Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate BWI76_RS14050 BWI76_RS14050 AP endonuclease, family 2
Query= reanno::Phaeo:GFF712 (297 letters) >FitnessBrowser__Koxy:BWI76_RS14050 Length = 307 Score = 243 bits (620), Expect = 4e-69 Identities = 117/307 (38%), Positives = 181/307 (58%), Gaps = 11/307 (3%) Query: 1 MTIRIGNAPCSWGVEFAQDPRNPDWRSVLKDCAEAGYKGIELGPVGYMPEDPAILRDALA 60 MTI I NAPCSWGV+ ++P P W VL++ A AGYK IELGP Y+P L AL Sbjct: 1 MTIHIANAPCSWGVDDPKNPYLPPWPKVLEEAATAGYKSIELGPWSYLPTRADELSAALN 60 Query: 61 EYDLELIGGVVFRAFHDPDQWDDVLDGAHRTCKAL-QAHGAQ----------HLVLIDSI 109 + L L+ G +F + + ++++ H C+ L Q A+ +LV+ID Sbjct: 61 KQGLSLVAGTIFDDLVSEENFANIVELTHNLCRNLSQVPSAEKTPGNPFQPPYLVIIDFG 120 Query: 110 SPRRAPTAGRASEAEQMNHAEWSAFRDRLATVAQIGTEEYGLTVGIHAHAAGFMDFEPEL 169 +P+RA AGR A +++ A+W D + T++++ +EYG+ IH HA G ++F E+ Sbjct: 121 NPQRAKYAGRGELAPRLSPADWQRMIDHIITISKLAWQEYGVRPVIHPHAGGCIEFADEI 180 Query: 170 ERLLNEVDDKILKICFDTGHHSYAGFDPVAFMKRHMDRISYMHFKDIDPKVKADVIAKRT 229 + L ++ ++ +C DTGH Y+G DP++++ RH DR+ Y+HFKD+DP+V VI++ Sbjct: 181 DLLATQIPHEVAGLCLDTGHLYYSGMDPISWLDRHFDRLDYLHFKDVDPQVFESVISRGI 240 Query: 230 NFYDACGQGIFCNLGEGDVDFPAVRQLLVDTGFSGWCTVEQDCDPTLDPDPVGDARANRE 289 +F+ AC +G+ C LG G +D+PAVR L G+ GW T+EQ+ DP + + Sbjct: 241 DFFSACAEGVMCPLGSGAIDYPAVRAFLDKRGYQGWITIEQERDPRNVEGSLQAVTESLR 300 Query: 290 YLESIGF 296 YL S+GF Sbjct: 301 YLRSVGF 307 Lambda K H 0.322 0.140 0.445 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: 305 Number of extensions: 18 Number of successful extensions: 2 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: 297 Length of database: 307 Length adjustment: 27 Effective length of query: 270 Effective length of database: 280 Effective search space: 75600 Effective search space used: 75600 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 (21.9 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