Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate WP_038217084.1 Q392_RS28980 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= CharProtDB::CH_024869 (274 letters) >NCBI__GCF_000745855.1:WP_038217084.1 Length = 277 Score = 356 bits (913), Expect = e-103 Identities = 179/274 (65%), Positives = 212/274 (77%), Gaps = 4/274 (1%) Query: 2 QQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKID-GQWVTHQWLK 60 QQLQ II+ A+E RA ++P A +AV VIA L++G LRVA + GQW HQW+K Sbjct: 3 QQLQQIIDAAWEDRANLSPTQAPKEVADAVEHVIAELNNGHLRVATREGVGQWTVHQWVK 62 Query: 61 KAVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN 120 KAVLLSFR+ DN+ I+ ++DKVP KF+ + G R+VPPA R+G+F+A+ Sbjct: 63 KAVLLSFRLKDNEQIQAGSLGFYDKVPTKFSHLSANELRDSGVRIVPPAIARRGSFVAKG 122 Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180 +LMPSYVNIGAYV EGTMVDTWATVGSCAQ+G NVHLSGGVG+GGVLEPLQANPTIIED Sbjct: 123 AILMPSYVNIGAYVGEGTMVDTWATVGSCAQVGANVHLSGGVGLGGVLEPLQANPTIIED 182 Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240 NCFIGARSEVVEGVIVEE SV+ MGVYIGQST I++R+TGEI YGRVPAGSVV+SGNLP Sbjct: 183 NCFIGARSEVVEGVIVEENSVLGMGVYIGQSTPIFNRDTGEISYGRVPAGSVVISGNLPK 242 Query: 241 K---DGKYSLYCAVIVKKVDAKTRGKVGINELLR 271 K YS Y A+IVK VDA+TR K +N+LLR Sbjct: 243 KTKAGQDYSTYAAIIVKTVDAQTRSKTSLNDLLR 276 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: 283 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: 277 Length adjustment: 25 Effective length of query: 249 Effective length of database: 252 Effective search space: 62748 Effective search space used: 62748 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_038217084.1 Q392_RS28980 (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.28975.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-133 430.2 0.3 1.9e-133 430.0 0.3 1.0 1 lcl|NCBI__GCF_000745855.1:WP_038217084.1 Q392_RS28980 2,3,4,5-tetrahydrop Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745855.1:WP_038217084.1 Q392_RS28980 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 ! 430.0 0.3 1.9e-133 1.9e-133 1 269 [. 4 276 .. 4 277 .] 0.98 Alignments for each domain: == domain 1 score: 430.0 bits; conditional E-value: 1.9e-133 TIGR00965 1 slqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfrit 68 +lq+ii+ a+e ra++ p+++ +v +av+++ia+l++g lrva + +gqw v++wvkkavllsfr++ lcl|NCBI__GCF_000745855.1:WP_038217084.1 4 QLQQIIDAAWEDRANLSPTQAPKEVADAVEHVIAELNNGHLRVATREgVGQWTVHQWVKKAVLLSFRLK 72 699*******************************************989******************** PP TIGR00965 69 dnqvlndavnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtm 137 dn+ ++ + ++dkv+tkf+ + +e++++g+r vp+a++rrg+f+ak +lmpsyvnigayv egtm lcl|NCBI__GCF_000745855.1:WP_038217084.1 73 DNEQIQAGSLGFYDKVPTKFSHLSANELRDSGVRIVPPAIARRGSFVAKGAILMPSYVNIGAYVGEGTM 141 ********************************************************************* PP TIGR00965 138 vdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfi 206 vdtwatvgscaq+g nvhlsggvg+ggvleplqa+p+iiedncfigarse+vegvivee sv+ mgv+i lcl|NCBI__GCF_000745855.1:WP_038217084.1 142 VDTWATVGSCAQVGANVHLSGGVGLGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEENSVLGMGVYI 210 ********************************************************************* PP TIGR00965 207 gqstkivdretgeiiygrvpagsvvvsgslps..kdgk.kslycavivkkvdaktrgkvsinellr 269 gqst i++r+tgei ygrvpagsvv+sg+lp k g+ +s y a+ivk vda+tr+k+s+n+llr lcl|NCBI__GCF_000745855.1:WP_038217084.1 211 GQSTPIFNRDTGEISYGRVPAGSVVISGNLPKktKAGQdYSTYAAIIVKTVDAQTRSKTSLNDLLR 276 *******************************955566448*************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (277 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: 8.25 // [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