GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glc-kinase in Bacteroides thetaiotaomicron VPI-5482

Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate 352021 BT2493 ROK family transcriptional repressor, with glucokinase domain (NCBI ptt file)

Query= BRENDA::Q8R8N4
         (312 letters)



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

 Score =  191 bits (484), Expect = 3e-53
 Identities = 116/314 (36%), Positives = 178/314 (56%), Gaps = 10/314 (3%)

Query: 3   IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGIS--VK 60
           +G+D+GGTN   G+V+  G IIA+ S  T    GY   A    E+   LL  +  +  V 
Sbjct: 11  VGIDIGGTNTVFGIVDARGTIIASSSIKTA---GYPTAAEYADEVCKNLLPLIIANGGVD 67

Query: 61  DVKSMGIGVPGVADNEKGIVIRAVNLFWTKV-PLAKEIRKYIDLPIYMENDANVAALAEA 119
            ++ +G+G P   +   G +  A NL W  + PLA    + + +P  + NDAN AA+ E 
Sbjct: 68  KIRGIGVGAPN-GNYYTGTIEFAPNLPWKGILPLAAMFEERLGIPTALTNDANAAAIGEM 126

Query: 120 TFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGC 179
           T+GA RG K  + ITLGTGVGSG +++G++  G   FA E+GH++   +G  C CG+ GC
Sbjct: 127 TYGAARGMKDFIMITLGTGVGSGIVINGQMVYGHDGFAGELGHVIARRDGRVCGCGRKGC 186

Query: 180 FETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEY 239
            ETY SAT + R  ++      +  +L+  N   E IT+K+V DAA Q D+ A +IFE  
Sbjct: 187 LETYCSATGVARTAREFLAARTDASLLR--NIPAENITSKDVYDAAVQGDKLAQEIFEFT 244

Query: 240 VKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAEL 299
              L   + + I    PE I+L GG+A +GD+++KP++K + +NIL        +  +EL
Sbjct: 245 GNILGEALADAIAFSSPEAIVLFGGLAKSGDYIMKPIQKAIDDNILNIYKGKTKLLVSEL 304

Query: 300 -GNDAGIIGAAILS 312
             +DA ++GA+ L+
Sbjct: 305 KDSDAAVLGASALA 318


Lambda     K      H
   0.318    0.140    0.397 

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: 334
Number of extensions: 13
Number of successful extensions: 3
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: 312
Length of database: 326
Length adjustment: 28
Effective length of query: 284
Effective length of database: 298
Effective search space:    84632
Effective search space used:    84632
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, 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