Align Probable 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_085122149.1 B9O00_RS09055 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Query= SwissProt::Q92RN8 (212 letters) >NCBI__GCF_900177295.1:WP_085122149.1 Length = 208 Score = 176 bits (446), Expect = 3e-49 Identities = 93/197 (47%), Positives = 123/197 (62%) Query: 11 RPLIAILRGLKPEEAEGVVGALIETGFTAIEIPLNSPDPFRSIETAVKMAPAGCLIGAGT 70 R L+AILRGL PEEA V AL+E G +E+PLNSP PF SI + +GAGT Sbjct: 2 RELMAILRGLTPEEAPAVGEALVEAGIQRLEVPLNSPRPFESIALLAERLGGRAEVGAGT 61 Query: 71 VLTTAQVERLADVGGRLMVSPNVEPAVIRLAATKGMVTMPGVFTPTEALAAAAAGASGLK 130 VLT +V ++ GR +VSPN + +I G+ + PG FT TE L AAAAGA+ LK Sbjct: 62 VLTPGEVRKVRAARGRFVVSPNTDRVIIEATRDAGLDSYPGAFTATECLVAAAAGATALK 121 Query: 131 FFPASVLGPSGITAIRAVLPGDLEIAAVGGVSEVNFADYAAIGIRSFGLGSSLYKPGMSA 190 FPA +LGP+G+ A++AV+P L + AVGG+ + + Y G FGLGS+LYK G +A Sbjct: 122 LFPAFLLGPAGVAALKAVMPPALALYAVGGIDAPDLSAYRRAGCIGFGLGSNLYKLGRAA 181 Query: 191 GDVRQRAIATLAAYDAV 207 G+V A + AYDA+ Sbjct: 182 GEVGAAARRLVEAYDAL 198 Lambda K H 0.318 0.136 0.387 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: 151 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: 212 Length of database: 208 Length adjustment: 21 Effective length of query: 191 Effective length of database: 187 Effective search space: 35717 Effective search space used: 35717 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 (21.7 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Apr 09 2024. 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