Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_041097708.1 SUTH_RS05530 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000828635.1:WP_041097708.1 Length = 390 Score = 340 bits (872), Expect = 4e-98 Identities = 180/398 (45%), Positives = 254/398 (63%), Gaps = 15/398 (3%) Query: 23 YVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLH 82 ++M+TYGR PVA G+GCRL+D +GKSYLD +AGIA TLGH HP L++A+S Q+ +L Sbjct: 3 HLMNTYGRLPVAFTHGQGCRLFDEQGKSYLDALAGIAVNTLGHNHPRLVKALSNQVARLI 62 Query: 83 HISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVI 142 H SNLY I E A + + S D+VFFCNSG EANEAAIKL R Y H +EQP I Sbjct: 63 HTSNLYRISEAEAASDRLAALSGMDEVFFCNSGCEANEAAIKLARMYGH--QQGVEQPAI 120 Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVA 202 + + +FHGRTLAT++ATG K Q F+PL GF VP++D+ A+E+ + E N V Sbjct: 121 IVMEHAFHGRTLATLSATGNRKVQAGFEPLVSGFVRVPFDDLAAIEQ----LAERNPNVV 176 Query: 203 AIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIEP 262 A++ E +QGEGG+ ++ +A+R+ICD L ++DEVQ G+GRTG ++ +++ GI P Sbjct: 177 AVLFEPIQGEGGINLAHNDFMRALRKICDRKNWLFMVDEVQCGIGRTGVWFAHQHAGILP 236 Query: 263 DIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQENLL 321 D+ T AKGL G+PIGA + A VF PG H STFGGNP +C AAL ++ +E + L+ Sbjct: 237 DVMTLAKGLGSGVPIGACLAAGRAAGVFKPGNHGSTFGGNPLACVAALTTLDVVEADGLM 296 Query: 322 ENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLLL 381 GE +R GL++ F +VRG GL+ G+E L+ ++V+ +E GLL+ Sbjct: 297 ARATMLGETIRGGLRSGLAGTSGFVEVRGDGLMIGIE----LDRPCGDLVRRGLESGLLI 352 Query: 382 APAGPKVLRFVPPLIVSAAE----INEAIALLDQTLAA 415 KV+R +P L++S AE + +AL+ + L A Sbjct: 353 NVTADKVVRLLPALVMSDAEGAELVTGLVALIKEFLGA 390 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: 424 Number of extensions: 20 Number of successful extensions: 4 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: 390 Length adjustment: 31 Effective length of query: 387 Effective length of database: 359 Effective search space: 138933 Effective search space used: 138933 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 Apr 09 2024. The underlying query database was built on Apr 09 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