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= 043673
         (252 letters)

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

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



>pdb|2YY3|A Chain A, Crystal Structure Of Translation Elongation Factor Ef-1
           Beta From Pyrococcus Horikoshii
 pdb|2YY3|B Chain B, Crystal Structure Of Translation Elongation Factor Ef-1
           Beta From Pyrococcus Horikoshii
 pdb|2YY3|C Chain C, Crystal Structure Of Translation Elongation Factor Ef-1
           Beta From Pyrococcus Horikoshii
          Length = 91

 Score = 30.4 bits (67), Expect = 0.90,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 12/58 (20%)

Query: 164 VNLENMFSKYARTVPDKLTLGEVWNLTEGNRLAFDLFGWVAAKLEWILLYILARDEEG 221
           VNL+ +  K  + +P+K  L +V    E   +AF   G VA K      Y+L RDEEG
Sbjct: 19  VNLDELEEKLKKVIPEKYGLAKV----EREPIAF---GLVALKF-----YVLGRDEEG 64


>pdb|4DOJ|A Chain A, Crystal Structure Of Betp In Outward-Facing Conformation
 pdb|4DOJ|B Chain B, Crystal Structure Of Betp In Outward-Facing Conformation
 pdb|4DOJ|C Chain C, Crystal Structure Of Betp In Outward-Facing Conformation
          Length = 566

 Score = 29.3 bits (64), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 5/42 (11%)

Query: 58  PDTYHPNGTPGHMHHGLSVLQQHVAFFDQDDNGIIYPWETYS 99
           P T++ NG PGH  H + V      F     +  ++PW  Y+
Sbjct: 133 PLTFYRNGVPGHDEHNVGVAMSTTMF-----HWTLHPWAIYA 169


>pdb|3P03|A Chain A, Crystal Structure Of Betp-G153d With Choline Bound
 pdb|3P03|B Chain B, Crystal Structure Of Betp-G153d With Choline Bound
 pdb|3P03|C Chain C, Crystal Structure Of Betp-G153d With Choline Bound
          Length = 566

 Score = 29.3 bits (64), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 5/42 (11%)

Query: 58  PDTYHPNGTPGHMHHGLSVLQQHVAFFDQDDNGIIYPWETYS 99
           P T++ NG PGH  H + V      F     +  ++PW  Y+
Sbjct: 133 PLTFYRNGVPGHDEHNVGVAMSTTMF-----HWTLHPWAIYA 169


>pdb|2WIT|A Chain A, Crystal Structure Of The Sodium-coupled Glycine Betaine
           Symporter Betp From Corynebacterium Glutamicum With
           Bound Substrate
 pdb|2WIT|B Chain B, Crystal Structure Of The Sodium-coupled Glycine Betaine
           Symporter Betp From Corynebacterium Glutamicum With
           Bound Substrate
 pdb|2WIT|C Chain C, Crystal Structure Of The Sodium-coupled Glycine Betaine
           Symporter Betp From Corynebacterium Glutamicum With
           Bound Substrate
          Length = 566

 Score = 29.3 bits (64), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 5/42 (11%)

Query: 58  PDTYHPNGTPGHMHHGLSVLQQHVAFFDQDDNGIIYPWETYS 99
           P T++ NG PGH  H + V      F     +  ++PW  Y+
Sbjct: 133 PLTFYRNGVPGHDEHNVGVAXSTTXF-----HWTLHPWAIYA 169


>pdb|4AIN|A Chain A, Crystal Structure Of Betp With Asymmetric Protomers.
 pdb|4AIN|B Chain B, Crystal Structure Of Betp With Asymmetric Protomers.
 pdb|4AIN|C Chain C, Crystal Structure Of Betp With Asymmetric Protomers
          Length = 539

 Score = 28.9 bits (63), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 5/42 (11%)

Query: 58  PDTYHPNGTPGHMHHGLSVLQQHVAFFDQDDNGIIYPWETYS 99
           P T++ NG PGH  H + V      F     +  ++PW  Y+
Sbjct: 122 PLTFYRNGVPGHDEHNVGVAMSTTMF-----HWTLHPWAIYA 158


>pdb|1AXK|A Chain A, Engineered Bacillus Bifunctional Enzyme Gluxyn-1
 pdb|1AXK|B Chain B, Engineered Bacillus Bifunctional Enzyme Gluxyn-1
          Length = 394

 Score = 27.3 bits (59), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 30/111 (27%), Positives = 44/111 (39%), Gaps = 27/111 (24%)

Query: 95  WETYSGLRQIGFNIIASLVLAFVINLGLTYPTLPGWFPSPLLPIYI---------HNIHR 145
           W T S  R I +N        +  N G  Y TL GW  SPL+  Y+            ++
Sbjct: 198 WTTGSPFRTINYN-----AGVWAPN-GNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYK 251

Query: 146 SKHGSDSGTYD--TEGRYTPVNLENMFSKYARTVPDKLTLGEVWNLTEGNR 194
               SD GTYD  T  RY   +++           D+ T  + W++ +  R
Sbjct: 252 GTVKSDGGTYDIYTTTRYNAPSIDG----------DRTTFTQYWSVRQSKR 292


  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    0.139    0.434 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,314,738
Number of Sequences: 62578
Number of extensions: 365011
Number of successful extensions: 736
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 735
Number of HSP's gapped (non-prelim): 23
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
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: 50 (23.9 bits)