Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011973917.1 MAEO_RS06130 aspartate aminotransferase family protein
Query= curated2:O27392 (390 letters) >NCBI__GCF_000017185.1:WP_011973917.1 Length = 432 Score = 152 bits (384), Expect = 2e-41 Identities = 106/306 (34%), Positives = 161/306 (52%), Gaps = 19/306 (6%) Query: 22 PIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRLIHSSNIYYTR 81 P +++ K + D++GN YID +GHA+ +A A+ Q + ++ T Sbjct: 39 PFFVNNAKDYYLVDVDGNKYIDYCLAYGPAVLGHANENIANAVIEQLKH--GTAYGCPTE 96 Query: 82 EQVELAKLLTAISP-HDRVFFANSGAEANEGAIKLARKFTGKSEIIAAENSFHGRT--LA 138 +++ LAK + P + V F NSG EA AI+LAR T +++II + ++HG + Sbjct: 97 KEITLAKEIIKRMPCAEMVRFVNSGTEATMSAIRLARGITKRNKIIKFDGAYHGAHDYVL 156 Query: 139 TVTATGQKKYSEPFRP-LPEGF-KHV---PYGDIGAMADAVG---DETAAIILEPVQGEG 190 + +G + P P +PE KH P+ D A+ + + DE A II+EPV G Sbjct: 157 VKSGSGALTHGAPNSPGIPEDTTKHTILAPFNDKDAIVEIIKNNKDEIACIIVEPVMGNV 216 Query: 191 GVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAMFASQLFGVEPDITTVAKAMGG 250 G I P E YLK ++E+ +N+++LI DEV TGF R A + +GV PD+ TV K MGG Sbjct: 217 GCIPPREDYLKFLREITEENNIILIFDEVITGF-RIAKGGAQEYYGVVPDLATVGKIMGG 275 Query: 251 GYPIGAVLANERVAMAFEPGD---HGSTFGGNPWGCAAAIATIEVLMDE--KLPERAAKM 305 G+PIGA++ + + F P TF GNP A I T++ L D ++AK Sbjct: 276 GFPIGAIVGKKELMENFSPNGTIYQAGTFNGNPISMTAGIETLKNLDDNFYSTTSKSAKK 335 Query: 306 GSYFLG 311 S F+G Sbjct: 336 LSDFIG 341 Lambda K H 0.320 0.138 0.404 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: 412 Number of extensions: 21 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: 390 Length of database: 432 Length adjustment: 31 Effective length of query: 359 Effective length of database: 401 Effective search space: 143959 Effective search space used: 143959 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 (21.8 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