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_013450265.1 CALNI_RS00660 glutamine-hydrolyzing GMP synthase
Query= curated2:P26923 (196 letters) >NCBI__GCF_000183405.1:WP_013450265.1 Length = 516 Score = 74.7 bits (182), Expect = 3e-18 Identities = 50/154 (32%), Positives = 77/154 (50%), Gaps = 13/154 (8%) Query: 47 VRGLDPERIIISPGPGNPIKREDFGICSEVIGEFTDRPILGVCLGHQGIFHYFGGVVG-- 104 ++ P+ II+S GP + + +D +C + + E + PILG+C G Q I +FGGVV Sbjct: 44 IQAFSPKGIILSGGPSS-VYDKDAPLCDKRVFEL-NLPILGICYGMQLICQFFGGVVSPA 101 Query: 105 ----YGEPVHGKISEVFHDGSELFRGVPNPFRATRYHSLRCECSGVPEDILVSASAPDGT 160 YG +++F D +L N H R E +PE + + Sbjct: 102 QQREYGRSEIMLKNDIFFDNLKLSG---NKLTVWMSHGDRLE--KIPEQFEIIGWTDNAP 156 Query: 161 IMAIRHRQYPVYGLQFHPESAGTPHGRDILENFL 194 I A++H+ P+Y +QFHPE A T G IL+NF+ Sbjct: 157 IAAMKHKDKPIYAIQFHPEVAHTDQGDTILKNFV 190 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: 287 Number of extensions: 16 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: 516 Length adjustment: 27 Effective length of query: 169 Effective length of database: 489 Effective search space: 82641 Effective search space used: 82641 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 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