Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate SMc02404 SMc02404 dihydrodipicolinate synthase
Query= BRENDA::Q8UGL3 (294 letters) >FitnessBrowser__Smeli:SMc02404 Length = 294 Score = 478 bits (1229), Expect = e-140 Identities = 235/294 (79%), Positives = 265/294 (90%) Query: 1 MFKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVV 60 MFKGSIPAL+TPFT GSVD +F AHVEWQI EGS+GLVPVGTTGESPTLSHDEHK+VV Sbjct: 1 MFKGSIPALVTPFTAAGSVDADSFVAHVEWQIKEGSHGLVPVGTTGESPTLSHDEHKKVV 60 Query: 61 ELCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTPYYNKPTQKGLFAHFS 120 ELC+E +A+RVPVIAGAGSNNT EAIELA HA++AGADA+LVVTPYYNKPTQKGLFAHF+ Sbjct: 61 ELCVEASARRVPVIAGAGSNNTIEAIELAQHAEKAGADAILVVTPYYNKPTQKGLFAHFA 120 Query: 121 AVAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHKNIIGVKDATGKLDRVSEQRISCGK 180 A+AE+VKLPIVIYNIP RSVVDMS ETM AL KAH I+GVKDATG+++RVSEQR++CGK Sbjct: 121 AIAESVKLPIVIYNIPGRSVVDMSVETMAALAKAHPTIVGVKDATGRIERVSEQRMACGK 180 Query: 181 DFVQLSGEDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALEYQDRLMPL 240 FVQLSGED TALGFNAHGGVGCISVTANVAPRLC+EFQ A LAG+YAKALE QD+LMPL Sbjct: 181 AFVQLSGEDATALGFNAHGGVGCISVTANVAPRLCAEFQEATLAGNYAKALELQDKLMPL 240 Query: 241 HRAIFMEPGVCGTKYALSKTRGGNRRVRSPLMSTLEPATEAAIDAALKHAGLMN 294 H+AIF+EPGVCG KYAL++ + VRSPL+S LEPAT +AIDAAL+HAGLMN Sbjct: 241 HKAIFLEPGVCGAKYALNRLGRMSFTVRSPLLSALEPATASAIDAALRHAGLMN 294 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: 366 Number of extensions: 6 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: 294 Length of database: 294 Length adjustment: 26 Effective length of query: 268 Effective length of database: 268 Effective search space: 71824 Effective search space used: 71824 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 SMc02404 SMc02404 (dihydrodipicolinate 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.20790.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-99 318.3 0.1 1.8e-99 318.2 0.1 1.0 1 lcl|FitnessBrowser__Smeli:SMc02404 SMc02404 dihydrodipicolinate syn Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02404 SMc02404 dihydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 318.2 0.1 1.8e-99 1.8e-99 1 280 [. 4 284 .. 4 290 .. 0.96 Alignments for each domain: == domain 1 score: 318.2 bits; conditional E-value: 1.8e-99 TIGR00674 1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtg 75 g+++Al+TPf + gsvd +++ +e qi++g+ ++v+vGtTGEs+tLs++E+kkv+e+ ve ++ rvpviaG+g lcl|FitnessBrowser__Smeli:SMc02404 4 GSIPALVTPFTAAGSVDADSFVAHVEWQIKEGSHGLVPVGTTGESPTLSHDEHKKVVELCVEASARRVPVIAGAG 78 589************************************************************************ PP TIGR00674 76 snateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLae 150 sn+t eaiel+++aek+g+d++lvvtPyYnkPtq+Gl++hf aiae+v+lPi++Yn+P+R++v++++et+++La+ lcl|FitnessBrowser__Smeli:SMc02404 79 SNNTIEAIELAQHAEKAGADAILVVTPYYNKPTQKGLFAHFAAIAESVKLPIVIYNIPGRSVVDMSVETMAALAK 153 **************************************************************************9 PP TIGR00674 151 eve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdte 224 ++ iv++K+a+g +ervse + ++ f+ lsG+Da++l + a G+ G iSV++nvap++++e+ +a+l+g+++ lcl|FitnessBrowser__Smeli:SMc02404 154 AHPtIVGVKDATGRIERVSEQRMACGKAFVQLSGEDATALGFNAHGGVGCISVTANVAPRLCAEFQEATLAGNYA 228 8888*********************************************************************** PP TIGR00674 225 eareihqkllklfkalfietNPipvKtalallgliekdelRlPLte.lseekkeklk 280 +a+e++ kl++l+ka+f+e+ + K+al+ lg + ++R PL l+ + + ++ lcl|FitnessBrowser__Smeli:SMc02404 229 KALELQDKLMPLHKAIFLEPGVCGAKYALNRLGRMSF-TVRSPLLSaLEPATASAID 284 ************************************9.*****86504445555555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (294 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.26 // [ok]
This GapMind analysis is from Apr 09 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