAD 88 (112)
T ss_dssp HHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCS--SCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHH
Confidence 367778888875 99999999999999999999 777899999999999999999999974 36999999999999999
Q ss_pred HHHHcCCCccCC
Q 016894 363 MVARHARGIKIP 374 (381)
Q Consensus 363 ~Ir~qsr~IRlP 374 (381)
.+|++.+...+|
T Consensus 89 ~~R~~~~~~~~~ 100 (112)
T 2o7g_A 89 HIRHVRSRPRTT 100 (112)
T ss_dssp HTC---------
T ss_pred HHHHhhcccccc
Confidence 999876554443
No 11
>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=98.65 E-value=1.2e-08 Score=85.33 Aligned_cols=54 Identities=24% Similarity=0.458 Sum_probs=44.5
Q ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccC
Q 016894 319 GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (381)
Q Consensus 319 g~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRl 373 (381)
|++.+|++|+|+++||+++.+||+.+ .+|.||++.+|++.+.++++++.+..+.
T Consensus 1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~ 54 (164)
T 3mzy_A 1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHM 54 (164)
T ss_dssp ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC--
T ss_pred CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccch
Confidence 67899999999999999999999988 6899999999999999999987544333
No 12
>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1
Probab=98.54 E-value=6.1e-08 Score=75.18 Aligned_cols=76 Identities=8% Similarity=-0.039 Sum_probs=66.7
Q ss_pred HhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016894 291 AFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 291 ~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
..|+. +.++|+..|.+.+..+|.++.+...+.||++||.++.+++.+..|++. ..|.+|++..+++.+.+.++++.
T Consensus 7 ~~g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~ 83 (87)
T 1h3l_A 7 TAERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQ 83 (87)
T ss_dssp HHHHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC---
T ss_pred CcccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhc
Confidence 34554 999999999999999999999888899999999999999999999975 47999999999999999988754
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=97.70 E-value=2e-06 Score=73.95 Aligned_cols=69 Identities=9% Similarity=0.024 Sum_probs=62.8
Q ss_pred HHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHc
Q 016894 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (381)
Q Consensus 297 re~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~q 367 (381)
++.|+..|.+.|..+|.++.+...+.+|++||+++.+|+++++|++.. .|.+|++..+++.+.+.+|+.
T Consensus 3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~ 71 (157)
T 2lfw_A 3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADG 71 (157)
T ss_dssp GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTT
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhcc
Confidence 457889999999999999988888999999999999999999999763 599999999999999999875
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=97.19 E-value=5.6e-05 Score=71.38 Aligned_cols=73 Identities=11% Similarity=-0.036 Sum_probs=64.0
Q ss_pred cHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHc
Q 016894 293 GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (381)
Q Consensus 293 G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~q 367 (381)
|+. ++++|+..|.+.++.+|.+|.+...+.+|++||.++-+|+...+|++. ..|.+|.+...++.+.+.+|+.
T Consensus 18 g~~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~~ 91 (286)
T 3n0r_A 18 GSEMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQL 91 (286)
T ss_dssp --CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC--
T ss_pred CCcCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhcccc
Confidence 443 899999999999999999999888899999999999999999999974 3699999999999999888753
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=49.89 E-value=6.4 Score=41.11 Aligned_cols=31 Identities=13% Similarity=0.134 Sum_probs=13.6
Q ss_pred hHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHH
Q 016894 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVA 253 (381)
Q Consensus 223 ~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~ 253 (381)
++|+=|++..|+ ||||.++|++|++.|+.+.
T Consensus 96 dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~ 127 (613)
T 3iyd_F 96 DPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127 (613)
T ss_dssp ---------C--------CSSSTTTHHHHHHH
T ss_pred CcHHHHHHHhcccccCCchhHHHHHHHHHHhH
Confidence 345667766665 8999999999999999875
No 16
>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}
Probab=42.54 E-value=35 Score=26.35 Aligned_cols=35 Identities=17% Similarity=0.193 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHH
Q 016894 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (381)
Q Consensus 255 Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~ 289 (381)
|+-++..+++..|.+||..+.|++.|++...+.+-
T Consensus 10 L~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~ 44 (77)
T 2jt1_A 10 ISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLY 44 (77)
T ss_dssp HHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHH
T ss_pred HHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHH
Confidence 44455556555689999999999999987665443
No 17
>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}
Probab=35.29 E-value=66 Score=24.83 Aligned_cols=38 Identities=11% Similarity=0.196 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHh
Q 016894 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (381)
Q Consensus 255 Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~ 292 (381)
++++..-+.......++..++|+..|++...|.+.++.
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 44556667777788899999999999999998887765
No 18
>3knw_A Putative transcriptional regulator (TETR/ACRR FAM; TETR-like protein, MCSG, PSI, structural genomics, protein S initiative; 2.45A {Acinetobacter SP}
Probab=31.38 E-value=2.1e+02 Score=23.22 Aligned_cols=78 Identities=13% Similarity=-0.028 Sum_probs=49.0
Q ss_pred HhC-CcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHH-HhhcCC
Q 016894 265 ESG-KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQG-AERFDH 342 (381)
Q Consensus 265 ~~g-r~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikA-vekFDp 342 (381)
+.| ...|..+.|+++|++...+-.-...-++....++..+..-+..........+.+..+.+......++.. +...++
T Consensus 29 ~~G~~~~ti~~IA~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 108 (212)
T 3knw_A 29 RKGFVGVGLQEILKTSGVPKGSFYHYFESKEAFGCELLKHYISDYQIRLNQLWTTETSARDKLMNYLQCWVKDPATEQSW 108 (212)
T ss_dssp HHCSTTCCHHHHHHHHTCCHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHC-------
T ss_pred HcCCccCCHHHHHHHhCCChHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHHhhccc
Confidence 346 578999999999999998887776555556666666555555544444344667777766666666555 443343
No 19
>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}
Probab=30.76 E-value=91 Score=23.80 Aligned_cols=37 Identities=16% Similarity=0.163 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhCC-cCchhHHHHHcCCCHHHHHHHHHh
Q 016894 256 ERIKTTLEKESGK-AASLNCWAQAAGVSERVLKQHLAF 292 (381)
Q Consensus 256 e~~r~~L~~~~gr-~ps~~ewA~aagl~~eeL~~~l~~ 292 (381)
+++..-+++.... .++..++|+..|++...|.+.++.
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 4455556666666 889999999999999999887765
No 20
>2zc2_A DNAD-like replication protein; GI 24377835, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Streptococcus mutans UA159}
Probab=30.35 E-value=1.1e+02 Score=22.93 Aligned_cols=60 Identities=18% Similarity=0.180 Sum_probs=39.6
Q ss_pred HHHHHhCCcCch------hHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCC-CHHH
Q 016894 261 TLEKESGKAASL------NCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGI-PFSD 324 (381)
Q Consensus 261 ~L~~~~gr~ps~------~ewA~aagl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~-d~ED 324 (381)
..+...|+.|+. ..|-...|++.+.+..+++.. .. -=..+.++|.+|++.+...|+ +.+|
T Consensus 9 ~~e~~~gr~ls~~e~~~i~~w~~~~~~~~elI~~A~~~a---~~-~~~~s~~Yi~~Il~~W~~~gi~T~e~ 75 (78)
T 2zc2_A 9 DFERELGRMLSPFELEDLQKTVSDDKTDPDLVRSALREA---VF-NGKTNWNYIQAILRNWRHEGISTLRQ 75 (78)
T ss_dssp HHHHHHTSCCCHHHHHHHHHHHTTTCCCHHHHHHHHHHH---HH-HTCCCHHHHHHHHHHHHHTTCCSHHH
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHH---HH-cCCCCHHHHHHHHHHHHHcCCCCHHH
Confidence 344556887775 457767778877776665432 21 113568999999999988876 4444
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=29.27 E-value=94 Score=24.00 Aligned_cols=38 Identities=11% Similarity=0.128 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHh
Q 016894 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (381)
Q Consensus 255 Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~ 292 (381)
+.++..-+.......++..+.|+..|++...|.+.++.
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 34455566677788899999999999999998887765
No 22
>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}
Probab=29.18 E-value=86 Score=24.17 Aligned_cols=38 Identities=11% Similarity=0.031 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhC-CcCchhHHHHHcCCCHHHHHHHHHh
Q 016894 255 LERIKTTLEKESG-KAASLNCWAQAAGVSERVLKQHLAF 292 (381)
Q Consensus 255 Le~~r~~L~~~~g-r~ps~~ewA~aagl~~eeL~~~l~~ 292 (381)
+.++...+..... ..++.+++|+..|++...|.+.++.
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 4455566667777 7899999999999999999888775
No 23
>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=27.43 E-value=2.4e+02 Score=22.55 Aligned_cols=76 Identities=14% Similarity=-0.102 Sum_probs=47.9
Q ss_pred HHhC-CcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhh
Q 016894 264 KESG-KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAER 339 (381)
Q Consensus 264 ~~~g-r~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvek 339 (381)
.+.| ...|..+.|+++|++...+-.-...-++....++.....-+............+..+.+....-.++..+..
T Consensus 21 ~~~G~~~~t~~~IA~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 97 (199)
T 3qbm_A 21 NVSGYAGTAISDIMAATGLEKGGIYRHFESKEQLALAAFDYAAEKVRERFAVGLAGHKHTVDTIIAFLDVFRSYAER 97 (199)
T ss_dssp HHHCSTTCCHHHHHHHHTCCHHHHHTTCSSHHHHHHHHHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHGGGTC
T ss_pred HHhCcCcCCHHHHHHHhCCCccHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHccCccHHHHHHHHHHHHHHHhhh
Confidence 3446 568999999999999888877665544455666666555554444444444456666666555555444433
No 24
>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}
Probab=27.31 E-value=67 Score=25.08 Aligned_cols=38 Identities=24% Similarity=0.203 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHh
Q 016894 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (381)
Q Consensus 255 Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~ 292 (381)
+.++..-+.+.....++..++|+.+|++...|.+.++.
T Consensus 9 i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 46 (113)
T 3oio_A 9 LTEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQ 46 (113)
T ss_dssp HHHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44455566666778899999999999999998887765
No 25
>3nxc_A HTH-type protein SLMA; nucleoid occlusion, cell division, TETR family member, DNA B protein; 2.50A {Escherichia coli}
Probab=23.90 E-value=2.2e+02 Score=23.08 Aligned_cols=74 Identities=19% Similarity=0.077 Sum_probs=34.9
Q ss_pred HHHHhC-CcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHH
Q 016894 262 LEKESG-KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQ 335 (381)
Q Consensus 262 L~~~~g-r~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLik 335 (381)
|..+.| ...|..+.|+++|++...+-.-...-++....++.....-+..........+.+..+.+..-...++.
T Consensus 37 lf~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 111 (212)
T 3nxc_A 37 LESSDGSQRITTAKLAASVGVSEAALYRHFPSKTRMFDSLIEFIEDSLITRINLILKDEKDTTARLRLIVLLLLG 111 (212)
T ss_dssp HHC------CCHHHHHHHTTSCHHHHHTTCSSHHHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHH
T ss_pred HHhcCChhhcCHHHHHHHhCCChhHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHH
Confidence 433346 67899999999999877665544433333344443333333322222222223444444444444433
No 26
>3ppb_A Putative TETR family transcription regulator; DNA-binding, helix-turn-helix motif, HTH motif, DNA/RNA-BIND helical bundle fold; HET: MSE PG4; 2.10A {Shewanella loihica}
Probab=22.07 E-value=3e+02 Score=21.79 Aligned_cols=73 Identities=15% Similarity=0.004 Sum_probs=48.9
Q ss_pred HHhC-CcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHH
Q 016894 264 KESG-KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQG 336 (381)
Q Consensus 264 ~~~g-r~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikA 336 (381)
.+.| ...|..+.|+.+|++...+-.-...-++....++.....-+..........+.+..+.+......++..
T Consensus 23 ~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 96 (195)
T 3ppb_A 23 VSQGFHGTSTATIAREAGVATGTLFHHFPSKEQLLEQLFLGVKQEFADAIQASVSSRGDLKQDAEQLWFAALTW 96 (195)
T ss_dssp HHTCSTTSCHHHHHHHHTCCHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHTCCCCSCHHHHHHHHHHHHHHH
T ss_pred HhcCcccCCHHHHHHHhCCChhHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHHHHHHHHH
Confidence 3446 678899999999999988877766544566666666666555555555455566666666555554443
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=21.97 E-value=1.1e+02 Score=24.61 Aligned_cols=38 Identities=18% Similarity=0.176 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHh
Q 016894 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (381)
Q Consensus 255 Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~ 292 (381)
+.++..-+.......++.+++|+..|++...|.+.++.
T Consensus 13 i~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 50 (129)
T 1bl0_A 13 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 50 (129)
T ss_dssp HHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHH
T ss_pred HHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 45556666677778899999999999999999888775
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=21.80 E-value=1.1e+02 Score=24.20 Aligned_cols=37 Identities=22% Similarity=0.186 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHh
Q 016894 256 ERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (381)
Q Consensus 256 e~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~ 292 (381)
.++..-+.......++..++|+.+|++...|.+.++.
T Consensus 10 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~ 46 (120)
T 3mkl_A 10 TRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLRE 46 (120)
T ss_dssp HHHHHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred HHHHHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4455556666677889999999999999888877755
No 29
>3dcf_A Transcriptional regulator of the TETR/ACRR family; YP_290855.1, structural genomics, joint center for structural genomics, JCSG; 2.50A {Thermobifida fusca YX}
Probab=21.48 E-value=3.3e+02 Score=22.06 Aligned_cols=76 Identities=16% Similarity=-0.024 Sum_probs=47.0
Q ss_pred HHhC-CcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhh
Q 016894 264 KESG-KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAER 339 (381)
Q Consensus 264 ~~~g-r~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvek 339 (381)
.+.| ...|..+.|+.+|++...+-.-...-++....++.....-+..........+.+..+-+...+..++..+..
T Consensus 45 ~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~sK~~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 121 (218)
T 3dcf_A 45 REKGYYATSLDDIADRIGFTKPAIYYYFKSKEDVLFAIVNSIVDEALERFHAIAAGPGSPGERIHALLVEHTRTILR 121 (218)
T ss_dssp HHTCTTTCCHHHHHHHHTCCHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHHHTSSSCHHHHHHHHHHHHHHHHHH
T ss_pred HHcCcccCcHHHHHHHhCCCHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHc
Confidence 3446 568999999999999988877666544455555555544444444443344556666555555555554443
No 30
>3eup_A Transcriptional regulator, TETR family; structural genomics, MCSG, protein structure initiative, midwest center for STRU genomics; 1.99A {Cytophaga hutchinsonii}
Probab=21.37 E-value=1.8e+02 Score=23.47 Aligned_cols=73 Identities=7% Similarity=-0.063 Sum_probs=43.3
Q ss_pred CcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhc
Q 016894 268 KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERF 340 (381)
Q Consensus 268 r~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekF 340 (381)
...|..+.|+++|++...+-.-...-+.....++.....-+..........+.+..+.+..-...++..+...
T Consensus 30 ~~~ti~~IA~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 102 (204)
T 3eup_A 30 AGTSLTDLTEATNLTKGSIYGNFENKEAVAIAAFDYNWGHVKSVLTAKVQACNTYKEMLLVYSSMYNDADGSL 102 (204)
T ss_dssp HHCCHHHHHHHHTCCHHHHTTTSSSHHHHHHHHHHHHHHHHHHHHHHHHTTCSSHHHHHTCHHHHHHGGGGTT
T ss_pred ccCCHHHHHHHhCCCcHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhcc
Confidence 3568899999999998777665554444555555555544444444433344566666555555555544443
No 31
>1sgm_A Putative HTH-type transcriptional regulator YXAF; structural genomics, PSI, protein structure initiative; 2.00A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1
Probab=21.30 E-value=3.1e+02 Score=21.68 Aligned_cols=76 Identities=14% Similarity=0.009 Sum_probs=44.6
Q ss_pred HhC-CcCchhHHHHHcCCCHHHHHHHHHh-cHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhc
Q 016894 265 ESG-KAASLNCWAQAAGVSERVLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERF 340 (381)
Q Consensus 265 ~~g-r~ps~~ewA~aagl~~eeL~~~l~~-G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekF 340 (381)
+.| ...|..+.|+++|++...+-.-... -+.....++.....-+............+..+-+....-.++..+...
T Consensus 21 ~~G~~~~t~~~Ia~~agvs~~t~Y~~F~~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 98 (191)
T 1sgm_A 21 LQGYHATGLNQIVKESGAPKGSLYHFFPNGKEELAIEAVTYTGKIVEHLIQQSMDESSDPVEAIQLFIKKTASQFDNT 98 (191)
T ss_dssp HHCTTTCCHHHHHHHHCCCSCHHHHSTTTCHHHHHHHHHHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHTTSSG
T ss_pred HcCccccCHHHHHHHHCCCchhHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHhcccc
Confidence 346 5689999999999998888777764 444445555544444333333222233455666655555555544433
No 32
>3pas_A TETR family transcription regulator; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.90A {Marinobacter aquaeolei}
Probab=20.24 E-value=3.2e+02 Score=21.55 Aligned_cols=70 Identities=19% Similarity=0.016 Sum_probs=39.5
Q ss_pred hC-CcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHH
Q 016894 266 SG-KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQ 335 (381)
Q Consensus 266 ~g-r~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLik 335 (381)
.| ...|..+.|+++|++...+-.-...-+.....++.....-+..........+.+..+.+..-...++.
T Consensus 24 ~G~~~~t~~~Ia~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 94 (195)
T 3pas_A 24 HGFSATSVGKIAKAAGLSPATLYIYYEDKEQLLLATFYYVSDQVIDAALDSFSRGKDLREGLRRQWHTLFR 94 (195)
T ss_dssp HHHHHCCHHHHHHHHTSCHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHH
T ss_pred cChHhcCHHHHHHHhCCCchHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 35 45789999999999988887766654444555554444433333322222344544444444433333
No 33
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1
Probab=20.09 E-value=36 Score=32.32 Aligned_cols=19 Identities=16% Similarity=0.141 Sum_probs=14.4
Q ss_pred CCCcHHHHHHHHHhHHHHH
Q 016894 236 LTIARNEAEMSKGVQVVAN 254 (381)
Q Consensus 236 lLtaeEE~eL~~~iq~~~~ 254 (381)
|||.|.|++++++|+.+..
T Consensus 1 LLTREgEI~IAKRIE~G~~ 19 (339)
T 1sig_A 1 GSHMEGEIDIAKRIEDGIN 19 (339)
T ss_dssp ---CCTHHHHHHHHHHHHH
T ss_pred CCChHHHHHHHHHHHHHHH
Confidence 7999999999999998654
Done!