Align Acetylornithine aminotransferase, chloroplastic/mitochondrial; ACOAT; Acetylornithine transaminase; AOTA; Protein HOPW1-1-INTERACTING 1; EC 2.6.1.11 (characterized)
to candidate WP_012113062.1 XAUT_RS05230 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::Q9M8M7 (457 letters) >NCBI__GCF_000017645.1:WP_012113062.1 Length = 469 Score = 152 bits (383), Expect = 3e-41 Identities = 133/440 (30%), Positives = 191/440 (43%), Gaps = 73/440 (16%) Query: 73 YARAPVVLSSGKGCKLFDPEGKEYLDCASGIAVNALGHGDPDWLRAVTEQAGVLAHVSNV 132 Y P + +G ++D E + +LD + G+ +P A+ Q L V++ Sbjct: 34 YTEEPKIFERCEGSFIYDDEDRAFLDLQMWYSAVNFGYANPRLNEAMRRQLDRLPQVASQ 93 Query: 133 YYTIPQIELAKRLVASSFA-----DRVFFCNSGTEANEAAIKFSRKFQRFTHPEDKEVAT 187 Y +IELA + + A RV F G +A E ++K R A Sbjct: 94 YLHREKIELAAEIAEGAMARFGHKGRVHFNVGGAQAIEDSLKLVRN------------AC 141 Query: 188 G----FIAFTNSFHGRTLGALALTSKEQYRTPF------EPIMP---------GVTFLEY 228 G AF +HGRTLGA A+TS +YR F +P G+T EY Sbjct: 142 GGKSLMFAFEGGYHGRTLGASAITSSYRYRRRFGHFGERAHFIPFPYHFRGPRGMTKEEY 201 Query: 229 GN--IQAATDLIRSG------------KIAAVFVEPIQGEGGIYSATKEFLQSLRSACDA 274 G+ ++ L S + AA +VEPIQG GG F L+ D Sbjct: 202 GHRCVEQFARLFESEYNGVWDPKAGQCEYAAFYVEPIQGTGGYVIPPANFFPELKEVLDR 261 Query: 275 AGSLLVFDEVQCGLGRTGLMWAYEAFGVTPDIMTVAKPLAGGL-PIGAVLVTEKV--AET 331 G LLV DE+Q G RTG +WA E FGV PDI+ K L GL P+ + E + + Sbjct: 262 HGILLVVDEIQMGFYRTGKLWAIEHFGVAPDIIVFGKALTNGLNPLSGLWAREALINPQA 321 Query: 332 INYGDHGSTFAGSPLVCSAAIAVMDKVSKPSFLSSVSNKGRYFRDLLVKKLGGNSHVKEV 391 G STF +PL + A+ M + + F +SV+ KG F D L + ++ V +V Sbjct: 322 FPPGSTHSTFNANPLGTAVALEAMRMMREEDFATSVAEKGARFLDGLKELKAKHAIVGDV 381 Query: 392 RGEGLIIGVEL------DVPASSLVDACRDSGL------------LILTAG--KGNVVRI 431 G GL + VE+ P+ ++VD D L L+L G NV+ + Sbjct: 382 DGLGLALRVEICEPHDSYTPSKAIVDRMVDEALKGDLVHGGERYGLVLDIGGYHKNVITL 441 Query: 432 VPPLVISEEEIERAVEIMSQ 451 P L IS EI+ A+ +M Q Sbjct: 442 APALTISHAEIDLALALMDQ 461 Lambda K H 0.318 0.135 0.385 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: 442 Number of extensions: 25 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: 457 Length of database: 469 Length adjustment: 33 Effective length of query: 424 Effective length of database: 436 Effective search space: 184864 Effective search space used: 184864 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 (21.7 bits) S2: 51 (24.3 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