Alignments for a candidate for actP in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Pseudomonas putida KT2440

Align Cation acetate symporter (characterized, see rationale)
to candidate PP_1743 PP_1743 acetate permease

Query= uniprot:A0A166PH03
         (552 letters)



>FitnessBrowser__Putida:PP_1743
          Length = 554

 Score =  985 bits (2547), Expect = 0.0
 Identities = 510/554 (92%), Positives = 527/554 (95%), Gaps = 2/554 (0%)

Query: 1   MIRRLMAL--LSIAAFAPGVWAAEALTGAVQKQPLNVSAILMFVAFVGATLCITYWASKR 58
           MIR++ AL  L+  AFAP VWAA+ALTG VQKQPLNVSAI MFVAFV  TL ITYWASKR
Sbjct: 1   MIRQVKALAVLACGAFAPAVWAADALTGEVQKQPLNVSAIAMFVAFVAFTLGITYWASKR 60

Query: 59  NNSAADYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPI 118
           N SA+DYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPI
Sbjct: 61  NKSASDYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPI 120

Query: 119 ILFLIAERLRNLGKYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLL 178
           ILFLIAERLRNLGKYTFADVASYRLGQ +IR+LSA GSLVVVAFYLIAQMVGAGKLI+LL
Sbjct: 121 ILFLIAERLRNLGKYTFADVASYRLGQKEIRTLSASGSLVVVAFYLIAQMVGAGKLIELL 180

Query: 179 FGLDYHVAVILVGILMCMYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNA 238
           FGLDYHVAVILVGILMC+YVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHV FDFN 
Sbjct: 181 FGLDYHVAVILVGILMCLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVGFDFNT 240

Query: 239 LFSEAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARK 298
           LFSEAIKVH KGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARK
Sbjct: 241 LFSEAIKVHAKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARK 300

Query: 299 SVLYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALMGGNNMAAVHLANAVGGSVF 358
           SVLYATGFIGYFYILTFIIGFGAILLVSTNP FKDAAGAL+GGNNMAAVHLANAVGGSVF
Sbjct: 301 SVLYATGFIGYFYILTFIIGFGAILLVSTNPEFKDAAGALLGGNNMAAVHLANAVGGSVF 360

Query: 359 LGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANEKDEIRVSKITTIALAVL 418
           LGFISAVAFATILAVVAGLTLAGASAVSHDLYASV +KGKAN+KDEIRVSKITT+AL VL
Sbjct: 361 LGFISAVAFATILAVVAGLTLAGASAVSHDLYASVWRKGKANDKDEIRVSKITTVALGVL 420

Query: 419 AIGLGILFEKQNIAFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMVGGWLGLVSAVGL 478
           AIGLGILFEKQNIAFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAM+GGWLGLVSAV L
Sbjct: 421 AIGLGILFEKQNIAFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMIGGWLGLVSAVTL 480

Query: 479 MVLGPTIWVQILGHEKAIFPYEYPALFSMAIAFVGIWFFSVTDKSAEGVNERALFFPQFV 538
           M+LGPTIWVQILGHEK I+PYEYPALFSMAIAFV IWFFSVTDKS    +ERALFFPQFV
Sbjct: 481 MILGPTIWVQILGHEKPIYPYEYPALFSMAIAFVSIWFFSVTDKSKAAEDERALFFPQFV 540

Query: 539 RSQTGLGASGAVSH 552
           RSQTGLGASGAVSH
Sbjct: 541 RSQTGLGASGAVSH 554


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: 1162
Number of extensions: 50
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: 554
Length adjustment: 36
Effective length of query: 516
Effective length of database: 518
Effective search space:   267288
Effective search space used:   267288
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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
the source code
instructions for running GapMind on your computer

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