BLASTP 2.2.18 [Mar-02-2008]


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= 0067.0013.p
         (222 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H...    82   4e-17
gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal...    69   2e-13
gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal...    56   2e-09
gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal...    55   5e-09

>gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase
           [Herbaspirillum seropedicae SmR1]
          Length = 433

 Score = 81.6 bits (200), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 44/98 (44%), Positives = 61/98 (62%), Gaps = 2/98 (2%)

Query: 3   LPQDETGNCPLFARALADWLQSQGVSFVLGTSVQQIEYAGGAVTGLRTANGMLTADAYVV 62
           LP DETG+C LF   LA   +  GV F  G  +  +  AGG + G+     ++ AD+YVV
Sbjct: 192 LPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVCGKELVQADSYVV 251

Query: 63  ACASASVALVKPL-GL-RLPVYPVKGYAITVPVSDATA 98
           A  S S  L+  + GL  +PVYP+KGY+ITVP++DA+A
Sbjct: 252 ALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASA 289


>gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small
           subunit [Herbaspirillum seropedicae SmR1]
          Length = 421

 Score = 69.3 bits (168), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 54/91 (59%), Gaps = 1/91 (1%)

Query: 6   DETGNCPLFARALADWLQSQ-GVSFVLGTSVQQIEYAGGAVTGLRTANGMLTADAYVVAC 64
           +E G+CP F RAL   +Q+     F+ G  +  +   G A++ ++  N  ++A  +V+A 
Sbjct: 195 EEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQAGNEWISAQRFVLAL 254

Query: 65  ASASVALVKPLGLRLPVYPVKGYAITVPVSD 95
            + S    + L LRLP+YP+KGY+ITVP+ D
Sbjct: 255 GADSADFARQLDLRLPLYPLKGYSITVPLED 285


>gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small
           subunit [Herbaspirillum seropedicae SmR1]
          Length = 423

 Score = 56.2 bits (134), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 54/99 (54%), Gaps = 4/99 (4%)

Query: 1   MLLPQDETGNCPLFARALADWLQSQGVSFVLGTSVQQI--EYAGGAVTGLRTAN--GMLT 56
           +  P D  GN  LFA+ + +  Q+ GVSF   ++V  I  E+ G     +++ +    LT
Sbjct: 191 LYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGGRVTLEVQSPHLASHLT 250

Query: 57  ADAYVVACASASVALVKPLGLRLPVYPVKGYAITVPVSD 95
            DA VVA   AS AL++PL   LP+  ++ Y+  VPV +
Sbjct: 251 MDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKN 289


>gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small
           subunit [Herbaspirillum seropedicae SmR1]
          Length = 436

 Score = 55.1 bits (131), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 43/112 (38%), Positives = 59/112 (52%), Gaps = 11/112 (9%)

Query: 6   DETGNCPLFARALADWLQSQGVSFVLGTSVQQI--EYAGGA--VTGLRTAN-----GMLT 56
           DE+G+       LA      GV F   T++ ++  E AG A  VTG+   N      +L 
Sbjct: 195 DESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAAARVTGVEIINPDGRHEVLK 254

Query: 57  ADAYVVACASASVALVKPLGLRLPVYPVKGYAITVPVSDATAQNRMAVTLTD 108
           AD +VVA  S S  LVKPLG+ L +YP KGY+ T  +++  A     V+LTD
Sbjct: 255 ADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAP--TVSLTD 304


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.319    0.132    0.394 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 496,916
Number of extensions: 14353
Number of successful extensions: 78
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 75
Number of HSP's successfully gapped: 4
Length of query: 222
Length of database: 1,619,870
Length adjustment: 82
Effective length of query: 140
Effective length of database: 1,231,600
Effective search space: 172424000
Effective search space used: 172424000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 129 (54.3 bits)