GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DVU3032 in Magnetospirillum magneticum AMB-1

Align LUD_dom domain-containing protein (characterized, see rationale)
to candidate WP_011386480.1 AMB_RS20895 lactate utilization protein

Query= uniprot:Q726S4
         (209 letters)



>NCBI__GCF_000009985.1:WP_011386480.1
          Length = 216

 Score = 72.0 bits (175), Expect = 8e-18
 Identities = 41/103 (39%), Positives = 61/103 (59%), Gaps = 2/103 (1%)

Query: 105 LAGIDIGFTHVTMGIAETGTCVVSSNSEELRLASMISEFHVAVLPKSKIVATSYDAEATL 164
           +A  D   T    GIA+TG+ V+   S+E RL S++   HVA++ +S +  T   AE   
Sbjct: 113 VAKADAALTTARGGIAQTGSLVLWPTSDEPRLMSLLPPIHVALVEESSL--TDSLAETIR 170

Query: 165 NELMGTGKPHYTAFISGPSRTADIERVLSLGVHGPLELHLILV 207
            +   +G P     +SGPS+TADIE+ L+ GVHGP EL ++L+
Sbjct: 171 VQGWASGMPTNAVLVSGPSKTADIEQTLAYGVHGPKELIVLLI 213


Lambda     K      H
   0.317    0.132    0.371 

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: 95
Number of extensions: 3
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: 209
Length of database: 216
Length adjustment: 21
Effective length of query: 188
Effective length of database: 195
Effective search space:    36660
Effective search space used:    36660
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: 41 (21.7 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Sep 17 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