GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Microvirga lotononidis WSM3557

Align glucokinase; EC 2.7.1.2 (characterized)
to candidate WP_009489786.1 MICLODRAFT_RS05260 ROK family transcriptional regulator

Query= CharProtDB::CH_014478
         (324 letters)



>NCBI__GCF_000262405.1:WP_009489786.1
          Length = 386

 Score =  141 bits (356), Expect = 2e-38
 Identities = 84/262 (32%), Positives = 133/262 (50%), Gaps = 21/262 (8%)

Query: 49  DIAKAIDKKLNDL-GEVKSR---LVGIGIGAPGPVNFANGSIEVAVNLGWEKFPIKDILE 104
           D+++A+   + DL GE+  R   +  IG+   G V+   G +  + NLGW   P++ +L 
Sbjct: 114 DLSQAVSLGIQDLTGEIGRRPMDIRAIGVSISGLVD-TEGHLAQSPNLGWHDVPLRKLLR 172

Query: 105 VETSLPVVVDNDANIAAIGEMWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAG 164
                P+ + N++N AAI E   G G    + L V  G+GVGGG+I +G + +G  G +G
Sbjct: 173 KTVKHPLYIGNNSNSAAIAEQMFGHGTETDNFLYVESGSGVGGGLILDGSLYRGAAGFSG 232

Query: 165 EIGHITSIPEGGAPCNCGKTGCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVT 224
           EIGHI  +P GG PC CG +GCL    +   I+R    +  +   P+E+    E   +VT
Sbjct: 233 EIGHIKVVP-GGRPCRCGSSGCLSAYVADHAILRQLQHDGVDIHTPAEILARAEAGDKVT 291

Query: 225 SKDVFDAARSKDGLAMHVVDKVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVR 284
                          +  +++   HLGLALAN  N LNP  IVLGGG++R    ++  +R
Sbjct: 292 ---------------LATLEEAGNHLGLALANLVNLLNPPLIVLGGGLARFAPHIMPSLR 336

Query: 285 DYFKRFAFPRVAQGAELAIATL 306
                 + P   +   + ++T+
Sbjct: 337 QTLSAMSMPAPLRACSIEVSTV 358


Lambda     K      H
   0.316    0.137    0.404 

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: 290
Number of extensions: 19
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: 324
Length of database: 386
Length adjustment: 29
Effective length of query: 295
Effective length of database: 357
Effective search space:   105315
Effective search space used:   105315
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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