Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate WP_041439343.1 TCUR_RS05775 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= CharProtDB::CH_024869 (274 letters) >NCBI__GCF_000024385.1:WP_041439343.1 Length = 278 Score = 217 bits (553), Expect = 2e-61 Identities = 121/274 (44%), Positives = 174/274 (63%), Gaps = 16/274 (5%) Query: 4 LQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVA--EKIDGQWVTHQWLKK 61 + +I+ +ERR +++P + D R A+ + L+D+G RVA + Q V + K+ Sbjct: 9 IPGVIDELWERRDQLSPDDGDA--RAAIVAAVDLIDTGRARVAFVDPATDQVVVDERAKR 66 Query: 62 AVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARNT 121 A+LLSF++ + + Y D++P+K + EG RVVP A R GA++A Sbjct: 67 AILLSFKVLGMVRAQVGDFHYHDRIPLKT--------RLEGVRVVPGAIARWGAYLAPGV 118 Query: 122 VLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDN 181 VLMPS+ NIGAYVD GTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEP A P ++ED+ Sbjct: 119 VLMPSFTNIGAYVDSGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPPNAVPVVVEDD 178 Query: 182 CFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETG-EIHYGRVPAGSVVVSGNLPS 240 FIG+R VV+G V G+ + G + ++TR++D ETG E+ G PA SV VSG Sbjct: 179 AFIGSRCMVVDGARVRRGAKLGAGAILTKTTRVFDVETGEELPRGEAPAWSVCVSGTRTK 238 Query: 241 K--DGKYSLYCAVIVKKV-DAKTRGKVGINELLR 271 K G++ + C +++K++ + + K+ +NE+LR Sbjct: 239 KFPGGEFGMPCLLVLKRLEEGQQHDKLALNEILR 272 Lambda K H 0.318 0.136 0.391 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: 241 Number of extensions: 14 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: 274 Length of database: 278 Length adjustment: 25 Effective length of query: 249 Effective length of database: 253 Effective search space: 62997 Effective search space used: 62997 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