Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate WP_007734084.1 C1M55_RS04085 4-hydroxy-2-oxovalerate aldolase
Query= BRENDA::P9WMK5 (346 letters) >NCBI__GCF_002893965.1:WP_007734084.1 Length = 347 Score = 567 bits (1460), Expect = e-166 Identities = 285/333 (85%), Positives = 303/333 (90%) Query: 5 WDVRITDTSLRDGSHHKRHQFTKDEVGAIVAALDAAGVPVIEVTHGDGLGGSSFNYGFSK 64 WD+R+TDTSLRDGSHHKRHQFT DEV AIV ALD AGVPVIEVTHGDGLGGSSFNYGFSK Sbjct: 11 WDIRVTDTSLRDGSHHKRHQFTVDEVRAIVGALDGAGVPVIEVTHGDGLGGSSFNYGFSK 70 Query: 65 TPEQELIKLAAATAKEARIAFLMLPGVGTKDDIKEARDNGGSICRIATHCTEADVSIQHF 124 TPEQELIK A TA A+IAFLMLPG+G KDDI A+DNG SICRIATHCTEADVSIQHF Sbjct: 71 TPEQELIKAAVETATNAKIAFLMLPGLGIKDDIVIAQDNGASICRIATHCTEADVSIQHF 130 Query: 125 GLARELGLETVGFLMMAHTIAPEKLAAQARIMADAGCQCVYVVDSAGALVLDGVADRVSA 184 GLARE GLETVGFLMMAH+I PEKLA QARIMADAGCQCVYVVDSAGALVL+ V+DRV A Sbjct: 131 GLARERGLETVGFLMMAHSIPPEKLAKQARIMADAGCQCVYVVDSAGALVLEQVSDRVEA 190 Query: 185 LVAELGEDAQVGFHGHENLGLGVANSVAAVRAGAKQIDGSCRRFGAGAGNAPVEALIGVF 244 LV ELG DAQVGFHGHENLGLGVANS+AAVRAGAKQIDGS RRFGAGAGNAPVEA +GV Sbjct: 191 LVQELGNDAQVGFHGHENLGLGVANSIAAVRAGAKQIDGSTRRFGAGAGNAPVEAFVGVC 250 Query: 245 DKIGVKTGIDFFDIADAAEDVVRPAMPAECLLDRNALIMGYSGVYSSFLKHAVRQAERYG 304 DKIGVKTGIDFF IADAAEDVVRPAMP ECLLDR AL+MGY+GVYSSFLKHA RQAERYG Sbjct: 251 DKIGVKTGIDFFAIADAAEDVVRPAMPQECLLDRQALMMGYAGVYSSFLKHAERQAERYG 310 Query: 305 VPASALLHRAGQRKLIGGQEDQLIDIALEIKRE 337 V ++ LL RAG+RKL+GGQEDQLIDIALE++RE Sbjct: 311 VSSAELLVRAGKRKLVGGQEDQLIDIALELQRE 343 Lambda K H 0.320 0.136 0.393 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: 495 Number of extensions: 17 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: 347 Length adjustment: 29 Effective length of query: 317 Effective length of database: 318 Effective search space: 100806 Effective search space used: 100806 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_007734084.1 C1M55_RS04085 (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.2719779.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-162 524.0 5.5 9.3e-162 523.8 5.5 1.0 1 NCBI__GCF_002893965.1:WP_007734084.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_007734084.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 523.8 5.5 9.3e-162 9.3e-162 3 333 .. 13 343 .. 11 344 .. 0.99 Alignments for each domain: == domain 1 score: 523.8 bits; conditional E-value: 9.3e-162 TIGR03217 3 ltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaaeavk 75 +++td++LrdGsh++rhqft++evrai+ aLd agv++iev+hGdGLggss+nyGfs++ ++eli+aa+e+++ NCBI__GCF_002893965.1:WP_007734084.1 13 IRVTDTSLRDGSHHKRHQFTVDEVRAIVGALDGAGVPVIEVTHGDGLGGSSFNYGFSKTPEQELIKAAVETAT 85 89*********************************************************************** PP TIGR03217 76 kakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmaspeklaeq 148 +ak+a l+lPG+g ++++ a+d+G++++r+athcteadvs qh++lare gletvgfLmm+h+++pekla+q NCBI__GCF_002893965.1:WP_007734084.1 86 NAKIAFLMLPGLGIKDDIVIAQDNGASICRIATHCTEADVSIQHFGLARERGLETVGFLMMAHSIPPEKLAKQ 158 ************************************************************************* PP TIGR03217 149 akllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatridasl 221 a+++ + G+++vyvvdsaGal++e+v+drv+al ++l ++++vG+h+henl+l+vansi+av++Ga++id+s NCBI__GCF_002893965.1:WP_007734084.1 159 ARIMADAGCQCVYVVDSAGALVLEQVSDRVEALVQELGNDAQVGFHGHENLGLGVANSIAAVRAGAKQIDGST 231 ************************************************************************* PP TIGR03217 222 aglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGvyssflrhaer 294 +++GagaGnap+e++v+v+d++G++tg+d+f+++daaedvvrP +++++ +dr+al++GyaGvyssfl+haer NCBI__GCF_002893965.1:WP_007734084.1 232 RRFGAGAGNAPVEAFVGVCDKIGVKTGIDFFAIADAAEDVVRPAMPQECLLDRQALMMGYAGVYSSFLKHAER 304 ************************************************************************* PP TIGR03217 295 aaekygvdardilvelGrrklvgGqedmivdvaldlake 333 +ae+ygv+++++lv+ G+rklvgGqed+++d+al+l++e NCBI__GCF_002893965.1:WP_007734084.1 305 QAERYGVSSAELLVRAGKRKLVGGQEDQLIDIALELQRE 343 ************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (334 nodes) Target sequences: 1 (347 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: 00:00:00.00 # Mc/sec: 13.03 // [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