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 BPHYT_RS16945 BPHYT_RS16945 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Query= SwissProt::Q6BF16 (205 letters) >FitnessBrowser__BFirm:BPHYT_RS16945 Length = 226 Score = 171 bits (434), Expect = 7e-48 Identities = 92/196 (46%), Positives = 122/196 (62%) Query: 8 PLIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAGTV 67 PLIAI+RG+TP +A H A+ +AGF VE+PLNSPQ SI AI A++GAGTV Sbjct: 25 PLIAIMRGVTPADAAEHGQALYEAGFRIVEVPLNSPQPFDSIAAIRKVLPADAIVGAGTV 84 Query: 68 LKPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEAGAQALKI 127 L P VD + G +LIV P+ EV+ A GM PG AT EAF AL+ GA LK+ Sbjct: 85 LHPSFVDDVKSAGGELIVMPHSDPEVVSAAKARGMACAPGVATPNEAFIALKNGADVLKM 144 Query: 128 FPSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQSVE 187 FP+ G Q +KA +AV+ +++ + VGG+TP+N+ ++ AG G GLGS LY+ GQS Sbjct: 145 FPAEQLGCQVVKAWRAVIAAEVPLVPVGGITPDNMGPFLSAGANGFGLGSALYKPGQSAA 204 Query: 188 RTAQQAAAFVKAYREA 203 TA A A++ R A Sbjct: 205 VTASHAKAYINGLRIA 220 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: 152 Number of extensions: 3 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: 226 Length adjustment: 22 Effective length of query: 183 Effective length of database: 204 Effective search space: 37332 Effective search space used: 37332 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 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