GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Geobacter daltonii FRC-32

Align 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate WP_012645274.1 GEOB_RS00845 thiolase family protein

Query= SwissProt::P76503
         (436 letters)



>NCBI__GCF_000022265.1:WP_012645274.1
          Length = 396

 Score = 99.8 bits (247), Expect = 1e-25
 Identities = 82/259 (31%), Positives = 124/259 (47%), Gaps = 24/259 (9%)

Query: 181 GLRMGDTAEQMAKTYGITREQQDALAHRSHQRAAQAWS-DGKLKEEVMTAF---IPPYKQ 236
           G  M  TAE +AK +GITREQ D L  R +++  QA + D + ++  M      I   K 
Sbjct: 155 GEAMIRTAENVAKEFGITREQCDELTLRRYEQYQQALAGDREFQKRYMFPVEVQISKKKT 214

Query: 237 PLVEDNNIRGNSSLADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLV 296
             +E +     ++    A L+P      G +T    T   DG   + + T  +AKEL   
Sbjct: 215 ITLEADEGVMATTKEGLAGLKPVLP--DGVLTFGAQTFPADGNCGISVTTREKAKELSAN 272

Query: 297 PLGYLRSYAFT-AIDVWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQ 355
           P   ++  +F  A      M    A S  +AL++AG+ +SD+  +  H  FAA  LA  +
Sbjct: 273 PSLEIQIVSFGFARTKKAHMAAAVAPSAQMALDKAGIKVSDIKAVKTHNPFAANDLAMAK 332

Query: 356 LLGSERFAREALGRAHATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGG 415
            LG                 +D +  N  G S+ YGHP A TGAR++ + + EL  +GGG
Sbjct: 333 ELG-----------------MDVNTMNNYGSSLIYGHPQAPTGARLMIEGIEELAVKGGG 375

Query: 416 FGLVTACAAGGLGAAMVLE 434
           + L + CAAG   A++VL+
Sbjct: 376 YLLFSGCAAGDTAASVVLK 394


Lambda     K      H
   0.319    0.133    0.377 

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: 351
Number of extensions: 13
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: 436
Length of database: 396
Length adjustment: 31
Effective length of query: 405
Effective length of database: 365
Effective search space:   147825
Effective search space used:   147825
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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