Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_009566395.1 RSPH17029_RS03635 aminodeoxychorismate/anthranilate synthase component II
Query= reanno::pseudo6_N2E2:Pf6N2E2_4510 (258 letters) >NCBI__GCF_000015985.1:WP_009566395.1 Length = 195 Score = 60.8 bits (146), Expect = 2e-14 Identities = 57/169 (33%), Positives = 76/169 (44%), Gaps = 32/169 (18%) Query: 82 APGTAHDPARDATTLPLIRAAVDAGIPVLGICRGFQEMNVAFGGSLHQKVHEVGTFIDHR 141 +PG DPA LPL AA +A IP+LG+C G Q + AFGG + + HE Sbjct: 50 SPGPC-DPAAAGICLPLTAAAAEARIPLLGVCLGHQTIGQAFGGKV-VRCHE-------- 99 Query: 142 EDDTQAVDVQYGPAHAVHIQPGGVLAGLGLPQRIEVNSIHSQGIER--LAPGLRAEAVAP 199 + +G A+H + GV A GLP HS +ER L L A Sbjct: 100 --------IVHGKMGAMHHEGKGVFA--GLPSPFLATRYHSLVVERDSLPDCLEVTAWLE 149 Query: 200 DGLIEAV---SVPGGKAFALGVQWHPEWEVSSNPHYLAIFQAFGDACRA 245 DG I + S+P GVQ+HPE S + H + + F D+ RA Sbjct: 150 DGTIMGLRHKSLP-----IEGVQFHPESIASEHGHQM--LRTFLDSARA 191 Lambda K H 0.319 0.136 0.413 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: 155 Number of extensions: 13 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: 258 Length of database: 195 Length adjustment: 22 Effective length of query: 236 Effective length of database: 173 Effective search space: 40828 Effective search space used: 40828 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: 46 (22.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.
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