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 H281DRAFT_05919 H281DRAFT_05919 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Burk376:H281DRAFT_05919 Length = 594 Score = 464 bits (1195), Expect = e-135 Identities = 253/572 (44%), Positives = 361/572 (63%), Gaps = 19/572 (3%) Query: 9 RKLRSQEWY---GGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65 R+LRSQEW+ +Y ++ +L GRP+IGI T SD+ PCN H E Sbjct: 7 RRLRSQEWFDDPANADMTALYVERFMNYGLTREELQSGRPIIGIAQTGSDLAPCNRHHIE 66 Query: 66 LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125 LA + KAG+ +AGG P+E PV +E + RPTA + RNLA L + E + G P+DG VL Sbjct: 67 LATRTKAGIRDAGGIPMEFPVHPLAEQSRRPTAALDRNLAYLGLVEILHGFPLDGVVLTT 126 Query: 126 GCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185 GCDKTTP+ LM AA+ D+P+IV++GGPML+G+ +G+RVGSGT +W ++ AGE+ Sbjct: 127 GCDKTTPACLMAAATVDMPAIVLSGGPMLDGWHQGKRVGSGTVIWHARNLLAAGEIDYEG 186 Query: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245 F+E + S S G CNTMGTA +M S+AEALGM+L G A+IP R MA TG+RIV Sbjct: 187 FMELTTASSPSIGHCNTMGTALSMNSLAEALGMSLPGCASIPAAYRERGQMAYATGKRIV 246 Query: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305 +V+DD++PS+IMTK AFENAI +A+G S+N HL+AIA +G++LSL+DW R G Sbjct: 247 DLVRDDVRPSKIMTKAAFENAIVVASALGASSNCPPHLIAIARHMGVELSLNDWQRVGEK 306 Query: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWN 365 VP IVN MP+G+YL E F AGG+P VL+ L AGL+H+D LTVSG+ + + + Sbjct: 307 VPLIVNCMPAGEYLGESFHRAGGVPAVLRELDRAGLVHRDCLTVSGQVIGAIADNAAQPD 366 Query: 366 EDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHL----LVHKG-------RAVV 414 DVI ++ L G +VL GN A++K S L G RA+V Sbjct: 367 RDVIKTTDEPLKHGAGFIVLSGNFF-DSAIMKMSVVGDAFRNTYLSEPGAENSFETRAIV 425 Query: 415 FEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRI 474 F+ +DY ++IND +L+ID++CI+V++ G GYPG AEV NM P +++++GI + + Sbjct: 426 FDGPEDYHSRINDPSLNIDQHCILVIRGAGTVGYPGSAEVVNMAPPAELVRQGITSLPTM 485 Query: 475 SDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAE 534 D R SGT+ +L+ SPEAA+GG LA+++ GD I +D+ R +++ + ++ELARR Sbjct: 486 GDGRQSGTSASPSILNMSPEAAIGGGLALLQTGDRIRVDLNTRTVNVLVDEDELARR--R 543 Query: 535 WQPNHDLP--TSGYAFLHQQHVEGADTGADLD 564 + D+P + + L++Q V TG L+ Sbjct: 544 ETVSFDIPPAQTPWQELYRQTVGQLSTGGCLE 575 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: 974 Number of extensions: 53 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: 579 Length of database: 594 Length adjustment: 37 Effective length of query: 542 Effective length of database: 557 Effective search space: 301894 Effective search space used: 301894 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