GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Lacinutrix algicola AKS293

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_055437058.1 ASC41_RS12920 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>NCBI__GCF_001418085.1:WP_055437058.1
          Length = 392

 Score =  226 bits (575), Expect = 1e-63
 Identities = 147/399 (36%), Positives = 221/399 (55%), Gaps = 21/399 (5%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGA 62
           E VIVS ARTPIG ++ GAL+      L   AI+ A+++  ++P+ V++V+MG  +Q G 
Sbjct: 4   EVVIVSAARTPIG-SFLGALSTIPAPKLGAIAIKGALEKINLNPELVQEVLMGNVVQAG- 61

Query: 63  TGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISL 122
           TG   AR+A + AG+P T   TTI++ CASG++ +  AA+S+     EI V GG E++SL
Sbjct: 62  TGQAPARQAAIFAGIPNTVPCTTINKVCASGMKTVMQAAQSIALGDAEIVVAGGMENMSL 121

Query: 123 VQN-------DKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEYSLE 173
           + +        K      VD   +    DVY   AM  +A+  A +Y  SRE QD Y+++
Sbjct: 122 IPHYFHARSATKFGPATMVDGMQKDGLVDVYDQQAMGVSADACATKYEFSREDQDAYAIQ 181

Query: 174 SQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGL 233
           S +R+AAA + GKFN+EI P++      D         D+ +++DE  +     + +  L
Sbjct: 182 SYKRSAAAWEAGKFNNEIVPVAVPQRRGD---------DVIVTEDEEYK-NVRMDKIPTL 231

Query: 234 KAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIG 293
           +A   +  T+TA NAS ++DGA A V+MS + A   GLK L   +G      EP+     
Sbjct: 232 RAAFTKEGTVTAANASTINDGAGAMVLMSREKANELGLKVLATIKGYADAAHEPEWFTTA 291

Query: 294 PVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYG 353
           P  A+P+ L + GL + D+  +E NEAF++  L     LG++   +NVNGGA+S+GHP G
Sbjct: 292 PSIALPKALNKAGLDIKDVDFFEFNEAFSIVGLANMKILGLNDSNVNVNGGAVSLGHPLG 351

Query: 354 MSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
            SG R+    L    +  AK     +C GGG  SA + E
Sbjct: 352 CSGVRILITLLNVLEQNDAKIGAAAICNGGGGASALVLE 390


Lambda     K      H
   0.316    0.134    0.378 

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: 395
Number of extensions: 18
Number of successful extensions: 4
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: 395
Length of database: 392
Length adjustment: 31
Effective length of query: 364
Effective length of database: 361
Effective search space:   131404
Effective search space used:   131404
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