Aligments for a candidate for glt in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for glt in Pseudomonas simiae WCS417

Align Amino acid:proton symporter (characterized, see rationale)
to candidate GFF3721 PS417_19045 amino acid:proton symporter

Query= uniprot:A0A0N9WTL5
         (431 letters)



>FitnessBrowser__WCS417:GFF3721
          Length = 420

 Score =  731 bits (1887), Expect = 0.0
 Identities = 379/413 (91%), Positives = 393/413 (95%)

Query: 1   MKKNKLPRRIAMGIALGVLVGWACHHFAGSEQSAKEIASYFSMVTDIFLRMIKMIIAPLV 60
           M KNKLPRRIA+GIALGVLVGWACHH+AGSEQ+AK +A YFSMVTDIFLRMIKMIIAPLV
Sbjct: 1   MNKNKLPRRIAVGIALGVLVGWACHHYAGSEQAAKALAGYFSMVTDIFLRMIKMIIAPLV 60

Query: 61  FATLVGGIASMGNSRSVGRIGARAMAWFVTASVVSLLIGMGLVNLFQPGAGLNMDVAQHA 120
           FATLVGGIASMGNSRSVGRIG RAM WFVTAS+VSL++GM LVNLFQPGAGLNM V QHA
Sbjct: 61  FATLVGGIASMGNSRSVGRIGMRAMLWFVTASLVSLMLGMALVNLFQPGAGLNMQVVQHA 120

Query: 121 TAAVPVNTGDFSLKAFIGHVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRIT 180
           TAAVPVNTGDFSLK FI HVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRIT
Sbjct: 121 TAAVPVNTGDFSLKTFISHVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRIT 180

Query: 181 DSIEELAKVMFKITDYVMAFAPIGVFAAIASAITTQGLGLLVDYGKLIAEFYLGILILWA 240
           D+++ELAKVMFKITDYVMAFAPIGVFAAIASAITT GLGLL DY KLIAEFYLGI +LW 
Sbjct: 181 DTVDELAKVMFKITDYVMAFAPIGVFAAIASAITTNGLGLLADYAKLIAEFYLGIALLWV 240

Query: 241 LLFGAGYLFLGRSVFHLGKLIREPILLAFSTASSESAYPKTIEALEKFGAPKRVSSFVLP 300
           LLF AGYLFLGRSVF LGKLIREPILLAFSTASSESAYPKT+EALEKFGAPKRVSSFVLP
Sbjct: 241 LLFAAGYLFLGRSVFTLGKLIREPILLAFSTASSESAYPKTMEALEKFGAPKRVSSFVLP 300

Query: 301 LGYSFNLDGSMMYQAFAILFIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVVVA 360
           LGYSFNLDGSMMYQAFAI+FIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVVVA
Sbjct: 301 LGYSFNLDGSMMYQAFAIMFIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVVVA 360

Query: 361 ATLPMFNLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSESHEEADE 413
           ATLPMFNLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSE+ EE  E
Sbjct: 361 ATLPMFNLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSEAEEEPAE 413


Lambda     K      H
   0.325    0.138    0.392 

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: 647
Number of extensions: 16
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: 431
Length of database: 420
Length adjustment: 32
Effective length of query: 399
Effective length of database: 388
Effective search space:   154812
Effective search space used:   154812
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources