Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate BPHYT_RS15405 BPHYT_RS15405 aminotransferase
Query= curated2:B1I544 (392 letters) >FitnessBrowser__BFirm:BPHYT_RS15405 Length = 398 Score = 170 bits (431), Expect = 6e-47 Identities = 121/392 (30%), Positives = 186/392 (47%), Gaps = 14/392 (3%) Query: 6 AKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQ 65 A R+ + P+ + + A + G D+I +GIG+PD P+ +IEAA L+ Q Sbjct: 12 AARVDAIQPFYVMELAKEAALLERDGRDIIHMGIGEPDFTAPEPVIEAAASALRRGVT-Q 70 Query: 66 YPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPD 125 Y S+ G+ A R A++ YA +GV++DP R VV+ G+ + VD D VL+PD Sbjct: 71 YTSALGLHALREAISAHYADFYGVDVDPARIVVTA-GASAALLLACAALVDRDDEVLMPD 129 Query: 126 PGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVAS 185 P YP I A G P VP F A + + + + P+NPTG Sbjct: 130 PCYPCNRHFVIAAEGRPVMVPSGPAERFQLTAADVERLWNEHTRGVLLASPSNPTGTSIE 189 Query: 186 KEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMT 245 R+V R G D Y +++D +P S L + I +S SK +NMT Sbjct: 190 PAELERIVKAVRARGGFTIVDEIYQGLSYDA-KPVSALSFG---DDVITVNSFSKYFNMT 245 Query: 246 GWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGV-QSLCEMYRERRD 304 GWR GW G V A +L NL + Q+AA+A + ++ + ++ RRD Sbjct: 246 GWRLGWLVVPPGMVSAFEKLAQNLFICASALAQHAALACFEPETIAIYEARRQEFKRRRD 305 Query: 305 LVVDTLNDLGWRL-TRPRATFYIWAPV-----PAGHDASSFAEMVLEKAGVVITPGTGYG 358 + L LG+ + P FY++A A D+++ + +L AGVV+ PG +G Sbjct: 306 FIAPALESLGFSVPVMPDGAFYVYADCRTVAHSAAGDSAALTKAMLHDAGVVLVPGMDFG 365 Query: 359 TYG-EGYFRISLTLPTPRLVEAMERLRGCLGR 389 T+ + Y R+S P+L EA++RL G+ Sbjct: 366 THAPKDYIRLSYATAYPKLEEAVDRLAKLFGK 397 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: 291 Number of extensions: 13 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: 398 Length adjustment: 31 Effective length of query: 361 Effective length of database: 367 Effective search space: 132487 Effective search space used: 132487 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