Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_041277544.1 DP_RS02690 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:Q8R7C1 (393 letters) >NCBI__GCF_000025945.1:WP_041277544.1 Length = 459 Score = 199 bits (505), Expect = 2e-55 Identities = 138/420 (32%), Positives = 215/420 (51%), Gaps = 52/420 (12%) Query: 17 PIMLVKGEGTRVWDSEGNAYLDFVAG-IAVNSLGHCHPALVEAIKKQAETLIHCSNLYWN 75 P+++V+G+G R+ D+ GN +LD V+G + ++G+ ++ A++ Q L + + + Sbjct: 34 PMVVVEGKGMRIKDANGNEFLDAVSGGVWTVNVGYGRESIANAVRDQLVKLCYFAGSAGS 93 Query: 76 EKQIELARMISENSFG-GKVFFANSGAEANEGAIKLARKYASLKYGGKRYKIITAKNSFH 134 + A + + G +V+++NSG+EANE K+ R+ A L+ GK+ KII +H Sbjct: 94 VPGAQFAEALLDKMPGMDRVYYSNSGSEANEKCFKIIRQLAHLEGDGKKNKIIYRDRDYH 153 Query: 135 GRTFGALTATGQEKYHKGFGPLLAGF---------------KYVPLN-----DIEALYEA 174 G T GAL++TGQ + +GP GF KY N +E L +A Sbjct: 154 GTTIGALSSTGQFERKAQYGPFAPGFVELTNCCCYRCPFGKKYGECNIECAHALEDLIQA 213 Query: 175 VDDE-VCAIMLEVIQGEGGIHEATPEYVKAVRKICDENDLLFILDEVQTGIGRTGKLFGY 233 E V I+LE I GG+ PEY +R+ICD + +L +DEV G+GRTGK FGY Sbjct: 214 EGPETVGGIILEPITAGGGVIVPVPEYFPIIREICDRHGVLLHIDEVVCGLGRTGKWFGY 273 Query: 234 EHYGVVPDIMTLAKGLGGGFPIGAIVAKEDKAVF-----KPGD------HASTFGGNPLA 282 +H+ VVPD++T+AKG+ G+ G +AVF P D STFGG Sbjct: 274 QHFDVVPDMVTMAKGVASGY-AGISCTTTTEAVFDRFKADPSDKMHYFRDISTFGGCTAG 332 Query: 283 CAAGIAVLNEVTKDGFLEGVDKKGKYFREGLETLQKKHKVVKEIRGKGLMVGCE------ 336 AA + + + ++ L+ V K G YF + L L+ K++++ ++RGKGL G E Sbjct: 333 PAAALENMAIIIRENLLDNVVKMGDYFSDRLFELKDKYEIIGDVRGKGLFQGLELVKDRT 392 Query: 337 ----VDLEDASEIVLKALEKGLLINSVS-------HNVLRFVPPLIVTEEEIDEALQILD 385 VD A+ + K +I + +N L F P LI ++ EIDE + LD Sbjct: 393 TKEPVDESVAAGVAGHCAAKSRVIIGRTNRSFEKHNNTLAFSPALISSKTEIDEVINALD 452 Lambda K H 0.319 0.139 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: 452 Number of extensions: 29 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: 393 Length of database: 459 Length adjustment: 32 Effective length of query: 361 Effective length of database: 427 Effective search space: 154147 Effective search space used: 154147 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 09 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