Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_085639309.1 MGEO_RS14630 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_002115805.1:WP_085639309.1 Length = 504 Score = 130 bits (327), Expect = 1e-34 Identities = 83/261 (31%), Positives = 130/261 (49%), Gaps = 9/261 (3%) Query: 186 GFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLT----YRLGRRHNTPVRSFLLQL 241 G+++ V A + I AG +V+ ++ + DFPL YR RR N F Sbjct: 233 GYKQAVEKAKEYIRAGDIFQVVPAQ----RWTQDFPLPPFALYRSLRRTNPSPFMFYFNF 288 Query: 242 GGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAIS 301 GG + +G SPE++ V V I P+AGTR G PA D DL +++KE EH + Sbjct: 289 GGFQVIGASPEILVRVFGSEVTI-RPIAGTRPRGATPAEDDALEADLLADAKECAEHLML 347 Query: 302 VRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVT 361 + ++ +A+ G+ + + V H+ S + L D ++AL A PA T Sbjct: 348 LDLGRNDVGRVAKIGTVRPTEKFIIERYSHVMHIVSNVVGELSDDHDALSALLAGLPAGT 407 Query: 362 ASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAG 421 SG PK +E I L+ RG+Y G V SA G +D + LR A + +++AG G Sbjct: 408 VSGAPKVRAMEIIDELEPEKRGIYGGGVGYFSAGGDMDMCIALRTALVKDKKLYIQAGGG 467 Query: 422 IIEESEPEREFEETCEKLSTL 442 ++ +S+PE E++ET K + + Sbjct: 468 VVYDSDPEAEYQETVHKSNAI 488 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: 450 Number of extensions: 23 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: 450 Length of database: 504 Length adjustment: 33 Effective length of query: 417 Effective length of database: 471 Effective search space: 196407 Effective search space used: 196407 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 Jul 26 2024. The underlying query database was built on Jul 25 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