Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate WP_005816432.1 DHAF_RS21345 deoxyribose-phosphate aldolase
Query= BRENDA::C7E719 (220 letters) >NCBI__GCF_000021925.1:WP_005816432.1 Length = 215 Score = 216 bits (549), Expect = 3e-61 Identities = 116/213 (54%), Positives = 154/213 (72%), Gaps = 2/213 (0%) Query: 1 MNIAALIDHTLLRADATKDEITKLTAEAKKYQFASVCVNPAWVAYAAEQLAGTGVATCTV 60 MN+A +IDHTLL+ +AT+ +I L EAK+++FA+VC+NPA++ AA+ L G+GV TV Sbjct: 1 MNLAGMIDHTLLKPEATEKDIVNLCHEAKQHKFATVCINPAYICTAAKLLHGSGVGVATV 60 Query: 61 IGFPLGANTSATKAFETKDAIANGATEVDMVINIGALKARDLQLVEQDIRAVVEAA--AG 118 IGFPLGA + K E A A+GA EVD+VINIG K+ + + V +DI VEAA G Sbjct: 61 IGFPLGATMTEIKVQEIFAAKAHGAREVDIVINIGWAKSGNWEAVAKDITRAVEAAHCCG 120 Query: 119 TLVKVIIETSLLTDEEKVLACELSVKAGANFVKTSTGFSTGGATVEDVALMRKTVGPEIG 178 +KVIIETSLLT+EEK A E+ +GA+++KTSTGF+ GGATVEDV ++ VG + Sbjct: 121 VTIKVIIETSLLTEEEKQKAAEIVKASGADYIKTSTGFAGGGATVEDVRNLKAWVGQSVK 180 Query: 179 VKASGGVRSLEDVQKLVEAGASRIGASSGVKII 211 VKASGG+RS E ++VEAGA R+G SSGV+II Sbjct: 181 VKASGGIRSRETALQMVEAGADRLGTSSGVQII 213 Lambda K H 0.313 0.127 0.340 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: 203 Number of extensions: 12 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: 220 Length of database: 215 Length adjustment: 22 Effective length of query: 198 Effective length of database: 193 Effective search space: 38214 Effective search space used: 38214 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: 45 (21.9 bits)
Align candidate WP_005816432.1 DHAF_RS21345 (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.8545.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-83 264.4 8.4 3.4e-83 264.3 8.4 1.0 1 lcl|NCBI__GCF_000021925.1:WP_005816432.1 DHAF_RS21345 deoxyribose-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_005816432.1 DHAF_RS21345 deoxyribose-phosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 264.3 8.4 3.4e-83 3.4e-83 2 210 .. 3 213 .. 2 214 .. 0.98 Alignments for each domain: == domain 1 score: 264.3 bits; conditional E-value: 3.4e-83 TIGR00126 2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLkgteveictvvgFPlGastte 70 la +iDht lk+++te+di +lc+eAk++kfa+vc+np+y+ A++lL+g+ v ++tv+gFPlGa+ te lcl|NCBI__GCF_000021925.1:WP_005816432.1 3 LAGMIDHTLLKPEATEKDIVNLCHEAKQHKFATVCINPAYICTAAKLLHGSGVGVATVIGFPLGATMTE 71 7889***************************************************************** PP TIGR00126 71 vkllEakeaieeGAdEvDvviniaalkdkneevviedikavveaca..kvllKvilEtalLtdeekkkA 137 +k+ E +a ++GA EvD+vini++ k++n+e+v +di vea+ +v++Kvi+Et+lLt+eek+kA lcl|NCBI__GCF_000021925.1:WP_005816432.1 72 IKVQEIFAAKAHGAREVDIVINIGWAKSGNWEAVAKDITRAVEAAHccGVTIKVIIETSLLTEEEKQKA 140 **************************************9999986667********************* PP TIGR00126 138 seisieagadfvKtstgfsakgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasaa 206 +ei + +gad++Ktstgf+ +gAtvedvr +k vg++v+vKasGG+r e+al+++eaga+r+g+s + lcl|NCBI__GCF_000021925.1:WP_005816432.1 141 AEIVKASGADYIKTSTGFAGGGATVEDVRNLKAWVGQSVKVKASGGIRSRETALQMVEAGADRLGTSSG 209 ********************************************************************* PP TIGR00126 207 vaii 210 v+ii lcl|NCBI__GCF_000021925.1:WP_005816432.1 210 VQII 213 **97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (215 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: 00:00:00.00 # Mc/sec: 6.91 // [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