Align xylonate dehydratase monomer (EC 4.2.1.82) (characterized)
to candidate 7024896 Shewana3_2070 dihydroxy-acid dehydratase (RefSeq)
Query= metacyc::MONOMER-20629 (591 letters) >FitnessBrowser__ANA3:7024896 Length = 586 Score = 428 bits (1101), Expect = e-124 Identities = 244/593 (41%), Positives = 349/593 (58%), Gaps = 18/593 (3%) Query: 1 MSNRTPRRFRSRDWFDNPDHIDMTALYLERFMNYGITPEELRSGKPIIGIAQTGSDISPC 60 M+N+ P+ RS WF + D +Y N GI PE KP+IGI T S+++PC Sbjct: 10 MNNKKPKTLRSASWFGSDDKNGF--MYRSWMKNQGI-PEHHFQNKPVIGICNTWSELTPC 66 Query: 61 NRIHLDLVQRVRDGIRDAGGIPMEFPVHPIFENCRRPTAALDRNLSYLGLVETLHGYPID 120 N +L QRV++GIR+AGGIP+EFPV E+ RP+A L RNL+ + E + G PID Sbjct: 67 NGHLRELAQRVKNGIREAGGIPVEFPVFSNGESNLRPSAMLTRNLAAMDTEEAIRGNPID 126 Query: 121 AVVLTTGCDKTTPAGIMAATTVNIPAIVLSGGPMLDGWHENELVGSGTVIWRSRRKLAAG 180 VVL GCDKTTPA +M A + ++P IV++GGPML+G H+ + VGSGT++W ++ AG Sbjct: 127 GVVLLVGCDKTTPALLMGAASCDLPTIVVTGGPMLNGKHKGKDVGSGTLVWELHQEYKAG 186 Query: 181 EITEEEFIDRAASSAPSAGHCNTMGTASTMNAVAEALGLSLTGCAAIPAPYRERGQMAYK 240 I+ F++ A + S G CNTMGTASTM + E LG+SL A IPA R +A+ Sbjct: 187 NISLAAFMNAEADMSRSTGTCNTMGTASTMACMVETLGVSLPHNATIPAVDSRRQVLAHM 246 Query: 241 TGQRIVDLAYDDVKPLDILTKQAFENAIALVAAAGGSTNAQPHIVAMARHAGVEITADDW 300 +G RIVD+ +D+ IL++ AF NAI + AA GGSTNA H+ A+A GVE++ DDW Sbjct: 247 SGMRIVDMVKEDLTLSKILSRDAFINAIKVNAAIGGSTNAVIHLKAIAGRIGVELSLDDW 306 Query: 301 RAAYDIPLIVNMQPAGKYLGERFHRAGGAPAVLWELLQQGRLHGDVLTVTGKTMSENLQG 360 R Y +P IVN++P+G+YL E F+ AGG PAVL +L + L + LTV ++ +N++ Sbjct: 307 RHGYTVPTIVNLKPSGQYLMEDFYYAGGLPAVLRQLFEHDLLSKNTLTVNAASLWDNVKE 366 Query: 361 RETSDREVIFPYHEPLAEKAGFLVLKGNLFDFAIMKSSVIGEEFRKRYLSQPGQEGVFEA 420 ++EVI PL E G VL+GNL + +VI +L Q Sbjct: 367 APCYNQEVIMSLENPLVENGGIRVLRGNL----APRGAVIKPSAASAHLMQ------HRG 416 Query: 421 RAIVFDGSDDYHKRINDPALEIDERCILVIRGAGPIGWPGSAEVVNMQPPDHLLKKGIMS 480 +A+VF+ DDY+ RI DP L+IDE I+V++ GP G+PG AEV NM P LLKKGI Sbjct: 417 KAVVFESFDDYNARIGDPELDIDENSIMVLKNCGPKGYPGMAEVGNMGLPPKLLKKGIKD 476 Query: 481 LPTLGDGRQSGTADSPSILNASPESAIGGGLSWLRTGDTIRIDLNTGRCDALVDEATIAA 540 + + D R SGTA +L+ +PE+ G L+ ++ GD I +D G + + + A Sbjct: 477 MVRISDARMSGTAFGTVVLHVAPEAQALGPLAAVQNGDMIALDTYAGTLQLEISDQELQA 536 Query: 541 R--KQDGIPAVPATMTPWQEIYRAHASQLDTGGVLEFAVKYQDLAAKLPRHNH 591 R K + ++P + +++ H Q D G +F V + A++P H+H Sbjct: 537 RLAKLATVKSIPVN-GGYLSLFKEHVLQADEGCDFDFLVGCR--GAEIPAHSH 586 Lambda K H 0.319 0.136 0.411 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: 888 Number of extensions: 37 Number of successful extensions: 3 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: 591 Length of database: 586 Length adjustment: 37 Effective length of query: 554 Effective length of database: 549 Effective search space: 304146 Effective search space used: 304146 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: 53 (25.0 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