Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate WP_011317589.1 AVA_RS03685 deoxyribose-phosphate aldolase
Query= BRENDA::C7E719 (220 letters) >NCBI__GCF_000204075.1:WP_011317589.1 Length = 226 Score = 192 bits (487), Expect = 6e-54 Identities = 98/211 (46%), Positives = 145/211 (68%), Gaps = 2/211 (0%) Query: 1 MNIAALIDHTLLRADATKDEITKLTAEAKKYQFASVCVNPAWVAYAAEQLAGTGVATCTV 60 ++IA IDH LL AT +++ + +A +Y FASVC+ P +V AAE L G CTV Sbjct: 8 IDIAPFIDHALLTPTATPEQVDQWCEQADRYNFASVCLYPTYVKQAAEFLHGKKPKVCTV 67 Query: 61 IGFPLGANTSATKAFETKDAIANGATEVDMVINIGALKARDLQLVEQDIRAVVEAAAGTL 120 IGFP GA T + K +E +A+ NGATE+D+VIN+G LK+ + + V ++I + E G + Sbjct: 68 IGFPTGATTRSVKLYEALEAVENGATELDVVINLGCLKSGNTEAVHREIAEICE-ETGQV 126 Query: 121 VKVIIETSLLTDEEKVLACELSVKAGANFVKTSTGFSTGGATVEDVALMRKTVGPEIGVK 180 VKVI+ET+LLTD EK +A ++++ AGA F+KT+TG++ GGATV DV L+++ +G+K Sbjct: 127 VKVILETNLLTDAEKKIAADIAMDAGATFLKTNTGWN-GGATVADVRLLKEITRERVGIK 185 Query: 181 ASGGVRSLEDVQKLVEAGASRIGASSGVKII 211 ASGG+R+L L+ AGA+R+G S G+ +I Sbjct: 186 ASGGIRTLNQALDLILAGATRLGTSRGIDLI 216 Lambda K H 0.313 0.127 0.340 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: 153 Number of extensions: 9 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: 220 Length of database: 226 Length adjustment: 22 Effective length of query: 198 Effective length of database: 204 Effective search space: 40392 Effective search space used: 40392 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_011317589.1 AVA_RS03685 (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.8697.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-83 265.5 0.6 1.7e-83 265.2 0.6 1.0 1 lcl|NCBI__GCF_000204075.1:WP_011317589.1 AVA_RS03685 deoxyribose-phosphat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204075.1:WP_011317589.1 AVA_RS03685 deoxyribose-phosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.2 0.6 1.7e-83 1.7e-83 2 210 .. 10 216 .. 9 217 .. 0.98 Alignments for each domain: == domain 1 score: 265.2 bits; conditional E-value: 1.7e-83 TIGR00126 2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLkgteveictvvgFPlGastte 70 +a +iDh+ l++ +t+e++++ c++A +y+fa+vc++p+yv++A+e L+g++ ++ctv+gFP+Ga+t + lcl|NCBI__GCF_000204075.1:WP_011317589.1 10 IAPFIDHALLTPTATPEQVDQWCEQADRYNFASVCLYPTYVKQAAEFLHGKKPKVCTVIGFPTGATTRS 78 6899***************************************************************** PP TIGR00126 71 vkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdeekkkAse 139 vkl+Ea ea+e+GA+E+Dvvin++ lk++n+e+v ++i+ + e + + +KvilEt lLtd ekk A++ lcl|NCBI__GCF_000204075.1:WP_011317589.1 79 VKLYEALEAVENGATELDVVINLGCLKSGNTEAVHREIAEICEET-GQVVKVILETNLLTDAEKKIAAD 146 *********************************************.999******************** PP TIGR00126 140 isieagadfvKtstgfsakgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasaava 208 i+++aga f+Kt tg++ +gAtv+dvrl+k++ +++vg+KasGG+rt ++al+li aga+r+g+s+++ lcl|NCBI__GCF_000204075.1:WP_011317589.1 147 IAMDAGATFLKTNTGWN-GGATVADVRLLKEITRERVGIKASGGIRTLNQALDLILAGATRLGTSRGID 214 *****************.*************************************************98 PP TIGR00126 209 ii 210 +i lcl|NCBI__GCF_000204075.1:WP_011317589.1 215 LI 216 76 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (226 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: 00:00:00.00 # Mc/sec: 9.97 // [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