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= psy17914
         (469 letters)

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

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



>pdb|2VX7|A Chain A, Cellvibrio Japonicus Mannanase Cjman26c Mannobiose-Bound
           Form
          Length = 396

 Score = 29.6 bits (65), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 68  FTSYVSVYNSFMKIVFIAASYGTVYLMYIKFKATYDHNHDTF---RGLLSESDPTVLWTF 124
             +Y+  + +F + +    + G  +   I F+  ++HN D F   +G  SE D   LW F
Sbjct: 163 LKAYLDTFVAFNEGLADVDAQGNKHYPPIIFRPWHEHNGDWFWWGKGHASEQDYIALWRF 222

Query: 125 SIY 127
           +++
Sbjct: 223 TVH 225


>pdb|2VX4|A Chain A, Cellvibrio Japonicus Mannanase Cjman26c Native Form
 pdb|2VX6|A Chain A, Cellvibrio Japonicus Mannanase Cjman26c Gal1man4-Bound
           Form
          Length = 396

 Score = 29.3 bits (64), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 68  FTSYVSVYNSFMKIVFIAASYGTVYLMYIKFKATYDHNHDTF---RGLLSESDPTVLWTF 124
             +Y+  + +F + +    + G  +   I F+  ++HN D F   +G  SE D   LW F
Sbjct: 163 LKAYLDTFVAFNEGLADVDAQGNKHYPPIIFRPWHEHNGDWFWWGKGHASEQDYIALWRF 222

Query: 125 SIY 127
           +++
Sbjct: 223 TVH 225


>pdb|2VX5|A Chain A, Cellvibrio Japonicus Mannanase Cjman26c Mannose-Bound Form
          Length = 396

 Score = 29.3 bits (64), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 70  SYVSVYNSFMKIVFIAASYGTVYLMYIKFKATYDHNHDTF---RGLLSESDPTVLWTFSI 126
           +Y+  + +F + +    + G  +   I F+  ++HN D F   +G  SE D   LW F++
Sbjct: 165 AYLDTFVAFNEGLADVDAQGNKHYPPIIFRPWHEHNGDWFWWGKGHASEQDYIALWRFTV 224

Query: 127 Y 127
           +
Sbjct: 225 H 225


>pdb|2JLN|A Chain A, Structure Of Mhp1, A Nucleobase-Cation-Symport-1 Family
           Transporter
 pdb|2JLO|A Chain A, Structure Of Mhp1, A Nucleobase-Cation-Symport-1 Family
           Transporter, In A Closed Conformation With
           Benzylhydantoin
          Length = 501

 Score = 28.5 bits (62), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 14/69 (20%), Positives = 32/69 (46%)

Query: 387 SICTSLEVSLQTRVVCVVTLYRALYLLNWVYRYYSEDYLDLIAIVAGVVQTALYCDFFYL 446
           ++C++       +   +V+    L ++ W +      +L+L+A   G +   +  D+F +
Sbjct: 325 TLCSTFPRVFTFKTGVIVSAVVGLLMMPWQFAGVLNTFLNLLASALGPLAGIMISDYFLV 384

Query: 447 YITRVSLRD 455
              R+SL D
Sbjct: 385 RRRRISLHD 393


  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
   0.331    0.144    0.447 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,080,577
Number of Sequences: 62578
Number of extensions: 516956
Number of successful extensions: 1052
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1047
Number of HSP's gapped (non-prelim): 8
length of query: 469
length of database: 14,973,337
effective HSP length: 102
effective length of query: 367
effective length of database: 8,590,381
effective search space: 3152669827
effective search space used: 3152669827
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (25.0 bits)