Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate GFF3393 PS417_17365 gluconolactonase
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >FitnessBrowser__WCS417:GFF3393 Length = 291 Score = 155 bits (393), Expect = 8e-43 Identities = 102/299 (34%), Positives = 152/299 (50%), Gaps = 19/299 (6%) Query: 1 MNVQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAF 60 MN +L+VD + +GE +W +++W DI L TG +W P+ L C A Sbjct: 1 MNAELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIAR 60 Query: 61 TADPQQLLIGLESRLAFFNLST---GTIAP--ICRIEDDLPSTRLNDGRCDRQGRFVFGT 115 T D + G+E+ FF L+ G++ + +E RLNDGRCDRQGRF G+ Sbjct: 61 T-DAGNWVAGMET--GFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGS 117 Query: 116 LNEDAG-RAPIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDS--MAGKIMV 172 + + G A + YR T L N + FS DG+ MY DS + +I Sbjct: 118 MVLNMGLNAAEGTLYRY-TSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWA 176 Query: 173 CDYDTASGAVGGQRVFADVAQP-GGPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVV 231 DYD +G +RVF D+ + G PDG+ +DA+G W + R++PDGR+DR + Sbjct: 177 FDYDIDTGTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSL 236 Query: 232 AIPTSQPSCVAFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVRF 290 +P +P+ AFGG++ DTL+VT+ + S + +G +FA+ V GLPE F Sbjct: 237 TVPVKKPTMCAFGGSRLDTLFVTSIRDDQSEQS-----LSGGVFALN-PGVVGLPEPTF 289 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: 299 Number of extensions: 13 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: 291 Length adjustment: 26 Effective length of query: 266 Effective length of database: 265 Effective search space: 70490 Effective search space used: 70490 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