GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglB in Pseudomonas fluorescens FW300-N2E2

Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate Pf6N2E2_1455 Xylose ABC transporter, periplasmic xylose-binding protein XylF

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



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1455 Xylose ABC
           transporter, periplasmic xylose-binding protein XylF
          Length = 333

 Score =  226 bits (575), Expect = 8e-64
 Identities = 130/320 (40%), Positives = 187/320 (58%), Gaps = 6/320 (1%)

Query: 9   ALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSAKQ 68
           ALA  +   MA A    +G S  + + ERW  D     AA E   A      A ++  KQ
Sbjct: 12  ALALLSLPVMADAAHPKIGFSIDDLRLERWSRDRDYFVAAAEKLDAKVFVQSADANEQKQ 71

Query: 69  LSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYLTFDNV 127
           +S IE+LI++GVD ++++  +A  +  AV  A   GI VV+YDRLI +     Y++FDN 
Sbjct: 72  ISQIENLISRGVDVIVIVPFNATVLTNAVAEAKKAGIKVVSYDRLILNADIDAYISFDNE 131

Query: 128 EVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAYTD 187
           +VG MQA  VL+A P GNY ++ G+PTD NA  LR GQ +++Q AID GDIKIVG+ +  
Sbjct: 132 KVGEMQASGVLKAAPKGNYFLLGGAPTDNNAKVLREGQMKVLQPAIDKGDIKIVGQQWVK 191

Query: 188 GWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQDGDHAA 246
            W P  A   +E  LT N+NK+D +VASND TAGG + AL AQ M G + +SGQD D AA
Sbjct: 192 EWNPTEALSIVENALTRNNNKIDGIVASNDATAGGAIQALAAQKMAGKVPISGQDADLAA 251

Query: 247 LNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAGTELTARFLE 306
           + RV  GTQT++V+K  + +   AA ++V++A      +    ++       ++    L 
Sbjct: 252 VKRVIDGTQTMTVYKPLKLIASEAAKLSVQLAR----NEKPTFSSQYDNGSKKVDTILLT 307

Query: 307 PIPVTADNLSVVVDAGWITK 326
           P P+T DN+ ++   G+ TK
Sbjct: 308 PTPLTKDNIDLLEKDGFYTK 327


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: 209
Number of extensions: 7
Number of successful extensions: 4
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: 333
Length adjustment: 28
Effective length of query: 313
Effective length of database: 305
Effective search space:    95465
Effective search space used:    95465
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