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 Ga0059261_2649 Ga0059261_2649 Dihydroxyacid dehydratase/phosphogluconate dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Korea:Ga0059261_2649 Length = 618 Score = 447 bits (1149), Expect = e-130 Identities = 243/537 (45%), Positives = 341/537 (63%), Gaps = 15/537 (2%) Query: 9 RKLRSQEWYGGTSR---DVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65 RKLRS W+ +Y +L +L GRP+IGI T SD++PCN H Sbjct: 27 RKLRSAAWFDNPDNIDMTALYLERYLNFGLSLKELRSGRPIIGIAQTGSDLSPCNRHHLV 86 Query: 66 LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125 LAE+V+ G+ +AGG +E PV E RPTA + RNLA L + EA+ G P+DG VL + Sbjct: 87 LAERVREGIRDAGGIAIEFPVHPIQETGKRPTAGLDRNLAYLGLVEALYGYPLDGVVLTI 146 Query: 126 GCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185 GCDKTTP+ LM AA+ ++P+I ++ GPMLNG+ +GER GSGT +WK +M+ AGE+ E Sbjct: 147 GCDKTTPACLMAAATVNIPAIALSVGPMLNGWHKGERTGSGTIVWKARQMLAAGEIDDDE 206 Query: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245 F+ AS + S+G CNTMGTA+TM S+AEALGM+L G+AAIP R+ +A TG R V Sbjct: 207 FIRLVASSAPSTGYCNTMGTATTMNSLAEALGMSLPGSAAIPAPHRDRQEVAYQTGLRAV 266 Query: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305 ++V+ D+KPS+I+T++AFENAI N+AIGGSTNA IHL AIA +G+DL +D W G Sbjct: 267 ELVRADVKPSDILTREAFENAIVVNSAIGGSTNAPIHLAAIARHIGVDLPIDAWQEKGHA 326 Query: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWN 365 VP +VNL P+G+YL E+++ AGG+P V+ +L +AGL+H+DA TV+G+++ + V + Sbjct: 327 VPLLVNLQPAGEYLGEDYYRAGGVPAVVSQLIDAGLIHEDAGTVNGKSIGANCRGVAIED 386 Query: 366 EDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKGRAVV 414 E VI P + L + G +VLRGNL + A++K S S +G AVV Sbjct: 387 EKVIRPFAQPLKDAAGFIVLRGNLF-ESAIMKTSVISDEFRDRYLSNPDDPDAFEGPAVV 445 Query: 415 FEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRI 474 F+ +DY A+I+D L I ++ M+ GP GYPG AEV NM P ++++GI + I Sbjct: 446 FDGPEDYHARIDDPALGITPETLLFMRGAGPVGYPGAAEVVNMRPPAYLIREGIHALPCI 505 Query: 475 SDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARR 531 D R SGT+ +L+ SPEAA G LA+++ GD + +D+ + I ELA R Sbjct: 506 GDGRQSGTSGSPSILNASPEAAAMGGLALIRTGDRVRIDLGKGTADVLIPSAELAER 562 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: 1046 Number of extensions: 56 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: 618 Length adjustment: 37 Effective length of query: 542 Effective length of database: 581 Effective search space: 314902 Effective search space used: 314902 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