Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate RR42_RS02275 RR42_RS02275 aspartate aminotransferase
Query= BRENDA::Q8TQ40 (389 letters) >FitnessBrowser__Cup4G11:RR42_RS02275 Length = 397 Score = 124 bits (310), Expect = 6e-33 Identities = 103/360 (28%), Positives = 158/360 (43%), Gaps = 14/360 (3%) Query: 34 DVIDLGVGDPDLPTHPHIVEAMREAVCDPKTHQYPSYAGMPEFREAAAEWCKKYKGIELD 93 DV+ G+ D T I +A A+ T Y G+ R A A++ G Sbjct: 39 DVLPFWFGESDQVTPAFIRDAASRALAGGATF-YTHNLGIAPLRSALADYVSALHG---- 93 Query: 94 PATEVLSLIGSKEAVAHIPLA---FVNPGDVVLYTDPGYPVYKIGTLFAGGEPYSLPLK- 149 AT + +++ + V + LA PGD + P +P G E ++ L Sbjct: 94 -ATALDNVVVTSAGVNALMLAAQLVAGPGDRAVAVTPLWPNLVEIPKILGAEVETVSLDY 152 Query: 150 AENSFLPDLDSIPADILKRAKLFFFNYPNNPTSATADMKFFEKVVEFCKKNDIIAVHDNA 209 + + DLD + A + +L N PNNPT + V+ C+++ I + D Sbjct: 153 GAHGWTLDLDKLLAALTPDTRLLMINSPNNPTGWVMSRADQQAVLAHCRRHGIWIIADEV 212 Query: 210 YSQMVY---DGYDAPSFLAAEGAMDIGIELYSHSKTYNMTGWRLGFAVGSKALIKGLGKV 266 Y ++ Y DG APSFL + I + S SK + MTGWRLG+ V AL LGK+ Sbjct: 213 YERLYYGKGDGAIAPSFLDIASRDERVICVNSFSKAWLMTGWRLGWMVLPAALTDDLGKL 272 Query: 267 KSNVDSGVFDAIQIAGIAALSSSQACVDDTNKIYEERRNVLIEGLTAM-GLEVKPPKATF 325 S +Q AGI A+ +A + R+ L+ L + G++V P+ Sbjct: 273 VEYNTSCAPSFVQEAGIVAVREGEAFTRELVGRLRAARDHLVSALAVVPGVDVHAPEGAM 332 Query: 326 YVWAPVPTGFTSIEFAKLLLEEAGIVATPGVGFGDAGEGYVRFALTKPVERIKEAVERMK 385 YV+ + S+ K L+ EA + PG FGD GEG+VR+ R+ E V R++ Sbjct: 333 YVFFRLAGASDSLALCKQLVREARLGLAPGSAFGDEGEGFVRWCYACDPARLDEGVRRLR 392 Lambda K H 0.319 0.137 0.409 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: 351 Number of extensions: 22 Number of successful extensions: 3 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: 389 Length of database: 397 Length adjustment: 31 Effective length of query: 358 Effective length of database: 366 Effective search space: 131028 Effective search space used: 131028 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 (21.7 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