Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate 350423 BT0895 dihydrodipicolinate synthase (NCBI ptt file)
Query= SwissProt::Q9X1K9 (294 letters) >FitnessBrowser__Btheta:350423 Length = 297 Score = 251 bits (642), Expect = 1e-71 Identities = 130/289 (44%), Positives = 185/289 (64%), Gaps = 4/289 (1%) Query: 3 RGVGTAIVTPFKNGE-LDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVSR 61 +G+G A++TPFK E +D ++ RLV Y L+N + L VLGTT E+PT+ E+E++ + Sbjct: 7 KGMGVALITPFKEDESVDYDALMRLVDYLLQNNADFLCVLGTTAETPTLTEEEKKTIKKM 66 Query: 62 TLEIVDGKIPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYNKPTQEGLYQHYKYI 121 ++ V+G+IP+++G G N+T ++ +K + G + +L V PYYNKP+QEG+YQHYK I Sbjct: 67 VIDRVNGRIPILLGVGGNNTRAIVETLKNDDFTGVDAILSVVPYYNKPSQEGIYQHYKAI 126 Query: 122 SERTDLGIVVYNVPGRTGVNVLPETAARIAADLKNVVGIKEANPDIDQIDRTVSLTKQAR 181 SE T+L IV+YNVPGRTGVN+ ET RIA + NV+ IKEA+ +I Q+D + K Sbjct: 127 SEATELPIVLYNVPGRTGVNMTAETTLRIARNFSNVIAIKEASGNITQMD---DIIKNKP 183 Query: 182 SDFMVWSGNDDRTFYLLCAGGDGVISVVSNVAPKQMVELCAEYFSGNLEKSREVHRKLRP 241 +F V SG+D TF L+ G GVISV+ N P++ + G+ + +H + Sbjct: 184 DNFNVISGDDGITFPLITLGAVGVISVIGNAFPREFSRMTRLALQGDFANALTIHHRFTE 243 Query: 242 LMKALFVETNPIPVKAALNLMGFIENELRLPLVPASEKTVELLRNVLKE 290 L LFV+ NP VK+ LN MG IEN+LRLPLVP T E +R VL E Sbjct: 244 LFDLLFVDGNPAGVKSMLNAMGMIENKLRLPLVPTRITTFEAIRKVLNE 292 Lambda K H 0.316 0.135 0.378 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: 267 Number of extensions: 16 Number of successful extensions: 3 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: 297 Length adjustment: 26 Effective length of query: 268 Effective length of database: 271 Effective search space: 72628 Effective search space used: 72628 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 (21.5 bits) S2: 48 (23.1 bits)
Align candidate 350423 BT0895 (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.30361.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-102 328.2 0.1 1.8e-102 328.0 0.1 1.0 1 lcl|FitnessBrowser__Btheta:350423 BT0895 dihydrodipicolinate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350423 BT0895 dihydrodipicolinate synthase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 328.0 0.1 1.8e-102 1.8e-102 4 285 .. 11 292 .. 8 293 .. 0.99 Alignments for each domain: == domain 1 score: 328.0 bits; conditional E-value: 1.8e-102 TIGR00674 4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsnat 79 +AliTPfked+svd++al +l++++++++ d + v+GtT E++tL+ eEkk++ +++++ v++r+p++ G+g+n+t lcl|FitnessBrowser__Btheta:350423 11 VALITPFKEDESVDYDALMRLVDYLLQNNADFLCVLGTTAETPTLTEEEKKTIKKMVIDRVNGRIPILLGVGGNNT 86 8*************************************************************************** PP TIGR00674 80 eeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeve.i 154 + +e k + +gvd++l+v+PyYnkP+qeG+y+h+kai e++elPi+lYnvP+Rtgv+++ et++r+a++ + + lcl|FitnessBrowser__Btheta:350423 87 RAIVETLKNDDFTGVDAILSVVPYYNKPSQEGIYQHYKAISEATELPIVLYNVPGRTGVNMTAETTLRIARNFSnV 162 ***********************************************************************9988* PP TIGR00674 155 vaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteeareih 230 +aiKeasg+++++ i++ ++++f+v sGdD +t ++++lGa GviSV++n p+e++ m + al+gd+++a+ ih lcl|FitnessBrowser__Btheta:350423 163 IAIKEASGNITQMDDIIKNKPDNFNVISGDDGITFPLITLGAVGVISVIGNAFPREFSRMTRLALQGDFANALTIH 238 **************************************************************************** PP TIGR00674 231 qkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285 +++++lf+ lf++ NP +vK +l+++g+ie+ +lRlPL+++ + e +++vl+e lcl|FitnessBrowser__Btheta:350423 239 HRFTELFDLLFVDGNPAGVKSMLNAMGMIEN-KLRLPLVPTRITTFEAIRKVLNE 292 *******************************.*****************999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (297 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 7.48 // [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