GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF3593
          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 (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:

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