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_013722264.1 ALIDE2_RS13370 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P26922 (196 letters) >NCBI__GCF_000204645.1:WP_013722264.1 Length = 392 Score = 81.3 bits (199), Expect = 2e-20 Identities = 56/162 (34%), Positives = 77/162 (47%), Gaps = 12/162 (7%) Query: 14 NLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAGICLPLIDAAAKAA 73 N++ L E G +L V + T +EA+AL+P+GI LS GP DP+ + A A Sbjct: 214 NILRMLAERGCKLTVVPAQT-TAQEALALKPDGIFLSNGPGDPEPCTYAIEATRAFLAAG 272 Query: 74 VPLMGVCLGHQAIGQPFGGTVVRAPVPMHGKVDRMFHQGRGVLKDLPSPF--RATRYHSL 131 +PL G+CLGHQ + G + P HG H G +K L S ++ H Sbjct: 273 IPLFGICLGHQIMALALGAQTFKMP---HG-----HHGGNHPVKTLASGHVCITSQNHGF 324 Query: 132 IVERATLPACLEVTG-ETEDGLIMALSHRELPIHGVQFHPES 172 VE ATLPA + T DG + L + P Q HPE+ Sbjct: 325 AVEAATLPASVRATHVSLFDGTLQGLECTDKPAFSFQGHPEA 366 Lambda K H 0.321 0.140 0.420 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: 217 Number of extensions: 11 Number of successful extensions: 1 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: 196 Length of database: 392 Length adjustment: 25 Effective length of query: 171 Effective length of database: 367 Effective search space: 62757 Effective search space used: 62757 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