Align galactaro-1,5-lactonase (characterized)
to candidate SMc04142 SMc04142 hypothetical protein
Query= reanno::WCS417:GFF3393 (291 letters) >FitnessBrowser__Smeli:SMc04142 Length = 294 Score = 149 bits (377), Expect = 6e-41 Identities = 101/283 (35%), Positives = 139/283 (49%), Gaps = 8/283 (2%) Query: 4 ELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWS-AATGHVAAWTAPQMLACIARTD 62 E ++D+R V E PV+ N L++VDI + L R + GHV WT Sbjct: 8 ECLLDSRCDVAESPVFDERRNCLFFVDIGRSALHRVDLSGAGHVE-WTIEGGACSTGLAR 66 Query: 63 AGNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNM 122 +G V P D T +AA+E D RLNDG+ G FW G+M ++ Sbjct: 67 SGRLVLAQRDRVVLFDP--DAGAVTREIAAIEPDIADTRLNDGKVGPDGAFWVGTMH-DV 123 Query: 123 GLNAAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDID 182 +LYR + A +++G + NGLA+S DG ++ SDS W FD Sbjct: 124 PDRRPVASLYRVSPEGAVERKVEGVVCSNGLAWSGDGSLLFHSDSRGAWIDRWQFDPA-- 181 Query: 183 TGTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPVKK 242 TG S RR + + GRPDGAA DA+ YW AG+++RFSP+GRL + PV Sbjct: 182 TGALSGRRRLASLDEASGRPDGAATDAEAHYWSAGVSAGIVNRFSPEGRLVGTHRFPVPA 241 Query: 243 PTMCAFGGSRLDTLFVTSIRD-DQSEQSLSGGVFALNPGVVGL 284 PTM F G L TL VTS+R +++ SGG+F V G+ Sbjct: 242 PTMPCFAGPDLKTLLVTSLRPAGIGKENRSGGIFVARSPVAGV 284 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: 366 Number of extensions: 16 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: 294 Length adjustment: 26 Effective length of query: 265 Effective length of database: 268 Effective search space: 71020 Effective search space used: 71020 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