Align galactaro-1,5-lactonase (characterized)
to candidate WP_012403004.1 BPHY_RS18670 SMP-30/gluconolactonase/LRE family protein
Query= reanno::WCS417:GFF3393 (291 letters) >NCBI__GCF_000020045.1:WP_012403004.1 Length = 296 Score = 180 bits (456), Expect = 4e-50 Identities = 112/291 (38%), Positives = 150/291 (51%), Gaps = 16/291 (5%) Query: 4 ELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDA 63 E ++ A A+GECP W L+WVDI L + TG P+ + C + T+ Sbjct: 5 ECVLPAAAALGECPRWDERRAKLWWVDIQAPALHAFDPKTGQDTMLPMPENIGCFSLTED 64 Query: 64 GNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMG 123 ++AGM TG F L G + L A E+P R NDGRCD GRFW G++ Sbjct: 65 DGFIAGMRTGIFLLDAK--GQVVRKLCANPENPATS-RFNDGRCDAHGRFWLGTLDEPKA 121 Query: 124 LNAAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDIDT 183 NAA LY Y +GA G +T NG+AFSPD R Y SD+ I+ YD+D+ Sbjct: 122 GNAA--ALYCYGNGALTKVDA-GLLTSNGMAFSPDYRWCYHSDTPRFT--IYRHSYDVDS 176 Query: 184 GTPSNRRVFVDMHK---HLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPV 240 G R +V GRPDGA+VD++G YW + G + R SPDG++ + + Sbjct: 177 GEVGPREEWVKFEPTPTDRGRPDGASVDSEGFYWAALYEGGRVVRISPDGKVVETHPLAA 236 Query: 241 KKPTMCAFGGSRLDTLFVTSIRDDQSEQSL-----SGGVFALNPGVVGLPE 286 + PTMC FGG L TL+VT+ R +S + L SG VFA+ V GL E Sbjct: 237 RCPTMCTFGGDDLRTLYVTTARQGRSAEELEQYPQSGAVFAMRVSVPGLIE 287 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: 327 Number of extensions: 21 Number of successful extensions: 4 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: 296 Length adjustment: 26 Effective length of query: 265 Effective length of database: 270 Effective search space: 71550 Effective search space used: 71550 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 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