Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_015928360.1 MNOD_RS08070 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000022085.1:WP_015928360.1 Length = 392 Score = 213 bits (541), Expect = 1e-59 Identities = 134/362 (37%), Positives = 184/362 (50%), Gaps = 5/362 (1%) Query: 31 GVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPSSAGMPAYRRAVADWYARRFGVE 90 G DVI+LGIG PD+PTP H++EAA K L+ +H Y + G+ R AVA RR VE Sbjct: 30 GRDVINLGIGQPDMPTPPHVVEAAVKALR-DGHHGYTPATGILPLREAVARDIRRRLDVE 88 Query: 91 LDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILAGGIPHPVPLTAG 150 + P V+ + G K + F +PG +L PDPG+P+Y G P P+P+ Sbjct: 89 VSPD-SVMIVPGGKVTMFAAILMFGEPGAEILYPDPGFPIYRSMIEFTGATPVPIPIREA 147 Query: 151 NGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKEFFARVV-DFAREYGILVCHDAAY 209 NGF A R +++ +N P NPTG V K R+V A + + D Y Sbjct: 148 NGFAFSAEETLALITPRTRLVILNSPANPTGGVTPKAEIDRLVAGLAAHPNVALLSDEIY 207 Query: 210 SEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTGWRAGWAAGNAGAVEALGRLKSNL 269 + +DG R S L R+ I SKTY MTGWR GW+ A EA +L N Sbjct: 208 GTMTYDGERHHSLLAYPEIRDRLIYLDGASKTYAMTGWRLGWSVWPAPFYEAARKLAVNS 267 Query: 270 DSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDL-GWRLTRPRATFYIWA 328 S V Q+A IAAL+GPQD V ++ + RR +VV+ LN L G P+ FY + Sbjct: 268 FSCVNAATQWAGIAALDGPQDAVAAMMAEFDRRRLIVVEGLNRLPGISCITPKGAFYAFP 327 Query: 329 PVP-AGHDASSFAEMVLEKAGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERLRGCL 387 + G A + A +LE+AGV G +G +GEGY R+S ++ A+ER+ L Sbjct: 328 NIARTGWKAKALASALLEEAGVATIGGPDFGVHGEGYLRLSYANSAENILRALERMGEFL 387 Query: 388 GR 389 R Sbjct: 388 AR 389 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: 359 Number of extensions: 21 Number of successful extensions: 5 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: 392 Length adjustment: 31 Effective length of query: 361 Effective length of database: 361 Effective search space: 130321 Effective search space used: 130321 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