Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_068462644.1 APY04_RS11160 aminodeoxychorismate synthase component I
Query= curated2:O66849 (494 letters) >NCBI__GCF_001541235.1:WP_068462644.1 Length = 614 Score = 189 bits (479), Expect = 3e-52 Identities = 108/276 (39%), Positives = 162/276 (58%), Gaps = 8/276 (2%) Query: 218 WRSNFTKEEFEDIVKKAKEYIAQGDVIQVVLSQRFRKRFKGNPDNIYRVLRFLNPSPYMY 277 W E F+ +++K I GD+ Q+ L+ + R + G+P + LR Y Sbjct: 139 WNEQQYVERFDQVIEK----IRAGDIYQLNLTFKARFKLSGSPLTFFLDLRQKQRVAYGG 194 Query: 278 YLDFDQLKVIGSSPEILVRLEEGRIETRPIAGTRKRGRTEEEDKRLEEDLLSDEKERAEH 337 +D ++ V+ +SPE+ + E + TRP+ GT R TEE D + + L D K+RAE+ Sbjct: 195 IVDTGEMTVLSASPELFIEQEGRTVFTRPMKGTAPRAGTEEADAQAKLQLAGDVKQRAEN 254 Query: 338 LMLVDLARNDIGRVAKTGSVRVENFMRIERYSHVMHIVSDVVGELREGYDALDVLKATFP 397 LM+VDL RNDIGR+A+ GSV V + +E Y + + S V L+EG D ++++ FP Sbjct: 255 LMIVDLMRNDIGRIAEVGSVEVTDLFTVETYKTLHQMTSGVRATLQEGIDISELMRGIFP 314 Query: 398 AGTVSGAPKVRAMQIIEELENERRGIYAGSVGYISFQGNMDMAIAIRTAV-YRDRDIFVQ 456 G+V GAPK+RAM++I ELE E RG+Y G++GYIS +G +AIRTAV +R+ D + Sbjct: 315 PGSVIGAPKIRAMELIRELETEPRGVYCGAIGYISPEGRSLFNVAIRTAVIFRNADGEMG 374 Query: 457 AGAGIVADSVPEKEWEETVNKAKAL---MKAIEIAE 489 G+G+V DS KE+ E + K K L +K E+ E Sbjct: 375 IGSGVVYDSQGPKEYAECLLKMKFLTDPVKRFELIE 410 Lambda K H 0.318 0.138 0.390 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: 625 Number of extensions: 20 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: 494 Length of database: 614 Length adjustment: 36 Effective length of query: 458 Effective length of database: 578 Effective search space: 264724 Effective search space used: 264724 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 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