GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctQ in Arenimonas metalli CF5-1

Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), small permease component (characterized)
to candidate WP_034212613.1 N787_RS08370 TRAP transporter small permease subunit

Query= reanno::PV4:5208944
         (212 letters)



>NCBI__GCF_000747155.1:WP_034212613.1
          Length = 173

 Score = 57.8 bits (138), Expect = 1e-13
 Identities = 47/160 (29%), Positives = 71/160 (44%), Gaps = 18/160 (11%)

Query: 17  LITAMTLLVFVEVIARFFFNTGFLWIQELTLTICGWFVLFGMSYGVKVGAHIGVDAFVKK 76
           L   +  LVF  V+AR+ FN G +  QE  L +     L G+ Y ++   H+ VD F ++
Sbjct: 27  LAAVLVALVFGLVLARYAFNAGSVAAQEAVLWLHASLFLLGLGYTLRHDGHVRVDVFSQR 86

Query: 77  LPAQGR-KYTAILAVAICLIYCGMFLVGSWDYLAKMYQIGVPMEDIDLPHFLIGGLDGDF 135
             A+ R + T    +A+ L +C   L  SWDY+A  +       D        GGL G  
Sbjct: 87  WSARTRARVTFAATLALLLPFCVFMLAMSWDYVAASWSAREGSRD-------PGGLPG-- 137

Query: 136 AWEYLRIDVEEPAVPLWTSQSILLIGFILLTWRFLQLALA 175
            W  L+         L  S ++L +  + L  R L +A A
Sbjct: 138 -WYLLK-------ALLPVSAALLFLQGVALALRSLSVAFA 169


Lambda     K      H
   0.329    0.144    0.453 

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: 87
Number of extensions: 8
Number of successful extensions: 2
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: 212
Length of database: 173
Length adjustment: 20
Effective length of query: 192
Effective length of database: 153
Effective search space:    29376
Effective search space used:    29376
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: 44 (21.6 bits)

This GapMind analysis is from Sep 24 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