Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_011308530.1 MBAR_RS19240 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000195895.1:WP_011308530.1 Length = 547 Score = 133 bits (335), Expect = 1e-35 Identities = 89/266 (33%), Positives = 129/266 (48%), Gaps = 4/266 (1%) Query: 180 VSDDPSG---FRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRS 236 VSD +G F V A + I AG +V+LSR E Y R N Sbjct: 275 VSDCNAGKKKFEDSVVQAKEHIFAGDIFQVVLSRKCEFTLEQSPFELYMQLRAINPSPYM 334 Query: 237 FLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIV 296 ++ + G + +G SPE + V + +IT P+AGT G+ A D + + KE Sbjct: 335 YIFEFGDLAIVGASPETLLTVH-ERTLITNPIAGTCPRGKTEAEDEAFAAHMMHDEKERA 393 Query: 297 EHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEAL 356 EH + V ++ + E GS V +FM V + VQH+ S + L P D+ A A+ Sbjct: 394 EHVMLVDLGRNDVRMVTESGSVKVSEFMKVLKYSHVQHIESKVIGTLRPECDQFDAFRAI 453 Query: 357 FPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWL 416 FPA T SG PK +E I L+ PRG+Y G V S +G D A+ +R G + + Sbjct: 454 FPAGTLSGAPKIRAMEIISELETSPRGIYGGGVGYYSWNGDADFAIVIRTIIVQGKKASV 513 Query: 417 RAGAGIIEESEPEREFEETCEKLSTL 442 +AGAGI+ +S+P EF ET K+ + Sbjct: 514 QAGAGIVADSDPGYEFRETERKMGAM 539 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: 479 Number of extensions: 21 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 450 Length of database: 547 Length adjustment: 34 Effective length of query: 416 Effective length of database: 513 Effective search space: 213408 Effective search space used: 213408 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: 52 (24.6 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