Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate H281DRAFT_02907 H281DRAFT_02907 arginine:pyruvate transaminase
Query= curated2:Q30ZX9 (388 letters) >FitnessBrowser__Burk376:H281DRAFT_02907 Length = 395 Score = 188 bits (478), Expect = 2e-52 Identities = 112/370 (30%), Positives = 189/370 (51%), Gaps = 6/370 (1%) Query: 20 QIDKVKAEVAARGVDIISLGIGDPDMPTPDFVIEALKKAAEKPANHQYPSYTGMLAFRQE 79 +I +V + AA G D+I L +GDPD TP ++E A H Y + +G R Sbjct: 19 EIHRVAQQAAANGNDVIVLSVGDPDFATPAPIVERAIDALRGGDTH-YSAVSGRDPLRAA 77 Query: 80 VANWYKRRYAVELDPKTEVLTLIGSKEGIAHFPTAFVNPGDLVLVCPPCYPVYAIASRFM 139 +A R + +LT G++ G+ + GD V+V P Y Y R Sbjct: 78 IAEEQARMTGCTVSAANVILTA-GAQNGVFATSLCLLEAGDEVIVPEPMYLTYEACVRAA 136 Query: 140 GGVVQELPLLEENDFLPDLDAVDEATWEKARCIFVNYPNNPTAAMAPRSFFEKLIGIARK 199 G + +P+ F D DA++ A + + IF P NPT + PR+ E++ +A + Sbjct: 137 GATLVPVPVDPARAFHLDCDALERAVTPRTKAIFFATPCNPTGVVMPRADLERIARLACE 196 Query: 200 HNVIVVHDAAYTEMYYNENNRPLSIMEIPGAMDVAIEFNSLSKPYNMTGWRIAMAVGNAS 259 H++ V+ D Y ++ + + +SIM +PG + + SLSK + M GWR+ A+G Sbjct: 197 HDLWVLSDEVYADLTFEREH--VSIMSLPGMAERTVTLGSLSKSHAMAGWRVGWAIGPTQ 254 Query: 260 LVAGLGKVKENMDSGAFQAVQEAAIVALRDGDAFLAEIRDIYRKRRDTVIAALNKI-GIT 318 L+ +G++ M G +Q+AA+ AL++ + +A++RDIYR+RRD V L+++ + Sbjct: 255 LIEHMGRLALAMLYGLPGFIQQAALTALQEKSSIVAQMRDIYRRRRDVVFERLSRVPRLR 314 Query: 319 CRVPEASLYVWARVP-EGYTSSDFVTRVLQETGVVMTPGNGFGAAGEGYFRISLTVNDER 377 C +PEA +++ V G + DF ++ + GV + + FG G+ R+ V++ R Sbjct: 315 CLLPEAGMFMMVDVSGTGLDTVDFTWQLFRAQGVSVLDASAFGETANGFVRLGFVVDEAR 374 Query: 378 LEEAVSRIAS 387 L EA RIA+ Sbjct: 375 LAEACERIAA 384 Lambda K H 0.320 0.136 0.403 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: 339 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: 388 Length of database: 395 Length adjustment: 31 Effective length of query: 357 Effective length of database: 364 Effective search space: 129948 Effective search space used: 129948 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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