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= psy4231
(247 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FCS|A Chain A, Structure Of Complete Ectodomain Of Integrin Aiibb3
pdb|3FCS|C Chain C, Structure Of Complete Ectodomain Of Integrin Aiibb3
Length = 959
Score = 30.0 bits (66), Expect = 1.4, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 179 IGHLYFFLTFKYPQEMGGPALLSTPAFMYKWFPNERTTVHGFGQVPRRP----AEPTSAG 234
+G +Y FL + P +G P+LL T +Y F + + G + R A G
Sbjct: 325 VGRVYLFLQPRGPHALGAPSLLLTGTQLYGRFG---SAIAPLGDLDRDGYNDIAVAAPYG 381
Query: 235 GRSWGRGNVL 244
G S GRG VL
Sbjct: 382 GPS-GRGQVL 390
>pdb|4DKT|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With
N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1e)-2-
Fluoroethanimidoyl]-L-Ornithinamide
Length = 668
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 179 IGHLYFFLTF-KYPQEMGGPALLSTPAFMYKWFPNERTTVHG 219
+GH+ FL+F P G LL++P YK F ++ HG
Sbjct: 474 VGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHG 515
>pdb|2DEW|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With Histone H3 N-Terminal Tail Including Arg8
pdb|2DEX|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With Histone H3 N-Terminal Peptide Including
Arg17
pdb|2DEY|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With Histone H4 N-Terminal Tail Including Arg3
Length = 671
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 179 IGHLYFFLTF-KYPQEMGGPALLSTPAFMYKWFPNERTTVHG 219
+GH+ FL+F P G LL++P YK F ++ HG
Sbjct: 477 VGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHG 518
>pdb|1WD9|A Chain A, Calcium Bound Form Of Human Peptidylarginine Deiminase
Type4 (pad4)
pdb|1WDA|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase
Type4 (Pad4) In Complex With Benzoyl-L-Arginine Amide
Length = 670
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 179 IGHLYFFLTF-KYPQEMGGPALLSTPAFMYKWFPNERTTVHG 219
+GH+ FL+F P G LL++P YK F ++ HG
Sbjct: 476 VGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHG 517
>pdb|1WD8|A Chain A, Calcium Free Form Of Human Peptidylarginine Deiminase
Type4 (Pad4)
Length = 670
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 179 IGHLYFFLTF-KYPQEMGGPALLSTPAFMYKWFPNERTTVHG 219
+GH+ FL+F P G LL++P YK F ++ HG
Sbjct: 476 VGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHG 517
>pdb|3APN|A Chain A, Crystal Structure Of The Human Wild-Type Pad4 Protein
Length = 666
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 179 IGHLYFFLTF-KYPQEMGGPALLSTPAFMYKWFPNERTTVHG 219
+GH+ FL+F P G LL++P YK F ++ HG
Sbjct: 472 VGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHG 513
>pdb|3APM|A Chain A, Crystal Structure Of The Human Snp Pad4 Protein
Length = 666
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 179 IGHLYFFLTF-KYPQEMGGPALLSTPAFMYKWFPNERTTVHG 219
+GH+ FL+F P G LL++P YK F ++ HG
Sbjct: 472 VGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHG 513
>pdb|2DW5|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With
N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine
Amide
pdb|3B1T|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With O-Cl-Amidine
pdb|3B1U|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With O-F-Amidine
Length = 671
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 179 IGHLYFFLTF-KYPQEMGGPALLSTPAFMYKWFPNERTTVHG 219
+GH+ FL+F P G LL++P YK F ++ HG
Sbjct: 477 VGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHG 518
>pdb|2VC2|A Chain A, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist L-739758
pdb|2VDK|A Chain A, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDL|A Chain A, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDM|A Chain A, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Tirofiban
pdb|2VDN|A Chain A, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Eptifibatide
pdb|2VDO|A Chain A, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide, Hhlggakqagdv
pdb|2VDP|A Chain A, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide,Lggakqagdv
pdb|2VDQ|A Chain A, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv
pdb|2VDR|A Chain A, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Lggakqrgdv
Length = 452
Score = 27.3 bits (59), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 179 IGHLYFFLTFKYPQEMGGPALLSTPAFMYKWF 210
+G +Y FL + P +G P+LL T +Y F
Sbjct: 325 VGRVYLFLQPRGPHALGAPSLLLTGTQLYGRF 356
>pdb|3FCU|A Chain A, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
pdb|3FCU|C Chain C, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
pdb|3FCU|E Chain E, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
pdb|3NID|A Chain A, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NID|C Chain C, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NIF|A Chain A, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIF|C Chain C, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|A Chain A, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|C Chain C, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3T3M|A Chain A, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3M|C Chain C, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|A Chain A, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|C Chain C, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
Length = 457
Score = 27.3 bits (59), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 179 IGHLYFFLTFKYPQEMGGPALLSTPAFMYKWF 210
+G +Y FL + P +G P+LL T +Y F
Sbjct: 325 VGRVYLFLQPRGPHALGAPSLLLTGTQLYGRF 356
>pdb|1TYE|A Chain A, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
pdb|1TYE|C Chain C, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
pdb|1TYE|E Chain E, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
Length = 452
Score = 27.3 bits (59), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 179 IGHLYFFLTFKYPQEMGGPALLSTPAFMYKWF 210
+G +Y FL + P +G P+LL T +Y F
Sbjct: 325 VGRVYLFLQPRGPHALGAPSLLLTGTQLYGRF 356
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
0.331 0.147 0.506
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,089,585
Number of Sequences: 62578
Number of extensions: 341785
Number of successful extensions: 584
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 578
Number of HSP's gapped (non-prelim): 14
length of query: 247
length of database: 14,973,337
effective HSP length: 96
effective length of query: 151
effective length of database: 8,965,849
effective search space: 1353843199
effective search space used: 1353843199
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 50 (23.9 bits)