GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguK in Pseudomonas fluorescens FW300-N2C3

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate AO356_24685 AO356_24685 2-dehydro-3-deoxygluconokinase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_24685
          Length = 326

 Score =  463 bits (1192), Expect = e-135
 Identities = 238/307 (77%), Positives = 254/307 (82%)

Query: 1   MPDIDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGN 60
           M + D+LSFGETMAM VA+  GDLA V  FHKRIAGADSNVAIGL+RLGFKVAWLSRVG 
Sbjct: 1   MSEFDVLSFGETMAMLVADQRGDLASVDQFHKRIAGADSNVAIGLSRLGFKVAWLSRVGA 60

Query: 61  DSLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAIS 120
           DSLGRFV  TL  EGLDCR V  DP HPTGFQ KS    G DP+VEYFRR SAASHL++ 
Sbjct: 61  DSLGRFVTQTLENEGLDCRHVAVDPEHPTGFQFKSLTVDGSDPQVEYFRRSSAASHLSVG 120

Query: 121 DLDPALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALM 180
            + PALL ARH+HATGI PALS +ARE+S  LM   R+AG S+SFDPNLRP+LW SE+ M
Sbjct: 121 SIAPALLDARHVHATGIVPALSGTAREMSFELMSRMRAAGRSLSFDPNLRPSLWGSESTM 180

Query: 181 IREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQL 240
           I  INRLAALAHWVLPGL EGRLLTG DDPADIAAFYLDQGAE VVIKLGA GAYYRT L
Sbjct: 181 ITAINRLAALAHWVLPGLGEGRLLTGFDDPADIAAFYLDQGAEIVVIKLGADGAYYRTAL 240

Query: 241 DAGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEG 300
           D G + GVPVAQVVDTVGAGDGFAVGLISALLE R I EAVQRANWIGSRAVQSRGDMEG
Sbjct: 241 DQGVIPGVPVAQVVDTVGAGDGFAVGLISALLEGRAITEAVQRANWIGSRAVQSRGDMEG 300

Query: 301 LPLRHEL 307
           LP R EL
Sbjct: 301 LPTRIEL 307


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: 453
Number of extensions: 15
Number of successful extensions: 1
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: 326
Length adjustment: 28
Effective length of query: 292
Effective length of database: 298
Effective search space:    87016
Effective search space used:    87016
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