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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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