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= 041561
         (156 letters)

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

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



>pdb|3BYD|A Chain A, Crystal Structure Of Beta-Lactamase Oxy-1-1 From
           Klebsiella Oxytoca
          Length = 267

 Score = 27.7 bits (60), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 99  CSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA 156
           CS +G V A   +    E + EV  K L   K DLVVW   ++   + S + LA+ +A
Sbjct: 48  CS-TGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSP-ITEKHLQSGMTLAELSA 103


>pdb|1RY9|A Chain A, Spa15, A Type Iii Secretion Chaperone From Shigella
           Flexneri
 pdb|1RY9|B Chain B, Spa15, A Type Iii Secretion Chaperone From Shigella
           Flexneri
 pdb|1RY9|C Chain C, Spa15, A Type Iii Secretion Chaperone From Shigella
           Flexneri
 pdb|1RY9|D Chain D, Spa15, A Type Iii Secretion Chaperone From Shigella
           Flexneri
          Length = 145

 Score = 26.6 bits (57), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 15/79 (18%)

Query: 39  DIFVGSAPINIY----CNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVA 94
           D+ + S+  NI      N   + NE++  +  +EY++  + +  D +     HDG+ F  
Sbjct: 75  DVKLQSSAYNILNLMLMNFSYSINELVELHRSDEYLQLRVVIKDDYV-----HDGIVFAE 129

Query: 95  ILTPCSHSGLVYAEVEIFN 113
           IL         Y  +EI N
Sbjct: 130 ILHE------FYQRMEILN 142


>pdb|2XGA|A Chain A, Mtsl Spin-Labelled Shigella Flexneri Spa15
 pdb|2XGA|B Chain B, Mtsl Spin-Labelled Shigella Flexneri Spa15
          Length = 153

 Score = 26.6 bits (57), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 15/79 (18%)

Query: 39  DIFVGSAPINIY----CNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVA 94
           D+ + S+  NI      N   + NE++  +  +EY++  + +  D +     HDG+ F  
Sbjct: 83  DVKLQSSAYNILNLMLMNFSYSINELVELHRSDEYLQLRVVIKDDYV-----HDGIVFAE 137

Query: 95  ILTPCSHSGLVYAEVEIFN 113
           IL         Y  +EI N
Sbjct: 138 ILHE------FYQRMEILN 150


>pdb|2H5E|A Chain A, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3
 pdb|2H5E|B Chain B, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3
 pdb|2O0F|A Chain A, Docking Of The Modified Rf3 X-Ray Structure Into Cryo-Em
           Map Of E.Coli 70s Ribosome Bound With Rf3
 pdb|3ZVO|Y Chain Y, Crystal Structure Of The Hybrid State Of Ribosome In
           Complex With The Guanosine Triphosphatase Release Factor
           3
 pdb|3SFS|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
           State On A Rotated Conformation Of The Ribosome
          Length = 529

 Score = 26.6 bits (57), Expect = 6.9,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 20/40 (50%)

Query: 34  DGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQA 73
           D   N++ +G API     CG  +  + H Y +  Y+ Q+
Sbjct: 156 DEVENELKIGCAPITWPIGCGKLFKGVYHLYKDETYLYQS 195


>pdb|3UOQ|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
           State On A Rotated Conformation Of The Ribosome (Without
           Viomycin)
          Length = 534

 Score = 26.6 bits (57), Expect = 6.9,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 20/40 (50%)

Query: 34  DGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQA 73
           D   N++ +G API     CG  +  + H Y +  Y+ Q+
Sbjct: 156 DEVENELKIGCAPITWPIGCGKLFKGVYHLYKDETYLYQS 195


>pdb|2AJA|A Chain A, X-Ray Structure Of An Ankyrin Repeat Family Protein Q5zsv0
           From Legionella Pneumophila. Northeast Structural
           Genomics Consortium Target Lgr21.
 pdb|2AJA|B Chain B, X-Ray Structure Of An Ankyrin Repeat Family Protein Q5zsv0
           From Legionella Pneumophila. Northeast Structural
           Genomics Consortium Target Lgr21
          Length = 376

 Score = 25.8 bits (55), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 69  YVEQAISLYKDIIASGVKHDGVTFVAILTPCS 100
           Y   A  L+ D    G+K + + FVA +T CS
Sbjct: 74  YNRNAKQLWSDAHKKGIKSEVICFVAAITGCS 105


  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
   0.322    0.137    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,783,047
Number of Sequences: 62578
Number of extensions: 186388
Number of successful extensions: 387
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 382
Number of HSP's gapped (non-prelim): 8
length of query: 156
length of database: 14,973,337
effective HSP length: 91
effective length of query: 65
effective length of database: 9,278,739
effective search space: 603118035
effective search space used: 603118035
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: 47 (22.7 bits)