Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate H281DRAFT_05978 H281DRAFT_05978 Sugar lactone lactonase YvrE
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >FitnessBrowser__Burk376:H281DRAFT_05978 Length = 303 Score = 189 bits (481), Expect = 5e-53 Identities = 109/281 (38%), Positives = 156/281 (55%), Gaps = 5/281 (1%) Query: 13 LGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAFTADPQQLLIGLE 72 LGE ++W +++Q ++W D + D +G +SW M E + A L++G+ Sbjct: 27 LGESIIWDEKTQLLWWVDGIGQSIHRLDISSGAKKSWPMQEEIGSIGLRAKGG-LIVGMR 85 Query: 73 SRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDAGRAPIASFYRLN 132 S FF+ TG + + R + + P R NDG+CDR GR+ GT+ E A P +RL+ Sbjct: 86 SGFYFFSPETGELTEVARPDAERPKNRFNDGKCDRHGRYWSGTV-EAAAYTPRGRLFRLD 144 Query: 133 TDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTASGAVGGQRVFADVA 192 DL +L + I N + FS D +LMY DS + +I V DYD+ GA+ +R FA+V Sbjct: 145 PDLK-PKLIMEGITCINGLSFSPDNRLMYMTDSFSCQIDVFDYDSVDGAIYNRRKFAEVP 203 Query: 193 QPGGP-DGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQPSCVAFGGAQFDTL 251 G DGST+DA+G W+A G V RY P GRID V+ +P + S + FGG DTL Sbjct: 204 LGRGICDGSTVDADGCFWSANMDGWCVTRYDPRGRIDMVINLPVRRVSSLCFGGPDLDTL 263 Query: 252 YVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVRFAG 292 ++TTA MS ++ A P AG + AV V+GLPE F G Sbjct: 264 FITTARRRMSEKELAQQPLAGNVLAVR-PGVKGLPEPEFLG 303 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: 296 Number of extensions: 11 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: 303 Length adjustment: 26 Effective length of query: 266 Effective length of database: 277 Effective search space: 73682 Effective search space used: 73682 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