GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Burkholderia phytofirmans PsJN

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate BPHYT_RS32650 BPHYT_RS32650 aldehyde dehydrogenase

Query= uniprot:Q88CC3
         (496 letters)



>FitnessBrowser__BFirm:BPHYT_RS32650
          Length = 499

 Score =  649 bits (1674), Expect = 0.0
 Identities = 333/493 (67%), Positives = 378/493 (76%), Gaps = 2/493 (0%)

Query: 5   LLERLGVAAEAYTQGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPR 64
           +L  LG+A  A   GD  VH+PI G  I  V     AE    + +A+ A+ AWR+VPAPR
Sbjct: 6   ILADLGIAHAAQA-GDIAVHSPITGDLIGRVASNTVAEVDTALARAKEAYTAWRNVPAPR 64

Query: 65  RGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTI 124
           RGELVRL G  LRE K  LG ++++E GKI QEGLGEVQEMIDICDFAVGLSRQLYGLTI
Sbjct: 65  RGELVRLLGNRLREKKQALGSIITLETGKILQEGLGEVQEMIDICDFAVGLSRQLYGLTI 124

Query: 125 ASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALA 184
           ASERPGH M ETWHP+G   VISAFNFP AVW+WN ALALV GN+V+WKPSEKTPLTALA
Sbjct: 125 ASERPGHRMAETWHPMGTCVVISAFNFPAAVWSWNAALALVCGNAVIWKPSEKTPLTALA 184

Query: 185 CQALFEKALKAFGDAPAGLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAA 244
              +  +AL+ FGDAPAGL  L+ GGR+ G  +V DPR  +VSATGST MGR VG  VA 
Sbjct: 185 VNQILTEALQEFGDAPAGLTALINGGRDVGAKLVADPRASIVSATGSTEMGRTVGVEVAK 244

Query: 245 RFGRSILELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVA 304
           RFGRS+LELGGNNA I+  +AD +LA+RGILFSAVGTAGQRCT+LRRL VH S+ D+ + 
Sbjct: 245 RFGRSLLELGGNNAGIVTQTADHELAMRGILFSAVGTAGQRCTSLRRLFVHESVYDKTIE 304

Query: 305 RVKAAYGKVRIGDP-RKDNLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPN 363
           R+K  Y KV IG+P  K  L+GPLIDKQS+  MQ AL +A  EGG+VFGGER     Y N
Sbjct: 305 RLKQLYSKVPIGNPLEKGTLMGPLIDKQSYGRMQEALQQATAEGGKVFGGERVDVKGYEN 364

Query: 364 AYYVSPAIAEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIRE 423
            YYV PAI EMP+Q+ VV  ETFAPILYVL Y DF +A+  NN    GLSSC+FTTD+RE
Sbjct: 365 GYYVRPAIVEMPSQTSVVLKETFAPILYVLRYTDFADAVEANNAAVHGLSSCVFTTDLRE 424

Query: 424 AERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRQTNTVNY 483
           AERF S SGSDCGIANVNIG SGAEIGGAFGGEKETGGGRESGSDAWK YMRR TNTVNY
Sbjct: 425 AERFLSDSGSDCGIANVNIGPSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNTVNY 484

Query: 484 SRELPLAQGIVFD 496
           S  LPLAQGI F+
Sbjct: 485 SSALPLAQGIDFN 497


Lambda     K      H
   0.318    0.135    0.396 

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: 794
Number of extensions: 41
Number of successful extensions: 2
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: 496
Length of database: 499
Length adjustment: 34
Effective length of query: 462
Effective length of database: 465
Effective search space:   214830
Effective search space used:   214830
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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:

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