Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate WP_002889295.1 KVAR_RS20940 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= CharProtDB::CH_024869 (274 letters) >NCBI__GCF_000025465.1:WP_002889295.1 Length = 274 Score = 531 bits (1367), Expect = e-156 Identities = 265/274 (96%), Positives = 272/274 (99%) Query: 1 MQQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLK 60 MQQLQN+IE+AFERRA+ITPAN DTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLK Sbjct: 1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLK 60 Query: 61 KAVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN 120 KAVLLSFRINDNQVI+GAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN Sbjct: 61 KAVLLSFRINDNQVIDGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN 120 Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED Sbjct: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180 Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240 NCFIGARSEVVEGVIVEEGSVISMGVY+GQST+IYDRETGE+ YGRVPAGSVVVSGNLPS Sbjct: 181 NCFIGARSEVVEGVIVEEGSVISMGVYLGQSTKIYDRETGEVFYGRVPAGSVVVSGNLPS 240 Query: 241 KDGKYSLYCAVIVKKVDAKTRGKVGINELLRTID 274 KDGKYSLYCAVIVKKVDAKTRGKVGINELLRTID Sbjct: 241 KDGKYSLYCAVIVKKVDAKTRGKVGINELLRTID 274 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: 382 Number of extensions: 5 Number of successful extensions: 1 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: 274 Length adjustment: 25 Effective length of query: 249 Effective length of database: 249 Effective search space: 62001 Effective search space used: 62001 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)
Align candidate WP_002889295.1 KVAR_RS20940 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase)
to HMM TIGR00965 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00965.hmm # target sequence database: /tmp/gapView.473.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00965 [M=271] Accession: TIGR00965 Description: dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-167 541.3 2.4 2.5e-167 541.1 2.4 1.0 1 lcl|NCBI__GCF_000025465.1:WP_002889295.1 KVAR_RS20940 2,3,4,5-tetrahydrop Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_002889295.1 KVAR_RS20940 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransfe # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 541.1 2.4 2.5e-167 2.5e-167 1 271 [] 3 273 .. 3 273 .. 1.00 Alignments for each domain: == domain 1 score: 541.1 bits; conditional E-value: 2.5e-167 TIGR00965 1 slqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritd 69 +lq++ie+aferra+i+pa+++++++eavn++ia ldsgalrvaek+dgqw++++w+kkavllsfri+d lcl|NCBI__GCF_000025465.1:WP_002889295.1 3 QLQNVIESAFERRADITPANVDTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRIND 71 69******************************************************************* PP TIGR00965 70 nqvlndavnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmv 138 nqv+++a+++yfdkv++kfadyde++f+++g+r+vp+a+vr+gafia+n+vlmpsyvnigayvdegtmv lcl|NCBI__GCF_000025465.1:WP_002889295.1 72 NQVIDGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARNTVLMPSYVNIGAYVDEGTMV 140 ********************************************************************* PP TIGR00965 139 dtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfig 207 dtwatvgscaqigknvhlsggvgiggvleplqa+p+iiedncfigarse+vegviveegsvismgv++g lcl|NCBI__GCF_000025465.1:WP_002889295.1 141 DTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLG 209 ********************************************************************* PP TIGR00965 208 qstkivdretgeiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellrti 271 qstki+dretge++ygrvpagsvvvsg+lpskdgk+slycavivkkvdaktrgkv+inellrti lcl|NCBI__GCF_000025465.1:WP_002889295.1 210 QSTKIYDRETGEVFYGRVPAGSVVVSGNLPSKDGKYSLYCAVIVKKVDAKTRGKVGINELLRTI 273 **************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (274 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.17 // [ok]
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