Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_010532310.1 ON01_RS17455 isochorismate synthase
Query= curated2:Q9YGB3 (433 letters) >NCBI__GCF_000224785.1:WP_010532310.1 Length = 461 Score = 149 bits (376), Expect = 2e-40 Identities = 104/297 (35%), Positives = 152/297 (51%), Gaps = 12/297 (4%) Query: 144 LVERARREESRLED------GGSEVIST-DAGMEEFVEIVRAGKEYIYSGDVFQVVLSRE 196 L R +R E+ L D GG+ V ST D EE+ + V+ +YI DV ++VL+RE Sbjct: 166 LASRIKRMENTLCDDSVYIPGGTGVESTEDIAPEEWKQTVKFATDYIKQSDVDKIVLARE 225 Query: 197 YRVRTDLDA--LEIYKRLVELNPSPYTFILEFE-KTVVGASPETMGSVEGRTFKINPIAG 253 V+ +A + L+E + Y F E + VG+SPE + + +AG Sbjct: 226 LLVKLSDNAQITPVLGNLIETQTNSYVFAFERDGDCFVGSSPERLVRQDKNEVLSTCLAG 285 Query: 254 TAPRGRTGEEDRELEKALLSDEKERAEHVMLVDLARNDVRRVSKPGSVRLTRFFDVLKYS 313 TAPRG+T +ED ++ +LL DEK R+EH +V + R + R + V LK Sbjct: 286 TAPRGKTQKEDAKIGNSLLHDEKNRSEHDFVVKMIRQSMERYCRAVDVPDKPVIYPLK-- 343 Query: 314 HVQHIESEVVGELDEGKNAFDAMEAAFPAGTLTGAPKIRAMEIIDELERSRRKVYGGAVG 373 ++QH+ + V L EG + FD + P L G P+ +++E I ER R YG VG Sbjct: 344 NLQHLYTPVKATLKEGYSIFDIIGKLHPTPALGGVPREKSLEFIRNQERLDRGWYGAPVG 403 Query: 374 YFSLTGDADMAIAIRMAEIEGRKASVRAGAGIVADSVPEKEFFETENKMRAVLKALG 430 + + A+AIR I+G +AS+ AG GIV DS PE E+ ET K +L LG Sbjct: 404 WLDSNASGEFAVAIRSGLIQGDQASLFAGCGIVRDSDPEAEYEETNIKFTPMLSVLG 460 Lambda K H 0.318 0.137 0.384 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: 397 Number of extensions: 14 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: 433 Length of database: 461 Length adjustment: 33 Effective length of query: 400 Effective length of database: 428 Effective search space: 171200 Effective search space used: 171200 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 Jul 26 2024. The underlying query database was built on Jul 25 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