Align Salicylate synthase; Chorismate mutase; CM; EC 5.4.99.5; Isochorismate synthase/isochorismate lyase; EC 4.2.99.21; EC 5.4.4.2; Mycobactin synthase protein (uncharacterized)
to candidate Dsui_0219 Dsui_0219 anthranilate synthase component I
Query= curated2:Q73XV3 (450 letters) >FitnessBrowser__PS:Dsui_0219 Length = 491 Score = 141 bits (355), Expect = 5e-38 Identities = 84/252 (33%), Positives = 129/252 (51%), Gaps = 1/252 (0%) Query: 187 YRDRVASAVAEIAAGRYHKVILSRCLQVPFAVDFPSTYRLARRHNTPVRSFLLRLGGIRA 246 ++ VA A I G +V+LS+ + PF+ S YR R N + Sbjct: 221 FKQAVAKAKEYITEGDIMQVVLSQRMTKPFSASPLSLYRALRTLNPSPYMYYFDFEDFHV 280 Query: 247 VGYSPELVAAVRHDGVVVTEPLAGTRAFGRGALHDRQARDDLESNSKEIVEHAISVRSSL 306 VG SPE++ + D V V P+AGTR G D +DL ++ KEI EH + Sbjct: 281 VGASPEILTRLEGDTVTV-RPIAGTRKRGATPEEDAALAEDLLADQKEIAEHVQLLDLGR 339 Query: 307 QEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMDALEALFPAVTASGIP 366 ++ +A+ G+ +T+ M++ V H+ S V G+L +D L+A FPA T SG P Sbjct: 340 NDVGRVAQTGSVKLTERMSIERYSHVMHIVSNVEGKLQAGLSALDVLKAAFPAGTLSGAP 399 Query: 367 KAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHDGKTWLRAGAGIIEES 426 K +E I L+ RG+Y GA+ + +G +D A+ +R A DG+ ++AGAGI+ +S Sbjct: 400 KVRAMEIIDELEPVKRGIYGGAIGYLGFNGDMDLAIAIRTAVIKDGQLHVQAGAGIVADS 459 Query: 427 TPEREFEETCEK 438 P E++ET K Sbjct: 460 DPTSEWQETQNK 471 Lambda K H 0.318 0.135 0.391 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: 427 Number of extensions: 22 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: 491 Length adjustment: 33 Effective length of query: 417 Effective length of database: 458 Effective search space: 190986 Effective search space used: 190986 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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