Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase; ADH synthase; ADHS; ADTH synthase; EC 2.2.1.10 (characterized)
to candidate WP_018124637.1 B149_RS0107855 fructose-bisphosphate aldolase
Query= SwissProt::Q6LZE3 (272 letters) >NCBI__GCF_000375485.1:WP_018124637.1 Length = 265 Score = 314 bits (805), Expect = 1e-90 Identities = 146/260 (56%), Positives = 195/260 (75%), Gaps = 1/260 (0%) Query: 10 VGKLIRLERIFDKKSEKTVIIPMDHGVSSGPLDGIKDMRITTNAVADGGANAVLGHKGLV 69 +GK +R+ERI ++ + +T+++P+DHGV+ GP+ G+ D+R T N VA+GGANA+L HKG+ Sbjct: 3 LGKAVRMERIMNRNNGRTIVVPIDHGVTVGPIYGLVDLRKTVNQVAEGGANAMLMHKGIP 62 Query: 70 RHGHRGYGRDIGLIIHMSAGTSISPDPNKKVIVTTVEDAMRMGADAVSLHVNVGAESDFE 129 R HR YG DIGLIIH+SA TS+SP PN K +V TVEDA+ +GADAVSLH+N+G E++ Sbjct: 63 RCSHRNYGPDIGLIIHLSASTSLSPYPNAKTLVATVEDALSLGADAVSLHINLGDETEPR 122 Query: 130 MYRDLGLISETCEHWGMPLIAMMYPRGPKIKDEKDPEVVAHAARLGAELGADIIKTNYTG 189 M DLG + WGMP++AMMY RGPK+ DE DP VVAH AR+G ELGADI+K NYTG Sbjct: 123 MLADLGAVCSEANKWGMPVLAMMYARGPKVTDEYDPAVVAHCARVGVELGADIVKVNYTG 182 Query: 190 DPDTFKEVVKG-CPAPIVIAGGPKTNTDEEFLQMVKDAMHAGGKGVASGRNVFQHKDVKG 248 PD+F+ VV G C P+VIAGGPK +D + +QMV D++ AGG G++ GRN+FQH D Sbjct: 183 APDSFRNVVNGACGVPVVIAGGPKLESDRDIVQMVHDSIQAGGSGLSVGRNIFQHADPSR 242 Query: 249 ITSAICKIVHEDVEVEEALK 268 I A+ K+VHED V+ A++ Sbjct: 243 IVKALHKVVHEDWSVDAAME 262 Lambda K H 0.317 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: 315 Number of extensions: 17 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: 272 Length of database: 265 Length adjustment: 25 Effective length of query: 247 Effective length of database: 240 Effective search space: 59280 Effective search space used: 59280 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: 41 (21.6 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 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