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= psy3080
         (118 letters)

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

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



>pdb|2VDC|A Chain A, The 9.5 A Resolution Structure Of Glutamate Synthase From
           Cryo-Electron Microscopy And Its Oligomerization
           Behavior In Solution: Functional Implications.
 pdb|2VDC|B Chain B, The 9.5 A Resolution Structure Of Glutamate Synthase From
           Cryo-Electron Microscopy And Its Oligomerization
           Behavior In Solution: Functional Implications.
 pdb|2VDC|C Chain C, The 9.5 A Resolution Structure Of Glutamate Synthase From
           Cryo-Electron Microscopy And Its Oligomerization
           Behavior In Solution: Functional Implications.
 pdb|2VDC|D Chain D, The 9.5 A Resolution Structure Of Glutamate Synthase From
           Cryo-Electron Microscopy And Its Oligomerization
           Behavior In Solution: Functional Implications.
 pdb|2VDC|E Chain E, The 9.5 A Resolution Structure Of Glutamate Synthase From
           Cryo-Electron Microscopy And Its Oligomerization
           Behavior In Solution: Functional Implications.
 pdb|2VDC|F Chain F, The 9.5 A Resolution Structure Of Glutamate Synthase From
           Cryo-Electron Microscopy And Its Oligomerization
           Behavior In Solution: Functional Implications
          Length = 1472

 Score = 30.4 bits (67), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 38  YPQLEQEMFVNIFYLRHL-CDTAKFPDWPINQPIMLL 73
           YP L  E F + F + H    T  FP WP+ QP  +L
Sbjct: 192 YPDLLDERFESDFAIYHQRYSTNTFPTWPLAQPFRML 228


>pdb|1EA0|A Chain A, Alpha Subunit Of A. Brasilense Glutamate Synthase
 pdb|1EA0|B Chain B, Alpha Subunit Of A. Brasilense Glutamate Synthase
          Length = 1479

 Score = 30.4 bits (67), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 38  YPQLEQEMFVNIFYLRHL-CDTAKFPDWPINQPIMLL 73
           YP L  E F + F + H    T  FP WP+ QP  +L
Sbjct: 192 YPDLLDERFESDFAIYHQRYSTNTFPTWPLAQPFRML 228


>pdb|2R91|A Chain A, Crystal Structure Of Kd(P)ga From T.Tenax
 pdb|2R91|D Chain D, Crystal Structure Of Kd(P)ga From T.Tenax
 pdb|2R91|B Chain B, Crystal Structure Of Kd(P)ga From T.Tenax
 pdb|2R91|C Chain C, Crystal Structure Of Kd(P)ga From T.Tenax
 pdb|2R94|A Chain A, Crystal Structure Of Kd(P)ga From T.Tenax
 pdb|2R94|D Chain D, Crystal Structure Of Kd(P)ga From T.Tenax
 pdb|2R94|B Chain B, Crystal Structure Of Kd(P)ga From T.Tenax
 pdb|2R94|C Chain C, Crystal Structure Of Kd(P)ga From T.Tenax
          Length = 286

 Score = 26.9 bits (58), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 3   RLLIGKIAAHIADFTPRLR--GNNRAVYQFCGIPAVRYPQLEQEMFVNIFYLRHLCDTAK 60
           R +I ++A+  AD    L     +R       +P   +P+L +       Y R LC    
Sbjct: 65  RRVIVQVASLNADEAIALAKYAESRGAEAVASLPPYYFPRLSERQIAK--YFRDLCSAVS 122

Query: 61  FPDWPINQPIMLLKDV 76
            P +  N P  + +DV
Sbjct: 123 IPVFLYNYPAAVGRDV 138


>pdb|2IUS|A Chain A, E. Coli Ftsk Motor Domain
 pdb|2IUS|B Chain B, E. Coli Ftsk Motor Domain
 pdb|2IUS|C Chain C, E. Coli Ftsk Motor Domain
 pdb|2IUS|D Chain D, E. Coli Ftsk Motor Domain
 pdb|2IUS|E Chain E, E. Coli Ftsk Motor Domain
 pdb|2IUS|F Chain F, E. Coli Ftsk Motor Domain
          Length = 512

 Score = 26.6 bits (57), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 12/27 (44%), Positives = 16/27 (59%)

Query: 50  FYLRHLCDTAKFPDWPINQPIMLLKDV 76
            YLR + D AKF D P    ++L KD+
Sbjct: 129 VYLREVLDNAKFRDNPSPLTVVLGKDI 155


>pdb|4E4U|A Chain A, Crystal Structure Of A Putative Mandelate RacemaseMUCONATE
           Lactonizing Enzyme (Target Psi-200780) From Burkholderia
           Sar-1
          Length = 412

 Score = 26.2 bits (56), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 22/45 (48%)

Query: 73  LKDVLEAWKAEVERKPPEMSVDDAYEALGLTRGSHHEENIVRKAY 117
           ++ V E + A    K     +DD +E   L R  HH E + R+AY
Sbjct: 34  IEGVGEIYSATFGPKAMAPIIDDVFERHLLNRDPHHVERLFRQAY 78


  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
   0.325    0.140    0.442 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,771,697
Number of Sequences: 62578
Number of extensions: 142753
Number of successful extensions: 385
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 380
Number of HSP's gapped (non-prelim): 8
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)