Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate 5210398 Shew_2839 carbamoyl phosphate synthase small subunit (RefSeq)
Query= curated2:Q9YGB2 (192 letters) >FitnessBrowser__PV4:5210398 Length = 390 Score = 73.6 bits (179), Expect = 4e-18 Identities = 48/147 (32%), Positives = 70/147 (47%), Gaps = 9/147 (6%) Query: 25 VKVVPNTITVGELRRLDPDGVIISPGPGHPLERREVGNSPEIVLEAGVPILGVCLGHQII 84 V VVP E+ ++PDG+ +S GPG P + + L+ +P+ G+CLGHQ++ Sbjct: 224 VTVVPAQTPAAEVLAMNPDGIFLSNGPGDPEPCDYAIEAIQAFLKTDIPLFGICLGHQLL 283 Query: 85 ATAFGGKVGRVK-PRHGKASPVKHDGKGVLRGIKNPLTAGRYHSLAVLE--VPREFDVSA 141 A A G K ++K HG PV + KG N + + H A E +P V+ Sbjct: 284 ALASGAKTLKMKFGHHGANHPVSNLEKG------NVMITSQNHGFAADETSLPANVKVTH 337 Query: 142 VSLDDNVVMGIRHRKLPIEGLQFHPES 168 SL D + GI P Q HPE+ Sbjct: 338 KSLFDGSLQGIHLTDKPAFSFQGHPEA 364 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: 171 Number of extensions: 13 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: 192 Length of database: 390 Length adjustment: 25 Effective length of query: 167 Effective length of database: 365 Effective search space: 60955 Effective search space used: 60955 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