Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate Pf1N1B4_4353 Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)
Query= reanno::pseudo3_N2E3:AO353_29305 (253 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4353 Length = 253 Score = 495 bits (1274), Expect = e-145 Identities = 241/253 (95%), Positives = 249/253 (98%) Query: 1 MALKPLIGVTACVKQIGLHPYHVSGDKYLRAVSVAALGLPVVIPSLGELTEIDELLAHLD 60 MA KPLIGVTAC+KQIGLHPYHVSGDKYLRAVSVAALGLPVVIPSLGELTEID+LLA LD Sbjct: 1 MAFKPLIGVTACIKQIGLHPYHVSGDKYLRAVSVAALGLPVVIPSLGELTEIDDLLAQLD 60 Query: 61 GLLLTGSPSNVEPFHYQGPASAPGTDHDPARDSTTLPLLRAAIAAGVPVLGICRGFQEMN 120 GLLLTGSPSNVEPFHYQGPASAPGTDHDP RD+TTLPLLRAAIAAGVPVLGICRGFQEMN Sbjct: 61 GLLLTGSPSNVEPFHYQGPASAPGTDHDPQRDATTLPLLRAAIAAGVPVLGICRGFQEMN 120 Query: 121 VAFGGSLHQKVHELPGMLDHREADHPDLAVQYAPAHAVSVQPGGVFQALELPPVFQVNSI 180 VAFGGSLHQKVHELPGMLDHREADHPDLAVQYAPAHAVSVQPGGVF+AL+LP VFQVNSI Sbjct: 121 VAFGGSLHQKVHELPGMLDHREADHPDLAVQYAPAHAVSVQPGGVFEALDLPQVFQVNSI 180 Query: 181 HSQGIDRLAPGLRAEAIAPDGLIEAISVEHSKAFALGVQWHPEWQVLANPPYLSIFQAFG 240 HSQGIDRLAPGLRAEA+APDGLIEAISVEHSKAFA+GVQWHPEWQVL+NPPYLSIFQAFG Sbjct: 181 HSQGIDRLAPGLRAEAVAPDGLIEAISVEHSKAFAVGVQWHPEWQVLSNPPYLSIFQAFG 240 Query: 241 DACRQRAALRNTR 253 DACRQRAALRNTR Sbjct: 241 DACRQRAALRNTR 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: 433 Number of extensions: 19 Number of successful extensions: 1 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: 253 Length adjustment: 24 Effective length of query: 229 Effective length of database: 229 Effective search space: 52441 Effective search space used: 52441 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: 46 (22.3 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