Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_011158428.1 TX73_RS14685 2-dehydro-3-deoxyphosphooctonate aldolase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000195775.1:WP_011158428.1 Length = 287 Score = 110 bits (274), Expect = 6e-29 Identities = 79/249 (31%), Positives = 121/249 (48%), Gaps = 24/249 (9%) Query: 122 IVGPCAVESYEQVAEVAAAAKKQGIKILRGGAFKP------RTSPYDFQGLGVEG-LQIL 174 I GPC +ES EVA+A K+ ++ G +K RTS +GLG++ L I Sbjct: 27 IAGPCQLESRAHALEVASALKEIATRLGIGLVYKTSFDKANRTSAASARGLGLDAALPIF 86 Query: 175 KRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGL 234 + D L V++++ A + +D++QI A + +LL AA A + V +K+G Sbjct: 87 AEIRDHLGLPVLTDVHENEQCARAAEAVDILQIPAFLCRQTDLLLAAAATGRIVNVKKGQ 146 Query: 235 AATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTL--DISAVPILKQETHLPVFV 292 + N I GN ++++ ERG+ + NTL D+ A+PI+ + T PV Sbjct: 147 FLAPWDMGNVVSKITHAGNSKVLVTERGV----SFGYNTLVSDMRALPIMAKTTGAPVIF 202 Query: 293 DVTHST-----------GRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIP 341 D THS G R+ + A+AA+A+G GV E HPDP A SD + + Sbjct: 203 DATHSVQQPGGKGTSSGGEREYVPVLARAAVAVGVAGVFIETHPDPDHAPSDGPNMVPLR 262 Query: 342 EFEKWLNEL 350 EFE + L Sbjct: 263 EFEALIKTL 271 Lambda K H 0.316 0.134 0.369 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: 225 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: 358 Length of database: 287 Length adjustment: 28 Effective length of query: 330 Effective length of database: 259 Effective search space: 85470 Effective search space used: 85470 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: 48 (23.1 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