Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate WP_090439171.1 BLS63_RS02445 2-oxo-3-hexenedioate decarboxylase
Query= BRENDA::Q1XGK3 (264 letters) >NCBI__GCF_900100495.1:WP_090439171.1 Length = 264 Score = 489 bits (1259), Expect = e-143 Identities = 244/264 (92%), Positives = 256/264 (96%) Query: 1 MNRTLTREQVLALAEHIENAELNVHDIGKVTNDFPEMTFADAYDVQWEIRRRKEARGNKI 60 MNRTLTREQVLALAEHIENAEL+ HDI KVTND+P+MTFADAYDVQWEIRRRKEARGNKI Sbjct: 1 MNRTLTREQVLALAEHIENAELHAHDISKVTNDYPDMTFADAYDVQWEIRRRKEARGNKI 60 Query: 61 VGLKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVDCSKLIHPKIEAEISVVTKAPL 120 VGLKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVD SKLIHPKIEAEIS VTKAPL Sbjct: 61 VGLKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVDTSKLIHPKIEAEISFVTKAPL 120 Query: 121 HGPGCHLGDVIAAIDYVIPTVEVIDSRYENFKFDLISVVADNASSTRFITGGRMASLEEV 180 HGPGCH+G V+AA D+VIPTVEVIDSRYENFKFDLISVVADNASSTRFITGG+MA++ ++ Sbjct: 121 HGPGCHIGQVLAATDFVIPTVEVIDSRYENFKFDLISVVADNASSTRFITGGQMANVADL 180 Query: 181 DLRTLGVVMEKNGEVVELGAGAAVLGHPLSSVAMLANLLAERGEHIPAGTFIMTGGITAA 240 DLRTLGVVMEKNGEVVELGAGAAVLGHP SSVAMLANLLAERGEHIPAG+FIMTGGITAA Sbjct: 181 DLRTLGVVMEKNGEVVELGAGAAVLGHPASSVAMLANLLAERGEHIPAGSFIMTGGITAA 240 Query: 241 VPVAPGDNITVRYQGLGSVSARFI 264 VPVAPGDNITVRYQGLGSVSARFI Sbjct: 241 VPVAPGDNITVRYQGLGSVSARFI 264 Lambda K H 0.319 0.136 0.395 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: 354 Number of extensions: 1 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: 264 Length of database: 264 Length adjustment: 25 Effective length of query: 239 Effective length of database: 239 Effective search space: 57121 Effective search space used: 57121 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: 47 (22.7 bits)
Align candidate WP_090439171.1 BLS63_RS02445 (2-oxo-3-hexenedioate decarboxylase)
to HMM TIGR03218 (dmpH: 4-oxalocrotonate decarboxylase (EC 4.1.1.77))
# 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/TIGR03218.hmm # target sequence database: /tmp/gapView.23071.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03218 [M=263] Accession: TIGR03218 Description: catechol_dmpH: 4-oxalocrotonate decarboxylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-157 508.7 0.2 1.7e-157 508.5 0.2 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090439171.1 BLS63_RS02445 2-oxo-3-hexenedioa Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090439171.1 BLS63_RS02445 2-oxo-3-hexenedioate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 508.5 0.2 1.7e-157 1.7e-157 1 263 [] 1 263 [. 1 263 [. 1.00 Alignments for each domain: == domain 1 score: 508.5 bits; conditional E-value: 1.7e-157 TIGR03218 1 leltltreqiealaehvenaeleareitkitdeyPdldfadaydiqaeirrrklarGakvvGlkaGlts 69 +++tltreq+ alaeh+enael+a++i k+t++yPd++fadayd+q+eirrrk+arG+k+vGlk+Glts lcl|NCBI__GCF_900100495.1:WP_090439171.1 1 MNRTLTREQVLALAEHIENAELHAHDISKVTNDYPDMTFADAYDVQWEIRRRKEARGNKIVGLKMGLTS 69 689****************************************************************** PP TIGR03218 70 kakmkqmGvetpvfGfladyfsvpdggeiktselihPkveaeiafvlkaelkgpgchigdvlaatdfvl 138 +akm+qmGvetp++Gfladyfsvpdgg ++ts+lihPk+eaei+fv+ka+l+gpgchig+vlaatdfv+ lcl|NCBI__GCF_900100495.1:WP_090439171.1 70 WAKMAQMGVETPIYGFLADYFSVPDGGVVDTSKLIHPKIEAEISFVTKAPLHGPGCHIGQVLAATDFVI 138 ********************************************************************* PP TIGR03218 139 pavevidsrykdfkfdlksvvadnassarfvtGgraaavedldlrtlGvvleknGevvalgagaavlGh 207 p+vevidsry++fkfdl+svvadnass+rf+tGg++a+v+dldlrtlGvv+eknGevv+lgagaavlGh lcl|NCBI__GCF_900100495.1:WP_090439171.1 139 PTVEVIDSRYENFKFDLISVVADNASSTRFITGGQMANVADLDLRTLGVVMEKNGEVVELGAGAAVLGH 207 ********************************************************************* PP TIGR03218 208 paaavamlanllaergeeiPaGslilsggiteavavaaGdsvtvrvqelgsvslrf 263 pa++vamlanllaerge+iPaGs+i++ggit+av va+Gd++tvr+q+lgsvs+rf lcl|NCBI__GCF_900100495.1:WP_090439171.1 208 PASSVAMLANLLAERGEHIPAGSFIMTGGITAAVPVAPGDNITVRYQGLGSVSARF 263 *******************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (264 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: 8.16 // [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