Align galactaro-1,5-lactonase (characterized)
to candidate RR42_RS33665 RR42_RS33665 gluconolactonase
Query= reanno::WCS417:GFF3393 (291 letters) >FitnessBrowser__Cup4G11:RR42_RS33665 Length = 300 Score = 344 bits (883), Expect = 1e-99 Identities = 166/292 (56%), Positives = 203/292 (69%), Gaps = 5/292 (1%) Query: 4 ELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDA 63 +LI D RNAVGE P W LYW DIP L W AA + W P+M CIA A Sbjct: 8 DLIADVRNAVGESPFWDTQTQCLYWSDIPARTLFEWRAANAAIRTWELPEMAGCIAPASA 67 Query: 64 GNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMG 123 G +VAGM++G F L P DGS+ + LA+V HP MR NDGRCDRQGRFWAG+M L+M Sbjct: 68 GGFVAGMQSGLFHLQPQPDGSMASRRLASVAHPAPSMRFNDGRCDRQGRFWAGTMHLDMH 127 Query: 124 LNAAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDIDT 183 + G++YR+ + Q++G I NG+A+SPDGRTMY SDSHP VQ IWAFDYD Sbjct: 128 PAQSIGSVYRFDARGLQQ-QIEGLIVPNGMAWSPDGRTMYLSDSHPDVQAIWAFDYDAAN 186 Query: 184 GTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPVKKP 243 G S RR+++DM ++ GRPDGAAVD DGCYWIC NDAG++HRF+P+GRLDRS+ +PVKKP Sbjct: 187 GVASRRRLWIDMRQYPGRPDGAAVDVDGCYWICGNDAGVVHRFTPEGRLDRSIALPVKKP 246 Query: 244 TMCAFGGSRLDTLFVTSIR----DDQSEQSLSGGVFALNPGVVGLPEPTFTL 291 MCAFGG+ + TLFVTSIR Q+EQ L+GGVFA+ PGV G+ E F L Sbjct: 247 AMCAFGGADMKTLFVTSIRPADASVQAEQPLAGGVFAVRPGVAGIAERAFQL 298 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: 421 Number of extensions: 24 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: 300 Length adjustment: 26 Effective length of query: 265 Effective length of database: 274 Effective search space: 72610 Effective search space used: 72610 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