Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_012282524.1 HM1_RS06545 acetylornithine transaminase
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000019165.1:WP_012282524.1 Length = 432 Score = 386 bits (991), Expect = e-112 Identities = 193/398 (48%), Positives = 273/398 (68%), Gaps = 16/398 (4%) Query: 22 QYVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKL 81 +YVM+TYGR P+++ KG+G RLWD +G+ YLDF+AG+A +LGH HP ++ A+ Q L Sbjct: 12 KYVMNTYGRLPISLVKGQGARLWDADGREYLDFLAGLAVNSLGHCHPKVVDALQQQAATL 71 Query: 82 HHISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTV--SDFLEQ 139 H+SNLY+I Q LAQ +VE+S ADKVFFCNSGAEANE AIKL RKYA SD E Sbjct: 72 LHVSNLYWIEPQVQLAQVLVENSFADKVFFCNSGAEANEGAIKLARKYAKKTWGSDKYE- 130 Query: 140 PVILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNR 199 I++ + SFHGRTLAT+TAT QPKYQK ++PLP GF YVP+ D++ALE AI+ Sbjct: 131 --IITMEKSFHGRTLATVTATAQPKYQKDYEPLPQGFRYVPFGDLKALERAISP------ 182 Query: 200 RVAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLG 259 AI++E +QGEGGV + +++ + ++ N +LL+ DEVQ G+GRTGK + +E+ G Sbjct: 183 HTCAILVEPVQGEGGVNLAEPSFWQGLAKLAAANKLLLIFDEVQCGLGRTGKLFAHEHYG 242 Query: 260 IEPDIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQE 318 + P I T AK LAGG P+GA++ D A F PG+HASTFGGNP AAA+AV++ L + Sbjct: 243 VTPHIMTLAKALAGGAPMGALLATDDVANAFQPGDHASTFGGNPLVAAAAVAVMDVLLND 302 Query: 319 NLLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKG 378 L++N L+ L EKYP+ ++VRG GL+ + +L+ ++V +EKG Sbjct: 303 GLMDNCREMAAYFMGHLRRLQEKYPFITEVRGLGLM----VACELDRPGADIVANCLEKG 358 Query: 379 LLLAPAGPKVLRFVPPLIVSAAEINEAIALLDQTLAAM 416 L++ VLRF+PPLI++ A+++EA+A+L++ LA++ Sbjct: 359 LIINCTAGNVLRFLPPLIINKADVDEAVAVLEEVLASV 396 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: 507 Number of extensions: 18 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: 432 Length adjustment: 32 Effective length of query: 386 Effective length of database: 400 Effective search space: 154400 Effective search space used: 154400 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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