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= psy6561
         (223 letters)

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

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



>pdb|3BP5|B Chain B, Crystal Structure Of The Mouse Pd-1 And Pd-L2 Complex
 pdb|3BP6|B Chain B, Crystal Structure Of The Mouse Pd-1 Mutant And Pd-L2
           Complex
          Length = 202

 Score = 27.3 bits (59), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 9/68 (13%)

Query: 57  VPADVSSPRSPSSQIYITEKKVIRGQHSLQFGCDLFNEHYVEYCFVYVSQDSTGAVSDVK 116
           VPA+ S  R+P     +T    ++ Q S  F C  +N H  E          T A+ D  
Sbjct: 142 VPANTSHIRTPEGLYQVTSVLRLKPQPSRNFSCMFWNAHMKEL---------TSAIIDPL 192

Query: 117 SDCVPTYP 124
           S   P  P
Sbjct: 193 SRMEPKVP 200


>pdb|3RNQ|B Chain B, Crystal Structure Of The Complex Between The Extracellular
           Domains Of Mouse Pd-1 Mutant And Pd-L2
          Length = 201

 Score = 27.3 bits (59), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 9/68 (13%)

Query: 57  VPADVSSPRSPSSQIYITEKKVIRGQHSLQFGCDLFNEHYVEYCFVYVSQDSTGAVSDVK 116
           VPA+ S  R+P     +T    ++ Q S  F C  +N H  E          T A+ D  
Sbjct: 141 VPANTSHIRTPEGLYQVTSVLRLKPQPSRNFSCMFWNAHMKEL---------TSAIIDPL 191

Query: 117 SDCVPTYP 124
           S   P  P
Sbjct: 192 SRMEPKVP 199


  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
   0.319    0.132    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,194,671
Number of Sequences: 62578
Number of extensions: 233963
Number of successful extensions: 547
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 545
Number of HSP's gapped (non-prelim): 3
length of query: 223
length of database: 14,973,337
effective HSP length: 95
effective length of query: 128
effective length of database: 9,028,427
effective search space: 1155638656
effective search space used: 1155638656
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: 49 (23.5 bits)