Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase
Query= curated2:Q8TUZ5 (389 letters) >MicrobesOnline__882:208056 Length = 542 Score = 208 bits (529), Expect = 3e-58 Identities = 140/420 (33%), Positives = 214/420 (50%), Gaps = 52/420 (12%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYN- 77 P + +G + D +GN Y+D V+ + NV GH HP + EA++ Q++R+ H + L Sbjct: 84 PCIIDAADGNHLIDTDGNRYLDGVSSLWTNVHGHRHPHIDEAIRRQLDRVAHSTLLGLGG 143 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF--------TGCTKFIAFEG 129 P E A L AP L +VF+ +SG+ +VE A+K+A ++ T+ +AF Sbjct: 144 TPSIELAARLTAIAPAGLTRVFYSDSGSTAVEAALKIAFQYHRQAPEGDARRTRVMAFSN 203 Query: 130 GFHGRTMGALSATWKPEFREPFEPLVPEFEHVP--------------------YGDVNAV 169 +HG T+G++S F + PL+ + P G+V + Sbjct: 204 AYHGDTIGSVSLGGMSLFHGIYGPLLFDPVRAPAPHCYRCPADLRPETCGMACLGEVERL 263 Query: 170 EKAIDDDTAAVIVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQF 228 + + AV+VEP VQG AG+ + P G+LR LR+LCD HG+ ++ DEV G G+TG Sbjct: 264 MRHHGHELCAVVVEPLVQGAAGMLVQPRGWLRGLRDLCDRHGVFMVADEVAVGFGKTGTM 323 Query: 229 FAFEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPG-------DHGSTFGGNPL 280 FA E E V+PD++CLAKG+ GG +P+ AT+ E + + F G HG T+ GN L Sbjct: 324 FACEQEGVVPDMLCLAKGITGGYLPLAATLVTEHIHDGFLGGYADFRTFFHGHTYTGNAL 383 Query: 281 ACAAVCAAVSTVLEENLPEAAERKGKLAMRILSEAEDV--VEEVRGRGLMMGVEVGDDER 338 ACAA A++ EE E + + +L+ D+ V ++R G+M G+E+ D Sbjct: 384 ACAAALASLDVFEEERTLETLRPRIERLATLLAPLNDLPHVGDIRRVGVMTGIELVADRE 443 Query: 339 AKD-----------VAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADALRA 387 + V E RG +V GDV+ L+PPL I E ELE + + A+ A Sbjct: 444 TRTPYRPEERIGHRVTLEARRRGVIVR-PLGDVMVLMPPLSITETELETLVHTVRGAIIA 502 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: 502 Number of extensions: 36 Number of successful extensions: 7 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: 542 Length adjustment: 33 Effective length of query: 356 Effective length of database: 509 Effective search space: 181204 Effective search space used: 181204 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: 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