Align galactaro-1,5-lactonase (characterized)
to candidate PP_1170 PP_1170 Gluconolactonase
Query= reanno::WCS417:GFF3393 (291 letters) >FitnessBrowser__Putida:PP_1170 Length = 293 Score = 389 bits (998), Expect = e-113 Identities = 188/292 (64%), Positives = 216/292 (73%), Gaps = 4/292 (1%) Query: 1 MNAELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIAR 60 MN ELIVDARN GE PVW PGE ALYWVDIP L RW AA G W +MLACIAR Sbjct: 1 MNCELIVDARNGTGESPVWHPGEQALYWVDIPARQLHRWQAADGKHQCWQGDEMLACIAR 60 Query: 61 TDAGNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVL 120 + G WVAGME+G FQL DGSLD+ LL+ V+H + MR NDGRCDRQGRFWAG+M+L Sbjct: 61 SGQG-WVAGMESGIFQLQAKADGSLDSRLLSNVQHAQAGMRFNDGRCDRQGRFWAGTMLL 119 Query: 121 NMGLNAAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYD 180 +M A G LYR+ H Q DG I NGLAFSPDG+ MY SDSHP VQ++WAFDYD Sbjct: 120 DMQQGAHVGALYRHDGEGHLHLQQDGMIVPNGLAFSPDGKRMYLSDSHPNVQKVWAFDYD 179 Query: 181 IDTGTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPV 240 D+GTP + +FVDM + GRPDGAA+D DGCYWIC NDAG IHRF+P+GRLDRSL+VPV Sbjct: 180 TDSGTPHGKHLFVDMRNYPGRPDGAAIDQDGCYWICGNDAGQIHRFTPEGRLDRSLSVPV 239 Query: 241 KKPTMCAFGGSRLDTLFVTSIRD---DQSEQSLSGGVFALNPGVVGLPEPTF 289 KKP MCAFGG+ LD L+VTSIR D S+Q L+GGVFAL+PG GL EP + Sbjct: 240 KKPAMCAFGGASLDILYVTSIRPTGIDLSDQPLAGGVFALDPGTKGLEEPAY 291 Lambda K H 0.321 0.137 0.443 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: 475 Number of extensions: 20 Number of successful extensions: 3 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: 293 Length adjustment: 26 Effective length of query: 265 Effective length of database: 267 Effective search space: 70755 Effective search space used: 70755 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