Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_043828100.1 RSPH17029_RS09530 gamma-glutamyl-gamma-aminobutyrate hydrolase family protein
Query= reanno::pseudo3_N2E3:AO353_29305 (253 letters) >NCBI__GCF_000015985.1:WP_043828100.1 Length = 252 Score = 184 bits (467), Expect = 2e-51 Identities = 97/232 (41%), Positives = 129/232 (55%) Query: 19 HPYHVSGDKYLRAVSVAALGLPVVIPSLGELTEIDELLAHLDGLLLTGSPSNVEPFHYQG 78 +P H G AV++ + LP++IP+ ++ELL DG LLTG NV P Y Sbjct: 14 YPVHAGGTMNSEAVALVSGCLPLIIPTDPTFVTVEELLDLCDGFLLTGGRPNVHPSEYGE 73 Query: 79 PASAPGTDHDPARDSTTLPLLRAAIAAGVPVLGICRGFQEMNVAFGGSLHQKVHELPGML 138 + + ARD+ TLPL+RA + G P LGICRGFQE+NVA GG+LH ++ +LPG + Sbjct: 74 DETPAHGSFERARDAITLPLVRACVERGQPFLGICRGFQEVNVAMGGTLHPEIRDLPGRM 133 Query: 139 DHREADHPDLAVQYAPAHAVSVQPGGVFQALELPPVFQVNSIHSQGIDRLAPGLRAEAIA 198 +HR + ++A H V PGGVF L N++H QGI R + + A Sbjct: 134 NHRMPPDGTIEEKFALRHPVRFTPGGVFHRLMAAEEVMTNTLHGQGIARAGQRIVIDGTA 193 Query: 199 PDGLIEAISVEHSKAFALGVQWHPEWQVLANPPYLSIFQAFGDACRQRAALR 250 PDG EAI VE +K F L VQWHPEW ++P +F AFG A R A R Sbjct: 194 PDGTPEAIYVEGAKGFTLSVQWHPEWNAASDPVSRPLFAAFGAAVRDWAECR 245 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: 229 Number of extensions: 9 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: 252 Length adjustment: 24 Effective length of query: 229 Effective length of database: 228 Effective search space: 52212 Effective search space used: 52212 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 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