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_011842504.1 RSPH17029_RS18285 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_000015985.1:WP_011842504.1 Length = 599 Score = 432 bits (1112), Expect = e-125 Identities = 248/542 (45%), Positives = 333/542 (61%), Gaps = 19/542 (3%) Query: 8 PRKLRSQEWYGGTS---RDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLR 64 P +LRS+ W+ +Y +L +L G+P+IGI T SD++PCN H Sbjct: 9 PDQLRSRLWFNNPDDPEMTALYLERYLNYGLTRAELQGGKPIIGIAQTGSDLSPCNRHHI 68 Query: 65 ELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLL 124 ELA++V+ G+ AGG P+E+PV E RPTA + RNLA L + EA+ G P+DG VL Sbjct: 69 ELAKRVRDGITAAGGIPMEIPVHPIQETGKRPTASLDRNLAYLGLVEALHGYPIDGVVLT 128 Query: 125 VGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQA 184 +GCDKTTP+LLM AA+ ++P+I + GPMLNG+ RGER GSGT +W+ E++ GE+ + Sbjct: 129 IGCDKTTPALLMAAATVNIPAIAYSVGPMLNGWHRGERAGSGTAVWRARELLARGEIDEE 188 Query: 185 EFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRI 244 F E AS + S G CNTMGTASTM S+AE LGM L G+AAIP R M TGRRI Sbjct: 189 GFYELVASSAPSVGYCNTMGTASTMNSLAEVLGMQLPGSAAIPAPYRERGQMGHATGRRI 248 Query: 245 VQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGR 304 V+MV +DL+PS+I+T++AFENAI +A+GGSTNA IHL A+A G+ L DDW R G Sbjct: 249 VEMVWEDLRPSDILTREAFENAIVACSALGGSTNAPIHLNAVARHAGVALDNDDWQRLGH 308 Query: 305 DVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLL-HKDALTVSGETVWDEVKDVVN 363 VP +VNL P+G YL E+F+ AGG+P VL L A LL H +A TV G + + + Sbjct: 309 AVPLLVNLQPAGTYLGEDFYRAGGVPAVLGELLAADLLPHPEAPTVFGTPL--SAGAMRS 366 Query: 364 WNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVH-----------KGRA 412 DVI P + L G + L GNL A++K S SP +G Sbjct: 367 LETDVIRPVVEPLKGEAGFINLSGNLF-DSAIMKTSVISPDFRARYLSDPADPEAFEGTV 425 Query: 413 VVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMV 472 VF+ + + A I+D L + E+ ++VM+ GP GYPG AEV NM P +LK+GI + Sbjct: 426 FVFDGPEHFHAVIDDPALGMGEDAVLVMRGAGPLGYPGAAEVVNMRPPAYLLKRGIPAVP 485 Query: 473 RISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEEL-ARR 531 I D R SGT+ +L+ SPEAA GG LA+++NGD I +D+ R+ + + DEEL ARR Sbjct: 486 CIGDGRQSGTSGSPSILNASPEAAAGGGLALLRNGDRIRVDLRRGRVDVLLPDEELEARR 545 Query: 532 LA 533 A Sbjct: 546 TA 547 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: 1010 Number of extensions: 67 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: 599 Length adjustment: 37 Effective length of query: 542 Effective length of database: 562 Effective search space: 304604 Effective search space used: 304604 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