Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate WP_085634854.1 MGEO_RS01140 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_002115805.1:WP_085634854.1 Length = 587 Score = 297 bits (761), Expect = 7e-85 Identities = 187/534 (35%), Positives = 283/534 (52%), Gaps = 51/534 (9%) Query: 44 RPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRN 103 +P++G+ W++ PCN L A+ VK GV +A G P E + ++ M + Sbjct: 41 QPLVGVATCWNEAAPCNIALNRQAQAVKMGVKQAFGTPREFTTITVTDGIAMGHEGMRSS 100 Query: 104 LA-----ALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYF 158 LA A VE +RG D V L GCDK+ P ++M ++PS+ + GG +L G Sbjct: 101 LASREAIADTVELTMRGHCYDAVVGLAGCDKSLPGMMMAMVRLNVPSVFIYGGSILPG-- 158 Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEA-----------------EASMSRSSGTCN 201 + + E + ++T + EA E S+G C Sbjct: 159 ------KAPQVAEIPEDFRTRDLTVQDMFEAVGRHQNNELSDKALDMLERVACPSAGACG 212 Query: 202 TMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQ 261 TA+TMA ++EA+G+AL ++ +P R + +GR ++ +++ ++K +I+T++ Sbjct: 213 GQFTANTMACVSEAIGLALFNSSGMPAPYESRDAYGEASGRAVMDLIEQNIKARDIVTRE 272 Query: 262 AFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLME 321 A ENA R A GGSTNA +HL AIA GI+ L+D +D P V+L P G Y+ + Sbjct: 273 ALENAARVVACTGGSTNAGLHLPAIAHEAGIEFYLEDVCDIFKDTPYFVDLKPGGTYVAK 332 Query: 322 EFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNED--VILPAEKALTSS 379 + + AGG+PVV+K L +AGL+H+D +T S T+ +E+ D + D VI E +T + Sbjct: 333 DLYDAGGIPVVMKELRKAGLIHEDCVTASTRTIGEEL-DRIEREADGKVIYSIETPITKT 391 Query: 380 GGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMV 439 GG+V L+GNLAP+GA++K + + G A VFE +D A + D E ++V Sbjct: 392 GGVVGLKGNLAPEGAIVKVAGIKAEDQIFTGPARVFECEEDAFAAVK--ARDYKEGEVIV 449 Query: 440 MKNCGPKGYPGMAE-------VGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVVLHTS 492 ++N GP G PGM E + G+ KV I+D R SG G V H Sbjct: 450 IRNEGPAGGPGMREMLATTAALSGQGMGKKV--------ALITDGRFSGATRGFCVGHVG 501 Query: 493 PEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQ-PNHDLPTSG 545 PEAA+GGP+A++KNGDMI +D N L +D+SDEELA+R A+W P + TSG Sbjct: 502 PEAALGGPIALLKNGDMITIDAVNGSLSVDLSDEELAQRKADWTGPRETIYTSG 555 Lambda K H 0.318 0.135 0.408 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: 903 Number of extensions: 54 Number of successful extensions: 6 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: 579 Length of database: 587 Length adjustment: 36 Effective length of query: 543 Effective length of database: 551 Effective search space: 299193 Effective search space used: 299193 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 24 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