GapMind for catabolism of small carbon sources

 

Aligments for a candidate for argT in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate Pf6N2E2_2958 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)

Query= reanno::pseudo6_N2E2:Pf6N2E2_2958
         (260 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2958
           Lysine-arginine-ornithine-binding periplasmic protein
           precursor (TC 3.A.1.3.1)
          Length = 260

 Score =  511 bits (1316), Expect = e-150
 Identities = 260/260 (100%), Positives = 260/260 (100%)

Query: 1   MKKALLTLSALALCMAAGVATAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAIC 60
           MKKALLTLSALALCMAAGVATAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAIC
Sbjct: 1   MKKALLTLSALALCMAAGVATAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAIC 60

Query: 61  AELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKAIDFSSELFSGPTAYVFKK 120
           AELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKAIDFSSELFSGPTAYVFKK
Sbjct: 61  AELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKAIDFSSELFSGPTAYVFKK 120

Query: 121 GSGLSEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYADLTSGRLDAA 180
           GSGLSEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYADLTSGRLDAA
Sbjct: 121 GSGLSEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYADLTSGRLDAA 180

Query: 181 IQDMLQAELGFLKSPKGEGYEVSKPVDSELLPSKTAIGIRKGNSELKALLNKGIKALHDD 240
           IQDMLQAELGFLKSPKGEGYEVSKPVDSELLPSKTAIGIRKGNSELKALLNKGIKALHDD
Sbjct: 181 IQDMLQAELGFLKSPKGEGYEVSKPVDSELLPSKTAIGIRKGNSELKALLNKGIKALHDD 240

Query: 241 GKYAEIQKKHFGDLNLYSGK 260
           GKYAEIQKKHFGDLNLYSGK
Sbjct: 241 GKYAEIQKKHFGDLNLYSGK 260


Lambda     K      H
   0.313    0.132    0.368 

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: 398
Number of extensions: 9
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: 260
Length of database: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 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