GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas simiae WCS417

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate GFF4143 PS417_21220 acetyl-CoA acetyltransferase

Query= BRENDA::Q0KAI3
         (392 letters)



>FitnessBrowser__WCS417:GFF4143
          Length = 401

 Score =  287 bits (735), Expect = 3e-82
 Identities = 168/412 (40%), Positives = 244/412 (59%), Gaps = 31/412 (7%)

Query: 1   MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60
           M QA+I DAIR+P G+ K   A   +    L+A ++  L  R+ LD   VDD++ GCVT 
Sbjct: 1   MTQALIFDAIRTPRGKGKADGALHSVKPVNLVAGLLTALARRSDLDTHQVDDIVLGCVTP 60

Query: 61  AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120
            G+Q A   + A L A +   V    I+R C S  +AV+  A  + +G  D+V+  G+ES
Sbjct: 61  IGDQGADIAKTAALVADWDISVAGVQINRFCASGLEAVNVGAMKVRSGFEDLVVVGGVES 120

Query: 121 MSRVPMGSARIGQNPYGP--SMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHE 178
           MSRVPMGS   G     P  +M + + P    QG+ A+L+A     +R D+D+++  S +
Sbjct: 121 MSRVPMGSDG-GAWVLDPQTNMHSHFTP----QGIGADLIATLEGFTRDDVDAFALHSQQ 175

Query: 179 LAATARESGAFRREILGISTPNGLV--EQDETIRPGTSVEKLGTLQASFRNDELSARFPQ 236
            AA AR  G+F + ++ +   NG+V  + DE IR  +++E LG L+ SF          Q
Sbjct: 176 KAARARADGSFNKSLIAVQDQNGIVLLDHDEFIRGDSTLEGLGKLKPSFE------MMGQ 229

Query: 237 IGWNVTA----------------GNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDV 280
           +G++ TA                GN+S I DGA+ ML+ SE+  + LGL+PRAR VA  V
Sbjct: 230 MGFDATALRVYSHVERIHHVHTPGNSSGIVDGAALMLIGSEAKGRELGLQPRARIVATAV 289

Query: 281 CGDDPVMMLTAPIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPR 340
              DP +MLT P PA+++A+ K+GL+++ ID +E+NEAFA V L + + +G D AR+N  
Sbjct: 290 TSTDPTIMLTGPAPATRKALAKAGLRIEDIDLFEVNEAFASVVLKFIKDMGIDAARVNVN 349

Query: 341 GGAIALGHPLGASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392
           GG+IA+GHPLGA+G  ++ T+L  LE   QRYGL ++C  GGM  ATIIERL
Sbjct: 350 GGSIAMGHPLGATGCAILGTLLDELEVRQQRYGLATLCVGGGMGIATIIERL 401


Lambda     K      H
   0.318    0.132    0.384 

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: 421
Number of extensions: 21
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: 392
Length of database: 401
Length adjustment: 31
Effective length of query: 361
Effective length of database: 370
Effective search space:   133570
Effective search space used:   133570
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