Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate Ga0059261_1558 Ga0059261_1558 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__Korea:Ga0059261_1558 Length = 389 Score = 303 bits (775), Expect = 7e-87 Identities = 176/380 (46%), Positives = 224/380 (58%), Gaps = 13/380 (3%) Query: 11 TTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPLRRAI 70 TT+F MS+ A +GA+NLGQGFPD +G +++AA DA+ NQYPP G LR+AI Sbjct: 14 TTIFETMSSRARAMGAINLGQGFPDGEGCVPVIRAAADALTTRSNQYPPMAGLPALRQAI 73 Query: 71 AAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAG 130 A RH +D PE EV+VT GATEAIAA+ L+ PG EV+LI+P YD+Y P+V AG Sbjct: 74 ATHYTRHQQLDLSPE-EVIVTSGATEAIAASFTALIAPGDEVILIQPLYDAYLPLVQRAG 132 Query: 131 AHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVA 190 L P + L AL A PRTR +++N+P NP GA LS ELA +A V Sbjct: 133 GVARLARLEPGS--WRLTPAALEAAAGPRTRLIVVNNPVNPAGAKLSHGELADLAAFCVE 190 Query: 191 ANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACGPAEL 250 +L+ I DEV+EH+V+D ARH+PL GM +RT+ I SA K+F TGWK+GW C A L Sbjct: 191 RDLIAICDEVWEHVVYDSARHIPLIAMPGMRDRTVKIGSAGKIFALTGWKVGWMCAAAPL 250 Query: 251 IAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEIGFAVH 310 A + A Q+L++ Q AVA L+T+DAW+A + RDRLAAGLT G+ V Sbjct: 251 AAVLARAHQFLTFSTAPNLQWAVAEGLETQDAWIADSIVGFQRSRDRLAAGLTAAGYRVL 310 Query: 311 DSYGTYFLCADPRPLGYD-DSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQADVWNHL 369 S T+FL D G FC L E++GVAAIP+SAF A HL Sbjct: 311 PSGATWFLSIDLAASGIALHDAAFCDRLVEEIGVAAIPVSAFYAEAP---------VTHL 361 Query: 370 VRFTFCKRDDTLDEAIRRLS 389 R F K D LD AI R+S Sbjct: 362 ARLCFAKADAVLDTAIERMS 381 Lambda K H 0.321 0.135 0.405 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: 435 Number of extensions: 25 Number of successful extensions: 6 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: 397 Length of database: 389 Length adjustment: 31 Effective length of query: 366 Effective length of database: 358 Effective search space: 131028 Effective search space used: 131028 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 (21.9 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