GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysA in Burkholderia phytofirmans PsJN

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate BPHYT_RS00645 BPHYT_RS00645 diaminopimelate decarboxylase

Query= curated2:P19572
         (415 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS00645 BPHYT_RS00645
           diaminopimelate decarboxylase
          Length = 402

 Score =  146 bits (368), Expect = 1e-39
 Identities = 122/388 (31%), Positives = 191/388 (49%), Gaps = 27/388 (6%)

Query: 3   TFSYRDAELFAEGVALSRIAERFG-TPTYVYSRAHIEAQYRAYADALAGMPHLVCFAVKA 61
           TF  R   L   G+ + ++A+R G TP + Y R+ I+ + R     L     L  +++KA
Sbjct: 4   TFLQRPPGLQFNGIDVRQLADRAGQTPFFAYDRSAIDTRVRELRSLLPSAMQLH-YSIKA 62

Query: 62  NSNLGVLNVLARLGAGFDIVSRGELERVLAAGGDPAKVVFSGVGKTRDDMRRALEVGVHC 121
           N    V++ LA+   GFD+ S  E+   L AG  P  + F+G GK+ DD+RRA+  GV+ 
Sbjct: 63  NPMPAVIHYLAQRVDGFDVASAQEMALALDAGATPDSIGFAGPGKSHDDLRRAVASGVN- 121

Query: 122 FNVESGEELERLQRVAAELGVKAPVSLRVNPDVDAQTHPYISTGLKENKFGIAIDEAEAV 181
            +VES  +L  +  +  ELGV+  V +R+NPD     H  +  G     FG+ +D+  A+
Sbjct: 122 VHVESDTQLRLVTALGWELGVQPNVVIRINPDFQV-GHSGMRMGGSAAPFGVDVDQIPAL 180

Query: 182 YARAAELDHLEVIGVDCHI--GSQLTQLEPFLDALERLLGLVDRLAGK-GIGIRHLDLGG 238
                EL+  EV     H+  GSQ       ++A  + + L+ RLA      +R ++LGG
Sbjct: 181 ---LHELETREVALAGFHVFWGSQCLHASTIIEAQRQSVDLILRLASDLPRPLRFVNLGG 237

Query: 239 GLGVRYRDEQPPL--------AGDYIRAIRERLHGRDLTLVFEPGRSIVANAGVLLTRVE 290
           G G+ Y   + PL          D++  + ERL G   T + E GR +V  AG+ + RV 
Sbjct: 238 GFGIPYFPGETPLDTKVVCEAMHDWLPRLCERLPG--TTPILELGRYLVGEAGIYVCRVI 295

Query: 291 YLKHTEHKDFAIVDAAMNDLIRPA------LYQAWMDVQAVRPRDAAPRRYDLVGPICET 344
             K +  + F I D  ++  +  +      L + +  V   RP   +  R  +VG +C  
Sbjct: 296 DRKVSRGRTFVITDGGLHHHLAASGNFGQVLRRNFPVVIGNRPDGISRERCYVVGCLCTP 355

Query: 345 GDFLAKDRDLALAE-GDLLAVRSAGAYG 371
            D LA D +L  A  GD + V+ +GAYG
Sbjct: 356 LDRLADDVELPEAHIGDFVVVKQSGAYG 383


Lambda     K      H
   0.321    0.139    0.400 

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: 382
Number of extensions: 22
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: 415
Length of database: 402
Length adjustment: 31
Effective length of query: 384
Effective length of database: 371
Effective search space:   142464
Effective search space used:   142464
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory