Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_043458620.1 H537_RS0111980 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000430725.1:WP_043458620.1 Length = 392 Score = 281 bits (719), Expect = 2e-80 Identities = 161/388 (41%), Positives = 224/388 (57%), Gaps = 12/388 (3%) Query: 4 SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63 SRL TT+F MSALA GAVNLGQGFPD +G P+++ A DA+ G+NQYPP G Sbjct: 17 SRLPQVGTTIFTVMSALAHAHGAVNLGQGFPDFEGDPRLVDAVADAMRSGLNQYPPMAGV 76 Query: 64 APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123 LR A+A + + +G YD +TE+ VT GAT+AI A+L V PG EV+++EP YDSY+ Sbjct: 77 PALRAAVADKVQALYGHRYDADTEITVTAGATQAILTAILCCVHPGDEVIVLEPCYDSYA 136 Query: 124 PVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAA 183 P + +AG V VPL P F D + A+TPRTR LI+N+PHNP +V + E+ Sbjct: 137 PNIELAGGTVVRVPLTPG--SFRPDLKRIAAAITPRTRLLIVNTPHNPGASVWTRQEMQQ 194 Query: 184 IAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGW 243 +AEI ++++++DEVYEH+V+D H+ A +A R +SS K ++ TGWK+G+ Sbjct: 195 LAEILRPTDVLLLSDEVYEHMVYDGRAHVSAASVAELAARAFIVSSFGKTYHVTGWKVGF 254 Query: 244 ACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLT 303 PA L A R Q+ + P Q +A + + A L + +RD AGL Sbjct: 255 VAAPAPLSAEFRKVHQFNVFTVNTPMQHGLARYM-ADPAPYLELGAFYQRKRDLFRAGLQ 313 Query: 304 EIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQA 363 + G+YF C D L EFC L ++GVAAIP+SAF AG Q+ Sbjct: 314 ATRLRPLQTEGSYFQCVDYSALSDLPEAEFCRFLTTEIGVAAIPLSAF---YAGGFEQR- 369 Query: 364 DVWNHLVRFTFCKRDDTLDEAIRRLSVL 391 +VRF F K+D+TL A++RL+ L Sbjct: 370 -----VVRFCFAKKDETLQTALQRLARL 392 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: 425 Number of extensions: 21 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: 392 Length adjustment: 31 Effective length of query: 366 Effective length of database: 361 Effective search space: 132126 Effective search space used: 132126 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