Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate WP_012277177.1 SHAL_RS10910 4-hydroxy-2-oxovalerate aldolase
Query= BRENDA::P51017 (346 letters) >NCBI__GCF_000019185.1:WP_012277177.1 Length = 340 Score = 555 bits (1429), Expect = e-163 Identities = 275/337 (81%), Positives = 306/337 (90%) Query: 1 MNLHGKSVILHDMSLRDGMHAKRHQISLEQMVAVATGLDQAGMPLIEITHGDGLGGRSIN 60 MNL GK VILHDMSLRDGMHA++HQI+L++MV VATGLD AG+PLIE+THGDGLGG S+N Sbjct: 1 MNLTGKKVILHDMSLRDGMHARQHQITLKEMVDVATGLDAAGVPLIEVTHGDGLGGASLN 60 Query: 61 YGFPAHSDEEYLRAVIPQLKQAKVSALLLPGIGTVDHLKMALDCGVSTIRVATHCTEADV 120 YGFPAH+DEEYL AVIP++KQAKVSALLLPGIGTVDHL+MA GV+TIRVATHCTEADV Sbjct: 61 YGFPAHTDEEYLSAVIPKMKQAKVSALLLPGIGTVDHLRMAHQLGVNTIRVATHCTEADV 120 Query: 121 SEQHIGMARKLGVDTVGFLMMAHMISAEKVLEQAKLMESYGANCIYCTDSAGYMLPDEVS 180 S QHI ++R LG+DTVGFLMMAHM+S EK+LEQAKLMESYGANCIYCTDSAGYMLP +V+ Sbjct: 121 SGQHIALSRDLGLDTVGFLMMAHMVSPEKLLEQAKLMESYGANCIYCTDSAGYMLPGDVT 180 Query: 181 EKIGLLRAELNPATEVGFHGHHNMGMAIANSLAAIEAGAARIDGSVAGLGAGAGNTPLEV 240 I LR EL T++GFHGHHNMGM+IANSLAAIEAGA RIDGSVAGLGAGAGNTPLEV Sbjct: 181 SHIERLRGELKSDTQIGFHGHHNMGMSIANSLAAIEAGAERIDGSVAGLGAGAGNTPLEV 240 Query: 241 FVAVCKRMGVETGIDLYKIMDVAEDLVVPMMDQPIRVDRDALTLGYAGVYSSFLLFAQRA 300 FVAV +RM V G++LY IMDVAEDLV PMMDQPIR+DRDALTLGYAGVYSSFLLFAQRA Sbjct: 241 FVAVLERMQVHHGVNLYDIMDVAEDLVTPMMDQPIRIDRDALTLGYAGVYSSFLLFAQRA 300 Query: 301 EKKYGVSARDILVELGRRGTVGGQEDMIEDLALDMAR 337 EKKYGV ARDIL+ELGRRGTVGGQEDMI+D A++MAR Sbjct: 301 EKKYGVPARDILLELGRRGTVGGQEDMIDDTAMNMAR 337 Lambda K H 0.320 0.135 0.386 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: 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: 346 Length of database: 340 Length adjustment: 29 Effective length of query: 317 Effective length of database: 311 Effective search space: 98587 Effective search space used: 98587 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_012277177.1 SHAL_RS10910 (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.2726525.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-168 546.6 6.9 1.2e-168 546.5 6.9 1.0 1 NCBI__GCF_000019185.1:WP_012277177.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000019185.1:WP_012277177.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 546.5 6.9 1.2e-168 1.2e-168 1 333 [. 6 338 .. 6 339 .. 0.99 Alignments for each domain: == domain 1 score: 546.5 bits; conditional E-value: 1.2e-168 TIGR03217 1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaaea 73 kk++++d++LrdG+ha +hq+t +e++++a++Ld+agv+ iev+hGdGLgg+slnyGf+a++d+e+++a++ + NCBI__GCF_000019185.1:WP_012277177.1 6 KKVILHDMSLRDGMHARQHQITLKEMVDVATGLDAAGVPLIEVTHGDGLGGASLNYGFPAHTDEEYLSAVIPK 78 6899********************************************************************* PP TIGR03217 74 vkkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmaspekla 146 +k+akv++lllPGigtv++l++a+++Gv+++rvathcteadvs qhi+l+r+lgl+tvgfLmm+hm+spekl NCBI__GCF_000019185.1:WP_012277177.1 79 MKQAKVSALLLPGIGTVDHLRMAHQLGVNTIRVATHCTEADVSGQHIALSRDLGLDTVGFLMMAHMVSPEKLL 151 ************************************************************************* PP TIGR03217 147 eqakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatrida 219 eqakl+esyGa+++y++dsaG++lp dv+++++ l+ +lk++t++G+h+h+n+++++ans++a+e+Ga+rid+ NCBI__GCF_000019185.1:WP_012277177.1 152 EQAKLMESYGANCIYCTDSAGYMLPGDVTSHIERLRGELKSDTQIGFHGHHNMGMSIANSLAAIEAGAERIDG 224 ************************************************************************* PP TIGR03217 220 slaglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGvyssflrha 292 s+aglGagaGn+plev+vavl+r+ +++gv+l+ ++d+aed+v+P++d+p+r+dr+altlGyaGvyssfl++a NCBI__GCF_000019185.1:WP_012277177.1 225 SVAGLGAGAGNTPLEVFVAVLERMQVHHGVNLYDIMDVAEDLVTPMMDQPIRIDRDALTLGYAGVYSSFLLFA 297 ************************************************************************* PP TIGR03217 293 eraaekygvdardilvelGrrklvgGqedmivdvaldlake 333 +ra++kygv+ardil+elGrr +vgGqedmi d+a+++a+e NCBI__GCF_000019185.1:WP_012277177.1 298 QRAEKKYGVPARDILLELGRRGTVGGQEDMIDDTAMNMARE 338 **************************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (334 nodes) Target sequences: 1 (340 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: 00:00:00.00 # Mc/sec: 22.05 // [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