Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate H281DRAFT_01183 H281DRAFT_01183 Sugar lactone lactonase YvrE
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >FitnessBrowser__Burk376:H281DRAFT_01183 Length = 293 Score = 192 bits (488), Expect = 8e-54 Identities = 104/290 (35%), Positives = 161/290 (55%), Gaps = 5/290 (1%) Query: 2 NVQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAFT 61 N+ + + LGE LW DR Q ++W D HA + D + R W MP ++ A Sbjct: 5 NISICGESRDALGESPLWDDRKQILYWIDSHARLVKARDMEANTLREWKMPSQIGAIAL- 63 Query: 62 ADPQQLLIGLESRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDAG 121 + +LL+ L S F + TG + + P+ RLNDGR DR+GR V G++ Sbjct: 64 CESGRLLVALVSSFVFLDTDTGELTNFVDVTHPAPNMRLNDGRVDREGRLVLGSMALGR- 122 Query: 122 RAPIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTASGA 181 R P Y+L+ + L+ L I I+NS CFS DG+ +Y DS++ ++ Y +++G Sbjct: 123 REPAGELYQLDGEGNLKVLDT-GICITNSTCFSPDGQYLYFSDSLSCQLRRYAYHSSAGT 181 Query: 182 VGGQRVFADVAQ-PGGPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQPSC 240 + + +F D GPDG+TIDA+G LW A ++ R+ PDGR+DR++ +PT P+C Sbjct: 182 LSERTLFVDTTSLKSGPDGATIDADGNLWTALVISGQLARFTPDGRLDRIIDLPTVYPTC 241 Query: 241 VAFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVRF 290 + GG DT++VT+ + +A ++ +P AGA+ A+ VRGLPE RF Sbjct: 242 PSIGGPALDTIFVTSISDSGNA-LKSQNPNAGAVVAITGTGVRGLPECRF 290 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: 295 Number of extensions: 20 Number of successful extensions: 5 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: 293 Length adjustment: 26 Effective length of query: 266 Effective length of database: 267 Effective search space: 71022 Effective search space used: 71022 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