Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_010529287.1 ON01_RS01750 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000224785.1:WP_010529287.1 Length = 467 Score = 122 bits (307), Expect = 2e-32 Identities = 85/261 (32%), Positives = 129/261 (49%), Gaps = 3/261 (1%) Query: 183 DPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLG 242 D F V +A D I G ++V+LS+ ++ D YR R+ N F + Sbjct: 199 DKQHFMHNVEIAKDHIKNGDIYQVVLSQRMKAAMQGDPFTFYRKLRKVNPSPYMFYINFD 258 Query: 243 GIRALGYSPE-LVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAIS 301 LG SPE L+ D ++T P+AGTR G D R++L ++ KEI EH + Sbjct: 259 DYVVLGASPESLIETSGRD--IMTNPIAGTRPRGSTTDGDGALRNELLTDEKEISEHRML 316 Query: 302 VRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVT 361 V S ++ + E S +V +M V V H+ S + +L + AL A PA T Sbjct: 317 VDLSRNDLGRVCEIDSVSVPTYMKVENYQHVMHMVSEVHGKLAEGFTSIDALIACLPAGT 376 Query: 362 ASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAG 421 SG PK ++ I L++ RG Y+G V +S + L+ AL +R+ +L+AGAG Sbjct: 377 VSGAPKIRAMQIINDLEKVKRGAYAGGVGYISFNDNLNIALAIRSLIVKENFAYLQAGAG 436 Query: 422 IIEESEPEREFEETCEKLSTL 442 I+ +S+PE E+ ET K +L Sbjct: 437 IVYDSDPETEYNETLHKARSL 457 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: 386 Number of extensions: 13 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: 467 Length adjustment: 33 Effective length of query: 417 Effective length of database: 434 Effective search space: 180978 Effective search space used: 180978 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