Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate RR42_RS27850 RR42_RS27850 2-oxo-hepta-3-ene-1,7-dioate hydratase
Query= BRENDA::B0VXM8 (267 letters) >FitnessBrowser__Cup4G11:RR42_RS27850 Length = 267 Score = 174 bits (440), Expect = 2e-48 Identities = 106/260 (40%), Positives = 146/260 (56%), Gaps = 8/260 (3%) Query: 9 LYRKFAELLNEAEREKREVARITEEVPDLSAEEAYKIQEELIKIKTNSGHRIIGPKMGLT 68 L + A L+ AE+ ++++ +I+ + PD++ E+AY IQ E + K + G I G K+GLT Sbjct: 6 LIHQIAHRLHGAEQSRQQIRQISLDHPDITIEDAYAIQREWLAHKLSEGRTIKGHKIGLT 65 Query: 69 SQAKMAQMKVKEPIYGYLFDYMFVPSGGAIHMSELIHPKVEVEIAFILGEDLEGPHVTST 128 S+A ++ EP YG L D MF G I I P+VEVE+AF+L + L+GP+ T Sbjct: 66 SRAMQLSSQIDEPDYGTLLDDMFFQDGATIPPGRFIVPRVEVELAFVLDKPLKGPNCTLF 125 Query: 129 QVLSATKYVAPALEIIDSRYQ--DFTFTLP----DVIADNASSSRVVIGNTMTPIHSLKT 182 V AT YV PALEIID+R D P D IADNA+++ VV+G P+ Sbjct: 126 DVYDATAYVIPALEIIDARSHGIDPDSKRPRKVFDTIADNAANAGVVMGG--RPVRPFDV 183 Query: 183 DLDLIGAALYINGELKACGAGAAVFNHPANSVAVLANMLARKGERLKAGDIILTGGITEA 242 DL + A + NG ++ G A V NHPAN VA LAN L G L+AG++IL G T Sbjct: 184 DLRWVSAIMSRNGVIEETGVAAGVLNHPANGVAWLANKLHPHGVGLEAGEVILGGSFTRP 243 Query: 243 IQLSAGDTVIGQLDQLGDVS 262 + S GDT LG V+ Sbjct: 244 VAASPGDTFHVDYGALGAVA 263 Lambda K H 0.316 0.134 0.364 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: 165 Number of extensions: 5 Number of successful extensions: 3 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: 267 Length of database: 267 Length adjustment: 25 Effective length of query: 242 Effective length of database: 242 Effective search space: 58564 Effective search space used: 58564 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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