Align L-rhamnonate dehydratase (EC 4.2.1.90) (characterized)
to candidate RR42_RS23065 RR42_RS23065 L-rhamnose 1-epimerase
Query= metacyc::MONOMER-16232 (397 letters) >FitnessBrowser__Cup4G11:RR42_RS23065 Length = 391 Score = 215 bits (548), Expect = 2e-60 Identities = 124/340 (36%), Positives = 190/340 (55%), Gaps = 18/340 (5%) Query: 60 GTLVVEIEAEDGTVGFA-VTTGGEPAAYIVEKHLARFLEGRAPTDYEKIWDQMYFSTQYY 118 G LVVE+E + G VG A I++++LA + G+ P D E +W +MY T + Sbjct: 46 GWLVVEVETDTGLVGIGNCALAPRVAKEIIDQYLAPIVIGQDPFDNEYLWQKMYRRTHAW 105 Query: 119 GRKGLVVNAISGVDLALWDLLGKLRQEPVYHLLGGAVRDELQFYATG-----------AR 167 GRKG+ + AIS VD+ALWDL+GK +PV+ LLGG ++++ YA+ A Sbjct: 106 GRKGIGMAAISAVDIALWDLMGKAVGKPVFKLLGGRTKEKIWCYASKLYNNDDRDAFLAE 165 Query: 168 PDKAKEFGFIGGKMPLHHGPAEGVEGLKKNIAELADMRSKVGDDFWLMWDCWMALDVDYA 227 + GF KM +GP +G G++KNI ++ +R VGD +M +C+M ++YA Sbjct: 166 AQSYLDQGFTAMKMRFGYGPKDGPAGMQKNIEQVRLLRELVGDGVDIMLECYMGWTLEYA 225 Query: 228 TRLAIAAHDFGLKWIEEAISPDDYWGYQQLKRNVPKGMLVTTGEHEATRWGFRMLMEMDC 287 R+ +F +W+EE + DD GY +LK+ P ++ GEHE T +GF+ L+E Sbjct: 226 RRMIPRLAEFNPRWLEEPVIADDIEGYAELKKMSP--FPISGGEHEFTSYGFKDLLERRA 283 Query: 288 CDIIQPDVGWCGGVTELLKISALADAHGKMVVPHGSSVYSYHFVITRHNSPFAEFLMMHP 347 D+IQ D GG+T KI+A+A+A V+PH +++YH + SP +EF +H Sbjct: 284 VDVIQYDTNRVGGITAAQKINAMAEAWSVPVIPHAGQMHNYHLTMASTASPMSEFFPVH- 342 Query: 348 GPTEV-VPMFHPQLLGEPVPDNGRMKVSALDKPGFGVDLN 386 EV +F+ GEP PDNG +++ + PG G+ LN Sbjct: 343 -DVEVGNELFYYIFKGEPAPDNGYLQLDD-NLPGLGLTLN 380 Lambda K H 0.322 0.140 0.451 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: 438 Number of extensions: 20 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: 397 Length of database: 391 Length adjustment: 31 Effective length of query: 366 Effective length of database: 360 Effective search space: 131760 Effective search space used: 131760 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: 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