Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate WP_009397183.1 BLS63_RS10115 4-hydroxy-2-oxovalerate aldolase
Query= BRENDA::P51017 (346 letters) >NCBI__GCF_900100495.1:WP_009397183.1 Length = 346 Score = 659 bits (1699), Expect = 0.0 Identities = 331/346 (95%), Positives = 340/346 (98%) Query: 1 MNLHGKSVILHDMSLRDGMHAKRHQISLEQMVAVATGLDQAGMPLIEITHGDGLGGRSIN 60 MNL GK+V LHDMSLRDGMHAKRHQISLEQM+AVATGLD AGMPLIEITHGDGLGGRSIN Sbjct: 1 MNLQGKNVTLHDMSLRDGMHAKRHQISLEQMIAVATGLDAAGMPLIEITHGDGLGGRSIN 60 Query: 61 YGFPAHSDEEYLRAVIPQLKQAKVSALLLPGIGTVDHLKMALDCGVSTIRVATHCTEADV 120 YGFPAHSDEEYLRAVIP+LKQAKVSALLLPGIGTVDHLKMALDCGVSTIRVATHCTEADV Sbjct: 61 YGFPAHSDEEYLRAVIPRLKQAKVSALLLPGIGTVDHLKMALDCGVSTIRVATHCTEADV 120 Query: 121 SEQHIGMARKLGVDTVGFLMMAHMISAEKVLEQAKLMESYGANCIYCTDSAGYMLPDEVS 180 SEQHIGM+RKLG DTVGFLMMAHMISAEKVLEQA+LMESYGANCIYCTDSAGYMLPDEVS Sbjct: 121 SEQHIGMSRKLGADTVGFLMMAHMISAEKVLEQARLMESYGANCIYCTDSAGYMLPDEVS 180 Query: 181 EKIGLLRAELNPATEVGFHGHHNMGMAIANSLAAIEAGAARIDGSVAGLGAGAGNTPLEV 240 EKIGLLRAELNPATE+GFHGHHNMGMAIANSLAAIEAGA+RIDGSVAGLGAGAGNTPLEV Sbjct: 181 EKIGLLRAELNPATEIGFHGHHNMGMAIANSLAAIEAGASRIDGSVAGLGAGAGNTPLEV 240 Query: 241 FVAVCKRMGVETGIDLYKIMDVAEDLVVPMMDQPIRVDRDALTLGYAGVYSSFLLFAQRA 300 FVAVCKRMGVETGIDLYKIMDVAED+VVPMMDQPIRVDRDALTLGYAGVYSSFLLFAQRA Sbjct: 241 FVAVCKRMGVETGIDLYKIMDVAEDIVVPMMDQPIRVDRDALTLGYAGVYSSFLLFAQRA 300 Query: 301 EKKYGVSARDILVELGRRGTVGGQEDMIEDLALDMARARQQQKVSA 346 EKKYGV ARDILVELGRRGTVGGQEDMIEDLALDM+RARQ QKVSA Sbjct: 301 EKKYGVPARDILVELGRRGTVGGQEDMIEDLALDMSRARQNQKVSA 346 Lambda K H 0.320 0.135 0.386 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: 573 Number of extensions: 16 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: 346 Length of database: 346 Length adjustment: 29 Effective length of query: 317 Effective length of database: 317 Effective search space: 100489 Effective search space used: 100489 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_009397183.1 BLS63_RS10115 (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.12093.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-175 566.8 5.9 8.7e-175 566.6 5.9 1.0 1 lcl|NCBI__GCF_900100495.1:WP_009397183.1 BLS63_RS10115 4-hydroxy-2-oxoval Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_009397183.1 BLS63_RS10115 4-hydroxy-2-oxovalerate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 566.6 5.9 8.7e-175 8.7e-175 1 333 [. 6 338 .. 6 339 .. 0.99 Alignments for each domain: == domain 1 score: 566.6 bits; conditional E-value: 8.7e-175 TIGR03217 1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdleliea 69 k++t++d++LrdG+ha+rhq++ e++ a+a++Ld+ag++ ie++hGdGLgg+s+nyGf+a+sd+e+++a lcl|NCBI__GCF_900100495.1:WP_009397183.1 6 KNVTLHDMSLRDGMHAKRHQISLEQMIAVATGLDAAGMPLIEITHGDGLGGRSINYGFPAHSDEEYLRA 74 5799***************************************************************** PP TIGR03217 70 aaeavkkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmsh 138 ++ +k+akv++lllPGigtv++lk+a d+Gv+++rvathcteadvseqhi+++r+lg +tvgfLmm+h lcl|NCBI__GCF_900100495.1:WP_009397183.1 75 VIPRLKQAKVSALLLPGIGTVDHLKMALDCGVSTIRVATHCTEADVSEQHIGMSRKLGADTVGFLMMAH 143 ********************************************************************* PP TIGR03217 139 maspeklaeqakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansi 207 m+s+ek+ eqa+l+esyGa+++y++dsaG++lp++v++++ l+++l+p+te+G+h+h+n+++a+ans+ lcl|NCBI__GCF_900100495.1:WP_009397183.1 144 MISAEKVLEQARLMESYGANCIYCTDSAGYMLPDEVSEKIGLLRAELNPATEIGFHGHHNMGMAIANSL 212 ********************************************************************* PP TIGR03217 208 vaveeGatridaslaglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrea 276 +a+e+Ga+rid+s+aglGagaGn+plev+vav++r+G+etg+dl+k++d+aed+v+P++d+p+rvdr+a lcl|NCBI__GCF_900100495.1:WP_009397183.1 213 AAIEAGASRIDGSVAGLGAGAGNTPLEVFVAVCKRMGVETGIDLYKIMDVAEDIVVPMMDQPIRVDRDA 281 ********************************************************************* PP TIGR03217 277 ltlGyaGvyssflrhaeraaekygvdardilvelGrrklvgGqedmivdvaldlake 333 ltlGyaGvyssfl++a+ra++kygv+ardilvelGrr +vgGqedmi d+ald++++ lcl|NCBI__GCF_900100495.1:WP_009397183.1 282 LTLGYAGVYSSFLLFAQRAEKKYGVPARDILVELGRRGTVGGQEDMIEDLALDMSRA 338 ******************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (334 nodes) Target sequences: 1 (346 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.49 // [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