GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas fluorescens FW300-N2C3

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate AO356_20395 AO356_20395 acetyl-CoA acetyltransferase

Query= BRENDA::Q0KAI3
         (392 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20395
          Length = 401

 Score =  287 bits (735), Expect = 3e-82
 Identities = 164/410 (40%), Positives = 240/410 (58%), Gaps = 27/410 (6%)

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

Query: 61  AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120
            GEQ A   + A L A +   V    ++R C S  +AV+ AA  + +G  D+V+A G+ES
Sbjct: 61  VGEQGADIAKTAALVANWDVSVAGVQLNRFCASGLEAVNLAAMKVRSGFEDLVVAGGVES 120

Query: 121 MSRVPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELA 180
           MSRVPMGS       +    ++      + QG+ A+L+A     SR D+D Y+  S + A
Sbjct: 121 MSRVPMGS---DGGAWALDPQSNLQGHFIPQGIGADLIATLEGFSREDVDRYALHSQQKA 177

Query: 181 ATARESGAFRREILGISTPNGLV--EQDETIRPGTSVEKLGTLQASFRNDELSARFPQIG 238
           A AR  G+F + ++ +   NG+V  + DE IR  +++E LG L+ SF          Q+G
Sbjct: 178 ARARADGSFDKSLVAVRDQNGIVLLDHDEFIRADSTLEGLGKLKPSFE------AMGQMG 231

Query: 239 WNVTA----------------GNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCG 282
           ++ TA                GN+S I DGA+ ML+ SE+  + +GL+PRAR VA  V  
Sbjct: 232 FDGTALRVYSHVERIHHVHTPGNSSGIVDGAALMLIGSEAKGRAMGLQPRARIVATAVTS 291

Query: 283 DDPVMMLTAPIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGG 342
            DP +MLT P PA+++A+ K+GL+++ ID +E+NEAFA V L + R +  DPA++N  GG
Sbjct: 292 TDPTIMLTGPAPATRKALAKAGLRVEDIDLFEVNEAFASVVLKFIRDMAIDPAKVNVNGG 351

Query: 343 AIALGHPLGASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392
           +IALGHPLGA+G  ++ T+L  LE    RYGL ++C  GGM  AT+IERL
Sbjct: 352 SIALGHPLGATGCAILGTLLDELEARRLRYGLATLCVGGGMGIATVIERL 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: 426
Number of extensions: 23
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