Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate BPHYT_RS24155 BPHYT_RS24155 5-dehydro-4-deoxyglucarate dehydratase
Query= BRENDA::Q7CU96 (298 letters) >FitnessBrowser__BFirm:BPHYT_RS24155 Length = 305 Score = 96.7 bits (239), Expect = 6e-25 Identities = 79/272 (29%), Positives = 131/272 (48%), Gaps = 8/272 (2%) Query: 12 GISGVPVTAYDADGEISFDITAEAYARVARAGIHNIVAAGNTGEFYALTPAEILTVYEAA 71 G+ PVT +D G+ D AE +A G + AG TGEF++LT + V + A Sbjct: 14 GLLSFPVTDFDEQGDFRADTYAERLEWLAPYGASALFVAGGTGEFFSLTHNDYSNVVKTA 73 Query: 72 IKGVDGIAPVTAAIGRSQREAIAMARTAKELGASAVMSHQPVDPFAAPQSQIAYFLGLAE 131 + G P+ A G R AIA A+ A+ GA+ ++ A + A+ + + Sbjct: 74 TEVCKGKVPILAGAGGPTRVAIAYAQEAERHGANGILLMPHYLTEACQEGIAAHAEEVCK 133 Query: 132 D-SALPLVAYVRADGFAVDDMVR--LSSHPNVAGIKFATTDIMLLSRAIAASDADGALYI 188 + ++ Y RA+ DM+ PN+ G K +I + +I D Y+ Sbjct: 134 SVPNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMV-SIRRRLGDRFSYL 192 Query: 189 CGL--AESWAPAFAAVGARGFTSGLVNVAPHFSMQVHEALMAGDFDSARKIVEKIEL-FE 245 GL AE +A A+ A+G ++S + N P +M + A+ A D + K++++ L + Sbjct: 193 GGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATVGKLIDEFFLPYL 252 Query: 246 RLRTRYRNGANVTVVKEAMEIMGLAVGPVRAP 277 +R R R G V++VK +++G + GPVRAP Sbjct: 253 AIRNR-RAGYAVSIVKAGAKLVGHSAGPVRAP 283 Lambda K H 0.321 0.134 0.381 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: 208 Number of extensions: 13 Number of successful extensions: 2 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: 298 Length of database: 305 Length adjustment: 27 Effective length of query: 271 Effective length of database: 278 Effective search space: 75338 Effective search space used: 75338 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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