GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Actinomyces timonensis 7400942

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_017177032.1 A1QA_RS0100780 ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_000295095.1:WP_017177032.1
          Length = 328

 Score = 83.6 bits (205), Expect = 5e-21
 Identities = 73/246 (29%), Positives = 107/246 (43%), Gaps = 27/246 (10%)

Query: 13  SPESSLLLA---QGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIR 69
           SP+ SL  A    GL K+FG +RAVD  D+ V  G I   +GPNGAGK+T  +++  F  
Sbjct: 14  SPDPSLAPAVEVAGLVKTFGPVRAVDGIDLRVAPGEIVAFLGPNGAGKSTALDVILGFST 73

Query: 70  PDQGEVLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPR 129
           PD G     G     LAP Q A     R  +   +L      E  LL D   T  + +  
Sbjct: 74  PDAGSARVFG-----LAPAQAA-----RELRTGAILQ-----EGGLLPD--YTVRQTITA 116

Query: 130 LINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLIL 189
           +          R  R    A+ E  G+           SGG+R+ L +A AL+ NP L++
Sbjct: 117 VAAM-------RGARHDIPAVEELAGISPILGRKVVKCSGGERQRLRLALALLGNPDLMV 169

Query: 190 LDEPAAGVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGT 249
           LDEP AG++ T        I          L   H +         + ++  GR +A G+
Sbjct: 170 LDEPTAGMDVTARRSFWAAIRERAAGNKAVLFATHYLQEAADFADRIVIINRGRIIASGS 229

Query: 250 PEQIQS 255
            + +++
Sbjct: 230 VDDVRA 235


Lambda     K      H
   0.319    0.136    0.389 

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: 186
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: 267
Length of database: 328
Length adjustment: 26
Effective length of query: 241
Effective length of database: 302
Effective search space:    72782
Effective search space used:    72782
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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