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= 011454
(485 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 = 137 bits (345), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 75/239 (31%), Positives = 138/239 (57%), Gaps = 23/239 (9%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
A++++V +N+RLV+SIA++Y N G DL+Q G IGL++ ++KF+ +G+K STY WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
IRQ ++R++ + +RT+R+P H+ E + L R ++ L+E G P+ + +AE + M + K+
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 384 RNATEVLA-------------------YIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 424
R ++ +I D +E P +L+ + ++ L
Sbjct: 495 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLE-LPLDSATTESLRAATHD-VLAGLT 552
Query: 425 EREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 482
RE +++R+ +G+D T E++ K+ ++RER+RQ+ AL KL+H +R + + + L
Sbjct: 553 AREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 136 bits (343), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 75/239 (31%), Positives = 138/239 (57%), Gaps = 23/239 (9%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
A++++V +N+RLV+SIA++Y N G DL+Q G IGL++ ++KF+ +G+K STY WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
IRQ ++R++ + +RT+R+P H+ E + L R ++ L+E G P+ + +AE + M + K+
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 384 RNATEVLA-------------------YIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 424
R ++ +I D +E P +L+ + ++ L
Sbjct: 495 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLE-LPLDSATTESLRAATHD-VLAGLT 552
Query: 425 EREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 482
RE +++R+ +G+D T E++ K+ ++RER+RQ+ AL KL+H +R + + + L
Sbjct: 553 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611
>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|Q Chain Q, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
Length = 332
Score = 129 bits (324), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 103/328 (31%), Positives = 168/328 (51%), Gaps = 39/328 (11%)
Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGL----------SLDDHKLR--LKERLGCEPS 240
++ Y+ + LLT E + L++K++ G+ LD +R ++ ++
Sbjct: 5 VRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTAR 64
Query: 241 MEQLAASLRISRPELQSILM---ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 297
+E++ L+ EL+ L E AR+ L+ +N+RLV+SIA++Y G DL+Q
Sbjct: 65 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQE 124
Query: 298 GLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNA 356
G GL+R +EKF+ + FK STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A
Sbjct: 125 GNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTA 184
Query: 357 KLRLEEKGVTPSVDRIA-------------EYLNMSQKKVRNAT----EVLAYIADNRVE 399
+ +E G PS + IA E L ++Q+ V T E ++ D +
Sbjct: 185 RQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPD 244
Query: 400 NN---PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSR 455
N P L +E+ K + L ERE +++L GL D T E++ G++R
Sbjct: 245 ENLPSPVEAAAQSLLSEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTR 303
Query: 456 ERVRQVGLVALEKLK-HAARKKKMEAML 482
ER+RQ+ AL KLK H +R +K+ L
Sbjct: 304 ERIRQIENKALRKLKYHESRTRKLRDFL 331
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 128 bits (322), Expect = 7e-30, Method: Compositional matrix adjust.
Identities = 87/249 (34%), Positives = 133/249 (53%), Gaps = 26/249 (10%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 191 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 250
Query: 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIA--- 373
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G PS + IA
Sbjct: 251 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAM 310
Query: 374 ----------EYLNMSQKKVRNATEV--------LAYIADNRVENNPWHGVDDWALKDEV 415
E L ++Q+ V T + +I D + +P L +E+
Sbjct: 311 GPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENL-PSPVEAAAQSLLSEEL 369
Query: 416 NKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAA 473
K + L ERE +++L GL D T E++ G++RER+RQ+ AL KLK H +
Sbjct: 370 EK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHES 428
Query: 474 RKKKMEAML 482
R +K+ L
Sbjct: 429 RTRKLRDFL 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 = 127 bits (320), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 86/249 (34%), Positives = 133/249 (53%), Gaps = 26/249 (10%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 176 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 235
Query: 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIA--- 373
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G P+ + IA
Sbjct: 236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 295
Query: 374 ----------EYLNMSQKKVRNATEV--------LAYIADNRVENNPWHGVDDWALKDEV 415
E L ++Q+ V T + +I D + +P L +E+
Sbjct: 296 GPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHL-PSPVDAATQSLLSEEL 354
Query: 416 NKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAA 473
K + L ERE +++L GL D T E++ G++RER+RQ+ AL KLK H +
Sbjct: 355 EK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHES 413
Query: 474 RKKKMEAML 482
R +K+ L
Sbjct: 414 RTRKLRDFL 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 = 127 bits (320), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 86/249 (34%), Positives = 133/249 (53%), Gaps = 26/249 (10%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 176 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 235
Query: 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIA--- 373
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G P+ + IA
Sbjct: 236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 295
Query: 374 ----------EYLNMSQKKVRNATEV--------LAYIADNRVENNPWHGVDDWALKDEV 415
E L ++Q+ V T + +I D + +P L +E+
Sbjct: 296 GPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHL-PSPVDAATQSLLSEEL 354
Query: 416 NKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAA 473
K + L ERE +++L GL D T E++ G++RER+RQ+ AL KLK H +
Sbjct: 355 EK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHES 413
Query: 474 RKKKMEAML 482
R +K+ L
Sbjct: 414 RTRKLRDFL 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 = 127 bits (319), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 86/249 (34%), Positives = 133/249 (53%), Gaps = 26/249 (10%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 196 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 255
Query: 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIA--- 373
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G P+ + IA
Sbjct: 256 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 315
Query: 374 ----------EYLNMSQKKVRNATEV--------LAYIADNRVENNPWHGVDDWALKDEV 415
E L ++Q+ V T + +I D + +P L +E+
Sbjct: 316 GPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHL-PSPVDAATQSLLSEEL 374
Query: 416 NKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAA 473
K + L ERE +++L GL D T E++ G++RER+RQ+ AL KLK H +
Sbjct: 375 EK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHES 433
Query: 474 RKKKMEAML 482
R +K+ L
Sbjct: 434 RTRKLRDFL 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 = 107 bits (266), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 72/226 (31%), Positives = 118/226 (52%), Gaps = 35/226 (15%)
Query: 185 SPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL----------SLDDHKLR---- 230
P + + ++ Y+ + LLT E + L++K++ G+ LD +R
Sbjct: 1 GPHMTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVR 60
Query: 231 --------------LKERLGCEP-SMEQLAASLRISRPELQ---SILMECSLAREKLVMS 272
LKE+ +P ++E++ L+ EL+ I E AR+ L+ +
Sbjct: 61 AKILGTARIQKIPGLKEK--PDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEA 118
Query: 273 NVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRA 332
N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK STY WWIRQ ++RA
Sbjct: 119 NLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRA 178
Query: 333 LVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLN 377
+ + +RT+R+P H+ E + L R A+ +E G PS + IAE +
Sbjct: 179 IADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMG 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 = 106 bits (264), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 52/121 (42%), Positives = 77/121 (63%), Gaps = 1/121 (0%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK
Sbjct: 100 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 159
Query: 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
STY WWIRQ ++RA+ + +RT+R+P H+ E + L R A+ +E G PS + IAE +
Sbjct: 160 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAM 219
Query: 377 N 377
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 = 89.4 bits (220), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 77/224 (34%), Positives = 117/224 (52%), Gaps = 28/224 (12%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
AR++++ N+RLV S+ QR+ N G + DL Q G IGLL+ ++KFD S K STY
Sbjct: 29 ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEE-KGVTPSVDRIAEYLNMS---- 379
I + R L ++ T+++ L E IR AK L + +G P+V IA++L +S
Sbjct: 89 IIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 380 ---QKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVN-------KLIIVTLGERERE 429
Q+ VR T + + +N + +P +D A DE + K I L ERER
Sbjct: 148 VLAQEAVRLPTSIHETVYEN--DGDPITLLDQIADADEASWFDKIALKKAIEELDERERL 205
Query: 430 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEK--LKH 471
I+ L Y D+ T +++ R+G+S QV + LEK L+H
Sbjct: 206 IVYLRYYKDQ---TQSEVASRLGIS-----QVQMSRLEKKILQH 241
>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 = 85.5 bits (210), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 37/81 (45%), Positives = 54/81 (66%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
I E AR+ L+ +N+RLV+SIA++Y G DL+Q G GL+R +EKF+ +GF
Sbjct: 99 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAF 158
Query: 318 STYVYWWIRQGVSRALVENSR 338
STY WWIRQ ++RA+ + +R
Sbjct: 159 STYATWWIRQAINRAIADQAR 179
>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: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
A++++V +N+RLV+SIA++Y N G DL+Q G IGL++ ++KF+ +G+K STY WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 325 IRQGVSRALVENSR 338
IRQ ++R++ + +R
Sbjct: 326 IRQAITRSIADQAR 339
>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 73
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 1/65 (1%)
Query: 419 IIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477
++ TL +RE ++RL +GLD T E++ K G++RER+RQ+ AL KL+H +R K+
Sbjct: 8 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKR 67
Query: 478 MEAML 482
++ +
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: 411 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKL 469
+++E+ K ++ TL RE ++R+ YGL D + T E++ + ++RER+RQ+ + AL KL
Sbjct: 8 MREELEK-VLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKL 66
Query: 470 KHAARKKKMEAML 482
+H +R K ++++L
Sbjct: 67 RHPSRSKYLKSLL 79
>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
Length = 81
Score = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 419 IIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477
++ L RE +++R+ +G+D T E++ K+ ++RER+RQ+ AL KL+H +R +
Sbjct: 15 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 74
Query: 478 MEAML 482
+ + 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: 419 IIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477
++ L RE +++R+ +G+D T E++ K+ ++RER+RQ+ AL KL+H +R +
Sbjct: 2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61
Query: 478 MEAML 482
+ + L
Sbjct: 62 LRSFL 66
>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 = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 56/231 (24%), Positives = 112/231 (48%), Gaps = 32/231 (13%)
Query: 264 LAREKLVMSNVRLVMSIA---QRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
+ RE+L++ + LV +IA +++ D+ DL+ G+IGL++ ++ + + Y
Sbjct: 12 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 71
Query: 321 VYWWIRQGVS---RALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYL 376
+ I+ + R+L SR +R E+ I+ +L+EK G P+ + +A+ L
Sbjct: 72 IKLRIKGAIYDYLRSLDFGSRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKEL 125
Query: 377 NMSQKK------------VRNATEVLAYIADNRVENNPWH-GVDDWALKDEVNKLI---I 420
+S ++ + + EV A + E P V++ +K E+ + + +
Sbjct: 126 GISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTNVEEEVIKRELTEKVKEAV 185
Query: 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471
L ERE+ +I+L + E L ++++K + S RV Q+ ALE+L+
Sbjct: 186 SKLPEREKLVIQLIFY---EELPAKEVAKILETSVSRVSQLKAKALERLRE 233
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
+LKE+LG EP+ E++A L IS EL L + N ++S+ + + +
Sbjct: 107 KLKEKLGREPTDEEVAKELGISTEELFKTLDKI----------NFSYILSLEEVFRDFAR 156
Query: 290 DMADLV 295
D ++L+
Sbjct: 157 DYSELI 162
>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: 419 IIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474
++ 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: 419 IIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471
++ 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 = 0.003, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 423 LGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAM 481
L ERE ++++ GL D T E++ G++RER+RQ+ AL KL+H +R +K+
Sbjct: 11 LSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRHPSRSEKLRDF 70
Query: 482 L 482
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: 288 GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327
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 = 37.0 bits (84), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
Query: 423 LGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAARKKKMEA 480
L ERE +++L GL D T E++ G++RER+RQ+ AL KLK H +R +K+
Sbjct: 11 LSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRD 70
Query: 481 ML 482
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 = 36.2 bits (82), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
Query: 423 LGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAARKKKMEA 480
L ERE ++++ GL D T E++ G++RER+RQ+ AL KLK H +R +K+
Sbjct: 11 LSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRD 70
Query: 481 ML 482
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 = 35.0 bits (79), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 38/180 (21%), Positives = 77/180 (42%), Gaps = 18/180 (10%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
L NG ++ +PE I+ LK ++L + G++ D+ +R+
Sbjct: 56 LGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVN----------NAGITRDNLLMRM 105
Query: 232 KERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 291
KE + L + R+S+ L+ ++ + R+ +++ V S+ N G
Sbjct: 106 KEEEWSDIMETNLTSIFRLSKAVLRGMMKK----RQGRIIN----VGSVVGTMGNAGQAN 157
Query: 292 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351
+ 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 = 35.0 bits (79), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 38/180 (21%), Positives = 77/180 (42%), Gaps = 18/180 (10%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
L NG ++ +PE I+ LK ++L + G++ D+ +R+
Sbjct: 56 LGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVN----------NAGITRDNLLMRM 105
Query: 232 KERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 291
KE + L + R+S+ L+ ++ + R+ +++ V S+ N G
Sbjct: 106 KEEEWSDIMETNLTSIFRLSKAVLRGMMKK----RQGRIIN----VGSVVGTMGNAGQAN 157
Query: 292 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351
+ 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 = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 41/183 (22%), Positives = 80/183 (43%), Gaps = 24/183 (13%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVK---GVVSEELLTHAEVVRLSKKIKTGLSLDDHK 228
L NG ++ +PE I+ LK GV + L+ +A++ R D+
Sbjct: 56 LGDNGKGMALNVTNPESIEAVLKAITDEFGGV--DILVNNADITR-----------DNLL 102
Query: 229 LRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMG 288
+R+KE + L + R+S+ L+ ++ + R+ +++ V S+ N G
Sbjct: 103 MRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKK----RQGRIIN----VGSVVGTMGNAG 154
Query: 289 ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE 348
+ G+IG + + + +S+G ++T +I +++AL + RT L
Sbjct: 155 QANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAG 214
Query: 349 RLG 351
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 = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 38/180 (21%), Positives = 76/180 (42%), Gaps = 18/180 (10%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
L NG ++ +PE I+ LK ++L + G++ D+ +R+
Sbjct: 56 LGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVN----------NAGITRDNLLMRM 105
Query: 232 KERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 291
KE + L + R+S+ L+ ++ + R+ +++ V S+ N G
Sbjct: 106 KEEEWSDIMETNLTSIFRLSKAVLRGMMKK----RQGRIIN----VGSVVGTMGNAGQAN 157
Query: 292 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351
+ 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 = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 41/183 (22%), Positives = 79/183 (43%), Gaps = 24/183 (13%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVK---GVVSEELLTHAEVVRLSKKIKTGLSLDDHK 228
L NG ++ +PE I+ LK GV + L+ +A + R D+
Sbjct: 56 LGDNGKGMALNVTNPESIEAVLKAITDEFGGV--DILVNNAAITR-----------DNLL 102
Query: 229 LRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMG 288
+R+KE + L + R+S+ L+ ++ + R+ +++ V S+ N G
Sbjct: 103 MRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKK----RQGRIIN----VGSVVGTMGNAG 154
Query: 289 ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE 348
+ G+IG + + + +S+G ++T +I +++AL + RT L
Sbjct: 155 QANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAG 214
Query: 349 RLG 351
RLG
Sbjct: 215 RLG 217
>pdb|3KR3|H Chain H, Crystal Structure Of Igf-Ii Antibody Complex
Length = 251
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 297 GGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRAL 333
GGL+ + ++ GF S Y+ WW+RQ + L
Sbjct: 9 GGLVQPGGSLRLSCAASGFTFSNYIMWWVRQAPGKGL 45
>pdb|3GIZ|H Chain H, Crystal Structure Of The Fab Fragment Of Anti-Cd20
Antibody Ofatumumab
Length = 222
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 31/126 (24%), Positives = 48/126 (38%), Gaps = 23/126 (18%)
Query: 297 GGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRAL------VENSRTLRLPNHLHERL 350
GGL+ R + ++ GF + Y W+RQ + L NS ++ + + R
Sbjct: 9 GGLVQPGRSLRLSCAASGFTFNDYAMHWVRQAPGKGLEWVSTISWNSGSIGYADSVKGRF 68
Query: 351 GLIR-NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDW 409
+ R NAK L YL M +R L Y A + N ++G+D W
Sbjct: 69 TISRDNAKKSL--------------YLQM--NSLRAEDTALYYCAKDIQYGNYYYGMDVW 112
Query: 410 ALKDEV 415
V
Sbjct: 113 GQGTTV 118
>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 = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329
+G+L DSS ++ Y IR V
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIRSKV 355
>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 = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 11/85 (12%)
Query: 245 AASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR 304
+AS + P L L EKL N+ L+ ++ + N+ + ++L+ G +G+L
Sbjct: 282 SASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL- 333
Query: 305 GIEKFDSSKGFKISTYVYWWIRQGV 329
DSS ++ Y IR V
Sbjct: 334 ---SMDSSNVLQLIVDAYGKIRSKV 355
>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 = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329
+G+L DSS ++ Y IR V
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIRSKV 355
>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 = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329
+G+L DSS ++ Y IR V
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIRSKV 355
>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 = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 38/180 (21%), Positives = 71/180 (39%), Gaps = 18/180 (10%)
Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
L NG ++ +PE I+ LK ++L + G++ D+ R
Sbjct: 53 LGDNGKGXALNVTNPESIEAVLKAITDEFGGVDILVN----------NAGITRDNLLXRX 102
Query: 232 KERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 291
KE + L + R+S+ ++L R+ +++ V S+ N G
Sbjct: 103 KEEEWSDIXETNLTSIFRLSK----AVLRGXXKKRQGRIIN----VGSVVGTXGNAGQAN 154
Query: 292 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351
+ G+IG + + +S+G ++T +I ++AL + RT L RLG
Sbjct: 155 YAAAKAGVIGFTKSXAREVASRGVTVNTVAPGFIETDXTKALNDEQRTATLAQVPAGRLG 214
>pdb|3IJE|B Chain B, Crystal Structure Of The Complete Integrin Alhavbeta3
Ectodomain Plus An Alpha/beta Transmembrane Fragment
Length = 695
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329
+G+L DSS ++ Y IR V
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIRSKV 355
>pdb|4G1M|B Chain B, Re-Refinement Of Alpha V Beta 3 Structure
Length = 692
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329
+G+L DSS ++ Y IR V
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIRSKV 355
>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 = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329
+G+L DSS ++ Y IR V
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIRSKV 355
>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 = 2.5, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329
+G+L DSS ++ Y IR V
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIRSKV 355
>pdb|4G1E|B Chain B, Crystal Structure Of Integrin Alpha V Beta 3 With
Coil-Coiled Tag
Length = 738
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329
+G+L DSS ++ Y IR V
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIRSKV 355
>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 = 3.2, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 297 GGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRAL 333
GGL+ + ++ GF S YV WW+RQ + L
Sbjct: 9 GGLVQPGGSLRLSCAASGFTFSRYVMWWVRQAPGKGL 45
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.131 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,280,093
Number of Sequences: 62578
Number of extensions: 457841
Number of successful extensions: 1801
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 41
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1744
Number of HSP's gapped (non-prelim): 53
length of query: 485
length of database: 14,973,337
effective HSP length: 103
effective length of query: 382
effective length of database: 8,527,803
effective search space: 3257620746
effective search space used: 3257620746
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)