GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoA in Pedobacter sp. GW460-11-11-14-LB5

Align 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16; EC 4.1.2.55) (characterized)
to candidate CA265_RS19860 CA265_RS19860 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase

Query= metacyc::MONOMER-4906
         (205 letters)



>FitnessBrowser__Pedo557:CA265_RS19860
          Length = 219

 Score =  107 bits (268), Expect = 1e-28
 Identities = 66/213 (30%), Positives = 116/213 (54%), Gaps = 20/213 (9%)

Query: 9   KHKIV-AVLRA--------NSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLK 59
           KHKI+ A+L          +S   + E    +++ GV + E T     A    K+L  ++
Sbjct: 4   KHKILDAILEQGMLPLFYQDSESGSVEILRTLYKAGVRVFEYTNRGKSALPNFKKLKEIR 63

Query: 60  EK---GAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTE 116
           +       +G GT+ +       +E+G +FIV+P ++  +++   + G+ ++PG MTPTE
Sbjct: 64  DAEMPDLYLGIGTIKTPADANAFIEAGTDFIVAPIVNPAVAEIANKIGMLWIPGCMTPTE 123

Query: 117 LVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGV--NLDNVCEWFKAGVLA 174
           +  A +    ++K+FP  ++GP+F+ ++K  F    F+PTGGV  N DN+  WFK+GV A
Sbjct: 124 ISVAQEHKAMLIKIFPANILGPEFISSIKDLFAGQLFMPTGGVEINADNLKTWFKSGVCA 183

Query: 175 VGVGSALV------KGTPDEVREKAKAFVEKIR 201
           VG+GS L+      KG  +E+ +  K  ++ I+
Sbjct: 184 VGMGSKLISKDVMSKGLYEELFDNTKLALDLIQ 216


Lambda     K      H
   0.318    0.136    0.393 

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: 131
Number of extensions: 5
Number of successful extensions: 2
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: 205
Length of database: 219
Length adjustment: 21
Effective length of query: 184
Effective length of database: 198
Effective search space:    36432
Effective search space used:    36432
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 (21.7 bits)
S2: 45 (21.9 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