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= psy4861
(101 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2Z4F|A Chain A, Solution Structure Of The Discoidin Domain Of Ddr2
Length = 173
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 20 GAWCPKNQITTEP---REWIEINLHFVHVITATGVQGRFGNGQGAEFTEAYLIDYWRPKL 76
GAWCP +I EP +E+++I+LH +H IT G QGR G G EF Y I+Y R
Sbjct: 49 GAWCP--EIPVEPDDLKEFLQIDLHTLHFITLVGTQGRHAGGHGIEFAPMYKINYSRDGT 106
Query: 77 GKWVRYKDAKGNEM 90
+W+ +++ G ++
Sbjct: 107 -RWISWRNRHGKQV 119
>pdb|2WUH|A Chain A, Crystal Structure Of The Ddr2 Discoidin Domain Bound To A
Triple-Helical Collagen Peptide
Length = 178
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 20 GAWCPKNQITTEP---REWIEINLHFVHVITATGVQGRFGNGQGAEFTEAYLIDYWRPKL 76
GAWCP +I EP +E+++I+LH +H IT G QGR G G EF Y I+Y R
Sbjct: 58 GAWCP--EIPVEPDDLKEFLQIDLHTLHFITLVGTQGRHAGGHGIEFAPMYKINYSRDGT 115
Query: 77 GKWVRYKDAKGNEM 90
+W+ +++ G ++
Sbjct: 116 -RWISWRNRHGKQV 128
>pdb|4AG4|A Chain A, Crystal Structure Of A Ddr1-Fab Complex
Length = 351
Score = 56.6 bits (135), Expect = 4e-09, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 20 GAWCPKNQITTEPREWIEINLHFVHVITATGVQGRFGNGQGAEFTEAYLIDYWRPKLGKW 79
GAWCP + + E+++++L +H++ G QGR G G EF+ +Y + Y R +W
Sbjct: 46 GAWCPAGSVFPKEEEYLQVDLQRLHLVALVGTQGRHAGGLGKEFSRSYRLRYSRDGR-RW 104
Query: 80 VRYKDAKGNEMYS 92
+ +KD G E+ S
Sbjct: 105 MGWKDRWGQEVIS 117
>pdb|2QQM|A Chain A, Crystal Structure Of The A2b1b2 Domains From Human
Neuropilin-1
Length = 450
Score = 30.8 bits (68), Expect = 0.20, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 14 RTDYNGGAWCPKNQITTEPREWIEINLHFVHVITATGVQG 53
R +Y W P REWI+++L + +TA G QG
Sbjct: 171 RLNYPENGWTPGED---SYREWIQVDLGLLRFVTAVGTQG 207
>pdb|2ORX|A Chain A, Structural Basis For Ligand Binding And Heparin Mediated
Activation Of Neuropilin
pdb|2ORZ|A Chain A, Structural Basis For Ligand Binding And Heparin Mediated
Activation Of Neuropilin
Length = 314
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 14 RTDYNGGAWCPKNQITTEPREWIEINLHFVHVITATGVQG 53
R +Y W P REWI+++L + +TA G QG
Sbjct: 35 RLNYPENGWTPGED---SYREWIQVDLGLLRFVTAVGTQG 71
>pdb|2QQI|A Chain A, Crystal Structure Of The B1b2 Domains From Human
Neuropilin-1
Length = 318
Score = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 14 RTDYNGGAWCPKNQITTEPREWIEINLHFVHVITATGVQG 53
R +Y W P REWI+++L + +TA G QG
Sbjct: 39 RLNYPENGWTPGED---SYREWIQVDLGLLRFVTAVGTQG 75
>pdb|1KEX|A Chain A, Crystal Structure Of The B1 Domain Of Human Neuropilin-1
Length = 155
Score = 29.3 bits (64), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 14 RTDYNGGAWCPKNQITTEPREWIEINLHFVHVITATGVQG 53
R +Y W P REWI+++L + +TA G QG
Sbjct: 35 RLNYPENGWTPGED---SYREWIQVDLGLLRFVTAVGTQG 71
>pdb|3I97|A Chain A, B1 Domain Of Human Neuropilin-1 Bound With Small
Molecule Eg
pdb|3I97|B Chain B, B1 Domain Of Human Neuropilin-1 Bound With Small
Molecule Eg
Length = 158
Score = 29.3 bits (64), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 14 RTDYNGGAWCPKNQITTEPREWIEINLHFVHVITATGVQG 53
R +Y W P REWI+++L + +TA G QG
Sbjct: 38 RLNYPENGWTPGED---SYREWIQVDLGLLRFVTAVGTQG 74
>pdb|2QQN|A Chain A, Neuropilin-1 B1 Domain In Complex With A Vegf-Blocking
Fab
Length = 159
Score = 29.3 bits (64), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 14 RTDYNGGAWCPKNQITTEPREWIEINLHFVHVITATGVQG 53
R +Y W P REWI+++L + +TA G QG
Sbjct: 39 RLNYPENGWTPGED---SYREWIQVDLGLLRFVTAVGTQG 75
>pdb|4DEQ|A Chain A, Structure Of The Neuropilin-1VEGF-A Complex
pdb|4DEQ|B Chain B, Structure Of The Neuropilin-1VEGF-A Complex
Length = 218
Score = 29.3 bits (64), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 33 REWIEINLHFVHVITATGVQG 53
REWI+++L + +TA G QG
Sbjct: 54 REWIQVDLGLLRFVTAVGTQG 74
>pdb|4GZ9|A Chain A, Mouse Neuropilin-1, Extracellular Domains 1-4 (A1a2b1b2)
pdb|4GZA|H Chain H, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
Length = 577
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 14 RTDYNGGAWCPKNQITTEPREWIEINLHFVHVITATGVQG 53
R +Y W P +EWI+++L + +TA G QG
Sbjct: 289 RLNYPENGWTPGEDSY---KEWIQVDLGLLRFVTAVGTQG 325
>pdb|1X5Z|A Chain A, Solution Structure Of The Fibronectin Type-Iii Domain Of
Human Protein Tyrosine Phosphatase, Receptor Type, D
Isoform 4 Variant
Length = 115
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 6/65 (9%)
Query: 43 VHVITATGVQGRFGNGQGAEFTEAYLIDYWRPKLGKWVR-----YKDAK-GNEMYSYVQT 96
+ VIT TGV G+ N + +E ++ W P + YKD + G E ++
Sbjct: 9 IQVITQTGVPGQPLNFKAEPESETSILLSWTPPRSDTIANYELVYKDGEHGEEQRITIEP 68
Query: 97 GTLWR 101
GT +R
Sbjct: 69 GTSYR 73
>pdb|3CDZ|B Chain B, Crystal Structure Of Human Factor Viii
Length = 684
Score = 26.6 bits (57), Expect = 3.7, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 15/85 (17%)
Query: 4 RYEEIYEDMVRTDYNGG--AWCPKNQITTEPREWIEINL---HFVHVITATGVQGRFGNG 58
+Y + + R Y+G AW T EP WI+++L +H I G + +F +
Sbjct: 394 QYGQWAPKLARLHYSGSINAWS-----TKEPFSWIKVDLLAPMIIHGIKTQGARQKFSSL 448
Query: 59 QGAEFTEAYLIDYWRPKLGKWVRYK 83
++F Y +D KW Y+
Sbjct: 449 YISQFIIMYSLDG-----KKWQTYR 468
>pdb|2R7E|B Chain B, Crystal Structure Analysis Of Coagulation Factor Viii
Length = 770
Score = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 15/85 (17%)
Query: 4 RYEEIYEDMVRTDYNGG--AWCPKNQITTEPREWIEINL---HFVHVITATGVQGRFGNG 58
+Y + + R Y+G AW T EP WI+++L +H I G + +F +
Sbjct: 480 QYGQWAPKLARLHYSGSINAWS-----TKEPFSWIKVDLLAPMIIHGIKTQGARQKFSSL 534
Query: 59 QGAEFTEAYLIDYWRPKLGKWVRYK 83
++F Y +D KW Y+
Sbjct: 535 YISQFIIMYSLDG-----KKWQTYR 554
>pdb|3CSK|A Chain A, Structure Of Dpp Iii From Saccharomyces Cerevisiae
Length = 711
Score = 25.8 bits (55), Expect = 5.6, Method: Composition-based stats.
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 69 IDYWRPKLGKW 79
++YW PK GKW
Sbjct: 564 LEYWNPKTGKW 574
>pdb|1U0M|A Chain A, Crystal Structure Of 1,3,6,8-Tetrahydroxynaphthalene
Synthase (Thns) From Streptomyces Coelicolor A3(2): A
Bacterial Type Iii Polyketide Synthase (Pks) Provides
Insights Into Enzymatic Control Of Reactive Polyketide
Intermediates
pdb|1U0M|B Chain B, Crystal Structure Of 1,3,6,8-Tetrahydroxynaphthalene
Synthase (Thns) From Streptomyces Coelicolor A3(2): A
Bacterial Type Iii Polyketide Synthase (Pks) Provides
Insights Into Enzymatic Control Of Reactive Polyketide
Intermediates
Length = 382
Score = 25.8 bits (55), Expect = 6.6, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 46 ITATGVQGRFGNGQGAEFTEAYLIDYWRPKLGKWVRY 82
I A V+GR G G E +YLI PK W+ Y
Sbjct: 200 IAAAVVRGRGGTGVRLERNGSYLI----PKTEDWIMY 232
>pdb|1SHN|A Chain A, Crystal Structure Of Shrimp Alkaline Phosphatase With
Phosphate Bound
pdb|1SHN|B Chain B, Crystal Structure Of Shrimp Alkaline Phosphatase With
Phosphate Bound
pdb|1SHQ|A Chain A, Crystal Structure Of Shrimp Alkaline Phosphatase With
Magnesium In M3
pdb|1SHQ|B Chain B, Crystal Structure Of Shrimp Alkaline Phosphatase With
Magnesium In M3
Length = 478
Score = 25.0 bits (53), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 3 KRYEEIYEDMVRTDYNGGAWCPKNQITTEPREW-IEINLHFVHVIT 47
KRYE ED+ ++ + PK+ +T + + I +N F H+ T
Sbjct: 405 KRYEPTEEDLKDINFRYASAAPKHSVTHDGTDVGIWVNGPFAHLFT 450
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
0.319 0.137 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,606,400
Number of Sequences: 62578
Number of extensions: 147638
Number of successful extensions: 304
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 289
Number of HSP's gapped (non-prelim): 26
length of query: 101
length of database: 14,973,337
effective HSP length: 67
effective length of query: 34
effective length of database: 10,780,611
effective search space: 366540774
effective search space used: 366540774
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)