GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Pseudomonas fluorescens FW300-N2E3

Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate AO353_21745 AO353_21745 ketodeoxygluconokinase

Query= SwissProt::P45416
         (310 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21745
          Length = 311

 Score =  299 bits (766), Expect = 5e-86
 Identities = 159/303 (52%), Positives = 203/303 (66%), Gaps = 5/303 (1%)

Query: 3   TKNIAIIGECMIELSQKG-ADLNRGFGGDTLNTAVYISRQVKPDALDVHYVTALGTDSFS 61
           T  IA+IGECMIEL Q+    L + FGGDTLNTAVY+SR++  D   V YVTALG DSFS
Sbjct: 11  TPRIALIGECMIELQQRADGSLQQSFGGDTLNTAVYLSREMG-DGATVDYVTALGDDSFS 69

Query: 62  SEMMASWQKEGVKTDLIQRLDNKLPGLYFIETDATGERTFYYWRNDAAARYWLESPDADT 121
             M  SW +EG+   ++QRL  +LPGLY I+TDA+GER F YWRN+AA R    +P A  
Sbjct: 70  DAMCQSWSEEGIGLGMVQRLPGRLPGLYCIQTDASGERRFLYWRNEAAVRDCFTTPAAAP 129

Query: 122 ISQQLAQFDYIYLSGISLAILNQASRARLLTVLRACRANGGKVIFDNNYRPRLWQSKEET 181
           I   LA +D +Y SGI+LA+L +A R +L+  L   R    +++FDNNYRPRLW S E+ 
Sbjct: 130 ILAALADYDVLYFSGITLAVLGEAGRKKLIETLIEARQRDARIVFDNNYRPRLWSSVEQA 189

Query: 182 RQAYSDMLACTDIAFLTLDDEDMLWGELPVDEVLKRTHGAGVMEVVIKRGADACLVSIQG 241
           R AY ++L   D+A LT+DDE  L+G      V       G+ EVV+KRGA+ CL+   G
Sbjct: 190 RTAYREVLPYVDLALLTVDDEQALFGFSDEAAVFAAYEQIGIPEVVLKRGAEPCLIRCDG 249

Query: 242 EALLEVPAIKLPKEKVVDTTAAGDSFSAGYLSVRLNGGSAQDAAKRGHLTASTVIQYRGA 301
           E+  EVPA+++  E+VVDTTAAGDSFSA YL+ RL G S  +AA+ GH  AS VIQ  GA
Sbjct: 250 ES-FEVPALRV--ERVVDTTAAGDSFSAAYLASRLRGASPAEAAEAGHRLASRVIQVPGA 306

Query: 302 IIP 304
           +IP
Sbjct: 307 LIP 309


Lambda     K      H
   0.318    0.134    0.390 

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: 285
Number of extensions: 11
Number of successful extensions: 4
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: 310
Length of database: 311
Length adjustment: 27
Effective length of query: 283
Effective length of database: 284
Effective search space:    80372
Effective search space used:    80372
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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