Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate N515DRAFT_1410 N515DRAFT_1410 methionine aminotransferase
Query= SwissProt::P16524 (393 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_1410 N515DRAFT_1410 methionine aminotransferase Length = 381 Score = 171 bits (433), Expect = 3e-47 Identities = 113/364 (31%), Positives = 185/364 (50%), Gaps = 13/364 (3%) Query: 21 SNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKK 80 S L +H+ ++L G PDF P ++ A +A+ E Y P G LR+ + L ++ Sbjct: 19 SQLAVEHQ-AVNLGQGFPDFEPPQALREAIARAMAEGRNQYAPGIGLPTLREQIALKTER 77 Query: 81 KADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIV 140 DA E+ +T+GA++A+ AA ++ GDEVI+ P Y YEP+I L GAK V + Sbjct: 78 MYGRRIDAAGEVTVTSGATEALFAAIAAVVRAGDEVIVFDPAYDSYEPVIELQGAKAVHI 137 Query: 141 DTTSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSD 200 T F + + + DA+TP T+ +++ P NP+G LS +L +AA+++ + VLSD Sbjct: 138 PLTVPSFGVDWQRVRDAVTPRTRMILINSPHNPSGAVLSAADLDQLAAIVRDTEIVVLSD 197 Query: 201 EIYSELTYDRP-HYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVH 257 E+Y + +D H S+ + L ++IV++ K++ TGW++G+ AP ++ KVH Sbjct: 198 EVYEHIVFDGALHQSVLRHAELAARSIVVSSFGKTYHCTGWKLGYAVAPAALSAEFRKVH 257 Query: 258 QYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMG----LDVVKPSG 313 QY C +Q A E + + + L + Y+ + D + L++ LDV P G Sbjct: 258 QYLTFCTFHPAQVAFAEFMASTPEHYLELPAFYQAKRDR-FRALIAPSRFKLLDV--PGG 314 Query: 314 AFYIFPSIKSFGMTSFDFSMALLEDAGVALVPGSSF--STYGEGYVRLSFACSMDTLREG 371 F + F L++ GVA +P + F + VRL FA S T+ Sbjct: 315 YFQLVDYSAIRDEPDVTFCEWLVKQGGVAAIPLAPFYETAPDTRLVRLCFAKSDATMDAA 374 Query: 372 LDRL 375 +RL Sbjct: 375 AERL 378 Lambda K H 0.319 0.135 0.388 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: 305 Number of extensions: 12 Number of successful extensions: 2 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: 393 Length of database: 381 Length adjustment: 30 Effective length of query: 363 Effective length of database: 351 Effective search space: 127413 Effective search space used: 127413 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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