Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_089301469.1 CHB84_RS10975 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_900188115.1:WP_089301469.1 Length = 416 Score = 194 bits (493), Expect = 4e-54 Identities = 136/406 (33%), Positives = 209/406 (51%), Gaps = 31/406 (7%) Query: 12 MNTYSR-FPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQV--ERL 68 + +YSR +PV +G+ ++ ++ Y+D AG GH +P + +A+ + + + + Sbjct: 11 VRSYSRGWPVVFHRAQGSWLYTEDDKPYLDFFAGAGALNYGHNNPVLKQALLDYISSDGV 70 Query: 69 IHCSNLYYNEPQAEAARLLAEAA--PKDLN-KVFFCN-SGTESVECAIKLARKFTGCTKF 124 H +++ + + L E P+DL+ KV F G +VE A+KLARK TG Sbjct: 71 THSLDMH-TVAKRDFLNALDEVVFGPRDLHYKVTFPGPGGANAVEAALKLARKVTGKEAV 129 Query: 125 IAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPYG--------DVNAVEKAIDD- 175 I F FHG T+GALS T R + +PY D E+ +DD Sbjct: 130 INFTNAFHGMTLGALSVTGNSMKRGGAGIPLVHATPMPYASYFGGAYPDFLYFERLLDDS 189 Query: 176 -----DTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFA 230 + AAVIVE VQGE G+ +LR L E+C +LLIVD+VQ G GRTG FF+ Sbjct: 190 GSGLNEPAAVIVETVQGEGGINAAELDWLRSLDEICKRREILLIVDDVQMGCGRTGPFFS 249 Query: 231 FEHEDVLPDIVCLAKGLGG-GVPVGATIAREEVAEAFEPGDHGSTFGGNPLACAAVCAAV 289 FE + PD++CL+K +GG G+P+ T+ R ++ + + PG+H TF G A A+ Sbjct: 250 FEDAGIKPDMICLSKSIGGYGLPLALTLIRPDL-DVWAPGEHNGTFRGISPAFVTAAEAL 308 Query: 290 STV-----LEENLPEAAERKGKLAMRILSEAEDVVEEVRGRGLMMGVEVGDDERAKDVAR 344 T LE++ ER G + I E D+ +GRGL G+E D E A V Sbjct: 309 RTFWTDDSLEKSTRAKGERVGAVLTEIADEHADLGLVAKGRGLARGLEFPDGETADKVCA 368 Query: 345 EMLDRGALVNVT--SGDVIRLVPPLVIGEDELEKALAELADALRAS 388 +RG L+ + G+V +L+PPL + +DE+E L + +++ A+ Sbjct: 369 AAFERGLLMETSGPDGEVAKLLPPLTVTDDEVEHGLGIIKESVAAT 414 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: 435 Number of extensions: 20 Number of successful extensions: 6 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: 416 Length adjustment: 31 Effective length of query: 358 Effective length of database: 385 Effective search space: 137830 Effective search space used: 137830 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 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