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 SMc04144 SMc04144 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Smeli:SMc04144 Length = 574 Score = 563 bits (1452), Expect = e-165 Identities = 277/560 (49%), Positives = 381/560 (68%), Gaps = 3/560 (0%) Query: 8 PRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELA 67 P + RS W+G HR L GY H +PVI I+NTWSD+ PC+ HLR A Sbjct: 7 PEEFRSFRWFGVKDLRAFGHRSRLYQMGYDHAELANKPVIAIINTWSDINPCHAHLRARA 66 Query: 68 EKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGC 127 E+VK GVW+AGGFP+E+P S +E +PT M+YRN A+ VEE IR P+DG VLL GC Sbjct: 67 EEVKRGVWQAGGFPIELPAMSLAETYVKPTTMLYRNFLAMEVEELIRSHPVDGVVLLAGC 126 Query: 128 DKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFL 187 DKTTP +MGA DLP+I V GPML G +RG +GSG+ +WK+ +AG +T+ E+ Sbjct: 127 DKTTPGTIMGAIQVDLPTIFVPAGPMLRGNYRGRMLGSGSDVWKYWAEKEAGRVTENEWS 186 Query: 188 EAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQM 247 E E ++RS GTC TMGTASTM ++A+ LG++L G +AIP D+ MA L+G RIV+M Sbjct: 187 EMERGIARSFGTCMTMGTASTMTALADTLGLSLPGASAIPAADAGHARMAALSGARIVEM 246 Query: 248 VKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVP 307 V +DLKPS+I+T +AFENA+ + A+ GSTNA+IHL+AIA R G+ L+LDD+DR +VP Sbjct: 247 VFEDLKPSDILTAKAFENALAVHMAMAGSTNAMIHLIAIARRCGVPLTLDDFDRVSAEVP 306 Query: 308 TIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNED 367 + N+ P+G++LME+F+YAGGL + K+L LLH V G T+ + + + Sbjct: 307 VLCNIRPTGEFLMEDFYYAGGLIALWKQL--KPLLHTGERNVIG-TIGGALDEAEVHLPE 363 Query: 368 VILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKIND 427 VI P ++ + + GG +L+GNLAP+G V+KP+AA P LL H+G A+VF+D D +ND Sbjct: 364 VIRPLDRPVAARGGTAILKGNLAPQGCVMKPAAADPALLQHRGPALVFDDYDAMMKAVND 423 Query: 428 DNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV 487 D+LD+ + +M+++N GP G PGM E G + +P K+LK+G+ DMVRISDARMSGT+YG Sbjct: 424 DDLDVTADTVMILRNAGPVGGPGMPEWGMLPIPRKLLKEGVRDMVRISDARMSGTSYGAC 483 Query: 488 VLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYA 547 +LH +PEA VGGPLA V+NGD+I LDV R + L++ E+ RRLAEW+P + GY Sbjct: 484 ILHVAPEAYVGGPLAAVRNGDIIALDVARRTITLEVDQAEIERRLAEWRPPERDYSRGYL 543 Query: 548 FLHQQHVEGADTGADLDFLK 567 +H +H++ A G D FL+ Sbjct: 544 KMHAEHIQQAPEGCDFTFLQ 563 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: 1016 Number of extensions: 42 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