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= 020126
(330 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 = 81.6 bits (200), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 50/153 (32%), Positives = 84/153 (54%), Gaps = 15/153 (9%)
Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLS----------LDDHKLR--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 GLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
G GL+R +EKF+ + FK STY WWIRQ+I+
Sbjct: 125 GNQGLIRAVEKFEYKRRFKFSTYATWWIRQAIN 157
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 80.9 bits (198), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 51/66 (77%)
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 IRQSIS 330
IRQ+I+
Sbjct: 435 IRQAIT 440
>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 = 80.9 bits (198), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 51/66 (77%)
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 IRQSIS 330
IRQ+I+
Sbjct: 435 IRQAIT 440
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 80.9 bits (198), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 51/66 (77%)
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 IRQSIS 330
IRQ+I+
Sbjct: 326 IRQAIT 331
>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 = 80.1 bits (196), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 55/178 (30%), Positives = 90/178 (50%), Gaps = 34/178 (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 NVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
N+RLV+SIA++Y G DL+Q G GL+R +EKF+ + FK STY WWIRQ+I+
Sbjct: 119 NLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAIN 176
>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 = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 35/73 (47%), Positives = 49/73 (67%)
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 STYVYWWIRQSIS 330
STY WWIRQ+I+
Sbjct: 236 STYATWWIRQAIN 248
>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 = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 35/73 (47%), Positives = 49/73 (67%)
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 STYVYWWIRQSIS 330
STY WWIRQ+I+
Sbjct: 236 STYATWWIRQAIN 248
>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 = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 35/73 (47%), Positives = 49/73 (67%)
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 STYVYWWIRQSIS 330
STY WWIRQ+I+
Sbjct: 256 STYATWWIRQAIN 268
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 35/73 (47%), Positives = 49/73 (67%)
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 STYVYWWIRQSIS 330
STY WWIRQ+I+
Sbjct: 251 STYATWWIRQAIN 263
>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 = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 35/73 (47%), Positives = 49/73 (67%)
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 STYVYWWIRQSIS 330
STY WWIRQ+I+
Sbjct: 159 STYATWWIRQAIN 171
>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 = 79.0 bits (193), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 35/73 (47%), Positives = 49/73 (67%)
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 STYVYWWIRQSIS 330
STY WWIRQ+I+
Sbjct: 160 STYATWWIRQAIN 172
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 57.8 bits (138), Expect = 9e-09, 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 = 36.6 bits (83), Expect = 0.020, 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|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|C Chain C, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|E Chain E, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|G Chain G, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1SC5|A Chain A, Sigma-28(Flia)FLGM COMPLEX
Length = 239
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 264 LAREKLVMSNVRLVMSIA---QRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
+ RE+L++ + LV +IA +++ D+ DL+ G+IGL++ ++ + + Y
Sbjct: 12 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 71
Query: 321 VYWWIRQSI 329
+ I+ +I
Sbjct: 72 IKLRIKGAI 80
Score = 31.2 bits (69), Expect = 0.89, 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|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 = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/90 (24%), 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 IGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
+G+L DSS ++ Y IR +
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 = 1.5, Method: Compositional matrix adjust.
Identities = 22/90 (24%), 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 IGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
+G+L DSS ++ Y IR +
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 = 1.5, Method: Compositional matrix adjust.
Identities = 22/90 (24%), 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 IGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
+G+L DSS ++ Y IR +
Sbjct: 330 VGVL----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 = 1.6, Method: Compositional matrix adjust.
Identities = 22/90 (24%), 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 IGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
+G+L DSS ++ Y IR +
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 = 1.6, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 323
L EKL N+ L+ ++ + N+ + ++L+ G +G+L DSS ++ Y
Sbjct: 294 LMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVL----SMDSSNVLQLIVDAYG 349
Query: 324 WIRQSI 329
IR +
Sbjct: 350 KIRSKV 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 = 1.6, Method: Compositional matrix adjust.
Identities = 22/90 (24%), 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 IGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
+G+L DSS ++ Y IR +
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIRSKV 355
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 22/90 (24%), 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 IGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
+G+L DSS ++ Y IR +
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 = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/90 (24%), 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 IGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
+G+L DSS ++ Y IR +
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 = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/90 (24%), 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 IGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
+G+L DSS ++ Y IR +
Sbjct: 330 VGVL----SMDSSNVLQLIVDAYGKIRSKV 355
>pdb|3KR3|H Chain H, Crystal Structure Of Igf-Ii Antibody Complex
Length = 251
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 311 SSKGFKISTYVYWWIRQS 328
++ GF S Y+ WW+RQ+
Sbjct: 23 AASGFTFSNYIMWWVRQA 40
>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 = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
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-WWIRQSI 329
S KG ++ W RQS+
Sbjct: 169 LHSDKGGNFEAALWQQWDRQSL 190
>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 = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 297 GGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 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
0.315 0.129 0.353
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,815,928
Number of Sequences: 62578
Number of extensions: 257072
Number of successful extensions: 847
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 814
Number of HSP's gapped (non-prelim): 36
length of query: 330
length of database: 14,973,337
effective HSP length: 99
effective length of query: 231
effective length of database: 8,778,115
effective search space: 2027744565
effective search space used: 2027744565
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: 52 (24.6 bits)