GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rbsC in Pseudomonas simiae WCS417

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family (characterized, see rationale)
to candidate GFF3593 PS417_18395 ABC transporter permease

Query= uniprot:A0A1N7UNQ5
         (325 letters)



>lcl|FitnessBrowser__WCS417:GFF3593 PS417_18395 ABC transporter
           permease
          Length = 325

 Score =  615 bits (1587), Expect = 0.0
 Identities = 325/325 (100%), Positives = 325/325 (100%)

Query: 1   MKTTTSPGKTGGNFYGLGTYLGLAGALLAMIALFSVLSDHFLSYDTFSTLANQIPDLMVL 60
           MKTTTSPGKTGGNFYGLGTYLGLAGALLAMIALFSVLSDHFLSYDTFSTLANQIPDLMVL
Sbjct: 1   MKTTTSPGKTGGNFYGLGTYLGLAGALLAMIALFSVLSDHFLSYDTFSTLANQIPDLMVL 60

Query: 61  AVGMTFILIIGGIDLSVGSVLALAASAVSVAILGWGWSVLPAAVLGMGCAALAGTITGSI 120
           AVGMTFILIIGGIDLSVGSVLALAASAVSVAILGWGWSVLPAAVLGMGCAALAGTITGSI
Sbjct: 61  AVGMTFILIIGGIDLSVGSVLALAASAVSVAILGWGWSVLPAAVLGMGCAALAGTITGSI 120

Query: 121 TVAWRIPSFIVSLGVLEMARGVAYQMTGSRTAYIGDSFAWLSNPIAFGISPSFIIALLVI 180
           TVAWRIPSFIVSLGVLEMARGVAYQMTGSRTAYIGDSFAWLSNPIAFGISPSFIIALLVI
Sbjct: 121 TVAWRIPSFIVSLGVLEMARGVAYQMTGSRTAYIGDSFAWLSNPIAFGISPSFIIALLVI 180

Query: 181 IAAQLVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISRLE 240
           IAAQLVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISRLE
Sbjct: 181 IAAQLVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISRLE 240

Query: 241 AADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKR 300
           AADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKR
Sbjct: 241 AADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKR 300

Query: 301 IITGAVIVIAVVLDTYRSQRASRRG 325
           IITGAVIVIAVVLDTYRSQRASRRG
Sbjct: 301 IITGAVIVIAVVLDTYRSQRASRRG 325


Lambda     K      H
   0.324    0.139    0.399 

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: 501
Number of extensions: 11
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: 325
Length of database: 325
Length adjustment: 28
Effective length of query: 297
Effective length of database: 297
Effective search space:    88209
Effective search space used:    88209
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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