GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Dinoroseobacter shibae DFL-12

Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate 3608607 Dshi_2000 D-xylose ABC transporter, periplasmic substrate-binding protein (RefSeq)

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



>FitnessBrowser__Dino:3608607
          Length = 340

 Score =  561 bits (1445), Expect = e-164
 Identities = 284/334 (85%), Positives = 301/334 (90%), Gaps = 1/334 (0%)

Query: 8   SALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSAK 67
           +A+  A   + A+A DVTVGVSWSNFQEERWKTDEAAIKAALEA GATYVSADAQSSSAK
Sbjct: 8   AAIVAAGVTTSAYA-DVTVGVSWSNFQEERWKTDEAAIKAALEAAGATYVSADAQSSSAK 66

Query: 68  QLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRAFYLTFDNV 127
           QLSD+ESLIAQGVDALI+LAQD+QAIGPAVQAAADEGIPVV YDRLIED RAFYLTFDNV
Sbjct: 67  QLSDVESLIAQGVDALIILAQDSQAIGPAVQAAADEGIPVVGYDRLIEDPRAFYLTFDNV 126

Query: 128 EVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAYTD 187
           EVGRMQARAVLE  P GNYVMIKGSPTDPNADFLRGGQQEI+Q AID+G I IVGEAYTD
Sbjct: 127 EVGRMQARAVLEQAPEGNYVMIKGSPTDPNADFLRGGQQEILQDAIDAGKITIVGEAYTD 186

Query: 188 GWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEGIAVSGQDGDHAAL 247
           GWLPANAQRNMEQILTA DN+VDAVVASNDGTAGGVVAALTAQGMEGI VSGQDGDHAAL
Sbjct: 187 GWLPANAQRNMEQILTAQDNQVDAVVASNDGTAGGVVAALTAQGMEGIPVSGQDGDHAAL 246

Query: 248 NRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAGTELTARFLEP 307
           NRVAKGTQTVSVWKDARDLG+AA  IAV MA G  M D+ G  +WTSP GTELTARFL P
Sbjct: 247 NRVAKGTQTVSVWKDARDLGRAAGEIAVAMANGTAMADIEGATSWTSPGGTELTARFLAP 306

Query: 308 IPVTADNLSVVVDAGWITKEALCQGVTNGPAPCN 341
           +PVTADNL+ VVDA WIT+E LCQGVT+GPAPCN
Sbjct: 307 VPVTADNLTAVVDAQWITQETLCQGVTDGPAPCN 340


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: 440
Number of extensions: 19
Number of successful extensions: 1
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: 340
Length adjustment: 28
Effective length of query: 313
Effective length of database: 312
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:

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