Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_092481937.1 BM299_RS02765 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::Q2RK33 (390 letters) >NCBI__GCF_900115975.1:WP_092481937.1 Length = 414 Score = 213 bits (541), Expect = 1e-59 Identities = 128/378 (33%), Positives = 188/378 (49%), Gaps = 7/378 (1%) Query: 7 IRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYPT 66 +R +PP R +AE R +ISLG+G+PD TP H+ + + Y + Sbjct: 14 VRSVPPSGIRRFFDLVAETR----GVISLGVGEPDFVTPWHIREACIYSLEKGYT-MYTS 68 Query: 67 SEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPGY 126 + GLL R+AVA +R Y V +P+ E++ +G E + + PGD L+P+P Y Sbjct: 69 NWGLLELREAVAADLERTYNVKYNPKNEILITVGVSEALDLAMRALLVPGDEVLIPEPSY 128 Query: 127 PVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADLKF 186 Y T LAGG FMP + N F + S + R K++ + YPNNPTGAV + + Sbjct: 129 VSYAPCTTLAGGVPVFMPTSMENNFRISADQVRSAITPRTKVLLLCYPNNPTGAVMEREE 188 Query: 187 FQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGWR 246 ++ E A +DLIV D Y +TY G PG +E + N SK Y MTGWR Sbjct: 189 LAKIAEVAVEHDLIVISDEIYDRLTYVGEHT-CLASLPGMQERTVLLNGFSKAYAMTGWR 247 Query: 247 LGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDIIVE 306 +G+A G D I A+ +I Q A + AL Q G+ + Y RR ++V+ Sbjct: 248 VGYAAGNPDFIGAMTKIHQYSMLCTPITGQMAALEALKNGQPGMRRMVGHYNRRRHLVVQ 307 Query: 307 GFNSLGWHLEKPKATFYVWAPVP-RGYTSASFAEMVLEKAGVIITPGNGYGNYGEGYFRI 365 F +G +P FY + V G S FAE +L++ V + PGN +G GEG+ R+ Sbjct: 308 AFRDMGVPCFEPGGAFYAFPQVSVTGLGSEEFAEELLKQEQVALVPGNAFGRSGEGFARV 367 Query: 366 ALTISKERMQEAIERLRR 383 + S + + EA R+ R Sbjct: 368 SYAASLDDLSEAFRRMAR 385 Lambda K H 0.320 0.139 0.421 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: 407 Number of extensions: 21 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: 390 Length of database: 414 Length adjustment: 31 Effective length of query: 359 Effective length of database: 383 Effective search space: 137497 Effective search space used: 137497 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