Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_028583710.1 G494_RS0105395 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000429965.1:WP_028583710.1 Length = 429 Score = 176 bits (446), Expect = 1e-48 Identities = 129/417 (30%), Positives = 208/417 (49%), Gaps = 41/417 (9%) Query: 10 YHMNTYSRFPVTLVP---GEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVE 66 +H T P+ + P G R+ ++G ID ++ + G+CHP + A EQ++ Sbjct: 15 WHPYTSMTQPLPVFPVASAAGVRLTLEDGQTLIDGMSSWWSVIHGYCHPVLDRAAHEQLD 74 Query: 67 RLIHCS-NLYYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCT--- 122 R+ H + P E R L +P+ L+KVF C+SG+ SVE A+K+A ++ Sbjct: 75 RMSHVMFGGLTHGPAVELGRRLVAISPEPLDKVFLCDSGSVSVEVALKMALQYWHSLGKP 134 Query: 123 ---KFIAFEGGFHGRTMGALSATWKPE-FREPFEPLVPEFEHVPYG-----------DVN 167 + + GG+HG T A+S FE +P+ P D+ Sbjct: 135 RKHRLLTIRGGYHGDTFHAMSVCDPVNGMHSLFEGALPKQLFAPRPSCRYDQQWQAEDLE 194 Query: 168 AVEKAIDD---DTAAVIVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMG 223 +E+ +++ + AAVIVEP VQG G+ I +L+ LR LCD +G+LLI DE+ +G G Sbjct: 195 EMERLLEEHHQELAAVIVEPLVQGAGGMWIYHPDYLKGLRSLCDSYGVLLICDEIATGFG 254 Query: 224 RTGQFFAFEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGD-----HGSTFGG 277 RTG+ FA +H + PDI+C+ K + GG + + AT+A E+A G HG TF G Sbjct: 255 RTGRMFAVDHAGIAPDIMCVGKAITGGYMTLAATLATTEIAVTISKGASGVFMHGPTFMG 314 Query: 278 NPLACAAVCAAVSTVLEENLPEAAERKGKLAMRILSE-----AEDVVEEVRGRGLMMGVE 332 NPLACA A++ + +E ER G + ++ +E A V +VR G + VE Sbjct: 315 NPLACAVASASLGLLQDE---PWQERVGAIEAQLTAELAPARALSTVSDVRVLGGIGVVE 371 Query: 333 VGDDERAKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADALRASG 389 + + + R +++G + G ++ ++PP +I ++L L +A SG Sbjct: 372 LKEPVDMARLQRFFVEQGVWIR-PFGRLLYIMPPYIISPEDLSTLTRVLVEAAAGSG 427 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: 411 Number of extensions: 28 Number of successful extensions: 6 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: 429 Length adjustment: 31 Effective length of query: 358 Effective length of database: 398 Effective search space: 142484 Effective search space used: 142484 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 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