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= 040209
         (388 letters)

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

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



>pdb|1UJP|A Chain A, Crystal Structure Of Tryptophan Synthase A-Subunit From
           Thermus Thermophilus Hb8
 pdb|1WXJ|A Chain A, Crystal Structure Of Tryptophan Synthase A-Subunit With
           Indole-3- Propanol Phosphate From Thermus Thermophilus
           Hb8
          Length = 271

 Score = 35.0 bits (79), Expect = 0.076,   Method: Compositional matrix adjust.
 Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 4/86 (4%)

Query: 258 VVQNYSQWNL---VALHPNLQSVTQVFSFNYKPLNQYGYINDTGMFWGIEFYNDMLLQAG 314
           V+Q  S+  L   +++   L+ V +V +   KPL    Y+N   + WG E +  +  QAG
Sbjct: 61  VIQRASELALRKGMSVQGALELVREVRALTEKPLFLMTYLNPV-LAWGPERFFGLFKQAG 119

Query: 315 ESGNVQTEMLLHKDSGIFTFREGWGF 340
            +G +  ++   +D G+    +  G 
Sbjct: 120 ATGVILPDLPPDEDPGLVRLAQEIGL 145


>pdb|3SGG|A Chain A, Crystal Structure Of A Hypothetical Hydrolase (Bt_2193)
           From Bacteroides Thetaiotaomicron Vpi-5482 At 1.25 A
           Resolution
          Length = 536

 Score = 30.0 bits (66), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 4/45 (8%)

Query: 26  QGDEVIWNMWGAEATEQGNCSKFTGGQLPHCCEKSPVIVDLLPGA 70
            GD + +N+WG    +QG       GQ P     SP + DL P A
Sbjct: 310 DGDNIAFNLWG----QQGYXDHDLHGQFPLGYTISPSLYDLAPAA 350


>pdb|1PHO|A Chain A, Crystal Structures Explain Functional Properties Of Two E.
           Coli Porins
          Length = 330

 Score = 29.3 bits (64), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 30/130 (23%), Positives = 49/130 (37%), Gaps = 9/130 (6%)

Query: 214 HDPNKEQSPVVICSQHMCPVRVHWHVKQSYTQYWRVKITITNLNVVQNYSQW------NL 267
            D NK      + + H           QSY ++     T  N + +  Y +W      N 
Sbjct: 6   KDGNKLDVYGKVKAMHYMSDNASKDGDQSYIRFGFKGETQIN-DQLTGYGRWEAEFAGNK 64

Query: 268 VALHPNLQSVTQVFS-FNYKPLNQYGYINDTGMFWGIEFYNDMLLQAGESGNVQTEMLLH 326
                  Q     F+   YK L  + Y  + G  + +E + DM  + G   + QT+  + 
Sbjct: 65  AESDTAQQKTRLAFAGLKYKDLGSFDYGRNLGALYDVEAWTDMFPEFGGDSSAQTDNFMT 124

Query: 327 KD-SGIFTFR 335
           K  SG+ T+R
Sbjct: 125 KRASGLATYR 134


>pdb|2B3B|A Chain A, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN WITH
           Bound Glucose
 pdb|2B3B|B Chain B, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN WITH
           Bound Glucose
 pdb|2B3B|C Chain C, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN WITH
           Bound Glucose
 pdb|2B3B|D Chain D, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN WITH
           Bound Glucose
 pdb|2B3B|E Chain E, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN WITH
           Bound Glucose
 pdb|2B3B|F Chain F, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN WITH
           Bound Glucose
 pdb|2B3F|A Chain A, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN
           Bound With Galactose
 pdb|2B3F|B Chain B, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN
           Bound With Galactose
 pdb|2B3F|C Chain C, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN
           Bound With Galactose
 pdb|2B3F|D Chain D, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN
           Bound With Galactose
 pdb|2B3F|E Chain E, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN
           Bound With Galactose
 pdb|2B3F|F Chain F, Thermus Thermophilus GlucoseGALACTOSE BINDING PROTEIN
           Bound With Galactose
          Length = 400

 Score = 28.1 bits (61), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 13/31 (41%), Positives = 18/31 (58%)

Query: 67  LPGAPYNQQTANCCKGGVLSSLTQDPSKFVA 97
           L G+   Q T+N  KG + + L  DPSK+ A
Sbjct: 298 LVGSKEGQDTSNPLKGSIAARLDSDPSKYNA 328


>pdb|3TUG|A Chain A, Crystal Structure Of The Hect Domain Of Itch E3 Ubiquitin
           Ligase
          Length = 398

 Score = 28.1 bits (61), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 9/56 (16%)

Query: 94  KFVAGF-QMNVGGSADYTGFQMPENFTLGIPG--------YTCGNATEVPPSKFYS 140
           +FV G  ++ VGG AD  G   P+ F +   G        +TC N  ++PP K Y 
Sbjct: 324 QFVTGTCRLPVGGFADLMGSNGPQKFCIEKVGKENWLPRSHTCFNRLDLPPYKSYE 379


  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    0.136    0.456 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,705,051
Number of Sequences: 62578
Number of extensions: 551583
Number of successful extensions: 1012
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1010
Number of HSP's gapped (non-prelim): 8
length of query: 388
length of database: 14,973,337
effective HSP length: 101
effective length of query: 287
effective length of database: 8,652,959
effective search space: 2483399233
effective search space used: 2483399233
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)