Align L-fucono-1,5-lactonase; D-arabinolactonase (characterized)
to candidate H281DRAFT_01224 H281DRAFT_01224 Predicted metal-dependent hydrolase, TIM-barrel fold
Query= reanno::Smeli:SM_b21101 (278 letters) >FitnessBrowser__Burk376:H281DRAFT_01224 Length = 297 Score = 133 bits (335), Expect = 4e-36 Identities = 93/298 (31%), Positives = 144/298 (48%), Gaps = 25/298 (8%) Query: 2 IIDTHLHLIDKSALNYPWLAGVPA--------LDRDFLYATYAAEAKRVGVAASLHMEVD 53 ++D+H+HL D YPWL L D+L A EA + V +H+E + Sbjct: 3 VVDSHIHLWDLKTHRYPWLENPGVSFVGDARDLKHDYLLADLLGEAGDIDVKKVVHVEAN 62 Query: 54 VDPAEIELETREVARLAG--EPGSLLKGAIAACRPEDEGFAAYLERQEENAFVKGFRRVL 111 DPA+ ETR + +A E + +AA A LE A +G R++L Sbjct: 63 HDPADPVEETRWLQGIADRHESRGMPNAIVAAVDLSSADAPALLEAHASFANTRGIRQIL 122 Query: 112 HVVTDDLSE--------QPLFRENVKRLSGTRFTFDLCVLPHQIPKAIALADLAPDVQFI 163 +V + L + +P +REN L +FDL + P Q+ +A ALA D F Sbjct: 123 NVHENRLFDYVGRHFMREPQWRENFALLRRYDMSFDLQLYPSQMEEAAALARAHGDTHFA 182 Query: 164 LDHCGV----PDIKGHAEHPWRDHMTEIARHPNVVAKISGVVAYAEEDWALDSIRPYVEH 219 ++H G+ + G+ WRD M +A NV KISG+ + + W ++S+RPYV Sbjct: 183 VNHAGMFVDRDSVAGY--RAWRDGMGMLADCENVCVKISGLAMF-DHHWTVESLRPYVLE 239 Query: 220 TISVFGWDRVVWGSDWPVCTLGGNLSTWVAATQALIEGCSPQERRKLLSGNAQRIWNL 277 TI FG +R ++ S++PV L G+ + A ++EG S E+ L GNA+R + + Sbjct: 240 TIDTFGVERAMFASNFPVDRLFGSYAGLWHAYATIVEGASAAEKEALFCGNAERFYRI 297 Lambda K H 0.321 0.137 0.432 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: 226 Number of extensions: 18 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: 278 Length of database: 297 Length adjustment: 26 Effective length of query: 252 Effective length of database: 271 Effective search space: 68292 Effective search space used: 68292 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: 47 (22.7 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