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 3606698 Dshi_0129 dihydroxy-acid dehydratase (RefSeq)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Dino:3606698 Length = 577 Score = 308 bits (788), Expect = 5e-88 Identities = 204/576 (35%), Positives = 304/576 (52%), Gaps = 30/576 (5%) Query: 1 MKKKAEWPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCN 60 M K++ KL S+ G SR HR + G + +P++G+ W++ PCN Sbjct: 1 MLKRSFDKSKLPSRHVTEGPSRAP--HRSYYYAMGMTEEEIH-QPLVGVATCWNEAAPCN 57 Query: 61 GHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLA-----ALAVEEAIRG 115 L A+ VK GV +A G P E + ++ M +LA A VE +RG Sbjct: 58 IALSRQAQAVKMGVKQASGTPREFTTITVTDGIAMGHEGMRSSLASREAIADTVELTMRG 117 Query: 116 QPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEM 175 D V L GCDK+ P ++M ++PS+ + GG +L G GE V + +++ Sbjct: 118 HCYDAIVGLAGCDKSLPGMMMAMVRLNVPSVFIYGGSILPGRLNGEDV-TVQDVFEAVGK 176 Query: 176 VKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKV 235 +AG T AE E S+G C TA+TMA ++EA+G+AL +A P R Sbjct: 177 HQAGNYTDAELEVLERVACPSAGACGGQFTANTMACVSEAIGLALPNSAGAPAPYESRDQ 236 Query: 236 MAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLS 295 + +GR ++ +++ ++ +I+T+++ ENA R A GGSTNA +HL AIA GI+ + Sbjct: 237 YGEASGRAVMDLIEKGIRARDIVTRKSLENAARIVACTGGSTNAGLHLPAIAHEAGIEFT 296 Query: 296 LDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVW 355 L D RD P V+L P GKY+ ++ + AGG+PVV++ L AGL+H+D +TV+G ++ Sbjct: 297 LQDVCDIFRDTPYFVDLKPGGKYVAKDMYEAGGVPVVMRELRRAGLIHEDCMTVTGYSIG 356 Query: 356 DEVKDVVNWNED--VILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAV 413 +E+ D V D VI P + L+++GG+V L GNLAP+GA++K + S LV G A Sbjct: 357 EEL-DKVTLEADGRVIYPVDTPLSTTGGVVGLEGNLAPEGAIVKIAGMSDDQLVFTGPAR 415 Query: 414 VFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAE-------VGNMGLPPKVLKK 466 VFE +D + N E + V++N GP G PGM E + G+ KV Sbjct: 416 VFECEEDAFEAV--QNRAYAEGDVFVIRNEGPAGGPGMREMLATTAALSGQGMGKKV--- 470 Query: 467 GILDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDE 526 I+D R SG G V H PEAA GGP+A++K+GDMI +D L + +S++ Sbjct: 471 -----ALITDGRFSGATRGFCVGHVGPEAAHGGPIAMLKDGDMITIDALKGELSVALSED 525 Query: 527 ELARRLAEWQ-PNHDLPTSGYAFLHQQHVEGADTGA 561 ELA R W P + SG + + Q V GA GA Sbjct: 526 ELAARKDAWSGPRETIYASGALWKYAQLVGGARLGA 561 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: 906 Number of extensions: 58 Number of successful extensions: 7 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: 577 Length adjustment: 36 Effective length of query: 543 Effective length of database: 541 Effective search space: 293763 Effective search space used: 293763 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 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