GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2924
          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 (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:

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