Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate Pf1N1B4_3383 Mandelate racemase (EC 5.1.2.2)
Query= reanno::BFirm:BPHYT_RS16405 (382 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3383 Length = 391 Score = 134 bits (336), Expect = 6e-36 Identities = 109/356 (30%), Positives = 174/356 (48%), Gaps = 35/356 (9%) Query: 15 WCFLKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYL----IGKDPLLIEDHWQVMYRS 70 W +++ETD G+VG G + R A E + YL IG+DP E WQ MYR Sbjct: 47 WLVVEVETDTGLVGIGNCALAPRV-----AKEIIDTYLAPIAIGEDPFDNEYIWQKMYRQ 101 Query: 71 GFYRGGP-ITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYS--WIGGDRPSD 127 G I M+AI+ +D A+WDI GK P+ LLGG+ ++KI Y+ D Sbjct: 102 SHAWGRKGIGMAAISAIDIAIWDIMGKAVNKPVFKLLGGRTKEKIWTYASKLYANDNLDL 161 Query: 128 VANNARAVVERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREAVGPNIGIGVDFHGR 187 A+ + +GF A+KM + D ++ I V A+RE GP+I I ++ + Sbjct: 162 FLEEAQGYLNQGFTALKMRFGYGPK--DGPAGMRKNIEQVRALRELAGPDIDIMLECYMG 219 Query: 188 VHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSRWDFKHIL 247 A+ + +L ++ ++EEPV++++ E ++ PI+ GE ++ + FK +L Sbjct: 220 WTLEYARRMLPKLAEFEPRWLEEPVIADDIEGYIELKKMGIMPISGGEHEFTSYGFKDLL 279 Query: 248 SGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPL---GPIALATCLQIDAVSY 304 +D+IQ D + GGIT RKI ++AEA+ V + H + ++T A + Sbjct: 280 ERRAIDVIQYDTNRVGGITAARKINALAEAWSVPVIPHAGQMHNYHLTMSTTASPMAEFF 339 Query: 305 NAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYE----DGFVSIPQG-PGLGIEVNEE 355 F E GN+L Y VFK E G++ + PGLG+E+++E Sbjct: 340 PVFDVE--------VGNELFYY-----VFKGEPQPVKGYIQLDDNKPGLGLEISDE 382 Lambda K H 0.319 0.139 0.428 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: 444 Number of extensions: 27 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: 382 Length of database: 391 Length adjustment: 30 Effective length of query: 352 Effective length of database: 361 Effective search space: 127072 Effective search space used: 127072 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 (21.7 bits) S2: 50 (23.9 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