Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate Ga0059261_0522 Ga0059261_0522 Predicted metal-dependent hydrolase of the TIM-barrel fold
Query= BRENDA::A9CEQ7 (292 letters) >FitnessBrowser__Korea:Ga0059261_0522 Length = 295 Score = 112 bits (281), Expect = 8e-30 Identities = 86/283 (30%), Positives = 123/283 (43%), Gaps = 11/283 (3%) Query: 8 LSGTAPNPAFPRGAVDTQMHMYLP--GYPALPGGPGLPPGALPGPEDYRRLMQWLGIDRV 65 L + P P GAVD H++ P +P P LP A P+ L + LG R Sbjct: 13 LDPSKPRYTPPPGAVDAHCHVFGPMAQFPFSPKAKYLPQDA--DPDALFALRERLGFARN 70 Query: 66 IITQGNAHQRDNGNTLACVAEMGEAAHAVVIIDATTTEKDMEKLTAAGTVGAR---IMDL 122 +I Q + H DN TL +A V ++D ++ ++ L G G R + L Sbjct: 71 VIVQASCHGTDNRATLNGIAASNGTCRGVAVVDPAISDAGLDTLHEGGIRGVRFNFLKRL 130 Query: 123 PGGAVNLSELDAVDERAHAADWMVAVQFDGNGLLDHLPRLQKIRSRWVFDHHGKFFKGIR 182 A LD + R W V V F+ + L + P L I V DH G+ Sbjct: 131 VDDAPKDKFLD-IARRIQRLGWHVVVYFEADILEEMKPFLAAIPVPVVIDHMGRPDVRQG 189 Query: 183 TDGPEMAALLKLID-RGNLWFKFAGVYESSRKSWPYADVAAFSRVIAAHAPERIVWGTNW 241 DG +MAA L+D R ++W K PYAD R + P+R++WGT+W Sbjct: 190 PDGADMAAFRALLDSRDDIWTKVTCPDRLDPAGPPYADFVRSVRPLVEAYPDRVLWGTDW 249 Query: 242 PHNSVRETAAYPDDARLAELTLGWLPDEAARHRALVENPEALF 284 PH ++ E PDD L +L P +H+ LV+NP L+ Sbjct: 250 PHPNMEE--VLPDDGALVDLIPAIAPTAELQHKLLVDNPMRLY 290 Lambda K H 0.319 0.136 0.426 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: 266 Number of extensions: 24 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: 292 Length of database: 295 Length adjustment: 26 Effective length of query: 266 Effective length of database: 269 Effective search space: 71554 Effective search space used: 71554 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