Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_085773088.1 B1812_RS19660 aspartate aminotransferase family protein
Query= curated2:Q81M98 (386 letters) >NCBI__GCF_002117405.1:WP_085773088.1 Length = 480 Score = 224 bits (571), Expect = 4e-63 Identities = 136/323 (42%), Positives = 181/323 (56%), Gaps = 10/323 (3%) Query: 14 VEFVKGNGTKVIDNNGKQYLDFTSGIGVCNLGHCHPTVMKAVQEQLNDIWHISNLFTNSL 73 V F +G+G + D G QYLD SG GV LG HP V A+ E LN F S+ Sbjct: 58 VGFTRGDGAYLYDRAGAQYLDLMSGYGVFALGRNHPRVRDALIEVLNSQSANLAQFDVSV 117 Query: 74 QEEVAS--LLTENIALDYVFFCNSGAEANEAALKLARKHTGKSLVVTCEQSFHGRTFGTM 131 V + LL LD FF NSGAEA EAA+K AR TG+S +V C SFHG T G + Sbjct: 118 LAGVLAERLLARTPWLDKAFFANSGAEAVEAAIKFARYATGRSGIVHCAHSFHGLTCGAL 177 Query: 132 SATGQNKVKEGFGPLLPSFLHTPFNDIKALKEVMN-EEVAAVMVEVVQGEGGVIPADLSF 190 S G K+GFGPLL PF+D+ AL+E ++ +VAA +VE +QG+G IP + Sbjct: 178 SLNGDEIFKKGFGPLLSGVREIPFDDLGALEEALSGHDVAAFVVEPIQGKGVNIP-HADY 236 Query: 191 LKEIETLCKKFGSLFIIDEVQTGIGRTGTLFAYEQMGIDPHIVTTAKALGNG-IPVGAMI 249 L LCKK+G+LF+ DE+QTG+GRTG A E G++P +V AKAL G P+G + Sbjct: 237 LSSAAALCKKYGTLFVADEIQTGVGRTGKFLAIEHFGVEPDMVLLAKALSGGHAPIGVTL 296 Query: 250 GRKELGTSF-----TAGSHGSTFGGNYVAMAAAKEVLQVSKRLSFLKEVQEKGEYVLQKL 304 RK + + HGSTF N +AMAAA L V + ++ KG+ +L Sbjct: 297 TRKWIFDKVFDRMDRSVVHGSTFSKNDLAMAAALATLDVLEDEKLIENAAAKGDRLLASF 356 Query: 305 QEELQHVECIQNIRGKGLMVGIE 327 + + E + +RGKGLM+G+E Sbjct: 357 NKMAERYELVSAVRGKGLMIGVE 379 Lambda K H 0.319 0.136 0.388 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: 377 Number of extensions: 19 Number of successful extensions: 3 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: 386 Length of database: 480 Length adjustment: 32 Effective length of query: 354 Effective length of database: 448 Effective search space: 158592 Effective search space used: 158592 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 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