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= psy3691
(137 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QQK|A Chain A, Neuropilin-2 A1a2b1b2 Domains In Complex With A
Semaphorin-Blocking Fab
pdb|2QQL|A Chain A, Neuropilin-2 A1a2b1b2 Domains In Complex With A
Semaphorin-Blocking Fab
Length = 579
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 12 PGNYSIDVKCSWLIDASDTPNATIRLHFNS-FATE---CGWDHLYIFDGDSVHAPLLGVF 67
P +Y C W++ A + PN I L+FN F E C +D + I DGDS A LLG
Sbjct: 24 PQDYPSHQNCEWIVYAPE-PNQKIVLNFNPHFEIEKHDCKYDFIEIRDGDSESADLLGKH 82
Query: 68 SG 69
G
Sbjct: 83 CG 84
>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 = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 16/83 (19%)
Query: 2 SDKSG--IIIDGPG---------NYSIDVKCSWLIDASDTPNATIRLHFNSF----ATEC 46
SDK G I I+ PG +Y KC WLI A + P I ++FN +C
Sbjct: 6 SDKCGGTIKIENPGYLTSPGYPHSYHPSEKCEWLIQAPE-PYQRIMINFNPHFDLEDRDC 64
Query: 47 GWDHLYIFDGDSVHAPLLGVFSG 69
+D++ + DG++ L G F G
Sbjct: 65 KYDYVEVIDGENEGGRLWGKFCG 87
>pdb|3KQ4|B Chain B, Structure Of Intrinsic Factor-Cobalamin Bound To Its
Receptor Cubilin
pdb|3KQ4|D Chain D, Structure Of Intrinsic Factor-Cobalamin Bound To Its
Receptor Cubilin
pdb|3KQ4|F Chain F, Structure Of Intrinsic Factor-Cobalamin Bound To Its
Receptor Cubilin
Length = 457
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 1 LSDKSGIII--DGPGNYSIDVKCSWLIDASDTPNATIRLHFNSFATE----CGWDHLYIF 54
L+ SG I + P Y +C W + +S + L F F E C D+L ++
Sbjct: 238 LTTSSGTFISPNYPMPYYHSSECYWWLKSSH--GSAFELEFKDFHLEHHPNCTLDYLAVY 295
Query: 55 DGDSVHAPLLGVFSG 69
DG S ++ LL G
Sbjct: 296 DGPSSNSHLLTQLCG 310
Score = 25.8 bits (55), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 35 IRLHFNSFATECG-----WDHLYIFDGDSVHAPLLGVFSG 69
I +HF +F+ E D L I DG +PLLG+F G
Sbjct: 155 IAVHFTNFSLEEAIGNYYTDFLEIRDGGYEKSPLLGIFYG 194
>pdb|1KTZ|A Chain A, Crystal Structure Of The Human Tgf-Beta Type Ii Receptor
Extracellular Domain In Complex With Tgf-Beta3
pdb|1TGJ|A Chain A, Human Transforming Growth Factor-beta 3, Crystallized From
Dioxane
pdb|1TGK|A Chain A, Human Transforming Growth Factor Beta 3, Crystallized From
Peg 4000
pdb|2PJY|A Chain A, Structural Basis For Cooperative Assembly Of The Tgf-Beta
Signaling Complex
pdb|3EO1|C Chain C, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|F Chain F, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|I Chain I, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|L Chain L, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
Length = 112
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 42 FATECGWDHLYIFDGDSVHAPLLGVFSGLMYEGDYSIHRVP-DVKCFTITNELGNTGIQI 100
+A C Y+ D+ H+ +LG+++ L E S VP D++ TI +G T
Sbjct: 40 YANFCSGPCPYLRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVE 99
Query: 101 VLGNDFVQ 108
L N V+
Sbjct: 100 QLSNMVVK 107
>pdb|2BIB|A Chain A, Crystal Structure Of The Complete Modular Teichioic Acid
Phosphorylcholine Esterase Pce (Cbpe) From Streptococcus
Pneumoniae
Length = 547
Score = 27.7 bits (60), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 1 LSDKSGIIIDG--PGNYSIDVKCSWLIDASDTPNATIR 36
L + ++++G P Y++D +WL+D S +ATI+
Sbjct: 508 LKENGQLLVNGKTPEGYTVDSSGAWLVDVSIEKSATIK 545
>pdb|3NTD|A Chain A, Structure Of The Shewanella Loihica Pv-4 Nadh-Dependent
Persulfide Reductase C531s Mutant
pdb|3NTD|B Chain B, Structure Of The Shewanella Loihica Pv-4 Nadh-Dependent
Persulfide Reductase C531s Mutant
Length = 565
Score = 25.8 bits (55), Expect = 8.1, Method: Composition-based stats.
Identities = 27/140 (19%), Positives = 63/140 (45%), Gaps = 10/140 (7%)
Query: 1 LSDKSGIIIDGP----GNYSIDVKCSWLIDASDTPN--ATIRLHFNSFATECGWDHLYIF 54
++ +S +++ P ++++V+ + A D T+R + + +D L +
Sbjct: 53 IAQRSALVLQTPESFKARFNVEVRVKHEVVAIDRAAKLVTVRRLLDGSEYQESYDTLLLS 112
Query: 55 DGDSVHAPLLGVFSGLMYEGDYSIHRVPDVKCFTITNELGNTGIQIVLGNDFVQLWEVGN 114
G AP++ G+ +S+ +PD+ T ++ N V+G F+ L + +
Sbjct: 113 PG---AAPIVPPIPGVDNPLTHSLRNIPDMDRILQTIQMNNVEHATVVGGGFIGLEMMES 169
Query: 115 V-YLTHKNELYETSKDLISP 133
+ +L K L E + +++P
Sbjct: 170 LHHLGIKTTLLELADQVMTP 189
>pdb|2V4J|A Chain A, The Crystal Structure Of Desulfovibrio Vulgaris
Dissimilatory Sulfite Reductase Bound To Dsrc Provides
Novel Insights Into The Mechanism Of Sulfate Respiration
pdb|2V4J|D Chain D, The Crystal Structure Of Desulfovibrio Vulgaris
Dissimilatory Sulfite Reductase Bound To Dsrc Provides
Novel Insights Into The Mechanism Of Sulfate Respiration
Length = 437
Score = 25.4 bits (54), Expect = 8.9, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 68 SGLMYEGDY--SIHRVPDVKCFTITNELGNTGIQIVLGNDFVQLWEV 112
SG Y DY + + D++ +TN G+TG ++LG QL E+
Sbjct: 106 SGKYYSADYLRQLCDIWDLRGSGLTNMHGSTGDIVLLGTQTPQLEEI 152
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
0.320 0.141 0.442
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,806,968
Number of Sequences: 62578
Number of extensions: 201461
Number of successful extensions: 318
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 313
Number of HSP's gapped (non-prelim): 9
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
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: 46 (22.3 bits)