Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate WP_086510574.1 BZY95_RS14235 deoxyribose-phosphate aldolase
Query= BRENDA::P0A6L0 (259 letters) >NCBI__GCF_002151265.1:WP_086510574.1 Length = 257 Score = 282 bits (721), Expect = 6e-81 Identities = 146/258 (56%), Positives = 192/258 (74%), Gaps = 5/258 (1%) Query: 1 MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTL 60 MT+L+ ++ +AL LMDLT+LN+DD D + LC +A TP G+ AA+C+YP F+ AR+ L Sbjct: 1 MTELQQAARQALALMDLTSLNNDDNDTVIRELCARANTPAGHPAAVCVYPAFVSTARQAL 60 Query: 61 KEQGTP-EIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGF 119 EQG ++++ATVTNFPHG D++ A AETRAAIA GADEVDVVFPYRALMAG+ +VG Sbjct: 61 AEQGLAGKVKVATVTNFPHGEADVERAAAETRAAIAAGADEVDVVFPYRALMAGDAEVGR 120 Query: 120 DLVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATP 179 +LV+ACK C A +LKVI+ETGELK+ LI +A ++I GADF+KTSTGKVAVNAT Sbjct: 121 ELVEACKRECGDA--VLKVILETGELKEAGLIDRAGMLAIDGGADFLKTSTGKVAVNATL 178 Query: 180 ESARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASS 239 ++A+I++ I+ G + VGFK AGGVRTAEDA YL +A+ + GA+W H+RFGAS Sbjct: 179 DAAKILLTAIKASG--RDVGFKAAGGVRTAEDAAAYLQLAERVMGAEWITPAHFRFGASG 236 Query: 240 LLASLLKALGHGDGKSAS 257 LL SLL+ LG K ++ Sbjct: 237 LLGSLLETLGVEQDKGST 254 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: 205 Number of extensions: 8 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: 257 Length adjustment: 24 Effective length of query: 235 Effective length of database: 233 Effective search space: 54755 Effective search space used: 54755 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 WP_086510574.1 BZY95_RS14235 (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.19519.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-68 215.6 4.3 3.3e-68 215.3 4.3 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510574.1 BZY95_RS14235 deoxyribose-phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510574.1 BZY95_RS14235 deoxyribose-phosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 215.3 4.3 3.3e-68 3.3e-68 2 205 .. 11 224 .. 10 229 .. 0.95 Alignments for each domain: == domain 1 score: 215.3 bits; conditional E-value: 3.3e-68 TIGR00126 2 lakliDhtalkadtteedietlcaeAkky..kfaavcvnpsyvslAkelLk....gteveictvvgFPl 64 ++ l+D+t l++d+++ i +lca A ++ + aavcv+p++vs A++ L+ +v+++tv++FP+ lcl|NCBI__GCF_002151265.1:WP_086510574.1 11 ALALMDLTSLNNDDNDTVIRELCARANTPagHPAAVCVYPAFVSTARQALAeqglAGKVKVATVTNFPH 79 6789*************************88889****************97744349*********** PP TIGR00126 65 GasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdee 133 G+ + e +++E+++ai++GAdEvDvv++++al++++ ev+ e ++a++ c+++ lKvilEt++L++ lcl|NCBI__GCF_002151265.1:WP_086510574.1 80 GEADVERAAAETRAAIAAGADEVDVVFPYRALMAGDAEVGRELVEACKRECGDAVLKVILETGELKEAG 148 ********************************************************************9 PP TIGR00126 134 kk.kAseisieagadfvKtstgfsakgAtvedvrlmkkvvgd...evgvKasGGvrtaedalalieaga 198 ++ +A ++i++gadf+Ktstg++a++At++ ++++ +++ +vg+Ka+GGvrtaeda a+++ ++ lcl|NCBI__GCF_002151265.1:WP_086510574.1 149 LIdRAGMLAIDGGADFLKTSTGKVAVNATLDAAKILLTAIKAsgrDVGFKAAGGVRTAEDAAAYLQLAE 217 9989*******************************9988876677************************ PP TIGR00126 199 erigasa 205 +ga++ lcl|NCBI__GCF_002151265.1:WP_086510574.1 218 RVMGAEW 224 ****998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (257 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: 10.95 // [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