Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate PfGW456L13_2295 Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)
Query= BRENDA::Q13KT2 (263 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2295 Length = 270 Score = 105 bits (261), Expect = 1e-27 Identities = 87/285 (30%), Positives = 132/285 (46%), Gaps = 39/285 (13%) Query: 1 MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60 MP+ ++G LHY ID G P ++L+ S D +MWAPQ+AALS+ +RV+ D GH Sbjct: 1 MPFVTIDGQALHY-ID---QGTGPAVLLAGSYLWDQAMWAPQIAALSQQYRVIALDLWGH 56 Query: 61 GHS-EAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVAL 119 G S P G +++ L L L+D L I R GLS+GG+ G LA A RI + L Sbjct: 57 GQSGPLPVGTTSLDDLARQALVLLDHLDIERVTLVGLSVGGMWGARLALSAAQRINGLVL 116 Query: 120 CNTAARIGSPE------VWVPRAVKARTEGMHALADAVLPRWF-------TADYMEREPV 166 +T A PE + + ++ AL D V+P +F +A Y + Sbjct: 117 MDTYAG-AEPEPTRQYYFSLLKQIEEAGVITPALLDIVVPIFFRPGIDPQSALYRDFRAS 175 Query: 167 VLAMIRDVF---------VHTDKEGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAA 217 + A+ D + ++ S +DAA LV+ G D Sbjct: 176 LAALPADRLRESIAPMGRITFGRDDQLSRLGELDAA-----------TTLVMCGDQDKPR 224 Query: 218 TPAQGRELAQAIAGARYVELDASHISNIERADAFTKTVVDFLTEQ 262 P + RE+A+ I + +A HISN+E T+T++ FL ++ Sbjct: 225 PPGEAREMAELIGCPWVLVPEAGHISNLENPGFVTETLLAFLADR 269 Lambda K H 0.320 0.134 0.402 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: 175 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 263 Length of database: 270 Length adjustment: 25 Effective length of query: 238 Effective length of database: 245 Effective search space: 58310 Effective search space used: 58310 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)
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