GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Pseudomonas fluorescens FW300-N1B4

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate Pf1N1B4_1643 Amino acid ABC transporter, permease protein

Query= uniprot:Q31RP0
         (377 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1643
          Length = 229

 Score = 79.7 bits (195), Expect = 7e-20
 Identities = 43/123 (34%), Positives = 76/123 (61%), Gaps = 4/123 (3%)

Query: 252 LVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYV 311
           +  +T A+I EI+RG I ++P G+ EAA ALG++R++ L+ I++P+A R+ +P+ +++ +
Sbjct: 102 MTLHTAAYIAEILRGAIQAIPPGEIEAARALGMSRTKALFYIMLPRAARIGLPAYSNEVI 161

Query: 312 GFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGMNGLQQRL 371
              K S+LA  V   +L   A+T + +T  PVE+F    + YL +  V+  G     + L
Sbjct: 162 LMLKASALASTVTLLELTGMARTIIARTYLPVEIFFAAGMFYLLMAYVLVRGF----KLL 217

Query: 372 QRW 374
           +RW
Sbjct: 218 ERW 220


Lambda     K      H
   0.326    0.140    0.445 

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: 227
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 377
Length of database: 229
Length adjustment: 26
Effective length of query: 351
Effective length of database: 203
Effective search space:    71253
Effective search space used:    71253
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 (21.7 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