GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglF in Dinoroseobacter shibae DFL-12

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate 3608247 Dshi_1651 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= uniprot:A8LLL5
         (334 letters)



>lcl|FitnessBrowser__Dino:3608247 Dshi_1651
           binding-protein-dependent transport systems inner
           membrane component (RefSeq)
          Length = 334

 Score =  673 bits (1737), Expect = 0.0
 Identities = 334/334 (100%), Positives = 334/334 (100%)

Query: 1   MHPAFQGLITIIIGVGGCVGYFYFANQFLDKVLYPAKGPKAGRNINRANQIRPWIFLFPA 60
           MHPAFQGLITIIIGVGGCVGYFYFANQFLDKVLYPAKGPKAGRNINRANQIRPWIFLFPA
Sbjct: 1   MHPAFQGLITIIIGVGGCVGYFYFANQFLDKVLYPAKGPKAGRNINRANQIRPWIFLFPA 60

Query: 61  LFVLLLYLGYPVVETLRLSLLERVPGGGYQWVGLDNYAQMASEPKFWEAMRNNMFWLIVV 120
           LFVLLLYLGYPVVETLRLSLLERVPGGGYQWVGLDNYAQMASEPKFWEAMRNNMFWLIVV
Sbjct: 61  LFVLLLYLGYPVVETLRLSLLERVPGGGYQWVGLDNYAQMASEPKFWEAMRNNMFWLIVV 120

Query: 121 PALSTAFGLLAAQLTDRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDGRPIEQEQIGIL 180
           PALSTAFGLLAAQLTDRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDGRPIEQEQIGIL
Sbjct: 121 PALSTAFGLLAAQLTDRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDGRPIEQEQIGIL 180

Query: 181 NAIIVGLGGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRGIPEETIEAAIIDG 240
           NAIIVGLGGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRGIPEETIEAAIIDG
Sbjct: 181 NAIIVGLGGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRGIPEETIEAAIIDG 240

Query: 241 ASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWETQVLANYMFDKLFR 300
           ASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWETQVLANYMFDKLFR
Sbjct: 241 ASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWETQVLANYMFDKLFR 300

Query: 301 ANDWGVGSASAMVIMLLVTPILIWNIHSARKEMR 334
           ANDWGVGSASAMVIMLLVTPILIWNIHSARKEMR
Sbjct: 301 ANDWGVGSASAMVIMLLVTPILIWNIHSARKEMR 334


Lambda     K      H
   0.329    0.143    0.455 

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: 518
Number of extensions: 17
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: 334
Length of database: 334
Length adjustment: 28
Effective length of query: 306
Effective length of database: 306
Effective search space:    93636
Effective search space used:    93636
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 (21.8 bits)
S2: 49 (23.5 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 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