GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Cupriavidus basilensis 4G11

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate RR42_RS07645 RR42_RS07645 acetyl-CoA acetyltransferase

Query= SwissProt::Q0KBP1
         (394 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS07645 RR42_RS07645 acetyl-CoA
           acetyltransferase
          Length = 394

 Score =  707 bits (1826), Expect = 0.0
 Identities = 358/394 (90%), Positives = 379/394 (96%)

Query: 1   MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60
           MTREVVVVSGVRTAIGTFGGSLKD++P ++GA+VVREALARAQVSGDDVGHVVFGNVIQT
Sbjct: 1   MTREVVVVSGVRTAIGTFGGSLKDLSPTQMGAMVVREALARAQVSGDDVGHVVFGNVIQT 60

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
           EPRDMYLGRVAAV GGVTI+APALTVNRLCGSGLQAIVSAAQTILLGD DVAIGGGAESM
Sbjct: 61  EPRDMYLGRVAAVEGGVTIDAPALTVNRLCGSGLQAIVSAAQTILLGDADVAIGGGAESM 120

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
           SRAPYLA +ARWGARMGDA ++DMMLGALHDPFH IHMGVTAENVAKEYDISR QQDEAA
Sbjct: 121 SRAPYLAQSARWGARMGDAKMLDMMLGALHDPFHGIHMGVTAENVAKEYDISRVQQDEAA 180

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240
           LESHRRASAAI+AG+FKDQI+PV  KGRKGDVTFDTDEHVRHDA ++DMTKL+PVFVKEN
Sbjct: 181 LESHRRASAAIRAGHFKDQILPVTLKGRKGDVTFDTDEHVRHDAVMEDMTKLKPVFVKEN 240

Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300
           GTVTAGNASGLNDAAAAVV+MERAEAE+RGLKP+ARLVSY HAGVDPK MGIGPVPATK 
Sbjct: 241 GTVTAGNASGLNDAAAAVVLMERAEAEKRGLKPMARLVSYAHAGVDPKTMGIGPVPATKK 300

Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360
           ALERAGL V+DLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT
Sbjct: 301 ALERAGLTVADLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360

Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           VKAL+EL RVQGRYALVTMCIGGGQGIAAIFER+
Sbjct: 361 VKALYELQRVQGRYALVTMCIGGGQGIAAIFERL 394


Lambda     K      H
   0.318    0.134    0.381 

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: 635
Number of extensions: 8
Number of successful extensions: 1
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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