GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Dethiosulfovibrio salsuginis USBA 82

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_085544746.1 B9Y55_RS07490 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_900177735.1:WP_085544746.1
          Length = 253

 Score =  122 bits (305), Expect = 1e-32
 Identities = 81/238 (34%), Positives = 126/238 (52%), Gaps = 19/238 (7%)

Query: 24  LSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFNGDSI- 82
           L KSFG L  +    + V EG +  +IGP+G+GK+TL   + +    DQGE+   G  I 
Sbjct: 10  LHKSFGKLNVLKGVSLDVAEGEVVSVIGPSGSGKSTLARCICHLEDIDQGEIYLYGKRID 69

Query: 83  -GQLA-PHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQKEE 140
            G L+   Q  L G +  FQ   +   L+VLEN+ L+             I  R +  E 
Sbjct: 70  KGNLSWKEQSQLVGMI--FQQFNLFPHLSVLENITLSP------------IKVRGISGE- 114

Query: 141 RANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVNPT 200
           +AN E+A+ +L  VGL  K       LSGGQ++ + +ARAL   P++++ DEP + ++P 
Sbjct: 115 KAN-EEALELLSKVGLVDKKDSRPSELSGGQQQRVAIARALAMEPRIMVFDEPTSALDPE 173

Query: 201 LIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDPR 258
           L+G++ E I +  + G+T ++I H M     +   V  +A+G  +  GTPE+I   PR
Sbjct: 174 LVGEVLEVIADLAKSGMTMVIITHEMSFAKDVSDRVIFMADGVIVEQGTPEEILGKPR 231


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: 171
Number of extensions: 6
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: 253
Length adjustment: 24
Effective length of query: 243
Effective length of database: 229
Effective search space:    55647
Effective search space used:    55647
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