Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_028489903.1 Q394_RS0114525 aminodeoxychorismate synthase, component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000621325.1:WP_028489903.1 Length = 449 Score = 106 bits (265), Expect = 1e-27 Identities = 88/288 (30%), Positives = 129/288 (44%), Gaps = 12/288 (4%) Query: 159 EAIDRLLATGVREVPQSRSVDVS---DDPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVP 215 EAI ++ AT + R VS D P F V D I+AG +V LSR Sbjct: 153 EAIAKVDATSSSSPDKERPGGVSLSEDPPEHFTSGVERIRDYISAGDVFQVNLSRAWRGE 212 Query: 216 F-----AIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRADGVVITEPLAG 270 A+D YR R N + L + SPE + V +G V T P+AG Sbjct: 213 LHAEQRAVDL---YRQLRTTNPAPFACLADFHDFAIISSSPERLVRVH-NGTVDTRPIAG 268 Query: 271 TRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERG 330 TR G A D+ ++L ++ KE EH + + ++ I G+ V + MTV Sbjct: 269 TRPRGDNAADDQALLEELIAHPKERAEHIMLIDLERNDLGRICGYGTVKVDELMTVESYQ 328 Query: 331 SVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVV 390 V H+ S I+ +L + A+FP T +G PK +E I L++ RG Y+G+V Sbjct: 329 HVHHIVSNIQGKLREGMTPGQVIRAVFPGGTITGCPKVRCMEIIAELEQTGRGAYTGSVG 388 Query: 391 MLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETCEK 438 L+ +G +D + +R G R GAGI+ +S E +ET K Sbjct: 389 YLNHNGDMDLNILIRTMTLQGKHLQFRTGAGIVMDSVAPNELKETRHK 436 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: 400 Number of extensions: 17 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: 449 Length adjustment: 33 Effective length of query: 417 Effective length of database: 416 Effective search space: 173472 Effective search space used: 173472 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