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= psy11738
         (323 letters)

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

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



>pdb|2XEV|A Chain A, Crystal Structure Of The Tpr Domain Of Xanthomonas
           Campestris Ybgf
 pdb|2XEV|B Chain B, Crystal Structure Of The Tpr Domain Of Xanthomonas
           Campestris Ybgf
 pdb|2XEV|C Chain C, Crystal Structure Of The Tpr Domain Of Xanthomonas
           Campestris Ybgf
          Length = 129

 Score = 30.0 bits (66), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 3/79 (3%)

Query: 241 RKIANAIFDTLPTSSYEEALKYFLEAEKQHP-LFYSQNVLM-LGKTYMRLENYEQA-AYY 297
           R   N  FD L    Y++A + FL   + +P   Y+ N L  LG++Y    N++ A A +
Sbjct: 3   RTAYNVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQF 62

Query: 298 LEMTKNYPAVQEATKLLEK 316
            ++   YP   +A   L K
Sbjct: 63  RDLVSRYPTHDKAAGGLLK 81



 Score = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

Query: 158 RKIANAIFDTLPTSSYEEALKYFLEAEKQHP-LFYSQNVLM-LGKTYMRLENYEQA-AYY 214
           R   N  FD L    Y++A + FL   + +P   Y+ N L  LG++Y    N++ A A +
Sbjct: 3   RTAYNVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQF 62

Query: 215 LEMTKNYPV 223
            ++   YP 
Sbjct: 63  RDLVSRYPT 71


>pdb|3CV0|A Chain A, Structure Of Peroxisomal Targeting Signal 1 (Pts1) Binding
           Domain Of Trypanosoma Brucei Peroxin 5 (Tbpex5)complexed
           To T. Brucei Phosphoglucoisomerase (Pgi) Pts1 Peptide
 pdb|3CVL|A Chain A, Structure Of Peroxisomal Targeting Signal 1 (Pts1) Binding
           Domain Of Trypanosoma Brucei Peroxin 5 (Tbpex5)complexed
           To T. Brucei Phosphofructokinase (Pfk) Pts1 Peptide
 pdb|3CVN|A Chain A, Structure Of Peroxisomal Targeting Signal 1 (Pts1) Binding
           Domain Of Trypanosoma Brucei Peroxin 5 (Tbpex5)complexed
           To T. Brucei Glyceraldehyde-3-Phosphate Dehydrogenase
           (Gapdh) Pts1 Peptide
 pdb|3CVP|A Chain A, Structure Of Peroxisomal Targeting Signal 1 (Pts1) Binding
           Domain Of Trypanosoma Brucei Peroxin 5 (Tbpex5)complexed
           To Pts1 Peptide (10-Skl)
          Length = 327

 Score = 28.1 bits (61), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 42  YKEDVEIIWRLVRVKYNLATHSSSLS--DADKKQLILSAYFLVYNALPQHE 90
           Y   ++I    VRV YN+A   S++S  D   KQL+ + Y  V    P  E
Sbjct: 229 YNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGE 279


>pdb|3CVQ|A Chain A, Structure Of Peroxisomal Targeting Signal 1 (pts1) Binding
           Domain Of Trypanosoma Brucei Peroxin 5 (tbpex5)complexed
           To Pts1 Peptide (7- Skl)
          Length = 327

 Score = 28.1 bits (61), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 42  YKEDVEIIWRLVRVKYNLATHSSSLS--DADKKQLILSAYFLVYNALPQHE 90
           Y   ++I    VRV YN+A   S++S  D   KQL+ + Y  V    P  E
Sbjct: 229 YNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGE 279


>pdb|2OCB|A Chain A, Crystal Structure Of Human Rab9b In Complex With A Gtp
           Analogue
          Length = 180

 Score = 28.1 bits (61), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 3/41 (7%)

Query: 146 WCFEITDMPWYQRKIANAIFDTLPTSSYEEALKYFLEAEKQ 186
           WC E  D P+ +    +A  DT  T ++EEA++  L  E+Q
Sbjct: 141 WCMENGDYPYLE---TSAKDDTNVTVAFEEAVRQVLAVEEQ 178


  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
   0.316    0.130    0.372 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,801,952
Number of Sequences: 62578
Number of extensions: 342968
Number of successful extensions: 1260
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1237
Number of HSP's gapped (non-prelim): 34
length of query: 323
length of database: 14,973,337
effective HSP length: 99
effective length of query: 224
effective length of database: 8,778,115
effective search space: 1966297760
effective search space used: 1966297760
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)