Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate BWI76_RS20905 BWI76_RS20905 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::P0A6L2 (292 letters) >FitnessBrowser__Koxy:BWI76_RS20905 Length = 292 Score = 521 bits (1343), Expect = e-153 Identities = 255/292 (87%), Positives = 278/292 (95%) Query: 1 MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVV 60 MFTGSIVA+VTPMDE GNVCR+SLKKLIDYHVASGTSAIVSVGTTGESATL+H+EH DVV Sbjct: 1 MFTGSIVALVTPMDENGNVCRSSLKKLIDYHVASGTSAIVSVGTTGESATLSHEEHGDVV 60 Query: 61 MMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQEGLYQHFK 120 M TL+LADGRIPVIAGTGANATAEAISLT+RFNDSG+VGCLTVTPYYNRP+QEGL+QHFK Sbjct: 61 MQTLELADGRIPVIAGTGANATAEAISLTKRFNDSGVVGCLTVTPYYNRPTQEGLFQHFK 120 Query: 121 AIAEHTDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIKEATGNLTRVNQIKELVSDD 180 AIAEHTDLPQILYNVPSRTGCD+LPETVGRLA++KNIIGIKEATGNL+RV+QIKELVSDD Sbjct: 121 AIAEHTDLPQILYNVPSRTGCDMLPETVGRLAEIKNIIGIKEATGNLSRVHQIKELVSDD 180 Query: 181 FVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLH 240 F+LLSGDDA+ +DFMQLGGHGVISVT NVAAR+MA+MC+LA G FAEAR INQRLMPLH Sbjct: 181 FILLSGDDATGMDFMQLGGHGVISVTTNVAAREMAEMCRLALAGQFAEARAINQRLMPLH 240 Query: 241 NKLFVEPNPIPVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL 292 KLFVEPNPIPVKWACK LGLVATDTLRLPMTPIT++G + V AALKHAGLL Sbjct: 241 TKLFVEPNPIPVKWACKALGLVATDTLRLPMTPITENGTKVVTAALKHAGLL 292 Lambda K H 0.319 0.134 0.387 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: 411 Number of extensions: 10 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: 292 Length adjustment: 26 Effective length of query: 266 Effective length of database: 266 Effective search space: 70756 Effective search space used: 70756 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate BWI76_RS20905 BWI76_RS20905 (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.30005.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-128 412.8 0.1 3e-128 412.6 0.1 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS20905 BWI76_RS20905 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS20905 BWI76_RS20905 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.6 0.1 3e-128 3e-128 1 285 [. 4 288 .. 4 289 .. 0.99 Alignments for each domain: == domain 1 score: 412.6 bits; conditional E-value: 3e-128 TIGR00674 1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpvi 71 g+++Al+TP++e+g+v+ ++l+kli++++++g++aiv+vGtTGEsatLs+eE+ +v++ ++el+++r+pvi lcl|FitnessBrowser__Koxy:BWI76_RS20905 4 GSIVALVTPMDENGNVCRSSLKKLIDYHVASGTSAIVSVGTTGESATLSHEEHGDVVMQTLELADGRIPVI 74 589******************************************************************** PP TIGR00674 72 aGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslep 142 aGtg+nat+eai+ltk+++++gv g+l+vtPyYn+PtqeGl++hfkaiae+++lP+ilYnvPsRtg+++ p lcl|FitnessBrowser__Koxy:BWI76_RS20905 75 AGTGANATAEAISLTKRFNDSGVVGCLTVTPYYNRPTQEGLFQHFKAIAEHTDLPQILYNVPSRTGCDMLP 145 *********************************************************************** PP TIGR00674 143 etvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelke 213 etv rLae ++i++iKea+g+l+rv +ik+ +++df +lsGdDa+ +++++lG++GviSV++nva++e++e lcl|FitnessBrowser__Koxy:BWI76_RS20905 146 ETVGRLAEIKNIIGIKEATGNLSRVHQIKELVSDDFILLSGDDATGMDFMQLGGHGVISVTTNVAAREMAE 216 *********************************************************************** PP TIGR00674 214 mvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlk 284 m++ al+g+++ear i+q+l++l+++lf+e+NPipvK+a+++lgl+++d+lRlP+t+++e+ ++ ++++lk lcl|FitnessBrowser__Koxy:BWI76_RS20905 217 MCRLALAGQFAEARAINQRLMPLHTKLFVEPNPIPVKWACKALGLVATDTLRLPMTPITENGTKVVTAALK 287 *******************************************************************9998 PP TIGR00674 285 e 285 + lcl|FitnessBrowser__Koxy:BWI76_RS20905 288 H 288 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (292 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: 9.85 // [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