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 Ga0059261_0256 Ga0059261_0256 anthranilate synthase component I, non-proteobacterial lineages
Query= curated2:Q73XV3 (450 letters) >FitnessBrowser__Korea:Ga0059261_0256 Length = 508 Score = 151 bits (381), Expect = 5e-41 Identities = 113/334 (33%), Positives = 153/334 (45%), Gaps = 13/334 (3%) Query: 124 RLAPGTALARVFWPNGRIVVTREAIQLFGTSTGRRDDVLGVLGDG-VPGLRDASAVDVVT 182 RLA L WP TR+ + R D L +P A+++ Sbjct: 172 RLADSLFLVAPVWPGS----TRDPEARLADAAERIDATAARLATAPLPPKVAGDALEIAA 227 Query: 183 DPS----NYRDRVASAVAEIAAGRYHKVILSRCLQVPFAVDFPSTYRLARRHNTPVRSFL 238 P+ +Y VA A I AG +V+L++ PFA+ YR RR N + Sbjct: 228 RPTLADGDYAAMVARAKEYITAGDIFQVVLAQRFTAPFALPPIELYRALRRVNPSPFLYF 287 Query: 239 LRLGGIRAVGYSPELVAAVRHDGVVVTEPLAGTRAFGRGALHDRQARDDLESNSKEIVEH 298 L L G G SPE++ VR D V + P+AGTR G+ A D R L ++ KE EH Sbjct: 288 LDLPGFALTGSSPEILVRVRDDEVTI-RPIAGTRPRGKTAAEDEANRTSLLADPKERAEH 346 Query: 299 AISVRSSLQEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMDALEALFP 358 + + + +A+ GT VTD TV V H+ S V G+L D +DAL A FP Sbjct: 347 LMLLDLGRNDTGRVAQAGTVRVTDSYTVEFYSHVMHIVSNVVGKLRPDADALDALFAGFP 406 Query: 359 AVTASGIPKAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHDGKTWLRA 418 A T SG PK E I L+ RG Y+G V S DG++D+ + LR A DG + A Sbjct: 407 AGTVSGAPKVRACEIIAELEREQRGPYAGGVGYFSPDGSMDSCIVLRTAIVKDGTMHVTA 466 Query: 419 GAGIIEEST---PEREFEETCEKLSTLAPYLIAR 449 GAGI+ +S +RE E L A +AR Sbjct: 467 GAGIVADSDAAYEQRECEAKAGALFAAAREAVAR 500 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: 468 Number of extensions: 15 Number of successful extensions: 3 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: 508 Length adjustment: 34 Effective length of query: 416 Effective length of database: 474 Effective search space: 197184 Effective search space used: 197184 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