Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012709571.1 NGR_RS26550 ornithine--oxo-acid transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000018545.1:WP_012709571.1 Length = 401 Score = 285 bits (729), Expect = 2e-81 Identities = 161/397 (40%), Positives = 230/397 (57%), Gaps = 16/397 (4%) Query: 6 LIDKYHM---NTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVK 62 LI+ H+ + Y V L GEG VWD EGN Y+D ++ + GHCHP + +A+ Sbjct: 7 LIETEHLLGAHNYKPLDVVLTRGEGVFVWDIEGNRYLDCLSAYSAVNQGHCHPKIFKAMV 66 Query: 63 EQVERLIHCSNLYYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCT 122 EQ ++L S + N+ A +A A +KV NSG E+VE AIK RK+ Sbjct: 67 EQAQKLTLTSRAFRNDQLALFYEEIA--ALTGSHKVLPMNSGAEAVETAIKAVRKWGYEV 124 Query: 123 KFIAFE--------GGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPYGDVNAVEKAID 174 K +A + FHGRT+G + + P+ + F P P F VP+GD++A AI Sbjct: 125 KGVAADQAEIIVCANNFHGRTIGIVGFSTDPDSHDGFGPFAPGFRIVPFGDIDAFRAAIS 184 Query: 175 DDTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHE 234 ++T A +VEP+QGEAGV +PP G+ E+RELC +H + L++DE+Q+G+GRTG+ A EHE Sbjct: 185 ENTVAFLVEPIQGEAGVIVPPAGYFAEVRELCTKHAITLVLDEIQTGLGRTGKLLAEEHE 244 Query: 235 DVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGDHGSTFGGNPLACAAVCAAVSTVL 293 + D+ + K L GG PV A ++ EV +PG HGSTFGGNPLACA AA+ + Sbjct: 245 AIEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAIARAALKVLT 304 Query: 294 EENLPEAAERKGKLAMRILSE-AEDVVEEVRGRGLMMGVE-VGDDERAKDVAREMLDRGA 351 EE + E + R G+ M L++ +++ EVRGRGLM+ VE V + A+ + RG Sbjct: 305 EEGMIENSARMGERFMTGLTDIRSNIIREVRGRGLMLAVELVPEAGGARKYCEALKARGI 364 Query: 352 LVNVTSGDVIRLVPPLVIGEDELEKALAELADALRAS 388 L T GD IR+ PPLVI E++ AL + A L ++ Sbjct: 365 LAKDTHGDTIRIAPPLVITAGEVDWALEQFAAVLAST 401 Lambda K H 0.318 0.137 0.405 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: 376 Number of extensions: 22 Number of successful extensions: 6 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: 389 Length of database: 401 Length adjustment: 31 Effective length of query: 358 Effective length of database: 370 Effective search space: 132460 Effective search space used: 132460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Jul 25 2024. The underlying query database was built on Jul 25 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