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= psy12370
         (96 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 = 40.0 bits (92), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/41 (43%), Positives = 21/41 (51%)

Query: 52 NGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDVE 92
          +G   SP FP  YP   EC Y  +      I L FESFD+E
Sbjct: 19 SGVIKSPGFPEKYPNSLECTYIVFAPKMSEIILEFESFDLE 59


>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 = 40.0 bits (92), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/40 (45%), Positives = 20/40 (50%)

Query: 53  GTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDVE 92
           G   SP FP  YP   EC Y  +      I L FESFD+E
Sbjct: 138 GVIKSPGFPEKYPNSLECTYIIFAPKMSEIILEFESFDLE 177


>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 = 38.1 bits (87), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 50 HRNGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFES-FDVEGVP 95
           R GT TSP++P  YP+ +EC Y         + L FE  FD+E  P
Sbjct: 11 QRTGTITSPDYPNPYPKSSECSYTIDLEEGFMVTLQFEDIFDIEDHP 57


>pdb|4AQB|A Chain A, Mbl-Ficolin Associated Protein-1, Map-1 Aka Map44
          Length = 361

 Score = 36.6 bits (83), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 50  HRNGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFES-FDVEGVP 95
            R G  TSP+FP  YP+ +EC Y         + L FE  FD+E  P
Sbjct: 173 QRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQFEDIFDIEDHP 219



 Score = 29.3 bits (64), Expect = 0.65,   Method: Compositional matrix adjust.
 Identities = 15/41 (36%), Positives = 21/41 (51%)

Query: 53 GTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDVEG 93
          G   SP +P  YP D+E  +     +  RIKL F  F++E 
Sbjct: 10 GQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFNLES 50


>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 = 36.6 bits (83), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/44 (38%), Positives = 22/44 (50%)

Query: 52 NGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDVEGVP 95
          NGT  SP FP  YP + +C +    +    I L F  FD+E  P
Sbjct: 16 NGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLEHDP 59


>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 = 36.2 bits (82), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 50  HRNGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFES-FDVEGVP 95
            R G  TSP+FP  YP+ +EC Y         + L FE  FD+E  P
Sbjct: 173 QRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQFEDIFDIEDHP 219



 Score = 28.9 bits (63), Expect = 0.73,   Method: Compositional matrix adjust.
 Identities = 15/41 (36%), Positives = 21/41 (51%)

Query: 53 GTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDVEG 93
          G   SP +P  YP D+E  +     +  RIKL F  F++E 
Sbjct: 10 GQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFNLES 50


>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 = 36.2 bits (82), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/44 (38%), Positives = 22/44 (50%)

Query: 52  NGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDVEGVP 95
           NGT  SP FP  YP + +C +    +    I L F  FD+E  P
Sbjct: 135 NGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLEHDP 178



 Score = 29.6 bits (65), Expect = 0.46,   Method: Composition-based stats.
 Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 39 PCAFMFNSTGGHRNGTFTSPNFPGLYPRDTECHYFFYG-RNDERIKLVFES-FDVE 92
          PC    NS      G  TSP +P  YP    C +  Y    +++I L F   F++E
Sbjct: 5  PCGGRLNSKDA---GYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIE 57


>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 = 35.0 bits (79), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 25/44 (56%)

Query: 52  NGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDVEGVP 95
           +GTF SPN+P  Y   +EC+++    +    +L F+ F +E  P
Sbjct: 242 SGTFISPNYPMPYYHSSECYWWLKSSHGSAFELEFKDFHLEHHP 285



 Score = 32.0 bits (71), Expect = 0.096,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 21/40 (52%)

Query: 53 GTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDVE 92
          GT  SP  P +YP    C +    + +  I L+FE+F +E
Sbjct: 10 GTIQSPGHPNVYPHGINCTWHILVQPNHLIHLMFETFHLE 49


>pdb|2WNO|A Chain A, X-Ray Structure Of Cub_c Domain From Tsg-6
          Length = 149

 Score = 31.6 bits (70), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 15/41 (36%), Positives = 21/41 (51%)

Query: 55 FTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDVEGVP 95
          F SP FP  Y  +  C++    +  +RI L F  FD+E  P
Sbjct: 18 FKSPGFPNEYEDNQICYWHIRLKYGQRIHLSFLDFDLEDDP 58


>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 = 30.8 bits (68), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 51  RNGTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVF-ESFDVEGVP 95
           R+G  +SP +P  YP+ + C Y         I L F ESFDVE  P
Sbjct: 173 RSGFLSSPEYPQPYPKLSSCAYNIRLEEGFSITLDFVESFDVEMHP 218


>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 = 30.4 bits (67), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 19/40 (47%)

Query: 53 GTFTSPNFPGLYPRDTECHYFFYGRNDERIKLVFESFDVE 92
          G   SP FPG Y  D E  +        R++L F  FD+E
Sbjct: 13 GRLASPGFPGEYANDQERRWTLTAPPGYRLRLYFTHFDLE 52


>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 = 26.6 bits (57), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 5/29 (17%)

Query: 52  NGTFTSPNFPGLYPRDTECHYFFYGRNDE 80
           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
   0.323    0.141    0.451 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,284,558
Number of Sequences: 62578
Number of extensions: 136364
Number of successful extensions: 179
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 162
Number of HSP's gapped (non-prelim): 19
length of query: 96
length of database: 14,973,337
effective HSP length: 62
effective length of query: 34
effective length of database: 11,093,501
effective search space: 377179034
effective search space used: 377179034
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)