Align galactaro-1,5-lactonase (characterized)
to candidate WP_086511018.1 BZY95_RS16655 SMP-30/gluconolactonase/LRE family protein
Query= reanno::WCS417:GFF3393 (291 letters) >NCBI__GCF_002151265.1:WP_086511018.1 Length = 295 Score = 155 bits (393), Expect = 8e-43 Identities = 103/294 (35%), Positives = 147/294 (50%), Gaps = 15/294 (5%) Query: 4 ELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTA-PQMLACIARTD 62 E+ V+ ++GE PVW L+W DI G + W G + + + C+A + Sbjct: 7 EVAVELDMSLGESPVWSVARQTLFWADINNGHVYAWRPQQGGAPLRSELGEKVGCVALDE 66 Query: 63 AGNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNM 122 AG VA +G +L P N + Q R NDGRCD GR W G++ + Sbjct: 67 AG-LVAATASGILRL-PENGEPERLADNPEWKKAGQGNRFNDGRCDAAGRLWVGTIDADE 124 Query: 123 GLNAAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDID 182 +A LY G ++ G NGLAFSPD R +Y +DS L ++I + +D+D Sbjct: 125 ASPSA--ALYCLDKGELSR-RVTGLGISNGLAFSPDRRWLYHTDS--LSRRILRYPFDVD 179 Query: 183 TGTPSNRRVFVDMHKH--LGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPV 240 +GT +VD+ + G PDGAAVD++GCYW D G I RFSP+G L VP Sbjct: 180 SGTLGEGEAWVDLERLGLPGVPDGAAVDSEGCYWSALYDGGRIVRFSPEGELVAEHEVPC 239 Query: 241 KKPTMCAFGGSRLDTLFVTSI-----RDDQSEQSLSGGVFALNPGVVGLPEPTF 289 PTM AFGG+ L TL++T+ + ++ +G + + GV GL EP F Sbjct: 240 PHPTMVAFGGADLRTLYITTATQHLDAEGKARWPQAGSLLQMRTGVTGLAEPGF 293 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: 368 Number of extensions: 31 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: 295 Length adjustment: 26 Effective length of query: 265 Effective length of database: 269 Effective search space: 71285 Effective search space used: 71285 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