Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_019555867.1 F612_RS0100950 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:Q58131 (398 letters) >NCBI__GCF_000381085.1:WP_019555867.1 Length = 428 Score = 194 bits (494), Expect = 3e-54 Identities = 132/416 (31%), Positives = 225/416 (54%), Gaps = 35/416 (8%) Query: 12 KYHLQIYGRL---PVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKK-- 66 KY ++ G + P + + K E++D+ GK+Y+DF AG G N GH +PK+ +A+ Sbjct: 8 KYESEVRGYIRSFPTIFEKSKMAEIWDVSGKRYIDFFAGAGALNYGHNNPKINDAVISYL 67 Query: 67 QAETLIHTSNIYYTIPQIKLAKKLVE--LSGLDRAFFCNSGAEANEGAIKFARKYVSKVL 124 Q + + H ++ T+ + + V L D + GAI+ A K KV Sbjct: 68 QNDGIGHALDMG-TVAKRDFMESFVNNILKPRDLDYKLQFVGPTGTGAIEAALKIARKVK 126 Query: 125 GREGGEIISMYNAFHGRTLTTLAATPKPKYQDGFYPLPPGFKYVPFND--------IEAL 176 GR+ +I+S N FHG ++ +L+ T Y D Y +P VPF+ I L Sbjct: 127 GRK--QIMSFTNGFHGMSMGSLSITGNKYYHDESYGVPGYTTQVPFHKYLGDKVDTIAYL 184 Query: 177 KEAITDKT------AAIMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMG 230 ++ + D + AAI++E VQ EGGI+VA +++LK +R +CDD +I++I D++Q G G Sbjct: 185 RKILEDDSSGTELPAAIVLETVQAEGGINVAGEEWLKDLRQICDDFDILMIVDDIQVGNG 244 Query: 231 RTGRMFAFEHYGVEPDILTLAKALGGGVPIGAVVLKEEIAKALSYGDHGTTFGGNPLACS 290 R+G F+FE G++PDI+TL+K++G G P+ V+LK E+ + G+H TF GN LA Sbjct: 245 RSGDFFSFERAGIKPDIITLSKSIGAGHPMALVLLKPEL-DIWTAGEHSGTFRGNNLAFV 303 Query: 291 AALASVEVI---EELIKDDKVIEKGKYFIRKLENLIEKY-NFIKEVRGLGLMIGAELEFN 346 A+ +++ + K+ K+ K K ++++ L+ ++ I E RGLG++ GAE + Sbjct: 304 ASTVALDTYWSDDSFSKEVKI--KAKLVEQRMQKLVSRFPEIINETRGLGMIWGAEFKDP 361 Query: 347 G--ADIVKKMLEKGFLINC--TSDTVLRFLPPLIVEKEHIDALINALDEVFTEIKK 398 + I + E G +I +++FL PL++ +E I+ + L+ ++ K Sbjct: 362 SITSAICSQAFEDGLVIETAGAESDLIKFLGPLVMTEELINEGFDILENAIVKVLK 417 Lambda K H 0.320 0.141 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: 449 Number of extensions: 28 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: 398 Length of database: 428 Length adjustment: 31 Effective length of query: 367 Effective length of database: 397 Effective search space: 145699 Effective search space used: 145699 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: 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