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_011938751.1 GURA_RS09415 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P00901 (198 letters) >NCBI__GCF_000016745.1:WP_011938751.1 Length = 373 Score = 79.7 bits (195), Expect = 6e-20 Identities = 59/180 (32%), Positives = 84/180 (46%), Gaps = 12/180 (6%) Query: 14 YNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAGVSIEAILHFAGK 73 +N+++ L G +V V+ + A+ P+ I +S GP P IE I F GK Sbjct: 199 FNILRCLVSAGCDVTVVPAT-FPAEEALAMAPDGIFLSNGPGDPEPMHAVIENIRKFVGK 257 Query: 74 LPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTGLNNPLTVTRYHSLVV 133 PI G+CLGHQ +G GG V+ + HG PV + + TG + H V Sbjct: 258 KPIFGICLGHQLLGLVLGGRTVKLKFGNHGSNLPV----MDLATG--KVEITAQNHGFSV 311 Query: 134 KRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPE-SILTEQGHELFANFLK 192 +L E+ AHE+ + + G+RHK L I VQ HPE S H LF F++ Sbjct: 312 DIVSLSHACEL----AHENLNDQTVEGMRHKELPIFSVQHHPEASPGPHDSHYLFGRFVE 367 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: 203 Number of extensions: 10 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: 373 Length adjustment: 25 Effective length of query: 173 Effective length of database: 348 Effective search space: 60204 Effective search space used: 60204 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