GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kguK in Pseudomonas fluorescens FW300-N1B4

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate Pf1N1B4_4765 2-ketogluconate kinase (EC 2.7.1.13)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4765 2-ketogluconate
           kinase (EC 2.7.1.13)
          Length = 339

 Score =  479 bits (1233), Expect = e-140
 Identities = 242/307 (78%), Positives = 260/307 (84%)

Query: 1   MPDIDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGN 60
           M +IDILSFGETMAMFVAE  G+LA V HFHKRIAGADSNVAIGL+RLGF VAWLSRVG 
Sbjct: 1   MSEIDILSFGETMAMFVAEQNGELADVDHFHKRIAGADSNVAIGLSRLGFNVAWLSRVGA 60

Query: 61  DSLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAIS 120
           DSLGRFV+DTL  +GLDC  V  DP HPTGFQLKSR D G DP VEYFRRGSAASHL++ 
Sbjct: 61  DSLGRFVIDTLEKQGLDCSHVDIDPAHPTGFQLKSRTDDGSDPAVEYFRRGSAASHLSVQ 120

Query: 121 DLDPALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALM 180
            + P LL ARHLHATGIPPALS +ARE+S  LM   R+AG SVSFDPNLRP+LW SE  M
Sbjct: 121 SIAPQLLEARHLHATGIPPALSAAAREMSFELMTRMRNAGRSVSFDPNLRPSLWTSEQQM 180

Query: 181 IREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQL 240
           IREINRLAALAHWVLPGL+EGRLLTG +DPADIAAFYLDQGAEAV IKLG  GAYYRT L
Sbjct: 181 IREINRLAALAHWVLPGLSEGRLLTGFEDPADIAAFYLDQGAEAVAIKLGPAGAYYRTHL 240

Query: 241 DAGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEG 300
           D GFV GVPV  VVDTVGAGDGFAVGLISALLE+  + +AVQRANWIGSRAVQSRGDMEG
Sbjct: 241 DEGFVAGVPVETVVDTVGAGDGFAVGLISALLENHSVAQAVQRANWIGSRAVQSRGDMEG 300

Query: 301 LPLRHEL 307
           LP R E+
Sbjct: 301 LPTRLEM 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: 480
Number of extensions: 16
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: 339
Length adjustment: 28
Effective length of query: 292
Effective length of database: 311
Effective search space:    90812
Effective search space used:    90812
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: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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