Align L-arabinonolactonase (characterized, see rationale)
to candidate H281DRAFT_01183 H281DRAFT_01183 Sugar lactone lactonase YvrE
Query= uniprot:A0A1I2AUG6 (300 letters) >FitnessBrowser__Burk376:H281DRAFT_01183 Length = 293 Score = 181 bits (458), Expect = 2e-50 Identities = 112/294 (38%), Positives = 158/294 (53%), Gaps = 12/294 (4%) Query: 2 NARVVHHPANTLGEGILWCEREQALYWTDIQAATLWRHRPADGATRSWEMPERLGCLALC 61 N + + LGE LW +R+Q LYW D A + R W+MP ++G +ALC Sbjct: 5 NISICGESRDALGESPLWDDRKQILYWIDSHARLVKARDMEANTLREWKMPSQIGAIALC 64 Query: 62 EADGWLLLGLATRLAFFRPEDDLLLPLVSVEPDLPT-RLNDGACDRQGRFVFGTLHEPAA 120 E+ G LL+ L + F + L V V P RLNDG DR+GR V G++ A Sbjct: 65 ES-GRLLVALVSSFVFLDTDTGELTNFVDVTHPAPNMRLNDGRVDREGRLVLGSM---AL 120 Query: 121 GETRQPIGAFYRLNADLTLERLNLPGIGISNSVAFSPDGRTMYFCDSPSRVIQCCDYGDR 180 G R+P G Y+L+ + L+ L+ GI I+NS FSPDG+ +YF DS S ++ Y Sbjct: 121 GR-REPAGELYQLDGEGNLKVLDT-GICITNSTCFSPDGQYLYFSDSLSCQLRRYAYHSS 178 Query: 181 CG---EPRVFARVDDERGEPDGSAVDAQGCLWNAQWGLGRVVRYAPDGRVDRIVEVPATQ 237 G E +F + PDG+ +DA G LW A G++ R+ PDGR+DRI+++P Sbjct: 179 AGTLSERTLFVDTTSLKSGPDGATIDADGNLWTALVISGQLARFTPDGRLDRIIDLPTVY 238 Query: 238 PTRPAFGDSPLDTLYITSARDGLSSAALATQPLAGALFA-ADAGASGLPEPRFR 290 PT P+ G LDT+++TS D +A + P AGA+ A G GLPE RF+ Sbjct: 239 PTCPSIGGPALDTIFVTSISDS-GNALKSQNPNAGAVVAITGTGVRGLPECRFK 291 Lambda K H 0.321 0.139 0.451 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: 284 Number of extensions: 12 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: 300 Length of database: 293 Length adjustment: 26 Effective length of query: 274 Effective length of database: 267 Effective search space: 73158 Effective search space used: 73158 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: 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