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 RR42_RS18585 RR42_RS18585 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Cup4G11:RR42_RS18585 Length = 577 Score = 752 bits (1942), Expect = 0.0 Identities = 363/572 (63%), Positives = 451/572 (78%), Gaps = 2/572 (0%) Query: 8 PRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELA 67 P RSQ W+G RD +R WLKN+G PHD FDGRPVIGI NT+S++TPCN H R LA Sbjct: 8 PPTRRSQAWFGRLDRDGFLYRSWLKNRGIPHDQFDGRPVIGICNTYSELTPCNSHFRTLA 67 Query: 68 EKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGC 127 E+VK GVWEAGGFPLE PV S E RPTAM++RNLA++ VEE+IRG P+DG VLL+GC Sbjct: 68 EQVKIGVWEAGGFPLEFPVMSLGETMLRPTAMLFRNLASMDVEESIRGNPIDGVVLLMGC 127 Query: 128 DKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFL 187 DKTTP+L+MGAASCDLP+I V+GGPML+G FRG +GSGT +WK SE V+AG+M+Q +F Sbjct: 128 DKTTPALMMGAASCDLPTIGVSGGPMLSGKFRGGELGSGTDVWKMSEQVRAGQMSQEDFF 187 Query: 188 EAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQM 247 EAE+ M RS G C TMGTASTMASM EALGM+L GNAAIP VD RR V+A+ +GRRIV+M Sbjct: 188 EAESCMHRSHGHCMTMGTASTMASMVEALGMSLPGNAAIPAVDGRRNVLARASGRRIVEM 247 Query: 248 VKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVP 307 VKD+L S+I+T+ AFENAIR NAAIGGSTNAVIHLLAIAGR+G++L L+DWD G ++P Sbjct: 248 VKDNLVMSKILTRDAFENAIRVNAAIGGSTNAVIHLLAIAGRIGVELKLEDWDALGHELP 307 Query: 308 TIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNED 367 +++L PSG++LME+F+YAGGLP V++ L +L +DALTV+G+T+WD KD NWN + Sbjct: 308 CLLDLQPSGRHLMEDFYYAGGLPAVIREL--ESVLARDALTVNGKTLWDNCKDAPNWNRE 365 Query: 368 VILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKIND 427 VI ++ GI VLRGNL P GAV+KPSAA+P LL H GRAVVFE+ + +++D Sbjct: 366 VIHAFGAPFKANAGIAVLRGNLCPDGAVIKPSAATPALLKHTGRAVVFENSEHMHQRLDD 425 Query: 428 DNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV 487 ++LD+DE C++V+KNCGP+GYPGMAE GNM LPPKVL+KGI DMVR+SDARMSGTAYGTV Sbjct: 426 ESLDVDETCVLVLKNCGPRGYPGMAEAGNMPLPPKVLRKGITDMVRVSDARMSGTAYGTV 485 Query: 488 VLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYA 547 VLH +PEAA GGPLA+VK+GDM+ELDVP R+LHL + + EL RR A WQ G+ Sbjct: 486 VLHVAPEAAAGGPLALVKDGDMVELDVPMRKLHLHVDEAELQRRRAAWQAPALPMARGWT 545 Query: 548 FLHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579 L+ +HV+ A+ GAD+DFL G G AV KD+H Sbjct: 546 RLYVEHVQQANLGADMDFLVGKSGAAVPKDNH 577 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: 1168 Number of extensions: 47 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: 577 Length adjustment: 36 Effective length of query: 543 Effective length of database: 541 Effective search space: 293763 Effective search space used: 293763 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