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= 016321
(391 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 = 78.6 bits (192), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 49/151 (32%), Positives = 81/151 (53%), Gaps = 15/151 (9%)
Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGL----------SLDDHKLR--LKERLGCEPS 240
++ Y+ + LLT E + L++K++ G+ LD +R ++ ++
Sbjct: 5 VRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTAR 64
Query: 241 MEQLAASLRISRPELQ---SILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 297
+E++ L+ EL+ I E AR+ L+ +N+RLV+SIA++Y G DL+Q
Sbjct: 65 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQE 124
Query: 298 GLIGLLRGIEKFDSSKGFKISTYVYWWIRQV 328
G GL+R +EKF+ + FK STY WWIRQ
Sbjct: 125 GNQGLIRAVEKFEYKRRFKFSTYATWWIRQA 155
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 31/63 (49%), Positives = 48/63 (76%)
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 IRQ 327
IRQ
Sbjct: 435 IRQ 437
>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 = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 31/63 (49%), Positives = 48/63 (76%)
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 IRQ 327
IRQ
Sbjct: 435 IRQ 437
>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 = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 54/175 (30%), Positives = 87/175 (49%), Gaps = 34/175 (19%)
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 NVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327
N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK STY WWIRQ
Sbjct: 119 NLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQ 173
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 31/63 (49%), Positives = 48/63 (76%)
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 IRQ 327
IRQ
Sbjct: 326 IRQ 328
>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 = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 34/71 (47%), Positives = 46/71 (64%)
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 STYVYWWIRQV 328
STY WWIRQ
Sbjct: 236 STYATWWIRQA 246
>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 = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 34/71 (47%), Positives = 46/71 (64%)
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 STYVYWWIRQV 328
STY WWIRQ
Sbjct: 236 STYATWWIRQA 246
>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 = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 34/71 (47%), Positives = 46/71 (64%)
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 STYVYWWIRQV 328
STY WWIRQ
Sbjct: 256 STYATWWIRQA 266
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 34/71 (47%), Positives = 46/71 (64%)
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 STYVYWWIRQV 328
STY WWIRQ
Sbjct: 251 STYATWWIRQA 261
>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 = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 34/71 (47%), Positives = 46/71 (64%)
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 STYVYWWIRQV 328
STY WWIRQ
Sbjct: 159 STYATWWIRQA 169
>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 = 76.3 bits (186), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 34/70 (48%), Positives = 46/70 (65%)
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 STYVYWWIRQ 327
STY WWIRQ
Sbjct: 160 STYATWWIRQ 169
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 38/56 (67%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
AR++++ N+RLV S+ QR+ N G + DL Q G IGLL+ ++KFD S K STY
Sbjct: 29 ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTY 84
>pdb|3MZY|A Chain A, The Crystal Structure Of The Rna Polymerase Sigma-H Factor
F Fusobacterium Nucleatum To 2.5a
Length = 164
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 288 GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLI---CTFKQFI--AW 342
GA+ DLVQ G++GLL+ I+ +D +K S++ + IR+ + I T K +
Sbjct: 1 GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREXISAIRKANTQKHXVLNEA 59
Query: 343 LKTDVLLKNQLKFD 356
LKT+ +L++ FD
Sbjct: 60 LKTNAILEDSAYFD 73
>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 = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 264 LAREKLVMSNVRLVMSIA---QRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
+ RE+L++ + LV +IA +++ D+ DL+ G+IGL++ ++ + + Y
Sbjct: 12 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 71
Query: 321 VYWWIR 326
+ I+
Sbjct: 72 IKLRIK 77
Score = 30.4 bits (67), Expect = 1.6, 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|3V7O|A Chain A, Crystal Structure Of The C-Terminal Domain Of Ebola Virus
Vp30 (Strain Reston-89)
pdb|3V7O|B Chain B, Crystal Structure Of The C-Terminal Domain Of Ebola Virus
Vp30 (Strain Reston-89)
Length = 227
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 249 RISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308
+I +L+++L C++ K S + L+ R++ +G D AD V L ++
Sbjct: 116 QIEDSKLRALLTLCAVLTRKFSKSQLGLLCETHLRHEGLGQDQADSV-------LEVYQR 168
Query: 309 FDSSKGFKISTYVY-WWIRQVRLLLICTF 336
S KG ++ W RQ ++ I F
Sbjct: 169 LHSDKGGNFEAALWQQWDRQSLIMFISAF 197
>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 = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIR 326
+G+L DSS ++ Y IR
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIR 352
>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 = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIR 326
+G+L DSS ++ Y IR
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIR 352
>pdb|3IJE|B Chain B, Crystal Structure Of The Complete Integrin Alhavbeta3
Ectodomain Plus An Alpha/beta Transmembrane Fragment
Length = 695
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIR 326
+G+L DSS ++ Y IR
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIR 352
>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 = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIR 326
+G+L DSS ++ Y IR
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIR 352
>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 = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIR 326
+G+L DSS ++ Y IR
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIR 352
>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 = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIR 326
+G+L DSS ++ Y IR
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIR 352
>pdb|4G1E|B Chain B, Crystal Structure Of Integrin Alpha V Beta 3 With
Coil-Coiled Tag
Length = 738
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIR 326
+G+L DSS ++ Y IR
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIR 352
>pdb|4G1M|B Chain B, Re-Refinement Of Alpha V Beta 3 Structure
Length = 692
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIR 326
+G+L DSS ++ Y IR
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIR 352
>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 = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
S +AS + P L L EKL N+ L+ ++ + N+ + ++L+ G
Sbjct: 277 SDNHYSASTTMDYPSL-------GLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTT 329
Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIR 326
+G+L DSS ++ Y IR
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIR 352
>pdb|3KR3|H Chain H, Crystal Structure Of Igf-Ii Antibody Complex
Length = 251
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 311 SSKGFKISTYVYWWIRQV 328
++ GF S Y+ WW+RQ
Sbjct: 23 AASGFTFSNYIMWWVRQA 40
>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 = 28.1 bits (61), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 297 GGLIGLLRGIEKFDSSKGFKISTYVYWWIRQV 328
GGL+ + ++ GF S YV WW+RQ
Sbjct: 9 GGLVQPGGSLRLSCAASGFTFSRYVMWWVRQA 40
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.131 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,411,753
Number of Sequences: 62578
Number of extensions: 321285
Number of successful extensions: 907
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 874
Number of HSP's gapped (non-prelim): 35
length of query: 391
length of database: 14,973,337
effective HSP length: 101
effective length of query: 290
effective length of database: 8,652,959
effective search space: 2509358110
effective search space used: 2509358110
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)