GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ams in Bacteroides thetaiotaomicron VPI-5482

Align β-fructofuranosidase (BT1759) (EC 3.2.1.26|3.2.1.64|3.2.1.80) (characterized)
to candidate 351287 BT1759 levanase precursor (2,6-beta-D-fructofuranosidase) (NCBI ptt file)

Query= CAZy::AAO76866.1
         (610 letters)



>lcl|FitnessBrowser__Btheta:351287 BT1759 levanase precursor
           (2,6-beta-D-fructofuranosidase) (NCBI ptt file)
          Length = 610

 Score = 1266 bits (3277), Expect = 0.0
 Identities = 610/610 (100%), Positives = 610/610 (100%)

Query: 1   MNVFLPVKQLQTFLICFILMTISVSTRAADSPLLIKNLGEGHCLVRVNTSQNYLLLPVED 60
           MNVFLPVKQLQTFLICFILMTISVSTRAADSPLLIKNLGEGHCLVRVNTSQNYLLLPVED
Sbjct: 1   MNVFLPVKQLQTFLICFILMTISVSTRAADSPLLIKNLGEGHCLVRVNTSQNYLLLPVED 60

Query: 61  ASPDVRISMIVNNKEVKNFDVRLAIHKVDYFVPVDLSDFSGKTVSFKFKMNSNDPIRVNL 120
           ASPDVRISMIVNNKEVKNFDVRLAIHKVDYFVPVDLSDFSGKTVSFKFKMNSNDPIRVNL
Sbjct: 61  ASPDVRISMIVNNKEVKNFDVRLAIHKVDYFVPVDLSDFSGKTVSFKFKMNSNDPIRVNL 120

Query: 121 SPDNTACCKEMKLSDTFDTTNREKFRPTYHFSPLYGWMNDPNGMVYKDGEYHLFYQYNPY 180
           SPDNTACCKEMKLSDTFDTTNREKFRPTYHFSPLYGWMNDPNGMVYKDGEYHLFYQYNPY
Sbjct: 121 SPDNTACCKEMKLSDTFDTTNREKFRPTYHFSPLYGWMNDPNGMVYKDGEYHLFYQYNPY 180

Query: 181 GSKWGNMNWGHAISKDLVNWEHRPVAIAPDALGTIFSGSAVVDHNNTAGFGAGAIIAIYT 240
           GSKWGNMNWGHAISKDLVNWEHRPVAIAPDALGTIFSGSAVVDHNNTAGFGAGAIIAIYT
Sbjct: 181 GSKWGNMNWGHAISKDLVNWEHRPVAIAPDALGTIFSGSAVVDHNNTAGFGAGAIIAIYT 240

Query: 241 QNSDRQVQSIAYSTDNGRTFTKYENNPVLVSEARDFRDPKVFWYEATKRWIMVLAVGQEM 300
           QNSDRQVQSIAYSTDNGRTFTKYENNPVLVSEARDFRDPKVFWYEATKRWIMVLAVGQEM
Sbjct: 241 QNSDRQVQSIAYSTDNGRTFTKYENNPVLVSEARDFRDPKVFWYEATKRWIMVLAVGQEM 300

Query: 301 QIFSSPNLKDWAFESSFGEGYGAHGNVWECPDLFELPVEGTNEKKWVLLCSLGDGPFGDS 360
           QIFSSPNLKDWAFESSFGEGYGAHGNVWECPDLFELPVEGTNEKKWVLLCSLGDGPFGDS
Sbjct: 301 QIFSSPNLKDWAFESSFGEGYGAHGNVWECPDLFELPVEGTNEKKWVLLCSLGDGPFGDS 360

Query: 361 ATQYFIGSFDGKKFSCDNQPNVTKWMDWGKDHYATVTWSDAPDNRRIAIAWMSNWQYAND 420
           ATQYFIGSFDGKKFSCDNQPNVTKWMDWGKDHYATVTWSDAPDNRRIAIAWMSNWQYAND
Sbjct: 361 ATQYFIGSFDGKKFSCDNQPNVTKWMDWGKDHYATVTWSDAPDNRRIAIAWMSNWQYAND 420

Query: 421 VPTSQYRSPNSIPRDLSLFAIDGGIYLQSAPSPELLKLRGVSKKRSFKVNGTRIVKDLIP 480
           VPTSQYRSPNSIPRDLSLFAIDGGIYLQSAPSPELLKLRGVSKKRSFKVNGTRIVKDLIP
Sbjct: 421 VPTSQYRSPNSIPRDLSLFAIDGGIYLQSAPSPELLKLRGVSKKRSFKVNGTRIVKDLIP 480

Query: 481 NNEGAYEIELSLKNQQAEIIGFRLYNDKGEEVDMQYDMKEKKFSMDRRKSGEVNFNENFP 540
           NNEGAYEIELSLKNQQAEIIGFRLYNDKGEEVDMQYDMKEKKFSMDRRKSGEVNFNENFP
Sbjct: 481 NNEGAYEIELSLKNQQAEIIGFRLYNDKGEEVDMQYDMKEKKFSMDRRKSGEVNFNENFP 540

Query: 541 MLTWTAIEEDKDEMKLRLFVDRSSVEAFGDGGRFAMTNQVFPSEPYNHISFYSKGGAYKV 600
           MLTWTAIEEDKDEMKLRLFVDRSSVEAFGDGGRFAMTNQVFPSEPYNHISFYSKGGAYKV
Sbjct: 541 MLTWTAIEEDKDEMKLRLFVDRSSVEAFGDGGRFAMTNQVFPSEPYNHISFYSKGGAYKV 600

Query: 601 DSFVVYKLKK 610
           DSFVVYKLKK
Sbjct: 601 DSFVVYKLKK 610


Lambda     K      H
   0.318    0.135    0.419 

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: 1576
Number of extensions: 48
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: 610
Length of database: 610
Length adjustment: 37
Effective length of query: 573
Effective length of database: 573
Effective search space:   328329
Effective search space used:   328329
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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 preprint 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