GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglF in Sinorhizobium meliloti 1021

Align ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized)
to candidate SMc03062 SMc03062 alpha-glucoside ABC transporter permease

Query= reanno::Smeli:SMc03062
         (336 letters)



>lcl|FitnessBrowser__Smeli:SMc03062 SMc03062 alpha-glucoside ABC
           transporter permease
          Length = 336

 Score =  679 bits (1752), Expect = 0.0
 Identities = 336/336 (100%), Positives = 336/336 (100%)

Query: 1   MEQLIAAILTMVAGVLVCAAYFWSTNLVLDWIFPSKGKFGAVASRNLRIANSIRPWLFLA 60
           MEQLIAAILTMVAGVLVCAAYFWSTNLVLDWIFPSKGKFGAVASRNLRIANSIRPWLFLA
Sbjct: 1   MEQLIAAILTMVAGVLVCAAYFWSTNLVLDWIFPSKGKFGAVASRNLRIANSIRPWLFLA 60

Query: 61  PALLALTLYLVYPVVQSVWLSLHGRGGQNFVGLSNYSWMINDGEFRQSIFNNFLWLLVVP 120
           PALLALTLYLVYPVVQSVWLSLHGRGGQNFVGLSNYSWMINDGEFRQSIFNNFLWLLVVP
Sbjct: 61  PALLALTLYLVYPVVQSVWLSLHGRGGQNFVGLSNYSWMINDGEFRQSIFNNFLWLLVVP 120

Query: 121 ALSTFFGLIIAALTDRIWWGNIAKTLIFMPMAISFVGAAVIWKFIYDYRAAGSEQIGLLN 180
           ALSTFFGLIIAALTDRIWWGNIAKTLIFMPMAISFVGAAVIWKFIYDYRAAGSEQIGLLN
Sbjct: 121 ALSTFFGLIIAALTDRIWWGNIAKTLIFMPMAISFVGAAVIWKFIYDYRAAGSEQIGLLN 180

Query: 181 AIVVALGGEPQAWITLPFWNNFFLMVILIWIQTGFAMVILSAALRGIPEETIEAAVIDGA 240
           AIVVALGGEPQAWITLPFWNNFFLMVILIWIQTGFAMVILSAALRGIPEETIEAAVIDGA
Sbjct: 181 AIVVALGGEPQAWITLPFWNNFFLMVILIWIQTGFAMVILSAALRGIPEETIEAAVIDGA 240

Query: 241 NGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVLAMTNGQWQSQVLANLMFDWMFRG 300
           NGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVLAMTNGQWQSQVLANLMFDWMFRG
Sbjct: 241 NGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVLAMTNGQWQSQVLANLMFDWMFRG 300

Query: 301 GGDFGRGAAIAVVIMILVVPIMIWNIRNATRESGGH 336
           GGDFGRGAAIAVVIMILVVPIMIWNIRNATRESGGH
Sbjct: 301 GGDFGRGAAIAVVIMILVVPIMIWNIRNATRESGGH 336


Lambda     K      H
   0.330    0.142    0.466 

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: 706
Number of extensions: 24
Number of successful extensions: 2
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: 336
Length of database: 336
Length adjustment: 28
Effective length of query: 308
Effective length of database: 308
Effective search space:    94864
Effective search space used:    94864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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