Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate AZOBR_RS20195 AZOBR_RS20195 aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__azobra:AZOBR_RS20195 Length = 369 Score = 305 bits (780), Expect = 2e-87 Identities = 171/374 (45%), Positives = 223/374 (59%), Gaps = 14/374 (3%) Query: 17 MSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPLRRAIAAQRRR 76 MS L+ A+NLGQGFPDE GP +L A AI G NQYPP G+ LR+A+AA RR Sbjct: 1 MSRLSDEHKAINLGQGFPDERGPADVLDVAAKAILEGWNQYPPMMGTPDLRQALAAHGRR 60 Query: 77 HFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAGAHRVTV 136 +G+D D +TEVLVT GATEA+ A++LGL+EPG EV+L +P YDSY P+V +AG V Sbjct: 61 FYGLDIDWKTEVLVTSGATEALTASLLGLIEPGDEVVLFQPMYDSYLPIVRLAGGVPRFV 120 Query: 137 PL-VPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVAANLVV 195 L PD D +A A +P+T+ ++IN P NP V S EL +AE + Sbjct: 121 SLKAPDWSFTRADLEA---AFSPKTKLVLINDPLNPAAKVFSRAELELLAEFVQRFDAFA 177 Query: 196 ITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACGPAELIAGVR 255 + DEVYEH+VFD +H+PL GM +R + I SA K F+ TGWK+G+ G L+ V Sbjct: 178 VCDEVYEHIVFDGRQHIPLMTLPGMRDRCLKIGSAGKTFSLTGWKVGYVTGAPHLLQPVA 237 Query: 256 AAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEIGFAVHDSYGT 315 A QY+++ Q AVA L +DA+ A L + L+A+RDRLA GL +GF V S GT Sbjct: 238 KAHQYITFTTPPNLQTAVAYGLGKDDAYFAGLSSGLQAKRDRLADGLRAVGFEVLPSAGT 297 Query: 316 YFLCADPRPLGYDDSTE-FCAALPEKVGVAAIPMSAFCDPAAGQASQQADVWNHLVRFTF 374 YF+ AD P G+D + E FC L + GV AIP+ AF D +RF F Sbjct: 298 YFVVADVSPFGFDGNDEAFCRRLTAEAGVTAIPVGAFF---------VQDAPRSFIRFCF 348 Query: 375 CKRDDTLDEAIRRL 388 KRD+ LD A+ RL Sbjct: 349 SKRDEILDGAVERL 362 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: 396 Number of extensions: 17 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: 397 Length of database: 369 Length adjustment: 30 Effective length of query: 367 Effective length of database: 339 Effective search space: 124413 Effective search space used: 124413 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