GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Lacinutrix algicola AKS293

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_055437058.1 ASC41_RS12920 acetyl-CoA C-acyltransferase

Query= BRENDA::Q8S4Y1
         (403 letters)



>NCBI__GCF_001418085.1:WP_055437058.1
          Length = 392

 Score =  444 bits (1141), Expect = e-129
 Identities = 234/391 (59%), Positives = 292/391 (74%), Gaps = 3/391 (0%)

Query: 11  RDVCIVGVARTPMGGFLGSLSSLPATKLGSLAIAAALKRANVDPALVQEVVFGNVLSANL 70
           ++V IV  ARTP+G FLG+LS++PA KLG++AI  AL++ N++P LVQEV+ GNV+ A  
Sbjct: 3   KEVVIVSAARTPIGSFLGALSTIPAPKLGAIAIKGALEKINLNPELVQEVLMGNVVQAGT 62

Query: 71  GQAPARQAALGAGIPNSVICTTVNKVCASGMKAVMIAAQSIQLGINDVVVAGGMESMSNT 130
           GQAPARQAA+ AGIPN+V CTT+NKVCASGMK VM AAQSI LG  ++VVAGGME+MS  
Sbjct: 63  GQAPARQAAIFAGIPNTVPCTTINKVCASGMKTVMQAAQSIALGDAEIVVAGGMENMSLI 122

Query: 131 PKYLAEARKGSRFGHDSLVDGMLKDGLWDVYNDCGMGSCAELCAEKFQITREQQDDYAVQ 190
           P Y   AR  ++FG  ++VDGM KDGL DVY+   MG  A+ CA K++ +RE QD YA+Q
Sbjct: 123 PHYF-HARSATKFGPATMVDGMQKDGLVDVYDQQAMGVSADACATKYEFSREDQDAYAIQ 181

Query: 191 SFERGIAAQEAGAFTWEIVPVEVSGGRGRPSTIVDKDEGLGKFDAAKLRKLRPSFKENGG 250
           S++R  AA EAG F  EIVPV V   RG    IV +DE        K+  LR +F + G 
Sbjct: 182 SYKRSAAAWEAGKFNNEIVPVAVPQRRG-DDVIVTEDEEYKNVRMDKIPTLRAAFTKEG- 239

Query: 251 TVTAGNASSISDGAAALVLVSGEKALQLGLLVLAKIKGYGDAAQEPEFFTTAPALAIPKA 310
           TVTA NAS+I+DGA A+VL+S EKA +LGL VLA IKGY DAA EPE+FTTAP++A+PKA
Sbjct: 240 TVTAANASTINDGAGAMVLMSREKANELGLKVLATIKGYADAAHEPEWFTTAPSIALPKA 299

Query: 311 IAHAGLESSQVDYYEINEAFAVVALANQKLLGIAPEKVNVNGGAVSLGHPLGCSGARILI 370
           +  AGL+   VD++E NEAF++V LAN K+LG+    VNVNGGAVSLGHPLGCSG RILI
Sbjct: 300 LNKAGLDIKDVDFFEFNEAFSIVGLANMKILGLNDSNVNVNGGAVSLGHPLGCSGVRILI 359

Query: 371 TLLGILKKRNGKYGVGGVCNGGGGASALVLE 401
           TLL +L++ + K G   +CNGGGGASALVLE
Sbjct: 360 TLLNVLEQNDAKIGAAAICNGGGGASALVLE 390


Lambda     K      H
   0.316    0.134    0.382 

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: 483
Number of extensions: 14
Number of successful extensions: 3
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: 403
Length of database: 392
Length adjustment: 31
Effective length of query: 372
Effective length of database: 361
Effective search space:   134292
Effective search space used:   134292
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