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 HSERO_RS05155 HSERO_RS05155 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Query= SwissProt::Q92RN8 (212 letters) >FitnessBrowser__HerbieS:HSERO_RS05155 Length = 212 Score = 184 bits (468), Expect = 8e-52 Identities = 100/195 (51%), Positives = 128/195 (65%) Query: 13 LIAILRGLKPEEAEGVVGALIETGFTAIEIPLNSPDPFRSIETAVKMAPAGCLIGAGTVL 72 +IAILRG++ EAE + AL E+GF IE+PLNSP+P SI K PA C++GAGTVL Sbjct: 17 MIAILRGVRNAEAEAIGAALYESGFRIIEVPLNSPEPLLSITALRKSLPADCIVGAGTVL 76 Query: 73 TTAQVERLADVGGRLMVSPNVEPAVIRLAATKGMVTMPGVFTPTEALAAAAAGASGLKFF 132 AQVE++ D GG L+V P+ + AVIR A G+ + PGV T TEA AA GA LK F Sbjct: 77 KPAQVEQVKDAGGELIVMPHSDGAVIRAARDAGLYSAPGVATVTEAFAALDNGADVLKMF 136 Query: 133 PASVLGPSGITAIRAVLPGDLEIAAVGGVSEVNFADYAAIGIRSFGLGSSLYKPGMSAGD 192 PA LGP + A RAV+ D+ + VGG++ A + A G FGLGS+LY PG+SA Sbjct: 137 PAEQLGPQVVKAWRAVIARDIALLPVGGITPEGMAVFHAAGASGFGLGSALYTPGLSAEQ 196 Query: 193 VRQRAIATLAAYDAV 207 VRQRA A +AA+ A+ Sbjct: 197 VRQRAEAFVAAWKAL 211 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: 160 Number of extensions: 10 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: 212 Length adjustment: 21 Effective length of query: 191 Effective length of database: 191 Effective search space: 36481 Effective search space used: 36481 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 Sep 17 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