Align L-arabinonolactonase (characterized, see rationale)
to candidate H281DRAFT_05978 H281DRAFT_05978 Sugar lactone lactonase YvrE
Query= uniprot:A0A1I2AUG6 (300 letters) >FitnessBrowser__Burk376:H281DRAFT_05978 Length = 303 Score = 192 bits (487), Expect = 1e-53 Identities = 120/291 (41%), Positives = 156/291 (53%), Gaps = 10/291 (3%) Query: 5 VVHHPANTLGEGILWCEREQALYWTDIQAATLWRHRPADGATRSWEMPERLGCLALCEAD 64 VV + LGE I+W E+ Q L+W D ++ R + GA +SW M E +G + L A Sbjct: 19 VVDSTPDVLGESIIWDEKTQLLWWVDGIGQSIHRLDISSGAKKSWPMQEEIGSIGL-RAK 77 Query: 65 GWLLLGLATRLAFFRPEDDLLLPLVSVEPDLP-TRLNDGACDRQGRFVFGTLHEPAAGET 123 G L++G+ + FF PE L + + + P R NDG CDR GR+ GT+ AA T Sbjct: 78 GGLIVGMRSGFYFFSPETGELTEVARPDAERPKNRFNDGKCDRHGRYWSGTVE--AAAYT 135 Query: 124 RQPIGAFYRLNADLTLERLNLPGIGISNSVAFSPDGRTMYFCDSPSRVIQCCDYGDRCG- 182 P G +RL+ DL +L + GI N ++FSPD R MY DS S I DY G Sbjct: 136 --PRGRLFRLDPDLK-PKLIMEGITCINGLSFSPDNRLMYMTDSFSCQIDVFDYDSVDGA 192 Query: 183 --EPRVFARVDDERGEPDGSAVDAQGCLWNAQWGLGRVVRYAPDGRVDRIVEVPATQPTR 240 R FA V RG DGS VDA GC W+A V RY P GR+D ++ +P + + Sbjct: 193 IYNRRKFAEVPLGRGICDGSTVDADGCFWSANMDGWCVTRYDPRGRIDMVINLPVRRVSS 252 Query: 241 PAFGDSPLDTLYITSARDGLSSAALATQPLAGALFAADAGASGLPEPRFRG 291 FG LDTL+IT+AR +S LA QPLAG + A G GLPEP F G Sbjct: 253 LCFGGPDLDTLFITTARRRMSEKELAQQPLAGNVLAVRPGVKGLPEPEFLG 303 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: 339 Number of extensions: 22 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: 300 Length of database: 303 Length adjustment: 27 Effective length of query: 273 Effective length of database: 276 Effective search space: 75348 Effective search space used: 75348 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