GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Pseudomonas fluorescens FW300-N2C3

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 AO356_28555 AO356_28555 ketodeoxygluconokinase

Query= SwissProt::P37647
         (309 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28555
          Length = 333

 Score =  291 bits (744), Expect = 2e-83
 Identities = 148/306 (48%), Positives = 208/306 (67%), Gaps = 4/306 (1%)

Query: 4   KIAVIGECMIEL-SEKGADVKRGFGGDTLNTSVYIARQVDPAALTVHYVTALGTDSFSQQ 62
           K+A++GECMIE+  E G  + + FGGDTLNT+VY+AR     A+ V Y+TA+G+D+FS  
Sbjct: 18  KVALVGECMIEMRGEPGTAITQTFGGDTLNTAVYLARLNPHGAVAVDYMTAVGSDAFSVA 77

Query: 63  MLDAWHGENVDTSLTQRMENRLPGLYYIETDSTGERTFYYWRNEAAAKFWLESEQSAAIC 122
           M  +W  E +  +  + +E+ LPGLY+I+TD  GER F YWR EAAA+   E  ++  + 
Sbjct: 78  MRRSWLEEGIGDAHVRVIEDALPGLYFIQTDPHGERRFLYWRGEAAARRMFEGPEADVML 137

Query: 123 EELANFDYLYLSGISLAILSPTSREKLLSLLRECRANGGKVIFDNNYRPRLWASKEETQQ 182
           + LA++DY+YLSGISLAIL+P  R++L+  L   R  G +++FDNNYRP LW   E  +Q
Sbjct: 138 DALADYDYVYLSGISLAILTPEGRQRLIQALPRARRAGTRIVFDNNYRPHLWLDPESARQ 197

Query: 183 VYQQMLECTDIAFLTLDDEDALWGQQPVEDVIARTHNAGVKEVVVKRGADSCLVSIAGEG 242
           VY+ +L+ TD+A LT +D+ AL+G +  + + +     GV+EV +KRGA SCL+     G
Sbjct: 198 VYRDLLQLTDLALLTWEDDVALFGYRDPDALFSAYAQVGVREVALKRGAASCLIQ-CPTG 256

Query: 243 LVDVPAVKLPKEKVIDTTAAGDSFSAGYLAVRLTGGSAEDAAKRGHLTASTVIQYRGAII 302
             +VPA  +    V+DTTAAGDSFSA YLA RL GG  + AA+ GH  A+ V+QYRGA+I
Sbjct: 257 RFEVPAQTV--SHVVDTTAAGDSFSAAYLACRLRGGDPQQAARWGHRLAAQVVQYRGALI 314

Query: 303 PREAMP 308
           P+ AMP
Sbjct: 315 PQAAMP 320


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: 295
Number of extensions: 10
Number of successful extensions: 3
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: 333
Length adjustment: 28
Effective length of query: 281
Effective length of database: 305
Effective search space:    85705
Effective search space used:    85705
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