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= 013357
         (444 letters)

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

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



>pdb|3MKT|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
 pdb|3MKT|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
 pdb|3MKU|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
 pdb|3MKU|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
          Length = 460

 Score = 55.1 bits (131), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 67/304 (22%), Positives = 129/304 (42%), Gaps = 15/304 (4%)

Query: 51  LVRLAAPAVFVYLINNLMSLSTRVFCGHLGNLELAAASLGNS---GIQLFAYGLMLGMGS 107
           L++LA P +   +    M     +  G +  +++AA S+  S      LF  GL++    
Sbjct: 14  LIKLATPVLIASVAQTGMGFVDTIMAGGVSAIDMAAVSIAASIWLPSILFGVGLLM---- 69

Query: 108 AVETLCGQAYGAGRYEMLGVYMQRATFVLLATGVPVMMVYIFCKPMLILLGESTAVASAA 167
           A+  +  Q  GAGR   +   + +   + L   VP++ V    + ++  +    A+A+  
Sbjct: 70  ALVPVVAQLNGAGRQHKIPFEVHQGLILALLVSVPIIAVLFQTQFIIRFMDVEEAMATKT 129

Query: 168 ALFVYGLIPQIFAYAVNFPIQKFLQAQSIVLPSAYISAATXXXXXXXXXXXXY-KFGA-- 224
             +++ +I  + AY +   ++ F    S+  P+  I                Y KFGA  
Sbjct: 130 VGYMHAVIFAVPAYLLFQALRSFTDGMSLTKPAMVIGFIGLLLNIPLNWIFVYGKFGAPE 189

Query: 225 -GLIGASLVLSLSWYIIVGAQFAYILMSDKCKH--TWTGFSVQAFSGICEFLKLSGSSAV 281
            G +G  +  ++ ++I++     YI+ S +  H   +  F       +    +L    A 
Sbjct: 190 LGGVGCGVATAIVYWIMLLLLLFYIVTSKRLAHVKVFETFHKPQPKELIRLFRLGFPVAA 249

Query: 282 MLCLETWYFQILVLIAGLLDNPELALDSLSVCMAVSGLLFMVSVGFNAAASVRVSNELGA 341
            L  E   F ++ L+   L +  +A  +  V +  S L+FM  +   AA S+RV ++LG 
Sbjct: 250 ALFFEVTLFAVVALLVAPLGSTVVA--AHQVALNFSSLVFMFPMSIGAAVSIRVGHKLGE 307

Query: 342 GNPK 345
            + K
Sbjct: 308 QDTK 311


>pdb|4HUK|A Chain A, Mate Transporter Norm-ng In Complex With Tpp And Monobody
 pdb|4HUL|A Chain A, Mate Transporter Norm-ng In Complex With Cs+ And Monobody
 pdb|4HUM|A Chain A, Mate Transporter Norm-ng In Complex With Ethidium And
           Monobody
 pdb|4HUN|A Chain A, Mate Transporter Norm-ng In Complex With R6g And Monobody
          Length = 459

 Score = 34.3 bits (77), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 47  ELKLLVRLAAPAVFVYLINNLMSLSTRVFCGHLGNLELAAASLGNSGIQLFAYGLMLGMG 106
           E++LL  LA P +   +    +     V  G  G  +LAA +LG+S      Y   +G+ 
Sbjct: 12  EIRLLTALALPMLLAQVAQVGIGFVDTVMAGGAGKEDLAAVALGSSAFAT-VYITFMGIM 70

Query: 107 SAVETLCGQAYGAGR 121
           +A+  +  Q YGAG+
Sbjct: 71  AALNPMIAQLYGAGK 85


>pdb|4ECL|A Chain A, Crystal Structure Of The Cytoplasmic Domain Of Vancomycin
           Resistance Serine Racemase Vantg
 pdb|4ECL|B Chain B, Crystal Structure Of The Cytoplasmic Domain Of Vancomycin
           Resistance Serine Racemase Vantg
 pdb|4ECL|C Chain C, Crystal Structure Of The Cytoplasmic Domain Of Vancomycin
           Resistance Serine Racemase Vantg
 pdb|4ECL|D Chain D, Crystal Structure Of The Cytoplasmic Domain Of Vancomycin
           Resistance Serine Racemase Vantg
          Length = 374

 Score = 28.9 bits (63), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 11/86 (12%)

Query: 238 YIIVGAQFAYILMSDKCKHTWTGFS---VQAFSGICEFLKLSGSSAVMLCLETWYFQILV 294
           +I V   F ++  +D  +     F+   + +F  + ++LK SG +   + +++ Y     
Sbjct: 151 HIKVAGIFTHLCAADSLEENDVAFTNKQIGSFYKVLDWLKSSGLNIPKVHIQSSY----- 205

Query: 295 LIAGLLDNPELALDSLSVCMAVSGLL 320
              GLL+ PEL  D + V +A+ G+L
Sbjct: 206 ---GLLNYPELECDYIRVGVALYGVL 228


  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
   0.326    0.137    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,208,920
Number of Sequences: 62578
Number of extensions: 332721
Number of successful extensions: 740
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 736
Number of HSP's gapped (non-prelim): 4
length of query: 444
length of database: 14,973,337
effective HSP length: 102
effective length of query: 342
effective length of database: 8,590,381
effective search space: 2937910302
effective search space used: 2937910302
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)