Align Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94) (characterized)
to candidate AZOBR_RS02010 AZOBR_RS02010 glutamine amidotransferase
Query= reanno::MR1:200445 (253 letters) >FitnessBrowser__azobra:AZOBR_RS02010 Length = 253 Score = 297 bits (760), Expect = 2e-85 Identities = 148/248 (59%), Positives = 179/248 (72%), Gaps = 1/248 (0%) Query: 6 PLIGVIACNQRLGSHPFNIVGEKYLLGVVNGAKGWPLVIPSLGADQPIEAILARLDGILF 65 PLIGV AC + +G HPF++VG+KY+ V +GA G PL+IP+LG ++ + RLDG+L Sbjct: 5 PLIGVPACARMMGEHPFHVVGDKYVRAVSDGAGGMPLLIPALGTALDMDDVAGRLDGLLV 64 Query: 66 TGSPSNVEPHLYAGVPSEAGTHHDPKRDATTLPLIRAAIAAGVPVLGICRGFQEMNVAFG 125 TGSPSNVEPH Y G PSE GT HDP+RD TTLPLIRAA+ GVP+LGICRGFQE+NVA G Sbjct: 65 TGSPSNVEPHRYGGSPSEPGTLHDPERDDTTLPLIRAALEMGVPLLGICRGFQELNVALG 124 Query: 126 GSLHQKLHEVGHFIEHREDKEASLEVQYGPSHSITVEPGGVIYE-AWGRNSAEVNSVHTQ 184 G+LHQ++HEV + HREDKEA L VQYGPSHS+ + PGGV+ A G + VNS+H Q Sbjct: 125 GTLHQRVHEVPGYANHREDKEAPLAVQYGPSHSVRLTPGGVLERLAGGAAAVTVNSLHGQ 184 Query: 185 GVERLGIGLRPEACAPDGLVEAFSVIDATEFALGVQWHPEWKVSDNPFYLSIFNAFGDAC 244 GV+RL GL EA A DGLVEA V A FAL VQWHPEW+ +NP +I AFG A Sbjct: 185 GVDRLADGLIVEAMAEDGLVEAVRVAGAPAFALAVQWHPEWRFWENPLSAAILRAFGSAA 244 Query: 245 RRRATTRV 252 RA R+ Sbjct: 245 ADRARRRL 252 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: 306 Number of extensions: 7 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: 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