Alignments for a candidate for atoB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for atoB in Cupriavidus basilensis 4G11

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate RR42_RS36320 RR42_RS36320 acetyl-CoA acetyltransferase

Query= BRENDA::Q0K368
         (391 letters)



>FitnessBrowser__Cup4G11:RR42_RS36320
          Length = 392

 Score =  650 bits (1676), Expect = 0.0
 Identities = 324/392 (82%), Positives = 360/392 (91%), Gaps = 1/392 (0%)

Query: 1   MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60
           MAEAYIVAA RTAGGRKGGKL+GWHPADLAAQVL+ALV R+GADPAL++DVIMGCV Q G
Sbjct: 1   MAEAYIVAAARTAGGRKGGKLAGWHPADLAAQVLNALVARSGADPALIDDVIMGCVGQAG 60

Query: 61  EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120
           EQAGNVARNA+LAS+LP+SVPGTSVDRQCGSSQQALHFAAQAVMSG MDIVIAAGVESMT
Sbjct: 61  EQAGNVARNAVLASKLPQSVPGTSVDRQCGSSQQALHFAAQAVMSGTMDIVIAAGVESMT 120

Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180
           RVPMGL S LP KNGFG   SP ++ RYPGV+FSQFTGAEM++RKY L+R+ LD YAL+S
Sbjct: 121 RVPMGLPSTLPFKNGFGSSMSPAMQERYPGVKFSQFTGAEMMSRKYGLTRDDLDRYALES 180

Query: 181 HQRAIAATKSGRFTAEILPVEVRTADG-ANGEMHTTDEGVRYDATLESIGSVKLIAEGGR 239
           H+RAIAAT++GRF  EI+PV VR ADG ANGE+HT DEG+R++A+LESI SVKLI EGG 
Sbjct: 181 HRRAIAATQAGRFKDEIVPVAVRAADGSANGELHTVDEGIRFEASLESISSVKLIEEGGT 240

Query: 240 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVAL 299
           VTAASASQICDGAAGLMVVNEAGLKKLGVKPLAR+H M+V+GHDPV+MLEAPLPAT  AL
Sbjct: 241 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARIHHMSVLGHDPVIMLEAPLPATLRAL 300

Query: 300 KKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTT 359
            KAG++IGDIDLFE+NEAFAPVPLAWL+ TGADPAR+NV+GGAIALGHPLGGSGAKLMTT
Sbjct: 301 DKAGMKIGDIDLFEINEAFAPVPLAWLQTTGADPARMNVNGGAIALGHPLGGSGAKLMTT 360

Query: 360 LVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391
           LVHALH  GKRYGLQTMCEGGG+ANVTIVERL
Sbjct: 361 LVHALHAQGKRYGLQTMCEGGGMANVTIVERL 392


Lambda     K      H
   0.317    0.132    0.379 

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: 652
Number of extensions: 28
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: 391
Length of database: 392
Length adjustment: 31
Effective length of query: 360
Effective length of database: 361
Effective search space:   129960
Effective search space used:   129960
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources