GapMind for catabolism of small carbon sources

 

Aligments for a candidate for amaB in Pseudomonas fluorescens GW456-L13

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate PfGW456L13_3932 Aldehyde dehydrogenase A (EC 1.2.1.22)

Query= uniprot:Q88CC3
         (496 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3932 Aldehyde
           dehydrogenase A (EC 1.2.1.22)
          Length = 477

 Score =  198 bits (504), Expect = 3e-55
 Identities = 142/448 (31%), Positives = 214/448 (47%), Gaps = 28/448 (6%)

Query: 23  VHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKAD 82
           V  P  G+ ++ V      +    +  A +A + W   PA  R   +R     LRE+ A 
Sbjct: 24  VINPATGAVLSKVPASTAEDVERALAAACAAQKGWARKPANDRAGYLRRIAAKLRENVAH 83

Query: 83  LGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGV 142
           L   +++E GKI+     EV    D  D+    +R++ G  I S+R   ++     PLGV
Sbjct: 84  LARTITLEQGKISGLAEVEVNFTADYLDYMAEWARRIEGEIITSDRQNENIFLFRKPLGV 143

Query: 143 VGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKA-LKAFGDAPA 201
           V  I  +NFP  + A   A AL+ GN++V KPSE+TP         FE A L A  D P 
Sbjct: 144 VAGILPWNFPFFLIARKMAPALLTGNTIVIKPSEETPNNC------FEFARLVAETDLPP 197

Query: 202 GLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMIL 261
           G+  +V G  + G A+     V ++S TGS   G  +    A    +  LELGG    I+
Sbjct: 198 GVFNVVCGDGKVGAALSSHKGVDMISFTGSVDTGSRIMAAAAPNITKLNLELGGKAPAIV 257

Query: 262 APSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDP--R 319
              ADLDLAVR I  S +  +GQ C    R+ V R + D+ + R+ AA    R GDP  +
Sbjct: 258 LADADLDLAVRAIRDSRIINSGQVCNCAERVYVERKVADQFIERIAAAMSATRYGDPIAQ 317

Query: 320 KDNLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPAI-AEMPAQS 378
            D  +GPLI++Q  D++   +  A  +G  +  G  Q+AD  PN ++  P + A   A  
Sbjct: 318 PDVEMGPLINRQGLDSVNRKVRTALSQGASLISG-GQMAD-LPNGFHFQPTVLAGCRADM 375

Query: 379 DVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREA-------------- 424
           +++R E F P+L +   DD +EA+ L N+   GL+S I+T D+ +               
Sbjct: 376 EIMREEIFGPVLPIQIIDDLDEAIALANDCDYGLTSSIYTRDLSKTMQAMRELDFGETYV 435

Query: 425 --ERFQSASGSDCGIANVNIGTSGAEIG 450
             E F++  G   G+    IG +  + G
Sbjct: 436 NRENFEAMQGFHAGVRKSGIGGADGKHG 463


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: 494
Number of extensions: 24
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: 496
Length of database: 477
Length adjustment: 34
Effective length of query: 462
Effective length of database: 443
Effective search space:   204666
Effective search space used:   204666
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.

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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 preprint on GapMind for carbon sources, or view the source code.

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