GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate Pf6N2E2_2924 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:A0A159ZYE0
         (418 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2924 Branched-chain amino
           acid transport system permease protein LivM (TC
           3.A.1.4.1)
          Length = 418

 Score =  815 bits (2104), Expect = 0.0
 Identities = 418/418 (100%), Positives = 418/418 (100%)

Query: 1   MTRHLKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLF 60
           MTRHLKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLF
Sbjct: 1   MTRHLKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLF 60

Query: 61  STQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLI 120
           STQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLI
Sbjct: 61  STQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLI 120

Query: 121 LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATF 180
           LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATF
Sbjct: 121 LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATF 180

Query: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERK 240
           GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERK
Sbjct: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERK 240

Query: 241 AAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEI 300
           AAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEI
Sbjct: 241 AAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEI 300

Query: 301 ACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM 360
           ACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM
Sbjct: 301 ACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM 360

Query: 361 GSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK 418
           GSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK
Sbjct: 361 GSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK 418


Lambda     K      H
   0.331    0.145    0.439 

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: 801
Number of extensions: 26
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: 418
Length of database: 418
Length adjustment: 32
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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 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