Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_068175624.1 HTA01S_RS22760 aspartate aminotransferase family protein
Query= uniprot:A0A806JQF3 (400 letters) >NCBI__GCF_001592305.1:WP_068175624.1 Length = 462 Score = 211 bits (538), Expect = 3e-59 Identities = 159/430 (36%), Positives = 216/430 (50%), Gaps = 63/430 (14%) Query: 27 PIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHTSNLYATE 86 P+A+ SG G +TD G+TY+D GG AV+ LGH HP V A+ Q+ L + + T Sbjct: 27 PVAV-SGQGMTLTDASGKTYLDACGGAAVSCLGHGHPEVRAAMHAQIDRLTYAHTSFFTT 85 Query: 87 PGIALAEELVALL---GADQRTRVFFCNSGAEANEAAFKLSRL-------TGRTKLVAAH 136 +AEEL LL + V+F + G+EA EAA K++R R +A Sbjct: 86 ---GVAEELADLLIDTAPAGMSHVYFVSGGSEAVEAALKMARQYFVEIGQPQRRHFIARR 142 Query: 137 DAFHGRTMGSLALTGQPAKQTPFAPLPGDVTHVG----------------YGD--VDALA 178 ++HG T+G+LA+ G ++ F PL DVTHV YG V L+ Sbjct: 143 QSYHGNTLGALAVGGNAWRREQFQPLLIDVTHVAPCYEYRDRRADESAEQYGQRLVAELS 202 Query: 179 AAVD----DHTAAVFLEPIMGES-GVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRT 233 A++ + A E + G + GV+ GY R++ R G LL+LDEV GMGRT Sbjct: 203 EAIERLGPQNVMAFVAETVGGATAGVLTAVPGYFKGVRELCDRHGILLILDEVMCGMGRT 262 Query: 234 GAFFAHQHDGITPDVVTLAKGLGGGL-PIGACLAVGPAAELLTPG----LHGSTFGGNPV 288 G A + +G+ PD++T+AKGLGGG PIGA LA G G HG T+ G+ V Sbjct: 263 GTLHACEQEGVVPDLMTIAKGLGGGYQPIGAVLAQGRVVGAFRQGSGLFQHGHTYLGHAV 322 Query: 289 CAAAALAVLRVLASDGLVRRAEVLGKSLRHGIEA--LGHPLIDHVRGRGLLLGIALTAP- 345 AAALAV RV+ DGL+ + G +L+ ++ GHP + +RGRGL G+ L A Sbjct: 323 ACAAALAVQRVIQRDGLLAQVRERGAALQALLQQAFAGHPQVGDIRGRGLFWGLELVAER 382 Query: 346 ------------HAK-DAEATA-----RDAGYLVNAAAPDVIRLAPPLIIAEAQLDGFVA 387 HA+ +EA A G V+ D I LAPP I +EA L V Sbjct: 383 GSKRWFDPALRLHARVKSEAMAGGLMVYPMGGTVDGRCGDHILLAPPFIASEADLGEIVE 442 Query: 388 ALPAILDRAV 397 L A LDRAV Sbjct: 443 RLRAALDRAV 452 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: 527 Number of extensions: 33 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: 462 Length adjustment: 32 Effective length of query: 368 Effective length of database: 430 Effective search space: 158240 Effective search space used: 158240 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 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