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= 0001.0205.p
         (430 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309533|ref|YP_003773625.1| diaminopimelate decarboxylase [...   844   0.0  
gi|300312040|ref|YP_003776132.1| diaminopimelate decarboxylase [...   125   9e-30

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

 Score =  844 bits (2181), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/430 (95%), Positives = 420/430 (97%)

Query: 1   MSHFSYRNGALHAEQVSLQALAEQFGTPLYVYSKAALVENFSAYANACRTAGRADGAKGG 60
           MSHFSYRNG LHAEQVSL  LAEQFGTPLYVYSKAALVENFSAYANAC+ AGRADG KGG
Sbjct: 1   MSHFSYRNGVLHAEQVSLATLAEQFGTPLYVYSKAALVENFSAYANACQQAGRADGGKGG 60

Query: 61  ALVCYSVKSNSNLAVLNLLGKLGSGFDIVSAGELLRVVAAGGDARKVIFSGVGKGRDEMK 120
           ALVCYSVKSNSNLAVLNLLG+LGSGFDIVS GELLRVVAAGGDARKVIFSGVGKGRDEMK
Sbjct: 61  ALVCYSVKSNSNLAVLNLLGRLGSGFDIVSGGELLRVVAAGGDARKVIFSGVGKGRDEMK 120

Query: 121 LALEHDILCFNVESIPEVARLNEVAGALGKRARISLRVNPNVDAKTHPYISTGLKENKFG 180
           LALEHDILCFNVESIPEVARLNEVAGALGKRARISLRVNPNVDAKTHPYISTGLKENKFG
Sbjct: 121 LALEHDILCFNVESIPEVARLNEVAGALGKRARISLRVNPNVDAKTHPYISTGLKENKFG 180

Query: 181 VAYEDALNCYRTAAALPHIEVVGIDCHIGSQLLDDSPLLEALDKIIDMVDALEAEGIPIH 240
           VAYEDALNCYR AAALPHIEVVGIDCHIGSQLLDDSPLLEALDKIIDMVDALEAEGIPIH
Sbjct: 181 VAYEDALNCYRAAAALPHIEVVGIDCHIGSQLLDDSPLLEALDKIIDMVDALEAEGIPIH 240

Query: 241 HLDIGGGIGIRYDDEQPVAIGDYLARVFARVDAWRAKKYDGRPIQVMFEPGRSVVGNAGL 300
           HLDIGGGIGIRYDDEQPVAIGDYLARVFARVDAWRA KY GRPIQVMFEPGRSVVGNAGL
Sbjct: 241 HLDIGGGIGIRYDDEQPVAIGDYLARVFARVDAWRASKYQGRPIQVMFEPGRSVVGNAGL 300

Query: 301 LLTEVQYLKHGEEKNFAVVDAAMNDLMRPAMYEAWHGVQTVKENAGQPRIYDVVGPVCES 360
           LLTEVQYLKHGE KNFAVVDAAMNDLMRPAMYEAWHGV+TVKENAGQPRIYDVVGPVCES
Sbjct: 301 LLTEVQYLKHGEGKNFAVVDAAMNDLMRPAMYEAWHGVKTVKENAGQPRIYDVVGPVCES 360

Query: 361 GDWLARARELAIGEGDLLALMSAGAYGMTMASNYNTRGRAAEVLVDGQQAHLVRARENPA 420
           GDWLAR+RELAIGEGDLLALMSAGAYGMTMASNYNTRGRAAEVLVDG++AHL+RARENPA
Sbjct: 361 GDWLARSRELAIGEGDLLALMSAGAYGMTMASNYNTRGRAAEVLVDGERAHLIRARENPA 420

Query: 421 DLFALEKIVN 430
           DLFALEKIV+
Sbjct: 421 DLFALEKIVS 430


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

 Score =  125 bits (313), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 126/420 (30%), Positives = 193/420 (45%), Gaps = 36/420 (8%)

Query: 4   FSYRNGALHAEQVSLQALAEQFG-TPLYVYSKAALVENFSAYANACRTAGRADGAKGGAL 62
           F   +G LH   + L  LA + G TP YVY +A L+    A+  A   A  A        
Sbjct: 17  FPIVDGMLHVGGMPLDRLALRVGATPFYVYDRA-LLRARVAHLRAHLPAELA-------- 67

Query: 63  VCYSVKSNSNLAVLNLLGKLGSGFDIVSAGELLRVVAAGGDARKVIFSGVGKGRDEMKLA 122
           + YS+K+N   A++  + +L  GFD+ S GEL   +      + + F+G GK   E++ A
Sbjct: 68  LHYSIKANPMPALVQAMAQLVDGFDVASGGELATALDTPMPVQHISFTGPGKSLAELRRA 127

Query: 123 LEHDILCFNVESIPEVARLNEVAGALGKRARISLRVNPNVDAKTHPYISTGLKENKFGVA 182
           L   ++  +VES  E   +  +A  LG R  ++LR+NP  + K+   +  G     FGV 
Sbjct: 128 LAAGVM-LHVESEREAEAVAALAQELGVRPGVTLRINPPFELKSS-GMRMGGGAKPFGVD 185

Query: 183 YEDALNCYRTAAALPHIEVVGIDCHIGSQLLDDSPLLEALDKIIDMVDALEAE-GIPIHH 241
            E A    R  A    ++V G+    GSQ LD   ++ A     ++   L  E G+ +  
Sbjct: 186 AEAAPALLRWLAGQ-GVQVAGLQIFCGSQSLDAQAIMAAQSSSFELALQLAGEAGLSLRV 244

Query: 242 LDIGGGIGIRY-DDEQPV---AIGDYLARVFARVDAWRAKKYDGRPIQVMFEPGRSVVGN 297
           L+IGGG GI Y   E+ +    IG +LA+   R+ A   +      ++V+ E GR +VG 
Sbjct: 245 LNIGGGFGIPYFPGERALEIAPIGAHLAQWLPRLRALHPQ------LRVVMEMGRYLVGE 298

Query: 298 AGLLLTEVQYLKHGEEKNFAVVDAAMN----------DLMRPAMYEAWHGVQTVKENAGQ 347
           AGL ++ V   K    + F VVD  ++           ++R          Q  +   G 
Sbjct: 299 AGLYVSRVIDRKQSRGEVFLVVDGGLHHHLAASGNFGQVIRKNYPVTIVPQQPQRSGGGT 358

Query: 348 PRIYDVVGPVCESGDWLARAREL-AIGEGDLLALMSAGAYGMTMASN-YNTRGRAAEVLV 405
                VVGP+C   D LA    L A   GDL+ +  +GAYG++ +   +      AEVLV
Sbjct: 359 TERVSVVGPLCTPLDVLAAQMLLPAAAVGDLVVVFQSGAYGLSASPTAFLGHPAPAEVLV 418


  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    0.136    0.397 

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: 1,327,543
Number of extensions: 56318
Number of successful extensions: 185
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 182
Number of HSP's successfully gapped: 2
Length of query: 430
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 342
Effective length of database: 1,203,190
Effective search space: 411490980
Effective search space used: 411490980
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 (21.7 bits)
S2: 132 (55.5 bits)