Align Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 (characterized)
to candidate WP_011778085.1 MVAN_RS04090 deoxyribose-phosphate aldolase
Query= SwissProt::C0ZUQ6 (221 letters) >NCBI__GCF_000015305.1:WP_011778085.1 Length = 225 Score = 240 bits (613), Expect = 1e-68 Identities = 134/222 (60%), Positives = 164/222 (73%), Gaps = 8/222 (3%) Query: 7 TRSQVAAMVDHTLLKPEATAADVTALIDEARSLGVLAVCVSPSMLP---IRADGLVTAAV 63 +R++VAA+VDHTLLKPEAT AD+ AL+ EA LGV A+CVSP+ + + A A+V Sbjct: 5 SRARVAALVDHTLLKPEATEADIEALVTEAAELGVYAICVSPTFVAAVSLLAPDATVASV 64 Query: 64 VGFPSGKHHSLVKGAEARLAVDQGATEIDMVIDVGAAVAGDYSAVLADILTVREAMGESA 123 VGFPSGKH S +K EARLAV+ GA E+DMVIDVG A+AG+ AV +DI VR A E A Sbjct: 65 VGFPSGKHVSAIKAEEARLAVEAGAREVDMVIDVGCALAGELGAVRSDIAAVRAAAPE-A 123 Query: 124 ILKVILETAAL----SDEAIVECCRAAVRAGANFVKTSTGFHPAGGATVEAVELMARTVG 179 +LKVI+E+AA+ + +V+ CR A AGA+FVKTSTGFHP+GGA+V AVELMA VG Sbjct: 124 VLKVIVESAAILQISGEPLLVDICRVAEDAGADFVKTSTGFHPSGGASVRAVELMAGAVG 183 Query: 180 PGVGVKASGGIRTTQAALDMIAAGATRLGLSGTRAVLDGLTD 221 +GVKASGGIR+ A M+ AGATRLGLSGTRAVL G D Sbjct: 184 GRLGVKASGGIRSAADAAAMLDAGATRLGLSGTRAVLAGFPD 225 Lambda K H 0.317 0.130 0.353 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: 225 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: 221 Length of database: 225 Length adjustment: 22 Effective length of query: 199 Effective length of database: 203 Effective search space: 40397 Effective search space used: 40397 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: 46 (22.3 bits)
Align candidate WP_011778085.1 MVAN_RS04090 (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.4030532.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-61 192.4 5.8 3.9e-61 192.2 5.8 1.0 1 NCBI__GCF_000015305.1:WP_011778085.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000015305.1:WP_011778085.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 192.2 5.8 3.9e-61 3.9e-61 2 205 .. 9 215 .. 8 221 .. 0.92 Alignments for each domain: == domain 1 score: 192.2 bits; conditional E-value: 3.9e-61 TIGR00126 2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLkgteveictvvgFPlGasttevkll 74 +a l+Dht lk+++te+die+l++eA + +++a+cv p++v A+ L + ++++vvgFP+G++ + +k+ NCBI__GCF_000015305.1:WP_011778085.1 9 VAALVDHTLLKPEATEADIEALVTEAAELGVYAICVSPTFV--AAVSLLAPDATVASVVGFPSGKHVSAIKAE 79 6899************************************9..45556677899******************* PP TIGR00126 75 EakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtd...ee.kkkAseisie 143 Ea+ a+e+GA EvD+vi+++ +++ +v +di+av a+ ++ lKvi+E a + + e +++ ++++ + NCBI__GCF_000015305.1:WP_011778085.1 80 EARLAVEAGAREVDMVIDVGCALAGELGAVRSDIAAVRAAAPEAVLKVIVESAAILQisgEPlLVDICRVAED 152 ***************************************************98764311133256******** PP TIGR00126 144 agadfvKtstgfs.akgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasa 205 agadfvKtstgf +gA+v v+lm +vg+++gvKasGG+r a da a+++aga+r+g s NCBI__GCF_000015305.1:WP_011778085.1 153 AGADFVKTSTGFHpSGGASVRAVELMAGAVGGRLGVKASGGIRSAADAAAMLDAGATRLGLSG 215 ************9899********************************************875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (225 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: 10.77 // [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