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_028951110.1 Q385_RS0107710 glutamine-hydrolyzing GMP synthase
Query= curated2:Q57690 (197 letters) >NCBI__GCF_000619805.1:WP_028951110.1 Length = 511 Score = 79.3 bits (194), Expect = 1e-19 Identities = 56/189 (29%), Positives = 98/189 (51%), Gaps = 11/189 (5%) Query: 6 VLVIDNIDSFVWNLVQYVGTLGYKVKLVDNKITLDEIKKINPDRIIISPGPKTPKE--AG 63 ++++D + + + + L +++ ++EI K NP II S GP + E A Sbjct: 5 IVILDFGSQYTQLIARRIRELHIYSEILPYNTPVEEILKHNPKGIIFSGGPASVYEENAP 64 Query: 64 NCIKIIQEVDIPILGVCLGHQCIVEAFGGEVGRAKRVMHGKASLINHDGEGIFKDIPNPF 123 + + ++ +PILG+C G Q I FGGEV +A + +G+A + + E +F +IP Sbjct: 65 KPDERVYDLGLPILGICYGLQLITHHFGGEVVKADKHEYGRAEIQVLNHEDLFYEIPEFT 124 Query: 124 YGGRYHSLIAKEVPKELKITAKSLDDNYIMGVRHKKLPIEGVQFHPESILTESDNLKFPD 183 + H+ ++P+ +I A+S + Y VR+K+ I GVQFHPE + Sbjct: 125 HVWMSHADKVVKLPEGFEILARSFNAPY-AAVRNKEKKIWGVQFHPE--------VSHTL 175 Query: 184 LGLKLIKNF 192 LG +++KNF Sbjct: 176 LGKEILKNF 184 Lambda K H 0.319 0.142 0.421 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: 291 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: 197 Length of database: 511 Length adjustment: 27 Effective length of query: 170 Effective length of database: 484 Effective search space: 82280 Effective search space used: 82280 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 (21.7 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