Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate 5210372 Shew_2815 deoxyribose-phosphate aldolase (RefSeq)
Query= BRENDA::P0A6L0 (259 letters) >FitnessBrowser__PV4:5210372 Length = 257 Score = 343 bits (881), Expect = 2e-99 Identities = 179/248 (72%), Positives = 206/248 (83%), Gaps = 3/248 (1%) Query: 1 MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTL 60 M+DLK ++ +A++LMDLTTLNDDDTD+KVI LCH+AKTP GNTAAICIYPRFIPIARKTL Sbjct: 1 MSDLKKAAQKAIELMDLTTLNDDDTDQKVIELCHKAKTPAGNTAAICIYPRFIPIARKTL 60 Query: 61 KEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFD 120 E G EI+IATVTNFPHGNDDI IA+ ETRAA+AYGADEVDVVFPYRALM GNE VG++ Sbjct: 61 NEMGCEEIKIATVTNFPHGNDDIAIAVLETRAAVAYGADEVDVVFPYRALMEGNETVGYE 120 Query: 121 LVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPE 180 LVKACKEAC +VLLKVIIE+G L+D ALIRKASE+SI AGADFIKTSTGKV VNAT E Sbjct: 121 LVKACKEAC-GDDVLLKVIIESGVLQDPALIRKASELSIDAGADFIKTSTGKVEVNATLE 179 Query: 181 SARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSL 240 +A IMM VI + + VGFKPAGGVR A A+++L +A+ L G WA R +RFGASSL Sbjct: 180 AAEIMMTVIAEKNPK--VGFKPAGGVRDAAAAEEFLGVAERLLGKGWATPRTFRFGASSL 237 Query: 241 LASLLKAL 248 L +LL L Sbjct: 238 LNNLLHTL 245 Lambda K H 0.317 0.133 0.373 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: 242 Number of extensions: 5 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: 259 Length of database: 257 Length adjustment: 24 Effective length of query: 235 Effective length of database: 233 Effective search space: 54755 Effective search space used: 54755 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: 47 (22.7 bits)
Align candidate 5210372 Shew_2815 (deoxyribose-phosphate aldolase (RefSeq))
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))
# 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.carbon/TIGR00126.hmm # target sequence database: /tmp/gapView.17055.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00126 [M=211] Accession: TIGR00126 Description: deoC: deoxyribose-phosphate aldolase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-79 249.9 2.8 1.1e-78 249.6 2.8 1.0 1 lcl|FitnessBrowser__PV4:5210372 Shew_2815 deoxyribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5210372 Shew_2815 deoxyribose-phosphate aldolase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.6 2.8 1.1e-78 1.1e-78 3 207 .. 12 226 .. 10 229 .. 0.97 Alignments for each domain: == domain 1 score: 249.6 bits; conditional E-value: 1.1e-78 TIGR00126 3 akliDhtalkadtteedietlcaeAkky..kfaavcvnpsyvslAkelLk..gt.eveictvvgFPlGasttevkllE 75 +l+D+t+l++d+t++++++lc++Ak++ ++aa+c++p+++++A+++L+ g e++i+tv++FP+G++++ +++lE lcl|FitnessBrowser__PV4:5210372 12 IELMDLTTLNDDDTDQKVIELCHKAKTPagNTAAICIYPRFIPIARKTLNemGCeEIKIATVTNFPHGNDDIAIAVLE 89 689*************************99*******************988556*********************** PP TIGR00126 76 akeaieeGAdEvDvviniaalkdkneevviedikavveaca.kvllKvilEtalLtdeekk.kAseisieagadfvKt 151 +++a+++GAdEvDvv++++al+++ne v++e +ka++eac+ +vllKvi+E + L+d +++ kAse+si+agadf+Kt lcl|FitnessBrowser__PV4:5210372 90 TRAAVAYGADEVDVVFPYRALMEGNETVGYELVKACKEACGdDVLLKVIIESGVLQDPALIrKASELSIDAGADFIKT 167 *****************************************99****************988**************** PP TIGR00126 152 stgfsakgAtvedvrlmkkvvgd...evgvKasGGvrtaedalalieagaerigasaav 207 stg++ ++At+e +++m+ v+++ +vg+K++GGvr+a a +++ +++ ++g +a lcl|FitnessBrowser__PV4:5210372 168 STGKVEVNATLEAAEIMMTVIAEknpKVGFKPAGGVRDAAAAEEFLGVAERLLGKGWAT 226 *********************998889***************************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (257 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: 00:00:00.00 # Mc/sec: 7.81 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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