GapMind for catabolism of small carbon sources

 

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

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate H281DRAFT_06209 H281DRAFT_06209 carboxyvinyl-carboxyphosphonate phosphorylmutase

Query= curated2:Q9YFM7
         (308 letters)



>FitnessBrowser__Burk376:H281DRAFT_06209
          Length = 290

 Score =  212 bits (540), Expect = 7e-60
 Identities = 115/276 (41%), Positives = 167/276 (60%), Gaps = 3/276 (1%)

Query: 13  GLVLRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGAAITGS-LAMPDLGLITLSE 71
           G  LR  ++    ++ PGV N   A +AE  G+ A++++GA I  S L  PD+GL T++E
Sbjct: 6   GAFLRRTLQPSAALLLPGVSNALAARIAEEAGYAAVFVTGAGIANSYLGAPDIGLTTVTE 65

Query: 72  LAMFTSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQ 131
           +    + I   V +P+I DADTGFG A+NV RTVR  ERAGA  I +EDQ  PK+CGH +
Sbjct: 66  VGAHINAIREAVSIPIIADADTGFGNALNVMRTVRLFERAGANCIMLEDQTFPKRCGHFE 125

Query: 132 GKALISPEDMVKKIIAAVGAR--RDALIVARTDARGVEGFEKAVERAQLYVEAGADIIFP 189
           GKA++S E+M  KI AAV AR   D LI+ARTD+R +EGFE+++ER + Y +AGAD++F 
Sbjct: 126 GKAVVSIEEMTAKIKAAVDARANADTLIMARTDSRAIEGFERSLERIRTYRDAGADVLFV 185

Query: 190 EALTSLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKAS 249
           EA +SLEE     R      + NM   GKTP +   Q  E GY  VI+     +A++ A 
Sbjct: 186 EAPSSLEELARIPREAPGVQVCNMVIGGKTPLLPQAQLSELGYAGVIYANAALQAAMFAM 245

Query: 250 ETVLREIMEKGTQKDILDKLYTRTEFYDLIGYHDYE 285
           + VL  +   G+ +   D++ +  E   ++ +  Y+
Sbjct: 246 KNVLEHLRSHGSIEGREDQIMSFAERQKMVNFARYD 281


Lambda     K      H
   0.321    0.137    0.378 

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: 236
Number of extensions: 10
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: 308
Length of database: 290
Length adjustment: 27
Effective length of query: 281
Effective length of database: 263
Effective search space:    73903
Effective search space used:    73903
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 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