Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate RR42_RS27900 RR42_RS27900 4-hyroxy-2-oxovalerate aldolase
Query= metacyc::MONOMER-11384 (352 letters) >FitnessBrowser__Cup4G11:RR42_RS27900 Length = 338 Score = 622 bits (1604), Expect = 0.0 Identities = 306/333 (91%), Positives = 322/333 (96%) Query: 3 QQKLYISDVTLRDGSHAIRHQYTVEQVKQIARALDDAKVDSIEVAHGDGLQGGSFNYGFG 62 Q+K+YISDVTLRDGSHA+RHQY+VEQ +QIA+ALDDAKVDSIEVAHGDGLQG SFNYGFG Sbjct: 4 QKKIYISDVTLRDGSHAVRHQYSVEQARQIAKALDDAKVDSIEVAHGDGLQGSSFNYGFG 63 Query: 63 AHTDLEWIEAAASVVKHAKIATLLLPGIGTVHDLKAVYEAGVRVVRVATHCTEADISRQH 122 AHTDLEWIEA ASVVKHAKIATLLLPGIGTVHDLKA Y+AG R+VRVATHCTEAD+SRQH Sbjct: 64 AHTDLEWIEAVASVVKHAKIATLLLPGIGTVHDLKAAYDAGARIVRVATHCTEADVSRQH 123 Query: 123 IEYARHLGMEAVGFLMMSHMTTPQHLAQQAKLMESYGATVCYVVDSGGALSMNDVRDRFR 182 IEYARHLGMEAVGFLMMSHMTTPQ+LA QAKLMESYGAT CYVVDSGGAL+MNDVRDRFR Sbjct: 124 IEYARHLGMEAVGFLMMSHMTTPQNLAAQAKLMESYGATCCYVVDSGGALTMNDVRDRFR 183 Query: 183 AFKDVLKPETQTGMHAHHNLSLGVANSIVAVENGCDRVDASLAGMGAGAGNAPLEVFIAA 242 AFK VLKPETQTGMHAHHNLSLGVANSIVAVE GCDR+DASLAGMGAGAGNAPLEVFIAA Sbjct: 184 AFKAVLKPETQTGMHAHHNLSLGVANSIVAVEEGCDRIDASLAGMGAGAGNAPLEVFIAA 243 Query: 243 AERMGWNHGTDLYKLMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEMAASKY 302 AERMGW+HG DLYKLMDAADD+VRPLQDRPVRVDRETLALGYAGVYSSFLRHSE AASKY Sbjct: 244 AERMGWDHGCDLYKLMDAADDIVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEAAASKY 303 Query: 303 GLKTVDILVELGRRRMVGGQEDMIIDVALDLLK 335 GLKTVD+LVELGRRRMVGGQEDMI+DVALDLLK Sbjct: 304 GLKTVDVLVELGRRRMVGGQEDMIVDVALDLLK 336 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: 527 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: 352 Length of database: 338 Length adjustment: 29 Effective length of query: 323 Effective length of database: 309 Effective search space: 99807 Effective search space used: 99807 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_RS27900 RR42_RS27900 (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.3383.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-185 602.1 8.6 1.6e-185 601.9 8.6 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS27900 RR42_RS27900 4-hyroxy-2-oxovaler Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS27900 RR42_RS27900 4-hyroxy-2-oxovalerate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 601.9 8.6 1.6e-185 1.6e-185 1 334 [] 5 338 .] 5 338 .] 0.99 Alignments for each domain: == domain 1 score: 601.9 bits; conditional E-value: 1.6e-185 TIGR03217 1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdleliea 69 kk++i+dvtLrdGshavrhq+++e++r+ia+aLd+a+vd+ievahGdGL+gss+nyGf+a++dle+iea lcl|FitnessBrowser__Cup4G11:RR42_RS27900 5 KKIYISDVTLRDGSHAVRHQYSVEQARQIAKALDDAKVDSIEVAHGDGLQGSSFNYGFGAHTDLEWIEA 73 689****************************************************************** PP TIGR03217 70 aaeavkkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmsh 138 +a++vk+ak+a+lllPGigtv++lkaa+daG+++vrvathcteadvs+qhie+ar+lg+e+vgfLmmsh lcl|FitnessBrowser__Cup4G11:RR42_RS27900 74 VASVVKHAKIATLLLPGIGTVHDLKAAYDAGARIVRVATHCTEADVSRQHIEYARHLGMEAVGFLMMSH 142 ********************************************************************* PP TIGR03217 139 maspeklaeqakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansi 207 m++p++la qakl+esyGa++ yvvds+Gal+++dv+dr++a+k++lkpet++G+hah+nlsl+vansi lcl|FitnessBrowser__Cup4G11:RR42_RS27900 143 MTTPQNLAAQAKLMESYGATCCYVVDSGGALTMNDVRDRFRAFKAVLKPETQTGMHAHHNLSLGVANSI 211 ********************************************************************* PP TIGR03217 208 vaveeGatridaslaglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrea 276 vaveeG++ridaslag+GagaGnaplev++a+++r+G+++g+dl+kl+daa+d+vrPl+drpvrvdre+ lcl|FitnessBrowser__Cup4G11:RR42_RS27900 212 VAVEEGCDRIDASLAGMGAGAGNAPLEVFIAAAERMGWDHGCDLYKLMDAADDIVRPLQDRPVRVDRET 280 ********************************************************************* PP TIGR03217 277 ltlGyaGvyssflrhaeraaekygvdardilvelGrrklvgGqedmivdvaldlaker 334 l+lGyaGvyssflrh+e+aa+kyg++++d+lvelGrr++vgGqedmivdvaldl+k+r lcl|FitnessBrowser__Cup4G11:RR42_RS27900 281 LALGYAGVYSSFLRHSEAAASKYGLKTVDVLVELGRRRMVGGQEDMIVDVALDLLKAR 338 ******************************************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (334 nodes) Target sequences: 1 (338 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: 8.47 // [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