Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_011781954.1 MVAN_RS24155 aminodeoxychorismate synthase, component I
Query= curated2:P96556 (531 letters) >NCBI__GCF_000015305.1:WP_011781954.1 Length = 420 Score = 139 bits (351), Expect = 2e-37 Identities = 101/281 (35%), Positives = 139/281 (49%), Gaps = 26/281 (9%) Query: 232 WNEPE-------YLAALDRGKEAIVDGEVFQVVISRRFEMECGASPLDVY-RVLRNTNPS 283 W EP+ LA L EAI GEV+Q + +F +P+D + T P+ Sbjct: 145 WGEPDRHAHRRGVLACL----EAIAAGEVYQACVCTQFAGVLAGAPVDFFAEAAARTVPA 200 Query: 284 PYMYIFSLEDAAGRQYSIVGSSPEALVTVTGEDVITHPIAGSRPRGKTVDADKALAEELL 343 ++ AG ++ SPE + GE V + PI G+ P D A L Sbjct: 201 RAAFV------AGDWGAVASLSPELFLRRCGEAVTSSPIKGTLP-------DFADPATLR 247 Query: 344 ADQKERAEHLMLVDLSRNDLSKVCVAGSVDVTQFMEVERFSHIMHLVSTVVGRLAPTAKA 403 A K+ AE++M+VDL RNDL +V GSV V + + V + HLVSTV R+ Sbjct: 248 ASVKDVAENIMIVDLVRNDLGRVARTGSVSVPELLAVRPAPGVWHLVSTVSARVPEDTPT 307 Query: 404 YDVLKATFPAGTLSGAPKPRALRLLDELEPHRRGIYGGVVGYLDFAGDMDMAIAIRSALL 463 +L ATFP +++G PK RA LL EPHRRGIY G VG ++ +AIR+ Sbjct: 308 AVLLDATFPPASVTGTPKSRARGLLTGWEPHRRGIYCGTVGLASPVAGCELNVAIRTVEF 367 Query: 464 -REGRAYVQAGGGIVADSSNPAEAQETVNKAAAPLRAVHTA 503 +G A + GGGI ADS E +E ++KAA + AV A Sbjct: 368 GADGSAVLGVGGGITADSDPDLEWEECLHKAAPIVNAVPVA 408 Lambda K H 0.317 0.133 0.387 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: 575 Number of extensions: 29 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: 531 Length of database: 420 Length adjustment: 33 Effective length of query: 498 Effective length of database: 387 Effective search space: 192726 Effective search space used: 192726 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