GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguK in Cronobacter condimenti 1330

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate WP_007680610.1 BN137_RS02010 sugar kinase

Query= metacyc::MONOMER-12748
         (320 letters)



>NCBI__GCF_000319285.1:WP_007680610.1
          Length = 312

 Score =  343 bits (879), Expect = 4e-99
 Identities = 179/308 (58%), Positives = 218/308 (70%), Gaps = 2/308 (0%)

Query: 4   IDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSL 63
           +D+++ GE MAMFVA   GDLAQV+HF KR+AGA+ NVA GLARLG  V+W+SRVGNDS 
Sbjct: 5   LDVITIGEAMAMFVATEPGDLAQVEHFFKRVAGAELNVATGLARLGLNVSWVSRVGNDSF 64

Query: 64  GRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD 123
           GRFVL  L  EG+  R V  D   PTGFQLKS+   G DP VEYFR+GSAASHL+  D +
Sbjct: 65  GRFVLSQLEKEGISTRGVTIDDRFPTGFQLKSKVTDGTDPSVEYFRKGSAASHLSGEDFN 124

Query: 124 -PALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALMIR 182
            P    ARHLH +G+  ALS S+ EL  H     ++ G ++SFDPNLRP LW SEA M+ 
Sbjct: 125 APLFYSARHLHLSGVAAALSGSSYELLDHAARAMKTQGKTISFDPNLRPVLWKSEAEMVE 184

Query: 183 EINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQL-D 241
           ++N LA LA WVLPGL EG +LTG+  P  IA FYL +G +AVVIK GA GA+Y+T   +
Sbjct: 185 KLNHLATLADWVLPGLKEGHILTGQQHPEGIADFYLSRGVKAVVIKTGADGAWYQTASGE 244

Query: 242 AGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEGL 301
            G VE V V  VVDTVGAGDGFAVG+ISALLE + + +A  R N IG+ A+Q +GD EGL
Sbjct: 245 QGTVEAVKVDNVVDTVGAGDGFAVGVISALLEGKTLHQAATRGNKIGALAIQVQGDSEGL 304

Query: 302 PLRHELPE 309
           P R +L E
Sbjct: 305 PTRAQLGE 312


Lambda     K      H
   0.321    0.138    0.414 

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: 361
Number of extensions: 16
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: 320
Length of database: 312
Length adjustment: 27
Effective length of query: 293
Effective length of database: 285
Effective search space:    83505
Effective search space used:    83505
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 (21.9 bits)
S2: 48 (23.1 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