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 HSERO_RS05205 HSERO_RS05205 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__HerbieS:HSERO_RS05205 Length = 585 Score = 752 bits (1941), Expect = 0.0 Identities = 375/584 (64%), Positives = 454/584 (77%), Gaps = 11/584 (1%) Query: 4 KAEWPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHL 63 K + R LRS W+G ++ +R W+KNQG P F G+PVIGI NTWS++TPCN H Sbjct: 5 KKDKSRTLRSAGWFGTADKNGFMYRSWMKNQGIPDHEFQGKPVIGICNTWSELTPCNAHF 64 Query: 64 RELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVL 123 R++AE V+ G+ EAGGFP+E PVFS E+ RPTAM+ RNLA++ VEE+IRG P+D VL Sbjct: 65 RKIAEHVRRGIIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEESIRGNPIDAVVL 124 Query: 124 LVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQ 183 L GCDKTTP+LLMGAASCD+P+IVVTGGPMLNG +G +GSGT +W+ SE VKAGE+T Sbjct: 125 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHQGRDIGSGTVVWQLSEQVKAGEITI 184 Query: 184 AEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRR 243 +F+ AEA MSRS+GTCNTMGTASTMA MAE+LG++L NAAIP VD+RR V+A L+G R Sbjct: 185 HDFMAAEAGMSRSAGTCNTMGTASTMACMAESLGVSLPHNAAIPAVDARRYVLAHLSGMR 244 Query: 244 IVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCG 303 IV MV + L S+I+T++AFENAIRTNAAIGGSTNAVIHL AIAGR+G+DL L+DW R G Sbjct: 245 IVDMVWEGLTLSKILTRKAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVDLELEDWTRIG 304 Query: 304 RDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLL-HKDALTVSGETVWDEVKDVV 362 R PTIV+L PSG+YLMEEF+YAGGLP VL+RLGEA LL HKDALTV+G+T+WD VKD Sbjct: 305 RGTPTIVDLQPSGRYLMEEFYYAGGLPAVLRRLGEADLLPHKDALTVNGQTMWDNVKDAP 364 Query: 363 NWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYK 422 +N++V+ P K L GGI +LRGNLAP+GAVLKPSAA+P L+ H+GRAVVFED + YK Sbjct: 365 IYNDEVVRPLAKPLIEDGGICILRGNLAPRGAVLKPSAATPELMKHRGRAVVFEDFNHYK 424 Query: 423 AKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGT 482 +IND +LD+D +C++VMKN GPKGYPGMAEVGNMGLPPKVL G+ DMVRISDARMSGT Sbjct: 425 ERINDPDLDVDASCVLVMKNVGPKGYPGMAEVGNMGLPPKVLATGVKDMVRISDARMSGT 484 Query: 483 AYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARR-------LAEW 535 AYGTV+LH +PEAA GGPL +V++GD IELD +L LDIS+EE+ RR LAE Sbjct: 485 AYGTVILHVAPEAAAGGPLGIVQDGDFIELDAYAGKLQLDISEEEMKRRLEARAKVLAER 544 Query: 536 QPNHDLPTSGYAFLHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579 +P GY L+ V AD G D DFL GCRG AV K SH Sbjct: 545 KPE---MVGGYQSLYVDRVLQADEGCDFDFLVGCRGAAVPKHSH 585 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: 1155 Number of extensions: 61 Number of successful extensions: 4 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: 585 Length adjustment: 36 Effective length of query: 543 Effective length of database: 549 Effective search space: 298107 Effective search space used: 298107 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