Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_027457779.1 K420_RS0109050 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000519045.1:WP_027457779.1 Length = 385 Score = 250 bits (639), Expect = 4e-71 Identities = 156/388 (40%), Positives = 210/388 (54%), Gaps = 18/388 (4%) Query: 4 SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63 SR TT+F MS LAT GAVNL QGFPD P + A + G NQY P G Sbjct: 9 SRFPAMGTTIFTVMSRLATECGAVNLSQGFPDFQAEPALFDAVHRHMLAGRNQYAPMGGL 68 Query: 64 APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123 LR+AI + +G +D E+EV VT GAT+AI A+ V PG EV++ EP YDSY Sbjct: 69 PELRQAIVDKVATLYGPRFDVESEVTVTAGATQAIFTAIAAFVRPGDEVIVFEPVYDSYV 128 Query: 124 PVVAMAGAHRVTVPL-VPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELA 182 P + G V L PD +A D D +R + RTR +I+NSPHNPTG++L+A +L Sbjct: 129 PAIETVGGQAVFAQLRFPD---YAPDWDQVRGLINERTRMIIVNSPHNPTGSLLTAADLD 185 Query: 183 AIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIG 242 +A + ++V+++DEVYEH+VFD RH L +A R+I +SS K ++ TGWKIG Sbjct: 186 RLAGLVRGTDIVILSDEVYEHIVFDGERHASLCAHAELAVRSIVVSSFGKTYHITGWKIG 245 Query: 243 WACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGL 302 + GPA L+A R Q+ + AP Q A+A + + L +A+RD + Sbjct: 246 YVVGPAALMAEFRKVHQFNVFTVHAPSQLAIAEYMQDASRHL-GLAAFYQAKRDHFRQLM 304 Query: 303 TEIGFAVHDSYGTYFLCADPRPLGYDDSTE--FCAALPEKVGVAAIPMSAFCDPAAGQAS 360 F + GTYF A R G D + F L +VGVA IP+S F A G+ Sbjct: 305 AATPFTLLPCRGTYFQLA--RYAGMSDLPDRAFAEWLTREVGVAVIPVSVF--NADGRDD 360 Query: 361 QQADVWNHLVRFTFCKRDDTLDEAIRRL 388 Q +VRF F KR+ TL+ A+ RL Sbjct: 361 Q-------VVRFCFAKREATLEAAVERL 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: 385 Number of extensions: 23 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: 385 Length adjustment: 31 Effective length of query: 366 Effective length of database: 354 Effective search space: 129564 Effective search space used: 129564 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