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= psy5091
         (112 letters)

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

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



>pdb|3U9I|A Chain A, The Crystal Structure Of Mandelate RacemaseMUCONATE
           LACTONIZING Enzyme From Roseiflexus Sp.
 pdb|3U9I|B Chain B, The Crystal Structure Of Mandelate RacemaseMUCONATE
           LACTONIZING Enzyme From Roseiflexus Sp
          Length = 393

 Score = 26.9 bits (58), Expect = 3.0,   Method: Composition-based stats.
 Identities = 11/29 (37%), Positives = 18/29 (62%)

Query: 2   GDPNDKTLRKLEKDVLIEQMMRDIARTEK 30
           GDP+  T+R +E D+     +RD+A T +
Sbjct: 191 GDPDATTIRTMEHDLARIVAIRDVAPTAR 219


>pdb|3NIT|A Chain A, The Structure Of Ubr Box (Native1)
          Length = 90

 Score = 26.9 bits (58), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 10/29 (34%), Positives = 14/29 (48%)

Query: 28 TEKCAEFTEALEKCGRDNGWKGVFTCRKE 56
          T+ C EFT  +  CG +  W     C+ E
Sbjct: 60 TDICTEFTSGICDCGDEEAWNSPLHCKAE 88


>pdb|3NIH|A Chain A, The Structure Of Ubr Box (Riaaa)
 pdb|3NII|A Chain A, The Structure Of Ubr Box (Kiaa)
 pdb|3NIJ|A Chain A, The Structure Of Ubr Box (Hiaa)
 pdb|3NIK|A Chain A, The Structure Of Ubr Box (Reaa)
 pdb|3NIK|B Chain B, The Structure Of Ubr Box (Reaa)
 pdb|3NIK|D Chain D, The Structure Of Ubr Box (Reaa)
 pdb|3NIK|F Chain F, The Structure Of Ubr Box (Reaa)
 pdb|3NIL|A Chain A, The Structure Of Ubr Box (Rdaa)
 pdb|3NIL|B Chain B, The Structure Of Ubr Box (Rdaa)
 pdb|3NIL|D Chain D, The Structure Of Ubr Box (Rdaa)
 pdb|3NIL|F Chain F, The Structure Of Ubr Box (Rdaa)
 pdb|3NIM|A Chain A, The Structure Of Ubr Box (Rraa)
 pdb|3NIM|B Chain B, The Structure Of Ubr Box (Rraa)
 pdb|3NIM|D Chain D, The Structure Of Ubr Box (Rraa)
 pdb|3NIM|F Chain F, The Structure Of Ubr Box (Rraa)
 pdb|3NIN|A Chain A, The Structure Of Ubr Box (Rlges)
 pdb|3NIN|B Chain B, The Structure Of Ubr Box (Rlges)
 pdb|3NIS|A Chain A, The Structure Of Ubr Box (Native2)
 pdb|3NIS|B Chain B, The Structure Of Ubr Box (Native2)
 pdb|3NIS|D Chain D, The Structure Of Ubr Box (Native2)
 pdb|3NIS|F Chain F, The Structure Of Ubr Box (Native2)
          Length = 82

 Score = 26.6 bits (57), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 10/29 (34%), Positives = 14/29 (48%)

Query: 28 TEKCAEFTEALEKCGRDNGWKGVFTCRKE 56
          T+ C EFT  +  CG +  W     C+ E
Sbjct: 52 TDICTEFTSGICDCGDEEAWNSPLHCKAE 80


>pdb|2Z2L|B Chain B, Penicillin-Binding Protein 2x (Pbp2x) From Streptococcus
           Pneumoniae
 pdb|2Z2L|E Chain E, Penicillin-Binding Protein 2x (Pbp2x) From Streptococcus
           Pneumoniae
 pdb|2Z2M|B Chain B, Cefditoren-Acylated Penicillin-Binding Protein 2x (Pbp2x)
           From Streptococcus Pneumoniae
 pdb|2Z2M|E Chain E, Cefditoren-Acylated Penicillin-Binding Protein 2x (Pbp2x)
           From Streptococcus Pneumoniae
 pdb|2ZC3|B Chain B, Penicillin-Binding Protein 2x (Pbp 2x) Acyl-Enzyme Complex
           (Biapenem) From Streptococcus Pneumoniae
 pdb|2ZC3|E Chain E, Penicillin-Binding Protein 2x (Pbp 2x) Acyl-Enzyme Complex
           (Biapenem) From Streptococcus Pneumoniae
 pdb|2ZC4|B Chain B, Penicillin-Binding Protein 2x (Pbp 2x) Acyl-Enzyme Complex
           (Tebipenem) From Streptococcus Pneumoniae
 pdb|2ZC4|E Chain E, Penicillin-Binding Protein 2x (Pbp 2x) Acyl-Enzyme Complex
           (Tebipenem) From Streptococcus Pneumoniae
          Length = 385

 Score = 26.6 bits (57), Expect = 3.8,   Method: Composition-based stats.
 Identities = 10/24 (41%), Positives = 17/24 (70%)

Query: 3   DPNDKTLRKLEKDVLIEQMMRDIA 26
           DPND+T RK +K+++   + +D A
Sbjct: 245 DPNDQTARKSQKEIVGNPVSKDAA 268


>pdb|1PMD|A Chain A, Penicillin-Binding Protein 2x (Pbp-2x)
          Length = 675

 Score = 26.2 bits (56), Expect = 5.0,   Method: Composition-based stats.
 Identities = 10/24 (41%), Positives = 17/24 (70%)

Query: 3   DPNDKTLRKLEKDVLIEQMMRDIA 26
           DPND+T RK +K+++   + +D A
Sbjct: 410 DPNDQTARKSQKEIVGNPVSKDAA 433


>pdb|1PYY|A Chain A, Double Mutant Pbp2x T338aM339F FROM STREPTOCOCCUS
           PNEUMONIAE STRAIN R6 At 2.4 A Resolution
          Length = 702

 Score = 26.2 bits (56), Expect = 5.1,   Method: Composition-based stats.
 Identities = 10/24 (41%), Positives = 17/24 (70%)

Query: 3   DPNDKTLRKLEKDVLIEQMMRDIA 26
           DPND+T RK +K+++   + +D A
Sbjct: 437 DPNDQTARKSQKEIVGNPVSKDAA 460


>pdb|1QME|A Chain A, Penicillin-binding Protein 2x (pbp-2x)
 pdb|1QMF|A Chain A, Penicillin-Binding Protein 2x (Pbp-2x) Acyl-Enzyme Complex
          Length = 702

 Score = 26.2 bits (56), Expect = 5.2,   Method: Composition-based stats.
 Identities = 10/24 (41%), Positives = 17/24 (70%)

Query: 3   DPNDKTLRKLEKDVLIEQMMRDIA 26
           DPND+T RK +K+++   + +D A
Sbjct: 437 DPNDQTARKSQKEIVGNPVSKDAA 460


>pdb|2GK1|A Chain A, X-Ray Crystal Structure Of Ngt-Bound Hexa
 pdb|2GK1|C Chain C, X-Ray Crystal Structure Of Ngt-Bound Hexa
 pdb|2GK1|E Chain E, X-Ray Crystal Structure Of Ngt-Bound Hexa
 pdb|2GK1|G Chain G, X-Ray Crystal Structure Of Ngt-Bound Hexa
 pdb|2GJX|A Chain A, Crystallographic Structure Of Human Beta-Hexosaminidase A
 pdb|2GJX|D Chain D, Crystallographic Structure Of Human Beta-Hexosaminidase A
 pdb|2GJX|E Chain E, Crystallographic Structure Of Human Beta-Hexosaminidase A
 pdb|2GJX|H Chain H, Crystallographic Structure Of Human Beta-Hexosaminidase A
          Length = 507

 Score = 25.8 bits (55), Expect = 6.5,   Method: Composition-based stats.
 Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)

Query: 51  FTCRKENEKMKECMAHWYHNEDFRKEVTEMYLQQRTD 87
           FTC K N ++++ M      EDF K++   Y+Q   D
Sbjct: 304 FTCWKSNPEIQDFMRKKGFGEDF-KQLESFYIQTLLD 339


>pdb|3BXZ|A Chain A, Crystal Structure Of The Isolated Dead Motor Domains
          From Escherichia Coli Seca
 pdb|3BXZ|B Chain B, Crystal Structure Of The Isolated Dead Motor Domains
          From Escherichia Coli Seca
          Length = 471

 Score = 25.4 bits (54), Expect = 8.1,   Method: Composition-based stats.
 Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 7/46 (15%)

Query: 2  GDPNDKTLRKLEKDVLI----EQMMRDIARTE---KCAEFTEALEK 40
          G  ND+TLR++ K V I    E  M  ++  E   K AEF   LEK
Sbjct: 13 GSRNDRTLRRMRKVVNIINAMEPEMEKLSDEELKGKTAEFRARLEK 58


>pdb|1IPE|A Chain A, Tropinone Reductase-Ii Complexed With Nadph
 pdb|1IPE|B Chain B, Tropinone Reductase-Ii Complexed With Nadph
 pdb|1IPF|A Chain A, Tropinone Reductase-Ii Complexed With Nadph And
          Tropinone
 pdb|1IPF|B Chain B, Tropinone Reductase-Ii Complexed With Nadph And
          Tropinone
          Length = 259

 Score = 25.4 bits (54), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 9/38 (23%), Positives = 22/38 (57%), Gaps = 1/38 (2%)

Query: 50 VFTCRKENEKMKECMAHWYHNEDFRKEVTEMYLQQRTD 87
          V+TC +  +++ +C+  W  ++ F+ E +   L  R++
Sbjct: 35 VYTCSRNQKELNDCLTQW-RSKGFKVEASVCDLSSRSE 71


>pdb|2AE2|A Chain A, Tropinone Reductase-Ii Complexed With Nadp+ And
          Pseudotropine
 pdb|2AE2|B Chain B, Tropinone Reductase-Ii Complexed With Nadp+ And
          Pseudotropine
 pdb|2AE1|A Chain A, Tropinone Reductase-Ii
          Length = 260

 Score = 25.4 bits (54), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 9/38 (23%), Positives = 22/38 (57%), Gaps = 1/38 (2%)

Query: 50 VFTCRKENEKMKECMAHWYHNEDFRKEVTEMYLQQRTD 87
          V+TC +  +++ +C+  W  ++ F+ E +   L  R++
Sbjct: 36 VYTCSRNQKELNDCLTQW-RSKGFKVEASVCDLSSRSE 72


>pdb|1MIU|A Chain A, Structure Of A Brca2-dss1 Complex
          Length = 738

 Score = 25.0 bits (53), Expect = 9.9,   Method: Composition-based stats.
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 9/68 (13%)

Query: 20  QMMRDIARTEKCAEFTEALEKCGRDNG--------WKGVFTCRKENEKMKECMAHWYHNE 71
           QM+ D  +    +EF +ALE   ++ G        WK   T  K+ EK    ++ W  + 
Sbjct: 478 QMLNDKKQARIQSEFRKALESAEKEEGLSRDVTTVWKLRVTSYKKKEK-SALLSIWRPSS 536

Query: 72  DFRKEVTE 79
           D    +TE
Sbjct: 537 DLSSLLTE 544


  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
   0.316    0.132    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,317,588
Number of Sequences: 62578
Number of extensions: 121561
Number of successful extensions: 491
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 483
Number of HSP's gapped (non-prelim): 17
length of query: 112
length of database: 14,973,337
effective HSP length: 76
effective length of query: 36
effective length of database: 10,217,409
effective search space: 367826724
effective search space used: 367826724
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)