Align fructose-1,6-bisphosphate aldolase subunit (EC 4.1.2.13) (characterized)
to candidate WP_078717302.1 B5D49_RS08675 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase
Query= metacyc::MONOMER-11810 (281 letters) >NCBI__GCF_900167125.1:WP_078717302.1 Length = 270 Score = 166 bits (421), Expect = 4e-46 Identities = 95/264 (35%), Positives = 151/264 (57%), Gaps = 13/264 (4%) Query: 12 RLKRFFRRD-GRALIFAMDHGFEHGPTDFEPVWEHVNPRVIIRKVVRAGIDGVMMLPGLA 70 R++R RD GR ++ +DHG GP ++ V+ R + KV G + V+M GL Sbjct: 8 RMERIMNRDNGRLIVVPLDHGVTVGP-----IYGLVDLRDTVNKVADGGANAVLMHKGLP 62 Query: 71 RIAGDEVKPEVGLMIKLTSKTNLRPKPEQLLQSQLGFVDDAIKLGADAIAATVYWGSPQE 130 R + ++GL++ L++ T L P P ++ +G V+DAIKLGADA++ V G E Sbjct: 63 RCSHRGTGRDIGLIVHLSASTALSPTPNA--KTMVGTVEDAIKLGADAVSIHVNLGDESE 120 Query: 131 DVMMRQFAEIVSYAHDLGYPVVQFAYPRGPYIDEKYGKKEDYRVVMYGARAAAESGADMI 190 M+ + S A D G PV+ Y RGP + ++Y VV + AR E GAD++ Sbjct: 121 RSMLSDLGALCSRAGDWGMPVLAMLYARGPKVKDEYAPD----VVAHCARVGMELGADIV 176 Query: 191 KTYWTGSKETFAKVVEAAAGVPVLLSGGAKTENPVDFLKVVWEVIEAGGAGAVVGRNIFQ 250 K +TG E+F +V E VPV+++GG K ++ D +++V + ++AGGAG VGRNIFQ Sbjct: 177 KVNYTGDPESFQRVTEGCC-VPVVIAGGPKVDSNYDLVRMVHDSVQAGGAGISVGRNIFQ 235 Query: 251 RENPEPMIKALIRVIHRNEDPEEA 274 ++P ++++L +V+H E+A Sbjct: 236 HDHPARLVRSLYKVVHEGWSVEQA 259 Lambda K H 0.320 0.138 0.409 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: 196 Number of extensions: 10 Number of successful extensions: 5 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: 281 Length of database: 270 Length adjustment: 25 Effective length of query: 256 Effective length of database: 245 Effective search space: 62720 Effective search space used: 62720 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 Jul 25 2024. The underlying query database was built on Jul 25 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