GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdC in Marinobacter adhaerens HP15

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate GFF1672 HP15_1631 dihydrolipoamide acetyltransferase

Query= reanno::Marino:GFF1672
         (378 letters)



>lcl|FitnessBrowser__Marino:GFF1672 HP15_1631 dihydrolipoamide
           acetyltransferase
          Length = 378

 Score =  736 bits (1901), Expect = 0.0
 Identities = 378/378 (100%), Positives = 378/378 (100%)

Query: 1   MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60
           MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST
Sbjct: 1   MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60

Query: 61  ATASPVAAASRQRIPASPAVRRLVREHELNLSDIQGSGKDGRVLKADVLAYIEEGPKQAQ 120
           ATASPVAAASRQRIPASPAVRRLVREHELNLSDIQGSGKDGRVLKADVLAYIEEGPKQAQ
Sbjct: 61  ATASPVAAASRQRIPASPAVRRLVREHELNLSDIQGSGKDGRVLKADVLAYIEEGPKQAQ 120

Query: 121 NQAPADDAQTATTRSARRAPAADQEARVEPIRGIKAAMAKSMVKSATTIPHFIYSEDIDV 180
           NQAPADDAQTATTRSARRAPAADQEARVEPIRGIKAAMAKSMVKSATTIPHFIYSEDIDV
Sbjct: 121 NQAPADDAQTATTRSARRAPAADQEARVEPIRGIKAAMAKSMVKSATTIPHFIYSEDIDV 180

Query: 181 TDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEFPVLNSQLNDDVTEIHYLPQCNI 240
           TDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEFPVLNSQLNDDVTEIHYLPQCNI
Sbjct: 181 TDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEFPVLNSQLNDDVTEIHYLPQCNI 240

Query: 241 GMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAARSGRVSQEDLKGGTITISNIGAL 300
           GMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAARSGRVSQEDLKGGTITISNIGAL
Sbjct: 241 GMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAARSGRVSQEDLKGGTITISNIGAL 300

Query: 301 GGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVERAIMTVSWAGDHRIIDGGTIARFC 360
           GGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVERAIMTVSWAGDHRIIDGGTIARFC
Sbjct: 301 GGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVERAIMTVSWAGDHRIIDGGTIARFC 360

Query: 361 NRWKGYLESPQTMLLHMG 378
           NRWKGYLESPQTMLLHMG
Sbjct: 361 NRWKGYLESPQTMLLHMG 378


Lambda     K      H
   0.316    0.131    0.367 

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: 581
Number of extensions: 14
Number of successful extensions: 1
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: 378
Length of database: 378
Length adjustment: 30
Effective length of query: 348
Effective length of database: 348
Effective search space:   121104
Effective search space used:   121104
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 (21.6 bits)
S2: 50 (23.9 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