GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguK in Cupriavidus basilensis 4G11

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate RR42_RS09470 RR42_RS09470 2-dehydro-3-deoxygluconokinase

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



>FitnessBrowser__Cup4G11:RR42_RS09470
          Length = 314

 Score =  332 bits (851), Expect = 7e-96
 Identities = 170/302 (56%), Positives = 209/302 (69%), Gaps = 1/302 (0%)

Query: 2   PDIDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGND 61
           PD+D+++ GE M M VA   G L  VQ FHKR AGA++NVAIGL+RLG KV W SR+G+D
Sbjct: 3   PDLDVVTLGEAMLMLVAGEAGPLEGVQTFHKRTAGAETNVAIGLSRLGLKVGWASRLGDD 62

Query: 62  SLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISD 121
           S+ R++L  +R EG+DC  V C+P   TGFQ K R D G DP VEY RRGSAAS +    
Sbjct: 63  SMARYLLGEMRREGVDCSQVVCEPGERTGFQFKGRVDDGSDPPVEYHRRGSAASRMNPEH 122

Query: 122 LDPALLR-ARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALM 180
           LD   LR ARHLH TG+ PAL++  +  +   + T R+AG +VSFDPNLRPALW +  LM
Sbjct: 123 LDDRWLRRARHLHVTGVFPALAEGTQAATRQAIATMRAAGRTVSFDPNLRPALWATPELM 182

Query: 181 IREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQL 240
              +N LA    WVLPG+ EGR LTG  +P  IAAFY  +GA  VV+KLGA GAY+  + 
Sbjct: 183 RETLNNLAQQCDWVLPGIEEGRFLTGHAEPERIAAFYRGRGARLVVVKLGAEGAYFDGEA 242

Query: 241 DAGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEG 300
             G V    V +VVDTVGAGDGFAVG+ISALL+ R + +AV+R  WIG+RAVQ RGD EG
Sbjct: 243 GTGHVPAFSVERVVDTVGAGDGFAVGVISALLQGRTVADAVRRGAWIGARAVQVRGDTEG 302

Query: 301 LP 302
           LP
Sbjct: 303 LP 304


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: 379
Number of extensions: 15
Number of successful extensions: 2
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: 314
Length adjustment: 27
Effective length of query: 293
Effective length of database: 287
Effective search space:    84091
Effective search space used:    84091
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 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 (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