Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_028310255.1 H566_RS0102945 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000482785.1:WP_028310255.1 Length = 399 Score = 328 bits (841), Expect = 2e-94 Identities = 175/388 (45%), Positives = 252/388 (64%), Gaps = 14/388 (3%) Query: 23 YVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLH 82 +VM+TYGR P+ +A+GEG LWD +G+ YLD +AGIA LGHAHP L+ A++ QI KL Sbjct: 11 HVMNTYGRLPITLARGEGVWLWDEQGRKYLDGLAGIAVNGLGHAHPKLVAALTDQIGKLI 70 Query: 83 HISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTV-SDFLEQPV 141 H SN+Y + Q LA I S ++VFFC+SGAEANE AIKL R Y + DF++ V Sbjct: 71 HTSNIYGVRGQEDLADAICARSGMEEVFFCSSGAEANENAIKLARFYGYKQGKDFIKTVV 130 Query: 142 ILSAKSSFHGRTLATITATGQPKYQKHFDPLPDG-FAYVPYNDIRALEEAITDIDEGNRR 200 + ++++HGRT+AT+ AT PK +K F+P+ D F VP+N++ AI ++ E N Sbjct: 131 M---ENAWHGRTIATLAATDSPKARKGFEPMQDECFVRVPHNNL----AAIIEVAETNPE 183 Query: 201 VAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGI 260 + ++MLE LQGEGG+ VEY + +R++CDE G LL+LDEVQ GVGRTG ++GY++ GI Sbjct: 184 INSVMLEVLQGEGGINLASVEYLQGLRKLCDERGWLLILDEVQCGVGRTGTWFGYQHAGI 243 Query: 261 EPDIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQEN 319 EPD T AKGL G+PIGA+ + S A + PG +TFGGNP + A ++TLE++ Sbjct: 244 EPDAITLAKGLGSGVPIGALAVRGSAAKLIGPGNFGTTFGGNPLAMRAGTCTLQTLEEDG 303 Query: 320 LLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGL 379 LL++ G+ +RAG + E +D+RG GL+ G+E+ + +V A+E G Sbjct: 304 LLQHAVVIGDHIRAGFRAALEGVAGVTDIRGQGLMIGIELDRPCGV----IVTRALEAGF 359 Query: 380 LLAPAGPKVLRFVPPLIVSAAEINEAIA 407 L+ KV+R +PPLI++ AE + +A Sbjct: 360 LINVTRDKVVRLLPPLIMTTAEADLLVA 387 Lambda K H 0.319 0.136 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: 447 Number of extensions: 16 Number of successful extensions: 5 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: 418 Length of database: 399 Length adjustment: 31 Effective length of query: 387 Effective length of database: 368 Effective search space: 142416 Effective search space used: 142416 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: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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