Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_090220024.1 CV091_RS15865 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q8UGL3 (294 letters) >NCBI__GCF_002796795.1:WP_090220024.1 Length = 290 Score = 392 bits (1008), Expect = e-114 Identities = 206/293 (70%), Positives = 235/293 (80%), Gaps = 3/293 (1%) Query: 1 MFKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVV 60 MFKGS+PAL+TPF NG +D A VEWQI EGS LVPVGTTGESPTLS +EH+ VV Sbjct: 1 MFKGSMPALVTPFR-NGELDLDALKHLVEWQIGEGSTALVPVGTTGESPTLSLEEHETVV 59 Query: 61 ELCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTPYYNKPTQKGLFAHFS 120 E ++ AA RVPVIAGAGSNNT +AI L A +AGADA LVVTPYYNKPTQ+G+ AH+ Sbjct: 60 EEVVKAAAGRVPVIAGAGSNNTVDAIRLVEFAAKAGADAALVVTPYYNKPTQRGMLAHYK 119 Query: 121 AVAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHKNIIGVKDATGKLDRVSEQRISCGK 180 A+ + LPIVIYNIP RS+VDMSP TMG L K + IIGVKDATG + RVS+QR +CG Sbjct: 120 ALHDCADLPIVIYNIPGRSIVDMSPATMGELAKLPR-IIGVKDATGDIARVSQQRATCGA 178 Query: 181 DFVQLSGEDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALEYQDRLMPL 240 DF+QLSGED +ALGFNAHGGVGCISVTANVAPRLC+EFQAA LAGDYAKALEYQDRLMPL Sbjct: 179 DFMQLSGEDASALGFNAHGGVGCISVTANVAPRLCAEFQAATLAGDYAKALEYQDRLMPL 238 Query: 241 HRAIFMEPGVCGTKYALSKTRGGNRRVRSPLMSTLEPATEAAIDAALKHAGLM 293 H AIF EPGV G KYALSK + VR PL + LE +T+AA+DAA+KHAGL+ Sbjct: 239 HEAIFTEPGVAGAKYALSKLGLCSDEVRLPL-TGLEDSTKAALDAAMKHAGLL 290 Lambda K H 0.317 0.133 0.384 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: 347 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: 294 Length of database: 290 Length adjustment: 26 Effective length of query: 268 Effective length of database: 264 Effective search space: 70752 Effective search space used: 70752 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: 48 (23.1 bits)
Align candidate WP_090220024.1 CV091_RS15865 (4-hydroxy-tetrahydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
# 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/TIGR00674.hmm # target sequence database: /tmp/gapView.771019.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00674 [M=286] Accession: TIGR00674 Description: dapA: 4-hydroxy-tetrahydrodipicolinate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-100 321.4 0.0 2.1e-100 321.2 0.0 1.0 1 NCBI__GCF_002796795.1:WP_090220024.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002796795.1:WP_090220024.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 321.2 0.0 2.1e-100 2.1e-100 2 285 .. 5 286 .. 4 287 .. 0.99 Alignments for each domain: == domain 1 score: 321.2 bits; conditional E-value: 2.1e-100 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGt 74 +++Al+TPf++ + +d++al++l+e qi +g+ a+v+vGtTGEs+tLsleE+++v+e +v+ +++rvpviaG+ NCBI__GCF_002796795.1:WP_090220024.1 5 SMPALVTPFRNGE-LDLDALKHLVEWQIGEGSTALVPVGTTGESPTLSLEEHETVVEEVVKAAAGRVPVIAGA 76 789******9988.*********************************************************** PP TIGR00674 75 gsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkr 147 gsn+t +ai+l+++a+k+g+d++lvvtPyYnkPtq+G+++h+ka++++++lPi++Yn+P+R+ v+++p t+ + NCBI__GCF_002796795.1:WP_090220024.1 77 GSNNTVDAIRLVEFAAKAGADAALVVTPYYNKPTQRGMLAHYKALHDCADLPIVIYNIPGRSIVDMSPATMGE 149 ************************************************************************* PP TIGR00674 148 LaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaale 220 La+ ++i+++K+a+gd++rvs+ +a+ ++df lsG+Da +l + a G+ G iSV++nvap++++e+ +a+l+ NCBI__GCF_002796795.1:WP_090220024.1 150 LAKLPRIIGVKDATGDIARVSQQRATCGADFMQLSGEDASALGFNAHGGVGCISVTANVAPRLCAEFQAATLA 222 ************************************************************************* PP TIGR00674 221 gdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285 gd+++a+e + +l++l++a+f+e+ + K+al lgl+ e+RlPLt l++++k l++++k+ NCBI__GCF_002796795.1:WP_090220024.1 223 GDYAKALEYQDRLMPLHEAIFTEPGVAGAKYALSKLGLCSD-EVRLPLTGLEDSTKAALDAAMKH 286 ***************************************99.***************99999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (290 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 15.45 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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