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= psy4493
(323 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2V1X|B Chain B, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2WWY|A Chain A, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
pdb|2WWY|B Chain B, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
Length = 591
Score = 275 bits (702), Expect = 3e-74, Method: Compositional matrix adjust.
Identities = 141/335 (42%), Positives = 193/335 (57%), Gaps = 69/335 (20%)
Query: 48 DYPWSDRVRSVLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPTGK-------------- 93
D+PWS +V+ +L++ F L FRP QL IN+ + K+ ++MPTG
Sbjct: 25 DFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSD 84
Query: 94 ------------------LLKKKKIC-------------------LMTESSSLKLLYVSP 116
+LK+ I ++ ++S LKL+YV+P
Sbjct: 85 GFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP 144
Query: 117 EKLAKSKSFMTKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPIL 176
EK+AKSK FM++L+K Y+A RIA+DEVHCCS WGHDFRPDY+ L ILK FP+ ++
Sbjct: 145 EKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLI 204
Query: 177 GLTATATTKVMLDVQKMLQIEDCVVIKAPFNRPNLFYEVRIKPAAQKDCLDELADLMSRR 236
GLTATAT V+ D QK+L IE C A FNRPNL+YEVR KP+ +D ++++ L++ R
Sbjct: 205 GLTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGR 264
Query: 237 FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESN------------------VS 278
++ QSGIIY S K+ E + L+N G+ AYHA LE +
Sbjct: 265 YKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVAT 324
Query: 279 IAFGLGIDKPNVRFVIHHCLSKSMENFYQVSIAFG 313
+AFG+GIDKP+VRFVIHH +SKSMEN+YQ S G
Sbjct: 325 VAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAG 359
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 165 bits (417), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 102/327 (31%), Positives = 168/327 (51%), Gaps = 47/327 (14%)
Query: 11 VRSVLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPTDYPWS----------DRVRSVLK 60
+ VL+ F FRP Q I+ L +D +++MPT S + + V+
Sbjct: 13 AKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVS 72
Query: 61 SKFNLTDFRPNQLAAINIALLKKDAIIIMPTGKLLKKKKICLMTESSSLKLLYVSPEKLA 120
+L + +QL A +A A + T ++ ++ + ++LLY++PE+L
Sbjct: 73 PLISLMKDQVDQLQANGVA-----AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLM 127
Query: 121 KSKSFMTKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPILGLTA 180
+F+ L +A+DE HC S WGHDFRP+Y L L+ FP +P + LTA
Sbjct: 128 LD-NFLEHLAHWNPV----LLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTA 182
Query: 181 TATTKVMLDVQKMLQIEDCVVIKAPFNRPNLFYEV--RIKPAAQKDCLDELADLMSRRFR 238
TA D+ ++L + D ++ + F+RPN+ Y + + KP LD+L + + R
Sbjct: 183 TADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKFKP------LDQLMRYVQEQ-R 235
Query: 239 NQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIA 280
+SGIIY S + ED L+++G+ +AYHA LE+NV ++A
Sbjct: 236 GKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA 295
Query: 281 FGLGIDKPNVRFVIHHCLSKSMENFYQ 307
FG+GI+KPNVRFV+H + +++E++YQ
Sbjct: 296 FGMGINKPNVRFVVHFDIPRNIESYYQ 322
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 162 bits (410), Expect = 3e-40, Method: Compositional matrix adjust.
Identities = 101/327 (30%), Positives = 165/327 (50%), Gaps = 47/327 (14%)
Query: 11 VRSVLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPTDYPWS----------DRVRSVLK 60
+ VL+ F FRP Q I+ L +D +++ PT S + + V+
Sbjct: 13 AKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLLNGLTVVVS 72
Query: 61 SKFNLTDFRPNQLAAINIALLKKDAIIIMPTGKLLKKKKICLMTESSSLKLLYVSPEKLA 120
+L + +QL A +A A + T ++ ++ + ++LLY++PE+L
Sbjct: 73 PLISLXKDQVDQLQANGVA-----AACLNSTQTREQQLEVXTGCRTGQIRLLYIAPERLX 127
Query: 121 KSKSFMTKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPILGLTA 180
+F+ L +A+DE HC S WGHDFRP+Y L L+ FP +P LTA
Sbjct: 128 LD-NFLEHLAHWNPV----LLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFXALTA 182
Query: 181 TATTKVMLDVQKMLQIEDCVVIKAPFNRPNLFYEV--RIKPAAQKDCLDELADLMSRRFR 238
TA D+ ++L + D ++ + F+RPN+ Y + + KP LD+L + + R
Sbjct: 183 TADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYXLXEKFKP------LDQLXRYVQEQ-R 235
Query: 239 NQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIA 280
+SGIIY S + ED L+++G+ +AYHA LE+NV ++A
Sbjct: 236 GKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA 295
Query: 281 FGLGIDKPNVRFVIHHCLSKSMENFYQ 307
FG GI+KPNVRFV+H + +++E++YQ
Sbjct: 296 FGXGINKPNVRFVVHFDIPRNIESYYQ 322
>pdb|3LJ4|Y Chain Y, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|Z Chain Z, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|AA Chain a, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|BB Chain b, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|CC Chain c, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|DD Chain d, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|EE Chain e, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|FF Chain f, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|GG Chain g, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|HH Chain h, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|II Chain i, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|JJ Chain j, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|1VT0|KK Chain k, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|LL Chain l, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|MM Chain m, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|NN Chain n, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|OO Chain o, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|PP Chain p, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|QQ Chain q, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|RR Chain r, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|SS Chain s, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|TT Chain t, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|UU Chain u, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|VV Chain v, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
Length = 166
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%)
Query: 217 IKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 271
++P + +D +D+L +M+ +++ GII + E+ E + GLR SA A
Sbjct: 28 VEPQSMQDAVDDLEAMMAEWYQDGKGIITGYVFSDDENPPAEGDDHGLRSSAVSA 82
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 208 RPNLFYEVRIKPAAQKDCLDEL-ADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRV 266
RP + I K +D+L ++ R RN+ ++ T + K EDL + L+ G++V
Sbjct: 438 RPTGLLDPTIDVRPTKGQIDDLIGEIHERVERNERTLVTTLTKKMAEDLTDYLKEAGIKV 497
Query: 267 SAYHAKLES 275
+ H+++++
Sbjct: 498 AYLHSEIKT 506
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 208 RPNLFYEVRIKPAAQKDCLDEL-ADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRV 266
RP + I K +D+L ++ R RN+ ++ T + K EDL + L+ G++V
Sbjct: 413 RPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKV 472
Query: 267 SAYHAKLES 275
+ H+++++
Sbjct: 473 AYLHSEIKT 481
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 208 RPNLFYEVRIKPAAQKDCLDEL-ADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRV 266
RP + I K +D+L ++ R RN+ ++ T + K EDL + L+ G++V
Sbjct: 412 RPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKV 471
Query: 267 SAYHAKLES 275
+ H+++++
Sbjct: 472 AYLHSEIKT 480
>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSO|B Chain B, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|B Chain B, Crystal Structure Of A Translation Initiation Complex
Length = 395
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 44/172 (25%), Positives = 76/172 (44%), Gaps = 38/172 (22%)
Query: 160 YQYLSILKTMFPDVPILGLTAT-------ATTKVMLDVQKMLQIEDCVVIKAPFNRPNLF 212
YQ ++L P ++ L+AT TTK M + ++L +D + ++ F
Sbjct: 185 YQIFTLLP---PTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGI----KQF 237
Query: 213 YEVRIKPAAQK-DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 271
Y V ++ K +CL +L D +S +I+ + ++ E+L +LRN VSA ++
Sbjct: 238 Y-VNVEEEEYKYECLTDLYDSISVT----QAVIFCNTRRKVEELTTKLRNDKFTVSAIYS 292
Query: 272 KL---------------ESNVSIAFGL---GIDKPNVRFVIHHCLSKSMENF 305
L S + I+ L GID V VI++ L + EN+
Sbjct: 293 DLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 344
>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
pdb|1T5L|B Chain B, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
Length = 658
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 208 RPNLFYEVRIKPAAQKDCLDEL-ADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRV 266
RP + I K +D+L ++ R RN+ ++ T + K EDL + L+ G++V
Sbjct: 413 RPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKV 472
Query: 267 SAYHAKLES 275
+ H+++++
Sbjct: 473 AYLHSEIKT 481
>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
pdb|2FDC|B Chain B, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
Length = 658
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 208 RPNLFYEVRIKPAAQKDCLDEL-ADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRV 266
RP + I K +D+L ++ R RN+ ++ T + K EDL + L+ G++V
Sbjct: 413 RPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKV 472
Query: 267 SAYHAKLES 275
+ H+++++
Sbjct: 473 AYLHSEIKT 481
>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 = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 259 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 288
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>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 = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 259 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 288
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>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 = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 259 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 288
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 22/100 (22%)
Query: 224 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKL---------- 273
+CL +L D +S +I+ + ++ E+L +LRN VSA ++ L
Sbjct: 248 ECLTDLYDSISVT----QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXK 303
Query: 274 -----ESNVSIAFGL---GIDKPNVRFVIHHCLSKSMENF 305
S + I+ L GID V VI++ L + EN+
Sbjct: 304 EFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 343
>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 = 28.9 bits (63), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 259 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 288
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>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 = 28.9 bits (63), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 259 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 288
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|3IJE|B Chain B, Crystal Structure Of The Complete Integrin Alhavbeta3
Ectodomain Plus An Alpha/beta Transmembrane Fragment
Length = 695
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 259 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 288
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|4G1E|B Chain B, Crystal Structure Of Integrin Alpha V Beta 3 With
Coil-Coiled Tag
Length = 738
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 259 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 288
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 22/100 (22%)
Query: 224 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKL---------- 273
+CL +L D +S +I+ + ++ E+L +LRN VSA ++ L
Sbjct: 19 ECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMK 74
Query: 274 -----ESNVSIAFGL---GIDKPNVRFVIHHCLSKSMENF 305
S + I+ L GID V VI++ L + EN+
Sbjct: 75 EFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 114
>pdb|4G1M|B Chain B, Re-Refinement Of Alpha V Beta 3 Structure
Length = 692
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 259 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 288
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>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 = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 259 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 288
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|2BOL|A Chain A, Crystal Structure And Assembly Of Tsp36, A Metazoan Small
Heat Shock Protein
pdb|2BOL|B Chain B, Crystal Structure And Assembly Of Tsp36, A Metazoan Small
Heat Shock Protein
Length = 314
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 190 VQKMLQIEDCVVIKAPFNRPNLFYEVRIKPAAQKDCLDELADLMSRRF--RNQSGIIYTT 247
+Q + +D +VI+AP N PN + +++ P +K + +++ R+ +N+ G+ T
Sbjct: 171 IQATITTDDVLVIEAPVNEPN-YKAIKLSP--EKGLAIQPSEVQERQLAVKNKEGLEIVT 227
Query: 248 SIKECEDLREELR 260
+ + + EL+
Sbjct: 228 AEDGSKKIHLELK 240
>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|C Chain C, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|D Chain D, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|F Chain F, Crystal Structure Of The Eif4a-Pdcd4 Complex
Length = 388
Score = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 19/98 (19%)
Query: 226 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE----------- 274
LD L DL Q+ +I+ + ++ + L E++ R VSA H ++
Sbjct: 242 LDTLCDLYETLTITQA-VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREF 300
Query: 275 ----SNVSIAFGL---GIDKPNVRFVIHHCLSKSMENF 305
S V I L GID V VI++ L + EN+
Sbjct: 301 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 338
>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex
pdb|3V4R|B Chain B, Crystal Structure Of A Uvrb Dimer-Dna Complex
Length = 667
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 31/49 (63%)
Query: 227 DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES 275
D + ++ +R RN+ ++ T + K EDL + L+ G++V+ H+++++
Sbjct: 439 DLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKT 487
>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase
Activity Of Uvrb
pdb|2NMV|A Chain A, Damage Detection By The Uvrabc Pathway: Crystal Structure
Of Uvrb Bound To Fluorescein-Adducted Dna
Length = 661
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 31/49 (63%)
Query: 227 DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES 275
D + ++ +R RN+ ++ T + K EDL + L+ G++V+ H+++++
Sbjct: 433 DLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKT 481
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 19/98 (19%)
Query: 226 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE----------- 274
LD L DL Q+ +I+ + ++ + L E++ R VSA H ++
Sbjct: 268 LDTLCDLYETLTITQA-VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREF 326
Query: 275 ----SNVSIAFGL---GIDKPNVRFVIHHCLSKSMENF 305
S V I L GID V VI++ L + EN+
Sbjct: 327 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 364
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
0.324 0.137 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,775,118
Number of Sequences: 62578
Number of extensions: 321894
Number of successful extensions: 1030
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 994
Number of HSP's gapped (non-prelim): 29
length of query: 323
length of database: 14,973,337
effective HSP length: 99
effective length of query: 224
effective length of database: 8,778,115
effective search space: 1966297760
effective search space used: 1966297760
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (24.3 bits)