Align Acetylornithine aminotransferase 2; ACOAT 2; EC 2.6.1.11 (uncharacterized)
to candidate WP_026607161.1 METAC_RS0111610 aspartate aminotransferase family protein
Query= curated2:Q9A652 (405 letters) >NCBI__GCF_000427445.1:WP_026607161.1 Length = 446 Score = 151 bits (381), Expect = 4e-41 Identities = 127/422 (30%), Positives = 192/422 (45%), Gaps = 44/422 (10%) Query: 18 YNRAPLAFERGRGARLISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWHVSNI 77 + +AP + + EG LD AG+ GH+ +V ++AQA +L Sbjct: 28 FKQAPRIVASAKDMHYFTPEGRAILDGTAGLWCANAGHSRAPIVAAIQAQAAELDFAPPF 87 Query: 78 -YRIPEQEELADALCANSFADV--VFFTNSGTEAVECALKTARKYHSANGQPERIDIYGF 134 + P+ LA + A + D+ VFFTNSG+EAV+ ALK A YH+ G+ R + G Sbjct: 88 QFGHPKVFALASRVAALAPGDLDHVFFTNSGSEAVDTALKIALAYHNIRGEGARQRLIGR 147 Query: 135 DGSFHGRTYAAVNASGNPSYVDGFGPRLPGYSQLT----------------FGDH--DAI 176 + +HG + G + FG L G L +G H D + Sbjct: 148 ERGYHGVGFGGTAVGGMVANRKVFGALLAGVDHLPSTYNRAEQAFTKGEPEWGAHLADEL 207 Query: 177 KAAIA---SPTTAAIIVEPVQGEGGARSIPTQCLVGLRQLCDEHGVLLIYDEVQCGMGRT 233 + + + T AA+IVEP+ G G P L LR +CD++G+LLI+DEV CG GR Sbjct: 208 ERIVGLHDASTIAAVIVEPMAGSTGVLPAPKGYLERLRAICDKYGILLIFDEVICGFGRL 267 Query: 234 GKLFAYEWAEGGEPHIMAVAKAL-GGGFPIGACL-------ATTEAAKGMTVAAHGSTFG 285 G+ FA E G P ++ AK + G P+G L A + + HG T+ Sbjct: 268 GRAFAAE-RYGVLPDMITFAKGVTSGTVPMGGVLVRKGIYEAFMKGPEHAVELFHGYTYS 326 Query: 286 GNPLAMAVGKAALEIIKSPETLDNVKTVSGFFTQQLNGLKDRFPDVIVDVRGKGMLIGVK 345 G+PLA A G A L++ + + F+ ++ LK P+V+ D+R G+ + Sbjct: 327 GHPLACAAGLATLDLYVEEDLFARSAKLEPFWADAIHSLKG-LPNVL-DIRTVGLTAAID 384 Query: 346 L-----IPNNRDFMVL---ARDEKLLIAGGGDNCVRLLPPLNLTIEEASEAIAKLEKACE 397 L P R F + LL+ GD+ V L PPL ++ + E + K KA + Sbjct: 385 LAAKPDAPGKRGFEAMDHAFHQFDLLVRIAGDSLV-LTPPLIVSEAQIGEIVEKTGKAIK 443 Query: 398 AA 399 AA Sbjct: 444 AA 445 Lambda K H 0.318 0.135 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: 437 Number of extensions: 28 Number of successful extensions: 4 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: 405 Length of database: 446 Length adjustment: 32 Effective length of query: 373 Effective length of database: 414 Effective search space: 154422 Effective search space used: 154422 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 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