Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate 200395 SO1217 deoxyribose-phosphate aldolase (NCBI ptt file)
Query= BRENDA::P0A6L0 (259 letters) >FitnessBrowser__MR1:200395 Length = 256 Score = 342 bits (876), Expect = 6e-99 Identities = 178/252 (70%), Positives = 204/252 (80%), Gaps = 4/252 (1%) Query: 1 MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTL 60 MTDLK ++ RA++LMDLTTLNDDDTD+KVI LCH+A TP GNTAAICIYPRFIPIARKTL Sbjct: 1 MTDLKKAAQRAIELMDLTTLNDDDTDQKVIDLCHKAVTPAGNTAAICIYPRFIPIARKTL 60 Query: 61 KEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFD 120 E G +I+IATVTNFPHGNDDI IA+ ETRAA+AYGADEVDVVFPYRALM GNE VG++ Sbjct: 61 DELGAEDIQIATVTNFPHGNDDIAIAVLETRAAVAYGADEVDVVFPYRALMEGNETVGYE 120 Query: 121 LVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPE 180 LVKACKEAC VLLKVIIE+G L D LIR+ASE+SI+AGADFIKTSTGKV VNAT E Sbjct: 121 LVKACKEAC--GEVLLKVIIESGVLADPVLIRRASELSIEAGADFIKTSTGKVPVNATLE 178 Query: 181 SARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSL 240 +A IM+ VI + + VGFKPAGGVR A A ++L +A+ + GADW R +RFGASSL Sbjct: 179 AAEIMLTVISEKNTK--VGFKPAGGVRDAAQAAEFLGVAERILGADWVSPRTFRFGASSL 236 Query: 241 LASLLKALGHGD 252 L SLL L D Sbjct: 237 LNSLLHTLELAD 248 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: 224 Number of extensions: 6 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: 256 Length adjustment: 24 Effective length of query: 235 Effective length of database: 232 Effective search space: 54520 Effective search space used: 54520 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 200395 SO1217 (deoxyribose-phosphate aldolase (NCBI ptt file))
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.22757.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-78 246.9 1.8 8.6e-78 246.6 1.8 1.0 1 lcl|FitnessBrowser__MR1:200395 SO1217 deoxyribose-phosphate ald Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200395 SO1217 deoxyribose-phosphate aldolase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 246.6 1.8 8.6e-78 8.6e-78 2 206 .. 11 224 .. 10 228 .. 0.97 Alignments for each domain: == domain 1 score: 246.6 bits; conditional E-value: 8.6e-78 TIGR00126 2 lakliDhtalkadtteedietlcaeAkky..kfaavcvnpsyvslAkelLk..gt.eveictvvgFPlGasttevkllE 75 + +l+D+t+l++d+t+++++ lc++A+++ ++aa+c++p+++++A+++L g +++i+tv++FP+G++++ +++lE lcl|FitnessBrowser__MR1:200395 11 AIELMDLTTLNDDDTDQKVIDLCHKAVTPagNTAAICIYPRFIPIARKTLDelGAeDIQIATVTNFPHGNDDIAIAVLE 89 5689*************************99*******************988555*********************** PP TIGR00126 76 akeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdeekk.kAseisieagadfvKtst 153 +++a+++GAdEvDvv++++al+++ne v++e +ka++eac++vllKvi+E + L d ++ +Ase+sieagadf+Ktst lcl|FitnessBrowser__MR1:200395 90 TRAAVAYGADEVDVVFPYRALMEGNETVGYELVKACKEACGEVLLKVIIESGVLADPVLIrRASELSIEAGADFIKTST 168 ********************************************************998879***************** PP TIGR00126 154 gfsakgAtvedvrlmkkvvgd...evgvKasGGvrtaedalalieagaerigasaa 206 g++ ++At+e +++m v+ + +vg+K++GGvr+a +a +++ +++ +ga++ lcl|FitnessBrowser__MR1:200395 169 GKVPVNATLEAAEIMLTVISEkntKVGFKPAGGVRDAAQAAEFLGVAERILGADWV 224 *******************988889****************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (256 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.26 // [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