Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_037575899.1 BS73_RS24325 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000744815.1:WP_037575899.1 Length = 398 Score = 394 bits (1013), Expect = e-114 Identities = 214/388 (55%), Positives = 259/388 (66%), Gaps = 14/388 (3%) Query: 6 LRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGV-NQYPPGPGSA 64 L TT+FAEMSALAT GA+NLGQGFPD DGP + +AA A+ G NQYPPGPG Sbjct: 21 LEGMGTTIFAEMSALATTTGAINLGQGFPDTDGPEAVREAAVRALREGRGNQYPPGPGVP 80 Query: 65 PLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSP 124 LR A+A + R +G+D+DP+TEVLVT GATEAIAA++L L+EPG EV+ EPFYDSY+ Sbjct: 81 ELRAAVAEHQLRFYGLDFDPDTEVLVTAGATEAIAASMLALLEPGDEVIAFEPFYDSYAA 140 Query: 125 VVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAI 184 +AMAGA RV P F D D LR +TP TR L++NSPHNPTG VL EL AI Sbjct: 141 CIAMAGAKRV--PFTLRAPSFRPDLDELRALITPSTRLLLLNSPHNPTGMVLDDEELRAI 198 Query: 185 AEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWA 244 A +AV +L+V+TDEVYEHLVF+ A H P+A GM ERT++ISSA K F+ TGWK+GW Sbjct: 199 AALAVEHDLLVVTDEVYEHLVFEGA-HRPIAALPGMRERTVSISSAGKTFSFTGWKVGWV 257 Query: 245 CGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTE 304 A L+A VR AKQYL+YV PFQ AVA AL DA+ R SLR RRD L AGL Sbjct: 258 TAAAPLVAAVRTAKQYLTYVSAGPFQYAVAEALRLPDAYYEDFRASLRRRRDLLDAGLRA 317 Query: 305 IGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFC-DPAAGQASQQA 363 GF V++ GTYF+ D P G D+ FC +LPE+ GV A+P S F DP AG++ Sbjct: 318 AGFEVYEPQGTYFITTDIAPFGAKDAYAFCRSLPERCGVVAVPNSVFYDDPEAGRSQ--- 374 Query: 364 DVWNHLVRFTFCKRDDTLDEAIRRLSVL 391 VRFTFCK+++ L EA RL L Sbjct: 375 ------VRFTFCKKEEVLREAAARLQRL 396 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: 504 Number of extensions: 24 Number of successful extensions: 5 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: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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 Jul 26 2024. The underlying query database was built on Jul 25 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