Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_086511325.1 BZY95_RS18280 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:O66442 (376 letters) >NCBI__GCF_002151265.1:WP_086511325.1 Length = 421 Score = 192 bits (488), Expect = 1e-53 Identities = 136/416 (32%), Positives = 216/416 (51%), Gaps = 64/416 (15%) Query: 5 MNNYAR-LPVKFVRGKGVYLYDEEGKEYLDFVSGIGVNSLGHAYPKLTEALKEQVEK--L 61 + Y+R PV F + + L DE G+EY+DF++G G + GH P L +AL + ++ + Sbjct: 13 VRTYSRSFPVVFTKARNARLTDESGREYIDFLAGAGTLNYGHNNPHLKQALLDYLDSDGI 72 Query: 62 LHVSNLY---ENPWQEELAHKLVKHFWTEGKVFFAN-SGTESVEAAIKLARKYWRDKGKN 117 +H + + + + E L ++K + KV +GT +VEAAI+LAR + Sbjct: 73 VHGLDFWTAAKRDYLETLEEVILKPRGLDYKVHLPGPTGTNAVEAAIRLARV-----AQG 127 Query: 118 KWKFISFENSFHGRTYGSLSATGQPKFHK--GFEPL-------VPGFSYAKLNDIDSVYK 168 + +SF N FHG T GSL+ TG KF + G PL G+ + +D K Sbjct: 128 RHNIVSFTNGFHGVTMGSLATTGNRKFREATGGIPLQGSAFMPYDGYLGEHTDSLDYFEK 187 Query: 169 LLDEETAG------IIIEVIQGEGGVNEASEDFLSKLQEICKEKDVLLIIDEVQTGIGRT 222 LL + ++G +I+E +QGEGG+N A ++L +L+ IC++ D+LLI+D++Q G GRT Sbjct: 188 LLGDNSSGLDLPAAVIVETVQGEGGINVAGLEWLQRLERICRDNDILLIVDDIQAGCGRT 247 Query: 223 GEFYAYQHFNLKPDVIALAKGLGG-GVPIGAILAREEVAQSFTPGSHGSTFGGNPLAC-- 279 G+F++++H + PD++ +K L G G+P +L R E+ + PG + TF G LA Sbjct: 248 GKFFSFEHAGITPDIVTNSKSLSGFGLPFAHVLMRPEL-DKWKPGQYNGTFRGFNLAFAT 306 Query: 280 -------------------RAGTVVVDEVEKLLPHVREVGNYFKEKLKELGKGKVKGRGL 320 R G VV D +K+ + E G K +GRGL Sbjct: 307 AAAAMRQYWQDDTFERDVQRKGRVVEDRFQKIAALIGEYG----------VKATERGRGL 356 Query: 321 MLGLEL-ERECKDYV-LKALEKGLLINCT--AGKVLRFLPPLIIQKEHIDRAISVL 372 M G+++ E D + KA EKGL+I + AG+V++ L PL I E + + +L Sbjct: 357 MRGIDVGSGELADKITAKAFEKGLVIETSGQAGEVVKCLCPLTIPDEDLLEGLDIL 412 Lambda K H 0.318 0.139 0.409 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: 393 Number of extensions: 23 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: 376 Length of database: 421 Length adjustment: 31 Effective length of query: 345 Effective length of database: 390 Effective search space: 134550 Effective search space used: 134550 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 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