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 WP_011384218.1 AMB_RS09175 anthranilate synthase component I
Query= curated2:Q73XV3 (450 letters) >NCBI__GCF_000009985.1:WP_011384218.1 Length = 506 Score = 157 bits (397), Expect = 7e-43 Identities = 98/259 (37%), Positives = 134/259 (51%), Gaps = 1/259 (0%) Query: 184 PSNYRDRVASAVAEIAAGRYHKVILSRCLQVPFAVDFPSTYRLARRHNTPVRSFLLRLGG 243 P +Y V A IAAG +V+LS+ L VPF + S YR RR N F L LG Sbjct: 234 PEHYCRMVEKAQEYIAAGDIFQVVLSQRLAVPFRLPPFSLYRSLRRLNPSPFLFFLDLGE 293 Query: 244 IRAVGYSPELVAAVRHDGVVVTEPLAGTRAFGRGALHDRQARDDLESNSKEIVEHAISVR 303 + VG SPE++ +R D V + P+AGTR G+ D + DL ++ KE+ EH + + Sbjct: 294 FQLVGSSPEILVRLRDDKVTI-RPIAGTRRRGKTPAEDEELAADLLADPKELAEHLMLLD 352 Query: 304 SSLQEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMDALEALFPAVTAS 363 ++ +A GT VT MTV V H+ S V G++ D MDAL A FPA T S Sbjct: 353 LGRNDVGRVAAIGTVEVTKKMTVEYYSHVMHIVSNVEGKIREGCDAMDALMAGFPAGTTS 412 Query: 364 GIPKAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHDGKTWLRAGAGII 423 G PK +E I L+ R Y+GA+ +G +D + LR DG +++AGAGI+ Sbjct: 413 GAPKIRAMEIIDELETERRSFYAGAIGYFDGNGNMDTCIALRTTLVKDGTMYVQAGAGIV 472 Query: 424 EESTPEREFEETCEKLSTL 442 +S P E EE K L Sbjct: 473 ADSVPLSEHEECMNKARAL 491 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: 434 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: 506 Length adjustment: 33 Effective length of query: 417 Effective length of database: 473 Effective search space: 197241 Effective search space used: 197241 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