Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate RR42_RS32625 RR42_RS32625 4-hyroxy-2-oxovalerate aldolase
Query= metacyc::MONOMER-11384 (352 letters) >FitnessBrowser__Cup4G11:RR42_RS32625 Length = 349 Score = 577 bits (1486), Expect = e-169 Identities = 281/336 (83%), Positives = 311/336 (92%) Query: 2 TQQKLYISDVTLRDGSHAIRHQYTVEQVKQIARALDDAKVDSIEVAHGDGLQGGSFNYGF 61 TQ+KLYISDVTLRDGSHAIRHQY+++ V++IA ALD AKVDSIEVAHGDGL G SFNYGF Sbjct: 6 TQKKLYISDVTLRDGSHAIRHQYSLDDVRRIAAALDAAKVDSIEVAHGDGLAGSSFNYGF 65 Query: 62 GAHTDLEWIEAAASVVKHAKIATLLLPGIGTVHDLKAVYEAGVRVVRVATHCTEADISRQ 121 GAHTDLEWI AAA V+HAK+ATLLLPG+GTVHDL+A ++AG RVVRVATHCTEAD+SRQ Sbjct: 66 GAHTDLEWIAAAAETVRHAKVATLLLPGVGTVHDLRAAFDAGARVVRVATHCTEADVSRQ 125 Query: 122 HIEYARHLGMEAVGFLMMSHMTTPQHLAQQAKLMESYGATVCYVVDSGGALSMNDVRDRF 181 HIEYAR+LGM+ VGFLMMSHMTTP LAQQA+LMESYGA YVVDSGGAL+MNDVR+RF Sbjct: 126 HIEYARNLGMDTVGFLMMSHMTTPAALAQQARLMESYGAETVYVVDSGGALNMNDVRERF 185 Query: 182 RAFKDVLKPETQTGMHAHHNLSLGVANSIVAVENGCDRVDASLAGMGAGAGNAPLEVFIA 241 RAFKDVLKP+TQTGMHAHHNLSLGVANSIVAVE GCDR+DASLAGMGAGAGNAPLEVFIA Sbjct: 186 RAFKDVLKPQTQTGMHAHHNLSLGVANSIVAVEEGCDRIDASLAGMGAGAGNAPLEVFIA 245 Query: 242 AAERMGWNHGTDLYKLMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEMAASK 301 A R+GWNHG DLY LMDAAD++VRPLQDRPVRVDRETLALGYAGVYSSFLRH+E AA + Sbjct: 246 ATSRLGWNHGCDLYTLMDAADEIVRPLQDRPVRVDRETLALGYAGVYSSFLRHAEAAAGR 305 Query: 302 YGLKTVDILVELGRRRMVGGQEDMIIDVALDLLKQQ 337 Y LKTVDILVELG+RRMVGGQEDMI+DVALDL+ ++ Sbjct: 306 YALKTVDILVELGQRRMVGGQEDMIVDVALDLVARR 341 Lambda K H 0.319 0.133 0.383 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: 503 Number of extensions: 12 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: 352 Length of database: 349 Length adjustment: 29 Effective length of query: 323 Effective length of database: 320 Effective search space: 103360 Effective search space used: 103360 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 RR42_RS32625 RR42_RS32625 (4-hyroxy-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.27241.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-181 589.3 9.1 1.3e-181 589.1 9.1 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS32625 RR42_RS32625 4-hyroxy-2-oxovaler Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS32625 RR42_RS32625 4-hyroxy-2-oxovalerate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 589.1 9.1 1.3e-181 1.3e-181 1 333 [. 8 340 .. 8 341 .. 0.99 Alignments for each domain: == domain 1 score: 589.1 bits; conditional E-value: 1.3e-181 TIGR03217 1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdleliea 69 kkl+i+dvtLrdGsha+rhq++ ++vr+iaaaLd+a+vd+ievahGdGL+gss+nyGf+a++dle+i+a lcl|FitnessBrowser__Cup4G11:RR42_RS32625 8 KKLYISDVTLRDGSHAIRHQYSLDDVRRIAAALDAAKVDSIEVAHGDGLAGSSFNYGFGAHTDLEWIAA 76 689****************************************************************** PP TIGR03217 70 aaeavkkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmsh 138 aae+v++akva+lllPG+gtv++l+aa daG++vvrvathcteadvs+qhie+ar+lg++tvgfLmmsh lcl|FitnessBrowser__Cup4G11:RR42_RS32625 77 AAETVRHAKVATLLLPGVGTVHDLRAAFDAGARVVRVATHCTEADVSRQHIEYARNLGMDTVGFLMMSH 145 ********************************************************************* PP TIGR03217 139 maspeklaeqakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansi 207 m++p +la+qa+l+esyGa++vyvvds+Gal+++dv++r++a+k++lkp+t++G+hah+nlsl+vansi lcl|FitnessBrowser__Cup4G11:RR42_RS32625 146 MTTPAALAQQARLMESYGAETVYVVDSGGALNMNDVRERFRAFKDVLKPQTQTGMHAHHNLSLGVANSI 214 ********************************************************************* PP TIGR03217 208 vaveeGatridaslaglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrea 276 vaveeG++ridaslag+GagaGnaplev++a++ rlG+++g+dl++l+daa+++vrPl+drpvrvdre+ lcl|FitnessBrowser__Cup4G11:RR42_RS32625 215 VAVEEGCDRIDASLAGMGAGAGNAPLEVFIAATSRLGWNHGCDLYTLMDAADEIVRPLQDRPVRVDRET 283 ********************************************************************* PP TIGR03217 277 ltlGyaGvyssflrhaeraaekygvdardilvelGrrklvgGqedmivdvaldlake 333 l+lGyaGvyssflrhae+aa +y ++++dilvelG+r++vgGqedmivdvaldl+++ lcl|FitnessBrowser__Cup4G11:RR42_RS32625 284 LALGYAGVYSSFLRHAEAAAGRYALKTVDILVELGQRRMVGGQEDMIVDVALDLVAR 340 ******************************************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (334 nodes) Target sequences: 1 (349 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: 7.69 // [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