Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate PP_0858 PP_0858 putative methionine/glutamine aminotransferase
Query= BRENDA::Q7NDX4 (392 letters) >FitnessBrowser__Putida:PP_0858 Length = 382 Score = 106 bits (265), Expect = 1e-27 Identities = 78/273 (28%), Positives = 124/273 (45%), Gaps = 5/273 (1%) Query: 33 INMGIGDPDKPTPPVVLEAMHAAIDDPSTHN-YPPYKGTKAYREAAAAWFERRFGVGGFH 91 +N+ G PD P +L+A+ + + HN Y P G A R+ AA ER +G Sbjct: 27 LNLSQGFPDFNGPQALLDAVGRHV--AAGHNQYSPMTGLPALRQQVAAKVERLYGAR-VD 83 Query: 92 PDTEVISSIGSKEAIHNTFLAFVDPGDYTLIPDPAYPVYRTSTIFAGGEFFAMPLLPENQ 151 D EV + G+ EAI A V GD ++ DP Y Y S AGG + L + Sbjct: 84 ADQEVTITPGATEAIFCAIQAVVHAGDEVIVFDPCYDSYEPSVELAGGRCVHVQL-SDGD 142 Query: 152 LLPDLEAVPETVARKAKLLWLNYPNNPTGAVASLEFFEKVVHFAKKHDILVCHDNAYSEM 211 D + + ++ + +++ LN P+NP+GA+ + E +++ DI + D Y + Sbjct: 143 FRIDWQKFSDALSPRTRMVILNSPHNPSGALITREDLDQLAALIADRDIYLVSDEVYEHL 202 Query: 212 AYDGYKPPSILQVPGARDVAIEFLSCSKAYNMTGWRVGFVIGNRTGIAGLGQVKTNIDSG 271 YDG + S+L A S K Y++TGW+ G+VI A L +V ++ Sbjct: 203 VYDGVRHASVLAHEQLYSRAFVVSSFGKTYHVTGWKTGYVIAPPALSAELRKVHQYVNFC 262 Query: 272 VFKAIQQAAIAAFGLDDERLHALMAVYQNRRNI 304 +Q A E + L A YQ +R++ Sbjct: 263 GVTPLQCALADFMAGHPEHIDELPAFYQAKRDL 295 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: 301 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: 382 Length adjustment: 30 Effective length of query: 362 Effective length of database: 352 Effective search space: 127424 Effective search space used: 127424 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