Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_005453184.1 SACCYDRAFT_RS02235 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000244975.1:WP_005453184.1 Length = 410 Score = 197 bits (502), Expect = 3e-55 Identities = 126/392 (32%), Positives = 187/392 (47%), Gaps = 15/392 (3%) Query: 8 RIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYP 67 RI + P ++ KA+G VI G G PD PTP++I+EAA ++ NH Y Sbjct: 18 RIAGITPSATLAVDAKAKALKAEGRPVIGFGAGQPDFPTPEYIVEAAAAAVRDRGNHGYT 77 Query: 68 SSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPG 127 ++AG+P R A+A R G D + +V+ G K+ + +DPGD VL+ P Sbjct: 78 AAAGLPELREAIAAKTLRDSGFSCDASQVLVTN-GGKQAVYSAFATLLDPGDEVLLLAPY 136 Query: 128 YPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKE 187 + Y LAGG+P V G+ + + A R KV+ N P+NPTGAV ++E Sbjct: 137 WTTYPESITLAGGVPVQVTADESTGYRVTVEQLEAARTERTKVLLFNSPSNPTGAVYTRE 196 Query: 188 FFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSF-LEVAGAREVGIEFHSVSKTYNMTG 246 + +A E+ I V D Y + +DG + S V + + + V+KTY+MTG Sbjct: 197 QVEAIGRWAAEHDIWVITDEIYEHLVYDGVKAASLPTVVPELADRTLILNGVAKTYSMTG 256 Query: 247 WRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLV 306 WR GW G ++A +S+L V V Q AA+AA+ GP D V + + RR + Sbjct: 257 WRVGWIVGPQDVIKAASSFQSHLCGNVANVSQRAALAAVEGPLDVVHEMRAAFDSRRKKI 316 Query: 307 VDTLNDL-GWRLTRPRATFYIWAPVPA----------GHDASSFAEMVLEKAGVVITPGT 355 V L+++ P FY + V A D A+++L + V + PG Sbjct: 317 VSMLSEIPNVECPTPEGAFYAYPSVKAVLGKEIRGQRPADTVELADLILREVEVAVVPGE 376 Query: 356 GYGTYGEGYFRISLTLPTPRLVEAMERLRGCL 387 +GT GYFR S L LVE + R+ L Sbjct: 377 AFGT--PGYFRFSYALAEKDLVEGVTRVADLL 406 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: 328 Number of extensions: 10 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: 410 Length adjustment: 31 Effective length of query: 361 Effective length of database: 379 Effective search space: 136819 Effective search space used: 136819 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 10 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