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= 024155
         (271 letters)

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

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



>pdb|4A01|A Chain A, Crystal Structure Of The H-Translocating Pyrophosphatase
 pdb|4A01|B Chain B, Crystal Structure Of The H-Translocating Pyrophosphatase
          Length = 766

 Score = 29.3 bits (64), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 11/36 (30%), Positives = 18/36 (50%)

Query: 185 SNIPEFNKVECWGPLKEAVAGSSEAGGTRHEIRQET 220
           S I     ++ +GP+ +   G +E  G  H IR+ T
Sbjct: 491 STIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERT 526


>pdb|1T91|A Chain A, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
 pdb|1T91|B Chain B, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
 pdb|1T91|C Chain C, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
 pdb|1T91|D Chain D, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
 pdb|1YHN|A Chain A, Structure Basis Of Rilp Recruitment By Rab7
          Length = 207

 Score = 28.5 bits (62), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 20/86 (23%)

Query: 166 NLLNNHPELQEALVWVYFHSNIPEFNKVECWGPLKEAVAGSSEAGGT--RHEIRQETSIS 223
           +L N     + A  W Y  +NIP F         KEA+    +A  T  R+ ++QET + 
Sbjct: 128 DLENRQVATKRAQAWCYSKNNIPYFET-----SAKEAI-NVEQAFQTIARNALKQETEVE 181

Query: 224 NW-ELPEPCQ-----------ETCNC 237
            + E PEP +           E+C+C
Sbjct: 182 LYNEFPEPIKLDKNDRAKASAESCSC 207


>pdb|1VG0|B Chain B, The Crystal Structures Of The Rep-1 Protein In Complex
           With Monoprenylated Rab7 Protein
 pdb|1VG8|A Chain A, Gppnhp-Bound Rab7
 pdb|1VG8|B Chain B, Gppnhp-Bound Rab7
 pdb|1VG8|C Chain C, Gppnhp-Bound Rab7
 pdb|1VG8|D Chain D, Gppnhp-Bound Rab7
          Length = 207

 Score = 28.5 bits (62), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 20/86 (23%)

Query: 166 NLLNNHPELQEALVWVYFHSNIPEFNKVECWGPLKEAVAGSSEAGGT--RHEIRQETSIS 223
           +L N     + A  W Y  +NIP F         KEA+    +A  T  R+ ++QET + 
Sbjct: 128 DLENRQVATKRAQAWCYSKNNIPYFET-----SAKEAI-NVEQAFQTIARNALKQETEVE 181

Query: 224 NW-ELPEPCQ-----------ETCNC 237
            + E PEP +           E+C+C
Sbjct: 182 LYNEFPEPIKLDKNERAKASAESCSC 207


>pdb|3LAW|A Chain A, Structure Of Gtp-Bound L129f Mutant Rab7
 pdb|3LAW|B Chain B, Structure Of Gtp-Bound L129f Mutant Rab7
 pdb|3LAW|C Chain C, Structure Of Gtp-Bound L129f Mutant Rab7
 pdb|3LAW|D Chain D, Structure Of Gtp-Bound L129f Mutant Rab7
 pdb|3LAW|E Chain E, Structure Of Gtp-Bound L129f Mutant Rab7
          Length = 207

 Score = 27.3 bits (59), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 36/83 (43%), Gaps = 20/83 (24%)

Query: 169 NNHPELQEALVWVYFHSNIPEFNKVECWGPLKEAVAGSSEAGGT--RHEIRQETSISNW- 225
           N     + A  W Y  +NIP F         KEA+    +A  T  R+ ++QET +  + 
Sbjct: 131 NRQVATKRAQAWCYSKNNIPYFET-----SAKEAI-NVEQAFQTIARNALKQETEVELYN 184

Query: 226 ELPEPCQ-----------ETCNC 237
           E PEP +           E+C+C
Sbjct: 185 EFPEPIKLDKNDRAKASAESCSC 207


>pdb|3R3Q|A Chain A, Crystal Structure Of The Yeast Vps23 Uev Domain
 pdb|3R42|A Chain A, Crystal Structure Of The Yeast Vps23 Uev Domain In
          Complex With A Vps27 Psdp Peptide
          Length = 162

 Score = 27.3 bits (59), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 13/27 (48%), Positives = 17/27 (62%)

Query: 73 PRTYTLTHSDITSKLTLAISQTINNSQ 99
          PRT   THSD T +L L+I  TI+  +
Sbjct: 49 PRTRVFTHSDGTPQLLLSIYGTISTGE 75


  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
   0.318    0.133    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,196,378
Number of Sequences: 62578
Number of extensions: 335403
Number of successful extensions: 708
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 705
Number of HSP's gapped (non-prelim): 7
length of query: 271
length of database: 14,973,337
effective HSP length: 97
effective length of query: 174
effective length of database: 8,903,271
effective search space: 1549169154
effective search space used: 1549169154
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)