GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Pseudomonas simiae WCS417

Align Serine acetyltransferase, plasmid; SAT; EC 2.3.1.30 (characterized)
to candidate GFF220 PS417_01115 serine acetyltransferase

Query= SwissProt::Q59967
         (319 letters)



>FitnessBrowser__WCS417:GFF220
          Length = 308

 Score =  321 bits (822), Expect = 2e-92
 Identities = 173/300 (57%), Positives = 211/300 (70%), Gaps = 6/300 (2%)

Query: 16  WGLDSIVSALSQASTDPLPHH-LLSDQF--YPLPSRESLGLILHGLRSVLFPRHFGDPEL 72
           W L +IVS L  A       +  LS +     LPSRE++  IL  L   LFP   G  +L
Sbjct: 8   WQLQTIVSQLRSARDQWRTRNGRLSGEHGGRELPSREAVAQILESLCGALFPMRLGPVDL 67

Query: 73  SVETTHYFIGNTLDKTLNLLNEQIRRELWLQHVTQGTPEATPAVLSQHASELTQAFAQAL 132
             E+  +++G+TLD  LN L  Q R EL          ++   VL   A  L Q FA AL
Sbjct: 68  REESEDFYVGHTLDVALNALLGQARLELRYAARQGAKDDSEVDVL---AIRLIQDFALAL 124

Query: 133 PEIKRLLDSDVNAAYLGDPAAQSISEILFCYPGITAITFHRLAHRLYQLGLPLLARITAE 192
           P ++ LLD+DV AAY GDPAA+S+ E+L CYPG+ A+  HRLAH LY+ GLPLLARI+AE
Sbjct: 125 PSLRSLLDTDVLAAYHGDPAARSVDEVLLCYPGVLAVIHHRLAHHLYRAGLPLLARISAE 184

Query: 193 VSHSETGIDIHPGAAIGGSFFIDHGTGVVIGETCVIGDRVRIYQAVTLGAKSFPRDETGA 252
           ++HS TGIDIHPGA IG SFFIDHGTGVVIGET +IG+RVRIYQAVTLGAK FP DE G 
Sbjct: 185 IAHSATGIDIHPGAQIGPSFFIDHGTGVVIGETAIIGERVRIYQAVTLGAKRFPADEDGQ 244

Query: 253 LIKGQARHPVIEDDVVIYAGATLLGRITVGRGSTIGGNVWLTRSVPAGSFISQAQIRSDN 312
           L KG  RHP++EDDVVIYAGAT+LGRIT+G+GSTIGGNVWLTRSVPAG+ I+QA ++ ++
Sbjct: 245 LQKGHPRHPIVEDDVVIYAGATILGRITIGKGSTIGGNVWLTRSVPAGANITQANLQHED 304


Lambda     K      H
   0.320    0.137    0.405 

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: 342
Number of extensions: 15
Number of successful extensions: 2
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: 319
Length of database: 308
Length adjustment: 27
Effective length of query: 292
Effective length of database: 281
Effective search space:    82052
Effective search space used:    82052
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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