GapMind for catabolism of small carbon sources

 

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

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 Pf1N1B4_5638 2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45)

Query= SwissProt::P37647
         (309 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5638
           2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45)
          Length = 310

 Score =  296 bits (758), Expect = 4e-85
 Identities = 158/302 (52%), Positives = 202/302 (66%), Gaps = 5/302 (1%)

Query: 4   KIAVIGECMIELSEKG-ADVKRGFGGDTLNTSVYIARQVDPAALTVHYVTALGTDSFSQQ 62
           +IA+IGECMIEL ++    +++ FGGDTLNT+VY+AR++     TV YVTALG DSFS  
Sbjct: 13  RIALIGECMIELQQRADGTLQQSFGGDTLNTAVYLARELGDGG-TVDYVTALGDDSFSDA 71

Query: 63  MLDAWHGENVDTSLTQRMENRLPGLYYIETDSTGERTFYYWRNEAAAKFWLESEQSAAIC 122
           M  +W  EN+   + QR+  RLPGLY I+TD+ GER F+YWRNEAA +    +  +A I 
Sbjct: 72  MCQSWASENIGLDMVQRLPGRLPGLYCIQTDAAGERRFFYWRNEAAVRDCFTTPAAAPIL 131

Query: 123 EELANFDYLYLSGISLAILSPTSREKLLSLLRECRANGGKVIFDNNYRPRLWASKEETQQ 182
             L ++D LY SGI+LA+L    REKLL  L E R    +++FDNNYRPRLWAS EE Q 
Sbjct: 132 AALPDYDVLYFSGITLAVLGVQGREKLLETLIEARQRDARIVFDNNYRPRLWASIEEAQA 191

Query: 183 VYQQMLECTDIAFLTLDDEDALWGQQPVEDVIARTHNAGVKEVVVKRGADSCLVSIAGEG 242
            Y+ +L   D+A LT+DDE AL+       V A     G  EVV+KRGA++CL+   GE 
Sbjct: 192 AYRNVLPYIDLALLTVDDEQALFHFSDCAAVFAAYEQMGTPEVVLKRGAEACLIHCDGES 251

Query: 243 LVDVPAVKLPKEKVIDTTAAGDSFSAGYLAVRLTGGSAEDAAKRGHLTASTVIQYRGAII 302
             +VPA  +  E+V+DTTAAGDSFSA YLA RL GGS  +AA+ GH  AS VIQ  GA+I
Sbjct: 252 F-EVPAQVV--ERVVDTTAAGDSFSAAYLACRLKGGSPVEAAEAGHRLASRVIQVPGALI 308

Query: 303 PR 304
           PR
Sbjct: 309 PR 310


Lambda     K      H
   0.317    0.132    0.384 

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: 286
Number of extensions: 10
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: 309
Length of database: 310
Length adjustment: 27
Effective length of query: 282
Effective length of database: 283
Effective search space:    79806
Effective search space used:    79806
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 (21.6 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 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, the preprint on GapMind for carbon sources, 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