Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate WP_083709430.1 BW971_RS07470 polyprenol monophosphomannose synthase
Query= BRENDA::Q2PCE3 (246 letters) >NCBI__GCF_900156495.1:WP_083709430.1 Length = 280 Score = 84.7 bits (208), Expect = 2e-21 Identities = 70/224 (31%), Positives = 112/224 (50%), Gaps = 20/224 (8%) Query: 10 IVLATLNEIDNLPRLCSDIDSILKNTKIKYQLLFVDDNSSDGTREFIIEYCNKNKLSKY- 68 +++ T NE +NLP + + L + L VDD+S DGT + + + Sbjct: 40 VIIPTFNERENLPVITERLLGSLPGITV----LVVDDDSPDGTGDLADRLAADDPAGRIK 95 Query: 69 IFNEYKKSTLIARY-----QGINNADGKYIIL-MDSDLQHPPKYLLNIYNSLLKHNDIVI 122 + + K L Y QG++ DG +++ MD+D H P+ L + + + D+VI Sbjct: 96 VMHRTGKGGLGTAYLAGFRQGLD--DGFQVLVEMDADGSHAPEQLSRLLEKVNEGYDLVI 153 Query: 123 ASRYVKGGSTGNRKPIRGIISRGASLMAQLLLKSSRQIKDPISCYIGFRKG----LKLD- 177 SRYV GG N R ++SRGA+L A+L L SS + D + Y +R+ + LD Sbjct: 154 GSRYVPGGELVNWPRRRELLSRGANLYARLALGSS--VHDITAGYRAYRRAVLEKIALDT 211 Query: 178 IDEGWRGYEIGIFLRASNNNVKVKEIPYRFAERENGKSKVTSSV 221 +D ++I + RA +V E+P F ERE G+SK++ SV Sbjct: 212 VDSQGYCFQIDLAWRALQAGFRVGEVPITFTEREIGESKMSGSV 255 Lambda K H 0.320 0.140 0.396 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: 140 Number of extensions: 11 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: 246 Length of database: 280 Length adjustment: 25 Effective length of query: 221 Effective length of database: 255 Effective search space: 56355 Effective search space used: 56355 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: 47 (22.7 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