GapMind for catabolism of small carbon sources

 

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

Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate 352021 BT2493 ROK family transcriptional repressor, with glucokinase domain (NCBI ptt file)

Query= metacyc::MONOMER-19002
         (326 letters)



>lcl|FitnessBrowser__Btheta:352021 BT2493 ROK family transcriptional
           repressor, with glucokinase domain (NCBI ptt file)
          Length = 326

 Score =  609 bits (1571), Expect = e-179
 Identities = 299/326 (91%), Positives = 317/326 (97%)

Query: 1   MNSSMEKPYVVGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLI 60
           MNS+MEKPYVVGIDIGGTNTVFGIVDARGTIIAS ++KT  YPT  EYADEVCKNLLPLI
Sbjct: 1   MNSNMEKPYVVGIDIGGTNTVFGIVDARGTIIASSSIKTAGYPTAAEYADEVCKNLLPLI 60

Query: 61  IANGGVDKIKGIGIGAPNGNYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANA 120
           IANGGVDKI+GIG+GAPNGNYYTGTIEFAPNLPWKG+LPLA+MFEERLGIPTALTNDANA
Sbjct: 61  IANGGVDKIRGIGVGAPNGNYYTGTIEFAPNLPWKGILPLAAMFEERLGIPTALTNDANA 120

Query: 121 AAVGEMTYGAARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRICG 180
           AA+GEMTYGAARGMKDFIMITLGTGVGSGIVINGQ+VYGHDGFAGELGHVI RRDGR+CG
Sbjct: 121 AAIGEMTYGAARGMKDFIMITLGTGVGSGIVINGQMVYGHDGFAGELGHVIARRDGRVCG 180

Query: 181 CGRKGCLETYCSATGVARTAREFLAARTDASLLRNIPAESIVSKDVYDAAVQGDKLAQEI 240
           CGRKGCLETYCSATGVARTAREFLAARTDASLLRNIPAE+I SKDVYDAAVQGDKLAQEI
Sbjct: 181 CGRKGCLETYCSATGVARTAREFLAARTDASLLRNIPAENITSKDVYDAAVQGDKLAQEI 240

Query: 241 FEFTGNILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNIYKGKAKLL 300
           FEFTGNILGEALADAIAFSSPEAI+LFGGLAKSGDYIMKPI KA+++N+LNIYKGK KLL
Sbjct: 241 FEFTGNILGEALADAIAFSSPEAIVLFGGLAKSGDYIMKPIQKAIDDNILNIYKGKTKLL 300

Query: 301 VSELKDSDAAVLGASALAWELKDLRD 326
           VSELKDSDAAVLGASALAWELKDL++
Sbjct: 301 VSELKDSDAAVLGASALAWELKDLKE 326


Lambda     K      H
   0.318    0.138    0.399 

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: 519
Number of extensions: 10
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: 326
Length of database: 326
Length adjustment: 28
Effective length of query: 298
Effective length of database: 298
Effective search space:    88804
Effective search space used:    88804
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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