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_011973036.1 MAEO_RS01575 fructose-bisphosphate aldolase
Query= SwissProt::Q6LZE3 (272 letters) >NCBI__GCF_000017185.1:WP_011973036.1 Length = 271 Score = 437 bits (1125), Expect = e-128 Identities = 213/271 (78%), Positives = 245/271 (90%), Gaps = 1/271 (0%) Query: 1 MEMFDNIKNVGKLIRLERIFDKKSEKTVIIPMDHGVSSGPLDGIKDMRITTNAVADGGAN 60 M+MF+NIKN GKLIRLERIFDKKSEKTVIIPMDHGVSSGP+ G+KDMR N+VA+GGAN Sbjct: 1 MKMFNNIKNTGKLIRLERIFDKKSEKTVIIPMDHGVSSGPVAGLKDMRTAINSVAEGGAN 60 Query: 61 AVLGHKGLVRHGHRGYGRDIGLIIHMSAGTSISPDPNKKVIVTTVEDAMRMGADAVSLHV 120 +VL HKG+VRHGHRGYG+DIGLIIH+SAGT +SPDPN+KVIVT+VE+A+RMGADAVS+HV Sbjct: 61 SVLVHKGIVRHGHRGYGKDIGLIIHLSAGTGVSPDPNEKVIVTSVEEAIRMGADAVSVHV 120 Query: 121 NVGAESDFEMYRDLGLISETCEHWGMPLIAMMYPRGPKIKDEKDPEVVAHAARLGAELGA 180 N+GA +D +MY+DLG I+ETCE+WGMPLIAMMYPRG KI DEKDPE VAHAARLGAELGA Sbjct: 121 NMGAPTDCQMYQDLGKIAETCEYWGMPLIAMMYPRGEKITDEKDPEFVAHAARLGAELGA 180 Query: 181 DIIKTNYTGDPDTFKEVVKGCPAPIVIAGGPKTNTDEEFLQMVKDAMHAGGKGVASGRNV 240 DIIKTNYTGD D+FK+VVKGCPAPI+IAGG K +TD E+LQMVKD++ AGG GVASGRNV Sbjct: 181 DIIKTNYTGDIDSFKDVVKGCPAPIIIAGGAK-STDAEYLQMVKDSIEAGGAGVASGRNV 239 Query: 241 FQHKDVKGITSAICKIVHEDVEVEEALKEIK 271 FQHKDV GIT A +VHE+ +VEEALK IK Sbjct: 240 FQHKDVIGITKATAMVVHENADVEEALKVIK 270 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: 408 Number of extensions: 22 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: 271 Length adjustment: 25 Effective length of query: 247 Effective length of database: 246 Effective search space: 60762 Effective search space used: 60762 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