Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate BWI76_RS04130 BWI76_RS04130 2-deoxyribose-5-phosphate aldolase
Query= BRENDA::Q7WT44 (259 letters) >FitnessBrowser__Koxy:BWI76_RS04130 Length = 259 Score = 494 bits (1272), Expect = e-145 Identities = 251/259 (96%), Positives = 258/259 (99%) Query: 1 MTDLSASSLRALKLMDLTTLNDDDTNEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTL 60 MTDL+ASSLRALKLMDLTTLNDDDTNEKVIALCHQAKTPVGNTAA+CIYPRFIPIARKTL Sbjct: 1 MTDLTASSLRALKLMDLTTLNDDDTNEKVIALCHQAKTPVGNTAAVCIYPRFIPIARKTL 60 Query: 61 NAQGTPDIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALIAGNEQVGFD 120 N QGTPDIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALIAGNEQVGFD Sbjct: 61 NEQGTPDIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALIAGNEQVGFD 120 Query: 121 LVKACKEACAAANVLLKVIIETGELKEEALIRKASEISIKAGADFIKTSTGKVPVNATPE 180 LVKACKEACAAANVLLKVIIETGELKE+ALIRKASEI+IKAGADFIKTSTGKVPVNATPE Sbjct: 121 LVKACKEACAAANVLLKVIIETGELKEDALIRKASEIAIKAGADFIKTSTGKVPVNATPE 180 Query: 181 SARIMLEVIRDMGVQKTVGFKPAGGVRSAEDAQQFLAIADELFGADWADSRHYRFGASSL 240 SARIMLEVIRDMGVQ++VGFKPAGGVRSAEDAQ+FLAIADELFGADWADSRHYRFGASSL Sbjct: 181 SARIMLEVIRDMGVQQSVGFKPAGGVRSAEDAQKFLAIADELFGADWADSRHYRFGASSL 240 Query: 241 LASLLKALGHGDGKSASSY 259 LASLLKALGHGDGKSASSY Sbjct: 241 LASLLKALGHGDGKSASSY 259 Lambda K H 0.318 0.133 0.374 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: 328 Number of extensions: 4 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: 259 Length of database: 259 Length adjustment: 24 Effective length of query: 235 Effective length of database: 235 Effective search space: 55225 Effective search space used: 55225 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 BWI76_RS04130 BWI76_RS04130 (2-deoxyribose-5-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.15255.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-88 281.6 1.3 2e-88 281.4 1.3 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS04130 BWI76_RS04130 2-deoxyribose-5-ph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS04130 BWI76_RS04130 2-deoxyribose-5-phosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 281.4 1.3 2e-88 2e-88 2 210 .. 11 232 .. 10 233 .. 0.98 Alignments for each domain: == domain 1 score: 281.4 bits; conditional E-value: 2e-88 TIGR00126 2 lakliDhtalkadtteedietlcaeAkky..kfaavcvnpsyvslAkelLk..gt.eveictvvgFPlGas 67 ++kl+D+t+l++d+t+e++++lc++Ak++ ++aavc++p+++++A+++L+ gt +++i+tv++FP+G++ lcl|FitnessBrowser__Koxy:BWI76_RS04130 11 ALKLMDLTTLNDDDTNEKVIALCHQAKTPvgNTAAVCIYPRFIPIARKTLNeqGTpDIRIATVTNFPHGND 81 689**************************99*******************988999*************** PP TIGR00126 68 ttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveaca..kvllKvilEtalLtdeekk. 135 +++++l+E+++ai++GAdEvDvv++++al ++ne+v+++ +ka++eaca +vllKvi+Et++L++++++ lcl|FitnessBrowser__Koxy:BWI76_RS04130 82 DIDIALAETRAAIAYGADEVDVVFPYRALIAGNEQVGFDLVKACKEACAaaNVLLKVIIETGELKEDALIr 152 ************************************************999*****************988 PP TIGR00126 136 kAseisieagadfvKtstgfsakgAtvedvrlmkkvvgd.....evgvKasGGvrtaedalalieagaeri 201 kAsei+i+agadf+Ktstg++ ++At+e++r+m +v++d +vg+K++GGvr aeda++++++++e++ lcl|FitnessBrowser__Koxy:BWI76_RS04130 153 KASEIAIKAGADFIKTSTGKVPVNATPESARIMLEVIRDmgvqqSVGFKPAGGVRSAEDAQKFLAIADELF 223 **************************************9999999************************** PP TIGR00126 202 gasaavaii 210 ga++a+ ++ lcl|FitnessBrowser__Koxy:BWI76_RS04130 224 GADWADSRH 232 *****9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (259 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: 7.02 // [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