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= 033276
         (123 letters)

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

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



>pdb|1PV6|A Chain A, Crystal Structure Of Lactose Permease
 pdb|1PV6|B Chain B, Crystal Structure Of Lactose Permease
 pdb|1PV7|A Chain A, Crystal Structure Of Lactose Permease With Tdg
 pdb|1PV7|B Chain B, Crystal Structure Of Lactose Permease With Tdg
 pdb|2CFP|A Chain A, Sugar Free Lactose Permease At Acidic Ph
 pdb|2CFQ|A Chain A, Sugar Free Lactose Permease At Neutral Ph
          Length = 417

 Score = 32.7 bits (73), Expect = 0.056,   Method: Composition-based stats.
 Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 3/45 (6%)

Query: 70  IVDKCLKLFSSPFPLVICIK---SNHEIRISPVFMLILICLYIQV 111
           ++ K L +F  PF LV C K   S  E+R S    L+  C + Q+
Sbjct: 316 VILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQL 360


>pdb|2V8N|A Chain A, Wild-Type Structure Of Lactose Permease
 pdb|2V8N|B Chain B, Wild-Type Structure Of Lactose Permease
          Length = 417

 Score = 32.3 bits (72), Expect = 0.061,   Method: Composition-based stats.
 Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 3/45 (6%)

Query: 70  IVDKCLKLFSSPFPLVICIK---SNHEIRISPVFMLILICLYIQV 111
           ++ K L +F  PF LV C K   S  E+R S    L+  C + Q+
Sbjct: 316 VILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQL 360


>pdb|4FEV|A Chain A, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp1
 pdb|4FEV|B Chain B, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp1
 pdb|4FEV|C Chain C, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp1
 pdb|4FEV|D Chain D, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp1
 pdb|4FEV|E Chain E, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp1
 pdb|4FEV|F Chain F, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp1
 pdb|4FEX|A Chain A, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Tyrphostin Ag1478
 pdb|4FEX|B Chain B, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Tyrphostin Ag1478
 pdb|4FEX|C Chain C, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Tyrphostin Ag1478
 pdb|4FEX|D Chain D, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Tyrphostin Ag1478
 pdb|4FEX|E Chain E, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Tyrphostin Ag1478
          Length = 272

 Score = 30.0 bits (66), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 7/56 (12%)

Query: 4   SSKNNEIVDVSYVDDECS----EQSW--MLRSLSESTVACIT-GDYAMQNVILQMG 52
           S  NN +VD S  DDE +    EQ W  M + L  S  + +T GD+++ N+I   G
Sbjct: 155 SRMNNGLVDASDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEG 210


>pdb|4EJ7|A Chain A, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, Atp-Bound
 pdb|4EJ7|B Chain B, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, Atp-Bound
 pdb|4EJ7|C Chain C, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, Atp-Bound
          Length = 292

 Score = 28.5 bits (62), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 7/56 (12%)

Query: 4   SSKNNEIVDVSYVDDECS----EQSWML--RSLSESTVACIT-GDYAMQNVILQMG 52
           S  NN +VD S  DDE +    EQ W    + L  S  + +T GD+++ N+I   G
Sbjct: 175 SRXNNGLVDASDFDDERNGWPVEQVWKEXHKLLPFSPDSVVTHGDFSLDNLIFDEG 230


>pdb|4FEU|A Chain A, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Anthrapyrazolone Sp600125
 pdb|4FEU|B Chain B, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Anthrapyrazolone Sp600125
 pdb|4FEU|C Chain C, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Anthrapyrazolone Sp600125
 pdb|4FEU|D Chain D, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Anthrapyrazolone Sp600125
 pdb|4FEU|E Chain E, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Anthrapyrazolone Sp600125
 pdb|4FEU|F Chain F, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Anthrapyrazolone Sp600125
 pdb|4FEW|A Chain A, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp2
 pdb|4FEW|B Chain B, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp2
 pdb|4FEW|C Chain C, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp2
 pdb|4FEW|D Chain D, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp2
 pdb|4FEW|E Chain E, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp2
 pdb|4FEW|F Chain F, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor Pyrazolopyrimidine Pp2
 pdb|4GKH|A Chain A, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|B Chain B, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|C Chain C, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|D Chain D, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|E Chain E, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|F Chain F, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|G Chain G, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|H Chain H, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|I Chain I, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|J Chain J, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|K Chain K, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKH|L Chain L, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Na-Pp1
 pdb|4GKI|A Chain A, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|B Chain B, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|C Chain C, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|D Chain D, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|E Chain E, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|F Chain F, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|G Chain G, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|H Chain H, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|I Chain I, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|J Chain J, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|K Chain K, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
 pdb|4GKI|L Chain L, Crystal Structure Of The Aminoglycoside Phosphotransferase
           Aph(3')-Ia, With Substrate Kanamycin And Small Molecule
           Inhibitor 1-Nm-Pp1
          Length = 272

 Score = 28.5 bits (62), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 7/56 (12%)

Query: 4   SSKNNEIVDVSYVDDECS----EQSWML--RSLSESTVACIT-GDYAMQNVILQMG 52
           S  NN +VD S  DDE +    EQ W    + L  S  + +T GD+++ N+I   G
Sbjct: 155 SRXNNGLVDASDFDDERNGWPVEQVWKEXHKLLPFSPDSVVTHGDFSLDNLIFDEG 210


>pdb|2P0M|A Chain A, Revised Structure Of Rabbit Reticulocyte 15s-Lipoxygenase
 pdb|2P0M|B Chain B, Revised Structure Of Rabbit Reticulocyte 15s-Lipoxygenase
          Length = 662

 Score = 27.7 bits (60), Expect = 1.5,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 49  LQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLY 108
           +Q+  RL+ P GM+  Q       K   LF + F L+  IK+N  +         L+ L 
Sbjct: 245 VQLPARLVFPPGMEELQAQLEKELKAGTLFEADFALLDNIKANVILYCQQYLAAPLVMLK 304

Query: 109 IQVDTE-MPCLLHYH 122
           +Q D + MP ++  H
Sbjct: 305 LQPDGKLMPMVIQLH 319


>pdb|1LOX|A Chain A, Rabbit Reticulocyte 15-Lipoxygenase
          Length = 662

 Score = 27.7 bits (60), Expect = 1.5,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 49  LQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLY 108
           +Q+  RL+ P GM+  Q       K   LF + F L+  IK+N  +         L+ L 
Sbjct: 245 VQLPARLVFPPGMEELQAQLEKELKAGTLFEADFALLDNIKANVILYCQQYLAAPLVMLK 304

Query: 109 IQVDTE-MPCLLHYH 122
           +Q D + MP ++  H
Sbjct: 305 LQPDGKLMPMVIQLH 319


>pdb|4FGM|A Chain A, Crystal Structure Of The Aminopeptidase N Family Protein
           Q5qty1 From Idiomarina Loihiensis. Northeast Structural
           Genomics Consortium Target Ilr60
          Length = 597

 Score = 26.6 bits (57), Expect = 3.9,   Method: Composition-based stats.
 Identities = 8/18 (44%), Positives = 13/18 (72%)

Query: 105 ICLYIQVDTEMPCLLHYH 122
           +CL ++  T++PC LH H
Sbjct: 111 LCLAVEGQTDLPCELHLH 128


>pdb|3T1P|A Chain A, Crystal Structure Of An Alpha-1-Antitrypsin Trimer
          Length = 371

 Score = 25.8 bits (55), Expect = 6.7,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 3/52 (5%)

Query: 37  CITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICI 88
           CITG Y +++V+ Q+G+  +   G  +  +     +  LKL  +    V+CI
Sbjct: 269 CITGTYDLKSVLGQLGITKVFSNGADLSGVTE---EAPLKLSKAVHKAVLCI 317


  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
   0.327    0.140    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,457,761
Number of Sequences: 62578
Number of extensions: 113974
Number of successful extensions: 295
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 291
Number of HSP's gapped (non-prelim): 13
length of query: 123
length of database: 14,973,337
effective HSP length: 85
effective length of query: 38
effective length of database: 9,654,207
effective search space: 366859866
effective search space used: 366859866
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)