Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate WP_086511018.1 BZY95_RS16655 SMP-30/gluconolactonase/LRE family protein
Query= reanno::ANA3:7024914 (300 letters) >NCBI__GCF_002151265.1:WP_086511018.1 Length = 295 Score = 157 bits (396), Expect = 4e-43 Identities = 103/298 (34%), Positives = 147/298 (49%), Gaps = 12/298 (4%) Query: 7 GELLMTIPVGNRLGEGVLWDDLHQSIWWTDILSSVIYRFHLASRSLET-FPMPHRVGSFG 65 G + + + + LGE +W Q+++W DI + +Y + + +VG Sbjct: 4 GMIEVAVELDMSLGESPVWSVARQTLFWADINNGHVYAWRPQQGGAPLRSELGEKVGCVA 63 Query: 66 LTAKPTTLIVAFDIGIAIYDIEDQSLTWLAQPESHFAG--NRFNDGRIDRQGRFWAGTMV 123 L L+ A GI + PE AG NRFNDGR D GR W GT+ Sbjct: 64 LDE--AGLVAATASGILRLPENGEPERLADNPEWKKAGQGNRFNDGRCDAAGRLWVGTI- 120 Query: 124 EQRDTLQQTAALYCLDEKGHCHQHLTNLEISNGLCWSVDGRTLYHADSPKHQIYQYDFDI 183 D +AALYCLD KG + +T L ISNGL +S D R LYH DS +I +Y FD+ Sbjct: 121 -DADEASPSAALYCLD-KGELSRRVTGLGISNGLAFSPDRRWLYHTDSLSRRILRYPFDV 178 Query: 184 EQGLLSRKRLFASTSHHIFP---DGSDVDAAGYLWNAQWGGGQVVRYRPDGEVDLILKLP 240 + G L + P DG+ VD+ G W+A + GG++VR+ P+GE+ ++P Sbjct: 179 DSGTLGEGEAWVDLERLGLPGVPDGAAVDSEGCYWSALYDGGRIVRFSPEGELVAEHEVP 238 Query: 241 VTHPTSIAFGGEKRDLLIVTSAKHSLDASQLDQEPQAGDVFIYPLQGIYGVNSPRFCG 298 HPT +AFGG L +T+A LDA + PQAG + + G+ G+ P F G Sbjct: 239 CPHPTMVAFGGADLRTLYITTATQHLDAEGKARWPQAGSL-LQMRTGVTGLAEPGFKG 295 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: 311 Number of extensions: 17 Number of successful extensions: 6 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: 295 Length adjustment: 26 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 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 24 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