Align xylono-1,5-lactonase (EC 3.1.1.110) (characterized)
to candidate HSERO_RS05225 HSERO_RS05225 gluconolaconase
Query= metacyc::MONOMER-20630 (291 letters) >FitnessBrowser__HerbieS:HSERO_RS05225 Length = 292 Score = 129 bits (323), Expect = 1e-34 Identities = 97/295 (32%), Positives = 140/295 (47%), Gaps = 16/295 (5%) Query: 1 MTVTRVVDTSCRLGEGPVWHPDEKRLYWVDIESGRLHRYDPETG---AHDCPVETSVIAG 57 M V +VD LGEG +W + ++W DI + RL +DP+TG + P A Sbjct: 1 MNVQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYA- 59 Query: 58 VTIQRDGSLLAFMDRGRVGRVVDGDRRESARIVDS--PTRFNDVIADPAGRVFCGTMPSD 115 T L+ R + G RI D TR ND D GR GT+ D Sbjct: 60 FTADPQQLLIGLESRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNED 119 Query: 116 TAGGRL---FRLDTDGTVTTVET-GVGIPNGMGFTRDRERFYFTETEARTVYRYAYDEET 171 + +RL+TD T+ + + I N + F+ D + Y ++ A + YD + Sbjct: 120 AGRAPIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTAS 179 Query: 172 GAVSARERFVESPETPGLPDGMTVDSAGHIWSARWEGGCVVEYDADGTELGRFDVPTEKV 231 GAV + F + + PG PDG T+D+ G++W+A+W G VV Y DG +PT + Sbjct: 180 GAVGGQRVFADVAQ-PGGPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQP 238 Query: 232 TSVAFGGPDLDSLYVTTAGGDGDGSAGEGDESTGDAAGALFRLDVA-ATGRPEFR 285 + VAFGG D+LYVTTA +G + E + AGALF + +A G PE R Sbjct: 239 SCVAFGGAQFDTLYVTTA---HEGMSAE-QRAADPQAGALFAVALADVRGLPEVR 289 Lambda K H 0.317 0.138 0.420 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: 269 Number of extensions: 16 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: 291 Length of database: 292 Length adjustment: 26 Effective length of query: 265 Effective length of database: 266 Effective search space: 70490 Effective search space used: 70490 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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