Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013841823.1 DESRU_RS09145 aspartate aminotransferase family protein
Query= curated2:Q8TUE8 (395 letters) >NCBI__GCF_000215085.1:WP_013841823.1 Length = 470 Score = 259 bits (662), Expect = 1e-73 Identities = 161/397 (40%), Positives = 223/397 (56%), Gaps = 44/397 (11%) Query: 38 SKGKGAVVQDIYGKEYIDCVAGIAVNNVGHCHPTVVKAIQA--QAENLIHVSNLYYTEIQ 95 + G V D G EY+D + G N+GH HP +V ++ NL+ S + Sbjct: 53 TSASGVSVFDAQGNEYLDFLGGYGALNLGHNHPEIVAVLEKVHSRPNLLQTS---LNSLA 109 Query: 96 AEFAETLASITG--MERVFFCNSGAESVEAAMKLARVATGKSAFVAAEHSFHGRTIGALS 153 A A LA + ++R FFCNSGAE+VE A+KLAR+ATG+ F+ +SFHG+T GALS Sbjct: 110 AALAHNLAQLAPGPLQRSFFCNSGAEAVEGALKLARIATGRQKFIYCINSFHGKTFGALS 169 Query: 154 VTHKSMYRDPFMPPVSSETTFVPYSDAEAIRQAISENTAAV-ILEPIQGEGGINIPDPGY 212 VT + Y+ PF P + E VP+ D A++Q +S AA I+EPIQGEGGI P P Y Sbjct: 170 VTGRDKYQSPFRP-LMQECAAVPFGDLSALQQQLSSREAAAFIIEPIQGEGGIIEPPPRY 228 Query: 213 LKEVREICDETGALLIFDEVQTGFGRTGTWFCKEQFGVEPDIMSMSKAIGGG-FPMGAIA 271 L + +C + G LLI DEVQTGFGRTGT+F E + PDI+ ++K++GGG P GA Sbjct: 229 LARAKNLCAQYGTLLIADEVQTGFGRTGTFFASEAEDLVPDILCLAKSLGGGLIPAGAYI 288 Query: 272 AHNGI------NFGRG-QHASTFGGGPLACAAALASVKVIREEKLLERSKEMGAYFMKKL 324 + + N R H STFGG LACA AL +++V+ + L +++KE G YF KL Sbjct: 289 TSDELWRKAYGNMDRALLHTSTFGGNTLACAVALKTIEVLLNQNLCQQAKEKGEYFKSKL 348 Query: 325 AGMVRDD--VVEVRGKGLMIGVEIKYP---------CGKFVDFAREQ-------GVLVN- 365 + + EVRG+GLMIG+E + P K VD ++ G L N Sbjct: 349 NRLKEKYPLLKEVRGRGLMIGLEFQQPNLQNRRFVLTLKKVDQLIQEYMGSLIAGELFNQ 408 Query: 366 --------CTSDSVLRLVPPLVITKEQIDTVVDVLEQ 394 + +V+R+ PPL +T+EQ+D VV LE+ Sbjct: 409 HRIITAYTLNNPNVIRMEPPLTVTREQLDAVVIALEE 445 Lambda K H 0.319 0.135 0.391 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: 446 Number of extensions: 17 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 395 Length of database: 470 Length adjustment: 32 Effective length of query: 363 Effective length of database: 438 Effective search space: 158994 Effective search space used: 158994 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