Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate RR42_RS32645 RR42_RS32645 2-keto-4-pentenoate hydratase
Query= metacyc::MONOMER-15110 (260 letters) >FitnessBrowser__Cup4G11:RR42_RS32645 Length = 260 Score = 210 bits (534), Expect = 3e-59 Identities = 105/249 (42%), Positives = 161/249 (64%), Gaps = 1/249 (0%) Query: 6 IKDLARFLVDAEVEKKEVLKLTNEHPDLTVEDGYAIQEQLVQMKLEQGYRIVGPKMGLTS 65 I ++ L A +++ + LT +P+L+++D Y IQ +VQ +L+ G R++G K+G+TS Sbjct: 6 ILEIGASLHQALDQRQAIAPLTERYPELSIDDAYRIQLAMVQHRLDAGERVIGKKIGVTS 65 Query: 66 QAKMKQMNVNEPIYGYIFDYMV-VNGQELSMSELIHPKVEAEIAFILGKDIEGPGITGAQ 124 + M ++V +P +G++ MV +G ++ + LI PK E EIAF+L +D+EGPG+T A Sbjct: 66 RVVMDMLDVRQPDFGHLLSGMVHADGTAIAANTLIAPKAEGEIAFVLKEDLEGPGVTNAD 125 Query: 125 VLAATEYVVPALEIIDSRYQNFQFTLPDVIADNASSSRVFLGSTIKRPDNMELDLLGVTL 184 VL AT YV+P EI+DSR ++++ +PD +ADNASS LG P ++L +G+TL Sbjct: 126 VLRATAYVLPCFEIVDSRIRDWKIRIPDTVADNASSGVFVLGDAAVDPRGLDLGTVGMTL 185 Query: 185 SINGQIKDLGAGAAVVGHPANSVAMLANMLARKGLKLKAGQIILSGGITGAVMLNVGDSV 244 NG+I GAGAA +GHPAN+VA LAN L R G+ LK G++ILSG + V + GD + Sbjct: 186 EKNGEIVATGAGAAALGHPANAVAWLANTLGRLGIGLKKGEVILSGSLAAMVPVQAGDQL 245 Query: 245 TGKFDGLGT 253 G+G+ Sbjct: 246 RISLGGIGS 254 Lambda K H 0.317 0.137 0.374 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: 184 Number of extensions: 6 Number of successful extensions: 2 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: 260 Length of database: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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