Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_011316915.1 AVA_RS00085 aspartate aminotransferase
Query= curated2:B8CX89 (389 letters) >NCBI__GCF_000204075.1:WP_011316915.1 Length = 403 Score = 416 bits (1069), Expect = e-121 Identities = 184/386 (47%), Positives = 272/386 (70%) Query: 4 ADRIKNLPPYLFAEIDKMIARAKKEGVDVISFGIGDPDQPTPDNIINKMIEAVKDPSTHS 63 ADRI+ LPPY+FA +D++ A+A+++G+D+I G+G+PD TP +++ I+A+++P+ H Sbjct: 9 ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQNPANHG 68 Query: 64 YPSYEGMYEYRKTVADWYKNNYGRELDPDKEVVSLIGSKEGIAHLPFCYINPGDIALVPD 123 YP +EG +R+ + +WY YG LDPD E + L+GSKEG++HL Y+NPGD+ LVP Sbjct: 69 YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128 Query: 124 PGYPVYKTSVLLAGGKPVQVPLVEENNFLPDLKAIDEDIARKAKLFFINYPNNPTGAIAP 183 P YP + ++AGG + L EN++L DL AI E++ARKAK+ + NYP+NPTGA AP Sbjct: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188 Query: 184 EEFYEELIDFADKYDIIIAHDAAYSEIGLDGYNPPSFMQFEGAKKVGIEFNSLSKPFNMT 243 EF+EE++ FA KY+I++ HD Y+E+ DGY P S ++ GAK +G+EF++LSK +NM Sbjct: 189 REFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMA 248 Query: 244 GWRVGWAVGRSDVIESLGRIKTNIDSGIFEAIQYAGIEALTGPEDNIEKMTELYSKRRDL 303 GWRVG+ VG VI+ L +KTN+D GIF A+Q A AL P+ + ++ + Y RRD Sbjct: 249 GWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDF 308 Query: 304 LVEGLRELGWEVPVNKATFYIWAKVPEGYNSTEFSTHVFEKTGIFFTPGNGYGEFGEGYV 363 L++GL ELGW+VP KAT Y+W K P G ST+F+ ++ ++TG+ TPGN +G GEGYV Sbjct: 309 LIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGYV 368 Query: 364 RIALTVTEERIKEALERLKNSDIKFK 389 RI+L +R+ EAL R+K + I+++ Sbjct: 369 RISLIADCDRLGEALGRIKQAGIRYR 394 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: 544 Number of extensions: 22 Number of successful extensions: 1 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: 403 Length adjustment: 31 Effective length of query: 358 Effective length of database: 372 Effective search space: 133176 Effective search space used: 133176 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 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