Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate GFF3387 PGA1_c34400 aminotransferase class-III
Query= uniprot:A0A806JQF3 (400 letters) >FitnessBrowser__Phaeo:GFF3387 Length = 464 Score = 162 bits (410), Expect = 2e-44 Identities = 129/413 (31%), Positives = 192/413 (46%), Gaps = 50/413 (12%) Query: 35 GAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHTSNLYATE--PGIALA 92 G +TD +G +D + G+ +G+ + + RQM L + + + T P IALA Sbjct: 44 GVTLTDSEGNEILDAMAGLWCVNIGYGRDELADVAARQMRELPYYNTFFQTTHAPAIALA 103 Query: 93 EELVALLGADQRTRVFFCNSGAEANEAAFKLSRLTGRTK-------LVAAHDAFHGRTMG 145 + +A L D VFF SG+EAN+ ++ R K +++ + +HG ++G Sbjct: 104 AK-IAELAPDGLNHVFFAGSGSEANDTNIRMVRHYWAMKAKPTKSVIISRKNGYHGSSVG 162 Query: 146 SLALTGQPAKQTPFA-PLPGDVTHVGY-------GDVDA----------LAAAV----DD 183 S +L G A P+P D+ H+ GD+ A L A+ +D Sbjct: 163 SGSLGGMTAMHEQGGLPIP-DIHHINQPNWWAEGGDMSAEDFGLARAQELEQAILELGED 221 Query: 184 HTAAVFLEPIMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHDG 243 AA EP+ G GV+VPPA Y + I + LL+ DEV G GRTG +F Q G Sbjct: 222 RVAAFIAEPVQGAGGVIVPPATYWPEIQRICDKYEILLIADEVICGFGRTGNWFGSQSVG 281 Query: 244 ITPDVVTLAKGLGGG-LPIGACLAVGPAAELLTPG--LHGSTFGGNPVCAAAALAVLRVL 300 I PD++T+AKGL G PIG + A ++ G HG T+ G+PV AA AL LR+L Sbjct: 282 IRPDIMTIAKGLSSGYAPIGGSIVSDEIASVIGSGEFNHGYTYSGHPVAAAVALENLRIL 341 Query: 301 ASDGLVRRA-EVLGKSLRHGIEALG-HPLIDHVRGRGLLLGIALTAPHAKDAEATARD-- 356 + ++ +V L+ EAL HPL+ + G++ IALT A A A Sbjct: 342 EEENIIGHVRDVAAPYLKEKWEALADHPLVGEAKIVGMMGSIALTPNKATRAGFAAEGGT 401 Query: 357 ----------AGYLVNAAAPDVIRLAPPLIIAEAQLDGFVAALPAILDRAVGA 399 A LV D + ++PPL+I ++D +A LD A Sbjct: 402 VGYICRERCFANNLVMRHVGDRMIISPPLVITPEEIDTLIARARQSLDECYAA 454 Lambda K H 0.320 0.136 0.399 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: 21 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: 400 Length of database: 464 Length adjustment: 32 Effective length of query: 368 Effective length of database: 432 Effective search space: 158976 Effective search space used: 158976 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 (21.8 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