Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_011613413.1 TERY_RS19575 isochorismate synthase
Query= curated2:Q9Y8T0 (438 letters) >NCBI__GCF_000014265.1:WP_011613413.1 Length = 498 Score = 108 bits (270), Expect = 4e-28 Identities = 83/265 (31%), Positives = 129/265 (48%), Gaps = 10/265 (3%) Query: 173 FEAMVADALERIRAGEAFQVVLSR-VERYRVWG-SLFSAYERLADANPSPYLYYARLG-G 229 F+ VA ALE I + ++VL+ ++ Y +L + L P Y++ G G Sbjct: 238 FKKSVASALELINSNYLRKIVLAHAIDIYSQNNFNLIKSLNNLRFIYPDCYVFSISNGKG 297 Query: 230 RVIIGSSPELLVKLEAGRVETHPIAGTRPRGSTPIEDIELEVELLNDEKERAEHVMLVDL 289 + IG+SPE L+ + ++ T +AG+ PRG TP +D +L LL EK+ EH ++D Sbjct: 298 QNFIGASPERLISINNNQLVTDALAGSAPRGKTPSQDAKLANSLLCSEKDLREHQFVIDF 357 Query: 290 ARNDITRVSI-PGTVQVTSFMDIERYETVMHIVSRVEGVTRPSTTFVEALKALHPAGTVS 348 + + + P + + + + + H+ + + + +E L LHP V+ Sbjct: 358 IIKRLQYLGLKPNYLPQPNLLQL---SNIQHLWTPINAEVSQNIHLLEILAQLHPTPAVA 414 Query: 349 GAPKPRAMEIIAELEEEARGPYAGAIG-VAGSSAGEAAIVLRSAWLLDDGETLEARAGAG 407 G P+ A E I E R YA IG + GE + +RSA L DGE AGAG Sbjct: 415 GVPRDIAQEQIQNFETFDRSLYAAPIGWIDHQGNGEFTVGIRSA--LIDGERARLYAGAG 472 Query: 408 IVYDSKPEREYMETVQKLGSLKRAL 432 IV SKP++E E KL +L +AL Sbjct: 473 IVTGSKPDQELAEVQLKLQTLLKAL 497 Lambda K H 0.317 0.135 0.401 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: 317 Number of extensions: 11 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: 438 Length of database: 498 Length adjustment: 33 Effective length of query: 405 Effective length of database: 465 Effective search space: 188325 Effective search space used: 188325 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 (21.6 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