Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_013819183.1 METME_RS12875 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000214665.1:WP_013819183.1 Length = 390 Score = 252 bits (644), Expect = 1e-71 Identities = 143/382 (37%), Positives = 212/382 (55%), Gaps = 22/382 (5%) Query: 1 MPLY-RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59 MP Y R+ + RGEG ++WD G+RYLD +AGI V LGHAHP + +Q + ++ Sbjct: 6 MPTYARQTVTFDRGEGAWLWDSNGKRYLDALAGIAVCNLGHAHPAVHQALCKQSQTLIHT 65 Query: 60 GPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR-----LATGRSEIVAMT 114 ++ + E+ ++L + V+ NSG EA EAAIK AR I+ M Sbjct: 66 SNLYGVKLQAELADKLCRLSGMDNVFFCNSGAEANEAAIKIARKYGHEQGIDAPVILTMD 125 Query: 115 NAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAI--TKETAAVIFEPIQ 172 +FHGRT+G+LSAT K ++GF PL+PGF H+P+NN++A AI K A++ EP+Q Sbjct: 126 KSFHGRTMGALSATGNTKIKQGFAPLLPGFVHVPYNNIDAIISAIHADKNIVAILVEPVQ 185 Query: 173 GEGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKG 231 GEGG+ D +++ +R L ++ LL+ DE+Q+G+ RTG+FLA + + PD+ T+ K Sbjct: 186 GEGGVNIPDADYLNRIRALCDEHQLLLMLDEIQTGIGRTGEFLAYQRNQILPDVCTLAKA 245 Query: 232 IGNGFPVSLTLTDLE----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEKFM 287 +GNG P+ + + + G HGSTFGGNPLAC A L L L+ A K Sbjct: 246 LGNGVPIGACMARGKAAAILTAGNHGSTFGGNPLACSAALAVLDTLCSTDLIADADRKGK 305 Query: 288 EF---------SGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLP 338 +V R GLMIGI L P G V E+G+L+N + IRLLP Sbjct: 306 RICDAVTRQLEGNPHIVSIRHLGLMIGIELDAPCGELVGKALEQGLLINVTADNTIRLLP 365 Query: 339 PLIIEGDTLEEARKEIEGVLND 360 PL+I+ ++ + + ++ + Sbjct: 366 PLLIDDAQIDLLTETLSALIKE 387 Lambda K H 0.320 0.140 0.410 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: 347 Number of extensions: 18 Number of successful extensions: 6 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: 362 Length of database: 390 Length adjustment: 30 Effective length of query: 332 Effective length of database: 360 Effective search space: 119520 Effective search space used: 119520 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