Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_073039467.1 BUB04_RS11095 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_900129305.1:WP_073039467.1 Length = 388 Score = 417 bits (1072), Expect = e-121 Identities = 192/388 (49%), Positives = 278/388 (71%), Gaps = 3/388 (0%) Query: 1 MSFDWITPADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQA 60 M+F++ ADR++ LPPY+F +D LKA+ +G+D+I+LG+G+PD TP+ +++ +A Sbjct: 1 MAFEF---ADRVKNLPPYLFKEIDRLKAELIARGVDVINLGVGDPDLPTPKHIIERLKEA 57 Query: 61 LQDPKNHGYPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNP 120 +DP NH YP + G F+ A+ WY RR+GV LDP SE + L+GSKEG++HL +A++NP Sbjct: 58 AEDPANHQYPSYSGMNDFKGAVARWYKRRFGVDLDPASEVITLIGSKEGIAHLPLAFINP 117 Query: 121 GDVVLVPSPAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPS 180 GD+ L+PSPAYP + + AGG H + L EN +L DL AIP +VA++AK+L+ NYP+ Sbjct: 118 GDLALIPSPAYPVYGVAVMFAGGNTHEIPLLKENGFLPDLDAIPADVAKRAKLLFINYPN 177 Query: 181 NPTGATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHT 240 NPTGATA +FF+++VAFAR+Y++++ HD Y E+AFDGY+P S LE+PGAK++G+EFH+ Sbjct: 178 NPTGATAEADFFQKVVAFAREYDVIVCHDAAYTEMAFDGYRPMSFLEVPGAKEVGIEFHS 237 Query: 241 LSKTYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQ 300 LSKT NM GWR+GF VG+ V++GL +K+N+D G F A+Q A TAL+ + E+Q Sbjct: 238 LSKTCNMTGWRLGFAVGHAKVLEGLGQIKSNVDSGAFNAVQLAGITALESDQTCVKEMQA 297 Query: 301 RYRTRRDFLIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAF 360 Y+ RRD LI+GL E+G KAT Y+W P GM S F LL++ G+V TPG+ F Sbjct: 298 IYQERRDVLIRGLREVGLHAEPPKATFYVWCPTPQGMTSAQFTSLLLKEAGIVTTPGSGF 357 Query: 361 GVAGEGYVRISLIADCDRLGEALDRIKQ 388 G GEGYVR++L +R+ EA++RI++ Sbjct: 358 GAPGEGYVRMALTVSKERIQEAVERIRK 385 Lambda K H 0.321 0.140 0.427 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: 490 Number of extensions: 21 Number of successful extensions: 1 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: 403 Length of database: 388 Length adjustment: 31 Effective length of query: 372 Effective length of database: 357 Effective search space: 132804 Effective search space used: 132804 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