Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_019866214.1 METMI_RS0110330 aspartate aminotransferase family protein
Query= curated2:Q81M98 (386 letters) >NCBI__GCF_000384075.1:WP_019866214.1 Length = 463 Score = 234 bits (596), Expect = 5e-66 Identities = 147/393 (37%), Positives = 216/393 (54%), Gaps = 38/393 (9%) Query: 21 GTKVIDNNGKQYLDFTSGIGVCNLGHCHPTVMKAVQEQL-----NDIWHISNLFTNSLQE 75 G + D NG +YLD SG GV +G HPTV+ A+QE L N + ++ + L + Sbjct: 46 GQYLYDQNGTEYLDLLSGFGVFAIGRNHPTVISALQETLTLELPNLVQLDVSVLSGLLGQ 105 Query: 76 EVASLLTENIALDYVFFCNSGAEANEAALKLARKHTGKSLVVTCEQSFHGRTFGTMSATG 135 E+ EN L+ +FFCNSG EA EAA+K AR T + +V CE +HG T G++S G Sbjct: 106 EIVKTTPEN--LNKIFFCNSGTEAVEAAIKFARYTTKREKIVFCEHGYHGLTMGSLSLNG 163 Query: 136 QNKVKEGFGPLLPSFLHTPFNDIKALKEVMNE-EVAAVMVEVVQGEGGVIPADLSFLKEI 194 +N +EGFGPLLP PFND+ AL+ +++ +VAA +VE +QG+G +P D ++L E+ Sbjct: 164 ENIFREGFGPLLPGCSAIPFNDLGALEAALSQKDVAAFIVEPIQGKGVNLPDD-NYLPEV 222 Query: 195 ETLCKKFGSLFIIDEVQTGIGRTGTLFAYEQMGIDPHIVTTAKALGNG-IPVGAM-IGRK 252 E LCK++G+LF+ DEVQTG+GRTG +A + + P ++ AKAL G +PVGA+ I +K Sbjct: 223 ERLCKQYGTLFVADEVQTGLGRTGKFWAVDHWNVSPDMICMAKALSGGFVPVGAVAITQK 282 Query: 253 ELGTSFT----AGSHGSTFGGNYVAMAAAKEVLQVSKRLSFLKEVQEKGEYVLQKLQEEL 308 + T + A HGSTF N +AMAA L V + + G ++ L Sbjct: 283 IMDTVYNRMDRAVVHGSTFSKNNMAMAAGLATLHVLAEEKLVDNCAKVGTDIINSLNAMS 342 Query: 309 QHVECIQNIRGKGLMVGIE------CTHEVASFIEQLEKEGLL----------------- 345 E ++ RGKG+M+ IE T + A + + +GL Sbjct: 343 GKYEFLKEARGKGMMIAIEFKSPKSLTLKAAWAMLEAANKGLFCQMITIPLFKEHHILTQ 402 Query: 346 VLQAGPNVIRLLPPLIVTNEELEQAVYMIKKVV 378 V G NV++LLPPL +T ++ + V K + Sbjct: 403 VAGHGMNVVKLLPPLNLTQQDRDHIVTSFDKTI 435 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: 383 Number of extensions: 18 Number of successful extensions: 4 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: 463 Length adjustment: 32 Effective length of query: 354 Effective length of database: 431 Effective search space: 152574 Effective search space used: 152574 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