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_013093958.1 BC1002_RS31165 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_000092885.1:WP_013093958.1 Length = 594 Score = 464 bits (1195), Expect = e-135 Identities = 254/574 (44%), Positives = 356/574 (62%), Gaps = 15/574 (2%) Query: 5 AEWPRKLRSQEWYGGTSR---DVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNG 61 A PR+LRSQEW+ S +Y ++ +L GRP+IGI T SD+ PCN Sbjct: 3 ASTPRRLRSQEWFDDPSHADMTALYVERFMNYGLTREELQSGRPIIGIAQTGSDLAPCNR 62 Query: 62 HLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGC 121 H ELA + KAG+ +AGG P+E PV +E + RPTA + RNLA L + E + G P+DG Sbjct: 63 HHIELAARTKAGIRDAGGIPMEFPVHPLAEQSRRPTAALDRNLAYLGLVEILHGFPLDGV 122 Query: 122 VLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEM 181 VL GCDKTTP+ LM AA+ D+P+IV++GGPML+G+ G+RVGSGT +W ++ AGE+ Sbjct: 123 VLTTGCDKTTPACLMAAATVDMPAIVLSGGPMLDGWHDGKRVGSGTVIWHARNLLAAGEI 182 Query: 182 TQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTG 241 F+E + S S G CNTMGTA +M S+AEALGM+L G A+IP R MA TG Sbjct: 183 DYEGFMELTTASSPSIGHCNTMGTALSMNSLAEALGMSLPGCASIPAAYRERGQMAYATG 242 Query: 242 RRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDR 301 +RIV +V+DD++PS+IMTK+AFENAI +A+G STN HL+AIA +G++LSLDDW R Sbjct: 243 KRIVDLVRDDVRPSKIMTKEAFENAIVVASALGASTNCPPHLIAIARHMGVELSLDDWQR 302 Query: 302 CGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDV 361 G VP IVN MP+G+YL E F AGG+P V+ L +AGL+H++ LTVSG T+ + Sbjct: 303 VGEQVPLIVNCMPAGEYLGESFHRAGGVPAVMHELAKAGLVHEECLTVSGRTMGEIAAAA 362 Query: 362 VNWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKG 410 + +VI + L G +VL GN A++K S + Sbjct: 363 PAPDREVIKTTDDPLKHGAGFMVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENTFEA 421 Query: 411 RAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILD 470 RA+VF+ +DY A+IND L+IDE+CI+V++ G GYPG AEV NM P ++++GI Sbjct: 422 RAIVFDGPEDYHARINDPALEIDEHCILVIRGTGTVGYPGSAEVVNMAPPAALVRQGITS 481 Query: 471 MVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELAR 530 + + D R SGT+ +L+ SPEAAVGG LA+++ D I +D+ +R +++ + + ELAR Sbjct: 482 LPTLGDGRQSGTSASPSILNMSPEAAVGGGLALLRTNDRIRVDLNSRSVNVLVDEAELAR 541 Query: 531 RLAEWQPNHDLPTSGYAFLHQQHVEGADTGADLD 564 R Q + + L+++ V TG L+ Sbjct: 542 RRETVQFEIPPAQTPWQELYRKTVGQLSTGGCLE 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: 978 Number of extensions: 59 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 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