Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate WP_012112958.1 XAUT_RS04725 4-hydroxy-2-oxovalerate aldolase
Query= metacyc::MONOMER-3404 (345 letters) >NCBI__GCF_000017645.1:WP_012112958.1 Length = 344 Score = 474 bits (1220), Expect = e-138 Identities = 233/333 (69%), Positives = 269/333 (80%) Query: 8 KLYISDVTLRDGSHAIRHQYSIQNVQDIARALDKARVDSIEVTHGDGLQGSSFNYGFGAH 67 KLYI DVTLRDG HA+RHQY + + IARALD+ARVD+IE++HGDGL GS+FNYGFGAH Sbjct: 8 KLYIQDVTLRDGMHALRHQYDLAATRAIARALDRARVDAIEISHGDGLTGSTFNYGFGAH 67 Query: 68 SDLEWIEAAADVIQHARVTVLLVPGIGTVHDLKAAYDAGARSVRVATHCTEADVSRQHIE 127 D EWI A A+ HA VTVLL+PGIGTVHDLK AY+AGARSVRV THCTEADVSRQHIE Sbjct: 68 DDAEWIAAVAEECSHAVVTVLLIPGIGTVHDLKHAYEAGARSVRVCTHCTEADVSRQHIE 127 Query: 128 YARELGMDTVGFLMMSHMIPAEQLAAQGKLMETYGAQCIYMADSGGAMNMNDIRDRMRAF 187 ARELGMDT FLMM+HMIP E LA Q +LME+YGA+C+Y+ DS GA+ D R++ Sbjct: 128 AARELGMDTATFLMMAHMIPPEALAEQARLMESYGAECVYVTDSAGALLPEDYTARVKTL 187 Query: 188 KAVLNPQTQTGMHAHHNLSLGVANSIIAVEEGCDRIDASLAGMGAGAGNAPLEVFIAAAE 247 + L P+T+ G+H HHNL+LG+AN++ +E G R+DASLAGMGAGAGNAPLE IA Sbjct: 188 RDALRPETEIGVHTHHNLTLGIANAVAGIEAGAVRVDASLAGMGAGAGNAPLEALIAVLN 247 Query: 248 RLGWNHGTDLYTLMDAADDIVRPLQDRPVRVDRETLGLGYAGVYSSFLRHAEVAAAKYGL 307 R G + G DLY LMDAADD+VRPLQDRPVRVDRE+L LGYAGVYSSFLRHAE AA YG+ Sbjct: 248 RKGIDTGCDLYALMDAADDLVRPLQDRPVRVDRESLSLGYAGVYSSFLRHAENAAQTYGV 307 Query: 308 KTLDILVELGRRRMVGGQEDMIVDVALDLLAAR 340 T +IL ELGRRRMVGGQEDMIVDVALDL A+ Sbjct: 308 DTREILSELGRRRMVGGQEDMIVDVALDLAEAK 340 Lambda K H 0.320 0.135 0.389 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: 467 Number of extensions: 21 Number of successful extensions: 1 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: 345 Length of database: 344 Length adjustment: 29 Effective length of query: 316 Effective length of database: 315 Effective search space: 99540 Effective search space used: 99540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_012112958.1 XAUT_RS04725 (4-hydroxy-2-oxovalerate aldolase)
to HMM TIGR03217 (dmpG: 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39))
# 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/TIGR03217.hmm # target sequence database: /tmp/gapView.297740.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03217 [M=334] Accession: TIGR03217 Description: 4OH_2_O_val_ald: 4-hydroxy-2-oxovalerate 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-172 559.8 8.2 1.2e-172 559.6 8.2 1.0 1 NCBI__GCF_000017645.1:WP_012112958.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000017645.1:WP_012112958.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 559.6 8.2 1.2e-172 1.2e-172 2 333 .. 8 339 .. 7 340 .. 0.99 Alignments for each domain: == domain 1 score: 559.6 bits; conditional E-value: 1.2e-172 TIGR03217 2 kltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaaeav 74 kl+i+dvtLrdG+ha rhq++ raia+aLd+a+vdaie++hGdGL+gs++nyGf+a++d+e+i+a+ae++ NCBI__GCF_000017645.1:WP_012112958.1 8 KLYIQDVTLRDGMHALRHQYDLAATRAIARALDRARVDAIEISHGDGLTGSTFNYGFGAHDDAEWIAAVAEEC 80 789********************************************************************** PP TIGR03217 75 kkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmaspeklae 147 +a v+vll+PGigtv++lk+a++aG+++vrv thcteadvs+qhie+arelg++t +fLmm+hm++pe+lae NCBI__GCF_000017645.1:WP_012112958.1 81 SHAVVTVLLIPGIGTVHDLKHAYEAGARSVRVCTHCTEADVSRQHIEAARELGMDTATFLMMAHMIPPEALAE 153 ************************************************************************* PP TIGR03217 148 qakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatridas 220 qa+l+esyGa++vyv+dsaGallped ++rvk+l++al+pete+G+h+h+nl+l++an+++ +e+Ga r+das NCBI__GCF_000017645.1:WP_012112958.1 154 QARLMESYGAECVYVTDSAGALLPEDYTARVKTLRDALRPETEIGVHTHHNLTLGIANAVAGIEAGAVRVDAS 226 ************************************************************************* PP TIGR03217 221 laglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGvyssflrhae 293 lag+GagaGnaple+l+avl+r G++tg+dl++l+daa+d+vrPl+drpvrvdre+l+lGyaGvyssflrhae NCBI__GCF_000017645.1:WP_012112958.1 227 LAGMGAGAGNAPLEALIAVLNRKGIDTGCDLYALMDAADDLVRPLQDRPVRVDRESLSLGYAGVYSSFLRHAE 299 ************************************************************************* PP TIGR03217 294 raaekygvdardilvelGrrklvgGqedmivdvaldlake 333 +aa+ ygvd+r+il elGrr++vgGqedmivdvaldla++ NCBI__GCF_000017645.1:WP_012112958.1 300 NAAQTYGVDTREILSELGRRRMVGGQEDMIVDVALDLAEA 339 *************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (334 nodes) Target sequences: 1 (344 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: 13.62 // [ok]
This GapMind analysis is from Apr 09 2024. 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