Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_020562613.1 A3OW_RS0106480 alanine transaminase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000372865.1:WP_020562613.1 Length = 394 Score = 166 bits (419), Expect = 1e-45 Identities = 117/356 (32%), Positives = 167/356 (46%), Gaps = 11/356 (3%) Query: 3 VSRLRPYATTVFAEMSALATRIGA--VNLGQGFPDEDGPPKMLQAAQDAIA-GGVNQYPP 59 +SRL PY + E+ A A G ++ G G PD+ P ++ +A G ++Y Sbjct: 7 ISRLPPYVFNIVNELKAKARAAGEDIIDFGMGNPDQPTPDHIVNKLLEATKRGDTHRYSV 66 Query: 60 GPGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFY 119 G LR+AI + F VD DPETE +VT+G+ E +A L + PG VL+ P Y Sbjct: 67 SRGIPRLRKAICNWYQHRFDVDLDPETEAIVTIGSKEGLAHLALATLGPGDVVLVPNPAY 126 Query: 120 DSYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVT---PRTRALIINSPHNPTGAVL 176 + V +AGA VPL+P G F + L RA+ P+ + LI+N P NPT + Sbjct: 127 PIHPYGVVIAGADLRHVPLIP-GVDFI---EELHRAIVESWPKPKMLILNFPGNPTSQCV 182 Query: 177 SATELAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNC 236 I EIA N+ V+ D Y +VFD + + G + + S +K +N Sbjct: 183 ELDFFEKIIEIAKEHNIWVVHDIAYIDIVFDGYKAPSILQIKGAKDIAVEFFSLSKSYNM 242 Query: 237 TGWKIGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRD 296 GW++G+ CG +L++ + K YL Y P Q A AL+ V + + R RRD Sbjct: 243 PGWRVGFMCGNKQLVSALARIKSYLDYGTFTPIQIAAITALEGPQNCVRDIADMYRKRRD 302 Query: 297 RLAAGLTEIGFAVHDSYGTYFLCAD-PRPLGYDDSTEFCAALPEKVGVAAIPMSAF 351 L GLT G+ V T F+ A P P S EF L + VA P F Sbjct: 303 VLCEGLTAAGWPVAKPKATMFVWAPIPEPYRAMGSLEFSKKLLIEAKVAVAPGIGF 358 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: 388 Number of extensions: 14 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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 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