Align L-arabinolactonase (EC 3.1.1.15) / D-galactonolactonase (EC 3.1.1.25) (characterized)
to candidate RR42_RS33665 RR42_RS33665 gluconolactonase
Query= reanno::pseudo5_N2C3_1:AO356_20235 (291 letters) >FitnessBrowser__Cup4G11:RR42_RS33665 Length = 300 Score = 169 bits (429), Expect = 5e-47 Identities = 102/291 (35%), Positives = 141/291 (48%), Gaps = 19/291 (6%) Query: 6 VTEHRAKLGEGPFWDAPTQALYWVDIAGKQALRLIGANVEI--WQMPEHVSAFIPTQSGD 63 + + R +GE PFWD TQ LYW DI + AN I W++PE P +G Sbjct: 10 IADVRNAVGESPFWDTQTQCLYWSDIPARTLFEWRAANAAIRTWELPEMAGCIAPASAGG 69 Query: 64 ALVTLSSGVYRLDLDSPGLEPRLTLLCMADPQPGNRANEARCDPQGQLWLGTMQNNIGAE 123 + + SG++ L G L +A P P R N+ RCD QG+ W GTM Sbjct: 70 FVAGMQSGLFHLQPQPDGSMASRRLASVAHPAPSMRFNDGRCDRQGRFWAGTMHL----- 124 Query: 124 GEDLPIEHRSGGLFRVGSDGRVLPLLRGLGIPNTLLWSPDGTTVYFGDSL-DGTVYRHFI 182 D+ G ++R + G + + GL +PN + WSPDG T+Y DS D F Sbjct: 125 --DMHPAQSIGSVYRFDARG-LQQQIEGLIVPNGMAWSPDGRTMYLSDSHPDVQAIWAFD 181 Query: 183 YPEGN--LAPAEVWFGPHPRGG-PDGSAMDARGYIWNARWDGSCLLRLTPDGQVDRVIEL 239 Y N + +W G PDG+A+D G W D + R TP+G++DR I L Sbjct: 182 YDAANGVASRRRLWIDMRQYPGRPDGAAVDVDGCYWICGNDAGVVHRFTPEGRLDRSIAL 241 Query: 240 PVSRPTSCVFGGEDLKTLYITS-----AASPLGHPLDGAVLSMRVDVPGVA 285 PV +P C FGG D+KTL++TS A+ PL G V ++R V G+A Sbjct: 242 PVKKPAMCAFGGADMKTLFVTSIRPADASVQAEQPLAGGVFAVRPGVAGIA 292 Lambda K H 0.319 0.140 0.455 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: 399 Number of extensions: 28 Number of successful extensions: 4 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: 291 Length of database: 300 Length adjustment: 26 Effective length of query: 265 Effective length of database: 274 Effective search space: 72610 Effective search space used: 72610 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 (21.7 bits) S2: 48 (23.1 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