Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_011937171.1 GURA_RS01135 acetylornithine transaminase
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000016745.1:WP_011937171.1 Length = 396 Score = 409 bits (1050), Expect = e-118 Identities = 212/397 (53%), Positives = 273/397 (68%), Gaps = 12/397 (3%) Query: 21 DQYVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQK 80 D+Y+M TYGR+P+ KGEGC LWD +GK YLDF+AG+A LGH HP ++ A+ Q + Sbjct: 11 DKYIMRTYGRYPLVPVKGEGCYLWDADGKRYLDFLAGVAVNNLGHCHPRVVAALQKQAAE 70 Query: 81 LHHISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQP 140 L H SN Y+IP Q LA+ + HS AD+ FFCNSGAEANEAAIKL RKY+ ++ Sbjct: 71 LIHCSNYYHIPTQIELAEILCNHSFADRAFFCNSGAEANEAAIKLARKYSREKYG-QDRY 129 Query: 141 VILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRR 200 I++A +SFHGRT+AT++ATGQ K QK FDPL GF +VP+ND ALE+A+T Sbjct: 130 EIITALASFHGRTMATVSATGQEKVQKFFDPLLHGFLHVPFNDADALEKAVTP------N 183 Query: 201 VAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGI 260 AIMLE +QGEGGV D EYF+ VRRICDEN +LL+ DEVQVG+GRTGK + +E+ G+ Sbjct: 184 TCAIMLEPIQGEGGVVVPDAEYFRQVRRICDENNLLLIFDEVQVGIGRTGKLFAHEHFGV 243 Query: 261 EPDIFTSAKGLAGGIPIGAMMCK-DSCAVFNPGEHASTFGGNPFSCAAALAVVETLEQEN 319 PDI T AK LAGG PIG M+ + D A F PG H STFGGNP AA +AV+ T+ +E Sbjct: 244 TPDIMTLAKALAGGAPIGTMLAREDLAASFGPGTHGSTFGGNPLVTAAGVAVMRTILEEG 303 Query: 320 LLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGL 379 +L + GE L L+ L +K+P +DVRG GL+ GME L + + ++VK +E+G+ Sbjct: 304 ILNHTEEMGEYLMGELEGLKKKFPIITDVRGIGLMIGME----LSVPAGDIVKKGLERGV 359 Query: 380 LLAPAGPKVLRFVPPLIVSAAEINEAIALLDQTLAAM 416 LL A +VLRFVPPLIV E++E IA+LD LA M Sbjct: 360 LLNVAQDRVLRFVPPLIVGKKEVDEMIAVLDGILAEM 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: 473 Number of extensions: 12 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: 396 Length adjustment: 31 Effective length of query: 387 Effective length of database: 365 Effective search space: 141255 Effective search space used: 141255 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 12 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