Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117) (characterized)
to candidate Echvi_3551 Echvi_3551 Tetrahydrodipicolinate N-succinyltransferase
Query= BRENDA::Q8X8Y7 (274 letters) >FitnessBrowser__Cola:Echvi_3551 Length = 271 Score = 236 bits (602), Expect = 4e-67 Identities = 139/275 (50%), Positives = 180/275 (65%), Gaps = 17/275 (6%) Query: 3 QLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKI-DGQWVTHQWLKK 61 +L+ IIE A+E R + + + AV VI LD G +RVAE + DG+W + W+KK Sbjct: 2 ELKTIIENAWENRELLKEKDVEI----AVKTVIEDLDKGNIRVAEPLEDGEWQVNDWVKK 57 Query: 62 AVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARNT 121 AV+L F I + IE + DK+ +K DY K+G RVVP A R GAF+A+ Sbjct: 58 AVILYFPIQKMRTIEVGPFEFHDKMGLK-TDY-----AKQGVRVVPHAVARYGAFLAKGV 111 Query: 122 VLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDN 181 V+MPSYVNIGAYVD GTMVDTWATVGSCAQIGK+VHLSGGVGIGGVLEP+QA P IIED Sbjct: 112 VMMPSYVNIGAYVDSGTMVDTWATVGSCAQIGKDVHLSGGVGIGGVLEPVQAAPVIIEDG 171 Query: 182 CFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGD---IHYGRVPAGSVVVSGNL 238 F+G+R+ +VEGV V + +VI GV + S++I D TGD + G VP SVV+ G++ Sbjct: 172 AFVGSRAIIVEGVRVGKEAVIGAGVTLTASSKIID-VTGDEPKEYRGYVPPRSVVIPGSI 230 Query: 239 PSK--DGKYSLYCAVIVKKVDAKTRGKVGINELLR 271 K G+Y + CA+I+ + A T K +NE LR Sbjct: 231 TKKFAAGEYQVPCALIIGQRKASTDRKTSLNEALR 265 Lambda K H 0.318 0.136 0.392 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: 239 Number of extensions: 11 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 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