Align Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94) (characterized)
to candidate H281DRAFT_01080 H281DRAFT_01080 gamma-glutamyl-gamma-aminobutyrate hydrolase
Query= reanno::MR1:200445 (253 letters) >FitnessBrowser__Burk376:H281DRAFT_01080 Length = 256 Score = 279 bits (714), Expect = 4e-80 Identities = 136/243 (55%), Positives = 173/243 (71%), Gaps = 1/243 (0%) Query: 6 PLIGVIACNQRLGSHPFNIVGEKYLLGVVNGAKGWPLVIPSLGADQPIEAILARLDGILF 65 PLIG+ A G HP ++VGEKY+ +V+G++ L++P+LG Q E +LA +DG+ F Sbjct: 5 PLIGITADRTTTGHHPSHVVGEKYIAAIVDGSQALALLLPALGERQSTEDVLASVDGLFF 64 Query: 66 TGSPSNVEPHLYAGVPSEAGTHHDPKRDATTLPLIRAAIAAGVPVLGICRGFQEMNVAFG 125 TGS SN+EPH Y G P T HD RDATTLPL+RAAIAAGVPVL +CRG QEMNV FG Sbjct: 65 TGSYSNLEPHRYGGKPCAPDTLHDAARDATTLPLMRAAIAAGVPVLAVCRGLQEMNVVFG 124 Query: 126 GSLHQKLHEVGHFIEHREDKEASLEVQYGPSHSITVEPGGVIYE-AWGRNSAEVNSVHTQ 184 G+LHQ +H V F +HRE+KE L++QY PSH++ + GG++ A G N VNS+H Q Sbjct: 125 GTLHQSVHAVAGFSDHRENKEDRLDLQYAPSHTVLLTHGGLLQRLAHGANEVRVNSLHDQ 184 Query: 185 GVERLGIGLRPEACAPDGLVEAFSVIDATEFALGVQWHPEWKVSDNPFYLSIFNAFGDAC 244 G+E+LG+GL EA APDGL+EA SV A FALGVQWHPEWK + + +IF AFG+AC Sbjct: 185 GIEQLGMGLVVEATAPDGLIEAVSVSGARAFALGVQWHPEWKHASDLLSTAIFRAFGNAC 244 Query: 245 RRR 247 R R Sbjct: 245 RER 247 Lambda K H 0.320 0.139 0.429 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: 283 Number of extensions: 11 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: 256 Length adjustment: 24 Effective length of query: 229 Effective length of database: 232 Effective search space: 53128 Effective search space used: 53128 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