Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_037374750.1 A3GO_RS0105540 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q7NDX4 (392 letters) >NCBI__GCF_000428045.1:WP_037374750.1 Length = 383 Score = 123 bits (308), Expect = 1e-32 Identities = 88/293 (30%), Positives = 128/293 (43%), Gaps = 5/293 (1%) Query: 33 INMGIGDPDKPTPPVVLEAMHAAIDDPSTHN-YPPYKGTKAYREAAAAWFERRFGVGGFH 91 IN+G G PD P +LE + I HN Y P G REA AA E+ +G Sbjct: 30 INLGQGFPDFSAPQALLERVDHHIRQG--HNQYAPMAGVARLREAIAAKIEQSYG-RPVS 86 Query: 92 PDTEVISSIGSKEAIHNTFLAFVDPGDYTLIPDPAYPVYRTSTIFAGGEFFAMPLLPENQ 151 D EV + G+ A++ A V PGD ++ DPAY Y + +GG +PLLP Sbjct: 87 ADREVTVTPGATVALYCAITACVRPGDEVIVFDPAYDSYEPAIELSGGRAVHLPLLPP-A 145 Query: 152 LLPDLEAVPETVARKAKLLWLNYPNNPTGAVASLEFFEKVVHFAKKHDILVCHDNAYSEM 211 D + V + + + +++ LN P+NPTGA E + + DIL+ D Y + Sbjct: 146 FAVDWQRVKDAITPRTRMIILNSPHNPTGATLLAEDLATLAELVRDTDILLLSDEVYEHL 205 Query: 212 AYDGYKPPSILQVPGARDVAIEFLSCSKAYNMTGWRVGFVIGNRTGIAGLGQVKTNIDSG 271 YDG S+LQ A S K Y++TGW+ G+ I A L +V + Sbjct: 206 VYDGVTHQSLLQHDELAARAFVVFSFGKTYHVTGWKTGYCIAPAALTAELRKVHQYVTFV 265 Query: 272 VFKAIQQAAIAAFGLDDERLHALMAVYQNRRNIIVEGLRSLGWPLEAPKATLY 324 IQ A + L A YQ +R++ E + + K T + Sbjct: 266 AVTPIQLALADFMQSCPQHHQQLAAFYQRKRDLFCEQMAGSRFHFSPAKGTFF 318 Lambda K H 0.321 0.140 0.429 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: 322 Number of extensions: 13 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: 392 Length of database: 383 Length adjustment: 30 Effective length of query: 362 Effective length of database: 353 Effective search space: 127786 Effective search space used: 127786 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