Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate WP_012172161.1 AZC_RS18745 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P00901 (198 letters) >NCBI__GCF_000010525.1:WP_012172161.1 Length = 401 Score = 68.2 bits (165), Expect = 2e-16 Identities = 52/183 (28%), Positives = 82/183 (44%), Gaps = 18/183 (9%) Query: 15 NVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAGVSIEAILH--FAG 72 N+++ L G +V V+ + A + AL P+ + +S GP P+ G ++ A Sbjct: 223 NILRLLATAGCKVTVVPATT-SAADVLALQPDGVFLSNGPGDPAATGEYAVPVIRELIAK 281 Query: 73 KLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLG--VFTGLNNPLTVTRYHS 130 ++P G+CLGHQ IG A GG ++ Q HG PV G T +N H Sbjct: 282 EIPTFGICLGHQMIGLAVGGRTLKMHQGHHGANHPVKDLTTGKVEITSMN--------HG 333 Query: 131 LVVKRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPE-SILTEQGHELFAN 189 V R++LP + T + + + G+ + VQ+HPE S H LF Sbjct: 334 FAVDRDSLPANAQETHVSLFDGSNA----GIALADKPVFSVQYHPEASPGPRDSHYLFTR 389 Query: 190 FLK 192 F++ Sbjct: 390 FVE 392 Lambda K H 0.320 0.138 0.411 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: 193 Number of extensions: 12 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: 198 Length of database: 401 Length adjustment: 26 Effective length of query: 172 Effective length of database: 375 Effective search space: 64500 Effective search space used: 64500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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