GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Azohydromonas australica DSM 1124

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_043458116.1 H537_RS0103160 ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_000430725.1:WP_043458116.1
          Length = 331

 Score =  206 bits (524), Expect = 8e-58
 Identities = 112/241 (46%), Positives = 155/241 (64%), Gaps = 5/241 (2%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           +A L L  ++K Y    G    AV+ I L +  G +  L+GPSGCGK+TTLRM+AG E  
Sbjct: 5   LAHLELVALSKRY----GPGTPAVDAIDLQVRAGSYCCLLGPSGCGKTTTLRMIAGHEVA 60

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           TEG++ L  R +  + A  R  AM+FQSYAL+PH +   N++FGL+   G+     R R 
Sbjct: 61  TEGDILLGARNITDLDATQRGTAMMFQSYALFPHLNALDNVAFGLK-MRGVDAATRRARA 119

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
            E  D++ +     RKPG+LSGGQQQRVAL RA++ +P+V L+DEPLS LD  LR +MR 
Sbjct: 120 AELLDLVAMGAYAQRKPGELSGGQQQRVALARALITNPKVLLLDEPLSALDPFLRVKMRA 179

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           EL+R Q +LG + V+VTH Q EAM + D+V V++ G ++Q GTP   ++ P   FVA F+
Sbjct: 180 ELKRWQKDLGFSFVHVTHSQEEAMALADQVVVMNAGRIEQQGTPHQIFNAPRTEFVARFM 239

Query: 241 G 241
           G
Sbjct: 240 G 240


Lambda     K      H
   0.316    0.136    0.384 

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: 295
Number of extensions: 10
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: 383
Length of database: 331
Length adjustment: 29
Effective length of query: 354
Effective length of database: 302
Effective search space:   106908
Effective search space used:   106908
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 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