Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate GFF4233 Psest_4306 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= uniprot:A0A806JQF3 (400 letters) >FitnessBrowser__psRCH2:GFF4233 Length = 441 Score = 178 bits (452), Expect = 2e-49 Identities = 138/422 (32%), Positives = 201/422 (47%), Gaps = 50/422 (11%) Query: 15 WQAVMMNN-YGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQM 73 W N + P L S +G T DGR +D G+ GH + EAV++Q+ Sbjct: 15 WMPFTANRQFKASPRLLESAEGMYYTASDGRQVLDGTAGLWCCNAGHGRREISEAVSKQI 74 Query: 74 STLGHTSNLYATEP-GIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLS----RLTG 128 + + P LAE+L A+ + RVFF NSG+E+ + A K++ R G Sbjct: 75 AKMDFAPTFQMGHPLPFELAEKLAAI-SPEGLNRVFFTNSGSESADTALKIALAYQRAIG 133 Query: 129 ---RTKLVAAHDAFHGRTMGSLALTGQPAKQTPFAPLPGDVTHV---------------- 169 RT+L+ A+HG G +++ G + F P+ V H+ Sbjct: 134 QGSRTRLIGRELAYHGVGFGGMSVGGMANNRRAFGPMLPGVDHLPHTLDLQRNAFSRGLP 193 Query: 170 --GYGDVDALAAAVDDH----TAAVFLEPIMGESGVVVPPAGYLAAARDITARRGALLVL 223 G D L V H AAV +EP+ G +GV++PP GYL R+ITA+ G LL+ Sbjct: 194 QHGVERADELERLVTLHGAENIAAVIVEPMSGSAGVILPPVGYLQRLREITAKHGILLIF 253 Query: 224 DEVQTGMGRTGAFFAHQHDGITPDVVTLAKGL-GGGLPIGACLAVGPAAELLTPG----- 277 DEV TG GR G FA Q G+TPD++T AKGL G +P+GA LA + G Sbjct: 254 DEVITGFGRVGEAFAAQRWGVTPDILTCAKGLTNGAIPMGAVLAADHLFDAFMKGPESVI 313 Query: 278 --LHGSTFGGNPVCAAAALAVLRVLASDGLVRRAEVLGKSLRHGIEALGH-PLIDHVRGR 334 HG T+ G+PV AAALA ++ + L ++A L + + +L P + +R Sbjct: 314 EFFHGYTYSGHPVACAAALATQQIYQQENLFQKAIDLEPYWQEALFSLRDLPNVIDIRTV 373 Query: 335 GLLLGIALTAPHAK-------DAEATARDAGYLVNAAAPDVIRLAPPLIIAEAQLDGFVA 387 GL+ GI A HA + + G LV A+ D I L+P LI+ +A++D +A Sbjct: 374 GLVAGIQFAA-HADGVGKRGYEVFRECFEKGLLVRASG-DTIALSPALIVEKAEIDQMMA 431 Query: 388 AL 389 L Sbjct: 432 LL 433 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: 434 Number of extensions: 20 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: 400 Length of database: 441 Length adjustment: 32 Effective length of query: 368 Effective length of database: 409 Effective search space: 150512 Effective search space used: 150512 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: 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