Alignments for a candidate for livM in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for livM in Pseudomonas fluorescens FW300-N1B4

Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate Pf1N1B4_3216 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:A0A159ZYE0
         (418 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3216
          Length = 418

 Score =  764 bits (1973), Expect = 0.0
 Identities = 384/418 (91%), Positives = 403/418 (96%)

Query: 1   MTRHLKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLF 60
           MTR+LK ALFSALLVWAVAYPVLGLKLTIVGINLEVHGTS A L TIAVCS+LMFLRVLF
Sbjct: 1   MTRNLKQALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSTATLITIAVCSVLMFLRVLF 60

Query: 61  STQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLI 120
             QIS+ WK+SP LPV+PAKA+NFLTLPTTQRWI++ALI+GALVWPFFGSRGAVDIATL+
Sbjct: 61  DQQISSAWKASPNLPVMPAKATNFLTLPTTQRWIIIALIIGALVWPFFGSRGAVDIATLV 120

Query: 121 LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATF 180
           LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHY+GLSFWICLPIAGMMAATF
Sbjct: 121 LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYYGLSFWICLPIAGMMAATF 180

Query: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERK 240
           GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTD+TGGPNGISNI KPT FGL+F+R 
Sbjct: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDLTGGPNGISNIPKPTLFGLSFDRT 240

Query: 241 AAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEI 300
           AAEGLQTFHEYFGLEYNSINKVIFLYL+A+LL+L ALFVINRLLRMP+GRAWEALREDEI
Sbjct: 241 AAEGLQTFHEYFGLEYNSINKVIFLYLIAVLLSLFALFVINRLLRMPLGRAWEALREDEI 300

Query: 301 ACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM 360
           ACRALGLNPTVIKLSAFTLGA FAGFAGSFFAARQGLVTPESFTFIESA ILAIVVLGGM
Sbjct: 301 ACRALGLNPTVIKLSAFTLGACFAGFAGSFFAARQGLVTPESFTFIESATILAIVVLGGM 360

Query: 361 GSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK 418
           GSQLGV+LAA VMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK
Sbjct: 361 GSQLGVVLAATVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK 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: 752
Number of extensions: 27
Number of successful extensions: 2
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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Protein sequences (fasta format)
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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:

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