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) >FitnessBrowser__Dyella79:N515DRAFT_1410 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 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