Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate H281DRAFT_05322 H281DRAFT_05322 gluconolactonase (EC 3.1.1.17)
Query= reanno::ANA3:7024914 (300 letters) >FitnessBrowser__Burk376:H281DRAFT_05322 Length = 317 Score = 151 bits (381), Expect = 2e-41 Identities = 99/302 (32%), Positives = 148/302 (49%), Gaps = 26/302 (8%) Query: 19 LGEGVLWDDLHQSIWWTDILSSVIYRFHLASRSLETFPMPHRVGSFGLTAKPTTL----- 73 +GE +W Q+++W DI + I R + + + +P +V + T L Sbjct: 22 VGESPVWRVAEQALYWVDIPAQKIVRLVVETGKRSEWLLPEKVACIAFDRRGTVLAGCET 81 Query: 74 -IVAFDIGIAIYDIEDQSLTW----------LAQPESHFAGNRFNDGRIDRQGRFWAGTM 122 + A + + D Q++ LA P F RFNDGR DRQGRFWAGTM Sbjct: 82 ALFAVTLSGSSTDATAQAVRASEPVEVTGRKLAAPVFPFDDMRFNDGRCDRQGRFWAGTM 141 Query: 123 VEQRDTLQQTAALYCLDEKGHCHQHLTN-LEISNGLCWSVDGRTLYHADSP--KHQIYQY 179 V+ ALY D +G + + L NGL WS DG+T+Y +DS + QI+ + Sbjct: 142 VQDMSLANPAGALYRFDAQGVLSAPVVDGLITQNGLGWSPDGKTMYLSDSHPLRRQIWAF 201 Query: 180 DFDIEQGLLSRKRLFASTSHHI-FPDGSDVDAAGYLWNAQWGGGQVVRYRPDGEVDLILK 238 D+++E G + +R+FA +H++ PDG+ VDA G W G ++R+ P G++D + Sbjct: 202 DYEVETGEPNNRRVFADLNHYVGRPDGAAVDADGCYWICANDAGALLRFTPQGKLDRQIA 261 Query: 239 LPVTHPTSIAFGGEKRDLLIVTSAKHSLDASQLDQEPQAGDVFIYPLQGIYGVNSPRFCG 298 +P P AFGG D L VTS + AS+ D G +F G+ G+ P F G Sbjct: 262 VPAIKPAMCAFGGRDLDTLFVTSIRPGAGASEHD-----GHLFAV-RPGVSGLPEPEFAG 315 Query: 299 QL 300 L Sbjct: 316 DL 317 Lambda K H 0.322 0.139 0.441 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: 281 Number of extensions: 15 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: 317 Length adjustment: 27 Effective length of query: 273 Effective length of database: 290 Effective search space: 79170 Effective search space used: 79170 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