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= 009014
         (546 letters)

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

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



>pdb|2G77|A Chain A, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
           Gtpase Bound To Gdp And Alf3
          Length = 410

 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 2/96 (2%)

Query: 366 EPSRIYHAARLEDHEA--FWCFAGFMKKARHNFRLDEVGIRRQLSIVSKIIKCKDNHLYR 423
           +PS      ++ D EA  FWC    +++   N+   + GI RQ+  +S+++K  D  LY 
Sbjct: 181 DPSTYMVDEQITDLEADTFWCLTKLLEQITDNYIHGQPGILRQVKNLSQLVKRIDADLYN 240

Query: 424 HLEQLQAEDCFFVYRMVVVLFRRELTFEQTLCLWEV 459
           H +    E   F +R +  L  RE      + +W+ 
Sbjct: 241 HFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDT 276


>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
          Length = 396

 Score = 46.2 bits (108), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 46/103 (44%), Gaps = 2/103 (1%)

Query: 359 LKDYDHLEPSRIYHAARLEDHEA--FWCFAGFMKKARHNFRLDEVGIRRQLSIVSKIIKC 416
           + D +  +PS      ++ D EA  FWC    +++   N+   + GI RQ+  +S+++K 
Sbjct: 154 IDDVEIKDPSTYXVDEQITDLEADTFWCLTKLLEQITDNYIHGQPGILRQVKNLSQLVKR 213

Query: 417 KDNHLYRHLEQLQAEDCFFVYRMVVVLFRRELTFEQTLCLWEV 459
            D  LY H +    E   F +R    L  RE      +  W+ 
Sbjct: 214 IDADLYNHFQNEHVEFIQFAFRWXNCLLXREFQXGTVIRXWDT 256


>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 = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/80 (22%), Positives = 42/80 (52%)

Query: 380 EAFWCFAGFMKKARHNFRLDEVGIRRQLSIVSKIIKCKDNHLYRHLEQLQAEDCFFVYRM 439
           + +WC +  +   + N+   + GI+ ++ ++ +++   D  ++RHL+Q +     F +R 
Sbjct: 190 DTYWCMSKLLDGIQDNYTFAQPGIQMKVKMLEELVSRIDEQVHRHLDQHEVRYLQFAFRW 249

Query: 440 VVVLFRRELTFEQTLCLWEV 459
           +  L  RE+    T+ LW+ 
Sbjct: 250 MNNLLMREVPLRCTIRLWDT 269


>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
          Length = 346

 Score = 42.7 bits (99), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/80 (22%), Positives = 41/80 (51%)

Query: 380 EAFWCFAGFMKKARHNFRLDEVGIRRQLSIVSKIIKCKDNHLYRHLEQLQAEDCFFVYRM 439
           ++FWC +  +   + N+   + GI++++  + +++   D  ++ H  + + E   F +R 
Sbjct: 191 DSFWCMSKLLDGIQDNYTFAQPGIQKKVKALEELVSRIDEQVHNHFRRYEVEYLQFAFRW 250

Query: 440 VVVLFRRELTFEQTLCLWEV 459
           +  L  REL    T+ LW+ 
Sbjct: 251 MNNLLMRELPLRCTIRLWDT 270


>pdb|2ICS|A Chain A, Crystal Structure Of An Adenine Deaminase
          Length = 379

 Score = 31.6 bits (70), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 30/117 (25%), Positives = 52/117 (44%), Gaps = 9/117 (7%)

Query: 327 DAVRANSEWTIYSPSQAAVSEMK-AQRSAQIVG-LKDYDHLEPSRIYHAARLEDHEAFWC 384
           D +  N +     P + A+ E K A  +A I G  K+  HLEP     A  ++DH    C
Sbjct: 6   DLLIKNGQTVNGXPVEIAIKEKKIAAVAATISGSAKETIHLEPGTYVSAGWIDDH--VHC 63

Query: 385 FAGFMKKARHNFRLDEVGIRRQLSIV--SKIIKCKDNHLYRHLEQLQAEDCFFVYRM 439
           F    K A +    DE+G+++ ++ V  +     ++ H +  L Q    + F +  +
Sbjct: 64  FE---KXALYYDYPDEIGVKKGVTTVIDAGTTGAENIHEFYDLAQQAKTNVFGLVNI 117


  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    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,385,246
Number of Sequences: 62578
Number of extensions: 514798
Number of successful extensions: 1238
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1230
Number of HSP's gapped (non-prelim): 14
length of query: 546
length of database: 14,973,337
effective HSP length: 104
effective length of query: 442
effective length of database: 8,465,225
effective search space: 3741629450
effective search space used: 3741629450
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)