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= psy3386
(76 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QQM|A Chain A, Crystal Structure Of The A2b1b2 Domains From Human
Neuropilin-1
Length = 450
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 19/39 (48%)
Query: 10 NGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFD 48
+G SP FP YP EC Y + I L FESFD
Sbjct: 19 SGVIKSPGFPEKYPNSLECTYIVFAPKMSEIILEFESFD 57
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 18/39 (46%)
Query: 10 NGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFD 48
G SP FP YP EC Y + I L FESFD
Sbjct: 137 TGVIKSPGFPEKYPNSLECTYIIFAPKMSEIILEFESFD 175
>pdb|3POB|A Chain A, Crystal Structure Of Masp-1 Cub2 Domain In Complex With
The Collagen- Like Domain Of Mbl
pdb|3POE|A Chain A, Crystal Structure Of The Masp-1 Cub2 Domain Bound To
Ca2+
pdb|3POF|A Chain A, Crystal Structure Of Masp-1 Cub2 Domain Bound To Ca2+
pdb|3POF|B Chain B, Crystal Structure Of Masp-1 Cub2 Domain Bound To Ca2+
pdb|3POG|A Chain A, Crystal Structure Of The Masp-1 Cub2 Domain Bound To
Ca2+
pdb|3POG|B Chain B, Crystal Structure Of The Masp-1 Cub2 Domain Bound To
Ca2+
pdb|3POG|C Chain C, Crystal Structure Of The Masp-1 Cub2 Domain Bound To
Ca2+
pdb|3POI|A Chain A, Crystal Structure Of Masp-1 Cub2 Domain Bound To
Methylamine
pdb|3POI|B Chain B, Crystal Structure Of Masp-1 Cub2 Domain Bound To
Methylamine
pdb|3POJ|A Chain A, Crystal Structure Of Masp-1 Cub2 Domain Bound To
Ethylamine
pdb|3POJ|B Chain B, Crystal Structure Of Masp-1 Cub2 Domain Bound To
Ethylamine
Length = 115
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 21/42 (50%)
Query: 8 HRNGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDD 49
R GT TSP++P YP+ +EC Y + L FE D
Sbjct: 11 QRTGTITSPDYPNPYPKSSECSYTIDLEEGFMVTLQFEDIFD 52
>pdb|4AQB|A Chain A, Mbl-Ficolin Associated Protein-1, Map-1 Aka Map44
Length = 361
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 20/42 (47%)
Query: 8 HRNGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDD 49
R G TSP+FP YP+ +EC Y + L FE D
Sbjct: 173 QRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQFEDIFD 214
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 11 GTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFD 48
G SP +P YP D+E + + RIKL F F+
Sbjct: 10 GQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFN 47
>pdb|3DEM|A Chain A, Cub1-egf-cub2 Domain Of Human Masp-1/3
pdb|3DEM|B Chain B, Cub1-egf-cub2 Domain Of Human Masp-1/3
Length = 278
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 20/42 (47%)
Query: 8 HRNGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDD 49
R G TSP+FP YP+ +EC Y + L FE D
Sbjct: 173 QRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQFEDIFD 214
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 11 GTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFD 48
G SP +P YP D+E + + RIKL F F+
Sbjct: 10 GQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFN 47
>pdb|2QQO|A Chain A, Crystal Structure Of The A2b1b2 Domains From Human
Neuropilin-2
pdb|2QQO|B Chain B, Crystal Structure Of The A2b1b2 Domains From Human
Neuropilin-2
Length = 460
Score = 32.7 bits (73), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 19/39 (48%)
Query: 10 NGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFD 48
NGT SP FP YP + +C + + I L F FD
Sbjct: 16 NGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFD 54
>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 = 32.3 bits (72), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 19/39 (48%)
Query: 10 NGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFD 48
NGT SP FP YP + +C + + I L F FD
Sbjct: 135 NGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFD 173
>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 = 29.6 bits (65), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 10 NGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESF 47
GT SP P +YP C + + + I L+FE+F
Sbjct: 9 TGTIQSPGHPNVYPHGINCTWHILVQPNHLIHLMFETF 46
Score = 29.3 bits (64), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 10 NGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESF 47
+GTF SPN+P Y +EC+++ + +L F+ F
Sbjct: 242 SGTFISPNYPMPYYHSSECYWWLKSSHGSAFELEFKDF 279
>pdb|1SZB|A Chain A, Crystal Structure Of The Human Mbl-Associated Protein 19
(Map19)
pdb|1SZB|B Chain B, Crystal Structure Of The Human Mbl-Associated Protein 19
(Map19)
Length = 170
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 17/38 (44%)
Query: 11 GTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFD 48
G SP FPG Y D E + R++L F FD
Sbjct: 13 GRLASPGFPGEYANDQERRWTLTAPPGYRLRLYFTHFD 50
>pdb|1NT0|A Chain A, Crystal Structure Of The Cub1-Egf-Cub2 Region Of Masp2
pdb|1NT0|G Chain G, Crystal Structure Of The Cub1-Egf-Cub2 Region Of Masp2
Length = 286
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 9 RNGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVF-ESFD 48
R+G +SP +P YP+ + C Y I L F ESFD
Sbjct: 173 RSGFLSSPEYPQPYPKLSSCAYNIRLEEGFSITLDFVESFD 213
>pdb|7FAB|H Chain H, Crystal Structure Of Human Immunoglobulin Fragment Fab
New Refined At 2.0 Angstroms Resolution
Length = 217
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 46 SFDDWWWIWLRQ 57
SFDD++W W+RQ
Sbjct: 28 SFDDYYWTWVRQ 39
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 25.8 bits (55), Expect = 6.5, Method: Composition-based stats.
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 20 GLYPRDTECHYFFYGRNDERIKLVFESFDDWWWIWL 55
GL PR + + + +KL ES DD W + L
Sbjct: 13 GLVPRGSHMRILEFDEKRQAVKLHIESEDDLWLLHL 48
>pdb|3L8U|A Chain A, Crystal Structure Of Smu.1707c, A Putative Rrna
Methyltransferase From Streptococcus Mutans Ua159
pdb|3L8U|B Chain B, Crystal Structure Of Smu.1707c, A Putative Rrna
Methyltransferase From Streptococcus Mutans Ua159
Length = 182
Score = 25.4 bits (54), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 5/29 (17%)
Query: 10 NGTFTSPNFPGLYPRDTECHYFFYGRNDE 38
N T++ N+ D+E HYF +GR D+
Sbjct: 98 NKTYSDENYD-----DSEHHYFLFGREDK 121
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
0.328 0.145 0.543
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,924,161
Number of Sequences: 62578
Number of extensions: 112792
Number of successful extensions: 248
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 228
Number of HSP's gapped (non-prelim): 22
length of query: 76
length of database: 14,973,337
effective HSP length: 45
effective length of query: 31
effective length of database: 12,157,327
effective search space: 376877137
effective search space used: 376877137
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)