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_078716394.1 B5D49_RS04215 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_900167125.1:WP_078716394.1
          Length = 251

 Score =  207 bits (527), Expect = 2e-58
 Identities = 122/258 (47%), Positives = 163/258 (63%), Gaps = 10/258 (3%)

Query: 12  LTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLR 71
           L ++ +++ FGG+ A++ VSF    GEI  +IGPNGAGKTT+FN ITG Y P+ GR++  
Sbjct: 4   LKLDDVSIHFGGVQALSKVSFELGGGEILGLIGPNGAGKTTIFNVITGVYRPSSGRVSY- 62

Query: 72  HADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAG 131
             DG+  LL + P   +  KA +ARTFQNIRLF  M+ +EN +VAQH    R +G  +  
Sbjct: 63  --DGRS-LLGKRPHQIL--KAGIARTFQNIRLFTAMTAVENCMVAQH---CRTAGSVLGA 114

Query: 132 LLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLC 191
           +   P+  R E    + A   L  + + + AD  A NLPYG QR LEIARA+ + P  + 
Sbjct: 115 VFRTPAQRREESRTHERAMEALRFMGMEDKADEAARNLPYGRQRHLEIARALASHPQTIL 174

Query: 192 LDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDG 251
           LDEPAAGLNP ES EL  ++  I  +  I VLL+EHDM VVM +   VVV+DYG+ I+ G
Sbjct: 175 LDEPAAGLNPVESAELMRVIERIAAQ-GINVLLVEHDMKVVMGVCHRVVVMDYGQLIAKG 233

Query: 252 DPAFVKNDPAVIRAYLGE 269
            P  V+ DP VI AYLG+
Sbjct: 234 RPEEVQRDPKVIEAYLGQ 251


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: 179
Number of extensions: 9
Number of successful extensions: 4
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: 251
Length adjustment: 25
Effective length of query: 269
Effective length of database: 226
Effective search space:    60794
Effective search space used:    60794
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