Align 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; 2-oxo-3-deoxygalactonate 6-phosphate aldolase; 6-phospho-2-dehydro-3-deoxygalactonate aldolase; 6-phospho-2-keto-3-deoxygalactonate aldolase; KDPGal; EC 4.1.2.21 (characterized)
to candidate WP_057509056.1 ABB28_RS13180 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Query= SwissProt::Q6BF16 (205 letters) >NCBI__GCF_001431535.1:WP_057509056.1 Length = 206 Score = 213 bits (541), Expect = 3e-60 Identities = 110/196 (56%), Positives = 135/196 (68%) Query: 7 LPLIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAGT 66 LPLIAILRGITPDE AHV +IDAG +EIP NSP W S+ + A +GAGT Sbjct: 8 LPLIAILRGITPDEVRAHVRVLIDAGISQIEIPTNSPDWLGSVQLALQEADGHAEVGAGT 67 Query: 67 VLKPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEAGAQALK 126 VL VD LA G +L+VTPN + VI A G+ + G ATA+EAF A+ AGAQ LK Sbjct: 68 VLDIADVDRLADTGARLMVTPNTNPVVIAHARSRGLDIAAGFATASEAFAAVAAGAQRLK 127 Query: 127 IFPSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQSV 186 +FP+S FG Y++ALKAVLP D+ ++AVGG+ P NLA+++ AGCAGAGLG +LYRAGQ Sbjct: 128 LFPASQFGSGYVRALKAVLPGDVPLYAVGGIGPGNLAEYLQAGCAGAGLGGELYRAGQDA 187 Query: 187 ERTAQQAAAFVKAYRE 202 TAQ A AFV A R+ Sbjct: 188 ATTAQHADAFVAALRK 203 Lambda K H 0.319 0.134 0.399 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: 157 Number of extensions: 6 Number of successful extensions: 1 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: 206 Length adjustment: 21 Effective length of query: 184 Effective length of database: 185 Effective search space: 34040 Effective search space used: 34040 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 (21.8 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
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