Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_084217011.1 Q392_RS31975 aspartate aminotransferase family protein
Query= curated2:O27392 (390 letters) >NCBI__GCF_000745855.1:WP_084217011.1 Length = 432 Score = 185 bits (470), Expect = 2e-51 Identities = 140/423 (33%), Positives = 201/423 (47%), Gaps = 57/423 (13%) Query: 18 YTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRLI----- 72 + P +L G +G S +D +G+ +IGH +A AI Q L Sbjct: 16 FKASPRMLERAAGVFYQAQDGRSILDAVSGLWCVNIGHGRTMMAEAIARQVSTLDYAPMF 75 Query: 73 ---HSSNIYYTREQVELAKLLTAISPHDRVFFANSGAEANEGAIKLARKFTG------KS 123 HS+ Y +E A RVF NSG+EA + A+KLA KF +S Sbjct: 76 QMGHSTGFAYADRLLEFAP-----KGFGRVFLVNSGSEAVDTALKLALKFHKMRGEGQRS 130 Query: 124 EIIAAENSFHGRTLATVTATGQKKYSEPFRPLPEGFKHVPYGDI-------------GA- 169 ++ E S+HG ++ G + F PL G H+P+ GA Sbjct: 131 RLVGRERSYHGVGFGGISVGGMAANRKDFGPLLPGIDHLPHTHGLSENLFSRGQPPGGAY 190 Query: 170 MADAV--------GDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQT 221 +ADA+ AA+I+EPV G GV++PP GYL+ ++E+ +++ +LLI DEV T Sbjct: 191 LADALERIVQLHDASTIAAVIVEPVAGSAGVLVPPVGYLERLREITKKHGILLIFDEVIT 250 Query: 222 GFGRTGAMFASQLFGVEPDITTVAKAM-GGGYPIGAVLANERVAMAFE--PGD-----HG 273 GFGR G+ FA+ GV PD+ AKA+ G P+G VL N + F+ P D HG Sbjct: 251 GFGRLGSSFAADRMGVVPDMIVTAKAITNGTIPMGGVLINSEMLETFKNTPADQIDFYHG 310 Query: 274 STFGGNPWGCAAAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMI 333 T +P CAAA ++ + DE+L ERA K+ + + L G V DIR GLM Sbjct: 311 YTASAHPVACAAASVVLDAIEDEELLERAKKLEDCLEQSIHK-LRGHPLVHDIRNFGLMG 369 Query: 334 GIEIDGECAG------VVDAAREMGVLINCTAGKVIRIVPPLVIKKEEIDAAVDVLGHVI 387 +E+ + V+ A GVL+ T G I + P LV + + ID AV VL V+ Sbjct: 370 AVELTPDAVAGRRGLEVLQACFNKGVLVRAT-GDTIALAPALVSEAKHIDMAVGVLDGVL 428 Query: 388 SDL 390 + L Sbjct: 429 TSL 431 Lambda K H 0.320 0.138 0.404 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: 471 Number of extensions: 28 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: 390 Length of database: 432 Length adjustment: 31 Effective length of query: 359 Effective length of database: 401 Effective search space: 143959 Effective search space used: 143959 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 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