Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate BPHYT_RS07255 BPHYT_RS07255 4-oxalocrotonate decarboxylase
Query= metacyc::MONOMER-13363 (251 letters) >FitnessBrowser__BFirm:BPHYT_RS07255 Length = 257 Score = 297 bits (760), Expect = 2e-85 Identities = 156/240 (65%), Positives = 180/240 (75%) Query: 4 LDIHAISTALDNAARFQEEIDPLTPVHGFNLDDAYLIQRASIALRHARGELPVGIKLGFT 63 +D+ I+ LD AAR E I +T F+LDDAY+IQRASI R RGE VG+KLGFT Sbjct: 2 IDLDGIAARLDEAARQAEPIAQITAAAPFSLDDAYVIQRASIERRIHRGESMVGVKLGFT 61 Query: 64 SRAKMIQMGVDSLIWGLLTDAMLYEEGAVVDLSGFIHPRAEPEVCFLTKRDIDRPLTLLE 123 SRAKMIQMGVDSLIWG LTDAML E+G + L FIHPR EPEVCFLT R+IDRPLTLLE Sbjct: 62 SRAKMIQMGVDSLIWGWLTDAMLDEDGGRIALDRFIHPRVEPEVCFLTSREIDRPLTLLE 121 Query: 124 ASSYLEGVAPAIEIIDSRYRNFKFTLEDVVADNCSSAGLVVGALSSNITDLANLGVALRF 183 AS YLE VAPA+EIIDSRYR+F+FTLEDVVADNCSSAGLV+G + L N GV +R Sbjct: 122 ASRYLEAVAPAMEIIDSRYRDFRFTLEDVVADNCSSAGLVIGPWTRKFDGLRNAGVTMRI 181 Query: 184 NGKPMQIGSTGAILGDPLRSVVQASRLAARAEMVLPAGSLIMAGAATGCPSIDRRHACQC 243 +G+ +Q GST AILGDPLRS+VQASRL ++ + LPAGSLIMAGAAT + C Sbjct: 182 DGRLVQAGSTAAILGDPLRSIVQASRLLTQSGLALPAGSLIMAGAATAAHPLTANAHVHC 241 Lambda K H 0.323 0.137 0.400 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: 233 Number of extensions: 5 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: 251 Length of database: 257 Length adjustment: 24 Effective length of query: 227 Effective length of database: 233 Effective search space: 52891 Effective search space used: 52891 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 (21.9 bits) S2: 47 (22.7 bits)
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