GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4765
          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.

Links

Downloads

Related tools

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