GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Granulicella mallensis MP5ACTX8

Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate WP_150110915.1 ACIX8_RS18080 sugar kinase

Query= BRENDA::Q9WXS2
         (339 letters)



>NCBI__GCF_000178955.2:WP_150110915.1
          Length = 340

 Score =  157 bits (398), Expect = 3e-43
 Identities = 114/344 (33%), Positives = 168/344 (48%), Gaps = 21/344 (6%)

Query: 10  MLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQ-MGLDAYFVTKLPNNPLGDAAAGHL 68
           MLR  P +  RI  + +F V  GG E NVA  L +   L    VT L +NP+G      +
Sbjct: 1   MLRFDPGEG-RIVGSRNFRVWEGGGEYNVARGLRRCFDLRTAIVTALVDNPVGRLVEDLM 59

Query: 69  RKFGVKTDYI-------ARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121
            + GV   ++            R GIYFLE G   R    + DR  +AIS+ K  D DW+
Sbjct: 60  LQGGVDLSHVLWRDFDGVGREARNGIYFLERGFGVRGGMGMMDRGSTAISQMKPGDVDWD 119

Query: 122 KIL--DGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEAQK 179
           +I   +G +WFH  G+   L ++   ++ +A+  A   G  VS D NYR  LW     +K
Sbjct: 120 EIFQDEGVQWFHTGGVMAALSEDSTEVVREAMAAAKRHGTIVSFDCNYRPSLWKSRGGRK 179

Query: 180 VMIP----FMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKY-NF 234
             I      M  VDVL  +E DI   LG + +G    T     +++  +A  VT ++ N 
Sbjct: 180 GSIDVNRSLMPLVDVLFGHEGDIAATLGEASQGPVWHT----LDSFRAMAGRVTAEFGNL 235

Query: 235 KTVGITLRESISATVNYWSVMVFENGQPHFSNRYE-IHIVDRVGAGDSFAGALIYGSLMG 293
           K +  T+R   +A  N WS   +  G+ +   R++ + I+DRVG GDSFA  LIYG L G
Sbjct: 236 KVIASTVRRLHTANRNGWSAFGYAEGEAYEGLRFDDLEILDRVGGGDSFASGLIYGLLQG 295

Query: 294 FDSQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASGATSGRV 337
              +   +   A   L  T  GD  + ++ E+E+L +G ++G V
Sbjct: 296 KGMRYALDCGIAHGALAMTTAGDSSMATLPEVERLMAGGSAGTV 339


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: 307
Number of extensions: 14
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: 340
Length adjustment: 28
Effective length of query: 311
Effective length of database: 312
Effective search space:    97032
Effective search space used:    97032
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.

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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