Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_011032197.1 MM_RS01335 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B8CX89 (389 letters) >NCBI__GCF_000007065.1:WP_011032197.1 Length = 380 Score = 218 bits (556), Expect = 2e-61 Identities = 125/377 (33%), Positives = 206/377 (54%), Gaps = 5/377 (1%) Query: 6 RIKNLPPYLFAEIDKMIARAKKEGVDVISFGIGDPDQPTPDNIINKMIEAVKDPSTHSYP 65 R+K + I + R KEG DVI+F +G+PD TP NI + +A+ + TH P Sbjct: 5 RLKRVEESATIRISNIATRMIKEGTDVINFSLGEPDFDTPKNICDAAAKAMYEGKTHYAP 64 Query: 66 SYEGMYEYRKTVADWYKNNYGRELDPDKEVVSLIGSKEGIAHLPFCYINPGDIALVPDPG 125 S G+ E R +A+ + ++ +K+V+ G+K+GI + ++ GD AL+ DP Sbjct: 65 S-AGIPELRSAIAEKLRTENHLDVS-EKDVLVTPGAKQGIFEIMMGSLDDGDQALLFDPA 122 Query: 126 YPVYKTSVLLAGGKPVQVPLVEENNFLPDLKAIDEDIARKAKLFFINYPNNPTGAIAPEE 185 + Y + AG V VP V E FLPD A E I K KL +N P NPTG + ++ Sbjct: 123 WVTYDACIRFAGADTVWVPTVPEKGFLPDNFA--EYINDKTKLIVVNSPGNPTGGVFGKK 180 Query: 186 FYEELIDFADKYDIIIAHDAAYSEIGLDGYNPPSFMQFEGAKKVGIEFNSLSKPFNMTGW 245 + + D A +D+++ D Y +I D + S F+G ++ I N SK + MTGW Sbjct: 181 TLQCIADIAIDHDLLVVSDEIYEKIIYDREHI-SIGSFDGMQERTITVNGFSKAYAMTGW 239 Query: 246 RVGWAVGRSDVIESLGRIKTNIDSGIFEAIQYAGIEALTGPEDNIEKMTELYSKRRDLLV 305 R+G+ ++ + L +I+++ S +QY G+EAL GP++ ++ M + + RRD+L+ Sbjct: 240 RLGYLTAPPEIFKLLQKIQSHSVSSATTFVQYGGLEALQGPQEGVKAMVDRFKMRRDILI 299 Query: 306 EGLRELGWEVPVNKATFYIWAKVPEGYNSTEFSTHVFEKTGIFFTPGNGYGEFGEGYVRI 365 +GL ++G E FY +A V + N TE + + ++ + TPG +G GE ++RI Sbjct: 300 DGLNKMGLECKKPDGAFYAFANVSDYGNGTEVAEKLLKEAHVAVTPGIAFGSSGEDFIRI 359 Query: 366 ALTVTEERIKEALERLK 382 + + +RI+EAL+RL+ Sbjct: 360 SYATSIDRIREALDRLE 376 Lambda K H 0.316 0.139 0.414 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: 417 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: 389 Length of database: 380 Length adjustment: 30 Effective length of query: 359 Effective length of database: 350 Effective search space: 125650 Effective search space used: 125650 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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