GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Thermoactinomyces daqus H-18

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_033100059.1 JG50_RS0105240 acetyl-CoA C-acyltransferase

Query= BRENDA::Q8VCH0
         (424 letters)



>NCBI__GCF_000763315.1:WP_033100059.1
          Length = 392

 Score =  331 bits (848), Expect = 3e-95
 Identities = 189/390 (48%), Positives = 258/390 (66%), Gaps = 8/390 (2%)

Query: 37  DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDV-KLKPEQLGDISVGNVLQPG 95
           + V+V G RT +G+A +G  K T PD+L + V+  +++ V +  P+++ D+ +G     G
Sbjct: 3   EAVIVAGARTAVGKAHKGTLKTTRPDDLAAQVVKDLMRRVPQADPKEVEDVILGCAFPEG 62

Query: 96  A-GAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154
             G  MAR+    +G+P  VP  TVNR CSSGLQ +A  A  I     DI +A GVESM+
Sbjct: 63  EQGMNMARLVALRAGLPTDVPGMTVNRFCSSGLQTIAIAAEKIMCNFADIIIAGGVESMS 122

Query: 155 LSQRGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASAQ 214
           +   G +    +  L +    +  + MG T+E VA+R+ VSR+ QD FALAS QKA +A 
Sbjct: 123 MVPMGGYKPAPNPWLMDHLP-EAYMSMGHTAEEVAKRYNVSREDQDRFALASHQKAYAAI 181

Query: 215 SRGCFHAEIVPVT--TTVLNDKGDKKTI--TVSQDEGVRPSTTMQGLAKLKPAFKDGGST 270
             G F  EIVPVT  T V ++KG  +        DEGVRP T+++ L KL+PAF+ GG+ 
Sbjct: 182 QEGKFKDEIVPVTVKTHVFDEKGKLRVEERVFDTDEGVRPDTSLEVLGKLRPAFQSGGTV 241

Query: 271 TAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAALQ 330
           TAGNSSQ SDGAAAV++  R KAEELG+  L V R + + GV PDVMGIGP  A+P  L+
Sbjct: 242 TAGNSSQTSDGAAAVMVMSREKAEELGVEPLAVFRGFVLGGVDPDVMGIGPVAAVPKLLK 301

Query: 331 KAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVVTL 390
           K G+++++ID+ E+NEAFASQA+  + +LG+  + VN  GGAIALGHPLGCTGA+  V++
Sbjct: 302 KTGVSLDEIDLVELNEAFASQAIAVIRELGLNPDIVNVNGGAIALGHPLGCTGAKLTVSI 361

Query: 391 LNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420
           LNELKRR +R YG+V+MCIG GMGAA + E
Sbjct: 362 LNELKRRNKR-YGLVTMCIGGGMGAAGLIE 390


Lambda     K      H
   0.317    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: 456
Number of extensions: 22
Number of successful extensions: 5
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: 424
Length of database: 392
Length adjustment: 31
Effective length of query: 393
Effective length of database: 361
Effective search space:   141873
Effective search space used:   141873
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 (21.6 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