GapMind for catabolism of small carbon sources


Aligments for a candidate for hisQ in Synechococcus elongatus PCC 7942

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine

Query= reanno::pseudo6_N2E2:Pf6N2E2_2959
         (242 letters)

>lcl|FitnessBrowser__SynE:Synpcc7942_0247 Synpcc7942_0247 ABC-type
           permease for basic amino acids and glutamine
          Length = 377

 Score = 69.7 bits (169), Expect = 8e-17
 Identities = 43/126 (34%), Positives = 64/126 (50%)

           F A ++ L    GA+ TE  RG ILSVP GQ EAA A GL R Q    +V PQ +R  +P

            + + ++   K ++L   +G  DL   AQ     T +     ++  L YL I +  +  +

Query: 227 RWLERR 232
Sbjct: 365 NGLQQR 370

Lambda     K      H
   0.329    0.142    0.418 

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: 272
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: 242
Length of database: 377
Length adjustment: 27
Effective length of query: 215
Effective length of database: 350
Effective search space:    75250
Effective search space used:    75250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

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



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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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