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= 009449
(534 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 155 bits (392), Expect = 6e-38, Method: Compositional matrix adjust.
Identities = 89/244 (36%), Positives = 143/244 (58%), Gaps = 5/244 (2%)
Query: 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
G R+ LI++ LV+ +A+ Y G G+ F DL+Q GN G+++ E+F++ R +KFSTY
Sbjct: 89 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 148
Query: 353 QYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
+WIR++I++ +A AR I+IP + I+K+ + + L G+ P EIA+ G
Sbjct: 149 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGW 208
Query: 413 AEIRSASECLRIVG---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRIL 469
+ + E L+I S++ IGD ++ Y +F PD ++ SP E + + +++ + L
Sbjct: 209 -DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKAL 267
Query: 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRDL 528
L RE VL LR GL D R +LEE+G F V++E IR++E KA+ KL+ E+ R L
Sbjct: 268 SKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKL 327
Query: 529 SHFL 532
FL
Sbjct: 328 RDFL 331
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 154 bits (390), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 98/279 (35%), Positives = 157/279 (56%), Gaps = 18/279 (6%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
T+E+ GK SL + LK++L G R+ LI++ LV+ +A+ Y G
Sbjct: 170 TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 219
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377
G+ F DL+Q GN G+++ E+F++ R +KFSTY +WIR++I++ +A AR I+IP +
Sbjct: 220 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 279
Query: 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVG---SIDQKIGD 434
I+K+ + + L G+ P EIA+ G + + E L+I S++ IGD
Sbjct: 280 VETINKLSRTARQLQQELGREPSYEEIAEAMGPGW-DAKRVEETLKIAQEPVSLETPIGD 338
Query: 435 CLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSL 494
++ Y +F PD ++ SP E + + +++ + L L RE VL LR GL D R +L
Sbjct: 339 EKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTL 398
Query: 495 EEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRDLSHFL 532
EE+G F V++E IR++E KA+ KL+ E+ R L FL
Sbjct: 399 EEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFL 437
>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 = 152 bits (385), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 88/244 (36%), Positives = 142/244 (58%), Gaps = 5/244 (2%)
Query: 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
G R+ LI++ LV+ +A+ Y G G+ F DL+Q GN G+++ E+F++ R +KFSTY
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 353 QYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
+WIR++I++ +A AR I+IP + I+K+ + + L G+ P EIA+ G
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 413 AEIRSASECLRIVG---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRIL 469
+ + E L+I S++ IGD ++ Y +F PD + SP + + + +++ + L
Sbjct: 300 -DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKAL 358
Query: 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRDL 528
L RE VL LR GL D R +LEE+G F V++E IR++E KA+ KL+ E+ R L
Sbjct: 359 SKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKL 418
Query: 529 SHFL 532
FL
Sbjct: 419 RDFL 422
>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 = 152 bits (385), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 88/244 (36%), Positives = 142/244 (58%), Gaps = 5/244 (2%)
Query: 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
G R+ LI++ LV+ +A+ Y G G+ F DL+Q GN G+++ E+F++ R +KFSTY
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 353 QYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
+WIR++I++ +A AR I+IP + I+K+ + + L G+ P EIA+ G
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 413 AEIRSASECLRIVG---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRIL 469
+ + E L+I S++ IGD ++ Y +F PD + SP + + + +++ + L
Sbjct: 300 -DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKAL 358
Query: 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRDL 528
L RE VL LR GL D R +LEE+G F V++E IR++E KA+ KL+ E+ R L
Sbjct: 359 SKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKL 418
Query: 529 SHFL 532
FL
Sbjct: 419 RDFL 422
>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 = 152 bits (385), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 88/244 (36%), Positives = 142/244 (58%), Gaps = 5/244 (2%)
Query: 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
G R+ LI++ LV+ +A+ Y G G+ F DL+Q GN G+++ E+F++ R +KFSTY
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 353 QYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
+WIR++I++ +A AR I+IP + I+K+ + + L G+ P EIA+ G
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 413 AEIRSASECLRIVG---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRIL 469
+ + E L+I S++ IGD ++ Y +F PD + SP + + + +++ + L
Sbjct: 320 -DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKAL 378
Query: 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRDL 528
L RE VL LR GL D R +LEE+G F V++E IR++E KA+ KL+ E+ R L
Sbjct: 379 SKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKL 438
Query: 529 SHFL 532
FL
Sbjct: 439 RDFL 442
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 147 bits (370), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 74/237 (31%), Positives = 140/237 (59%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
++E++++ LV+ +A+ Y G+ F DL+Q GN+G+++ ++F++ RGYKFSTY +W
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
IR++I++ +A AR I+IP + I+K+ + + + G+ P E+A+ + +I
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 416 RSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSR 475
R + + S++ IGD ++ +F D +++ P + + ++ +L L +R
Sbjct: 495 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAR 554
Query: 476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
E +VL +R+G++ + +LEE+GK F V++E IR++E KA+ KLR L FL
Sbjct: 555 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 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 = 146 bits (369), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 74/237 (31%), Positives = 140/237 (59%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
++E++++ LV+ +A+ Y G+ F DL+Q GN+G+++ ++F++ RGYKFSTY +W
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
IR++I++ +A AR I+IP + I+K+ + + + G+ P E+A+ + +I
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 416 RSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSR 475
R + + S++ IGD ++ +F D +++ P + + ++ +L L +R
Sbjct: 495 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAR 554
Query: 476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
E +VL +R+G++ + +LEE+GK F V++E IR++E KA+ KLR L FL
Sbjct: 555 EAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611
>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 = 94.7 bits (234), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 53/152 (34%), Positives = 87/152 (57%), Gaps = 13/152 (8%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
T+E+ GK SL + LK++L G R+ LI++ LV+ +A+ Y G
Sbjct: 79 TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 128
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377
G+ F DL+Q GN G+++ E+F++ R +KFSTY +WIR++I++ +A AR I+IP +
Sbjct: 129 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 188
Query: 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTG 409
I+K+ + + L G+ P EIA+ G
Sbjct: 189 VETINKLSRTARQLQQELGREPSYEEIAEAMG 220
>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 = 94.4 bits (233), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 53/152 (34%), Positives = 87/152 (57%), Gaps = 13/152 (8%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
T+E+ GK SL + LK++L G R+ LI++ LV+ +A+ Y G
Sbjct: 83 TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 132
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377
G+ F DL+Q GN G+++ E+F++ R +KFSTY +WIR++I++ +A AR I+IP +
Sbjct: 133 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 192
Query: 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTG 409
I+K+ + + L G+ P EIA+ G
Sbjct: 193 VETINKLSRTARQLQQELGREPSYEEIAEAMG 224
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 78.2 bits (191), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 54/74 (72%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
++E++++ LV+ +A+ Y G+ F DL+Q GN+G+++ ++F++ RGYKFSTY +W
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 356 IRKSISKMVARHAR 369
IR++I++ +A AR
Sbjct: 326 IRQAITRSIADQAR 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 = 76.3 bits (186), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 32/77 (41%), Positives = 53/77 (68%)
Query: 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
G R+ LI++ LV+ +A+ Y G G+ F DL+Q GN G+++ E+F++ RG+ FSTY
Sbjct: 103 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAFSTYA 162
Query: 353 QYWIRKSISKMVARHAR 369
+WIR++I++ +A AR
Sbjct: 163 TWWIRQAINRAIADQAR 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 = 76.3 bits (186), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 63/229 (27%), Positives = 113/229 (49%), Gaps = 18/229 (7%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
R+E+I+ LV + + + G DL Q G +G+L+ ++FD + KFSTY
Sbjct: 29 ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
I I + + R +K+ L +KI+KA+ L+ + G+ P EIA + G+S ++
Sbjct: 89 IIGEIQRFL-RDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 416 RSASECLRIVGSIDQKI----GDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILES 471
A E +R+ SI + + GD + L+ D S + + +KK +E
Sbjct: 148 VLAQEAVRLPTSIHETVYENDGDPIT--LLDQIADADEASWFDKIA---LKK----AIEE 198
Query: 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
LD RER ++ LRY ++ ++ E+ +S+ + +LEKK + ++
Sbjct: 199 LDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHIK 243
>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
Maritima
Length = 87
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 34/78 (43%), Positives = 54/78 (69%)
Query: 457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516
MR M++++ ++L++L RE VL +RYGL D +PK+LEE+G+ F+V++E IR++E KA+
Sbjct: 4 MRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKAL 63
Query: 517 TKLRDSETCRDLSHFLVL 534
KLR + L L L
Sbjct: 64 RKLRHPSRSKYLKSLLSL 81
>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 73
Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 32/72 (44%), Positives = 50/72 (69%)
Query: 461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
MK+ + +L++L RE VL LR+GL+D R ++LEE+GK+F V++E IR++E KA+ KLR
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 521 DSETCRDLSHFL 532
+ L F+
Sbjct: 61 HPSRSKRLKDFM 72
>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 62
Score = 59.7 bits (143), Expect = 4e-09, Method: Composition-based stats.
Identities = 30/60 (50%), Positives = 46/60 (76%)
Query: 461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
MK+ + +L++L RE VL LR+GL+D R ++LEE+GK+F V++E IR++E KA+ KLR
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
Length = 81
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 42/65 (64%)
Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527
+L L +RE +VL +R+G++ + +LEE+GK F V++E IR++E KA+ KLR
Sbjct: 15 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 74
Query: 528 LSHFL 532
L FL
Sbjct: 75 LRSFL 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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 42/65 (64%)
Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527
+L L +RE +VL +R+G++ + +LEE+GK F V++E IR++E KA+ KLR
Sbjct: 2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61
Query: 528 LSHFL 532
L FL
Sbjct: 62 LRSFL 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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 39/53 (73%)
Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
+L L +RE +VL +R+G++ + +LEE+GK F V++E IR++E KA+ KLR
Sbjct: 16 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 68
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/64 (45%), Positives = 37/64 (57%)
Query: 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL 528
L L RE VL +R GL D R +LEE+G F V++E IR++E KA+ KLR L
Sbjct: 8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRHPSRSEKL 67
Query: 529 SHFL 532
FL
Sbjct: 68 RDFL 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 = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 31/65 (47%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRD 527
L L RE VL LR GL D R +LEE+G F V++E IR++E KA+ KL+ E+ R
Sbjct: 8 LSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRK 67
Query: 528 LSHFL 532
L FL
Sbjct: 68 LRDFL 72
>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 = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/65 (46%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRD 527
L L RE VL +R GL D R +LEE+G F V++E IR++E KA+ KL+ E+ R
Sbjct: 8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRK 67
Query: 528 LSHFL 532
L FL
Sbjct: 68 LRDFL 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 = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 55/234 (23%), Positives = 103/234 (44%), Gaps = 23/234 (9%)
Query: 297 REELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ 353
REELI PLV +A N + + DL+ G +G+++ + + Y++
Sbjct: 14 REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73
Query: 354 YWIRKSISKMVARHARGIKIPCKLNREISK-IQKARKALTNSHGKYPEDIEIAKYTGLSL 412
I+ +I + R + + RE + I++ + L G+ P D E+AK G+
Sbjct: 74 LRIKGAIYD----YLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGI-- 127
Query: 413 AEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP-----KEIVMRQHMKKDVFR 467
S E + + I+ L + +FA D S P +E V+++ + + V
Sbjct: 128 ----STEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTNVEEEVIKRELTEKVKE 183
Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521
+ L RE+ LV++ + P E+ K+ S + +L+ KA+ +LR+
Sbjct: 184 AVSKLPEREK--LVIQLIFYEELPAK--EVAKILETSVSRVSQLKAKALERLRE 233
>pdb|1YY5|A Chain A, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1YY5|B Chain B, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|A Chain A, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|B Chain B, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|C Chain C, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|D Chain D, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
Length = 513
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 221 TIFSAERAL--NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQ 277
IF E N + +T+A + E + V+ NL+ + + LE+E S K S+ CW+Q
Sbjct: 297 VIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQ 356
>pdb|1Z6L|A Chain A, Crystal Structure Of Fms1 In Complex With Its Substrate
pdb|1Z6L|B Chain B, Crystal Structure Of Fms1 In Complex With Its Substrate
pdb|3BI2|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI2|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI4|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI4|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI5|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI5|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BNM|B Chain B, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3r,3'r)-
Methylated Spermine
pdb|3BNM|A Chain A, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3r,3'r)-
Methylated Spermine
pdb|3BNU|B Chain B, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3s,3's)-
Methylated Spermine
pdb|3BNU|A Chain A, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3s,3's)-
Methylated Spermine
pdb|3CN8|B Chain B, Crystal Structure Of Fms1 In Complex With Spermidine
pdb|3CN8|A Chain A, Crystal Structure Of Fms1 In Complex With Spermidine
pdb|3CND|B Chain B, Crystal Structure Of Fms1 In Complex With N1-Acspermine
pdb|3CND|A Chain A, Crystal Structure Of Fms1 In Complex With N1-Acspermine
pdb|3CNP|B Chain B, Crystal Structure Of Fms1 In Complex With
S-n1-acmespermidine
pdb|3CNP|A Chain A, Crystal Structure Of Fms1 In Complex With
S-n1-acmespermidine
pdb|3CNS|A Chain A, Crystal Structure Of Fms1 In Complex With
S-Bz-Mespermidine
pdb|3CNS|B Chain B, Crystal Structure Of Fms1 In Complex With
S-Bz-Mespermidine
pdb|3CNT|B Chain B, Crystal Structure Of Fms1 In Complex With
R-Bz-Mespermidine
pdb|3CNT|A Chain A, Crystal Structure Of Fms1 In Complex With
R-Bz-Mespermidine
Length = 516
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 221 TIFSAERAL--NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQ 277
IF E N + +T+A + E + V+ NL+ + + LE+E S K S+ CW+Q
Sbjct: 297 VIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQ 356
>pdb|1RSG|A Chain A, Crystal Structure Of The Polyamine Oxidase Fms1 From Yeast
pdb|1RSG|B Chain B, Crystal Structure Of The Polyamine Oxidase Fms1 From Yeast
Length = 516
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 221 TIFSAERAL--NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQ 277
IF E N + +T+A + E + V+ NL+ + + LE+E S K S+ CW+Q
Sbjct: 297 VIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSXLEREDSQKHTSVTCWSQ 356
>pdb|4GDP|A Chain A, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|B Chain B, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|C Chain C, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|D Chain D, Yeast Polyamine Oxidase Fms1, N195a Mutant
Length = 516
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 221 TIFSAERAL--NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQ 277
IF E N + +T+A + E + V+ NL+ + + LE+E S K S+ CW+Q
Sbjct: 297 VIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQ 356
>pdb|4ECH|A Chain A, Yeast Polyamine Oxidase Fms1, H67q Mutant
pdb|4ECH|B Chain B, Yeast Polyamine Oxidase Fms1, H67q Mutant
Length = 516
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 221 TIFSAERAL--NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQ 277
IF E N + +T+A + E + V+ NL+ + + LE+E S K S+ CW+Q
Sbjct: 297 VIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQ 356
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
0.318 0.132 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,126,098
Number of Sequences: 62578
Number of extensions: 468678
Number of successful extensions: 1598
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1565
Number of HSP's gapped (non-prelim): 34
length of query: 534
length of database: 14,973,337
effective HSP length: 103
effective length of query: 431
effective length of database: 8,527,803
effective search space: 3675483093
effective search space used: 3675483093
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)