Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate WP_015927721.1 MNOD_RS04885 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= CharProtDB::CH_024869 (274 letters) >NCBI__GCF_000022085.1:WP_015927721.1 Length = 281 Score = 336 bits (861), Expect = 4e-97 Identities = 182/276 (65%), Positives = 205/276 (74%), Gaps = 9/276 (3%) Query: 4 LQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKI-DGQWVTHQWLKKA 62 L IE A+E RA + P TV REAV +ALLDSG RVAEK W +QWLKKA Sbjct: 6 LARTIEAAWEDRASVGPTTQGTV-REAVEAALALLDSGQARVAEKSGSADWQVNQWLKKA 64 Query: 63 VLLSFRINDNQVIEGAE--SRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN 120 VLLSFR+ND VI G + ++DKVP KF +D RF+ GFR VP A VR+G++IA Sbjct: 65 VLLSFRLNDMSVIPGGPGGAAWWDKVPSKFEGWDADRFRAAGFRAVPGAVVRRGSYIAPG 124 Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180 VLMPS+VN+GAYV EGTMVDTWAT+GSCAQ+GKN H+SGG GI GVLEPLQANP IIED Sbjct: 125 AVLMPSFVNLGAYVGEGTMVDTWATIGSCAQVGKNCHISGGAGIAGVLEPLQANPVIIED 184 Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240 NCFIGAR+EV EGVIV EGSV+SMGVYIG ST+I DR TGE+ YGRVP SVVVSG P Sbjct: 185 NCFIGARAEVAEGVIVGEGSVLSMGVYIGASTKIIDRATGEVMYGRVPPYSVVVSGTQPG 244 Query: 241 K---DGK--YSLYCAVIVKKVDAKTRGKVGINELLR 271 K DG SLYCAVIVK+VDA TR K GINELLR Sbjct: 245 KPLPDGTPGPSLYCAVIVKRVDAGTRAKTGINELLR 280 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: 278 Number of extensions: 13 Number of successful extensions: 4 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: 281 Length adjustment: 25 Effective length of query: 249 Effective length of database: 256 Effective search space: 63744 Effective search space used: 63744 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_015927721.1 MNOD_RS04885 (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.21638.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-130 420.4 0.0 1.8e-130 420.3 0.0 1.0 1 lcl|NCBI__GCF_000022085.1:WP_015927721.1 MNOD_RS04885 2,3,4,5-tetrahydrop Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000022085.1:WP_015927721.1 MNOD_RS04885 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 ! 420.3 0.0 1.8e-130 1.8e-130 2 269 .. 6 280 .. 5 281 .] 0.95 Alignments for each domain: == domain 1 score: 420.3 bits; conditional E-value: 1.8e-130 TIGR00965 2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfritd 69 l + ie a+e ra + p+++ +v+eav+ ++a ldsg+ rvaek +++w+vn+w+kkavllsfr++d lcl|NCBI__GCF_000022085.1:WP_015927721.1 6 LARTIEAAWEDRASVGPTTQG-TVREAVEAALALLDSGQARVAEKSgSADWQVNQWLKKAVLLSFRLND 73 6789************99865.69**********************789******************** PP TIGR00965 70 nqvlnda..vnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegt 136 v+ ++ + ++dkv++kf +d d+f+ ag+r+vpgavvrrg++ia vlmps+vn+gayv egt lcl|NCBI__GCF_000022085.1:WP_015927721.1 74 MSVIPGGpgGAAWWDKVPSKFEGWDADRFRAAGFRAVPGAVVRRGSYIAPGAVLMPSFVNLGAYVGEGT 142 ****98622689********************************************************* PP TIGR00965 137 mvdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvf 205 mvdtwat+gscaq+gkn+h+sgg+gi gvleplqa+pviiedncfigar+e++egviv egsv+smgv+ lcl|NCBI__GCF_000022085.1:WP_015927721.1 143 MVDTWATIGSCAQVGKNCHISGGAGIAGVLEPLQANPVIIEDNCFIGARAEVAEGVIVGEGSVLSMGVY 211 ********************************************************************* PP TIGR00965 206 igqstkivdretgeiiygrvpagsvvvsgslpsk...dgk..kslycavivkkvdaktrgkvsinellr 269 ig stki+dr tge++ygrvp +svvvsg+ p k dg +slycavivk+vda tr+k++inellr lcl|NCBI__GCF_000022085.1:WP_015927721.1 212 IGASTKIIDRATGEVMYGRVPPYSVVVSGTQPGKplpDGTpgPSLYCAVIVKRVDAGTRAKTGINELLR 280 *****************************998754446762269************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (281 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: 00:00:00.01 # Mc/sec: 6.68 // [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