Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Tetrahydrodipicolinate N-succinyltransferase; THDP succinyltransferase; THP succinyltransferase; Tetrahydropicolinate succinylase; EC 2.3.1.117 (characterized)
to candidate CA265_RS02995 CA265_RS02995 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= SwissProt::P56220 (274 letters) >FitnessBrowser__Pedo557:CA265_RS02995 Length = 273 Score = 231 bits (589), Expect = 1e-65 Identities = 135/272 (49%), Positives = 176/272 (64%), Gaps = 14/272 (5%) Query: 4 LQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAV 63 L+ +IE+A+E R + +N EA+ VI LD G +RVAE + W ++W+KKAV Sbjct: 6 LKKLIEAAWEDRTLLKYSNYC----EAIEAVIMGLDKGEIRVAEPVLNSWGINEWVKKAV 61 Query: 64 LLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVL 123 +L F I + K + Y+DK+ +K DY + G RVVP A+ R GAF+A+ ++ Sbjct: 62 ILYFPIREMKEIKSGPFVYHDKMDLK-TDY-----KATGVRVVPMASARYGAFLAKGVIM 115 Query: 124 MPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCF 183 MPSYVNIGAYVDEGTMVDTWATVGSCAQIGK VHLSGGVGIGGVLEP+QA P IIED+ F Sbjct: 116 MPSYVNIGAYVDEGTMVDTWATVGSCAQIGKRVHLSGGVGIGGVLEPVQAAPVIIEDDAF 175 Query: 184 IGARSEVVEGVIVEEGSVISMGVYLGQSTRIYD--RETGEIHYGRVPAGSVVVSGNLPSK 241 +G+R+ VVEGV VE +V+ V L ST+I D T + G VPA SVV+ G+ K Sbjct: 176 LGSRAIVVEGVKVEREAVLGANVVLTASTKIIDVTGPTPVEYKGIVPARSVVIPGSYTKK 235 Query: 242 --DGSYSLYCAVIVKKVDAKTRGKVGINELLR 271 G + + CA+I+ K T K +N+ LR Sbjct: 236 FPAGEFQVPCALIIGKRKESTDKKTSLNDALR 267 Lambda K H 0.318 0.136 0.393 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: 222 Number of extensions: 9 Number of successful extensions: 2 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: 274 Length of database: 273 Length adjustment: 25 Effective length of query: 249 Effective length of database: 248 Effective search space: 61752 Effective search space used: 61752 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 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