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 WP_012676639.1 PERMA_RS00580 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= SwissProt::P56220 (274 letters) >NCBI__GCF_000021565.1:WP_012676639.1 Length = 271 Score = 261 bits (666), Expect = 1e-74 Identities = 142/275 (51%), Positives = 184/275 (66%), Gaps = 14/275 (5%) Query: 1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLK 60 M++L+ +I ++E R + +AV + I LLD G +RVAEK DG+WV ++W+K Sbjct: 1 MEELKRLITESWENRELLKEKQYI----DAVRETIDLLDRGKIRVAEKRDGEWVVNEWVK 56 Query: 61 KAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARN 120 +A+LL F I D +VM+ YYDK+P+K +++ G RVVPPAT R G+FI + Sbjct: 57 QAILLYFPIQDMQVMEVGPFEYYDKIPLK------KNWKEAGVRVVPPATARYGSFIEKG 110 Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180 +LMPSYVNIGAYV GT+VDTWATVGSCAQ+GKNVHLSGGVGIGGVLEP A P IIED Sbjct: 111 AILMPSYVNIGAYVGSGTLVDTWATVGSCAQVGKNVHLSGGVGIGGVLEPPSAKPVIIED 170 Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGE-IHY-GRVPAGSVVVSGNL 238 NCFIG+R +VEG ++EE +V+ GV + STRI D E + Y GRVPA SVV+ G + Sbjct: 171 NCFIGSRCIIVEGAVIEEEAVLGAGVVITGSTRIIDVSGEEPVEYRGRVPARSVVIPGVM 230 Query: 239 PSK--DGSYSLYCAVIVKKVDAKTRGKVGINELLR 271 K G Y + A+I+ K T KV +NE LR Sbjct: 231 NKKFPAGEYGVPVALIIGKRKESTDKKVSLNEALR 265 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: 255 Number of extensions: 10 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: 274 Length of database: 271 Length adjustment: 25 Effective length of query: 249 Effective length of database: 246 Effective search space: 61254 Effective search space used: 61254 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 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