Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate 201041 SO1879 dihydrodipicolinate synthase (NCBI ptt file)
Query= BRENDA::A5F699 (292 letters) >FitnessBrowser__MR1:201041 Length = 294 Score = 345 bits (885), Expect = e-100 Identities = 173/291 (59%), Positives = 216/291 (74%) Query: 1 MFSGSIVALITPFTPDGEVDYISLKKLVDFHVDAGTDAIVSVGTTGESATLTVEEHVKVV 60 M +GSIVALITP DG VD+ SL++LV+FH+D GTDAIV+VGTTGESATL + EHV VV Sbjct: 1 MINGSIVALITPMNSDGSVDFASLERLVEFHIDQGTDAIVAVGTTGESATLPMNEHVTVV 60 Query: 61 AKTVEFAEGRLPIIAGTGANATHEAVTFSRLLNNTGIAGYLSVTPYYNKPTQEGLFLHYN 120 A+TV+FA GR+P+I G GANAT EA+ ++ L+ G+A L VTPYYNKPT +GL HY Sbjct: 61 AQTVKFAAGRIPVIGGNGANATAEAIELTKSLSKVGVAAMLGVTPYYNKPTPKGLVAHYK 120 Query: 121 AIAQETDIPVILYNVPGRTAVDMRPETVARLSEIKNIVALKDATGDLSRVAKHREMCKEG 180 A+A TDIP ILYNVPGRTAVDM+PETVA L + NI+ +K+ATGD+SRV + RE+C Sbjct: 121 AVAASTDIPQILYNVPGRTAVDMKPETVAELVSVSNIIGVKEATGDVSRVKRLRELCGND 180 Query: 181 FVLLSGDDATGLEFVKLGGQGVISVTNNIAAADMAKMMHLALDGKFDEAASINQRLMTLH 240 F+L SGDDAT EF+ LGG GVISV NNI M AL G + AASI++ L L+ Sbjct: 181 FMLYSGDDATASEFLLLGGNGVISVANNIVPKAFKAMCDAALAGNAELAASIDEPLRGLY 240 Query: 241 KNLFIESSPIPVKWAAHKMGLIANGDLRLPLTQLSEPARPIVAQALSEACI 291 LF E++PIPVKWAAH+MGLI G +RLPLT+LSE ++ +A++ A I Sbjct: 241 STLFCEANPIPVKWAAHRMGLIECGHIRLPLTELSEQCHGLLLEAMTRAQI 291 Lambda K H 0.318 0.134 0.379 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: 276 Number of extensions: 5 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: 292 Length of database: 294 Length adjustment: 26 Effective length of query: 266 Effective length of database: 268 Effective search space: 71288 Effective search space used: 71288 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 201041 SO1879 (dihydrodipicolinate synthase (NCBI ptt file))
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.18066.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-115 369.3 0.1 5.2e-115 369.2 0.1 1.0 1 lcl|FitnessBrowser__MR1:201041 SO1879 dihydrodipicolinate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:201041 SO1879 dihydrodipicolinate synthase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 369.2 0.1 5.2e-115 5.2e-115 1 279 [. 4 282 .. 4 289 .. 0.98 Alignments for each domain: == domain 1 score: 369.2 bits; conditional E-value: 5.2e-115 TIGR00674 1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsnat 79 g+++AliTP+++dgsvdfa+le+l+e++i++g+daiv+vGtTGEsatL ++E+++v+ +v+++++r+pvi G g+nat lcl|FitnessBrowser__MR1:201041 4 GSIVALITPMNSDGSVDFASLERLVEFHIDQGTDAIVAVGTTGESATLPMNEHVTVVAQTVKFAAGRIPVIGGNGANAT 82 589**************************************************************************** PP TIGR00674 80 eeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeveivaiK 158 +eaieltk ++k+gv+++l vtPyYnkPt +Gl++h+ka+a+++++P+ilYnvP+Rt+v+++petv++L++ +i+++K lcl|FitnessBrowser__MR1:201041 83 AEAIELTKSLSKVGVAAMLGVTPYYNKPTPKGLVAHYKAVAASTDIPQILYNVPGRTAVDMKPETVAELVSVSNIIGVK 161 ******************************************************************************* PP TIGR00674 159 easgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteeareihqkllklf 237 ea+gd++rv+++++ ++df ++sGdDa+++e+l+lG++GviSVa+n++pk +k m+ aal+g+ e a+ i++ l l+ lcl|FitnessBrowser__MR1:201041 162 EATGDVSRVKRLRELCGNDFMLYSGDDATASEFLLLGGNGVISVANNIVPKAFKAMCDAALAGNAELAASIDEPLRGLY 240 ******************************************************************************* PP TIGR00674 238 kalfietNPipvKtalallgliekdelRlPLtelseekkekl 279 ++lf+e+NPipvK+a++ +glie+ ++RlPLtelse+ + l lcl|FitnessBrowser__MR1:201041 241 STLFCEANPIPVKWAAHRMGLIECGHIRLPLTELSEQCHGLL 282 ***********************************9977655 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: 10.68 // [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