Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)
Query= curated2:B1I544 (392 letters) >FitnessBrowser__Miya:8501474 Length = 390 Score = 185 bits (470), Expect = 2e-51 Identities = 118/386 (30%), Positives = 195/386 (50%), Gaps = 17/386 (4%) Query: 8 RIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYP 67 R+ + P + + KA+GV V+SL +G+PD PTP+H+ EAA+ + +Y Sbjct: 6 RLTRIKPSATLAVNAKALELKAKGVQVVSLAVGEPDFPTPEHVREAAKTAID-QGFTRYT 64 Query: 68 SSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPG 127 G+P R+AV ++AR +GVE P V G K+ + +L C ++PGD VLVP P Sbjct: 65 QVPGIPELRQAVCGYFARFYGVEA-PMEATVVTNGGKQALYNLFQCLLNPGDEVLVPAPY 123 Query: 128 YPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKE 187 + Y LAGG+P V A GF + + +V+ +N P+NPTGA S+ Sbjct: 124 WVSYPALVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACYSRA 183 Query: 188 FFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIE----FHSVSKTYN 243 ++++A + V D Y + Y P + V E E + ++KT+ Sbjct: 184 ETDAIMEWAIARDLFVVSDEIYDRLV---YEPAEAVSVCDWWERHPENVAVVNGLAKTFA 240 Query: 244 MTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERR 303 MTGWR G+A + ++A+ +++ S + V Q AA+AAL GP D V+ + + +R RR Sbjct: 241 MTGWRVGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDAVEEMKKSFRRRR 300 Query: 304 DLVVDTLNDL-GWRLTRPRATFYIWAPV-----PAGHDASSFAEMVLEKAGVVITPGTGY 357 DL ++ G +P FY++A + PA D++S ++E+A V + PG + Sbjct: 301 DLAHGIVSSWPGVICPKPDGAFYLFADMRALFTPALPDSASLCTYIMEQANVALVPGAAF 360 Query: 358 GTYGEGYFRISLTLPTPRLVEAMERL 383 G + R S + L+ A++++ Sbjct: 361 G--DDACLRFSYAVSDDTLMIALDKV 384 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: 316 Number of extensions: 14 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: 390 Length adjustment: 31 Effective length of query: 361 Effective length of database: 359 Effective search space: 129599 Effective search space used: 129599 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