Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate BWI76_RS21760 BWI76_RS21760 SMP-30/gluconolactonase/LRE family protein
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >FitnessBrowser__Koxy:BWI76_RS21760 Length = 286 Score = 246 bits (628), Expect = 4e-70 Identities = 128/285 (44%), Positives = 168/285 (58%), Gaps = 10/285 (3%) Query: 8 DGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAFTADPQQL 67 D + LGE +WC+R++ ++WTDI L + + + W +PERL +A T + L Sbjct: 7 DARNLLGECPIWCERTRRIYWTDIEGCELLALEEDSSVVMRWSLPERLGSFALTENSDVL 66 Query: 68 LIGLESRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDAGRAPIAS 127 L+GL SR AF +L+TG P+ P TR DGRCDR+G FVFGT+++ I Sbjct: 67 LMGLASRFAFCDLNTGIFTPVVASPGG-PGTRTGDGRCDREGNFVFGTMDDGYPAKVIGR 125 Query: 128 FYRLNT-DLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTASGAVGGQR 186 F+RLN L++E L LP +AI NSICFS DG MY+CDSM G+IM CDY + + QR Sbjct: 126 FHRLNAATLSIETLPLPEVAIPNSICFSPDGSTMYYCDSMQGRIMCCDYPS----MNNQR 181 Query: 187 VFADVAQPGGPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQPSCVAFGGA 246 VF G PDGS +DA GY+WNA+WGG+RVVRY PDG + ++ P Q +C G Sbjct: 182 VFTATEGNGAPDGSCVDALGYVWNAEWGGSRVVRYRPDGTTESILPSPGVQSTCPTLAGE 241 Query: 247 QFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVRFA 291 F TLY T+A G+S R GAL A GLPE RF+ Sbjct: 242 AFTTLYCTSASVGLSVPSR----HDGALLRAESAVFPGLPESRFS 282 Lambda K H 0.322 0.138 0.437 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: 335 Number of extensions: 24 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: 292 Length of database: 286 Length adjustment: 26 Effective length of query: 266 Effective length of database: 260 Effective search space: 69160 Effective search space used: 69160 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 (21.9 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