Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_002721205.1 RSPH17029_RS13130 aspartate aminotransferase family protein
Query= curated2:Q58131 (398 letters) >NCBI__GCF_000015985.1:WP_002721205.1 Length = 459 Score = 199 bits (505), Expect = 2e-55 Identities = 134/422 (31%), Positives = 219/422 (51%), Gaps = 47/422 (11%) Query: 22 PVVLVEGKGMEVYDIDGKKYLDFLAG-IGVNNVGHCHPKVVEAIKKQAETLIHTSNIYYT 80 P ++VEGKGM V+D GK++LD ++G + NVG+ + A++ Q + + ++ + Sbjct: 36 PRIIVEGKGMRVWDAAGKEHLDAVSGGVWTVNVGYGRESIANAVRDQLIKMNYFAHSAGS 95 Query: 81 IPQIKLAKKLVE-LSGLDRAFFCNSGAEANEGAIKFARKYVSKVLGREGGEIISMYNAFH 139 IP + +K+L+E + GL R ++ NSG+EANE K R+ + G G+I+ +H Sbjct: 96 IPASRFSKRLIEKMPGLSRVYYSNSGSEANEKVFKMVRQISHRHHGGRKGKILFRERDYH 155 Query: 140 GRTLTTLAATPKPKYQDGFYPLPPGFKYVPFN-------DIE--------ALKEAIT--- 181 G T+T LA + +P+ + + PL PGF VP D+E A++E I Sbjct: 156 GTTITALATSGQPQRAEQYGPLTPGFVMVPHCLEYRKQWDVENYGERAADAIEEVILREG 215 Query: 182 -DKTAAIMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAFEH 240 D A+ +EPV GG+ V Y + V+++C +I+L DEV CG+GRTG F +++ Sbjct: 216 PDTIGALCLEPVTAGGGVIVPPAGYWERVQEICRKYDILLHIDEVVCGLGRTGTWFGYQN 275 Query: 241 YGVEPDILTLAKALGGG-------VPIGAV--VLKEEIAKALSYGDHGTTFGGNPLACSA 291 +GV+PD +T+AK + G V AV + K++ + +SY +TFGG A Sbjct: 276 FGVKPDFVTMAKGVASGYAAISCTVTTEAVFDMFKDDPSDPMSYFRDISTFGGCTAGPVA 335 Query: 292 ALASVEVIEELIKDDKVIEKGKYFIRKLENLIEKYNFIKEVRGLGLMIGAEL-------- 343 AL ++ +IE+ + ++ G + L L EK+ I +VRG GL GAEL Sbjct: 336 ALENMRIIEDEGLLENTLKMGARVVENLSALQEKHAVIGDVRGKGLFCGAELVADRATKE 395 Query: 344 ---EFNGADIVKKMLEKGFLINCTS------DTVLRFLPPLIVEKEHIDALINALDEVFT 394 E A +V ++ +G +I T+ + L P LI + ID + +A+D T Sbjct: 396 PMDEKRVAAVVADVMAQGVIIGMTNRSLPGFNNTLCLSPALIATPDDIDQITDAIDRALT 455 Query: 395 EI 396 + Sbjct: 456 RV 457 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: 433 Number of extensions: 30 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: 459 Length adjustment: 32 Effective length of query: 366 Effective length of database: 427 Effective search space: 156282 Effective search space used: 156282 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 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