Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate WP_012475712.1 CPHAMN1_RS11645 carbamoyl-phosphate synthase small subunit
Query= curated2:Q9YGB2 (192 letters) >NCBI__GCF_000020545.1:WP_012475712.1 Length = 366 Score = 88.2 bits (217), Expect = 2e-22 Identities = 55/159 (34%), Positives = 84/159 (52%), Gaps = 26/159 (16%) Query: 24 RVKVVPNTITVGELRRLDPDGVIISPGPGHPLER-----------REVGNSPEIVLEAGV 72 RV V+ T ++R L+PDG+ +S GPG P RE G+S A + Sbjct: 200 RVTVLNAGATADDIRDLNPDGLFLSNGPGDPFAVTYAIDTIRTLIRENGDS------APL 253 Query: 73 PILGVCLGHQIIATAFGGKVGRVK-PRHGKASPVKHDGKGVLRGIKNPLTAGRYHSLAV- 130 PI G+CLGHQ+++ A+G ++K HG PVK+ G + + H AV Sbjct: 254 PIFGICLGHQLLSLAYGANTYKLKFGHHGSNHPVKNLSTGSIE------ITSQNHGFAVE 307 Query: 131 -LEVPREFDVSAVSLDDNVVMGIRHRKLPIEGLQFHPES 168 +P E +++ ++L DN V G+RHR+LP +Q+HPE+ Sbjct: 308 MSSLPEELELTHLNLYDNTVEGVRHRELPCFSVQYHPEA 346 Lambda K H 0.320 0.141 0.422 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: 184 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: 192 Length of database: 366 Length adjustment: 25 Effective length of query: 167 Effective length of database: 341 Effective search space: 56947 Effective search space used: 56947 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