Align Anthranilate synthase beta subunit 1, chloroplastic; OsASB1; Anthranilate synthase, glutamine amidotransferase component 2-1; EC 4.1.3.27 (characterized)
to candidate WP_013707080.1 DESAC_RS10650 glutamine-hydrolyzing GMP synthase
Query= SwissProt::Q7XUS2 (288 letters) >NCBI__GCF_000195295.1:WP_013707080.1 Length = 515 Score = 72.8 bits (177), Expect = 2e-17 Identities = 56/195 (28%), Positives = 95/195 (48%), Gaps = 13/195 (6%) Query: 81 KQPIIVIDNYDSFTYNLCQYMGELGLNFEVYRNDELTIEDVKRKNPRGILISPGPGEPQD 140 + ++++D +T + + + EL + E++ + +E ++ PRGI++S GP + Sbjct: 6 RDKVLILDFGSQYTQLIARRIRELQVYCEIHPY-LMPLEQIEAFAPRGIILSGGPRSVYE 64 Query: 141 SGISL--QTVLELGPTIPIFGVCMGLQCIGEAFGGKIIRAPSGVMHGKSSPVRYDEELGK 198 G L + VLELGP P+ G+C GLQ + GGK+ A S K+ + ++ Sbjct: 65 PGAPLVSREVLELGP--PVLGICYGLQLLNHILGGKVSPAASREYGRKNFTISDHQD--- 119 Query: 199 ALFNGLPNPFTAARYHSLVIEQETFPHDALEATAWTEDGLIMAARHKKYRHIQGVQFHPE 258 LF GL + H I++ + + ++ G + R R I GVQFHPE Sbjct: 120 -LFAGLSPHESVWMSHGDHIDEIAPGLEIIGSSDTCPAGAVRDQR----RRIFGVQFHPE 174 Query: 259 SIITPEGKRIILNFV 273 TP G +I+ NF+ Sbjct: 175 VKHTPNGGKILANFL 189 Lambda K H 0.318 0.133 0.386 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: 314 Number of extensions: 18 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: 288 Length of database: 515 Length adjustment: 30 Effective length of query: 258 Effective length of database: 485 Effective search space: 125130 Effective search space used: 125130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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