Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_011382998.1 AMB_RS02875 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000009985.1:WP_011382998.1 Length = 400 Score = 165 bits (417), Expect = 2e-45 Identities = 125/400 (31%), Positives = 190/400 (47%), Gaps = 23/400 (5%) Query: 1 MSFVEAKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKI 60 M F+ A R+ + P + Q A+ KA G DVI LG G+PD TPD+I +AA K Sbjct: 1 MPFI-ADRLSAIKPSPTIAVTQKAAELKAAGRDVIGLGAGEPDFDTPDNI-KAAAKAAID 58 Query: 61 PANHQYPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDV 120 +Y AG R+A+A + R G++ + V +G K I + ++PGD Sbjct: 59 KGLTKYGPPAGTVDLRQAIAAKFKRENGLDYTADQVTVG-VGGKGVIFNAFMATINPGDE 117 Query: 121 VLVPDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPT 180 V+VP P + Y ++ GG P VP GF A + R K + +N P+NPT Sbjct: 118 VIVPAPYWVSYPDIALMFGGKPVFVPCPETAGFKLQPADLEKAITPRTKWLVLNSPSNPT 177 Query: 181 GAVASKEFFARVVD-FAREYGILVCHDAAYSEIAFDGYR--PPSFLEVAGAREVGIEFHS 237 GA S + + D R + + D Y + +D ++ P+ +E + + + Sbjct: 178 GAAYSWDEMKALTDVLLRHPHVWIMSDDMYEHLVYDDFKFCTPAQVEPK-LYDRTLTMNG 236 Query: 238 VSKTYNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCE 297 VSK Y MTGWR G+AAG A ++A+ ++S + + Q A++ ALNG QD + Sbjct: 237 VSKAYAMTGWRVGYAAGPAAIIKAINMIQSQSVTHTSSISQAASVEALNGTQDFIPKNAA 296 Query: 298 MYRERRDLVVDTLNDL-GWRLTRPRATFYIWAPVPAG------------HDASSFAEMVL 344 +++ RRDL+V LN G P FY++ P AG + + F +L Sbjct: 297 VFKRRRDLIVGLLNQCPGITCRTPEGAFYVY-PSCAGVIGKKTPDGKVIANDTDFVGALL 355 Query: 345 EKAGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERLR 384 E GV + G +G E YFRIS L +A ER++ Sbjct: 356 EAEGVAVVQGAAFGL--EPYFRISYATSDAALTKAAERIK 393 Lambda K H 0.321 0.139 0.430 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: 314 Number of extensions: 18 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: 392 Length of database: 400 Length adjustment: 31 Effective length of query: 361 Effective length of database: 369 Effective search space: 133209 Effective search space used: 133209 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