Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012965636.1 FERP_RS05655 aspartate aminotransferase family protein
Query= curated2:Q58131 (398 letters) >NCBI__GCF_000025505.1:WP_012965636.1 Length = 428 Score = 128 bits (321), Expect = 4e-34 Identities = 93/318 (29%), Positives = 157/318 (49%), Gaps = 24/318 (7%) Query: 22 PVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKKQAET-LIHTSNIYYT 80 P V G ++ D+DG+ Y D+ G +GH HP+V EA+K+Q E ++ + + Sbjct: 33 PFVPERAFGCKIVDVDGRVYTDYHLAFGPILLGHNHPEVNEAVKEQIEEGVLFGAGVCEL 92 Query: 81 IPQIKLAKKLVEL-SGLDRAFFCNSGAEANEGAIKFARKYVSKVLGREGGEIISMYNAFH 139 ++++A+KLVEL + F NSG EA AI+ +R Y E +II +H Sbjct: 93 --EVEVAEKLVELIPSAEMVTFVNSGTEATYHAIRLSRAYT------EREKIIKFEGCYH 144 Query: 140 G-RTLTTLAATPKPKYQDGFYPLPPGF--------KYVPFNDIEALKEAIT---DKTAAI 187 G P + YP G +PFND EA +E + ++ A + Sbjct: 145 GWHDYVAFNVNPPKEKMGRIYPQSRGILKAAYETTTVLPFNDKEAFEEYMAEHGEEVAGV 204 Query: 188 MIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAFEHYGVEPDI 247 ++EP+ G + +D+LK++R VLIFDE+ R E +GV PD+ Sbjct: 205 ILEPIPHSVGAIIPKRDFLKSLRKETKSYGSVLIFDEIITAF-RHNIHGVQEEFGVIPDL 263 Query: 248 LTLAKALGGGVPIGAVVLKEEIAKALSYGD-HGTTFGGNPLACSAALASVEVIEELIKDD 306 T+ K++G G P+ A+V KEEI + G T+ G+P + +A ++EV+E + Sbjct: 264 TTIGKSMGNGYPVAAIVGKEEIMSLVHNGVLVSGTYSGHPASLAAVKKTIEVLEREKVVE 323 Query: 307 KVIEKGKYFIRKLENLIE 324 + + G+ + + ++++IE Sbjct: 324 YISKLGEEYRKAIKDVIE 341 Lambda K H 0.320 0.141 0.409 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: 428 Number of extensions: 35 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: 398 Length of database: 428 Length adjustment: 31 Effective length of query: 367 Effective length of database: 397 Effective search space: 145699 Effective search space used: 145699 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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