GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Paucidesulfovibrio gracilis DSM 16080

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_078715619.1 B5D49_RS00080 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_900167125.1:WP_078715619.1
          Length = 263

 Score =  238 bits (606), Expect = 1e-67
 Identities = 132/266 (49%), Positives = 175/266 (65%), Gaps = 8/266 (3%)

Query: 10  PLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRL- 68
           P L V  L M FGGL A+N V      GEI A+IGPNGAGKTT FNCITG Y PT G + 
Sbjct: 4   PALDVRGLCMDFGGLRALNKVDLEVRQGEIAALIGPNGAGKTTFFNCITGIYAPTEGDIH 63

Query: 69  TLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFS 128
            L   + +  +  R P +    +  +ARTFQNIRLF  M+VLEN+++ +H +    +  S
Sbjct: 64  VLPDGENRVRINGRKPNH--VTELGMARTFQNIRLFPSMTVLENVMIGRHCR----NRSS 117

Query: 129 IAGLLGLPSYTRTEREAVDLAKY-WLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEP 187
           I G +    +TR + + V    Y  L+ V L  +A+  A NLPYGAQRRLEIARAM TEP
Sbjct: 118 ILGAVLRDGHTRRQEDEVISRSYEMLELVGLERWANELATNLPYGAQRRLEIARAMATEP 177

Query: 188 VMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRK 247
            +L LDEPAAG+NP+E+  L DL+ +IR+ + I VLLIEHDM +VM++SD + V+DYG++
Sbjct: 178 FLLLLDEPAAGMNPQETRRLKDLIDHIRETYHIAVLLIEHDMKMVMSVSDRIYVMDYGQR 237

Query: 248 ISDGDPAFVKNDPAVIRAYLGEEEDE 273
           I+ G P  V  +P VI+AYLGE+ D+
Sbjct: 238 IAAGSPEEVSKNPEVIKAYLGEDADD 263


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: 222
Number of extensions: 7
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: 294
Length of database: 263
Length adjustment: 25
Effective length of query: 269
Effective length of database: 238
Effective search space:    64022
Effective search space used:    64022
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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