Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_057507761.1 ABB28_RS05945 glutamine amidotransferase
Query= reanno::pseudo5_N2C3_1:AO356_13140 (258 letters) >NCBI__GCF_001431535.1:WP_057507761.1 Length = 253 Score = 244 bits (623), Expect = 1e-69 Identities = 127/250 (50%), Positives = 158/250 (63%), Gaps = 1/250 (0%) Query: 5 PLIGVTTCSRQMGLHAYHTSGDKYARAVATAAKGLPVLVPSLADLFPPSDILDALDGILL 64 PL+G+ T S G H + +G+KY RA+ AA PVL+PSL P D L + G+LL Sbjct: 5 PLVGLPTDSSLQGHHRFAMAGEKYVRALVDAAAVTPVLLPSLQPPLPAGDWLSRVHGLLL 64 Query: 65 TGSPSNVEPFHYQGPASAPGTAHDPARDATTLPLIRAAVEAGVPVLGICRGFQEMNVAFG 124 TG+ SN+EP HY G + PG HDPARD L+ A+ A +PVL ICRGFQE+NVA G Sbjct: 65 TGAVSNIEPQHYAGGRTWPGNLHDPARDGAAFSLLVHALAADLPVLAICRGFQELNVALG 124 Query: 125 GSLHQKVHEVGTFIDHREDDTQAVEVQYGPAHAVDIQPGGILAGLGLPQSIEVNSIHSQG 184 G+LH +VH V DHRED +VEVQYGPAH++ + GG LA +S VNS+H QG Sbjct: 125 GTLHPQVHRVEGRHDHREDPAASVEVQYGPAHSIALVAGGWLAQWHGARSAVVNSVHGQG 184 Query: 185 IERLAPGLRAEAVAPDGLIEAVSVPEGKAFALGVQWHPEWEVSSNPHYLAIFQAFGDACR 244 I+ LA L EA A DGL+EA +F LGVQWHPEW V+ NP Y A+F AFG ACR Sbjct: 185 IDSLADALLPEAHADDGLVEAAR-SRRHSFVLGVQWHPEWRVTHNPFYHAVFHAFGQACR 243 Query: 245 ARATQRDADA 254 R ++ A Sbjct: 244 QRQRRQQDSA 253 Lambda K H 0.318 0.135 0.406 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: 269 Number of extensions: 8 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: 258 Length of database: 253 Length adjustment: 24 Effective length of query: 234 Effective length of database: 229 Effective search space: 53586 Effective search space used: 53586 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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