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= 0007.0165.p
         (420 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312040|ref|YP_003776132.1| diaminopimelate decarboxylase [...   384   e-108
gi|300309533|ref|YP_003773625.1| diaminopimelate decarboxylase [...   122   6e-29

>gi|300312040|ref|YP_003776132.1| diaminopimelate decarboxylase
           [Herbaspirillum seropedicae SmR1]
          Length = 418

 Score =  384 bits (986), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 209/415 (50%), Positives = 271/415 (65%), Gaps = 10/415 (2%)

Query: 15  PYRSPIAA---AWPCTHDGEFAVGGMALSQVVDAVGGTPCYLYDRAYMAERVTRLRRALS 71
           P + P+ A   A+P   DG   VGGM L ++   VG TP Y+YDRA +  RV  LR  L 
Sbjct: 5   PRQKPLHAEQTAFPIV-DGMLHVGGMPLDRLALRVGATPFYVYDRALLRARVAHLRAHLP 63

Query: 72  QTVELYYAIKANPMPAVVAHVARLLNGLDVASAGEMRVALDAGVAAEKISFAGPGKSEEE 131
             + L+Y+IKANPMPA+V  +A+L++G DVAS GE+  ALD  +  + ISF GPGKS  E
Sbjct: 64  AELALHYSIKANPMPALVQAMAQLVDGFDVASGGELATALDTPMPVQHISFTGPGKSLAE 123

Query: 132 LLQAYASNVLVNVESRRELHLLAKMSERSGRAARIALRVNLPFELKASGMKMTGGARQFG 191
           L +A A+ V+++VES RE   +A +++  G    + LR+N PFELK+SGM+M GGA+ FG
Sbjct: 124 LRRALAAGVMLHVESEREAEAVAALAQELGVRPGVTLRINPPFELKSSGMRMGGGAKPFG 183

Query: 192 IDAEDVPRSIAETAALGLKLEGFHLFTGSQSLHAEAVIEAQRKSYECAREWAELTCEPIK 251
           +DAE  P  +   A  G+++ G  +F GSQSL A+A++ AQ  S+E A + A      ++
Sbjct: 184 VDAEAAPALLRWLAGQGVQVAGLQIFCGSQSLDAQAIMAAQSSSFELALQLAGEAGLSLR 243

Query: 252 SINLGGGLGIPYGDADARISEEEVVTHLNCLAEETRRDFDGVSLVLELGRYLVGEAGLYV 311
            +N+GGG GIPY   +  +    +  HL       R     + +V+E+GRYLVGEAGLYV
Sbjct: 244 VLNIGGGFGIPYFPGERALEIAPIGAHLAQWLPRLRALHPQLRVVMEMGRYLVGEAGLYV 303

Query: 312 SRVIDRKVSRGKTFLVVDGGMHQHLAASGNFGQVLRKNYPVAINGKLF------GNEVSS 365
           SRVIDRK SRG+ FLVVDGG+H HLAASGNFGQV+RKNYPV I  +          E  S
Sbjct: 304 SRVIDRKQSRGEVFLVVDGGLHHHLAASGNFGQVIRKNYPVTIVPQQPQRSGGGTTERVS 363

Query: 366 VVGPLCTPLDLLASNAKLGRAEQGDLVVIFQSGAYGRSASPSGFLGHPAVREALV 420
           VVGPLCTPLD+LA+   L  A  GDLVV+FQSGAYG SASP+ FLGHPA  E LV
Sbjct: 364 VVGPLCTPLDVLAAQMLLPAAAVGDLVVVFQSGAYGLSASPTAFLGHPAPAEVLV 418


>gi|300309533|ref|YP_003773625.1| diaminopimelate decarboxylase
           [Herbaspirillum seropedicae SmR1]
          Length = 430

 Score =  122 bits (306), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 118/383 (30%), Positives = 179/383 (46%), Gaps = 46/383 (12%)

Query: 48  GTPCYLYDRAYMAERVTRLRRALSQT---------VELYYAIKANPMPAVVAHVARLLNG 98
           GTP Y+Y +A + E  +    A  Q            + Y++K+N   AV+  + RL +G
Sbjct: 26  GTPLYVYSKAALVENFSAYANACQQAGRADGGKGGALVCYSVKSNSNLAVLNLLGRLGSG 85

Query: 99  LDVASAGEMRVALDAGVAAEKISFAGPGKSEEELLQAYASNVLV-NVESRRELHLLAKMS 157
            D+ S GE+   + AG  A K+ F+G GK  +E+  A   ++L  NVES  E+  L +++
Sbjct: 86  FDIVSGGELLRVVAAGGDARKVIFSGVGKGRDEMKLALEHDILCFNVESIPEVARLNEVA 145

Query: 158 ERSGRAARIALRVNLPFELKASGMKMTG-GARQFGIDAEDVPRSIAETAAL-GLKLEGFH 215
              G+ ARI+LRVN   + K      TG    +FG+  ED        AAL  +++ G  
Sbjct: 146 GALGKRARISLRVNPNVDAKTHPYISTGLKENKFGVAYEDALNCYRAAAALPHIEVVGID 205

Query: 216 LFTGSQSLHAEAVIEAQRKSYECAREWAELTCEPIKSINLGGGLGIPYGDADARISEEEV 275
              GSQ L    ++EA  K  +   +  E    PI  +++GGG+GI Y D       E+ 
Sbjct: 206 CHIGSQLLDDSPLLEALDKIIDMV-DALEAEGIPIHHLDIGGGIGIRYDD-------EQP 257

Query: 276 VTHLNCLAEETRR-------DFDG--VSLVLELGRYLVGEAGLYVSRVIDRKVSRGKTFL 326
           V   + LA    R        + G  + ++ E GR +VG AGL ++ V   K   GK F 
Sbjct: 258 VAIGDYLARVFARVDAWRASKYQGRPIQVMFEPGRSVVGNAGLLLTEVQYLKHGEGKNFA 317

Query: 327 VVDGGMHQHLAASGNFGQVLRKNYPVAINGKLFGNE------VSSVVGPLCTPLDLLASN 380
           VVD  M+           ++R     A +G     E      +  VVGP+C   D LA +
Sbjct: 318 VVDAAMN----------DLMRPAMYEAWHGVKTVKENAGQPRIYDVVGPVCESGDWLARS 367

Query: 381 AKLGRAEQGDLVVIFQSGAYGRS 403
            +L   E GDL+ +  +GAYG +
Sbjct: 368 RELAIGE-GDLLALMSAGAYGMT 389


  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
   0.318    0.134    0.384 

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: 1,338,125
Number of extensions: 57896
Number of successful extensions: 191
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 184
Number of HSP's successfully gapped: 2
Length of query: 420
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 332
Effective length of database: 1,203,190
Effective search space: 399459080
Effective search space used: 399459080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 132 (55.5 bits)