Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011841343.1 RSPH17029_RS09880 aspartate aminotransferase family protein
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000015985.1:WP_011841343.1 Length = 436 Score = 161 bits (407), Expect = 4e-44 Identities = 132/382 (34%), Positives = 183/382 (47%), Gaps = 35/382 (9%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNE 78 P+ +V GEG ++D +G Y+D +A LGHCHP VVEAV Q +L + Y +E Sbjct: 43 PLHIVRGEGVWLYDADGTAYLDAYNNVAS--LGHCHPRVVEAVARQAGQLATHTR-YLHE 99 Query: 79 PQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTKFIAFEGGFHGRTMGA 138 E A L P +L F +G+E+ + A++LA TG T I E +HG TMG Sbjct: 100 GVLELAERLLATLPPELGHAMFTCTGSEANDLALRLAFAATGGTGVIVTENAYHGVTMGV 159 Query: 139 LSATWKPEFREPFEPLVPEFEHVPYGDVN---------AVEKAIDD------DTAAVIVE 183 A P P PL VP D + AV A D AA+I++ Sbjct: 160 --AALSPSL-GPGVPLGAHVRTVPAPDPDKGADATFGAAVAAAAADLMRHGIRPAALILD 216 Query: 184 PVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQ-FFAFEHEDVLPDIVC 242 V GV P L G L I DEVQ G GRTG+ + F V+PD+V Sbjct: 217 TVFSSDGVFTHPTDTLAPAAAAIRAAGGLFIADEVQPGFGRTGEAMWGFLRHGVVPDMVS 276 Query: 243 LAKGLGGGVPVGATIAREEVAEAFEPG-DHGSTFGGNPLACAAVCAAVSTVLEENLPEAA 301 + K +G G PV A R E+AE F G + +TFGGN +A AA A + T+ E L A Sbjct: 277 MGKPMGNGYPVAALALRPELAERFGAGARYFNTFGGNAVAAAAALAVLDTLEAEGLQAHA 336 Query: 302 ERKG---KLAMRILSEAEDVVEEVRGRGLMMGVEVGDDE-RAKD------VAREMLDRGA 351 + G + + LS+ + + VRG GL +GVEV + E RA D + + + Sbjct: 337 LKVGGQFRADLSALSDRDPRLGAVRGAGLFLGVEVLEPESRAPDARMATRIVNGLREARV 396 Query: 352 LVNVTS--GDVIRLVPPLVIGE 371 L++ T G V+++ PPLV + Sbjct: 397 LISATGPHGHVLKIRPPLVFSD 418 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: 388 Number of extensions: 31 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: 436 Length adjustment: 31 Effective length of query: 358 Effective length of database: 405 Effective search space: 144990 Effective search space used: 144990 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 16 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