Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate AO353_24850 AO353_24850 aspartate aminotransferase
Query= BRENDA::A0LEA5 (388 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24850 Length = 396 Score = 158 bits (399), Expect = 3e-43 Identities = 108/361 (29%), Positives = 176/361 (48%), Gaps = 5/361 (1%) Query: 27 LTAKGVDVINLGVGDPDLPTPDHIIARLKTAAEDPSTHQYPSYSGMNDFKVSVAGWYKRR 86 L +G D++ L VGDPD TP I+ + +TH Y G + S+A +++R Sbjct: 27 LQEQGEDILLLSVGDPDFDTPVPIVQAAIDSLLSGNTH-YAEVRGKRALRESIAKRHQQR 85 Query: 87 FGVELDPLSEVLTLIGSKEGLAHFPLAVINPGDLALVPTPAYPVYHVATMFAGGESYFMP 146 G + +V L G++ L V+NPGD +V P Y Y G +P Sbjct: 86 SGQPVSA-DQVTVLAGAQCALFSVAQCVLNPGDEVIVAEPMYVTYEAVFGACGAVVIPVP 144 Query: 147 LVRENGFLPDLDSIPADVARRAKVMFINYPNNPTGATAERDFFEKVIAFAREYDVIVCHD 206 + ENGF + + A + R + + +N P+NP+GA+ R ++ + +D+ + D Sbjct: 145 VRSENGFRVLPEDVAARITPRTRALALNSPHNPSGASLPRTTWQALAELCIAHDLWLISD 204 Query: 207 AAYTEMAFGGYRPLSFLELPGAGEVGVEFHSLSKTYNMTGWRLGFAVGNADILAGLGQVK 266 Y+E+ F G +S LPG GE +SLSK++ MTGWR+G+ V + A L + Sbjct: 205 EVYSELLFEG-EHVSPASLPGMGERTATLNSLSKSHAMTGWRVGWVVAPPSLAAHLENLA 263 Query: 267 SNIDSGAFNAVQWAGITALEGDQGCVVEMQRIYKERLDILIEGLKRI-GLHPEVPRATFY 325 + G+ + VQ A + ALE + + M+ Y++R D++ E L G+ P P + Sbjct: 264 LCMLYGSPDFVQDAAVVALESNLPELAAMRDAYRQRRDLVCESLADCPGVRPLKPDGGMF 323 Query: 326 VWCP-TPPGYSSKDFSSLLLREAGIVATPGSGFGAPGEGYIRMALTVDKERVREAVERMR 384 V G S++ F+ LL G+ G FG G+IR+ L V E +R+A +R+ Sbjct: 324 VMVDIRETGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVVGAEPLRDACQRIA 383 Query: 385 K 385 + Sbjct: 384 R 384 Lambda K H 0.321 0.140 0.423 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: 369 Number of extensions: 17 Number of successful extensions: 4 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: 388 Length of database: 396 Length adjustment: 31 Effective length of query: 357 Effective length of database: 365 Effective search space: 130305 Effective search space used: 130305 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