Align 5-keto-2-deoxy-D-gluconate-6 phosphate aldolase (EC 4.1.2.29) (characterized)
to candidate 15891 b1773 predicted aldolase (NCBI)
Query= reanno::Phaeo:GFF707 (279 letters) >FitnessBrowser__Keio:15891 Length = 278 Score = 109 bits (272), Expect = 8e-29 Identities = 74/228 (32%), Positives = 108/228 (47%), Gaps = 6/228 (2%) Query: 18 YAVAGLVTLGWEDMRAYVAAAEAEGVPVILQAGPSCRVHTPLPILGKMFRHLAEGASVPV 77 YA+A E + + AAE PVI+ G +T M +A+ A+VPV Sbjct: 17 YAIAHFNVWNAEMLMGVIDAAEEAKSPVIISFGTGFVGNTSFEDFSHMMVSMAQKATVPV 76 Query: 78 VAHLDHGYTAEDCRIAIDSGFTSVMFDGSRNALDDNIAETAAIAGMAHAAGVSCEGEIGF 137 + H DHG + E A G S+M D S ++NI T H G+ E E+G Sbjct: 77 ITHWDHGRSMEIIHNAWTHGMNSLMRDASAFDFEENIRLTKEAVDFFHPLGIPVEAELGH 136 Query: 138 VGYSG--GEGSAG---TDPEEARRFAQETGVDAMAISVGNVHLQQDKEGGLDIDRIRAIE 192 VG E AG TDP++A F + TG D++A+++GN H E L+ + ++ + Sbjct: 137 VGNETVYEEALAGYHYTDPDQAAEFVERTGCDSLAVAIGNQHGVYTSEPQLNFEVVKRVR 196 Query: 193 AITEVPLVIHGGSGVPVAQRRMLARESRICKFNIGTELRMVFGAAMRD 240 VPLV+HG SG+ A + A I K NI TEL A+++ Sbjct: 197 DAVSVPLVLHGASGISDADIK-TAISLGIAKINIHTELCQAAMVAVKE 243 Lambda K H 0.320 0.135 0.393 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: 9 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: 279 Length of database: 278 Length adjustment: 25 Effective length of query: 254 Effective length of database: 253 Effective search space: 64262 Effective search space used: 64262 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: 47 (22.7 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