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= 043546
         (110 letters)

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

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



>pdb|2R8B|A Chain A, The Crystal Structure Of The Protein Atu2452 Of Unknown
           Function From Agrobacterium Tumefaciens Str. C58
 pdb|2R8B|B Chain B, The Crystal Structure Of The Protein Atu2452 Of Unknown
           Function From Agrobacterium Tumefaciens Str. C58
          Length = 251

 Score = 29.3 bits (64), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 27/58 (46%), Gaps = 10/58 (17%)

Query: 12  PQDPRMKPPAEDLARLGCERVLIFVAERDYLCPA--GKNYYEELKKRGWKGRVELVEH 67
           P +P++ P           RVLI   ERD +CP    K   E LK +G  G VE V H
Sbjct: 177 PFEPKISPAKP------TRRVLITAGERDPICPVQLTKALEESLKAQG--GTVETVWH 226


>pdb|4HLQ|A Chain A, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
           Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
 pdb|4HLQ|C Chain C, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
           Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
 pdb|4HLQ|E Chain E, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
           Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
 pdb|4HLQ|G Chain G, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
           Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
 pdb|4HLQ|I Chain I, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
           Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
          Length = 305

 Score = 27.3 bits (59), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 15/52 (28%), Positives = 22/52 (42%)

Query: 57  GWKGRVELVEHLDEKHVFYLRNPTCTNALELTNKFISFIKQNNGSLRSSIES 108
           G +    LVE L   H+    +PT  N   + N  +  I Q N  L   ++S
Sbjct: 158 GERLATSLVEKLSTHHLRDFMDPTMDNTKHILNYLMPIIDQVNPELHDFMQS 209


>pdb|4HL4|A Chain A, Crystal Structure Of The Human Tbc1d20 Rabgap Domain
          Length = 292

 Score = 26.9 bits (58), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 15/52 (28%), Positives = 22/52 (42%)

Query: 57  GWKGRVELVEHLDEKHVFYLRNPTCTNALELTNKFISFIKQNNGSLRSSIES 108
           G +    LVE L   H+    +PT  N   + N  +  I Q N  L   ++S
Sbjct: 145 GERLATSLVEKLSTHHLRDFMDPTMDNTKHILNYLMPIIDQVNPELHDFMQS 196


>pdb|4PBG|A Chain A, 6-Phospho-Beta-Galactosidase Form-Cst
 pdb|4PBG|B Chain B, 6-Phospho-Beta-Galactosidase Form-Cst
          Length = 468

 Score = 26.9 bits (58), Expect = 3.0,   Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 54  KKRGWKGRVELVEHLDEKHVFYLRNPTCTNALELT----NKFI 92
           K +G+KG + +V  L  K+ +   NP    A EL     NKFI
Sbjct: 204 KDKGYKGEIGVVHALPTKYPYDPENPADVRAAELEDIIHNKFI 246


>pdb|1PBG|A Chain A, The Three-Dimensional Structure Of 6-Phospho-Beta
           Galactosidase From Lactococcus Lactis
 pdb|1PBG|B Chain B, The Three-Dimensional Structure Of 6-Phospho-Beta
           Galactosidase From Lactococcus Lactis
 pdb|3PBG|A Chain A, 6-Phospho-Beta-Galactosidase Form-C
 pdb|3PBG|B Chain B, 6-Phospho-Beta-Galactosidase Form-C
          Length = 468

 Score = 26.9 bits (58), Expect = 3.0,   Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 54  KKRGWKGRVELVEHLDEKHVFYLRNPTCTNALELT----NKFI 92
           K +G+KG + +V  L  K+ +   NP    A EL     NKFI
Sbjct: 204 KDKGYKGEIGVVHALPTKYPYDPENPADVRAAELEDIIHNKFI 246


>pdb|2PBG|A Chain A, 6-Phospho-Beta-D-Galactosidase Form-B
          Length = 468

 Score = 26.9 bits (58), Expect = 3.1,   Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 54  KKRGWKGRVELVEHLDEKHVFYLRNPTCTNALELT----NKFI 92
           K +G+KG + +V  L  K+ +   NP    A EL     NKFI
Sbjct: 204 KDKGYKGEIGVVHALPTKYPYDPENPADVRAAELEDIIHNKFI 246


  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
   0.320    0.138    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,479,783
Number of Sequences: 62578
Number of extensions: 133005
Number of successful extensions: 250
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 244
Number of HSP's gapped (non-prelim): 7
length of query: 110
length of database: 14,973,337
effective HSP length: 74
effective length of query: 36
effective length of database: 10,342,565
effective search space: 372332340
effective search space used: 372332340
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: 45 (21.9 bits)