Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_026186023.1 THITHI_RS0103360 aminodeoxychorismate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000378965.1:WP_026186023.1 Length = 438 Score = 122 bits (306), Expect = 2e-32 Identities = 91/279 (32%), Positives = 127/279 (45%), Gaps = 4/279 (1%) Query: 172 VPQSRSVDVSDDPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLT--YRLGRR 229 VP S+D D P + VA + I G +V LSR + D P Y R Sbjct: 162 VPWPESLD-EDPPQRYLDGVAQVIRYIRDGDVFQVNLSRAWQARLGEDMPAADLYDRLRD 220 Query: 230 HNTPVRSFLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLE 289 N + L L G + + SPE + VR D V T P+AGTR G DR L Sbjct: 221 CNPAPFAALATLPGGQIVSSSPERLVRVRGDRVD-TRPIAGTRPRGARLEADRALATQLL 279 Query: 290 SNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDR 349 N+KE EH + + ++ + PGS V + MT+ V H+ S + RL Sbjct: 280 GNAKERAEHIMLLDLERNDLGRLCRPGSIRVDELMTLETYPHVHHIVSNVTGRLRAEVTP 339 Query: 350 MAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQ 409 + A+FP T +G PK +E I L+ RG Y+G++ L+ DG +D + +R Sbjct: 340 GEVIRAVFPGGTITGCPKVRCMEIIAELEGQGRGAYTGSLGYLNRDGDMDLNILIRTLVH 399 Query: 410 VGGRTWLRAGAGIIEESEPEREFEETCEKLSTLTPYLVA 448 G R GAGI+ +S+P RE EET K L LV+ Sbjct: 400 QGREIRFRTGAGIVADSDPRRELEETRHKAEGLRRMLVS 438 Lambda K H 0.319 0.135 0.386 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: 468 Number of extensions: 27 Number of successful extensions: 1 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: 450 Length of database: 438 Length adjustment: 32 Effective length of query: 418 Effective length of database: 406 Effective search space: 169708 Effective search space used: 169708 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: 51 (24.3 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