GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Planococcus halocryophilus Or1

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_008497300.1 B481_RS06650 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_000342445.1:WP_008497300.1
          Length = 310

 Score = 93.6 bits (231), Expect = 5e-24
 Identities = 80/273 (29%), Positives = 123/273 (45%), Gaps = 39/273 (14%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           +L  E LT +F   +AV++V+     GE   ++GPNGAGK+T  + I+    PT G + L
Sbjct: 1   MLKTEKLTKKFKDTLAVDEVTIELGQGESVGLLGPNGAGKSTAISMISTLIQPTSGDVRL 60

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
              +GK  L  + PG     +  +    Q I L+  +S  ENL                 
Sbjct: 61  ---NGKSVL--KKPG---EMRKVLGVVPQKIALYEELSAYENLKF-------------FG 99

Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190
            + GL      ER  + L    L   R  E     +G    G QRR+ +A AM  EP +L
Sbjct: 100 RIYGLSGKKLEERIQIVLELVGLSD-RQKELVKKYSG----GMQRRVNLAAAMLHEPEVL 154

Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250
            +DEP  G++P+    L + +  +  E  + VL   H M  V  + D V ++D+G+ I+ 
Sbjct: 155 IMDEPTVGIDPQSRNHLLETIRKLNREQGMTVLYTSHYMEEVEKLCDRVYIMDHGKVIAA 214

Query: 251 GDPAFVKNDPAVIRAYLGEEE------DEELPP 277
           G     K++   ++  L EEE      D+  PP
Sbjct: 215 G----TKDE---LKGVLSEEETVLIEFDQNYPP 240


Lambda     K      H
   0.319    0.137    0.397 

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: 181
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 294
Length of database: 310
Length adjustment: 27
Effective length of query: 267
Effective length of database: 283
Effective search space:    75561
Effective search space used:    75561
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 (21.8 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