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= 008888
         (550 letters)

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

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



>pdb|1C7G|A Chain A, Tyrosine Phenol-Lyase From Erwinia Herbicola
 pdb|1C7G|B Chain B, Tyrosine Phenol-Lyase From Erwinia Herbicola
 pdb|1C7G|C Chain C, Tyrosine Phenol-Lyase From Erwinia Herbicola
 pdb|1C7G|D Chain D, Tyrosine Phenol-Lyase From Erwinia Herbicola
          Length = 456

 Score = 30.4 bits (67), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 4/51 (7%)

Query: 354 IDLERLGTLLSDPGVQRVPGLCFFYTNIHQDGLTPILGHYIKNMRSLHKVT 404
           IDL +L TL+ + G + +  +C   T ++  G  P+    + NMR++H++ 
Sbjct: 158 IDLNKLATLIKEKGAENIAYICLAVT-VNLAGGQPV---SMANMRAVHEMA 204


>pdb|3U65|B Chain B, The Crystal Structure Of Tat-P(T) (Tp0957)
 pdb|3U65|A Chain A, The Crystal Structure Of Tat-P(T) (Tp0957)
          Length = 328

 Score = 30.0 bits (66), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 326 AISFFLAFIMFGWFNGRQKKIEYELTHKIDLERLGTLLSDPGVQRVPGLCFFYTNIHQDG 385
           +I  FL+  +F W  G  + I Y L  KI    +G L+SD    R+P     Y +     
Sbjct: 195 SIDGFLSVHLFTWATGFYRYISYALDTKICPAVIGMLISDGSWARIPSR---YHDAMLQA 251

Query: 386 LTPILGHYIKNMRSLHK 402
            T +      N+ +L +
Sbjct: 252 ATRVRQRLANNLETLDR 268


>pdb|4DI3|D Chain D, Crystal Structure Of A 2:1 Complex Of Treponema Pallidum
           Tatp(T) (Tp0957) Bound To Tatt (Tp0956)
 pdb|4DI3|E Chain E, Crystal Structure Of A 2:1 Complex Of Treponema Pallidum
           Tatp(T) (Tp0957) Bound To Tatt (Tp0956)
 pdb|4DI4|B Chain B, Crystal Structure Of A 3:1 Complex Of Treponema Pallidum
           Tatp(T) (Tp0957) Bound To Tatt (Tp0956)
          Length = 324

 Score = 29.6 bits (65), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 326 AISFFLAFIMFGWFNGRQKKIEYELTHKIDLERLGTLLSDPGVQRVPGLCFFYTNIHQDG 385
           +I  FL+  +F W  G  + I Y L  KI    +G L+SD    R+P     Y +     
Sbjct: 191 SIDGFLSVHLFTWATGFYRYISYALDTKICPAVIGMLISDGSWARIPSR---YHDAMLQA 247

Query: 386 LTPILGHYIKNMRSLHK 402
            T +      N+ +L +
Sbjct: 248 ATRVRQRLANNLETLDR 264


>pdb|3K1D|A Chain A, Crystal Structure Of Glycogen Branching Enzyme Synonym:
           1,4- Glucan:1,4-Alpha-D-Glucan 6-Glucosyl-Transferase
           From Mycob Tuberculosis H37rv
          Length = 722

 Score = 29.6 bits (65), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 6/35 (17%)

Query: 296 ALYFLVFFTMEGVYVSAVFTKI------PEGGWIP 324
           ALY+L  F ++G+ V AV + +      PEGGW P
Sbjct: 387 ALYWLQEFHIDGLRVDAVASMLYLDYSRPEGGWTP 421


>pdb|3RKO|A Chain A, Crystal Structure Of The Membrane Domain Of Respiratory
           Complex I From E. Coli At 3.0 Angstrom Resolution
 pdb|3RKO|E Chain E, Crystal Structure Of The Membrane Domain Of Respiratory
           Complex I From E. Coli At 3.0 Angstrom Resolution
          Length = 147

 Score = 29.3 bits (64), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 294 LVALYFLVFFTMEGVYVSAVFTKIPEGGWIPFAISFFLAFIMFG 337
           LVA++F V F +E +Y+ A  T I E GW+ F  +    F++  
Sbjct: 70  LVAMFF-VIFDVEALYLFAWSTSIRESGWVGFVEAAIFIFVLLA 112


  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
   0.328    0.143    0.443 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,613,014
Number of Sequences: 62578
Number of extensions: 634347
Number of successful extensions: 1389
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1386
Number of HSP's gapped (non-prelim): 5
length of query: 550
length of database: 14,973,337
effective HSP length: 104
effective length of query: 446
effective length of database: 8,465,225
effective search space: 3775490350
effective search space used: 3775490350
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: 54 (25.4 bits)