Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate 352790 BT3263 putative deoxyribose-phosphate aldolase (NCBI ptt file)
Query= BRENDA::P0A6L0 (259 letters) >lcl|FitnessBrowser__Btheta:352790 BT3263 putative deoxyribose-phosphate aldolase (NCBI ptt file) Length = 300 Score = 166 bits (420), Expect = 5e-46 Identities = 100/240 (41%), Positives = 138/240 (57%), Gaps = 14/240 (5%) Query: 15 MDLTTLNDDDTDEKVIALCHQAKT------PVGNTAAICIYPRFIPIARKTLKEQGTPEI 68 +DLTTLN D+DE V+ + + N AAIC+YP F I + TL+ G I Sbjct: 55 IDLTTLNSTDSDESVMHFTEKVNEFDNEFPDMKNVAAICVYPNFADIVKNTLQVDG---I 111 Query: 69 RIATVTN-FPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLVKACKE 127 IA V+ FP I++ +AET AIA GADE+D+V ++G+ + + ++ KE Sbjct: 112 NIACVSGGFPSSQTFIEVKVAETALAIADGADEIDIVISIGKFLSGDYETMCEEIQELKE 171 Query: 128 ACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESARIMME 187 C + LKVI+ETG LK + I+KAS +S+ +GADFIKTSTGK ATPE+A +M E Sbjct: 172 VCKERH--LKVILETGALKTASNIKKASILSMYSGADFIKTSTGKQQPAATPEAAYVMCE 229 Query: 188 VIRD--MGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLASLL 245 I++ +GFKPAGG+ T DA Y I E+ G +W + R +R G S L LL Sbjct: 230 AIKEYYQKTNNKIGFKPAGGINTVHDAIIYYTIVKEILGEEWLNNRLFRLGTSRLANLLL 289 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: 183 Number of extensions: 11 Number of successful extensions: 4 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: 300 Length adjustment: 26 Effective length of query: 233 Effective length of database: 274 Effective search space: 63842 Effective search space used: 63842 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 352790 BT3263 (putative 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.5570.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-53 168.0 1.8 1.4e-53 167.5 1.8 1.2 1 lcl|FitnessBrowser__Btheta:352790 BT3263 putative deoxyribose-phos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:352790 BT3263 putative deoxyribose-phosphate aldolase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 167.5 1.8 1.4e-53 1.4e-53 4 205 .. 53 271 .. 50 276 .. 0.94 Alignments for each domain: == domain 1 score: 167.5 bits; conditional E-value: 1.4e-53 TIGR00126 4 kliDhtalkadtteedietlcaeAkky........kfaavcvnpsyvslAkelLkgteveictvv.gFPlGastte 70 + iD+t+l++ + +e + + ++ ++ ++aa+cv+p++ ++ k++L+ ++i++v gFP+ ++ +e lcl|FitnessBrowser__Btheta:352790 53 NCIDLTTLNSTDSDESVMHFTEKVNEFdnefpdmkNVAAICVYPNFADIVKNTLQVDGINIACVSgGFPSSQTFIE 128 78****************9999988776667777789***************************846********* PP TIGR00126 71 vkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtd.eekkkAseisieag 145 vk++E+ ai+ GAdE+D+vi i+++ +++ e+ e+i+ ++e+c +++lKvilEt+ L+ +++kkAs +s+ +g lcl|FitnessBrowser__Btheta:352790 129 VKVAETALAIADGADEIDIVISIGKFLSGDYETMCEEIQELKEVCKERHLKVILETGALKTaSNIKKASILSMYSG 204 **********************************************************97626777********** PP TIGR00126 146 adfvKtstgfsakgAtvedvrlmkkvvgd.......evgvKasGGvrtaedalalieagaerigasa 205 adf+Ktstg+++ At+e + +m +++++ ++g+K++GG+ t+ da+ + + e +g ++ lcl|FitnessBrowser__Btheta:352790 205 ADFIKTSTGKQQPAATPEAAYVMCEAIKEyyqktnnKIGFKPAGGINTVHDAIIYYTIVKEILGEEW 271 ****************************99999999**********************999999877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (300 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: 00:00:00.01 # Mc/sec: 6.32 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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