GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Maridesulfovibrio zosterae DSM 11974

Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_027723082.1 H589_RS0116710 3-oxoacyl-ACP reductase FabG

Query= uniprot:A0A4P7ABK7
         (254 letters)



>NCBI__GCF_000425265.1:WP_027723082.1
          Length = 240

 Score = 97.8 bits (242), Expect = 2e-25
 Identities = 72/250 (28%), Positives = 121/250 (48%), Gaps = 24/250 (9%)

Query: 11  KTVLITAAAQGIGRASTELFAREGARVI----ATDISKTHLEELASIAGVETHLL--DVT 64
           K  LIT A++GIG A     A +G  +     + D       E     G +  LL  DVT
Sbjct: 3   KIALITGASKGIGAAIAVQLAEDGYDIWLNYRSDDAGAHKTAEQIKQHGQQCTLLKFDVT 62

Query: 65  DDDAIKALVAKVGTVDVLF---NCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVL 121
           D+ A++  ++ +    V +   N AG+     ++  D   W+    ++    F+  + V+
Sbjct: 63  DEKAVEENLSSLLEKKVPYIVVNNAGFTRDSIMMMMDSSDWNKVLQVHLTGFFNVTKPVV 122

Query: 122 PGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICP 181
             ML K+ G I+NIAS +    GVA +  Y A+KA ++G TKS+A +   + I  NA+ P
Sbjct: 123 SRMLRKRTGRIINIASTSGET-GVAGQTNYCAAKAGLIGATKSLAMEVAKRNILVNAVTP 181

Query: 182 GTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFT 241
           G I++  L++    + K T               P+ R+G  +EVA +  +L SD++++ 
Sbjct: 182 GFIDTDMLSELPVDEIKNT--------------IPLKRLGTPKEVAGVVSFLCSDKASYI 227

Query: 242 TGSIHMIDGG 251
           TG    ++GG
Sbjct: 228 TGQTIAVNGG 237


Lambda     K      H
   0.316    0.129    0.359 

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: 117
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: 254
Length of database: 240
Length adjustment: 24
Effective length of query: 230
Effective length of database: 216
Effective search space:    49680
Effective search space used:    49680
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: 46 (22.3 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