GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Pseudomonas fluorescens FW300-N2C3

Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate AO356_23200 AO356_23200 rhizopine-binding protein

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_23200
          Length = 308

 Score =  102 bits (254), Expect = 1e-26
 Identities = 92/281 (32%), Positives = 134/281 (47%), Gaps = 17/281 (6%)

Query: 9   ALAFAATASMAFAEDVTVGVSWSNFQEERWKT---DEAAIKAALEAKGATYVSADAQSSS 65
           AL+   T+  A A D+ +GVS S F ++ W T   +    KA     G T    DA+S  
Sbjct: 11  ALSLMLTSGAALA-DLKIGVSMSQF-DDTWLTYLRESMDKKAKSLPDGVTLQFEDARSDV 68

Query: 66  AKQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGR----AFY 121
            KQLS +ES I+Q VDALIV   D  A     +AA   GIP+V  +R  +D +       
Sbjct: 69  VKQLSQVESFISQKVDALIVNPVDTAATQRITKAAVAAGIPLVYVNRRPDDPKLPEGVVT 128

Query: 122 LTFDNVEVGRMQARAVLEAQ-PSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKI 180
           +  D++E GRMQ + + E     GN V++ G   + +      G ++++        IKI
Sbjct: 129 VASDDLEAGRMQMQYLAEKMGGKGNIVILLGDLANNSTANRTKGVKDVL---AKYPGIKI 185

Query: 181 VGEAYTDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGME--GIAVS 238
             E  T  WL       +   LT    +  AVVA+ND  A G   AL   G E   + ++
Sbjct: 186 EQE-QTGIWLRDKGMTLVNDWLT-QGREFQAVVANNDEMAIGAAMALKQAGTEKGSVLIA 243

Query: 239 GQDGDHAALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAE 279
           G DG    LN + KG   VSV++DA+     + + AV+M +
Sbjct: 244 GVDGTPDGLNAIKKGEMAVSVFQDAKGQADGSIDTAVKMVK 284


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: 210
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: 341
Length of database: 308
Length adjustment: 28
Effective length of query: 313
Effective length of database: 280
Effective search space:    87640
Effective search space used:    87640
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: 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