Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate WP_012277179.1 SHAL_RS10920 2-keto-4-pentenoate hydratase
Query= BRENDA::B0VXM8 (267 letters) >NCBI__GCF_000019185.1:WP_012277179.1 Length = 271 Score = 170 bits (430), Expect = 3e-47 Identities = 103/265 (38%), Positives = 149/265 (56%), Gaps = 8/265 (3%) Query: 4 TVKVSLYRKFAELLNEAEREKREVARITEEVPDLSAEEAYKIQEELIKIKTNSGHRIIGP 63 T SL AE L A R+ + ++E L+ ++AY+I ++ + N G ++IG Sbjct: 8 TTNSSLIEMHAEELLLALRKGEAITPLSERTTSLTIDDAYQISRLCLQQRENDGEQLIGK 67 Query: 64 KMGLTSQAKMAQMKVKEPIYGYLFDYMFVPSGGAIHMSE--LIHPKVEVEIAFILGEDLE 121 K+G+TS A + V +P +G+L + M +G I +S+ LI PK E EIAF L EDL Sbjct: 68 KIGVTSLAVQQMLNVHQPDFGFLTNSMHFNNGDCISLSKAKLIQPKAEGEIAFCLKEDLH 127 Query: 122 GPHVTSTQVLSATKYVAPALEIIDSRYQDFTFTLPDVIADNASSSRVVIGNTMTPIHSLK 181 GP VT+ VL AT +VAP EI+DSR +D+ ++ D +ADNAS VIG+T TP Sbjct: 128 GPGVTAQDVLDATLWVAPCFEIVDSRIEDWRISIVDTVADNASCGVFVIGDTHTP----P 183 Query: 182 TDLDLIGAALYI--NGELKACGAGAAVFNHPANSVAVLANMLARKGERLKAGDIILTGGI 239 ++DL A + I N + G G+AV HPA +VA L N L G K G+IIL+G + Sbjct: 184 REIDLAEAQMEIKKNSQFAGSGLGSAVQGHPAQAVAWLTNTLGEYGIPFKKGEIILSGAL 243 Query: 240 TEAIQLSAGDTVIGQLDQLGDVSLS 264 I +GD +++ LG S+S Sbjct: 244 APLIVAQSGDKFTMEIEGLGSCSIS 268 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: 178 Number of extensions: 10 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: 271 Length adjustment: 25 Effective length of query: 242 Effective length of database: 246 Effective search space: 59532 Effective search space used: 59532 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 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