Align dihydrodipicolinate synthase subunit (EC 4.3.3.7) (characterized)
to candidate Synpcc7942_1847 Synpcc7942_1847 dihydrodipicolinate synthase
Query= metacyc::MONOMER-6565 (289 letters) >FitnessBrowser__SynE:Synpcc7942_1847 Length = 299 Score = 287 bits (734), Expect = 2e-82 Identities = 144/289 (49%), Positives = 201/289 (69%), Gaps = 3/289 (1%) Query: 3 FGNIATAMVTPFDKNENIDFQKLSKLIDYLLNNGTDSLVVAGTTGESPTLSEEEKVALIQ 62 FG + TAM+TPF+ + + L +L+ G+D LV+ GTTGESPTL+ EE++ L + Sbjct: 7 FGRVITAMITPFNAEGQVAYDIAQSLAVHLVEQGSDGLVICGTTGESPTLTWEEELQLFR 66 Query: 63 YSVKEAAG-RAPIIAGTGSNNTKASIKLTKKAEEAGADAVMLVTPYYNKPSQEGMYRHFR 121 +VKEA G RA +IAGTGSN T+ +I T+ A G + + V PYYNKP QEG+Y HFR Sbjct: 67 -AVKEAVGDRAAVIAGTGSNCTREAIAATQSAATLGLNGSLQVVPYYNKPPQEGLYAHFR 125 Query: 122 AIAEET-SLPVMLYNVPGRTAASLAPETTIRLAEIPNIIAIKEASGDLDAITKIVAETPE 180 AIAE LP+MLYN+PGRT SL PET RLA +PN++AIK ASG+++ ++ + P+ Sbjct: 126 AIAEACPDLPLMLYNIPGRTGQSLQPETVARLASLPNVVAIKAASGNVEEVSALRQLLPD 185 Query: 181 DFAVYSGDDSLTLPALSVGARGIVSVASHIIGPEMQEMIKHYTEGNTAQAALIHQKLLPL 240 FA+YSGDDSLTLP L+VGA+G+VSVASH++GP++Q +I+ + GN A+A +H +L PL Sbjct: 186 SFAIYSGDDSLTLPMLAVGAQGVVSVASHLVGPQLQALIQAFEAGNVARAQQLHHQLYPL 245 Query: 241 MKGLFAAPNPSPLKTALQLKGLDVGSVRLPLIPLNEDERLRLSSLMNGL 289 K LF NP P++ A++L G +G RLPL+P + + R L+S + L Sbjct: 246 FKALFLTTNPIPVRAAMELLGWSIGLPRLPLVPASAEIRQALASCLTEL 294 Lambda K H 0.313 0.131 0.357 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: 3 Number of successful extensions: 2 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: 289 Length of database: 299 Length adjustment: 26 Effective length of query: 263 Effective length of database: 273 Effective search space: 71799 Effective search space used: 71799 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 bits)
Align candidate Synpcc7942_1847 Synpcc7942_1847 (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.20206.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-111 355.1 0.0 1.1e-110 355.0 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1847 Synpcc7942_1847 dihydrodipicolin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1847 Synpcc7942_1847 dihydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 355.0 0.0 1.1e-110 1.1e-110 2 285 .. 10 293 .. 9 294 .. 0.99 Alignments for each domain: == domain 1 score: 355.0 bits; conditional E-value: 1.1e-110 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 v+tA+iTPf+++g+v ++ ++l +++e+g+d++v++GtTGEs+tL++eE+ ++++ + e v +r v lcl|FitnessBrowser__SynE:Synpcc7942_1847 10 VITAMITPFNAEGQVAYDIAQSLAVHLVEQGSDGLVICGTTGESPTLTWEEELQLFRAVKEAVGDRAAV 78 89******************************************************************* PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeev.elPiilYnvPsRtgv 138 iaGtgsn+t+eai t+ a+ lg +g l+v+PyYnkP qeGly+hf aiae++ +lP++lYn+P+Rtg+ lcl|FitnessBrowser__SynE:Synpcc7942_1847 79 IAGTGSNCTREAIAATQSAATLGLNGSLQVVPYYNKPPQEGLYAHFRAIAEACpDLPLMLYNIPGRTGQ 147 ***************************************************999*************** PP TIGR00674 139 slepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnva 207 sl+petv+rLa+ +++vaiK asg++e+vs +++ +++f+++sGdD+ltl++la+Ga+Gv+SVas+++ lcl|FitnessBrowser__SynE:Synpcc7942_1847 148 SLQPETVARLASLPNVVAIKAASGNVEEVSALRQLLPDSFAIYSGDDSLTLPMLAVGAQGVVSVASHLV 216 ********************************************************************* PP TIGR00674 208 pkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekk 276 + +l+ +++a+ +g++++a+++h++l +lfkalf++tNPipv++a++llg+ + RlPL+++s e + lcl|FitnessBrowser__SynE:Synpcc7942_1847 217 GPQLQALIQAFEAGNVARAQQLHHQLYPLFKALFLTTNPIPVRAAMELLGWSIG-LPRLPLVPASAEIR 284 ******************************************************.9************* PP TIGR00674 277 eklkevlke 285 + l++ l+e lcl|FitnessBrowser__SynE:Synpcc7942_1847 285 QALASCLTE 293 ***999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (299 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: 00:00:00.01 # Mc/sec: 7.47 // [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