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= 006861
         (628 letters)

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

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



>pdb|2QFZ|A Chain A, Crystal Structure Of Human Tbc1 Domain Family Member 22a
 pdb|2QFZ|B Chain B, Crystal Structure Of Human Tbc1 Domain Family Member 22a
          Length = 345

 Score = 31.2 bits (69), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 22/95 (23%), Positives = 45/95 (47%), Gaps = 7/95 (7%)

Query: 217 KEIGSGYLSAFPTEQFDRLEALIPVWAPYYTIHKILAGLLDQYTYADNAEALRMTTWMVE 276
           +E+ +  +S  P E    +EA       Y+ + K+L G+ D YT+A     ++M   M+E
Sbjct: 169 EEVDTVDVSGVPAEVLCNIEA-----DTYWCMSKLLDGIQDNYTFA--QPGIQMKVKMLE 221

Query: 277 YFYNRVQNVIKKYSIERHWQTLNEEAGGMNDVLYK 311
              +R+   + ++  +   + L      MN++L +
Sbjct: 222 ELVSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMR 256


>pdb|3TX8|A Chain A, Crystal Structure Of A Succinyl-Diaminopimelate
           Desuccinylase (Arge) From Corynebacterium Glutamicum
           Atcc 13032 At 2.97 A Resolution
          Length = 369

 Score = 30.4 bits (67), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 6/61 (9%)

Query: 157 TARLPAPGEPYGGWEEPSCE--LRGHFVGHYLSA-SALMWASTHNESLKEKMSAVVSALS 213
            A L   GEP GGW E  C+  LR     H + A SA  W     ++   K+S ++S ++
Sbjct: 157 AADLALLGEPTGGWIEAGCQGNLRIKVTAHGVRAHSARSWLG---DNAXHKLSPIISKVA 213

Query: 214 A 214
           A
Sbjct: 214 A 214


>pdb|3IFL|L Chain L, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
           7:12a11) Complex
 pdb|3IFN|L Chain L, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
           40:12a11) Complex
          Length = 219

 Score = 29.6 bits (65), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 334 LGLLALQADDISGFH--SNTHIPIVIGSQMRYEVTGDQLHKTISMFFMDIVNSSHTYATG 391
           L +  ++A+D+  ++   ++H+P+  G+  + E+ G     T+S+F      SS    +G
Sbjct: 78  LKISRVEAEDLGIYYCFQSSHVPLTFGAGTKLELKGADAAPTVSIF----PPSSEQLTSG 133

Query: 392 GTSVGEFWSD--PKRL 405
           G SV  F ++  PK +
Sbjct: 134 GASVVCFLNNFYPKDI 149


>pdb|3GNM|L Chain L, The Crystal Structure Of The Jaa-f11 Monoclonal Antibody
           Fab Fragment
          Length = 219

 Score = 29.3 bits (64), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 8/76 (10%)

Query: 334 LGLLALQADDISGFH--SNTHIPIVIGSQMRYEVTGDQLHKTISMFFMDIVNSSHTYATG 391
           L +  ++ADD+  ++    +H+P   GS  + E+       T+S+F      SS    +G
Sbjct: 78  LKISRVEADDLGVYYCFQGSHVPFTFGSGTKLEIKRADAAPTVSIF----PPSSEQLTSG 133

Query: 392 GTSVGEFWSD--PKRL 405
           G SV  F ++  PK +
Sbjct: 134 GASVVCFLNNFYPKDI 149


  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    0.134    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,290,367
Number of Sequences: 62578
Number of extensions: 874803
Number of successful extensions: 1890
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1890
Number of HSP's gapped (non-prelim): 9
length of query: 628
length of database: 14,973,337
effective HSP length: 105
effective length of query: 523
effective length of database: 8,402,647
effective search space: 4394584381
effective search space used: 4394584381
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)