GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aceA in Paraburkholderia bryophila 376MFSha3.1

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate H281DRAFT_06209 H281DRAFT_06209 carboxyvinyl-carboxyphosphonate phosphorylmutase

Query= BRENDA::Q05957
         (318 letters)



>FitnessBrowser__Burk376:H281DRAFT_06209
          Length = 290

 Score =  204 bits (520), Expect = 2e-57
 Identities = 104/282 (36%), Positives = 169/282 (59%), Gaps = 1/282 (0%)

Query: 31  MHRLIEEHGSVLMPGVQDALSAAVVEKTGFHAAFVSGYSVSAAMLGLPDFGLLTTTEVVE 90
           + R ++   ++L+PGV +AL+A + E+ G+ A FV+G  ++ + LG PD GL T TEV  
Sbjct: 9   LRRTLQPSAALLLPGVSNALAARIAEEAGYAAVFVTGAGIANSYLGAPDIGLTTVTEVGA 68

Query: 91  ATRRITAAAPNLCVVVDGDTGGGGPLNVQRFIRELISAGAKGVFLEDQVWPKKCGHMRGK 150
               I  A  ++ ++ D DTG G  LNV R +R    AGA  + LEDQ +PK+CGH  GK
Sbjct: 69  HINAIREAV-SIPIIADADTGFGNALNVMRTVRLFERAGANCIMLEDQTFPKRCGHFEGK 127

Query: 151 AVVPAEEHALKIAAAREAIGDSDFFLVARTDARAPHGLEEGIRRANLYKEAGADATFVEA 210
           AVV  EE   KI AA +A  ++D  ++ARTD+RA  G E  + R   Y++AGAD  FVEA
Sbjct: 128 AVVSIEEMTAKIKAAVDARANADTLIMARTDSRAIEGFERSLERIRTYRDAGADVLFVEA 187

Query: 211 PANVDELKEVSAKTKGLRIANMIEGGKTPLHTPEEFKEMGFHLIAHSLTAVYATARALVN 270
           P++++EL  +  +  G+++ NM+ GGKTPL    +  E+G+  + ++  A+ A   A+ N
Sbjct: 188 PSSLEELARIPREAPGVQVCNMVIGGKTPLLPQAQLSELGYAGVIYANAALQAAMFAMKN 247

Query: 271 IMKILKEKGTTRDDLDQMATFSEFNELISLESWYEMESKFKN 312
           +++ L+  G+     DQ+ +F+E  ++++   +  +  +  N
Sbjct: 248 VLEHLRSHGSIEGREDQIMSFAERQKMVNFARYDALAKQCAN 289


Lambda     K      H
   0.316    0.131    0.373 

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: 184
Number of extensions: 7
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: 318
Length of database: 290
Length adjustment: 27
Effective length of query: 291
Effective length of database: 263
Effective search space:    76533
Effective search space used:    76533
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: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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