Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate WP_012590244.1 MSIL_RS06200 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= CharProtDB::CH_024869 (274 letters) >NCBI__GCF_000021745.1:WP_012590244.1 Length = 285 Score = 327 bits (837), Expect = 2e-94 Identities = 180/280 (64%), Positives = 205/280 (73%), Gaps = 13/280 (4%) Query: 4 LQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQ-----WVTHQW 58 L+ IIE AFE RA I V R+AV+ + LLD+G LRVAEKI G+ W HQW Sbjct: 6 LETIIEAAFEDRANINAQTQGDV-RKAVDAALHLLDAGKLRVAEKIAGESGPQSWRVHQW 64 Query: 59 LKKAVLLSFRINDNQVIEGAE--SRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAF 116 LKKAVLLSFR+ND I G + ++DKVP KFA + GFR VP VR+ A+ Sbjct: 65 LKKAVLLSFRLNDMGEIPGGPGGATWWDKVPSKFAGWGAKEHAAAGFRSVPSCVVRRSAY 124 Query: 117 IARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPT 176 IA VLMPS+VN+GAYVD+ TMVDTW TVGSCAQIGKNVHLSGGVGIGGVLEPLQANPT Sbjct: 125 IAPGVVLMPSFVNLGAYVDQNTMVDTWVTVGSCAQIGKNVHLSGGVGIGGVLEPLQANPT 184 Query: 177 IIEDNCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSG 236 IIED+CFIGARSE+VEGVIV EG+V+SMG +I ST+I DR TG+IH G VP SVVVSG Sbjct: 185 IIEDDCFIGARSEIVEGVIVGEGAVVSMGTFISASTKIIDRATGKIHIGYVPPFSVVVSG 244 Query: 237 NLPSK---DGK--YSLYCAVIVKKVDAKTRGKVGINELLR 271 NLP K DG SLYCAVIVK VDA+TR K IN+LLR Sbjct: 245 NLPGKPLPDGSPGPSLYCAVIVKTVDAQTRAKTAINDLLR 284 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: 12 Number of successful extensions: 6 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: 285 Length adjustment: 26 Effective length of query: 248 Effective length of database: 259 Effective search space: 64232 Effective search space used: 64232 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_012590244.1 MSIL_RS06200 (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.2980.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-122 394.2 0.1 1.8e-122 394.0 0.1 1.0 1 lcl|NCBI__GCF_000021745.1:WP_012590244.1 MSIL_RS06200 2,3,4,5-tetrahydrop Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021745.1:WP_012590244.1 MSIL_RS06200 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 ! 394.0 0.1 1.8e-122 1.8e-122 2 269 .. 6 284 .. 5 285 .] 0.94 Alignments for each domain: == domain 1 score: 394.0 bits; conditional E-value: 1.8e-122 TIGR00965 2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgq.....wkvnewvkkavllsf 65 l iie afe ra+i +++ +v++av ++ ld g+lrvaek++g+ w+v++w+kkavllsf lcl|NCBI__GCF_000021745.1:WP_012590244.1 6 LETIIEAAFEDRANINA-QTQGDVRKAVDAALHLLDAGKLRVAEKIAGEsgpqsWRVHQWLKKAVLLSF 73 6789**********975.56789***********************76444555*************** PP TIGR00965 66 ritdnqvlnd..avnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayv 132 r++d + + + + ++dkv++kfa + +e ag+r vp+ vvrr a+ia vvlmps+vn+gayv lcl|NCBI__GCF_000021745.1:WP_012590244.1 74 RLNDMGEIPGgpGGATWWDKVPSKFAGWGAKEHAAAGFRSVPSCVVRRSAYIAPGVVLMPSFVNLGAYV 142 ****988876224689***************************************************** PP TIGR00965 133 degtmvdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvis 201 d+ tmvdtw tvgscaqigknvhlsggvgiggvleplqa+p+iied+cfigarseivegviv eg+v+s lcl|NCBI__GCF_000021745.1:WP_012590244.1 143 DQNTMVDTWVTVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDDCFIGARSEIVEGVIVGEGAVVS 211 ********************************************************************* PP TIGR00965 202 mgvfigqstkivdretgeiiygrvpagsvvvsgslpsk...dgk..kslycavivkkvdaktrgkvsin 265 mg fi stki+dr tg+i+ g vp svvvsg+lp k dg+ +slycavivk vda+tr+k++in lcl|NCBI__GCF_000021745.1:WP_012590244.1 212 MGTFISASTKIIDRATGKIHIGYVPPFSVVVSGNLPGKplpDGSpgPSLYCAVIVKTVDAQTRAKTAIN 280 ***********************************9864558873358********************* PP TIGR00965 266 ellr 269 +llr lcl|NCBI__GCF_000021745.1:WP_012590244.1 281 DLLR 284 ***9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (285 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 0.00s 00:00:00.00 Elapsed: 00:00:00.06 # Mc/sec: 1.24 // [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