Align Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH; EC 4.1.2.28 (characterized)
to candidate BPHYT_RS29250 BPHYT_RS29250 dihydrodipicolinate synthase
Query= SwissProt::P39359 (301 letters) >FitnessBrowser__BFirm:BPHYT_RS29250 Length = 307 Score = 98.6 bits (244), Expect = 2e-25 Identities = 80/243 (32%), Positives = 124/243 (51%), Gaps = 18/243 (7%) Query: 1 MKKFSGIIPPVSSTFHRDGTLDKKAMREVADFLINKGVDGLFYLGTGGEFSQMNTAQRMA 60 M FSGI P+ + F DG +D A+R + G+ GL LGT GE + ++ A++ A Sbjct: 1 MSIFSGIWVPLITPF-ADGAVDHAALRALVRRYTGAGIAGLVALGTTGEPAALDAAEQDA 59 Query: 61 L-------AEEAVTIV-DGR-VPVLIGV-GSPSTDEAVKLAQHAQAYGADGIVAINPYYW 110 + A+ A + DG+ +PV+ GV G+ + V++ Q A G++ PYY Sbjct: 60 VLATILDEAQSAAHLARDGQALPVVAGVSGNHTASMRVRIGQ-LNALPLAGVLMAAPYYI 118 Query: 111 KVAPRNLDDYYQQIARSVTLPVILYNFPDLTGQDLTPETVTRLALQNENIVGIKDTIDSV 170 + + + ++ +A + PV+LY+ P TG L +T+ LA + I +KD Sbjct: 119 RPSQAGIVAHFMALADASEKPVVLYDIPYRTGVRLELDTLLALAT-HPRIQAVKDC---A 174 Query: 171 GHLRTMINTVKSVRPSFSVFCGYDDHLLNTMLLGGDGAITASANFAPELSVGIYRAWREG 230 G L T + ++ R V G D ++ NT+ LGG GAI ASA+ PE V +YRA G Sbjct: 175 GSLDTTLALIRDAR--LQVLAGEDINIFNTLCLGGSGAIAASAHVRPERFVEMYRALAAG 232 Query: 231 DLA 233 LA Sbjct: 233 RLA 235 Lambda K H 0.319 0.137 0.398 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: 206 Number of extensions: 11 Number of successful extensions: 3 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: 301 Length of database: 307 Length adjustment: 27 Effective length of query: 274 Effective length of database: 280 Effective search space: 76720 Effective search space used: 76720 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: 48 (23.1 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