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= 006546
         (641 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 = 40.8 bits (94), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 32/66 (48%)

Query: 145 VIEASSAMYHLLSVADSSLHSHLVELGVEPQYFGLRWLRVLFGREFSLGDLLIIWDEIFA 204
           ++     +  L+   D+ L++H     VE   F  RW+  L  REF +G ++ +WD   +
Sbjct: 220 ILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYLS 279

Query: 205 SDSSKV 210
             S +V
Sbjct: 280 ETSQEV 285


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

 Score = 37.4 bits (85), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 29/66 (43%)

Query: 145 VIEASSAMYHLLSVADSSLHSHLVELGVEPQYFGLRWLRVLFGREFSLGDLLIIWDEIFA 204
           ++     +  L+   D+ L++H     VE   F  RW   L  REF  G ++  WD   +
Sbjct: 200 ILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWXNCLLXREFQXGTVIRXWDTYLS 259

Query: 205 SDSSKV 210
             S +V
Sbjct: 260 ETSQEV 265


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

 Score = 34.3 bits (77), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 16/97 (16%)

Query: 105 MEHDAYCMFDALMVGSQGSVSMADFFAHSHADGSLTCLLPVIEAS-SAMYHLLSVADSSL 163
           +E D++     L+ G Q + + A                P I+    A+  L+S  D  +
Sbjct: 188 IEADSFWCMSKLLDGIQDNYTFAQ---------------PGIQKKVKALEELVSRIDEQV 232

Query: 164 HSHLVELGVEPQYFGLRWLRVLFGREFSLGDLLIIWD 200
           H+H     VE   F  RW+  L  RE  L   + +WD
Sbjct: 233 HNHFRRYEVEYLQFAFRWMNNLLMRELPLRCTIRLWD 269


>pdb|3QYB|A Chain A, X-Ray Crystal Structure Of Human Tbc1d4 (As160) Rabgap
           Domain
          Length = 301

 Score = 33.5 bits (75), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 163 LHSHLVELGVEPQYFGLRWLRVLFGREFSLGDLLIIWDEIFASDSSKVNK 212
           L++HL E  + P  +   W   LF  +FSLG +  ++D IF   +  + K
Sbjct: 200 LYNHLEENEISPSLYAAPWFLTLFASQFSLGFVARVFDIIFLQGTEVIFK 249


>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 = 32.3 bits (72), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 37/97 (38%), Gaps = 16/97 (16%)

Query: 105 MEHDAYCMFDALMVGSQGSVSMADFFAHSHADGSLTCLLPVIEASSAMYH-LLSVADSSL 163
           +E D Y     L+ G Q + + A                P I+    M   L+S  D  +
Sbjct: 187 IEADTYWCMSKLLDGIQDNYTFAQ---------------PGIQMKVKMLEELVSRIDEQV 231

Query: 164 HSHLVELGVEPQYFGLRWLRVLFGREFSLGDLLIIWD 200
           H HL +  V    F  RW+  L  RE  L   + +WD
Sbjct: 232 HRHLDQHEVRYLQFAFRWMNNLLMREVPLRCTIRLWD 268


>pdb|3NK6|A Chain A, Structure Of The Nosiheptide-Resistance Methyltransferase
 pdb|3NK6|B Chain B, Structure Of The Nosiheptide-Resistance Methyltransferase
 pdb|3NK7|A Chain A, Structure Of The Nosiheptide-Resistance Methyltransferase
           S-Adenosyl- L-Methionine Complex
 pdb|3NK7|B Chain B, Structure Of The Nosiheptide-Resistance Methyltransferase
           S-Adenosyl- L-Methionine Complex
          Length = 277

 Score = 31.2 bits (69), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 13/26 (50%), Positives = 20/26 (76%)

Query: 374 SDPTPRTVDNGTKHSRSSIRRSLLED 399
           SDP  + + + TKHSR+SI+ +L+ED
Sbjct: 14  SDPAVQRIIDVTKHSRASIKTTLIED 39


>pdb|3U44|A Chain A, Crystal Structure Of Addab-Dna Complex
 pdb|3U4Q|A Chain A, Structure Of Addab-Dna Complex At 2.8 Angstroms
          Length = 1232

 Score = 30.4 bits (67), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 8/67 (11%)

Query: 51  KKFLDSMEDEIGSHGNSVKVRSVDELDPEIQTIVQLSDAYG-----AEGELGIVLSEKFM 105
           KK L+ ++ +  +      ++S+ E+ P I+T+VQL  +YG     A+ E  I+    F 
Sbjct: 313 KKLLEKLKTDYFTRSPEQHLKSLAEMKPVIETLVQLVISYGKRFEAAKQEKSII---DFS 369

Query: 106 EHDAYCM 112
           + + YC+
Sbjct: 370 DLEHYCL 376


  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
   0.313    0.129    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,346,464
Number of Sequences: 62578
Number of extensions: 672975
Number of successful extensions: 1156
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1149
Number of HSP's gapped (non-prelim): 10
length of query: 641
length of database: 14,973,337
effective HSP length: 105
effective length of query: 536
effective length of database: 8,402,647
effective search space: 4503818792
effective search space used: 4503818792
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.8 bits)