Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate PP_5298 PP_5298 putative glutamine amidotransferase
Query= reanno::pseudo3_N2E3:AO353_29305 (253 letters) >FitnessBrowser__Putida:PP_5298 Length = 255 Score = 295 bits (754), Expect = 8e-85 Identities = 146/249 (58%), Positives = 178/249 (71%), Gaps = 2/249 (0%) Query: 5 PLIGVTACVKQIGLHPYHVSGDKYLRAVSVAALGLPVVIPSLGELTEIDELLAHLDGLLL 64 PLIGV+AC +Q+G + H GDKY+ A A GLP+++P+ ++ LLA L G++ Sbjct: 7 PLIGVSACRQQVGKNSSHTVGDKYVEAAGFA--GLPLILPARDGGSDTQALLARLHGIVF 64 Query: 65 TGSPSNVEPFHYQGPASAPGTDHDPARDSTTLPLLRAAIAAGVPVLGICRGFQEMNVAFG 124 TGSPSN+EP HY G S GT HD ARD TLPLL+AAIA GVPV ICRG+QE+NVA G Sbjct: 65 TGSPSNIEPHHYNGAPSVAGTRHDLARDRLTLPLLQAAIAVGVPVFCICRGYQELNVALG 124 Query: 125 GSLHQKVHELPGMLDHREADHPDLAVQYAPAHAVSVQPGGVFQALELPPVFQVNSIHSQG 184 GSLHQ+V ELPG LDHRE + L VQY P H+VS++PGG+F+ L L F+VNS+HSQG Sbjct: 125 GSLHQRVQELPGYLDHREPEDAPLEVQYGPRHSVSIEPGGLFERLGLVAQFEVNSLHSQG 184 Query: 185 IDRLAPGLRAEAIAPDGLIEAISVEHSKAFALGVQWHPEWQVLANPPYLSIFQAFGDACR 244 IDRLAPGLR EA APDGLIEA+S+ + F LGVQWHPEW+ NP L +FQAF +AC Sbjct: 185 IDRLAPGLRVEARAPDGLIEAVSMPAAPGFVLGVQWHPEWRFNENPVSLRLFQAFREACN 244 Query: 245 QRAALRNTR 253 AA R Sbjct: 245 AYAAREGLR 253 Lambda K H 0.320 0.138 0.419 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: 292 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: 253 Length of database: 255 Length adjustment: 24 Effective length of query: 229 Effective length of database: 231 Effective search space: 52899 Effective search space used: 52899 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. 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