GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Arenitalea lutea P7-3-5

Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate WP_019388253.1 P735_RS0111840 sugar kinase

Query= BRENDA::Q9WXS2
         (339 letters)



>NCBI__GCF_000283015.1:WP_019388253.1
          Length = 348

 Score =  305 bits (781), Expect = 1e-87
 Identities = 168/346 (48%), Positives = 222/346 (64%), Gaps = 8/346 (2%)

Query: 2   KVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLG 61
           KVVTFGEIMLRL+P    R  Q +SFD  YGG E+NVA  LA  G+D  FVT+LP N +G
Sbjct: 3   KVVTFGEIMLRLAPQGFLRFSQANSFDAIYGGGESNVAVSLANYGVDVDFVTRLPKNDIG 62

Query: 62  DAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121
           + A   +RK GV  D I  GG+R+GIYFLE GA  R SKVVYDRAHSAI+E K    DW+
Sbjct: 63  ECAMMEMRKRGVGVDKIVWGGDRLGIYFLETGAVSRGSKVVYDRAHSAIAEIKSGMIDWD 122

Query: 122 KILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEA---Q 178
            + +G  WFH++GITP + +    +  +A+K A+ KG+T+S DLNYRA+LW   +A   +
Sbjct: 123 AVFEGCEWFHWTGITPAISQGSADVCLEAVKAASAKGITISTDLNYRAKLWKYCDAAHRE 182

Query: 179 KVMIPFMEYVDVLIANEEDIEKVLGISVEGLDLKT--GKLNREAYAKIAEEVTRKY-NFK 235
           KVM     Y D+++ NEED E   GI  EG+ ++T    +  EA+  + E++  K+   K
Sbjct: 183 KVMTELTSYCDIVLGNEEDAEMHFGIKPEGITVQTQGHDVKAEAFLSVCEQMMEKFPRAK 242

Query: 236 TVGITLRESISATVNYWSVMVFENGQPHFSNRYEI-HIVDRVGAGDSFAGALIYGSL-MG 293
            V  TLR SISA+ N W+ ++++      + +Y+I  IVDRVG GDSF G LIYG L   
Sbjct: 243 KVITTLRGSISASHNTWAGVLYDGKTLFQTRQYQITDIVDRVGGGDSFMGGLIYGLLKYP 302

Query: 294 FDSQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASGATSGRVER 339
            D Q   +FA AASCLKHTI GD  ++++ E+EKL  G  SGRV R
Sbjct: 303 KDDQNALDFAVAASCLKHTIKGDANLVTVAEVEKLMGGDASGRVAR 348


Lambda     K      H
   0.319    0.136    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: 352
Number of extensions: 11
Number of successful extensions: 5
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: 339
Length of database: 348
Length adjustment: 29
Effective length of query: 310
Effective length of database: 319
Effective search space:    98890
Effective search space used:    98890
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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