GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk 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)



>FitnessBrowser__Btheta:352021
          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 (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