Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_315861777.1 H567_RS0104695 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000422285.1:WP_315861777.1 Length = 300 Score = 109 bits (272), Expect = 1e-28 Identities = 84/254 (33%), Positives = 127/254 (50%), Gaps = 21/254 (8%) Query: 116 DGQQRFIVGPCAVESYEQVAEVAAAAKKQG----IKILRGGAFKP--RTSPYDFQGLGVE 169 +G I GPC +E VA ++ G I ++ ++ RTS ++G G+E Sbjct: 42 EGPFFLIAGPCVIEDEAVALHVADRLRELGDDLDIPVIYKSSYDKANRTSLGSYRGPGLE 101 Query: 170 -GLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPV 228 GL+IL +V + LAV+S++ P + A + +DVIQI A + +L+ AA PV Sbjct: 102 KGLEILWKVKESTGLAVLSDVHRPEDMAAAAEVLDVIQIPAFLCRQTDLVVAAARTGLPV 161 Query: 229 LLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHL 288 LK+G + E A+ I++ GN+QI+L ERG +D+ A+ +++ Sbjct: 162 NLKKGQFLSPWEMGPASGKILAAGNEQILLTERGASF--GYNNLVVDMRAIAVMR-GLGF 218 Query: 289 PVFVDVTHST-----------GRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQ 337 PV D THS G+R+ + A+AA+A GADGV EVHPDP AL D Sbjct: 219 PVVFDATHSVQLPGGEGTCSGGQREFVGHLARAAVAAGADGVFMEVHPDPDQALCDGPNS 278 Query: 338 MAIPEFEKWLNELK 351 + I + L LK Sbjct: 279 LPIQDVRPLLRLLK 292 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: 240 Number of extensions: 10 Number of successful extensions: 2 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: 300 Length adjustment: 28 Effective length of query: 330 Effective length of database: 272 Effective search space: 89760 Effective search space used: 89760 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 09 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