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= 041400
         (95 letters)

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

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



>pdb|3ME1|A Chain A, Crystal Structure Of The Desulfovibro Vulgaris Urea
          Transporter In The P3(1) Space Group At 3.86
 pdb|3ME1|B Chain B, Crystal Structure Of The Desulfovibro Vulgaris Urea
          Transporter In The P3(1) Space Group At 3.86
 pdb|3ME1|C Chain C, Crystal Structure Of The Desulfovibro Vulgaris Urea
          Transporter In The P3(1) Space Group At 3.86
          Length = 335

 Score = 27.3 bits (59), Expect = 2.1,   Method: Composition-based stats.
 Identities = 8/15 (53%), Positives = 11/15 (73%)

Query: 51 RNPCIEFCNMCCKKC 65
          +NP IEFC+  C+ C
Sbjct: 6  KNPLIEFCDSVCRGC 20


>pdb|3M6E|A Chain A, F80a Mutant Of The Urea Transporter From Desulfovibrio
          Vulgaris
          Length = 340

 Score = 27.3 bits (59), Expect = 2.1,   Method: Composition-based stats.
 Identities = 8/15 (53%), Positives = 11/15 (73%)

Query: 51 RNPCIEFCNMCCKKC 65
          +NP IEFC+  C+ C
Sbjct: 11 KNPLIEFCDSVCRGC 25


>pdb|3K3F|A Chain A, Crystal Structure Of The Urea Transporter From
          Desulfovibrio Vulgaris
 pdb|3K3G|A Chain A, Crystal Structure Of The Urea Transporter From
          Desulfovibrio Vulgaris Bound To 1,3-Dimethylurea
          Length = 340

 Score = 27.3 bits (59), Expect = 2.1,   Method: Composition-based stats.
 Identities = 8/15 (53%), Positives = 11/15 (73%)

Query: 51 RNPCIEFCNMCCKKC 65
          +NP IEFC+  C+ C
Sbjct: 11 KNPLIEFCDSVCRGC 25


>pdb|3J16|B Chain B, Models Of Ribosome-Bound Dom34p And Rli1p And Their
          Ribosomal Binding Partners
          Length = 608

 Score = 26.9 bits (58), Expect = 3.0,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 16/49 (32%), Gaps = 16/49 (32%)

Query: 33 KPEQCASACNYRCSATSHRNPCIEF----------------CNMCCKKC 65
          KP++C   C   C        CIE                 C +C KKC
Sbjct: 17 KPKKCRQECKRSCPVVKTGKLCIEVTPTSKIAFISEILCIGCGICVKKC 65


  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
   0.320    0.133    0.499 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,776,587
Number of Sequences: 62578
Number of extensions: 91790
Number of successful extensions: 290
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 286
Number of HSP's gapped (non-prelim): 20
length of query: 95
length of database: 14,973,337
effective HSP length: 62
effective length of query: 33
effective length of database: 11,093,501
effective search space: 366085533
effective search space used: 366085533
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)