GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16935 in Paraburkholderia bryophila 376MFSha3.1

Align L-arabinose-binding periplasmic protein; Short=ABP; Flags: Precursor (characterized, see rationale)
to candidate H281DRAFT_06297 H281DRAFT_06297 L-arabinose-binding protein

Query= uniprot:B2SYR6
         (332 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06297 H281DRAFT_06297
           L-arabinose-binding protein
          Length = 332

 Score =  643 bits (1659), Expect = 0.0
 Identities = 317/331 (95%), Positives = 328/331 (99%)

Query: 1   MKRRIFLTLAAAATGVLFNAPVAQAADPVKIGFLVKQPEEPWFQDEWKFAEIAAKEKGFT 60
           MKRRIFLTLAAAA GV+FNAPVAQAADPVKIGFLVKQPEEPWFQDEWKFAEIAAKEKGFT
Sbjct: 1   MKRRIFLTLAAAAAGVVFNAPVAQAADPVKIGFLVKQPEEPWFQDEWKFAEIAAKEKGFT 60

Query: 61  LVKIGAPSGEKVMSAIDNLSAQKAQGFVICTPDVKLGPGIVAKAKADGLKMMTVDDRLVD 120
           LVKIGAPSGEKVMSAIDNLSAQKAQGFVICTPDVKLGPGIVAKAKADGLKMMTVDDRLVD
Sbjct: 61  LVKIGAPSGEKVMSAIDNLSAQKAQGFVICTPDVKLGPGIVAKAKADGLKMMTVDDRLVD 120

Query: 121 GAGKPIASVPHMGISAYNIGKQVGDGLAAEIKKRGWDMKDVGAIDVTYEQLPTAHDRTSG 180
           GAGKPIASVPHMGISAYNIGKQVGDGLAAEIKKRGWDMKDVGAIDVTYEQLPTAHDRTSG
Sbjct: 121 GAGKPIASVPHMGISAYNIGKQVGDGLAAEIKKRGWDMKDVGAIDVTYEQLPTAHDRTSG 180

Query: 181 ATDALIAAGFPKANIVMAPQAKTDTENAFNAANIALTKNPQFKHWVAYALNDEGVLGAVR 240
           ATDAL+AAGFPKAN++ APQAKTDTENAFNAANIALTKNPQFKHWVAYALNDEGVLGAVR
Sbjct: 181 ATDALLAAGFPKANVIAAPQAKTDTENAFNAANIALTKNPQFKHWVAYALNDEGVLGAVR 240

Query: 241 AAEGRGFKADNMIGIGIGGSDSALNEFKKPSPTGFYGTVIISPKRHGEETSTLMYDWITQ 300
           AAEGRGFKADNMIGIGIGGSDSALNEFKKP+PTGF+GTVIISPKRHGEET+TLMYDWITQ
Sbjct: 241 AAEGRGFKADNMIGIGIGGSDSALNEFKKPNPTGFFGTVIISPKRHGEETATLMYDWITQ 300

Query: 301 GKAPPPLTLTTGMLATRDNVADVRQKMGLAA 331
           GKAPPPLTLTTGMLATR+NV +VR+KMGLA+
Sbjct: 301 GKAPPPLTLTTGMLATRENVGEVREKMGLAS 331


Lambda     K      H
   0.316    0.133    0.391 

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: 573
Number of extensions: 8
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: 332
Length of database: 332
Length adjustment: 28
Effective length of query: 304
Effective length of database: 304
Effective search space:    92416
Effective search space used:    92416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 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