GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Burkholderia phytofirmans PsJN

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate BPHYT_RS17930 BPHYT_RS17930 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>FitnessBrowser__BFirm:BPHYT_RS17930
          Length = 420

 Score =  292 bits (748), Expect = 1e-83
 Identities = 160/388 (41%), Positives = 240/388 (61%), Gaps = 9/388 (2%)

Query: 13  TPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEI 72
           TP Y+Y    + +A+  Y  A  GR++ +  A+KANSNL++L++ A L +G D VS GE+
Sbjct: 29  TPLYVYSRAALTEAWNAYAGACAGRRASVHVAVKANSNLAVLNVFARLGAGFDIVSGGEL 88

Query: 73  QRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARI 132
            R L AG +    VFSGVGK A E+  AL   +   NVES  EL  +  +A ++G KA +
Sbjct: 89  ARVLAAGGRAENTVFSGVGKHADEMRDALAAGVKCFNVESIPELDRLNAVAAAMGKKAPV 148

Query: 133 SIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLD 192
           S+R+NP++DAKTHPYISTGLK NKFGV  ++A   +  A   A LE V +  HIGSQ+ +
Sbjct: 149 SLRVNPDVDAKTHPYISTGLKSNKFGVAFEDARATYQAAAAMANLEVVGIDCHIGSQITE 208

Query: 193 LEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQGL 252
           + P ++A  KV ++ + +   G+ +R  DVGGG+G++Y++E   ++ ++ + +L+ ++  
Sbjct: 209 VAPYLDAVDKVLELVEQIEQDGVKIRHIDVGGGLGITYDDETPPEIGEFVRTVLDRIEAR 268

Query: 253 ---DLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKHAIR 309
                 +  EPGRS+V  +G L+T+V + K    K F IVDA M D  RP++Y A HA  
Sbjct: 269 GHGHREVYFEPGRSLVGNAGMLLTRVEFLKPGAEKNFAIVDAAMTDLARPAMYEAYHA-- 326

Query: 310 VITPSKGREISP--CDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYN 367
            I P   R++     DVVGPVCES D +L    L  +EPGD +AI   GAYG  M+S YN
Sbjct: 327 -IDPVVKRDVPAHVYDVVGPVCESGD-WLGRERLLSVEPGDLLAIRSAGAYGFVMSSNYN 384

Query: 368 SRPKLLELALEDHKIRVIRKREALEDLW 395
           +RP+  E+ ++  ++ V+R RE ++ L+
Sbjct: 385 TRPRAAEVMVDGTQVHVVRAREEVKQLF 412


Lambda     K      H
   0.319    0.138    0.389 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 380
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 405
Length of database: 420
Length adjustment: 31
Effective length of query: 374
Effective length of database: 389
Effective search space:   145486
Effective search space used:   145486
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: 50 (23.9 bits)

Align candidate BPHYT_RS17930 BPHYT_RS17930 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

Software error:

../bin/blast/fastacmd -i /tmp/list.669.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.669.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.