Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_092482527.1 BM299_RS05865 LL-diaminopimelate aminotransferase
Query= BRENDA::A0LEA5 (388 letters) >NCBI__GCF_900115975.1:WP_092482527.1 Length = 390 Score = 416 bits (1069), Expect = e-121 Identities = 196/380 (51%), Positives = 273/380 (71%), Gaps = 3/380 (0%) Query: 6 AERLKLLPPYLFQEIDRLKAELTAKGVDVINLGVGDPDLPTPDHIIARLKTAAEDPSTHQ 65 A R++ L +F E++ +K ++ KG++VINLGVG PDLP HI+ + A ++P + Sbjct: 4 ARRIQNLSSAIFNEMEEIKKQVEQKGIEVINLGVGSPDLPPAPHIVEAMHRALDNPGNYH 63 Query: 66 YPSYSGMNDFKVSVAGWYKRRFGVELDPLSEVLTLIGSKEGLAHFPLAVINPGDLALVPT 125 YP G + +V WY++RFGVELDP +EVL L+GS++GLAH +A INPGD+ALVP Sbjct: 64 YPLV-GKPELHRAVTAWYRKRFGVELDPDNEVLALMGSQDGLAHIAMAYINPGDIALVPD 122 Query: 126 PAYPVYHVATMFAGGESYFMPLVRENGFLPDLDSIPADVARRAKVMFINYPNNPTGATAE 185 P YP+Y + + A G+ Y MPL+ +N FLPDL +IP +VAR+AK++++NYPNNP A A+ Sbjct: 123 PGYPIYACSILLAEGKIYPMPLLAKNNFLPDLKAIPEEVARQAKLLWVNYPNNPVAAAAD 182 Query: 186 RDFFEKVIAFAREYDVIVCHDAAYTEMAFGGYRPLSFLELPGAGEVGVEFHSLSKTYNMT 245 RDFF ++ FAREYD++VCHD AY E+AF G++P+SFLE+ GA EVG+EF+SLSKTYNM Sbjct: 183 RDFFTSLVDFAREYDILVCHDIAYCELAFDGFKPISFLEITGAREVGIEFYSLSKTYNMA 242 Query: 246 GWRLGFAVGNADILAGLGQVKSNIDSGAFNAVQWAGITALEGDQGCVVEMQRIYKERLDI 305 G R+GFAVGNA+IL GL +VK+NID G FN VQ AGI ALEG Q CV E Y+ R D+ Sbjct: 243 GCRIGFAVGNAEILQGLNRVKTNIDYGVFNVVQEAGIAALEGPQDCVRENAETYRRRRDV 302 Query: 306 LIEGLKRIGLHPEVPRATFYVWCPTPPGY--SSKDFSSLLLREAGIVATPGSGFGAPGEG 363 L++GL R+G PRA+ +VW P P G+ ++++F+ LL + G++ PG+ FG GEG Sbjct: 303 LVDGLARLGWKVPRPRASMFVWAPLPEGFNCTAREFALQLLHQTGVLVIPGTAFGEQGEG 362 Query: 364 YIRMALTVDKERVREAVERM 383 Y+R+AL ++ + AV R+ Sbjct: 363 YLRIALVREENVLARAVRRI 382 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: 508 Number of extensions: 20 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: 388 Length of database: 390 Length adjustment: 30 Effective length of query: 358 Effective length of database: 360 Effective search space: 128880 Effective search space used: 128880 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