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 AZOBR_RS31260 AZOBR_RS31260 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__azobra:AZOBR_RS31260 Length = 608 Score = 439 bits (1129), Expect = e-127 Identities = 241/539 (44%), Positives = 338/539 (62%), Gaps = 15/539 (2%) Query: 9 RKLRSQEWYGGTSRD---VIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65 R+LRS+ W+ +Y +L +L G P+IGI T SD++PCN H Sbjct: 17 RRLRSRAWFDNPDNPDMTALYLERYLNFGLTREELQSGAPIIGIAQTGSDLSPCNRHHLV 76 Query: 66 LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125 LAE+++ G+ AGG +E PV E RPTA + RNLA L + E + G P+DG VL + Sbjct: 77 LAERLREGIRTAGGIAIEFPVHPIQETGKRPTASIDRNLAYLGLVEVLHGYPLDGVVLTI 136 Query: 126 GCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185 GCDKTTP+ LM AA+ ++P+I ++ GPMLNG+FRGER GSGT +WK +M+ AGE+ Sbjct: 137 GCDKTTPACLMAAATVNIPAIALSVGPMLNGWFRGERTGSGTIVWKARQMMAAGEIDYQG 196 Query: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245 F+E AS + S+G CNTMGTASTM S+AE LGM L G+AAIP R+ TG+RIV Sbjct: 197 FIELVASSAPSTGYCNTMGTASTMNSLAEVLGMQLPGSAAIPAPYRERQQADYETGKRIV 256 Query: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305 +MV++DLKPS+I+T+ AF NAI N+AIGGSTNA IH+ AIA +G+ L+++DW G D Sbjct: 257 EMVREDLKPSDILTRDAFLNAIVVNSAIGGSTNAPIHINAIAKHIGVPLTVEDWQTHGHD 316 Query: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWN 365 VP +VNL P+G+YL E+F AGG+P V+ +L GL+ + A TV+G T+ + + + Sbjct: 317 VPLLVNLQPAGEYLGEDFHRAGGVPAVVAQLMGKGLIREGAPTVNGRTIGENCRRQPILD 376 Query: 366 EDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKGRAVV 414 VI P ++ L + G VVLRGNL A++K S S +G+ VV Sbjct: 377 TRVIHPIDEPLMPNAGFVVLRGNLF-GAAIMKTSVISDEFRERYLSNPQDPEAFEGKVVV 435 Query: 415 FEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRI 474 F+ +DY +I+D +L ID I+V++ GP GYPG AEV NM P ++K+G+ + I Sbjct: 436 FDGPEDYHHRIDDPSLGIDAYTILVIRGTGPIGYPGAAEVVNMRPPATLIKQGVHSLPCI 495 Query: 475 SDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLA 533 D R SGT+ +L+ SPEAA GG LA++++GD + +D+ + I + ELA R A Sbjct: 496 GDGRQSGTSGSPSILNASPEAAAGGGLALLRSGDRVRIDLRRGSADILIPEGELADRRA 554 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: 985 Number of extensions: 66 Number of successful extensions: 2 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: 608 Length adjustment: 37 Effective length of query: 542 Effective length of database: 571 Effective search space: 309482 Effective search space used: 309482 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