GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Pseudomonas simiae WCS417

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 GFF2379 PS417_12130 ketodeoxygluconokinase

Query= SwissProt::E0J5J4
         (309 letters)



>FitnessBrowser__WCS417:GFF2379
          Length = 309

 Score =  289 bits (739), Expect = 7e-83
 Identities = 162/305 (53%), Positives = 197/305 (64%), Gaps = 7/305 (2%)

Query: 1   MSKKIAVIGECMIELSEKG-ADVKRGFGGDTLNTSVYIARQVDPAALTVHYVTALGTDSF 59
           +S +IA+IGECMIEL  +    + + FGGDTLNT+VY+ R++     +V YVTALG DSF
Sbjct: 4   LSPRIALIGECMIELQHRADGSLHQSFGGDTLNTAVYLRRELGETG-SVDYVTALGDDSF 62

Query: 60  SQQMLDAWHGENVDTSLTQRMENRLPGLYYIETDSTGERTFYYWRNEAAAKFWLESEQSA 119
           S  M   W  E +     QR+  RLPGLY I+TD+ GER F YWRNEAA +    +  + 
Sbjct: 63  SDAMCKQWKDEGLGLGRVQRLPGRLPGLYCIQTDANGERKFLYWRNEAAVRDCFTTPAAE 122

Query: 120 AICEELANFDYLYLSGISLAILSPTSREKLLSLLRECRANGGKVIFDNNYRPRLWASKEE 179
            I   L ++D +Y SGI+LA+L    RE+LL  L E R  GGKV+FDNNYRPRLWA  E 
Sbjct: 123 PILAALPDYDVVYFSGITLAVLGDIGRERLLQTLVETRRRGGKVVFDNNYRPRLWAGIEA 182

Query: 180 TQQVYQQMLECTDIAFLTLDDEDALWGQQPVEDVIARTHNAGVKEVVVKRGADSCLVSIA 239
            +  Y ++L   DIA LT DDE AL+G    E V A     G+ EVV+KRGAD CL+  A
Sbjct: 183 ARTAYHRVLAEVDIALLTEDDERALFGYADSEQVFAA--YPGIDEVVLKRGADDCLIRWA 240

Query: 240 GEGLVDVPAVKLPKEKVIDTTAAGDSFSAGYLAVRLTGGSAENAAKRGHLTASTVIQYRG 299
           GE    VPAVK+  EKV+DTTAAGDSFSA YLA RL G S E AA  GH  AS VIQ  G
Sbjct: 241 GERFA-VPAVKV--EKVVDTTAAGDSFSAAYLASRLKGSSPEQAALAGHRLASRVIQVPG 297

Query: 300 AIIPR 304
           A+IPR
Sbjct: 298 ALIPR 302


Lambda     K      H
   0.316    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: 291
Number of extensions: 15
Number of successful extensions: 5
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: 309
Length adjustment: 27
Effective length of query: 282
Effective length of database: 282
Effective search space:    79524
Effective search space used:    79524
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 (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