GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF4143 PS417_21220 acetyl-CoA
           acetyltransferase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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