Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_245546805.1 A377_RS0107825 aminodeoxychorismate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000384235.1:WP_245546805.1 Length = 493 Score = 131 bits (330), Expect = 4e-35 Identities = 91/274 (33%), Positives = 136/274 (49%), Gaps = 5/274 (1%) Query: 172 VPQSRSVDVSDDP-SGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFA-IDFPLTYRLGRR 229 VP+ ++ DP F + V D I AG +V LSR EV P YR R+ Sbjct: 213 VPEIAVAEIHQDPPQRFTQGVDRIKDYILAGDVFQVNLSRQWEVDVKNASAPNVYRALRQ 272 Query: 230 HNTPVRSFLLQLGGIRALGYSPELVTAVRADGV-VITEPLAGTRALGRGPAIDRLARDDL 288 N + G + L SPE + V +DG V T P+AGTR D +L Sbjct: 273 ANPAPFAAYADFGDWQVLSSSPERL--VTSDGEHVATRPIAGTRRRSSDTEKDLALIREL 330 Query: 289 ESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSD 348 +++ KE+ EH + + ++ +++PGS AV + M + V H+ S I+ RL P + Sbjct: 331 QAHPKEVAEHIMLIDLERNDLGRLSQPGSVAVDELMAIETYQYVHHIVSNIQGRLQPGTS 390 Query: 349 RMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAY 408 + A FP T +G PK +E I L++ PR Y+G++ ++ DG LD+ + +R Sbjct: 391 PLDIFAATFPGGTITGCPKIRCMEIIAELEQTPREAYTGSLGYINRDGRLDSNILIRTFV 450 Query: 409 QVGGRTWLRAGAGIIEESEPEREFEETCEKLSTL 442 Q G R RAGAGI+ +S+PE+E ET K L Sbjct: 451 QQGERLRFRAGAGIVADSDPEKELAETRHKAKGL 484 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: 496 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: 493 Length adjustment: 33 Effective length of query: 417 Effective length of database: 460 Effective search space: 191820 Effective search space used: 191820 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