GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Planococcus halocryophilus Or1

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_008497300.1 B481_RS06650 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_000342445.1:WP_008497300.1
          Length = 310

 Score =  117 bits (293), Expect = 3e-31
 Identities = 72/238 (30%), Positives = 122/238 (51%), Gaps = 18/238 (7%)

Query: 18  LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77
           +L  + L+K F    AVD   I + +G   GL+GPNGAGK+T  +++S  I+P  G+V  
Sbjct: 1   MLKTEKLTKKFKDTLAVDEVTIELGQGESVGLLGPNGAGKSTAISMISTLIQPTSGDVRL 60

Query: 78  NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137
           NG S+ +       + G V   Q   +   L+  EN+          KF  R+      +
Sbjct: 61  NGKSVLKKPGEMRKVLGVVP--QKIALYEELSAYENL----------KFFGRIYGLSGKK 108

Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197
            EER        +LE VGL  + ++     SGG ++ + +A A++  P+++++DEP  G+
Sbjct: 109 LEER-----IQIVLELVGLSDRQKELVKKYSGGMQRRVNLAAAMLHEPEVLIMDEPTVGI 163

Query: 198 NPTLIGQICEHIVNWNR-QGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQ 254
           +P     + E I   NR QG+T L   H M+ +  LC  V+++  G+ +A GT ++++
Sbjct: 164 DPQSRNHLLETIRKLNREQGMTVLYTSHYMEEVEKLCDRVYIMDHGKVIAAGTKDELK 221


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: 179
Number of extensions: 9
Number of successful extensions: 3
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: 310
Length adjustment: 26
Effective length of query: 241
Effective length of database: 284
Effective search space:    68444
Effective search space used:    68444
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.

Links

Downloads

Related tools

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