Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117) (characterized)
to candidate WP_052666383.1 NITAL_RS11720 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase
Query= BRENDA::P9WP21 (317 letters) >NCBI__GCF_000969705.1:WP_052666383.1 Length = 356 Score = 357 bits (917), Expect = e-103 Identities = 200/352 (56%), Positives = 230/352 (65%), Gaps = 36/352 (10%) Query: 2 STVTGAAGIGLATLAADGS---VLDTWFPAPELTESGT----------SATSRLAVSDVP 48 +T A G+G+AT + G VLDTW+P L G AT+ + ++D Sbjct: 4 ATPRPAHGLGIATRSTRGEGTKVLDTWYPHARLDTPGARALADALGHGDATATIELTDEH 63 Query: 49 VELAALIGRDDD-------------------RRTETIAVRTVIGSLDDVAADPYDAYLRL 89 V G D+ RT +AV T + LD D +DAYLRL Sbjct: 64 VAALEQAGADEQLLTTVRQLVAAAQQPALAPTRTSRVAVATFVADLDAPPTDAHDAYLRL 123 Query: 90 HLLSHRLVAPHGLNAGGLFGVLTNVVWTNHGPCAIDGFEAVRARLRRRGP-VTVYGVDKF 148 HLLS R +APHG N G FG L NVVWT+ GPC DGFE +R L G V V VDKF Sbjct: 124 HLLSQRSIAPHGANLDGAFGALNNVVWTDLGPCDPDGFEQLRLELLAAGHRVRVTSVDKF 183 Query: 149 PRMVDYVVPTGVRIADADRVRLGAHLAPGTTVMHEGFVNYNAGTLGASMVEGRISAGVVV 208 PRM DYVVP GVR+ADADRVRLGAHLA GTTVMHEGFVN+NAGTLG+SMVEGRISAGVVV Sbjct: 184 PRMTDYVVPAGVRVADADRVRLGAHLAEGTTVMHEGFVNFNAGTLGSSMVEGRISAGVVV 243 Query: 209 GDGSDVGGGASIMGTLSGGGTHVISIGKRCLLGANSGLGISLGDDCVVEAGLYVTAGTRV 268 GDGSD+GG +SIMGTLSGGG ++ IG R LLGAN+G+GISLGDDCVVEAGLYVTAGT+V Sbjct: 244 GDGSDLGGSSSIMGTLSGGGKEIVRIGARTLLGANAGIGISLGDDCVVEAGLYVTAGTKV 303 Query: 269 TMPDSNSVKARELSGSSNLLFRRNSVSGAVEVLARDGQGI---ALNEDLHAN 317 T+P VKARELSG LLFRR+SVSG V V+ R+G LN LHAN Sbjct: 304 TLPGGEVVKARELSGRDGLLFRRDSVSGTVTVVEREGVTADWGGLNAALHAN 355 Lambda K H 0.318 0.136 0.397 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: 386 Number of extensions: 22 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: 317 Length of database: 356 Length adjustment: 28 Effective length of query: 289 Effective length of database: 328 Effective search space: 94792 Effective search space used: 94792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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