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= psy11311
         (499 letters)

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

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



>pdb|2EFK|A Chain A, Crystal Structure Of The Efc Domain Of Cdc42-Interacting
           Protein 4
          Length = 301

 Score = 31.2 bits (69), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 330 SQEGAFENVRMNLNGDQGQTIRQLISNNSIRRTCMCILSSPQSKRQHLVAVSHEKGKITL 389
           SQ+ +F  +   +N   GQ  R+L++ N   R C+ +    Q  +Q       E G+   
Sbjct: 66  SQQQSFVQILQEVNDFAGQ--RELVAENLSVRVCLELTKYSQEXKQERKXHFQE-GRRAQ 122

Query: 390 LQLSGLLKQIDSSKRKL 406
            QL    KQ+++SKRK 
Sbjct: 123 QQLENGFKQLENSKRKF 139


>pdb|3NY1|A Chain A, Structure Of The Ubr-Box Of The Ubr1 Ubiquitin Ligase
 pdb|3NY1|B Chain B, Structure Of The Ubr-Box Of The Ubr1 Ubiquitin Ligase
          Length = 77

 Score = 30.4 bits (67), Expect = 2.1,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 79  YHCHTCKMIDGVGVCSVCAQ-VCHKNHDIT-YSKFGNFFCDCGAKE 122
           Y C  C +     +C  C Q   HKNH    ++  G  FCDCG  E
Sbjct: 19  YSCRDCAIDPTCVLCMDCFQDSVHKNHRYKMHTSTGGGFCDCGDTE 64


>pdb|2D5W|A Chain A, The Crystal Structure Of Oligopeptide Binding Protein From
           Thermus Thermophilus Hb8 Complexed With Pentapeptide
 pdb|2D5W|B Chain B, The Crystal Structure Of Oligopeptide Binding Protein From
           Thermus Thermophilus Hb8 Complexed With Pentapeptide
          Length = 603

 Score = 28.5 bits (62), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 13/41 (31%), Positives = 27/41 (65%), Gaps = 2/41 (4%)

Query: 309 LQNMQHKFVENTDNLMVPVMGSQEGAFENVRMNLNGDQGQT 349
           +Q + ++F++NT++L+V V+G    A  +V +    DQG++
Sbjct: 244 VQKVVYRFIQNTNSLLVAVIGGSIDATSSVSLTF--DQGRS 282


  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    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,264,188
Number of Sequences: 62578
Number of extensions: 381887
Number of successful extensions: 722
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 722
Number of HSP's gapped (non-prelim): 4
length of query: 499
length of database: 14,973,337
effective HSP length: 103
effective length of query: 396
effective length of database: 8,527,803
effective search space: 3377009988
effective search space used: 3377009988
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)