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= 010092
(518 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 127 bits (320), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 86/280 (30%), Positives = 149/280 (53%), Gaps = 29/280 (10%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
++ E T ++ QVK + +G A A+ ++++ NLRLV+ + KKY G +F
Sbjct: 346 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 402
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIM 364
DL Q G GL+ A+D+FE +R ++ STY +WIR AI RS+ + T R+P + +
Sbjct: 403 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-----I 457
Query: 365 QVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE- 423
+ ++ R ++L E+ R PT EE+ + + + ++ R+V+K +K +S+ + G ++
Sbjct: 458 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517
Query: 424 ---EFINGIT---DVDGVENENQRQPAXXXXXXXXXXXXXKPKESLVIRQRFGLDGKGDR 477
+FI T +D E+ R +E+ V+R RFG+D D
Sbjct: 518 HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT------AREAKVLRMRFGIDMNTDH 571
Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
TL E+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 572 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611
>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 = 127 bits (319), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 86/280 (30%), Positives = 149/280 (53%), Gaps = 29/280 (10%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
++ E T ++ QVK + +G A A+ ++++ NLRLV+ + KKY G +F
Sbjct: 346 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 402
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIM 364
DL Q G GL+ A+D+FE +R ++ STY +WIR AI RS+ + T R+P + +
Sbjct: 403 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-----I 457
Query: 365 QVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE- 423
+ ++ R ++L E+ R PT EE+ + + + ++ R+V+K +K +S+ + G ++
Sbjct: 458 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517
Query: 424 ---EFINGIT---DVDGVENENQRQPAXXXXXXXXXXXXXKPKESLVIRQRFGLDGKGDR 477
+FI T +D E+ R +E+ V+R RFG+D D
Sbjct: 518 HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT------AREAKVLRMRFGIDMNTDY 571
Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
TL E+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 572 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 114 bits (284), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 87/267 (32%), Positives = 135/267 (50%), Gaps = 26/267 (9%)
Query: 264 QVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
++K+ L + G AAR LI+ NLRLV+ + KKY G F DL Q G +GLI A++
Sbjct: 184 ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVE 240
Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLF 379
+FE KRRF+ STY +WIR AI R++ + T R+P +++ ++ R +L
Sbjct: 241 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQ 295
Query: 380 ELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 437
EL R P+ EEI + G +R E +K ++ +SL + G ++ F D + +
Sbjct: 296 ELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPD 350
Query: 438 ENQRQPAXXXXXXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISRE 491
EN P K +E++V++ R GL + TL E+ ++RE
Sbjct: 351 ENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRE 410
Query: 492 MVRKHEVKGLMKLK-HPTRVDYLRQHM 517
+R+ E K L KLK H +R LR +
Sbjct: 411 RIRQIENKALRKLKYHESRTRKLRDFL 437
Score = 28.9 bits (63), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%), Gaps = 2/36 (5%)
Query: 240 QLQKDLGREPTDVELAEAT--NMSAAQVKKCLEVGR 273
QLQ++LGREP+ E+AEA A +V++ L++ +
Sbjct: 292 QLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQ 327
>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 = 112 bits (281), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 87/267 (32%), Positives = 135/267 (50%), Gaps = 26/267 (9%)
Query: 264 QVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
++K+ L + G AAR LI+ NLRLV+ + KKY G F DL Q G +GLI A++
Sbjct: 78 ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVE 134
Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLF 379
+FE KRRF+ STY +WIR AI R++ + T R+P +++ ++ R +L
Sbjct: 135 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQ 189
Query: 380 ELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 437
EL R P+ EEI + G +R E +K ++ +SL + G ++ F D + +
Sbjct: 190 ELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPD 244
Query: 438 ENQRQPAXXXXXXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISRE 491
EN P K +E++V++ R GL + TL E+ ++RE
Sbjct: 245 ENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRE 304
Query: 492 MVRKHEVKGLMKLK-HPTRVDYLRQHM 517
+R+ E K L KLK H +R LR +
Sbjct: 305 RIRQIENKALRKLKYHESRTRKLRDFL 331
Score = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%), Gaps = 2/36 (5%)
Query: 240 QLQKDLGREPTDVELAEAT--NMSAAQVKKCLEVGR 273
QLQ++LGREP+ E+AEA A +V++ L++ +
Sbjct: 186 QLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQ 221
>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 = 112 bits (279), Expect = 7e-25, Method: Compositional matrix adjust.
Identities = 85/256 (33%), Positives = 129/256 (50%), Gaps = 23/256 (8%)
Query: 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
G AAR LI+ NLRLV+ + KKY G F DL Q G +GLI A+++FE KRRF+ S
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 236
Query: 332 TYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEI 390
TY +WIR AI R++ + T R+P +++ ++ R +L EL R PT EEI
Sbjct: 237 TYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQELGREPTYEEI 291
Query: 391 IQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXX 448
+ G +R E +K ++ +SL + G ++ F D + +E+ P
Sbjct: 292 AEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDEHLPSPVDAAT 346
Query: 449 XXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502
K +E++V++ R GL + TL E+ ++RE +R+ E K L
Sbjct: 347 QSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALR 406
Query: 503 KLK-HPTRVDYLRQHM 517
KLK H +R LR +
Sbjct: 407 KLKYHESRTRKLRDFL 422
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 25/36 (69%), Gaps = 2/36 (5%)
Query: 240 QLQKDLGREPTDVELAEAT--NMSAAQVKKCLEVGR 273
QLQ++LGREPT E+AEA A +V++ L++ +
Sbjct: 277 QLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQ 312
>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 = 112 bits (279), Expect = 7e-25, Method: Compositional matrix adjust.
Identities = 85/256 (33%), Positives = 129/256 (50%), Gaps = 23/256 (8%)
Query: 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
G AAR LI+ NLRLV+ + KKY G F DL Q G +GLI A+++FE KRRF+ S
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 236
Query: 332 TYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEI 390
TY +WIR AI R++ + T R+P +++ ++ R +L EL R PT EEI
Sbjct: 237 TYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQELGREPTYEEI 291
Query: 391 IQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXX 448
+ G +R E +K ++ +SL + G ++ F D + +E+ P
Sbjct: 292 AEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDEHLPSPVDAAT 346
Query: 449 XXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502
K +E++V++ R GL + TL E+ ++RE +R+ E K L
Sbjct: 347 QSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALR 406
Query: 503 KLK-HPTRVDYLRQHM 517
KLK H +R LR +
Sbjct: 407 KLKYHESRTRKLRDFL 422
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 25/36 (69%), Gaps = 2/36 (5%)
Query: 240 QLQKDLGREPTDVELAEAT--NMSAAQVKKCLEVGR 273
QLQ++LGREPT E+AEA A +V++ L++ +
Sbjct: 277 QLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQ 312
>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 = 111 bits (278), Expect = 9e-25, Method: Compositional matrix adjust.
Identities = 85/256 (33%), Positives = 129/256 (50%), Gaps = 23/256 (8%)
Query: 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
G AAR LI+ NLRLV+ + KKY G F DL Q G +GLI A+++FE KRRF+ S
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 256
Query: 332 TYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEI 390
TY +WIR AI R++ + T R+P +++ ++ R +L EL R PT EEI
Sbjct: 257 TYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQELGREPTYEEI 311
Query: 391 IQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXX 448
+ G +R E +K ++ +SL + G ++ F D + +E+ P
Sbjct: 312 AEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDEHLPSPVDAAT 366
Query: 449 XXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502
K +E++V++ R GL + TL E+ ++RE +R+ E K L
Sbjct: 367 QSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALR 426
Query: 503 KLK-HPTRVDYLRQHM 517
KLK H +R LR +
Sbjct: 427 KLKYHESRTRKLRDFL 442
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 25/36 (69%), Gaps = 2/36 (5%)
Query: 240 QLQKDLGREPTDVELAEAT--NMSAAQVKKCLEVGR 273
QLQ++LGREPT E+AEA A +V++ L++ +
Sbjct: 297 QLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQ 332
>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 = 88.2 bits (217), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 59/157 (37%), Positives = 89/157 (56%), Gaps = 14/157 (8%)
Query: 264 QVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
++K+ L + G AAR LI+ NLRLV+ + KKY G F DL Q G +GLI A++
Sbjct: 97 ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVE 153
Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLF 379
+FE KRRF+ STY +WIR AI R++ + T R+P +++ ++ R +L
Sbjct: 154 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQ 208
Query: 380 ELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSL 414
EL R P+ EEI + G +R E +K ++ +SL
Sbjct: 209 ELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 245
Score = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%), Gaps = 2/36 (5%)
Query: 240 QLQKDLGREPTDVELAEAT--NMSAAQVKKCLEVGR 273
QLQ++LGREP+ E+AEA A +V++ L++ +
Sbjct: 205 QLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQ 240
>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 = 88.2 bits (217), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 59/157 (37%), Positives = 89/157 (56%), Gaps = 14/157 (8%)
Query: 264 QVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
++K+ L + G AAR LI+ NLRLV+ + KKY G F DL Q G +GLI A++
Sbjct: 93 ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVE 149
Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLF 379
+FE KRRF+ STY +WIR AI R++ + T R+P +++ ++ R +L
Sbjct: 150 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQ 204
Query: 380 ELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSL 414
EL R P+ EEI + G +R E +K ++ +SL
Sbjct: 205 ELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241
Score = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%), Gaps = 2/36 (5%)
Query: 240 QLQKDLGREPTDVELAEAT--NMSAAQVKKCLEVGR 273
QLQ++LGREP+ E+AEA A +V++ L++ +
Sbjct: 201 QLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQ 236
>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 = 74.3 bits (181), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 40/87 (45%), Positives = 54/87 (62%), Gaps = 6/87 (6%)
Query: 264 QVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
++K+ L + G AAR LI+ NLRLV+ + KKY G F DL Q G +GLI A++
Sbjct: 92 ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVE 148
Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMT 347
+FE KR F STY +WIR AI R++
Sbjct: 149 KFEYKRGFAFSTYATWWIRQAINRAIA 175
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 72.4 bits (176), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 39/102 (38%), Positives = 61/102 (59%), Gaps = 10/102 (9%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
++ E T ++ QVK + +G A A+ ++++ NLRLV+ + KKY G +F
Sbjct: 237 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 293
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT 347
DL Q G GL+ A+D+FE +R ++ STY +WIR AI RS+
Sbjct: 294 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 335
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 62.8 bits (151), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 63/241 (26%), Positives = 112/241 (46%), Gaps = 16/241 (6%)
Query: 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEP 324
+++ E + AR+++I+ N+RLV V++++ G DL Q G GL+ ++D+F+
Sbjct: 19 IRRSQEGDQEARDEIIEKNMRLVWSVVQRFLN---RGYEADDLFQIGCIGLLKSVDKFDL 75
Query: 325 KRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRV 384
+ STY + I I R + +V S S+ ++ +I++AK EL R
Sbjct: 76 SYDVKFSTYAVPMIIGEIQRFLRDDGTVKV-----SRSLKEMGNKIRKAKDELSKTRGRA 130
Query: 385 PTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA 444
PT EI + ISPE +V+ A + + S H E + IT +D + + ++
Sbjct: 131 PTVTEIADHLGISPE---DVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADE-ASW 186
Query: 445 XXXXXXXXXXXXXKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504
+E L++ R+ D+T E+A L IS+ + + E K L +
Sbjct: 187 FDKIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHI 242
Query: 505 K 505
K
Sbjct: 243 K 243
>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
Maritima
Length = 87
Score = 56.2 bits (134), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 42/57 (73%), Gaps = 2/57 (3%)
Query: 459 PKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 514
P+E++V+R R+GL DGK +TL E+ N++RE +R+ EVK L KL+HP+R YL+
Sbjct: 21 PREAMVLRMRYGLLDGK-PKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLK 76
>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
Length = 81
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
+E+ V+R RFG+D D TL E+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 21 AREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
+E+ V+R RFG+D D TL E+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 8 AREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 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 = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 37/56 (66%)
Query: 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 514
+E+ V+R RFG+D D TL E+ +++RE +R+ E K L KL+HP+R + LR
Sbjct: 22 AREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 77
>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 73
Score = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 35/58 (60%)
Query: 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
+E V+R RFGLD RTL E+ ++RE +R+ E K L KL+HP+R L+ M
Sbjct: 15 REENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 72
>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 62
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/48 (45%), Positives = 30/48 (62%)
Query: 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507
+E V+R RFGLD RTL E+ ++RE +R+ E K L KL+HP
Sbjct: 15 REENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 62
>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 = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 460 KESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
+E++V++ R GL DG+ + TL E+ ++RE +R+ E K L KL+HP+R + LR +
Sbjct: 14 REAMVLKMRKGLIDGR-EHTLEEVGAYFGVTRERIRQIENKALRKLRHPSRSEKLRDFL 71
>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 = 35.4 bits (80), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 3/61 (4%)
Query: 459 PKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK-HPTRVDYLRQH 516
+E++V++ R GL DG+ + TL E+ ++RE +R+ E K L KLK H +R LR
Sbjct: 13 EREAMVLKMRKGLIDGR-EHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDF 71
Query: 517 M 517
+
Sbjct: 72 L 72
>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 = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 3/61 (4%)
Query: 459 PKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK-HPTRVDYLRQH 516
+E++V++ R GL DG+ + TL E+ ++RE +R+ E K L KLK H +R LR
Sbjct: 13 EREAMVLKLRKGLIDGR-EHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDF 71
Query: 517 M 517
+
Sbjct: 72 L 72
>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 = 33.9 bits (76), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 11/64 (17%)
Query: 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYF 295
+V E+L++ LGREPTD E+A+ +S ++ K L+ K N +L +++ F
Sbjct: 103 EVVEKLKEKLGREPTDEEVAKELGISTEELFKTLD----------KINFSYIL-SLEEVF 151
Query: 296 QDFA 299
+DFA
Sbjct: 152 RDFA 155
Score = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 41/130 (31%), Positives = 56/130 (43%), Gaps = 19/130 (14%)
Query: 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGL 335
R +LI L LV + + +DL GV GLI A+D + R Y
Sbjct: 14 REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73
Query: 336 FWIRHAI---IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAK--LELLFE-LKRVPTDEE 389
I+ AI +RS+ S QVR + +R K +E L E L R PTDEE
Sbjct: 74 LRIKGAIYDYLRSLDFGS-------------RQVREKERRIKEVVEKLKEKLGREPTDEE 120
Query: 390 IIQGVNISPE 399
+ + + IS E
Sbjct: 121 VAKELGISTE 130
>pdb|2OM6|A Chain A, Hypothetical Protein (probable Phosphoserine Phosph
(ph0253) From Pyrococcus Horikoshii Ot3
pdb|2OM6|B Chain B, Hypothetical Protein (probable Phosphoserine Phosph
(ph0253) From Pyrococcus Horikoshii Ot3
Length = 235
Score = 28.5 bits (62), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501
KP+ESL I + D +G R +G A +N + VRK E +G
Sbjct: 174 KPEESLHIGDTYAEDYQGARKVGXWAVWINQEGDKVRKLEERGF 217
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
0.317 0.133 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,384,618
Number of Sequences: 62578
Number of extensions: 511012
Number of successful extensions: 1720
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1661
Number of HSP's gapped (non-prelim): 38
length of query: 518
length of database: 14,973,337
effective HSP length: 103
effective length of query: 415
effective length of database: 8,527,803
effective search space: 3539038245
effective search space used: 3539038245
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)