Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_073038500.1 BUB04_RS08170 putrescine aminotransferase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_900129305.1:WP_073038500.1 Length = 449 Score = 293 bits (751), Expect = 5e-84 Identities = 168/385 (43%), Positives = 229/385 (59%), Gaps = 15/385 (3%) Query: 18 FPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYN 77 F VT G+G+ + D G EYID + G + LG HP VV AVK Q++R S + Sbjct: 63 FAVTEWVGQGSILRDALGREYIDALGGFGLYSLGIRHPKVVAAVKAQLDRSPQYSQEMLD 122 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTKFIAFEGGFHGRTMG 137 +A +++A P D+ FF NSGTE+VE A+KLA+ +TG FIA GFHG+T+G Sbjct: 123 PLRAHLGKVIAAITPGDIQYGFFANSGTEAVEGAMKLAKFYTGKPGFIAMLRGFHGKTLG 182 Query: 138 ALSATWKPEFREPFEPLVPEFEHVPYGDVNAVE------KAIDDDTAAVIVEPVQGEAGV 191 +LS K FR+P PL+ HVP+GD +AVE KA+ D AAV+ EP+QGEAG Sbjct: 183 SLSLMGKSVFRQPLLPLLEGVRHVPFGDADAVEKALAAAKAVGDGIAAVVAEPIQGEAGA 242 Query: 192 RIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVCLAKGLGGG- 250 +PP+ F LRELCD +G+LLI DEVQ+G GRTG F +H DV PDI+C K LGGG Sbjct: 243 IVPPDDFWPRLRELCDHYGVLLIADEVQTGFGRTGTLFGVDHWDVTPDIMCFGKALGGGV 302 Query: 251 VPVGATIAREEVAEAFEPGD--HGSTFGGNPLACAAVCAAVSTVLEENLPEAAERKGKLA 308 VP+ A + ++ + EP H +T GGNPLACAA A ++ L E+LP A KG Sbjct: 303 VPMSAFFSTPKIWKVMEPNPFMHTTTTGGNPLACAAALAQITVTLGEDLPRQAAEKGDYV 362 Query: 309 MRILSEAE----DVVEEVRGRGLMMGVEVGDDERAKDVAREMLDRGALV--NVTSGDVIR 362 + L E + +++EVRG+GL++G+E DE VA + RG L +T+ IR Sbjct: 363 LGKLREFQSRFPQILQEVRGKGLLIGMEFPTDEVGFKVAAGLFSRGVLTAGTLTNAQTIR 422 Query: 363 LVPPLVIGEDELEKALAELADALRA 387 + P L I + L++ L L D L++ Sbjct: 423 IEPALNISYELLDELLNRLEDTLKS 447 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: 437 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: 389 Length of database: 449 Length adjustment: 32 Effective length of query: 357 Effective length of database: 417 Effective search space: 148869 Effective search space used: 148869 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