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_013009433.1 DACET_RS00400 glutamine-hydrolyzing GMP synthase
Query= curated2:P26923 (196 letters) >NCBI__GCF_000025725.1:WP_013009433.1 Length = 515 Score = 75.9 bits (185), Expect = 1e-18 Identities = 48/153 (31%), Positives = 74/153 (48%), Gaps = 2/153 (1%) Query: 42 VDIDYVRGLDPERIIISPGPGNPIKREDFGICSEVIGEFTDRPILGVCLGHQGIFHYFGG 101 V+ + ++ + II+S GP + ++ + EV P+LG+C GHQ YFGG Sbjct: 39 VEFEKIKEYGAKGIILSGGPASVYDKDAPKVSDEVYE--LGVPVLGICYGHQLTGMYFGG 96 Query: 102 VVGYGEPVHGKISEVFHDGSELFRGVPNPFRATRYHSLRCECSGVPEDILVSASAPDGTI 161 VV + +E++ D S+ F + S +PE A + + Sbjct: 97 VVAEADHREYGRAELYADKSDDFFADIEDDSFVVWMSHGDRLDKMPEGFKTIAKTDNAPV 156 Query: 162 MAIRHRQYPVYGLQFHPESAGTPHGRDILENFL 194 A+RH P+Y +QFHPE A T +GR ILENF+ Sbjct: 157 AAMRHETRPIYTIQFHPEVAHTKNGRQILENFV 189 Lambda K H 0.324 0.145 0.449 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: 286 Number of extensions: 15 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: 196 Length of database: 515 Length adjustment: 27 Effective length of query: 169 Effective length of database: 488 Effective search space: 82472 Effective search space used: 82472 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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