Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate GFF1137 HP15_1115 4-hydroxy-2-ketovalerate aldolase
Query= metacyc::MONOMER-3404 (345 letters) >FitnessBrowser__Marino:GFF1137 Length = 345 Score = 592 bits (1525), Expect = e-174 Identities = 291/345 (84%), Positives = 317/345 (91%) Query: 1 MTFNPGKKLYISDVTLRDGSHAIRHQYSIQNVQDIARALDKARVDSIEVTHGDGLQGSSF 60 MTFNPGKKLYISDVTLRDGSHAIRHQYSI+NVQDIARALDKA+VDSIEV HGDGLQGSSF Sbjct: 1 MTFNPGKKLYISDVTLRDGSHAIRHQYSIKNVQDIARALDKAKVDSIEVAHGDGLQGSSF 60 Query: 61 NYGFGAHSDLEWIEAAADVIQHARVTVLLVPGIGTVHDLKAAYDAGARSVRVATHCTEAD 120 NYGFGAH+DLEWIEA ++VI+HA++ LL+PGIGTVHDL AY+AGAR VRVATHCTEAD Sbjct: 61 NYGFGAHTDLEWIEAVSEVIEHAKIATLLLPGIGTVHDLDNAYNAGARIVRVATHCTEAD 120 Query: 121 VSRQHIEYARELGMDTVGFLMMSHMIPAEQLAAQGKLMETYGAQCIYMADSGGAMNMNDI 180 VSRQHIE+AR+LGMDTVGFLMMSHM + LA Q KLME YGA C+Y+ DSGGAMNMNDI Sbjct: 121 VSRQHIEHARKLGMDTVGFLMMSHMQTPQGLAEQAKLMEDYGATCLYVVDSGGAMNMNDI 180 Query: 181 RDRMRAFKAVLNPQTQTGMHAHHNLSLGVANSIIAVEEGCDRIDASLAGMGAGAGNAPLE 240 RDR RA K VL P+TQTGMHAHHNL+LGVANSI+AVEEGCDRIDASLAGMGAGAGNAPLE Sbjct: 181 RDRFRALKDVLKPETQTGMHAHHNLALGVANSIVAVEEGCDRIDASLAGMGAGAGNAPLE 240 Query: 241 VFIAAAERLGWNHGTDLYTLMDAADDIVRPLQDRPVRVDRETLGLGYAGVYSSFLRHAEV 300 V IAA +++GW HGTD+Y LMDAADDIVRPLQDRPVRVDRETL LGYAGVYSSFLRH+EV Sbjct: 241 VCIAAFDKMGWEHGTDVYALMDAADDIVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEV 300 Query: 301 AAAKYGLKTLDILVELGRRRMVGGQEDMIVDVALDLLAARKEQQA 345 AA KYGLK +DILVELG+RRMVGGQEDMIVDVALDLLAA+KEQ A Sbjct: 301 AAQKYGLKAVDILVELGKRRMVGGQEDMIVDVALDLLAAQKEQNA 345 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: 512 Number of extensions: 20 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: 345 Length adjustment: 29 Effective length of query: 316 Effective length of database: 316 Effective search space: 99856 Effective search space used: 99856 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 GFF1137 HP15_1115 (4-hydroxy-2-ketovalerate 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.16590.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-182 591.1 9.4 3.6e-182 590.9 9.4 1.0 1 lcl|FitnessBrowser__Marino:GFF1137 HP15_1115 4-hydroxy-2-ketovalera Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1137 HP15_1115 4-hydroxy-2-ketovalerate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 590.9 9.4 3.6e-182 3.6e-182 1 333 [. 7 339 .. 7 340 .. 0.99 Alignments for each domain: == domain 1 score: 590.9 bits; conditional E-value: 3.6e-182 TIGR03217 1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaaeavk 75 kkl+i+dvtLrdGsha+rhq+++++v++ia+aLd+a+vd+ievahGdGL+gss+nyGf+a++dle+iea++e+++ lcl|FitnessBrowser__Marino:GFF1137 7 KKLYISDVTLRDGSHAIRHQYSIKNVQDIARALDKAKVDSIEVAHGDGLQGSSFNYGFGAHTDLEWIEAVSEVIE 81 689************************************************************************ PP TIGR03217 76 kakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmaspeklaeqak 150 +ak+a+lllPGigtv++l++a++aG+++vrvathcteadvs+qhie+ar+lg++tvgfLmmshm++p+ laeqak lcl|FitnessBrowser__Marino:GFF1137 82 HAKIATLLLPGIGTVHDLDNAYNAGARIVRVATHCTEADVSRQHIEHARKLGMDTVGFLMMSHMQTPQGLAEQAK 156 *************************************************************************** PP TIGR03217 151 llesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatridaslaglG 225 l+e+yGa+++yvvds+Ga++++d++dr++alk++lkpet++G+hah+nl+l+vansivaveeG++ridaslag+G lcl|FitnessBrowser__Marino:GFF1137 157 LMEDYGATCLYVVDSGGAMNMNDIRDRFRALKDVLKPETQTGMHAHHNLALGVANSIVAVEEGCDRIDASLAGMG 231 *************************************************************************** PP TIGR03217 226 agaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGvyssflrhaeraaekyg 300 agaGnaplev +a++d++G+e+g+d+++l+daa+d+vrPl+drpvrvdre+l+lGyaGvyssflrh+e aa+kyg lcl|FitnessBrowser__Marino:GFF1137 232 AGAGNAPLEVCIAAFDKMGWEHGTDVYALMDAADDIVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEVAAQKYG 306 *************************************************************************** PP TIGR03217 301 vdardilvelGrrklvgGqedmivdvaldlake 333 ++a+dilvelG+r++vgGqedmivdvaldl+++ lcl|FitnessBrowser__Marino:GFF1137 307 LKAVDILVELGKRRMVGGQEDMIVDVALDLLAA 339 ******************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (334 nodes) Target sequences: 1 (345 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: 00:00:00.01 # Mc/sec: 11.27 // [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