Align Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 (characterized)
to candidate WP_007498018.1 BA79_RS10050 deoxyribose-phosphate aldolase
Query= SwissProt::P39121 (223 letters) >NCBI__GCF_000691145.1:WP_007498018.1 Length = 223 Score = 352 bits (903), Expect = e-102 Identities = 179/223 (80%), Positives = 196/223 (87%) Query: 1 MSLANIIDHTALKPHTQKADILKLIEEAKTYKFASVCVNPTWVELAAKELKGTGVDVCTV 60 M++A +IDHTALKP T KA I++L+EEAKTY+FASVCVNPTWV LAAKEL+GTGVDVCTV Sbjct: 1 MTIAKLIDHTALKPDTSKAAIMQLLEEAKTYQFASVCVNPTWVSLAAKELEGTGVDVCTV 60 Query: 61 IGFPLGANTTETKAFETKDAISKGATEVDMVINIAALKDKEDDVVEADIRGVVEAVAGKA 120 IGFPLGANTT KAFETKDAI GATEVDMVINIAALKD E D VE DIR VV+A GKA Sbjct: 61 IGFPLGANTTAVKAFETKDAIENGATEVDMVINIAALKDGEYDAVEQDIRAVVDAAKGKA 120 Query: 121 LVKVIIETCLLTDEEKERACRLAVSAGADFVKTSTGFSTGGATKEDIALMRKTVGPDIGV 180 LVKVIIETCLLTDEEK RAC L+V AGADFVKTSTGFSTGGAT EDIALMRKTVGPDIGV Sbjct: 121 LVKVIIETCLLTDEEKVRACELSVKAGADFVKTSTGFSTGGATAEDIALMRKTVGPDIGV 180 Query: 181 KASGGVRTKEDVDTMVEAGASRIGASAGVSIVKGENASGGDNY 223 KASGGVRTKEDV+ M AGA+RIGASAGVSI+KG+ ++ +Y Sbjct: 181 KASGGVRTKEDVEAMTAAGATRIGASAGVSIIKGDQSAPSKDY 223 Lambda K H 0.312 0.130 0.356 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: 269 Number of extensions: 7 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: 223 Length of database: 223 Length adjustment: 22 Effective length of query: 201 Effective length of database: 201 Effective search space: 40401 Effective search space used: 40401 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: 46 (22.3 bits)
Align candidate WP_007498018.1 BA79_RS10050 (deoxyribose-phosphate aldolase)
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.1975504.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-100 319.5 12.7 4.7e-100 319.3 12.7 1.0 1 NCBI__GCF_000691145.1:WP_007498018.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000691145.1:WP_007498018.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 319.3 12.7 4.7e-100 4.7e-100 2 210 .. 3 212 .. 2 213 .. 0.99 Alignments for each domain: == domain 1 score: 319.3 bits; conditional E-value: 4.7e-100 TIGR00126 2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLkgteveictvvgFPlGasttevkll 74 +akliDhtalk+dt +++i +l +eAk+y+fa+vcvnp++vslA+++L+gt v++ctv+gFPlGa+tt vk++ NCBI__GCF_000691145.1:WP_007498018.1 3 IAKLIDHTALKPDTSKAAIMQLLEEAKTYQFASVCVNPTWVSLAAKELEGTGVDVCTVIGFPLGANTTAVKAF 75 689********************************************************************** PP TIGR00126 75 EakeaieeGAdEvDvviniaalkdkneevviedikavveaca.kvllKvilEtalLtdeekkkAseisieaga 146 E+k+aie+GA+EvD+viniaalkd++ ++v++di+avv+a+ k+l+Kvi+Et+lLtdeek++A+e+s++aga NCBI__GCF_000691145.1:WP_007498018.1 76 ETKDAIENGATEVDMVINIAALKDGEYDAVEQDIRAVVDAAKgKALVKVIIETCLLTDEEKVRACELSVKAGA 148 *****************************************989***************************** PP TIGR00126 147 dfvKtstgfsakgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasaavaii 210 dfvKtstgfs++gAt ed++lm+k+vg+++gvKasGGvrt+ed+ a+ +aga+rigasa+v ii NCBI__GCF_000691145.1:WP_007498018.1 149 DFVKTSTGFSTGGATAEDIALMRKTVGPDIGVKASGGVRTKEDVEAMTAAGATRIGASAGVSII 212 *************************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (223 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: 10.43 // [ok]
This GapMind analysis is from Sep 24 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