BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 046578
(379 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|Y Chain Y, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 613
Score = 153 bits (386), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 81/242 (33%), Positives = 132/242 (54%)
Query: 137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLST 196
K R +++ ++ + LV+SIA Y +GL DLIQEG+IGL++ +F RGYK ST
Sbjct: 370 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 429
Query: 197 YVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNI 256
Y WWI+QAI R+IA+++RTIR+P M + K+ + + + + R PT E+AE + +
Sbjct: 430 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 489
Query: 257 HVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXXXX 316
+R ++ + PIS++ + D + D I +P
Sbjct: 490 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLA 549
Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKV 376
L+ REA +LR+ FG+D T + +E+G+ ++RERIRQI AL KL+ + L+
Sbjct: 550 GLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609
Query: 377 YM 378
++
Sbjct: 610 FL 611
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 152 bits (384), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 81/242 (33%), Positives = 132/242 (54%)
Query: 137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLST 196
K R +++ ++ + LV+SIA Y +GL DLIQEG+IGL++ +F RGYK ST
Sbjct: 370 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 429
Query: 197 YVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNI 256
Y WWI+QAI R+IA+++RTIR+P M + K+ + + + + R PT E+AE + +
Sbjct: 430 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 489
Query: 257 HVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXXXX 316
+R ++ + PIS++ + D + D I +P
Sbjct: 490 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLA 549
Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKV 376
L+ REA +LR+ FG+D T + +E+G+ ++RERIRQI AL KL+ + L+
Sbjct: 550 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609
Query: 377 YM 378
++
Sbjct: 610 FL 611
>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|Q Chain Q, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
Length = 332
Score = 143 bits (360), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 89/244 (36%), Positives = 131/244 (53%), Gaps = 3/244 (1%)
Query: 126 LDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAK 184
L L +Y + +E E+ ++ +I + LVVSIA Y G+GLS DLIQEG+ GL+R +
Sbjct: 75 LPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE 134
Query: 185 RFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRM 244
+F +R +K STY WWI+QAI RAIA+++RTIR+P M + K++ L + L R
Sbjct: 135 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 194
Query: 245 PTDSEIAEMLNIHVSTVRL--AIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV 302
P+ EIAE + R+ ++ + P+SL+ + D D IP + P
Sbjct: 195 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAA 254
Query: 303 XXXXXXXXXXXXXXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362
LSEREA +L+L GL + +E+G ++RERIRQI AL
Sbjct: 255 AQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKAL 314
Query: 363 TKLQ 366
KL+
Sbjct: 315 RKLK 318
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 142 bits (358), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 91/245 (37%), Positives = 134/245 (54%), Gaps = 5/245 (2%)
Query: 126 LDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAK 184
L L +Y + +E E+ ++ +I + LVVSIA Y G+GLS DLIQEG+ GL+R +
Sbjct: 181 LPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE 240
Query: 185 RFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRM 244
+F +R +K STY WWI+QAI RAIA+++RTIR+P M + K++ L + L R
Sbjct: 241 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 300
Query: 245 PTDSEIAEMLNIHVSTVRL--AIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV 302
P+ EIAE + R+ ++ + P+SL+ + D D IP + P
Sbjct: 301 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAA 360
Query: 303 XXXXXXXXXXXXXXTLSEREADILRLHFGL-DGQTPVSCKEIGRLLSLSRERIRQIRGIA 361
LSEREA +L+L GL DG+ + +E+G ++RERIRQI A
Sbjct: 361 AQSLLSEELEKALSKLSEREAMVLKLRKGLIDGRE-HTLEEVGAYFGVTRERIRQIENKA 419
Query: 362 LTKLQ 366
L KL+
Sbjct: 420 LRKLK 424
>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
Length = 423
Score = 142 bits (357), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 92/253 (36%), Positives = 137/253 (54%), Gaps = 7/253 (2%)
Query: 119 LDKENGELDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSI 177
+D++ L +Y + +E E+ ++ +I + LVVSIA Y G+GLS DLIQEG+
Sbjct: 159 IDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 218
Query: 178 GLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVL 237
GL+R ++F +R +K STY WWI+QAI RAIA+++RTIR+P M + K++ L
Sbjct: 219 GLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQL 278
Query: 238 SRRLRRMPTDSEIAEMLNIHVSTVRL--AIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295
+ L R PT EIAE + R+ ++ + P+SL+ + D D I PDE
Sbjct: 279 QQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFI--PDE 336
Query: 296 TMPERM--VXXXXXXXXXXXXXXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRER 353
+P + LSEREA +L+L GL + +E+G ++RER
Sbjct: 337 HLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRER 396
Query: 354 IRQIRGIALTKLQ 366
IRQI AL KL+
Sbjct: 397 IRQIENKALRKLK 409
>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|P Chain P, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|F Chain F, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|P Chain P, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|F Chain F, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|P Chain P, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|3EQL|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
Length = 423
Score = 142 bits (357), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 92/253 (36%), Positives = 137/253 (54%), Gaps = 7/253 (2%)
Query: 119 LDKENGELDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSI 177
+D++ L +Y + +E E+ ++ +I + LVVSIA Y G+GLS DLIQEG+
Sbjct: 159 IDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 218
Query: 178 GLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVL 237
GL+R ++F +R +K STY WWI+QAI RAIA+++RTIR+P M + K++ L
Sbjct: 219 GLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQL 278
Query: 238 SRRLRRMPTDSEIAEMLNIHVSTVRL--AIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295
+ L R PT EIAE + R+ ++ + P+SL+ + D D I PDE
Sbjct: 279 QQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFI--PDE 336
Query: 296 TMPERM--VXXXXXXXXXXXXXXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRER 353
+P + LSEREA +L+L GL + +E+G ++RER
Sbjct: 337 HLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRER 396
Query: 354 IRQIRGIALTKLQ 366
IRQI AL KL+
Sbjct: 397 IRQIENKALRKLK 409
>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 443
Score = 141 bits (356), Expect = 5e-34, Method: Compositional matrix adjust.
Identities = 92/253 (36%), Positives = 137/253 (54%), Gaps = 7/253 (2%)
Query: 119 LDKENGELDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSI 177
+D++ L +Y + +E E+ ++ +I + LVVSIA Y G+GLS DLIQEG+
Sbjct: 179 IDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 238
Query: 178 GLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVL 237
GL+R ++F +R +K STY WWI+QAI RAIA+++RTIR+P M + K++ L
Sbjct: 239 GLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQL 298
Query: 238 SRRLRRMPTDSEIAEMLNIHVSTVRL--AIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295
+ L R PT EIAE + R+ ++ + P+SL+ + D D I PDE
Sbjct: 299 QQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFI--PDE 356
Query: 296 TMPERM--VXXXXXXXXXXXXXXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRER 353
+P + LSEREA +L+L GL + +E+G ++RER
Sbjct: 357 HLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRER 416
Query: 354 IRQIRGIALTKLQ 366
IRQI AL KL+
Sbjct: 417 IRQIENKALRKLK 429
>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
Length = 241
Score = 107 bits (267), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 61/152 (40%), Positives = 92/152 (60%), Gaps = 3/152 (1%)
Query: 126 LDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAK 184
L L +Y + +E E+ ++ +I + LVVSIA Y G+GLS DLIQEG+ GL+R +
Sbjct: 90 LPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE 149
Query: 185 RFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRM 244
+F +R +K STY WWI+QAI RAIA+++RTIR+P M + K++ L + L R
Sbjct: 150 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 209
Query: 245 PTDSEIAEMLNIHVSTVRL--AIERTRHPISL 274
P+ EIAE + R+ ++ + P+SL
Sbjct: 210 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241
>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tacaat)
pdb|3UGP|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tataat)
pdb|4GOR|A Chain A, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
pdb|4GOR|B Chain B, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
Length = 245
Score = 107 bits (267), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 61/152 (40%), Positives = 92/152 (60%), Gaps = 3/152 (1%)
Query: 126 LDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAK 184
L L +Y + +E E+ ++ +I + LVVSIA Y G+GLS DLIQEG+ GL+R +
Sbjct: 94 LPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE 153
Query: 185 RFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRM 244
+F +R +K STY WWI+QAI RAIA+++RTIR+P M + K++ L + L R
Sbjct: 154 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 213
Query: 245 PTDSEIAEMLNIHVSTVRL--AIERTRHPISL 274
P+ EIAE + R+ ++ + P+SL
Sbjct: 214 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 245
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 85.5 bits (210), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 37/79 (46%), Positives = 54/79 (68%)
Query: 137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLST 196
K R +++ ++ + LV+SIA Y +GL DLIQEG+IGL++ +F RGYK ST
Sbjct: 261 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 320
Query: 197 YVYWWIKQAIIRAIANKSR 215
Y WWI+QAI R+IA+++R
Sbjct: 321 YATWWIRQAITRSIADQAR 339
>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2
pdb|3LES|B Chain B, 2f5 Epitope Scaffold Es2
pdb|3LEV|A Chain A, Hiv-1 Antibody 2f5 In Complex With Epitope Scaffold Es2
Length = 179
Score = 84.3 bits (207), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 43/91 (47%), Positives = 62/91 (68%), Gaps = 1/91 (1%)
Query: 126 LDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAK 184
L L +Y + +E E+ ++ +I + LVVSIA Y G+GLS DLIQEG+ GL+R +
Sbjct: 89 LPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE 148
Query: 185 RFNPERGYKLSTYVYWWIKQAIIRAIANKSR 215
+F +RG+ STY WWI+QAI RAIA+++R
Sbjct: 149 KFEYKRGFAFSTYATWWIRQAINRAIADQAR 179
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 68.6 bits (166), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 53/160 (33%), Positives = 78/160 (48%), Gaps = 3/160 (1%)
Query: 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
++E+++ II LV S+ + +G DL Q G IGLL+ +F+ K STY
Sbjct: 26 DQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYA 85
Query: 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
I I R + + T+++ S+ M KI +A + LS+ R PT +EIA+ L I
Sbjct: 86 VPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISP 144
Query: 259 STVRLAIERTRHPISLDGAV--TDRGCMTMQDIIPGPDET 296
V LA E R P S+ V D +T+ D I DE
Sbjct: 145 EDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEA 184
>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|C Chain C, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|E Chain E, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|G Chain G, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1SC5|A Chain A, Sigma-28(Flia)FLGM COMPLEX
Length = 239
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 60/233 (25%), Positives = 104/233 (44%), Gaps = 21/233 (9%)
Query: 143 QERIIRSYRSLVVSIATGYQG---KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
+E +I Y LV +IAT + + + ++DLI G IGL++ + E + Y+
Sbjct: 14 REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73
Query: 200 WWIKQAI---IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNI 256
IK AI +R++ SR +R +I E L +L R PTD E+A+ L I
Sbjct: 74 LRIKGAIYDYLRSLDFGSRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGI 127
Query: 257 HVSTVRLAIERTR--HPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXX 314
+ +++ + +SL+ D ++IP T E V
Sbjct: 128 STEELFKTLDKINFSYILSLEEVFRD-FARDYSELIPSS--TNVEEEVIKRELTEKVKEA 184
Query: 315 XXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
L ERE +++L F + + KE+ ++L S R+ Q++ AL +L++
Sbjct: 185 VSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLRE 233
>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 73
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/62 (43%), Positives = 41/62 (66%)
Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKV 376
TL++RE ++LRL FGLD + +E+G++ ++RERIRQI AL KL+ + LK
Sbjct: 11 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKD 70
Query: 377 YM 378
+M
Sbjct: 71 FM 72
>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
Length = 81
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 39/61 (63%)
Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY 377
L+ REA +LR+ FG+D T + +E+G+ ++RERIRQI AL KL+ + L+ +
Sbjct: 19 LTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 78
Query: 378 M 378
+
Sbjct: 79 L 79
>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of
Sigma 70, Rsd, In Complex With Sigma 70 Domain 4
Length = 68
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 39/61 (63%)
Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY 377
L+ REA +LR+ FG+D T + +E+G+ ++RERIRQI AL KL+ + L+ +
Sbjct: 6 LTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 65
Query: 378 M 378
+
Sbjct: 66 L 66
>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|OO Chain o, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
Length = 99
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 34/50 (68%)
Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
L+ REA +LR+ FG+D T + +E+G+ ++RERIRQI AL KL+
Sbjct: 20 LTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH 69
>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 62
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 24/51 (47%), Positives = 36/51 (70%)
Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
TL++RE ++LRL FGLD + +E+G++ ++RERIRQI AL KL+
Sbjct: 11 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 61
>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
Maritima
Length = 87
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 38/59 (64%)
Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLK 375
TLS REA +LR+ +GL P + +E+G+ +++RERIRQI AL KL+ + LK
Sbjct: 18 TLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLK 76
>pdb|3N97|A Chain A, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma
Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna
pdb|3N97|D Chain D, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma
Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna
Length = 72
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 36/61 (59%)
Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY 377
LSEREA +L++ GL + +E+G ++RERIRQI AL KL+ + L+ +
Sbjct: 11 LSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRHPSRSEKLRDF 70
Query: 378 M 378
+
Sbjct: 71 L 71
>pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With
Sigma-Region4 Of Thermus Aquaticus Bound To Dna
Length = 73
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/49 (46%), Positives = 31/49 (63%)
Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366
LSEREA +L+L GL + +E+G ++RERIRQI AL KL+
Sbjct: 11 LSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59
>pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment, Region 4
pdb|1KU7|A Chain A, Crystal Structure Of Thermus Aquatics Rna Polymerase
Sigmaa Subunit Region 4 Bound To-35 Element Dna
pdb|1KU7|D Chain D, Crystal Structure Of Thermus Aquatics Rna Polymerase
Sigmaa Subunit Region 4 Bound To-35 Element Dna
Length = 73
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 31/49 (63%)
Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366
LSEREA +L++ GL + +E+G ++RERIRQI AL KL+
Sbjct: 11 LSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59
>pdb|3MZY|A Chain A, The Crystal Structure Of The Rna Polymerase Sigma-H Factor
F Fusobacterium Nucleatum To 2.5a
Length = 164
Score = 31.6 bits (70), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 165 GLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAI 210
G +DL+QEG +GLL+ K F E S++ + I++ I AI
Sbjct: 1 GAEKEDLVQEGILGLLKAIK-FYDETKSSFSSFAFLCIRREXISAI 45
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.135 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,185,852
Number of Sequences: 62578
Number of extensions: 272896
Number of successful extensions: 831
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 800
Number of HSP's gapped (non-prelim): 24
length of query: 379
length of database: 14,973,337
effective HSP length: 100
effective length of query: 279
effective length of database: 8,715,537
effective search space: 2431634823
effective search space used: 2431634823
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)