Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_212636831.1 B9A12_RS05520 aspartate aminotransferase family protein
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_900176285.1:WP_212636831.1 Length = 449 Score = 196 bits (499), Expect = 8e-55 Identities = 140/433 (32%), Positives = 216/433 (49%), Gaps = 56/433 (12%) Query: 10 YHMNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLI 69 ++ N +PV + GEG +WD +GN YID G V LGH P ++EA+KEQ R+ Sbjct: 11 FYRNLRKTYPV-VDRGEGIHIWDKDGNRYIDGSGGACVVSLGHGVPEILEAMKEQAARIS 69 Query: 70 HCSNLYYNEPQAE--AARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF------TGC 121 ++ A A RL+ A L++V+F + G+E+VE A+K+ R++ Sbjct: 70 FAHGSHFTSEAARECADRLVRLAPDPSLSRVYFLSGGSEAVETAVKVVRQYWREVGRPDK 129 Query: 122 TKFIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHV--------PYGD-------- 165 K I+ FHG TMGA++ R + P H+ P+G Sbjct: 130 YKVISRWVSFHGNTMGAVALGGHTARRRHYHPHFLHTPHIEPAYCYRCPFGREPQTCSLE 189 Query: 166 -VNAVEKAID----DDTAAVIVEPVQGE-AGVRIPPEGFLRELRELCDEHGLLLIVDEVQ 219 +E+ I D AA I EPV G AG +P +G+ + +RE+CD + + LI DEV Sbjct: 190 CAEQLERTIKYEGPDAVAAFIAEPVVGATAGALVPRDGYWQRIREICDTYEVKLIADEVM 249 Query: 220 SGMGRTGQFFAFEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGD----HGST 274 +G+GRTG+ F +H V+PD++ AKGL G P+GA I +EE+ +A G HG T Sbjct: 250 TGVGRTGRNFCLDHWSVVPDVIVSAKGLSSGYTPLGAVIVKEEIHDAIRSGSGAFVHGHT 309 Query: 275 FGGNPLACAAVCAAVSTVLEENLPEAAERKGKLAMRILSE--AEDVVEEVRGRGLMMGVE 332 + NPL+ A A + + E++L G++ + L +V +VRG GL GVE Sbjct: 310 YSQNPLSVAVGAAVLRYLEEKDLIARCATMGEVFLEKLRGLLERPMVGDVRGLGLFAGVE 369 Query: 333 VGDDERAK-----------DVAREMLDRGAL-------VNVTSGDVIRLVPPLVIGEDEL 374 + ++ K VA+E RG + + +GD I L PP +I E+EL Sbjct: 370 LVQNKETKAPFAPSGKISARVAQEAFRRGLITYPGSGGADGINGDHILLAPPFIITEEEL 429 Query: 375 EKALAELADALRA 387 ++ + L +A++A Sbjct: 430 DEIVRILGEAIQA 442 Lambda K H 0.318 0.137 0.405 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: 482 Number of extensions: 29 Number of successful extensions: 8 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: 389 Length of database: 449 Length adjustment: 32 Effective length of query: 357 Effective length of database: 417 Effective search space: 148869 Effective search space used: 148869 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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