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= psy8434
         (114 letters)

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

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



>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 =  103 bits (258), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 50/113 (44%), Positives = 73/113 (64%)

Query: 1   YSQVVLDVNRSLKRFPPGIPIEXXXXXXXXXXXXXXKVIHAYPRLRYYQGYHDVAITFLL 60
           Y QV+LDV RSL+RFPPG+P E               ++   P+L YYQGYHD+ +TFLL
Sbjct: 96  YQQVLLDVRRSLRRFPPGMPEEQREGLQEELIDIILLILERNPQLHYYQGYHDIVVTFLL 155

Query: 61  VVGEMKAFRILEVLSNDHLSENMRDTMDETSYVLNYMFPLVNKRSSDLCEFLE 113
           VVGE  A  ++E LS  HL + M  TMD T ++LNY+ P++++ + +L +F++
Sbjct: 156 VVGERLATSLVEKLSTHHLRDFMDPTMDNTKHILNYLMPIIDQVNPELHDFMQ 208


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

 Score =  103 bits (258), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 50/113 (44%), Positives = 73/113 (64%)

Query: 1   YSQVVLDVNRSLKRFPPGIPIEXXXXXXXXXXXXXXKVIHAYPRLRYYQGYHDVAITFLL 60
           Y QV+LDV RSL+RFPPG+P E               ++   P+L YYQGYHD+ +TFLL
Sbjct: 83  YQQVLLDVRRSLRRFPPGMPEEQREGLQEELIDIILLILERNPQLHYYQGYHDIVVTFLL 142

Query: 61  VVGEMKAFRILEVLSNDHLSENMRDTMDETSYVLNYMFPLVNKRSSDLCEFLE 113
           VVGE  A  ++E LS  HL + M  TMD T ++LNY+ P++++ + +L +F++
Sbjct: 143 VVGERLATSLVEKLSTHHLRDFMDPTMDNTKHILNYLMPIIDQVNPELHDFMQ 195


>pdb|2F6D|A Chain A, Structure Of The Complex Of A Glucoamylase From
          Saccharomycopsis Fibuligera With Acarbose
 pdb|2FBA|A Chain A, Glucoamylase From Saccharomycopsis Fibuligera At Atomic
          Resolution
 pdb|1AYX|A Chain A, Crystal Structure Of Glucoamylase From Saccharomycopsis
          Fibuligera At 1.7 Angstroms
          Length = 492

 Score = 25.8 bits (55), Expect = 7.3,   Method: Composition-based stats.
 Identities = 11/20 (55%), Positives = 14/20 (70%)

Query: 47 YYQGYHDVAITFLLVVGEMK 66
          YYQ   D AITFL V+ E++
Sbjct: 64 YYQWTRDSAITFLTVLSELE 83


  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    0.141    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,742,870
Number of Sequences: 62578
Number of extensions: 80335
Number of successful extensions: 206
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 201
Number of HSP's gapped (non-prelim): 3
length of query: 114
length of database: 14,973,337
effective HSP length: 77
effective length of query: 37
effective length of database: 10,154,831
effective search space: 375728747
effective search space used: 375728747
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)