Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate WP_028950553.1 Q385_RS0104675 deoxyribose-phosphate aldolase
Query= BRENDA::Q877I0 (224 letters) >NCBI__GCF_000619805.1:WP_028950553.1 Length = 234 Score = 197 bits (502), Expect = 1e-55 Identities = 98/218 (44%), Positives = 152/218 (69%), Gaps = 4/218 (1%) Query: 6 IARYIDQTNLKPYATKEDIIKLCDEAIEYGFYAVCVNPYRVKLAKDYLREKNADVKVASV 65 I +YID + LKPY T +++ C +A+EY F ++C+NP+ VK+ L KN+ V V SV Sbjct: 11 INKYIDHSVLKPYITYQEVEDHCIKALEYQFASICINPFHVKICSQIL--KNSTVSVCSV 68 Query: 66 IGFPLGATPTEVKVFEAKRALEDGADELDMVINIGALKDKDYEYVKNDIAEVVKVAHERG 125 +GFPLG ++K+ EA +++EDG+ ELD+V NI A K KDY+YV+ ++ E++K + Sbjct: 69 VGFPLGLNTIDIKIKEALQSIEDGSRELDIVWNISAFKSKDYKYVEQELKEIIK--NTPN 126 Query: 126 AKVKVIIETCYLTEEEKVKACELAKEAGADFVKTSTGFGTGGATVEDVRLMRKVVGPEMG 185 KVI+ET YL++EEK A ++ AGA+++KTSTGF GA ++DV + +++ G ++ Sbjct: 127 IIHKVIVETAYLSQEEKKIALDIVINAGAEYIKTSTGFADKGADLQDVLMWKELAGKKIK 186 Query: 186 VKAAGGIRTYEQALEMIEAGANRIGTSSGVKIVEGAPD 223 +KA+GGI+ + ALE I+AG +RIGTSSG++IV+ D Sbjct: 187 IKASGGIKDLKTALEFIKAGCDRIGTSSGIEIVKEVRD 224 Lambda K H 0.315 0.134 0.372 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: 237 Number of extensions: 12 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: 224 Length of database: 234 Length adjustment: 23 Effective length of query: 201 Effective length of database: 211 Effective search space: 42411 Effective search space used: 42411 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: 42 (22.0 bits) S2: 46 (22.3 bits)
Align candidate WP_028950553.1 Q385_RS0104675 (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.1172858.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-71 226.2 2.3 1.8e-71 226.0 2.3 1.0 1 NCBI__GCF_000619805.1:WP_028950553.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000619805.1:WP_028950553.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 226.0 2.3 1.8e-71 1.8e-71 2 210 .. 11 219 .. 10 220 .. 0.99 Alignments for each domain: == domain 1 score: 226.0 bits; conditional E-value: 1.8e-71 TIGR00126 2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLkgteveictvvgFPlGasttevkll 74 ++k+iDh+ lk+ t +++e c +A +y+fa++c+np v++ ++Lk++ v++c+vvgFPlG +t+++k+ NCBI__GCF_000619805.1:WP_028950553.1 11 INKYIDHSVLKPYITYQEVEDHCIKALEYQFASICINPFHVKICSQILKNSTVSVCSVVGFPLGLNTIDIKIK 83 689********************************************************************** PP TIGR00126 75 EakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdeekkkAseisieagad 147 Ea ++ie G E+D+v ni+a+k+k+ + v++++k +++ + ++ Kvi+Eta+L +eekk A +i i+aga+ NCBI__GCF_000619805.1:WP_028950553.1 84 EALQSIEDGSRELDIVWNISAFKSKDYKYVEQELKEIIKNTPNIIHKVIVETAYLSQEEKKIALDIVINAGAE 156 ************************************************************************* PP TIGR00126 148 fvKtstgfsakgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasaavaii 210 ++Ktstgf+ kgA ++dv + k+ +g+++++KasGG+++ ++al++i+ag +rig+s +++i+ NCBI__GCF_000619805.1:WP_028950553.1 157 YIKTSTGFADKGADLQDVLMWKELAGKKIKIKASGGIKDLKTALEFIKAGCDRIGTSSGIEIV 219 ************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (234 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: 20.71 // [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