GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglB in Burkholderia phytofirmans PsJN

Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS32820 BPHYT_RS32820 xylose ABC transporter substrate-binding protein

Query= reanno::Phaeo:GFF3639
         (341 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS32820 BPHYT_RS32820 xylose ABC
           transporter substrate-binding protein
          Length = 342

 Score =  230 bits (587), Expect = 3e-65
 Identities = 131/325 (40%), Positives = 196/325 (60%), Gaps = 6/325 (1%)

Query: 7   VSALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSA 66
           +++L+  A  + A  +   +G    + + ERW  D     AA E  GA      A +S A
Sbjct: 19  LASLSLVAPLAHASKDHPEIGFCIDDLRVERWSRDRDYFVAAAEKLGAKVSVQSADASEA 78

Query: 67  KQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYLTFD 125
           +Q+S IE+LI++GVD ++++  +++ +G  V  A   GI VV+YDRLI D     Y++FD
Sbjct: 79  RQISQIENLISRGVDVIVIVPFNSKTLGNVVAEAKKAGIKVVSYDRLILDADVDAYISFD 138

Query: 126 NVEVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAY 185
           N +VG +QA+ V  AQP GNY ++ G+PTD NA  LR GQ +I++ AID GDIK+VG+ +
Sbjct: 139 NEKVGELQAQGVYNAQPKGNYFLLGGAPTDNNAKMLREGQLKILKPAIDKGDIKVVGQQW 198

Query: 186 TDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQDGDH 244
              W  + A R +E  LTAN+NK+DA+VASNDGTAGG + AL AQ M G + VSGQD D 
Sbjct: 199 VPEWSASTALRIVEDALTANNNKIDAIVASNDGTAGGAIQALAAQHMAGKVPVSGQDADL 258

Query: 245 AALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAGTELTARF 304
           AA+ RV  GTQT++V+K  + +   AA ++V +A+    G+     +       ++    
Sbjct: 259 AAVKRVIAGTQTMTVYKPLKLIAGEAAKLSVALAK----GEKPAFNSQYDNGKKKVDTVL 314

Query: 305 LEPIPVTADNLSVVVDAGWITKEAL 329
           L+P  +T  N+ VVV  G+ ++  L
Sbjct: 315 LQPTLLTKSNVDVVVKDGFYSQAQL 339


Lambda     K      H
   0.313    0.128    0.362 

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: 226
Number of extensions: 8
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: 341
Length of database: 342
Length adjustment: 29
Effective length of query: 312
Effective length of database: 313
Effective search space:    97656
Effective search space used:    97656
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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