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= 010835
(499 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 = 143 bits (360), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 80/247 (32%), Positives = 147/247 (59%), Gaps = 16/247 (6%)
Query: 256 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 315
A++++V +N+RLV+SIA++Y N G DL+Q G IGL++ ++KF+ +G+K STY WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 316 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 374
IRQ ++R++ + +RT+R+P H+ E + L R ++ L+E G P+ + +AE + M + K+
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 375 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN----PWHGVDDWALKDEVN 430
R KV + +E S+ G+ S++ D +E+ P +L+ +
Sbjct: 495 R-------KVLKIAKEPI-SMETPIGDDEDSHLGDF-IEDTTLELPLDSATTESLRAATH 545
Query: 431 KLIIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489
++ L RE +++R+ +G+D T E++ K+ ++RER+RQ+ AL KL+H +R
Sbjct: 546 D-VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 604
Query: 490 KKMEAML 496
+ + + L
Sbjct: 605 EVLRSFL 611
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 142 bits (357), Expect = 5e-34, Method: Compositional matrix adjust.
Identities = 80/247 (32%), Positives = 147/247 (59%), Gaps = 16/247 (6%)
Query: 256 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 315
A++++V +N+RLV+SIA++Y N G DL+Q G IGL++ ++KF+ +G+K STY WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 316 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 374
IRQ ++R++ + +RT+R+P H+ E + L R ++ L+E G P+ + +AE + M + K+
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 375 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN----PWHGVDDWALKDEVN 430
R KV + +E S+ G+ S++ D +E+ P +L+ +
Sbjct: 495 R-------KVLKIAKEPI-SMETPIGDDEDSHLGDF-IEDTTLELPLDSATTESLRAATH 545
Query: 431 KLIIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489
++ L RE +++R+ +G+D T E++ K+ ++RER+RQ+ AL KL+H +R
Sbjct: 546 D-VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 604
Query: 490 KKMEAML 496
+ + + L
Sbjct: 605 EVLRSFL 611
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 131 bits (330), Expect = 8e-31, Method: Compositional matrix adjust.
Identities = 89/254 (35%), Positives = 136/254 (53%), Gaps = 13/254 (5%)
Query: 249 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 308
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 191 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 250
Query: 309 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 367
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G PS + IAE +
Sbjct: 251 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAM 310
Query: 368 NMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN---PWHGVDDWA 424
R + + + +E SL G+ S+ D + N P
Sbjct: 311 GPGWDAKR-----VEETLKIAQEPV-SLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSL 364
Query: 425 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKL 483
L +E+ K + L ERE +++L GL D T E++ G++RER+RQ+ AL KL
Sbjct: 365 LSEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKL 423
Query: 484 K-HAARKKKMEAML 496
K H +R +K+ L
Sbjct: 424 KYHESRTRKLRDFL 437
>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 = 130 bits (327), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 89/254 (35%), Positives = 136/254 (53%), Gaps = 13/254 (5%)
Query: 249 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 308
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 85 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 144
Query: 309 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 367
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G PS + IAE +
Sbjct: 145 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAM 204
Query: 368 NMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN---PWHGVDDWA 424
R + + + +E SL G+ S+ D + N P
Sbjct: 205 GPGWDAKR-----VEETLKIAQEPV-SLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSL 258
Query: 425 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKL 483
L +E+ K + L ERE +++L GL D T E++ G++RER+RQ+ AL KL
Sbjct: 259 LSEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKL 317
Query: 484 K-HAARKKKMEAML 496
K H +R +K+ L
Sbjct: 318 KYHESRTRKLRDFL 331
>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 = 130 bits (327), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 87/253 (34%), Positives = 137/253 (54%), Gaps = 11/253 (4%)
Query: 249 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 308
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 176 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 235
Query: 309 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 367
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G P+ + IAE +
Sbjct: 236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 295
Query: 368 NM--SQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWAL 425
K+V + + SL+ + G+ +I D + +P L
Sbjct: 296 GPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGD----FIPDEHL-PSPVDAATQSLL 350
Query: 426 KDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484
+E+ K + L ERE +++L GL D T E++ G++RER+RQ+ AL KLK
Sbjct: 351 SEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 409
Query: 485 -HAARKKKMEAML 496
H +R +K+ L
Sbjct: 410 YHESRTRKLRDFL 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 = 130 bits (327), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 87/253 (34%), Positives = 137/253 (54%), Gaps = 11/253 (4%)
Query: 249 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 308
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 176 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 235
Query: 309 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 367
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G P+ + IAE +
Sbjct: 236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 295
Query: 368 NM--SQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWAL 425
K+V + + SL+ + G+ +I D + +P L
Sbjct: 296 GPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGD----FIPDEHL-PSPVDAATQSLL 350
Query: 426 KDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484
+E+ K + L ERE +++L GL D T E++ G++RER+RQ+ AL KLK
Sbjct: 351 SEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 409
Query: 485 -HAARKKKMEAML 496
H +R +K+ L
Sbjct: 410 YHESRTRKLRDFL 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 = 130 bits (327), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 87/253 (34%), Positives = 137/253 (54%), Gaps = 11/253 (4%)
Query: 249 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 308
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 196 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 255
Query: 309 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 367
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G P+ + IAE +
Sbjct: 256 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 315
Query: 368 NM--SQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWAL 425
K+V + + SL+ + G+ +I D + +P L
Sbjct: 316 GPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGD----FIPDEHL-PSPVDAATQSLL 370
Query: 426 KDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484
+E+ K + L ERE +++L GL D T E++ G++RER+RQ+ AL KLK
Sbjct: 371 SEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 429
Query: 485 -HAARKKKMEAML 496
H +R +K+ L
Sbjct: 430 YHESRTRKLRDFL 442
>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 = 106 bits (264), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 52/121 (42%), Positives = 77/121 (63%), Gaps = 1/121 (0%)
Query: 249 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 308
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 104 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 163
Query: 309 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 367
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G PS + IAE +
Sbjct: 164 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAM 223
Query: 368 N 368
Sbjct: 224 G 224
>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 = 105 bits (263), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 52/121 (42%), Positives = 77/121 (63%), Gaps = 1/121 (0%)
Query: 249 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 308
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 100 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 159
Query: 309 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 367
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G PS + IAE +
Sbjct: 160 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAM 219
Query: 368 N 368
Sbjct: 220 G 220
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 88.6 bits (218), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 81/233 (34%), Positives = 122/233 (52%), Gaps = 23/233 (9%)
Query: 256 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 315
AR++++ N+RLV S+ QR+ N G + DL Q G IGLL+ ++KFD S K STY
Sbjct: 29 ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 316 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEE-KGVTPSVDRIAEYLNMSQKKV 374
I + R L ++ T+++ L E IR AK L + +G P+V IA++L +S + V
Sbjct: 89 IIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 375 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII 434
A EA+ S+ + + +G P T IAD + W D ALK + +
Sbjct: 148 VLAQEAVRLPTSIHETVYEN-DGDPI-TLLDQIAD--ADEASW--FDKIALKKAIEE--- 198
Query: 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEK--LKH 485
L ERER I+ L Y D+ T +++ R+G+S QV + LEK L+H
Sbjct: 199 --LDERERLIVYLRYYKDQ---TQSEVASRLGIS-----QVQMSRLEKKILQH 241
>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 = 6e-17, Method: Compositional matrix adjust.
Identities = 33/74 (44%), Positives = 56/74 (75%)
Query: 256 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 315
A++++V +N+RLV+SIA++Y N G DL+Q G IGL++ ++KF+ +G+K STY WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 316 IRQGVSRALVENSR 329
IRQ ++R++ + +R
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 = 85.1 bits (209), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 37/81 (45%), Positives = 54/81 (66%)
Query: 249 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 308
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ +GF
Sbjct: 99 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAF 158
Query: 309 STYVYWWIRQGVSRALVENSR 329
STY WWIRQ ++RA+ + +R
Sbjct: 159 STYATWWIRQAINRAIADQAR 179
>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 73
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 1/65 (1%)
Query: 433 IIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491
++ TL +RE ++RL +GLD T E++ K G++RER+RQ+ AL KL+H +R K+
Sbjct: 8 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKR 67
Query: 492 MEAML 496
++ +
Sbjct: 68 LKDFM 72
>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
Maritima
Length = 87
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 50/73 (68%), Gaps = 2/73 (2%)
Query: 425 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKL 483
+++E+ K ++ TL RE ++R+ YGL D + T E++ + ++RER+RQ+ + AL KL
Sbjct: 8 MREELEK-VLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKL 66
Query: 484 KHAARKKKMEAML 496
+H +R K ++++L
Sbjct: 67 RHPSRSKYLKSLL 79
>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 = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 60/241 (24%), Positives = 116/241 (48%), Gaps = 29/241 (12%)
Query: 255 LAREKLVMSNVRLVMSIA---QRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 311
+ RE+L++ + LV +IA +++ D+ DL+ G+IGL++ ++ + + Y
Sbjct: 12 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 71
Query: 312 VYWWIRQGVS---RALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYL 367
+ I+ + R+L SR +R E+ I+ +L+EK G P+ + +A+ L
Sbjct: 72 IKLRIKGAIYDYLRSLDFGSRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKEL 125
Query: 368 NMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKD 427
+S TE + K +LD+ F + L E + D V++ +K
Sbjct: 126 GIS-------TEELFK--TLDKINFSYILSL-EEVFRDFARDYSELIPSSTNVEEEVIKR 175
Query: 428 EVNKLI---IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484
E+ + + + L ERE+ +I+L + E L ++++K + S RV Q+ ALE+L+
Sbjct: 176 ELTEKVKEAVSKLPEREKLVIQLIFY---EELPAKEVAKILETSVSRVSQLKAKALERLR 232
Query: 485 H 485
Sbjct: 233 E 233
>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
Length = 81
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 433 IIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491
++ L RE +++R+ +G+D T E++ K+ ++RER+RQ+ AL KL+H +R +
Sbjct: 15 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 74
Query: 492 MEAML 496
+ + L
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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 433 IIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491
++ L RE +++R+ +G+D T E++ K+ ++RER+RQ+ AL KL+H +R +
Sbjct: 2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61
Query: 492 MEAML 496
+ + L
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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 433 IIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488
++ L RE +++R+ +G+D T E++ K+ ++RER+RQ+ AL KL+H +R
Sbjct: 16 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 72
>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 62
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/54 (42%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 433 IIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485
++ TL +RE ++RL +GLD T E++ K G++RER+RQ+ AL KL+H
Sbjct: 8 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 61
>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 = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 437 LGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAM 495
L ERE ++++ GL D T E++ G++RER+RQ+ AL KL+H +R +K+
Sbjct: 11 LSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRHPSRSEKLRDF 70
Query: 496 L 496
L
Sbjct: 71 L 71
>pdb|3MZY|A Chain A, The Crystal Structure Of The Rna Polymerase Sigma-H Factor
F Fusobacterium Nucleatum To 2.5a
Length = 164
Score = 37.0 bits (84), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%), Gaps = 1/40 (2%)
Query: 279 GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 318
GA+ DLVQ G++GLL+ I+ +D +K S++ + IR+
Sbjct: 1 GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRR 39
>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 = 36.6 bits (83), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
Query: 437 LGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAARKKKMEA 494
L ERE +++L GL D T E++ G++RER+RQ+ AL KLK H +R +K+
Sbjct: 11 LSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRD 70
Query: 495 ML 496
L
Sbjct: 71 FL 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 = 35.8 bits (81), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
Query: 437 LGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAARKKKMEA 494
L ERE ++++ GL D T E++ G++RER+RQ+ AL KLK H +R +K+
Sbjct: 11 LSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRD 70
Query: 495 ML 496
L
Sbjct: 71 FL 72
>pdb|3TZC|A Chain A, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(Y155f) From Vibrio Cholerae
pdb|3TZC|B Chain B, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(Y155f) From Vibrio Cholerae
pdb|3TZC|C Chain C, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(Y155f) From Vibrio Cholerae
pdb|3TZC|D Chain D, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(Y155f) From Vibrio Cholerae
Length = 251
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 39/180 (21%), Positives = 76/180 (42%), Gaps = 27/180 (15%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
L NG ++ +PE I+ LK ++L + G++ D+ +R+
Sbjct: 56 LGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVN----------NAGITRDNLLMRM 105
Query: 232 KE---------RLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 282
KE L S R+S+ L+ ++ + R+ +++ V S+ N G
Sbjct: 106 KEEEWSDIMETNLTSIFRLSKAVLRGMMKK----RQGRIIN----VGSVVGTMGNAGQAN 157
Query: 283 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 342
+ G+IG + + + +S+G ++T +I +++AL + RT L RLG
Sbjct: 158 FAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAGRLG 217
>pdb|3RSH|A Chain A, Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)reductase
(Fabg) From Vibrio Cholerae O1 Complexed With Nadp+
(Space Group P62)
pdb|3RSH|B Chain B, Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)reductase
(Fabg) From Vibrio Cholerae O1 Complexed With Nadp+
(Space Group P62)
pdb|3RRO|A Chain A, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg) From Vibrio Cholerae
pdb|3RRO|B Chain B, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg) From Vibrio Cholerae
pdb|4I08|A Chain A, Crystal Structure Of Beta-Ketoacyl-Acyl Carrier Protein
Reductase (Fabg) From Vibrio Cholerae In Complex With
Nadph
pdb|4I08|B Chain B, Crystal Structure Of Beta-Ketoacyl-Acyl Carrier Protein
Reductase (Fabg) From Vibrio Cholerae In Complex With
Nadph
Length = 251
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 39/180 (21%), Positives = 76/180 (42%), Gaps = 27/180 (15%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
L NG ++ +PE I+ LK ++L + G++ D+ +R+
Sbjct: 56 LGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVN----------NAGITRDNLLMRM 105
Query: 232 KER---------LGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 282
KE L S R+S+ L+ ++ + R+ +++ V S+ N G
Sbjct: 106 KEEEWSDIMETNLTSIFRLSKAVLRGMMKK----RQGRIIN----VGSVVGTMGNAGQAN 157
Query: 283 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 342
+ G+IG + + + +S+G ++T +I +++AL + RT L RLG
Sbjct: 158 YAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAGRLG 217
>pdb|3U09|A Chain A, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(G92d) From Vibrio Cholerae
pdb|3U09|B Chain B, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(G92d) From Vibrio Cholerae
Length = 251
Score = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 79/183 (43%), Gaps = 33/183 (18%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVK---GVVSEELLTHAEVVRLSKKIKTGLSLDDHK 228
L NG ++ +PE I+ LK GV + L+ +A++ R D+
Sbjct: 56 LGDNGKGMALNVTNPESIEAVLKAITDEFGGV--DILVNNADITR-----------DNLL 102
Query: 229 LRLKER---------LGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMG 279
+R+KE L S R+S+ L+ ++ + R+ +++ V S+ N G
Sbjct: 103 MRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKK----RQGRIIN----VGSVVGTMGNAG 154
Query: 280 ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE 339
+ G+IG + + + +S+G ++T +I +++AL + RT L
Sbjct: 155 QANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAG 214
Query: 340 RLG 342
RLG
Sbjct: 215 RLG 217
>pdb|3TZH|A Chain A, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(F187a) From Vibrio Cholerae
pdb|3TZH|B Chain B, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(F187a) From Vibrio Cholerae
pdb|3TZH|C Chain C, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(F187a) From Vibrio Cholerae
pdb|3TZH|D Chain D, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(F187a) From Vibrio Cholerae
pdb|3TZH|E Chain E, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(F187a) From Vibrio Cholerae
pdb|3TZH|F Chain F, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(F187a) From Vibrio Cholerae
Length = 251
Score = 32.7 bits (73), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 39/180 (21%), Positives = 75/180 (41%), Gaps = 27/180 (15%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
L NG ++ +PE I+ LK ++L + G++ D+ +R+
Sbjct: 56 LGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVN----------NAGITRDNLLMRM 105
Query: 232 KE---------RLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 282
KE L S R+S+ L+ ++ + R+ +++ V S+ N G
Sbjct: 106 KEEEWSDIMETNLTSIFRLSKAVLRGMMKK----RQGRIIN----VGSVVGTMGNAGQAN 157
Query: 283 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 342
+ G+IG + + + +S+G ++T I +++AL + RT L RLG
Sbjct: 158 YAAAKAGVIGFTKSMAREVASRGVTVNTVAPGAIETDMTKALNDEQRTATLAQVPAGRLG 217
>pdb|3TZK|A Chain A, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(G92a) From Vibrio Cholerae
pdb|3TZK|B Chain B, Crystal Structure Of 3-Ketoacyl-(Acyl-Carrier-Protein)
Reductase (Fabg)(G92a) From Vibrio Cholerae
Length = 251
Score = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 78/183 (42%), Gaps = 33/183 (18%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVK---GVVSEELLTHAEVVRLSKKIKTGLSLDDHK 228
L NG ++ +PE I+ LK GV + L+ +A + R D+
Sbjct: 56 LGDNGKGMALNVTNPESIEAVLKAITDEFGGV--DILVNNAAITR-----------DNLL 102
Query: 229 LRLKER---------LGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMG 279
+R+KE L S R+S+ L+ ++ + R+ +++ V S+ N G
Sbjct: 103 MRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKK----RQGRIIN----VGSVVGTMGNAG 154
Query: 280 ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE 339
+ G+IG + + + +S+G ++T +I +++AL + RT L
Sbjct: 155 QANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAG 214
Query: 340 RLG 342
RLG
Sbjct: 215 RLG 217
>pdb|2VC2|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist L-739758
pdb|2VDK|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDL|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDM|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Tirofiban
pdb|2VDN|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Eptifibatide
pdb|2VDO|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide, Hhlggakqagdv
pdb|2VDP|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide,Lggakqagdv
pdb|2VDQ|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv
pdb|2VDR|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Lggakqrgdv
pdb|3FCU|B Chain B, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
pdb|3FCU|D Chain D, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
pdb|3FCU|F Chain F, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
Length = 461
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 60/144 (41%), Gaps = 22/144 (15%)
Query: 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 314
L EKL N+ L+ ++ + N+ + ++L+ G +G+L DSS ++ Y
Sbjct: 294 LMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL----SMDSSNVLQLIVDAYG 349
Query: 315 WIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD-----RIAEYLNM 369
IR V + + L E L L NA E V P + +I + ++
Sbjct: 350 KIRSKVELEVRD----------LPEELSLSFNATCLNNE--VIPGLKSCMGLKIGDTVSF 397
Query: 370 S-QKKVRNATEAIGKVFSLDREAF 392
S + KVR + K F++ F
Sbjct: 398 SIEAKVRGCPQEKEKSFTIKPVGF 421
>pdb|3T3M|B Chain B, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3M|D Chain D, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|B Chain B, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|D Chain D, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
Length = 472
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 60/144 (41%), Gaps = 22/144 (15%)
Query: 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 314
L EKL N+ L+ ++ + N+ + ++L+ G +G+L DSS ++ Y
Sbjct: 294 LMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL----SMDSSNVLQLIVDAYG 349
Query: 315 WIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD-----RIAEYLNM 369
IR V + + L E L L NA E V P + +I + ++
Sbjct: 350 KIRSKVELEVRD----------LPEELSLSFNATCLNNE--VIPGLKSCMGLKIGDTVSF 397
Query: 370 S-QKKVRNATEAIGKVFSLDREAF 392
S + KVR + K F++ F
Sbjct: 398 SIEAKVRGCPQEKEKSFTIKPVGF 421
>pdb|1TYE|B Chain B, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
pdb|1TYE|D Chain D, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
pdb|1TYE|F Chain F, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
Length = 440
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 60/144 (41%), Gaps = 22/144 (15%)
Query: 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 314
L EKL N+ L+ ++ + N+ + ++L+ G +G+L DSS ++ Y
Sbjct: 294 LMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL----SMDSSNVLQLIVDAYG 349
Query: 315 WIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD-----RIAEYLNM 369
IR V + + L E L L NA E V P + +I + ++
Sbjct: 350 KIRSKVELEVRD----------LPEELSLSFNATCLNNE--VIPGLKSCMGLKIGDTVSF 397
Query: 370 S-QKKVRNATEAIGKVFSLDREAF 392
S + KVR + K F++ F
Sbjct: 398 SIEAKVRGCPQEKEKSFTIKPVGF 421
>pdb|3KR3|H Chain H, Crystal Structure Of Igf-Ii Antibody Complex
Length = 251
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 288 GGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRAL 324
GGL+ + ++ GF S Y+ WW+RQ + L
Sbjct: 9 GGLVQPGGSLRLSCAASGFTFSNYIMWWVRQAPGKGL 45
>pdb|3NID|B Chain B, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NID|D Chain D, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NIF|B Chain B, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIF|D Chain D, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|B Chain B, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|D Chain D, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
Length = 471
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 60/144 (41%), Gaps = 22/144 (15%)
Query: 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 314
L EKL N+ L+ ++ + N+ + ++L+ G +G+L DSS ++ Y
Sbjct: 294 LMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL----SMDSSNVLQLIVDAYG 349
Query: 315 WIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD-----RIAEYLNM 369
IR V + + L E L L NA E V P + +I + ++
Sbjct: 350 KIRSKVELEVRD----------LPEELSLSFNATCLNNE--VIPGLKSCMGLKIGDTVSF 397
Query: 370 S-QKKVRNATEAIGKVFSLDREAF 392
S + KVR + K F++ F
Sbjct: 398 SIEAKVRGCPQEKEKSFTIKPVGF 421
>pdb|3IJE|B Chain B, Crystal Structure Of The Complete Integrin Alhavbeta3
Ectodomain Plus An Alpha/beta Transmembrane Fragment
Length = 695
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 60/144 (41%), Gaps = 22/144 (15%)
Query: 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 314
L EKL N+ L+ ++ + N+ + ++L+ G +G+L DSS ++ Y
Sbjct: 294 LMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL----SMDSSNVLQLIVDAYG 349
Query: 315 WIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD-----RIAEYLNM 369
IR V + + L E L L NA E V P + +I + ++
Sbjct: 350 KIRSKVELEVRD----------LPEELSLSFNATCLNNE--VIPGLKSCMGLKIGDTVSF 397
Query: 370 S-QKKVRNATEAIGKVFSLDREAF 392
S + KVR + K F++ F
Sbjct: 398 SIEAKVRGCPQEKEKSFTIKPVGF 421
>pdb|1JV2|B Chain B, Crystal Structure Of The Extracellular Segment Of Integrin
Alphavbeta3
pdb|1L5G|B Chain B, Crystal Structure Of The Extracellular Segment Of Integrin
Avb3 In Complex With An Arg-Gly-Asp Ligand
pdb|1M1X|B Chain B, Crystal Structure Of The Extracellular Segment Of Integrin
Alpha Vbeta3 Bound To Mn2+
pdb|1U8C|B Chain B, A Novel Adaptation Of The Integrin Psi Domain Revealed
From Its Crystal Structure
Length = 692
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 60/144 (41%), Gaps = 22/144 (15%)
Query: 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 314
L EKL N+ L+ ++ + N+ + ++L+ G +G+L DSS ++ Y
Sbjct: 294 LMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL----SMDSSNVLQLIVDAYG 349
Query: 315 WIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD-----RIAEYLNM 369
IR V + + L E L L NA E V P + +I + ++
Sbjct: 350 KIRSKVELEVRD----------LPEELSLSFNATCLNNE--VIPGLKSCMGLKIGDTVSF 397
Query: 370 S-QKKVRNATEAIGKVFSLDREAF 392
S + KVR + K F++ F
Sbjct: 398 SIEAKVRGCPQEKEKSFTIKPVGF 421
>pdb|4G1M|B Chain B, Re-Refinement Of Alpha V Beta 3 Structure
Length = 692
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 60/144 (41%), Gaps = 22/144 (15%)
Query: 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 314
L EKL N+ L+ ++ + N+ + ++L+ G +G+L DSS ++ Y
Sbjct: 294 LMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL----SMDSSNVLQLIVDAYG 349
Query: 315 WIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD-----RIAEYLNM 369
IR V + + L E L L NA E V P + +I + ++
Sbjct: 350 KIRSKVELEVRD----------LPEELSLSFNATCLNNE--VIPGLKSCMGLKIGDTVSF 397
Query: 370 S-QKKVRNATEAIGKVFSLDREAF 392
S + KVR + K F++ F
Sbjct: 398 SIEAKVRGCPQEKEKSFTIKPVGF 421
>pdb|4G1E|B Chain B, Crystal Structure Of Integrin Alpha V Beta 3 With
Coil-Coiled Tag
Length = 738
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 60/144 (41%), Gaps = 22/144 (15%)
Query: 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 314
L EKL N+ L+ ++ + N+ + ++L+ G +G+L DSS ++ Y
Sbjct: 294 LMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL----SMDSSNVLQLIVDAYG 349
Query: 315 WIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD-----RIAEYLNM 369
IR V + + L E L L NA E V P + +I + ++
Sbjct: 350 KIRSKVELEVRD----------LPEELSLSFNATCLNNE--VIPGLKSCMGLKIGDTVSF 397
Query: 370 S-QKKVRNATEAIGKVFSLDREAF 392
S + KVR + K F++ F
Sbjct: 398 SIEAKVRGCPQEKEKSFTIKPVGF 421
>pdb|3FCS|B Chain B, Structure Of Complete Ectodomain Of Integrin Aiibb3
pdb|3FCS|D Chain D, Structure Of Complete Ectodomain Of Integrin Aiibb3
Length = 690
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 60/144 (41%), Gaps = 22/144 (15%)
Query: 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 314
L EKL N+ L+ ++ + N+ + ++L+ G +G+L DSS ++ Y
Sbjct: 294 LMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL----SMDSSNVLQLIVDAYG 349
Query: 315 WIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD-----RIAEYLNM 369
IR V + + L E L L NA E V P + +I + ++
Sbjct: 350 KIRSKVELEVRD----------LPEELSLSFNATCLNNE--VIPGLKSCMGLKIGDTVSF 397
Query: 370 S-QKKVRNATEAIGKVFSLDREAF 392
S + KVR + K F++ F
Sbjct: 398 SIEAKVRGCPQEKEKSFTIKPVGF 421
>pdb|3HI5|H Chain H, Crystal Structure Of Fab Fragment Of Al-57
pdb|3HI6|H Chain H, Crystal Structure Of Intermediate Affinity I Domain Of
Integrin Lfa-1 With The Fab Fragment Of Its Antibody
Al-57
pdb|3HI6|X Chain X, Crystal Structure Of Intermediate Affinity I Domain Of
Integrin Lfa-1 With The Fab Fragment Of Its Antibody
Al-57
Length = 220
Score = 30.0 bits (66), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 288 GGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRAL 324
GGL+ + ++ GF S YV WW+RQ + L
Sbjct: 9 GGLVQPGGSLRLSCAASGFTFSRYVMWWVRQAPGKGL 45
>pdb|1K9X|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1K9X|B Chain B, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1K9X|C Chain C, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1K9X|D Chain D, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1KA2|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Mg
pdb|1KA4|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Nat-Pb
Length = 499
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 30/55 (54%)
Query: 200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECS 254
V+S ELL H E V L +K K +L++++ + L S+RI+R + E S
Sbjct: 55 VLSHELLLHPEFVNLVEKAKGLENLNEYERGIVRVLDRSIRIARAFPPEFIREVS 109
>pdb|3OP4|A Chain A, Crystal Structure Of Putative
3-Ketoacyl-(Acyl-Carrier-Protein) Reductase From Vibrio
Cholerae O1 Biovar Eltor Str. N16961 In Complex With
Nadp+
pdb|3OP4|B Chain B, Crystal Structure Of Putative
3-Ketoacyl-(Acyl-Carrier-Protein) Reductase From Vibrio
Cholerae O1 Biovar Eltor Str. N16961 In Complex With
Nadp+
Length = 248
Score = 28.9 bits (63), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 39/180 (21%), Positives = 70/180 (38%), Gaps = 27/180 (15%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
L NG ++ +PE I+ LK ++L + G++ D+ R
Sbjct: 53 LGDNGKGXALNVTNPESIEAVLKAITDEFGGVDILVN----------NAGITRDNLLXRX 102
Query: 232 KER---------LGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 282
KE L S R+S+ ++L R+ +++ V S+ N G
Sbjct: 103 KEEEWSDIXETNLTSIFRLSK----AVLRGXXKKRQGRIIN----VGSVVGTXGNAGQAN 154
Query: 283 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 342
+ G+IG + + +S+G ++T +I ++AL + RT L RLG
Sbjct: 155 YAAAKAGVIGFTKSXAREVASRGVTVNTVAPGFIETDXTKALNDEQRTATLAQVPAGRLG 214
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
0.316 0.131 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,046,111
Number of Sequences: 62578
Number of extensions: 496074
Number of successful extensions: 1727
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 41
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1672
Number of HSP's gapped (non-prelim): 48
length of query: 499
length of database: 14,973,337
effective HSP length: 103
effective length of query: 396
effective length of database: 8,527,803
effective search space: 3377009988
effective search space used: 3377009988
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: 53 (25.0 bits)