Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_013536761.1 THEAM_RS00005 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000185805.1:WP_013536761.1 Length = 492 Score = 144 bits (362), Expect = 8e-39 Identities = 94/266 (35%), Positives = 139/266 (52%), Gaps = 5/266 (1%) Query: 178 VDVSDDPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLT-YRLGRRHNTPVRS 236 V+ SD+ F + V A + I AG +V+LSR E PF D PLT YR R N Sbjct: 219 VNFSDEE--FMKAVERAKEYIRAGDIIQVVLSRRFEKPFYAD-PLTLYRAIRHVNPSPYM 275 Query: 237 FLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIV 296 + L + +G SPE++ ++ +G V T P+AGTR GR D +L ++ KE Sbjct: 276 YFLDYQDFQVVGASPEVLVRLK-NGRVETRPIAGTRRRGRTKEEDLALERELLNDEKERA 334 Query: 297 EHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEAL 356 EH + V + ++ +A+ GS V D M + V H+ S + L +D L+A Sbjct: 335 EHIMLVDLARNDVGRVAKVGSVKVTDLMVIERYSHVMHIVSNVVGELKEGADAFDVLKAC 394 Query: 357 FPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWL 416 FPA T SG PK +E I ++ RG+Y+GAV S DG +D A+ +R A + ++ Sbjct: 395 FPAGTVSGAPKVRAMEIIDEMEPSERGVYAGAVGYFSFDGNMDTAIAIRTAVVRRNKVYV 454 Query: 417 RAGAGIIEESEPEREFEETCEKLSTL 442 +AGAGI+ +S P+ E +ET K L Sbjct: 455 QAGAGIVADSVPQLEAKETVNKAKAL 480 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: 390 Number of extensions: 18 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: 492 Length adjustment: 33 Effective length of query: 417 Effective length of database: 459 Effective search space: 191403 Effective search space used: 191403 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