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_053937132.1 WG78_RS07225 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Query= SwissProt::Q6BF16 (205 letters) >NCBI__GCF_001294205.1:WP_053937132.1 Length = 205 Score = 267 bits (682), Expect = 1e-76 Identities = 137/201 (68%), Positives = 158/201 (78%) Query: 1 MQWQTKLPLIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKA 60 M + LPLIAILRGITP E AH+ A+IDAGF +EIPLNSP W SI V +G +A Sbjct: 1 MSNNSPLPLIAILRGITPQETPAHIEALIDAGFGLIEIPLNSPDWHSSIALAVRQFGQRA 60 Query: 61 LIGAGTVLKPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEA 120 IGAGTVL+P QVD LA++G +LIVTPN + VI RAVG+ + V GCATATEAFTAL+A Sbjct: 61 QIGAGTVLQPAQVDQLAQLGARLIVTPNTNPAVISRAVGHQLQVYAGCATATEAFTALQA 120 Query: 121 GAQALKIFPSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLY 180 GAQALKIFPSSAFGP YIKALKAVLP+ + V+AVGG+TP NLA ++ AGCAGAGLG DLY Sbjct: 121 GAQALKIFPSSAFGPAYIKALKAVLPAAVPVYAVGGITPANLADYMAAGCAGAGLGGDLY 180 Query: 181 RAGQSVERTAQQAAAFVKAYR 201 RAGQSV RTA+ A FV AYR Sbjct: 181 RAGQSVARTAELAREFVTAYR 201 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: 195 Number of extensions: 7 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: 205 Length adjustment: 21 Effective length of query: 184 Effective length of database: 184 Effective search space: 33856 Effective search space used: 33856 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