Align galactaro-1,5-lactonase (characterized)
to candidate WP_053939912.1 WG78_RS21560 lactonase family protein
Query= reanno::HerbieS:HSERO_RS15795 (352 letters) >NCBI__GCF_001294205.1:WP_053939912.1 Length = 402 Score = 147 bits (370), Expect = 6e-40 Identities = 106/340 (31%), Positives = 168/340 (49%), Gaps = 31/340 (9%) Query: 26 DSQDIYVLRLN-NDGSVNLIDKVDTGSTVMPLAISPDRKYLYASLRREPYAVASYAIDPA 84 + Q +Y+LR + G++ + + AIS D Y+ + + VA+YAID Sbjct: 55 NGQGVYLLRQDPQTGALQQVGVYPSVPNPAQFAISKDTLYVGSESPKHG-EVAAYAIDRR 113 Query: 85 SGKLKALSKAPLADNMA-NIATDRSGRYLLAASYFGNKISVNAIGSDGAVQTP------- 136 +G L ++ + + R LL A+Y +++ A+ DG++ Sbjct: 114 TGALTLRNQVDAQGKQTVYLGLINNQRQLLVANYGSGSVALFALAQDGSLGAASDVHQSV 173 Query: 137 -------PLAVIP--------TGKNAHSVQVDPANAFVFASNLGSDVILQYRFDPASGAV 181 P A + G +AH + DP+ F F+++LG D I Q+R D G + Sbjct: 174 GQPGAAHPAAAVEGSFAASDHNGPHAHMIAADPSGQFAFSTDLGLDRIYQWRIDAEHGKL 233 Query: 182 TPNTPPSV-ASKAGAGPRHFVFSPDQRFLYCANELDATVSTYAYDRQAGTLTLLGSDSAL 240 PN PP + AS AGAGPRHFVF D + LY NE +T++ Y D GTLT S S L Sbjct: 234 LPNDPPFINASSAGAGPRHFVFGADGKQLYLVNEEASTLTHYRLDTGKGTLTEAASLSTL 293 Query: 241 PEGFQSSEQLAAADLHLTPDGRFLYATERTSNTLTGYRVDRASGKLTRILNIPTE-TQPR 299 P GF+ + A+D+ +TPDGRF+Y R +++ + V A G L+ + T + PR Sbjct: 294 PPGFKGTS--FASDILITPDGRFVYVLNRLHDSIARFAV-AADGSLSWQDDTWTRGSYPR 350 Query: 300 AFNIDPQGRYLLAVGQKAG-LTSYAIDAASGTLTPLFRYT 338 +DP GR++ Q++ + ++ +DAASG + +YT Sbjct: 351 TLTLDPAGRFIYVANQRSDHIATFKLDAASGKVEFTGQYT 390 Lambda K H 0.316 0.131 0.375 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: 486 Number of extensions: 40 Number of successful extensions: 13 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: 352 Length of database: 402 Length adjustment: 30 Effective length of query: 322 Effective length of database: 372 Effective search space: 119784 Effective search space used: 119784 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: 50 (23.9 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