Align Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 (characterized)
to candidate 353951 BT4425 deoxyribose-phosphate aldolase (NCBI ptt file)
Query= SwissProt::P39121 (223 letters) >FitnessBrowser__Btheta:353951 Length = 238 Score = 224 bits (570), Expect = 1e-63 Identities = 115/212 (54%), Positives = 148/212 (69%), Gaps = 1/212 (0%) Query: 3 LANIIDHTALKPHTQKADILKLIEEAKTYKFASVCVNPTWVELAAKELKGTGVDVCTVIG 62 LA +IDHT LKP +I KL EA+ Y+FA V +NP VE K L+G+GV V IG Sbjct: 18 LAGMIDHTFLKPFGTAENIEKLCAEARQYQFAMVAINPAEVETCVKLLEGSGVRVGAAIG 77 Query: 63 FPLGANTTETKAFETKDAISKGATEVDMVINIAALKDKEDDVVEADIRGVVEAVAGKALV 122 FPLG NT E KAFET+DAI+KGATE+D VIN+ AL+ + D+V+ +I +V ++ Sbjct: 78 FPLGQNTVECKAFETRDAIAKGATEIDTVINVRALQKGQTDIVKKEIEDMVSICKPAGVI 137 Query: 123 -KVIIETCLLTDEEKERACRLAVSAGADFVKTSTGFSTGGATKEDIALMRKTVGPDIGVK 181 KVI+ETC LTDEEKE CR+A AG DFVKTSTGF T GA D+ALMR+ VGP IGVK Sbjct: 138 CKVILETCYLTDEEKETVCRIAKEAGVDFVKTSTGFGTAGANVHDVALMRRVVGPVIGVK 197 Query: 182 ASGGVRTKEDVDTMVEAGASRIGASAGVSIVK 213 A+GG+R + +++ GA+RIG S+G+ IV+ Sbjct: 198 AAGGIRDLDTALALIQVGATRIGTSSGIQIVE 229 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: 215 Number of extensions: 8 Number of successful extensions: 2 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: 238 Length adjustment: 23 Effective length of query: 200 Effective length of database: 215 Effective search space: 43000 Effective search space used: 43000 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 353951 BT4425 (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.2635.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-82 260.8 7.5 4.6e-82 260.6 7.5 1.0 1 lcl|FitnessBrowser__Btheta:353951 BT4425 deoxyribose-phosphate ald Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:353951 BT4425 deoxyribose-phosphate aldolase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.6 7.5 4.6e-82 4.6e-82 2 210 .. 18 228 .. 17 229 .. 0.99 Alignments for each domain: == domain 1 score: 260.6 bits; conditional E-value: 4.6e-82 TIGR00126 2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLkgteveictvvgFPlGasttevkllEak 77 la +iDht lk+ t e+ie+lcaeA +y+fa v +np+ v+ ++lL+g+ v++ + +gFPlG++t e k++E++ lcl|FitnessBrowser__Btheta:353951 18 LAGMIDHTFLKPFGTAENIEKLCAEARQYQFAMVAINPAEVETCVKLLEGSGVRVGAAIGFPLGQNTVECKAFETR 93 7899************************************************************************ PP TIGR00126 78 eaieeGAdEvDvviniaalkdkneevviedikavveaca..kvllKvilEtalLtdeekkkAseisieagadfvKt 151 +ai++GA+E+D vin++al+++++++v+++i+ +v +c +v KvilEt++Ltdeek++ ++i++eag+dfvKt lcl|FitnessBrowser__Btheta:353951 94 DAIAKGATEIDTVINVRALQKGQTDIVKKEIEDMVSICKpaGVICKVILETCYLTDEEKETVCRIAKEAGVDFVKT 169 **************************************8889********************************** PP TIGR00126 152 stgfsakgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasaavaii 210 stgf+++gA v dv+lm++vvg+ +gvKa+GG+r+ ++alali++ga+rig+s +++i+ lcl|FitnessBrowser__Btheta:353951 170 STGFGTAGANVHDVALMRRVVGPVIGVKAAGGIRDLDTALALIQVGATRIGTSSGIQIV 228 ********************************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (238 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 5.83 // [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