GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livF in Pseudomonas simiae WCS417

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate GFF1298 PS417_06595 ABC transporter ATP-binding protein

Query= uniprot:A0A159ZWL6
         (233 letters)



>lcl|FitnessBrowser__WCS417:GFF1298 PS417_06595 ABC transporter
           ATP-binding protein
          Length = 233

 Score =  444 bits (1142), Expect = e-130
 Identities = 228/233 (97%), Positives = 230/233 (98%)

Query: 1   MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60
           MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY
Sbjct: 1   MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60

Query: 61  MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQMDKVLHLF 120
           MGEELVGQ SS IMRKSIAVVPEGRRVF+RLTVEENLAMGGFFTDKGDYQEQMDKVLHLF
Sbjct: 61  MGEELVGQQSSQIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKGDYQEQMDKVLHLF 120

Query: 121 PRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR 180
           PRLKERF+QRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR
Sbjct: 121 PRLKERFSQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR 180

Query: 181 KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLGG 233
           KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGE LLTDPKVREAYLGG
Sbjct: 181 KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEQLLTDPKVREAYLGG 233


Lambda     K      H
   0.320    0.137    0.381 

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: 299
Number of extensions: 9
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: 233
Length of database: 233
Length adjustment: 23
Effective length of query: 210
Effective length of database: 210
Effective search space:    44100
Effective search space used:    44100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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 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