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= psy12771
(160 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3AFC|A Chain A, Mouse Semaphorin 6a Extracellular Domain
pdb|3AFC|B Chain B, Mouse Semaphorin 6a Extracellular Domain
pdb|3AL8|A Chain A, Plexin A2 SEMAPHORIN 6A COMPLEX
Length = 556
Score = 43.1 bits (100), Expect = 6e-05, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 15/73 (20%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
SG+A+CPYD + A++ + LYS T +F D VI+R+ +
Sbjct: 146 SGMARCPYDAKHANIALFADG-------KLYSATVTDFLAIDAVIYRS--------LGDS 190
Query: 136 TFKRTIKYDSKWL 148
RT+K+DSKWL
Sbjct: 191 PTLRTVKHDSKWL 203
>pdb|3OKW|A Chain A, Mouse Semaphorin 6a, Extracellular Domains 1-2
pdb|3OKW|B Chain B, Mouse Semaphorin 6a, Extracellular Domains 1-2
pdb|3OKY|B Chain B, Plexin A2 In Complex With Semaphorin 6a
Length = 565
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 15/73 (20%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
SG+A+CPYD + A++ + LYS T +F D VI+R+ L + T
Sbjct: 145 SGMARCPYDAKHANIALFADG-------KLYSATVTDFLAIDAVIYRS-LGDSPT----- 191
Query: 136 TFKRTIKYDSKWL 148
RT+K+DSKWL
Sbjct: 192 --LRTVKHDSKWL 202
>pdb|1Q47|A Chain A, Structure Of The Semaphorin 3a Receptor-Binding Module
pdb|1Q47|B Chain B, Structure Of The Semaphorin 3a Receptor-Binding Module
Length = 495
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 15/84 (17%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
+G K PYDP + ++ ++ LYSGT A+F D IFRT +
Sbjct: 139 NGRGKSPYDPKLLTASLLIDG-------ELYSGTAADFMGRDFAIFRT--------LGHH 183
Query: 136 TFKRTIKYDSKWLDSFKSLIAKII 159
RT ++DS+WL+ + + A +I
Sbjct: 184 HPIRTEQHDSRWLNDPRFISAHLI 207
>pdb|4GZA|G Chain G, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
Length = 538
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 15/84 (17%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
+G K PYDP + ++ ++ LYSGT A+F D IFRT +
Sbjct: 147 NGRGKSPYDPKLLTASLLIDG-------ELYSGTAADFMGRDFAIFRT--------LGHH 191
Query: 136 TFKRTIKYDSKWLDSFKSLIAKII 159
RT ++DS+WL+ + + A +I
Sbjct: 192 HPIRTEQHDSRWLNDPRFISAHLI 215
>pdb|4GZ8|A Chain A, Mouse Semaphorin 3a, Domains Sema-Psi-Ig
pdb|4GZ8|B Chain B, Mouse Semaphorin 3a, Domains Sema-Psi-Ig
Length = 667
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 15/84 (17%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
+G K PYDP + ++ ++ LYSGT A+F D IFRT +
Sbjct: 147 NGRGKSPYDPKLLTASLLIDG-------ELYSGTAADFMGRDFAIFRT--------LGHH 191
Query: 136 TFKRTIKYDSKWLDSFKSLIAKII 159
RT ++DS+WL+ + + A +I
Sbjct: 192 HPIRTEQHDSRWLNDPRFISAHLI 215
>pdb|1OLZ|A Chain A, The Ligand-Binding Face Of The Semaphorins Revealed By The
High Resolution Crystal Structure Of Sema4d
pdb|1OLZ|B Chain B, The Ligand-Binding Face Of The Semaphorins Revealed By The
High Resolution Crystal Structure Of Sema4d
pdb|3OL2|A Chain A, Receptor-Ligand Structure Of Human Semaphorin 4d With
Plexin B1
Length = 663
Score = 31.2 bits (69), Expect = 0.23, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 16/65 (24%)
Query: 61 NLTH---LGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKAD 117
NLT LG++E G +CP+DP + T++ V+ LYSGT+ F ++
Sbjct: 118 NLTSFKFLGKNE------DGKGRCPFDPAHSYTSVMVDG-------ELYSGTSYNFLGSE 164
Query: 118 TVIFR 122
+I R
Sbjct: 165 PIISR 169
>pdb|1H6K|A Chain A, Nuclear Cap Binding Complex
pdb|1H6K|B Chain B, Nuclear Cap Binding Complex
pdb|1H6K|C Chain C, Nuclear Cap Binding Complex
Length = 757
Score = 26.9 bits (58), Expect = 5.6, Method: Composition-based stats.
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 47 RGFTKVFFWKILENNLTHLGRH 68
R FT++F W+IL + + + +H
Sbjct: 611 RDFTRLFVWEILHSTIRKMNKH 632
>pdb|1N52|A Chain A, Cap Binding Complex
pdb|1N54|A Chain A, Cap Binding Complex M7gpppg Free
pdb|3FEX|A Chain A, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|A Chain A, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 790
Score = 26.9 bits (58), Expect = 5.6, Method: Composition-based stats.
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 47 RGFTKVFFWKILENNLTHLGRH 68
R FT++F W+IL + + + +H
Sbjct: 630 RDFTRLFVWEILHSTIRKMNKH 651
>pdb|1H2V|C Chain C, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
Length = 771
Score = 26.9 bits (58), Expect = 5.6, Method: Composition-based stats.
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 47 RGFTKVFFWKILENNLTHLGRH 68
R FT++F W+IL + + + +H
Sbjct: 611 RDFTRLFVWEILHSTIRKMNKH 632
>pdb|4F52|E Chain E, Structure Of A Glomulin-Rbx1-Cul1 Complex
pdb|4F52|F Chain F, Structure Of A Glomulin-Rbx1-Cul1 Complex
Length = 596
Score = 26.6 bits (57), Expect = 6.1, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 9/60 (15%)
Query: 84 DPNDNSTAIWVEKGNPGN--LPALYSGTN-------AEFTKADTVIFRTDLLNFTTGKKE 134
+ NDN T +W E GN N L L+ G N AE + DL + T +E
Sbjct: 488 NENDNQTGLWTELGNIENNFLKPLHIGLNMSKAHYEAEIKNSQEAQKSKDLCSITVSGEE 547
>pdb|1H2T|C Chain C, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|A Chain A, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|B Chain B, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
Length = 723
Score = 26.6 bits (57), Expect = 6.2, Method: Composition-based stats.
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 47 RGFTKVFFWKILENNLTHLGRH 68
R FT++F W+IL + + + +H
Sbjct: 611 RDFTRLFVWEILHSTIRKMNKH 632
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
0.321 0.139 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,978,137
Number of Sequences: 62578
Number of extensions: 200497
Number of successful extensions: 312
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 298
Number of HSP's gapped (non-prelim): 11
length of query: 160
length of database: 14,973,337
effective HSP length: 91
effective length of query: 69
effective length of database: 9,278,739
effective search space: 640232991
effective search space used: 640232991
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: 47 (22.7 bits)