Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate WP_110752346.1 C7477_RS11865 deoxyribose-phosphate aldolase
Query= BRENDA::P0A6L0 (259 letters) >NCBI__GCF_003217235.1:WP_110752346.1 Length = 256 Score = 238 bits (608), Expect = 7e-68 Identities = 130/256 (50%), Positives = 168/256 (65%), Gaps = 6/256 (2%) Query: 3 DLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTLKE 62 D ++ +LR L L+DLT L+D+ T + V L +A TP G+TAAICI+PRFI A+ L Sbjct: 5 DRRSLALRVLSLIDLTDLDDNSTAQGVAELSARAITPHGHTAAICIWPRFIETAKALLHG 64 Query: 63 QGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLV 122 G +R+ATV NFPHG DID LAETR AI+ GADE+D+V PYR A + ++ Sbjct: 65 TG---VRVATVVNFPHGGTDIDGVLAETRRAISDGADEIDLVLPYRDFAANGAALSRQMI 121 Query: 123 KACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESA 182 + K+ C V LKVI+ETG+L DEA I ASE++++ GADFIKTSTGKV +NATP + Sbjct: 122 GSVKKLCGR-KVKLKVILETGKLADEAAIESASEVALEEGADFIKTSTGKVEINATPAAL 180 Query: 183 RIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLA 242 RIM+E IR+ G G KPAGG+RT +DA +YL AD + G W +RFGAS LL Sbjct: 181 RIMLEAIRESG--SAAGVKPAGGIRTLDDAAQYLDFADAIMGEGWVKPETFRFGASKLLD 238 Query: 243 SLLKALGHGDGKSASS 258 +L LG G +ASS Sbjct: 239 DVLGQLGSGASSTASS 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: 211 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: 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 WP_110752346.1 C7477_RS11865 (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.3437139.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-66 208.1 0.2 6.8e-66 207.7 0.2 1.0 1 NCBI__GCF_003217235.1:WP_110752346.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003217235.1:WP_110752346.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 207.7 0.2 6.8e-66 6.8e-66 2 204 .. 13 222 .. 12 226 .. 0.97 Alignments for each domain: == domain 1 score: 207.7 bits; conditional E-value: 6.8e-66 TIGR00126 2 lakliDhtalkadtteedietlcaeAkky..kfaavcvnpsyvslAkelLkgteveictvvgFPlGasttevk 72 +++liD+t l++++t + +++l a A+++ ++aa+c+ p++++ Ak lL+gt v+++tvv+FP+G ++++ NCBI__GCF_003217235.1:WP_110752346.1 13 VLSLIDLTDLDDNSTAQGVAELSARAITPhgHTAAICIWPRFIETAKALLHGTGVRVATVVNFPHGGTDIDGV 85 5789************************9889***************************************** PP TIGR00126 73 llEakeaieeGAdEvDvviniaalkdkneevviedikavveaca.kvllKvilEtalLtdeekk.kAseisie 143 l+E++ ai+ GAdE+D+v++++ + ++ ++ + i +v++ c+ kv+lKvilEt++L de+ + +Ase+++e NCBI__GCF_003217235.1:WP_110752346.1 86 LAETRRAISDGADEIDLVLPYRDFAANGAALSRQMIGSVKKLCGrKVKLKVILETGKLADEAAIeSASEVALE 158 ********************************************9***************987769******* PP TIGR00126 144 agadfvKtstgfsakgAtvedvrlmkkvvgd...evgvKasGGvrtaedalalieagaerigas 204 gadf+Ktstg++ +At++ r+m +++++ gvK++GG+rt +da ++++ ++ +g NCBI__GCF_003217235.1:WP_110752346.1 159 EGADFIKTSTGKVEINATPAALRIMLEAIREsgsAAGVKPAGGIRTLDDAAQYLDFADAIMGEG 222 *****************************998889***********************999875 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 15.33 // [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