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= psy114
         (609 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3OKT|A Chain A, Mouse Plexin A2, Extracellular Domains 1-4
 pdb|3OKY|A Chain A, Plexin A2 In Complex With Semaphorin 6a
 pdb|4GZA|A Chain A, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
 pdb|4GZA|B Chain B, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
 pdb|4GZA|C Chain C, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
 pdb|4GZA|D Chain D, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
 pdb|4GZA|E Chain E, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
 pdb|4GZA|F Chain F, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
          Length = 681

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 43/114 (37%), Positives = 60/114 (52%), Gaps = 8/114 (7%)

Query: 197 RTLDLAIENLPELPGQLLCAFTIGETTVTTEAIKQTNG--VKCATPPTKDIPSIPVGQHN 254
           R L L + + P L   + CAF        TE   Q +G  V C +P  KD+P IP+ Q  
Sbjct: 545 RLLSLVVNDAPNLSEGIACAFG-----NLTEVEGQVSGSQVICISPGPKDVPVIPLDQDW 599

Query: 255 ITAKLSVRS-SNGPDFVTTKFMFFDCNTYSSCTQCVSSDFPCDWCVDGHRCTHD 307
              +L +RS   G  FV+T+F F++C+ +  C  CV+S F C WC   + CTHD
Sbjct: 600 FGLELQLRSKETGKIFVSTEFKFYNCSAHQLCLSCVNSAFRCHWCKYRNLCTHD 653


>pdb|3NVN|B Chain B, Molecular Mechanism Of Guidance Cue Recognition
 pdb|3NVQ|B Chain B, Molecular Mechanism Of Guidance Cue Recognition
 pdb|3NVQ|F Chain F, Molecular Mechanism Of Guidance Cue Recognition
          Length = 476

 Score = 32.7 bits (73), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%)

Query: 273 KFMFFDCNTYSSCTQCVSSDFP-CDWCVDGHRCT 305
           +    +CN + SC++C+++  P C WC    RCT
Sbjct: 415 RIRVANCNKHKSCSECLTATDPHCGWCHSLQRCT 448


>pdb|3OL2|B Chain B, Receptor-Ligand Structure Of Human Semaphorin 4d With
           Plexin B1
          Length = 528

 Score = 30.4 bits (67), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)

Query: 445 NCGLCLALPEKYGCGWCESSKRCEIFEQCDKG 476
           +C  CLA  + Y CGWC    RC    +C +G
Sbjct: 471 DCASCLAHRDPY-CGWCVLLGRCSRRSECSRG 501


>pdb|2UZX|B Chain B, Structure Of The Human Receptor Tyrosine Kinase Met In
           Complex With The Listeria Monocytogenes Invasion Protein
           Inlb: Crystal Form I
 pdb|2UZX|D Chain D, Structure Of The Human Receptor Tyrosine Kinase Met In
           Complex With The Listeria Monocytogenes Invasion Protein
           Inlb: Crystal Form I
 pdb|2UZY|B Chain B, Structure Of The Human Receptor Tyrosine Kinase Met In
           Complex With The Listeria Monocytogenes Invasion Protein
           Inlb: Low Resolution, Crystal Form Ii
 pdb|2UZY|D Chain D, Structure Of The Human Receptor Tyrosine Kinase Met In
           Complex With The Listeria Monocytogenes Invasion Protein
           Inlb: Low Resolution, Crystal Form Ii
          Length = 727

 Score = 29.3 bits (64), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 3/45 (6%)

Query: 432 VHVNIYKCRDLANNCGLCLALPEKYGCGWCESSKRCEIFEQCDKG 476
           + +N   CR    +C  CL+ P    CGWC    +C   E+C  G
Sbjct: 492 IPLNGLGCRHF-QSCSQCLSAPPFVQCGWCHD--KCVRSEECLSG 533


>pdb|3AL8|B Chain B, Plexin A2  SEMAPHORIN 6A COMPLEX
 pdb|3AL9|A Chain A, Mouse Plexin A2 Extracellular Domain
 pdb|3AL9|B Chain B, Mouse Plexin A2 Extracellular Domain
          Length = 539

 Score = 28.9 bits (63), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 1/28 (3%)

Query: 279 CNTYSSCTQCVSSDFP-CDWCVDGHRCT 305
           C  Y++C +C+SS  P C WC   + C+
Sbjct: 481 CEQYTTCGECLSSGDPHCGWCALHNMCS 508


>pdb|1SHY|B Chain B, The Crystal Structure Of Hgf Beta-Chain In Complex With
           The Sema Domain Of The Met Receptor
          Length = 551

 Score = 28.9 bits (63), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 3/45 (6%)

Query: 432 VHVNIYKCRDLANNCGLCLALPEKYGCGWCESSKRCEIFEQCDKG 476
           + +N   CR    +C  CL+ P    CGWC    +C   E+C  G
Sbjct: 489 IPLNGLGCRHF-QSCSQCLSAPPFVQCGWCHD--KCVRSEECLSG 530


  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    0.136    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,980,304
Number of Sequences: 62578
Number of extensions: 539856
Number of successful extensions: 940
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 929
Number of HSP's gapped (non-prelim): 15
length of query: 609
length of database: 14,973,337
effective HSP length: 105
effective length of query: 504
effective length of database: 8,402,647
effective search space: 4234934088
effective search space used: 4234934088
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: 54 (25.4 bits)