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= psy946
         (714 letters)

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

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



>pdb|3TW8|A Chain A, Gef Domain Of Dennd 1b In Complex With Rab Gtpase Rab35
 pdb|3TW8|C Chain C, Gef Domain Of Dennd 1b In Complex With Rab Gtpase Rab35
          Length = 391

 Score =  240 bits (612), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 115/226 (50%), Positives = 163/226 (72%), Gaps = 4/226 (1%)

Query: 279 LNTLPQDVKNLTEY-CAIEPVNMLHIFASMLYERRIVITSKRLSRVSACVQAANLVIYPM 337
           L T+P+  +NLTEY  A++  NML ++ASML+ERRIVI S +LS ++AC+  +  ++YPM
Sbjct: 162 LPTIPES-RNLTEYFVAVDVNNMLQLYASMLHERRIVIISSKLSTLTACIHGSAALLYPM 220

Query: 338 CWQHIFIPLMPRDLLDYLTAPMPYMVGLPEILLDSVRRNELGDVVLLNADTNVLTTPHDD 397
            WQHI+IP++P  LLDY  APMPY++G+   L++ V+   L DVV+LN DTN L +P  D
Sbjct: 221 YWQHIYIPVLPPHLLDYCCAPMPYLIGIHSSLIERVKNKSLEDVVMLNVDTNTLESPFSD 280

Query: 398 LNTLPQDVIATLKKQLRNKT--TGDGVARAFLRALVQLIGGYRDALKFHQGQEITFNDAA 455
           LN LP DV++ LK +L+ ++  TGDGVARAFLRA   L G YRDAL++  G+ ITF + +
Sbjct: 281 LNNLPSDVVSALKNKLKKQSTATGDGVARAFLRAQAALFGSYRDALRYKPGEPITFCEES 340

Query: 456 FVESRPAAMQPFLRKMLDLQIFQQFKEERLNMLNSGQGFTDEFERE 501
           FV+ R + M+ FL   ++LQ+F+QF + RL  LN+G+GF+D FE E
Sbjct: 341 FVKHRSSVMKQFLETAINLQLFKQFIDGRLAKLNAGRGFSDVFEEE 386



 Score =  221 bits (563), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 113/260 (43%), Positives = 167/260 (64%), Gaps = 8/260 (3%)

Query: 32  VLQKFPGSYKDESVLKNVPKFAYPCKLENTS----VEYYSFVLTDLDSKFTFGYCRHDPK 87
           VL KFP  + D+ +L++VPKF +P  +E  S     ++++FVLTD++SK  FG+CR    
Sbjct: 32  VLWKFPEDFGDQEILQSVPKFCFPFDVERVSQNQVGQHFTFVLTDIESKQRFGFCRLTSG 91

Query: 88  SDTSMVIISLLPWHESFYKLLNCVVEITNGSSPQLLWTFLEDIYNANIPEYGQIIYATSK 147
               + I+S LPW E +YKLLN + +         L   L  +YN  +P+    +   S 
Sbjct: 92  GTICLCILSYLPWFEVYYKLLNTLADYLAKELENDLNETLRSLYNHPVPKANTPV-NLSV 150

Query: 148 NTEYTCQAPNQYQLPSIPENKNLTEY-CAIEPVNMLHIFASMLYERRIVITSKRLSRVSA 206
           ++ +   AP+   LP+IPE++NLTEY  A++  NML ++ASML+ERRIVI S +LS ++A
Sbjct: 151 HSYFI--APDVTGLPTIPESRNLTEYFVAVDVNNMLQLYASMLHERRIVIISSKLSTLTA 208

Query: 207 CVQAANSVIYPMCWQHIFIPLMPRDLLDYLTAPMPYMVGLPEILLDSVRRNELGDVVLLN 266
           C+  + +++YPM WQHI+IP++P  LLDY  APMPY++G+   L++ V+   L DVV+LN
Sbjct: 209 CIHGSAALLYPMYWQHIYIPVLPPHLLDYCCAPMPYLIGIHSSLIERVKNKSLEDVVMLN 268

Query: 267 ADTNVLTTPHDDLNTLPQDV 286
            DTN L +P  DLN LP DV
Sbjct: 269 VDTNTLESPFSDLNNLPSDV 288


>pdb|4A27|A Chain A, Crystal Structure Of Human Synaptic Vesicle Membrane
           Protein Vat-1 Homolog-Like Protein
 pdb|4A27|B Chain B, Crystal Structure Of Human Synaptic Vesicle Membrane
           Protein Vat-1 Homolog-Like Protein
          Length = 349

 Score = 30.8 bits (68), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 7/70 (10%)

Query: 245 GLPEILLDSVRRNELGDVVLL----NADTNVLTTPHDDLNTLPQDVKNLTEYCAIEPVNM 300
           G+ E L DSV+  E+GD V+     NA   V+ TP + +  +P D+ + +E  A  P+N 
Sbjct: 70  GIVEALGDSVKGYEIGDRVMAFVNYNAWAEVVCTPVEFVYKIPDDM-SFSEAAAF-PMNF 127

Query: 301 LHIFASMLYE 310
           +  +  ML+E
Sbjct: 128 VTAYV-MLFE 136


  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
   0.321    0.136    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,541,365
Number of Sequences: 62578
Number of extensions: 876360
Number of successful extensions: 1831
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1819
Number of HSP's gapped (non-prelim): 15
length of query: 714
length of database: 14,973,337
effective HSP length: 106
effective length of query: 608
effective length of database: 8,340,069
effective search space: 5070761952
effective search space used: 5070761952
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)