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 GFF723 PGA1_c07380 dihydroxy-acid dehydratase IlvD
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Phaeo:GFF723 Length = 571 Score = 659 bits (1699), Expect = 0.0 Identities = 327/568 (57%), Positives = 422/568 (74%), Gaps = 2/568 (0%) Query: 12 RSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVK 71 R++ WYG +D HR W+KNQG+P FDGRP+IGI NTWS++TPCN LR+LAE VK Sbjct: 6 RNRAWYGKLDKDGFIHRSWMKNQGFPDHAFDGRPIIGICNTWSELTPCNSGLRDLAEGVK 65 Query: 72 AGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTT 131 GVWEAGGFP+E PV S E +PTAM++RNL A+ VEE+IR +DG VLL GCDKTT Sbjct: 66 RGVWEAGGFPVEFPVMSLGETQMKPTAMLFRNLLAMDVEESIRAYGIDGVVLLGGCDKTT 125 Query: 132 PSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEA 191 P LMGAAS DLP+IVV+ GPMLNG ++G+ +GSGT +WKFSE V+AGEMT +F+ AE+ Sbjct: 126 PGQLMGAASVDLPAIVVSSGPMLNGKWQGKDIGSGTDVWKFSEAVRAGEMTLQDFMAAES 185 Query: 192 SMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDD 251 MSRS G C TMGTASTMAS+ EA+GM+L NAA+P VD+RR +A LTG+RIV+MV++D Sbjct: 186 GMSRSKGVCMTMGTASTMASLVEAMGMSLPTNAALPAVDARRMALAHLTGKRIVEMVEED 245 Query: 252 LKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVN 311 +KPS+++T++AF NAI NAA+GGSTNAV+HLLA+AGRVG +LSLDD+D G D+P +VN Sbjct: 246 IKPSDVLTREAFVNAIMANAAVGGSTNAVVHLLALAGRVGAELSLDDFD-LGSDIPLLVN 304 Query: 312 LMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDVILP 371 MPSGKYLME+F YAGG+PVVLK+L + G L + TV G + + +N+DVI Sbjct: 305 CMPSGKYLMEDFCYAGGMPVVLKQLADNGHLRSNT-TVLGGDILAYAEGAECFNDDVIKS 363 Query: 372 AEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLD 431 ++ + + G+ VLRGNLAP GA++KPSAA+ HLL H+G A VFE I+D KA I+ D+L Sbjct: 364 FDEPVKPAAGLRVLRGNLAPNGAIVKPSAATDHLLEHEGVAHVFETIEDMKANIDRDDLP 423 Query: 432 IDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVVLHT 491 + ++ I+V+K GPKGYPGM EVGNM +P K++++G+ DM+RISD RMSGTA+GTV+LH Sbjct: 424 VTKDSILVLKGVGPKGYPGMPEVGNMPIPRKLVREGVRDMIRISDGRMSGTAFGTVILHV 483 Query: 492 SPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQ 551 SPE+ GGPL +V+ GD I + N L L +S+EEL R WQP T GYA L+ Sbjct: 484 SPESQAGGPLGLVQTGDRIRVSAKNGTLDLLVSEEELTARREAWQPEPLHYTRGYAKLYV 543 Query: 552 QHVEGADTGADLDFLKGCRGNAVGKDSH 579 V A+ GADLDFL G V ++SH Sbjct: 544 DSVLQAEKGADLDFLVGKDTRPVTRESH 571 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: 1062 Number of extensions: 50 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: 571 Length adjustment: 36 Effective length of query: 543 Effective length of database: 535 Effective search space: 290505 Effective search space used: 290505 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