Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate GFF707 PGA1_c07220 putative 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase
Query= BRENDA::Q8Y498 (284 letters) >FitnessBrowser__Phaeo:GFF707 Length = 279 Score = 159 bits (403), Expect = 5e-44 Identities = 102/280 (36%), Positives = 149/280 (53%), Gaps = 9/280 (3%) Query: 1 MPIVNMTDMLKKALAGKYAVGQFNINNLEWTQAILKAAEAEKAPVILGVSEGAAKYMGGF 60 M I + ++L+ AL YAV E +A + AAEAE PVIL + Sbjct: 1 MTIATLAEVLQPALRDGYAVAGLVTLGWEDMRAYVAAAEAEGVPVILQAGPSCRVHTP-L 59 Query: 61 KTVVKMTEGLVEDLKITVPVAIHLDHGSSFDSCKAAIDAGFSSVMIDGSHHPIDENIAMT 120 + KM L E +VPV HLDHG + + C+ AID+GF+SVM DGS + +D+NIA T Sbjct: 60 PILGKMFRHLAEGA--SVPVVAHLDHGYTAEDCRIAIDSGFTSVMFDGSRNALDDNIAET 117 Query: 121 KQVVDYAHAKGVSVEAEIGTVG-GDEDGVTGGINYADPQECLRVVKEANIDALAAALGSV 179 + AHA GVS E EIG VG +G G DP+E R +E +DA+A ++G+V Sbjct: 118 AAIAGMAHAAGVSCEGEIGFVGYSGGEGSAG----TDPEEARRFAQETGVDAMAISVGNV 173 Query: 180 HGPYHGEPVLGFDEMKEISELTGAPLVLHGGSGIPEHQIKK-AIELGHSKINVNTECQIV 238 H E L D ++ I +T PLV+HGGSG+P Q + A E K N+ TE ++V Sbjct: 174 HLQQDKEGGLDIDRIRAIEAITEVPLVIHGGSGVPVAQRRMLARESRICKFNIGTELRMV 233 Query: 239 WTAAVREKLATDDKVYDPRKVIGPGVDAIIKTVTEKIQEF 278 + AA+R+ + +D +D ++ D ++ ++ F Sbjct: 234 FGAAMRDAVNSDPDRFDRVSILSETHDPVVAAARSVLRAF 273 Lambda K H 0.314 0.134 0.383 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: 236 Number of extensions: 13 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: 284 Length of database: 279 Length adjustment: 26 Effective length of query: 258 Effective length of database: 253 Effective search space: 65274 Effective search space used: 65274 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: 42 (22.0 bits) S2: 47 (22.7 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