Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate Ac3H11_435 Carbamoyl-phosphate synthase small chain (EC 6.3.5.5)
Query= curated2:Q9YGB2 (192 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_435 Length = 405 Score = 72.8 bits (177), Expect = 8e-18 Identities = 47/148 (31%), Positives = 68/148 (45%), Gaps = 9/148 (6%) Query: 24 RVKVVPNTITVGELRRLDPDGVIISPGPGHPLERREVGNSPEIVLEAGVPILGVCLGHQI 83 +V VVP E+ ++PDGV +S GPG P + +++AGVP G+CLGHQI Sbjct: 243 KVTVVPAQTPAAEVLAMNPDGVFLSNGPGDPAPCDYAIEATRQIIDAGVPTFGICLGHQI 302 Query: 84 IATAFGGKVGRV-KPRHGKASPVKHDGKGVLRGIKNPLTAGRYHSLAV--LEVPREFDVS 140 +A A G ++ HG PVK G + + H AV +P + Sbjct: 303 MALASGATTFKMDNSHHGANHPVKDLDNGRVS------ITSQNHGFAVDMASLPATLRAT 356 Query: 141 AVSLDDNVVMGIRHRKLPIEGLQFHPES 168 +SL D + G+ P Q HPE+ Sbjct: 357 HISLFDGTLQGLARTDKPAFCFQGHPEA 384 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: 187 Number of extensions: 15 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: 405 Length adjustment: 25 Effective length of query: 167 Effective length of database: 380 Effective search space: 63460 Effective search space used: 63460 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 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