GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagB in Burkholderia phytofirmans PsJN

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate BPHYT_RS02735 BPHYT_RS02735 iron dicitrate transport regulator FecR

Query= reanno::BFirm:BPHYT_RS02735
         (335 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS02735 BPHYT_RS02735 iron
           dicitrate transport regulator FecR
          Length = 335

 Score =  632 bits (1630), Expect = 0.0
 Identities = 335/335 (100%), Positives = 335/335 (100%)

Query: 1   MLKEALASAETVAAQLTDTSRVEALAAKLAQQPRHVALTVARGSSDHAASYFASLTMSRL 60
           MLKEALASAETVAAQLTDTSRVEALAAKLAQQPRHVALTVARGSSDHAASYFASLTMSRL
Sbjct: 1   MLKEALASAETVAAQLTDTSRVEALAAKLAQQPRHVALTVARGSSDHAASYFASLTMSRL 60

Query: 61  GVPVASLPMSVATLQQAPLQVRDQLALAFSQSGKSPDLVGTMEALRKAGALTVAAVNVSG 120
           GVPVASLPMSVATLQQAPLQVRDQLALAFSQSGKSPDLVGTMEALRKAGALTVAAVNVSG
Sbjct: 61  GVPVASLPMSVATLQQAPLQVRDQLALAFSQSGKSPDLVGTMEALRKAGALTVAAVNVSG 120

Query: 121 SPLADACEFELPLVAGPELSVAATKSYIAMLSISAQLVAHWQKDAELLAALKTLPEALCT 180
           SPLADACEFELPLVAGPELSVAATKSYIAMLSISAQLVAHWQKDAELLAALKTLPEALCT
Sbjct: 121 SPLADACEFELPLVAGPELSVAATKSYIAMLSISAQLVAHWQKDAELLAALKTLPEALCT 180

Query: 181 AGKLDWSVAVEELRGIERMIVIGRGLGLAIAQEAALKLKETSGIQAEAFSSAEVRHGPME 240
           AGKLDWSVAVEELRGIERMIVIGRGLGLAIAQEAALKLKETSGIQAEAFSSAEVRHGPME
Sbjct: 181 AGKLDWSVAVEELRGIERMIVIGRGLGLAIAQEAALKLKETSGIQAEAFSSAEVRHGPME 240

Query: 241 LIDRDYPLLVFAPRGPEQAGLLQLARDMKARGARVLLAASVDVPEATLPLATTAHAALDP 300
           LIDRDYPLLVFAPRGPEQAGLLQLARDMKARGARVLLAASVDVPEATLPLATTAHAALDP
Sbjct: 241 LIDRDYPLLVFAPRGPEQAGLLQLARDMKARGARVLLAASVDVPEATLPLATTAHAALDP 300

Query: 301 IAAILSFYVMAAGLAAARGRNPDAPRHLNKVTETH 335
           IAAILSFYVMAAGLAAARGRNPDAPRHLNKVTETH
Sbjct: 301 IAAILSFYVMAAGLAAARGRNPDAPRHLNKVTETH 335


Lambda     K      H
   0.317    0.128    0.352 

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: 570
Number of extensions: 15
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: 335
Length of database: 335
Length adjustment: 28
Effective length of query: 307
Effective length of database: 307
Effective search space:    94249
Effective search space used:    94249
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: 49 (23.5 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 paper from 2022 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