Align 4-hydroxy-2-oxovalerate aldolase; EC 4.1.3.39 (characterized)
to candidate 14490 b0352 4-hydroxy-2-ketovalerate aldolase (NCBI)
Query= CharProtDB::CH_002284 (337 letters) >FitnessBrowser__Keio:14490 Length = 337 Score = 671 bits (1732), Expect = 0.0 Identities = 337/337 (100%), Positives = 337/337 (100%) Query: 1 MNGKKLYISDVTLRDGMHAIRHQYSLENVRQIAKALDDARVDSIEVAHGDGLQGSSFNYG 60 MNGKKLYISDVTLRDGMHAIRHQYSLENVRQIAKALDDARVDSIEVAHGDGLQGSSFNYG Sbjct: 1 MNGKKLYISDVTLRDGMHAIRHQYSLENVRQIAKALDDARVDSIEVAHGDGLQGSSFNYG 60 Query: 61 FGAHSDLEWIEAAADVVKHAKIATLLLPGIGTIHDLKNAWQAGARVVRVATHCTEADVSA 120 FGAHSDLEWIEAAADVVKHAKIATLLLPGIGTIHDLKNAWQAGARVVRVATHCTEADVSA Sbjct: 61 FGAHSDLEWIEAAADVVKHAKIATLLLPGIGTIHDLKNAWQAGARVVRVATHCTEADVSA 120 Query: 121 QHIQYARELGMDTVGFLMMSHMTTPENLAKQAKLMEGYGATCIYVVDSGGAMNMSDIRDR 180 QHIQYARELGMDTVGFLMMSHMTTPENLAKQAKLMEGYGATCIYVVDSGGAMNMSDIRDR Sbjct: 121 QHIQYARELGMDTVGFLMMSHMTTPENLAKQAKLMEGYGATCIYVVDSGGAMNMSDIRDR 180 Query: 181 FRALKAELKPETQTGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI 240 FRALKAELKPETQTGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI Sbjct: 181 FRALKAELKPETQTGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI 240 Query: 241 AAADKLGWQHGTDLYALMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHCETAAA 300 AAADKLGWQHGTDLYALMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHCETAAA Sbjct: 241 AAADKLGWQHGTDLYALMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHCETAAA 300 Query: 301 RYGLSAVDILVELGKRRMVGGQEDMIVDVALDLRNNK 337 RYGLSAVDILVELGKRRMVGGQEDMIVDVALDLRNNK Sbjct: 301 RYGLSAVDILVELGKRRMVGGQEDMIVDVALDLRNNK 337 Lambda K H 0.319 0.134 0.391 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: 560 Number of extensions: 15 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: 337 Length of database: 337 Length adjustment: 28 Effective length of query: 309 Effective length of database: 309 Effective search space: 95481 Effective search space used: 95481 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 14490 b0352 (4-hydroxy-2-ketovalerate aldolase (NCBI))
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.31718.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-185 601.0 7.4 3.4e-185 600.8 7.4 1.0 1 lcl|FitnessBrowser__Keio:14490 b0352 4-hydroxy-2-ketovalerate a Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:14490 b0352 4-hydroxy-2-ketovalerate aldolase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 600.8 7.4 3.4e-185 3.4e-185 1 333 [. 4 336 .. 4 337 .] 0.99 Alignments for each domain: == domain 1 score: 600.8 bits; conditional E-value: 3.4e-185 TIGR03217 1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaaeavkkakv 79 kkl+i+dvtLrdG+ha+rhq++ e+vr+ia+aLd+a+vd+ievahGdGL+gss+nyGf+a+sdle+ieaaa++vk+ak+ lcl|FitnessBrowser__Keio:14490 4 KKLYISDVTLRDGMHAIRHQYSLENVRQIAKALDDARVDSIEVAHGDGLQGSSFNYGFGAHSDLEWIEAAADVVKHAKI 82 689**************************************************************************** PP TIGR03217 80 avlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmaspeklaeqakllesyGad 158 a+lllPGigt+++lk+a +aG++vvrvathcteadvs+qhi++arelg++tvgfLmmshm++pe+la+qakl+e yGa+ lcl|FitnessBrowser__Keio:14490 83 ATLLLPGIGTIHDLKNAWQAGARVVRVATHCTEADVSAQHIQYARELGMDTVGFLMMSHMTTPENLAKQAKLMEGYGAT 161 ******************************************************************************* PP TIGR03217 159 vvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatridaslaglGagaGnaplevlv 237 ++yvvds+Ga++++d++dr++alk++lkpet++G+hah+nlsl+vansi+aveeG++ridaslag+GagaGnaplev++ lcl|FitnessBrowser__Keio:14490 162 CIYVVDSGGAMNMSDIRDRFRALKAELKPETQTGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI 240 ******************************************************************************* PP TIGR03217 238 avldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGvyssflrhaeraaekygvdardilvelGrrklv 316 a++d+lG+++g+dl++l+daa+d+vrPl+drpvrvdre+l+lGyaGvyssflrh+e+aa++yg++a+dilvelG+r++v lcl|FitnessBrowser__Keio:14490 241 AAADKLGWQHGTDLYALMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHCETAAARYGLSAVDILVELGKRRMV 319 ******************************************************************************* PP TIGR03217 317 gGqedmivdvaldlake 333 gGqedmivdvaldl ++ lcl|FitnessBrowser__Keio:14490 320 GGQEDMIVDVALDLRNN 336 **************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (334 nodes) Target sequences: 1 (337 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: 7.54 // [ok]
This GapMind analysis is from Sep 17 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