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 SMc00884 SMc00884 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Smeli:SMc00884 Length = 574 Score = 691 bits (1783), Expect = 0.0 Identities = 344/571 (60%), Positives = 432/571 (75%), Gaps = 2/571 (0%) Query: 9 RKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAE 68 ++LRS+ WYGGT +D HR W+KNQG+P +FDGRP+IGI NTWS++TPCN HLR LAE Sbjct: 6 KELRSRHWYGGTHKDGFIHRSWMKNQGFPDHVFDGRPIIGICNTWSELTPCNSHLRILAE 65 Query: 69 KVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCD 128 VK GVWEAGGFP+E PV S E RPTAM++RNL A+ VEEAIR +DG VLL GCD Sbjct: 66 GVKRGVWEAGGFPVEFPVSSLGETQMRPTAMLFRNLLAMDVEEAIRAYGIDGVVLLGGCD 125 Query: 129 KTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLE 188 KTTP LMGAAS DLP+IVV+ GPMLNG ++G+ +GSGT +WKFSE V+AGEM+ EF+ Sbjct: 126 KTTPGQLMGAASVDLPTIVVSSGPMLNGKWKGKDIGSGTDVWKFSEAVRAGEMSLQEFMA 185 Query: 189 AEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMV 248 AE+ MSRS G C TMGTA+TMAS+ EA+G++L NAA+P VD+RR ++ +TG+RIV+MV Sbjct: 186 AESGMSRSPGVCMTMGTATTMASIVEAMGLSLPTNAALPAVDARRMALSHMTGKRIVEMV 245 Query: 249 KDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPT 308 +DL+ S+I+TK+ FEN I NAA+GGSTNAV+H+LAIAGR GIDL L+D+DR G VP Sbjct: 246 HEDLRLSKILTKENFENGIIANAAVGGSTNAVVHMLAIAGRAGIDLCLEDFDRVGGQVPC 305 Query: 309 IVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDV 368 IVN MPSGKYL+E+ YAGGLP V+ R+ LLH DA TV G + + +N+DV Sbjct: 306 IVNCMPSGKYLIEDLAYAGGLPAVMNRIQH--LLHPDAPTVFGVPISKYWEAAEVYNDDV 363 Query: 369 ILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDD 428 I P + L ++ GI VL+GNLAP GAV+KPSAAS HLL H+G A VF+ I+D +AKI+D Sbjct: 364 IRPLDNPLRAAAGIRVLKGNLAPNGAVIKPSAASEHLLAHEGPAYVFDTIEDLRAKIDDP 423 Query: 429 NLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVV 488 +L + E+ I+V+K CGPKGYPGMAEVGNM +P ++++KG+ DMVRISDARMSGTA+GTVV Sbjct: 424 DLPVTEDTILVLKGCGPKGYPGMAEVGNMPIPRRLVEKGVRDMVRISDARMSGTAFGTVV 483 Query: 489 LHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAF 548 LH SPEA GGPLA+V+ GD I LD L+L +S+EELA R+A WQP GY Sbjct: 484 LHVSPEANAGGPLAIVRTGDRIRLDALKGELNLLVSEEELAARMAAWQPPEQKWHRGYYK 543 Query: 549 LHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579 L+ V AD GADLDFL G G+ V ++SH Sbjct: 544 LYHDTVLQADKGADLDFLVGKSGSEVLRESH 574 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: 1115 Number of extensions: 54 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: 574 Length adjustment: 36 Effective length of query: 543 Effective length of database: 538 Effective search space: 292134 Effective search space used: 292134 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