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= psy12371
         (72 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 = 39.3 bits (90), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/48 (37%), Positives = 23/48 (47%)

Query: 20 STNHTRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLEDFKLE 67
          S N+T P G   SP +P  YP  ++C Y   A     I +  E F LE
Sbjct: 12 SQNYTTPSGVIKSPGFPEKYPNSLECTYIVFAPKMSEIILEFESFDLE 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 = 39.3 bits (90), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/49 (36%), Positives = 24/49 (48%)

Query: 20  STNHTRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLEDFKLEK 68
           S N+T P G   SP +P  YP  ++C Y   A     I +  E F LE+
Sbjct: 130 SQNYTAPTGVIKSPGFPEKYPNSLECTYIIFAPKMSEIILEFESFDLEQ 178


>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 = 37.4 bits (85), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 24/48 (50%)

Query: 20 STNHTRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLEDFKLE 67
          S N T P G   SP +P  YP ++ C +T  A+ +  I +    F LE
Sbjct: 9  SKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLE 56


>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 = 37.0 bits (84), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 24/48 (50%)

Query: 20  STNHTRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLEDFKLE 67
           S N T P G   SP +P  YP ++ C +T  A+ +  I +    F LE
Sbjct: 128 SKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLE 175



 Score = 26.9 bits (58), Expect = 3.0,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 23 HTRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLE---DFKLEKGDVR 72
          +++  G   SP YP +YP+   C +   A  +   ++VL     F++EK D +
Sbjct: 11 NSKDAGYITSPGYPQDYPSHQNCEWIVYA-PEPNQKIVLNFNPHFEIEKHDCK 62


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

 Score = 32.3 bits (72), Expect = 0.071,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 23/44 (52%)

Query: 24 TRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLEDFKLE 67
          T P+  F SP +P+ Y  +  C +  R +  +RI +   DF LE
Sbjct: 12 TDPKQIFKSPGFPNEYEDNQICYWHIRLKYGQRIHLSFLDFDLE 55


>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 = 30.0 bits (66), Expect = 0.36,   Method: Composition-based stats.
 Identities = 14/44 (31%), Positives = 20/44 (45%)

Query: 24 TRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLEDFKLE 67
          T   G   SP +P+ YP  I C +    +    I ++ E F LE
Sbjct: 6  TESTGTIQSPGHPNVYPHGINCTWHILVQPNHLIHLMFETFHLE 49



 Score = 29.3 bits (64), Expect = 0.62,   Method: Composition-based stats.
 Identities = 14/46 (30%), Positives = 20/46 (43%)

Query: 22  NHTRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLEDFKLE 67
           N T   G F SP YP  Y    +C +  ++       +  +DF LE
Sbjct: 237 NLTTSSGTFISPNYPMPYYHSSECYWWLKSSHGSAFELEFKDFHLE 282


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

 Score = 29.3 bits (64), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 6/68 (8%)

Query: 1   MFHTDGHKLSGTTCDYQFVSTNHTRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVV 60
           + HTD       TC  +      T+  G   SP +P+ YP   +C YT        + + 
Sbjct: 154 ILHTDNR-----TCRVECSDNLFTQRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQ 208

Query: 61  LED-FKLE 67
            ED F +E
Sbjct: 209 FEDIFDIE 216



 Score = 29.3 bits (64), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 13/40 (32%), Positives = 20/40 (50%)

Query: 28 GRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLEDFKLE 67
          G+  SP YP +YP+D +  +        RI++    F LE
Sbjct: 10 GQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFNLE 49


>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 = 29.3 bits (64), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 13/41 (31%), Positives = 20/41 (48%)

Query: 28 GRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLEDFKLEK 68
          G+  SP YP +YP+D +  +        RI++    F LE 
Sbjct: 10 GQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFNLES 50



 Score = 28.9 bits (63), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 6/68 (8%)

Query: 1   MFHTDGHKLSGTTCDYQFVSTNHTRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVV 60
           + HTD       TC  +      T+  G   SP +P+ YP   +C YT        + + 
Sbjct: 154 ILHTDNR-----TCRVECSDNLFTQRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQ 208

Query: 61  LED-FKLE 67
            ED F +E
Sbjct: 209 FEDIFDIE 216


>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 = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 24 TRPQGRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLED-FKLE 67
          T+  G   SP YP+ YP   +C+YT        + +  ED F +E
Sbjct: 10 TQRTGTITSPDYPNPYPKSSECSYTIDLEEGFMVTLQFEDIFDIE 54


>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 = 14/40 (35%), Positives = 19/40 (47%)

Query: 28 GRFFSPRYPSNYPADIKCAYTFRARAQERIRVVLEDFKLE 67
          GR  SP +P  Y  D +  +T  A    R+R+    F LE
Sbjct: 13 GRLASPGFPGEYANDQERRWTLTAPPGYRLRLYFTHFDLE 52


>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 = 15/42 (35%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 27  QGRFFSPRYPSNYPADIKCAYTFRARAQERIRV-VLEDFKLE 67
            G   SP YP  YP    CAY  R      I +  +E F +E
Sbjct: 174 SGFLSSPEYPQPYPKLSSCAYNIRLEEGFSITLDFVESFDVE 215


  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
   0.325    0.138    0.435 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,325,432
Number of Sequences: 62578
Number of extensions: 77166
Number of successful extensions: 163
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 145
Number of HSP's gapped (non-prelim): 18
length of query: 72
length of database: 14,973,337
effective HSP length: 42
effective length of query: 30
effective length of database: 12,345,061
effective search space: 370351830
effective search space used: 370351830
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)