Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_092350282.1 BLU87_RS15000 aspartate aminotransferase family protein
Query= curated2:O27392 (390 letters) >NCBI__GCF_900107645.1:WP_092350282.1 Length = 463 Score = 199 bits (507), Expect = 1e-55 Identities = 139/416 (33%), Positives = 216/416 (51%), Gaps = 34/416 (8%) Query: 6 IIELERKFIMQTYTRQPIV-LSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAI 64 + E E+ FI Q+ + + L G+ ++D G SY+D F G + + +G+ HP V AI Sbjct: 38 LAEDEKYFIHQSLSTPCLTALERSHGSYLFDTNGKSYLD-FHGNSSHQVGYGHPHVVAAI 96 Query: 65 CHQAQRLIHSSNIYYTREQVELAKLLTAISPHD--RVFFANSGAEANEGAIKLARKFTGK 122 + QRL S + R VELAK L +SP + R+ FA G AN A+KLAR TG+ Sbjct: 97 TEEMQRLPFSPRRFTNRPAVELAKKLAQLSPGNLNRMLFAPGGTSANGIALKLARSVTGR 156 Query: 123 SEIIAAENSFHGRTLATVTATGQKKYSEPFRPLPEGFKHVP-----------------YG 165 + ++ ++FHG +L ++ G+ + PL G VP G Sbjct: 157 FKTLSFWDAFHGASLDAISVGGEALFRRNMGPLLPGCIQVPAPGSHCFGVDKLDWQKALG 216 Query: 166 DIGAMADAVGDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGR 225 I + GD AA I EP++ + IPP + + ++E+ ++ VLLI DE+ GR Sbjct: 217 YIEYVMVHEGD-VAAFIAEPMRCTT-IDIPPVQFWRQIREICDRHGVLLIFDEIPLCLGR 274 Query: 226 TGAMFASQLFGVEPDITTVAKAMGGG-YPIGAVLANERVAMAFEPGDHGSTFGGNPWGCA 284 TG MFA + + V PDI + K +GGG +P+ A L E + + T +P GCA Sbjct: 275 TGFMFACEYYAVVPDILCLGKGLGGGIFPMAATLIREDLEIDPAQALGHYTHEKSPVGCA 334 Query: 285 AAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEID---GEC 341 AA+AT+EV+ DE L +R+ ++G + L L ++ + +RGVGLM+GIEI G Sbjct: 335 AALATLEVIADEHLLQRSRELGRHTLAALHRLRSEHPLISAVRGVGLMLGIEITPPAGFT 394 Query: 342 AGVVDAAREM-------GVLINCTAGKVIRIVPPLVIKKEEIDAAVDVLGHVISDL 390 DAA ++ G+ +AG V+ + PPL I E+DAA++++ I+ + Sbjct: 395 CSATDAAEQILYAAFTQGLSFKISAGNVLTLTPPLTISDAEMDAALNIIAASIAQV 450 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: 456 Number of extensions: 17 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: 463 Length adjustment: 32 Effective length of query: 358 Effective length of database: 431 Effective search space: 154298 Effective search space used: 154298 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