GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Nocardioides daejeonensis MJ31

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_110208105.1 DNK54_RS16590 ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_003194585.1:WP_110208105.1
          Length = 263

 Score =  159 bits (403), Expect = 4e-44
 Identities = 91/240 (37%), Positives = 138/240 (57%), Gaps = 12/240 (5%)

Query: 28  FGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFNGDSIGQLAP 87
           FGG+ AV+ A     E  ITGLIGPNGAGKTT FN+++   RP  G V F G  + + A 
Sbjct: 13  FGGVTAVNQARFTADERRITGLIGPNGAGKTTCFNVITGLQRPTSGSVRFGGRDVTRTAV 72

Query: 88  HQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQKEERANREKA 147
           H+ A RG  RTFQ  +    LTV +N+ +A     G         F  + +   A  ++A
Sbjct: 73  HRRARRGMARTFQRLEAFGSLTVRDNVRVALDIAGG---------FGGLMRSSSARVDEA 123

Query: 148 MAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVNPTLIGQICE 207
              L+ VG+   A + A ++  G  +LLE+AR L+ +PKL+LLDEP++G++ +      E
Sbjct: 124 ---LDRVGISEYAAERADSIPTGTARLLELARCLVGDPKLLLLDEPSSGLDESETDAFGE 180

Query: 208 HIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDPRVLEAYLGDS 267
            ++    +G   L++EH+MD++MT+C  + VL  G  +  G+P ++++D RV  AYLG S
Sbjct: 181 LLIALASEGKAILMVEHDMDLVMTVCDDIHVLDFGEIICSGSPAEVRADARVQAAYLGAS 240


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: 162
Number of extensions: 3
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: 263
Length adjustment: 25
Effective length of query: 242
Effective length of database: 238
Effective search space:    57596
Effective search space used:    57596
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: 47 (22.7 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