Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_084276196.1 B8779_RS08465 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::O67216 (294 letters) >NCBI__GCF_900176045.1:WP_084276196.1 Length = 295 Score = 264 bits (674), Expect = 2e-75 Identities = 136/290 (46%), Positives = 194/290 (66%), Gaps = 3/290 (1%) Query: 3 QGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFA 62 +G++ ALITPFK+G+VD E LI+ +D+ D ++ GTTGES TLT +EH+K IE A Sbjct: 5 KGAMTALITPFKDGKVDEEKYAKLIQRQIDHAIDVVVPVGTTGESATLTHDEHKKCIEIA 64 Query: 63 VKRAAGR-IKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTV 121 V+ G KV+AG G N+THEA+ L A++ GAD L V PYYNKPTQ GLY+H+K + Sbjct: 65 VEVCKGTSTKVMAGAGSNSTHEAIDLAQFAQKAGADAILSVSPYYNKPTQEGLYQHYKAL 124 Query: 122 AQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESF 181 A VDIP+++YN+P RT V+I +T+F+L E ENI KE+T +++R E++ + E + Sbjct: 125 ANAVDIPVLLYNVPGRTGVDIKPETVFRLFDEVENIYGIKEATGSIERCVELLAKRPELY 184 Query: 182 SVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFK 241 V+SGDD++ P++A G GVISV N++P ++ L+ A L G F A+ I+ L D+ K Sbjct: 185 -VISGDDTINYPIIANGGMGVISVTANLLPDKMSMLVHAGLAGQFDTAKMINDELFDINK 243 Query: 242 VLFIETNPIPVKTACWMLGMCEK-EFRLPLTEMSPENENKLREVLKKYNL 290 LFIE+NPIP+K A + G+ + E+RLPL S EN K+ L KY + Sbjct: 244 ALFIESNPIPIKAAMYHAGLLDTLEYRLPLVPPSKENMAKIENALTKYKV 293 Lambda K H 0.318 0.136 0.390 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: 244 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: 295 Length adjustment: 26 Effective length of query: 268 Effective length of database: 269 Effective search space: 72092 Effective search space used: 72092 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 WP_084276196.1 B8779_RS08465 (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.238864.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-113 362.1 0.2 8.5e-113 361.9 0.2 1.0 1 NCBI__GCF_900176045.1:WP_084276196.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900176045.1:WP_084276196.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 361.9 0.2 8.5e-113 8.5e-113 2 285 .. 7 290 .. 6 291 .. 0.98 Alignments for each domain: == domain 1 score: 361.9 bits; conditional E-value: 8.5e-113 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvkn.rvpviaG 73 +tAliTPfk+ + vd ++++kli++qi++ +d +v+vGtTGEsatL+++E+kk+ie+ave++k+ +v+aG NCBI__GCF_900176045.1:WP_084276196.1 7 AMTALITPFKDGK-VDEEKYAKLIQRQIDHAIDVVVPVGTTGESATLTHDEHKKCIEIAVEVCKGtSTKVMAG 78 689******9988.**************************************************95689**** PP TIGR00674 74 tgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvk 146 +gsn+t+eai+l+++a+k+g+d++l+v+PyYnkPtqeGly+h+ka+a++v++P++lYnvP+Rtgv+++petv+ NCBI__GCF_900176045.1:WP_084276196.1 79 AGSNSTHEAIDLAQFAQKAGADAILSVSPYYNKPTQEGLYQHYKALANAVDIPVLLYNVPGRTGVDIKPETVF 151 ************************************************************************* PP TIGR00674 147 rLaeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaa 218 rL++eve i +iKea+g++er++e+ a+ + +++v sGdD+++ +i+a G+ GviSV++n++p++++ +v+a NCBI__GCF_900176045.1:WP_084276196.1 152 RLFDEVEnIYGIKEATGSIERCVELLAKRP-ELYVISGDDTINYPIIANGGMGVISVTANLLPDKMSMLVHAG 223 *****999*******************998.9***************************************** PP TIGR00674 219 legdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285 l+g+++ a+ i+ +l+++ kalfie+NPip+K+a++ +gl + e+RlPL++ s+e+ k++++l++ NCBI__GCF_900176045.1:WP_084276196.1 224 LAGQFDTAKMINDELFDINKALFIESNPIPIKAAMYHAGLLDTLEYRLPLVPPSKENMAKIENALTK 290 ***************************************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (295 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.62 // [ok]
This GapMind analysis is from Jul 25 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