Aligments for a candidate for actP in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Aligments for a candidate for actP in Pseudomonas fluorescens FW300-N1B4

Align Cation acetate symporter (characterized, see rationale)
to candidate Pf1N1B4_3673 Acetate permease ActP (cation/acetate symporter)

Query= uniprot:A0A166PH03
         (552 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3673
          Length = 552

 Score = 1068 bits (2761), Expect = 0.0
 Identities = 552/552 (100%), Positives = 552/552 (100%)

Query: 1   MIRRLMALLSIAAFAPGVWAAEALTGAVQKQPLNVSAILMFVAFVGATLCITYWASKRNN 60
           MIRRLMALLSIAAFAPGVWAAEALTGAVQKQPLNVSAILMFVAFVGATLCITYWASKRNN
Sbjct: 1   MIRRLMALLSIAAFAPGVWAAEALTGAVQKQPLNVSAILMFVAFVGATLCITYWASKRNN 60

Query: 61  SAADYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPIIL 120
           SAADYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPIIL
Sbjct: 61  SAADYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPIIL 120

Query: 121 FLIAERLRNLGKYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFG 180
           FLIAERLRNLGKYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFG
Sbjct: 121 FLIAERLRNLGKYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFG 180

Query: 181 LDYHVAVILVGILMCMYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALF 240
           LDYHVAVILVGILMCMYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALF
Sbjct: 181 LDYHVAVILVGILMCMYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALF 240

Query: 241 SEAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSV 300
           SEAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSV
Sbjct: 241 SEAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSV 300

Query: 301 LYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALMGGNNMAAVHLANAVGGSVFLG 360
           LYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALMGGNNMAAVHLANAVGGSVFLG
Sbjct: 301 LYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALMGGNNMAAVHLANAVGGSVFLG 360

Query: 361 FISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANEKDEIRVSKITTIALAVLAI 420
           FISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANEKDEIRVSKITTIALAVLAI
Sbjct: 361 FISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANEKDEIRVSKITTIALAVLAI 420

Query: 421 GLGILFEKQNIAFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMVGGWLGLVSAVGLMV 480
           GLGILFEKQNIAFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMVGGWLGLVSAVGLMV
Sbjct: 421 GLGILFEKQNIAFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMVGGWLGLVSAVGLMV 480

Query: 481 LGPTIWVQILGHEKAIFPYEYPALFSMAIAFVGIWFFSVTDKSAEGVNERALFFPQFVRS 540
           LGPTIWVQILGHEKAIFPYEYPALFSMAIAFVGIWFFSVTDKSAEGVNERALFFPQFVRS
Sbjct: 481 LGPTIWVQILGHEKAIFPYEYPALFSMAIAFVGIWFFSVTDKSAEGVNERALFFPQFVRS 540

Query: 541 QTGLGASGAVSH 552
           QTGLGASGAVSH
Sbjct: 541 QTGLGASGAVSH 552


Lambda     K      H
   0.327    0.140    0.415 

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: 1215
Number of extensions: 53
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: 552
Length of database: 552
Length adjustment: 36
Effective length of query: 516
Effective length of database: 516
Effective search space:   266256
Effective search space used:   266256
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 (21.7 bits)
S2: 53 (25.0 bits)

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

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

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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