Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_066920128.1 ACG33_RS07755 hypothetical protein
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_001579945.1:WP_066920128.1 Length = 481 Score = 135 bits (339), Expect = 4e-36 Identities = 87/259 (33%), Positives = 130/259 (50%), Gaps = 3/259 (1%) Query: 182 DDPSGFRRRVAVAVDEIAAGRYHKVILSRC--VEVPFAIDFPLTYRLGRRHNTPVRSFLL 239 D P + R V A+ IAAG ++ LSRC + + Y+ RR N + + Sbjct: 204 DPPEHYLRMVERALAYIAAGEIYQANLSRCWRARLRAGTEAHHVYQRLRRTNPGPFNAIA 263 Query: 240 QLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHA 299 + + + SPE + VRA G V T P+AGTR G PA D +L + KE EH Sbjct: 264 MIDEMAVISSSPERLVEVRA-GQVSTRPIAGTRPRGPNPAADTALLRELREHPKERAEHI 322 Query: 300 ISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPA 359 + + ++ I +PG+ V ++M++ V H+ S +R RL L A+FP Sbjct: 323 MLIDLERNDLGRICQPGTVRVDEYMSIESYTHVHHIVSNVRGRLREDVSPGEVLAAVFPG 382 Query: 360 VTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAG 419 T +G PK +E I L++ RG Y+G++ L+ DG +D + +R+ G LRAG Sbjct: 383 GTITGCPKVRCMEIIGELEQQARGAYTGSLGYLNLDGSMDLNILIRSLQLYGDTVSLRAG 442 Query: 420 AGIIEESEPEREFEETCEK 438 AGI+ +S P RE EET K Sbjct: 443 AGIVADSIPMRELEETRAK 461 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: 522 Number of extensions: 25 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: 481 Length adjustment: 33 Effective length of query: 417 Effective length of database: 448 Effective search space: 186816 Effective search space used: 186816 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 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