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 Ac3H11_604 L-arabonate dehydratase (EC 4.2.1.25)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_604 Length = 577 Score = 769 bits (1986), Expect = 0.0 Identities = 374/572 (65%), Positives = 456/572 (79%), Gaps = 1/572 (0%) Query: 9 RKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAE 68 RKLRS EW+G ++ +R W+KNQG P FDGRPVIGI NTWS++TPCN H R++AE Sbjct: 6 RKLRSAEWFGTADKNGFMYRSWMKNQGIPDHAFDGRPVIGICNTWSELTPCNAHFRKIAE 65 Query: 69 KVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCD 128 VK G++EAGGFP+E PVFS E+ RPTAM+ RNLA++ VEEAIRG P+D VLLVGCD Sbjct: 66 HVKRGIYEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDAVVLLVGCD 125 Query: 129 KTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLE 188 KTTP+LLMGAASCD+P+IVVTGGPMLNG G+ +GSGT +W+ E +KAGE+ + +F Sbjct: 126 KTTPALLMGAASCDVPAIVVTGGPMLNGKLDGKDIGSGTAVWRLHESLKAGEINEHQFFA 185 Query: 189 AEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMV 248 AEA MSRS+GTCNTMGTASTMA MAE+LG +L NAAIP VD+RR V+A ++G+RIV+M Sbjct: 186 AEAGMSRSAGTCNTMGTASTMACMAESLGTSLPHNAAIPAVDARRYVLAHMSGKRIVEMA 245 Query: 249 KDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPT 308 + L S+I+T++AFENAIRTNAAIGGSTNAVIHL AIAGR+G+ L L+DW R GR PT Sbjct: 246 HEGLTLSKILTREAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVQLDLEDWTRIGRGTPT 305 Query: 309 IVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLL-HKDALTVSGETVWDEVKDVVNWNED 367 +V+L PSG++LMEEF+YAGGLP VL+RLGE LL H +ALTV+G+++WD V++ +N++ Sbjct: 306 LVDLQPSGRFLMEEFYYAGGLPAVLRRLGENNLLPHPNALTVNGKSLWDNVREAPQYNDE 365 Query: 368 VILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKIND 427 VI P L + GGI +LRGNLAP+GAVLKPSAASP LL H+GRAVVFE+++ YK +I D Sbjct: 366 VIRPISNPLIADGGICILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLEHYKERIVD 425 Query: 428 DNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV 487 +NLDID +C+MV+KNCGPKGYPGMAEVGNMGLPPK+L++G+ DMVRISDARMSGTAYGTV Sbjct: 426 ENLDIDASCVMVLKNCGPKGYPGMAEVGNMGLPPKLLRQGVKDMVRISDARMSGTAYGTV 485 Query: 488 VLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYA 547 VLH +PEAA GGPLA V++GD IELD N RLHLDISDEELA RLA GY Sbjct: 486 VLHVAPEAAAGGPLAAVRDGDFIELDCENGRLHLDISDEELAARLAALANTDQGGRGGYQ 545 Query: 548 FLHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579 L+ HV AD G D DFL GCRG AV + SH Sbjct: 546 RLYVDHVLQADDGCDFDFLVGCRGAAVPRHSH 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: 1149 Number of extensions: 60 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