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 PfGW456L13_1217 Anthranilate synthase, aminase component (EC 4.1.3.27)
Query= curated2:Q73XV3 (450 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1217 Length = 493 Score = 138 bits (348), Expect = 3e-37 Identities = 83/253 (32%), Positives = 128/253 (50%), Gaps = 1/253 (0%) Query: 186 NYRDRVASAVAEIAAGRYHKVILSRCLQVPFAVDFPSTYRLARRHNTPVRSFLLRLGGIR 245 +Y V + I AG +V+ S+ + + F YR R N + G Sbjct: 225 DYEKAVDTIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFH 284 Query: 246 AVGYSPELVAAVRHDGVVVTEPLAGTRAFGRGALHDRQARDDLESNSKEIVEHAISVRSS 305 VG SPE++ V D ++ P+AGTR G D +DL S+ KEI EH + + Sbjct: 285 VVGSSPEVLVRVE-DNLITVRPIAGTRPRGANEEADLALEEDLLSDDKEIAEHLMLIDLG 343 Query: 306 LQEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMDALEALFPAVTASGI 365 + ++E G+ +T+ M + +V H+ S V+G+L + MDAL A+ PA T SG Sbjct: 344 RNDTGRVSEIGSVKLTEKMVIERYSNVMHIVSNVTGQLKSGLTAMDALRAILPAGTLSGA 403 Query: 366 PKAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHDGKTWLRAGAGIIEE 425 PK +E I L+ RG+Y GAV + +G +D A+ +R A +G+ ++AG GI+ + Sbjct: 404 PKIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVAD 463 Query: 426 STPEREFEETCEK 438 S P E+EET K Sbjct: 464 SVPALEWEETLNK 476 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: 429 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: 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 ( 7.3 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