Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_086510991.1 BZY95_RS16565 dihydroxy-acid dehydratase
Query= reanno::HerbieS:HSERO_RS05205 (585 letters) >NCBI__GCF_002151265.1:WP_086510991.1 Length = 581 Score = 981 bits (2536), Expect = 0.0 Identities = 473/579 (81%), Positives = 529/579 (91%) Query: 7 DKSRTLRSAGWFGTADKNGFMYRSWMKNQGIPDHEFQGKPVIGICNTWSELTPCNAHFRK 66 D+ R LRSA WFG+ADKNGFMYRSWMKNQGIPDHEF+GKP+IGICNTWSELTPCNAHFRK Sbjct: 3 DRKRPLRSAQWFGSADKNGFMYRSWMKNQGIPDHEFEGKPIIGICNTWSELTPCNAHFRK 62 Query: 67 IAEHVRRGIIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEESIRGNPIDAVVLLT 126 +AEHV++G++EAGGFPVEFPVFSNGES LRPTAM TRNLASMDVEESIRGNP+DAVVLL Sbjct: 63 LAEHVKKGVLEAGGFPVEFPVFSNGESLLRPTAMFTRNLASMDVEESIRGNPLDAVVLLV 122 Query: 127 GCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHQGRDIGSGTVVWQLSEQVKAGEITIHD 186 GCDKTTPALLMGAASCD+P IVV+GGPMLNGKH+GRDIGSGTVVWQLSEQVKAG+I+IH+ Sbjct: 123 GCDKTTPALLMGAASCDIPTIVVSGGPMLNGKHEGRDIGSGTVVWQLSEQVKAGKISIHE 182 Query: 187 FMAAEAGMSRSAGTCNTMGTASTMACMAESLGVSLPHNAAIPAVDARRYVLAHLSGMRIV 246 FM+AEAGMSRSAGTCNTMGTASTMACMAE+LG SLPHNAAIPAVDARRYVLAHLSG RIV Sbjct: 183 FMSAEAGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHLSGNRIV 242 Query: 247 DMVWEGLTLSKILTRKAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVDLELEDWTRIGRG 306 +MV E L LSK+LTR+AFENAIRTNAAIGGSTNAVIHLKAIAGRIGV+L+L+DW+RIGRG Sbjct: 243 EMVEEDLRLSKVLTRQAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVELDLDDWSRIGRG 302 Query: 307 TPTIVDLQPSGRYLMEEFYYAGGLPAVLRRLGEADLLPHKDALTVNGQTMWDNVKDAPIY 366 TPT+VDLQPSGR+LMEEFYYAGGLPAVLRRLGEAD LPH++ALTVNG+T+WDNVK+AP+Y Sbjct: 303 TPTLVDLQPSGRFLMEEFYYAGGLPAVLRRLGEADRLPHREALTVNGRTLWDNVKEAPLY 362 Query: 367 NDEVVRPLAKPLIEDGGICILRGNLAPRGAVLKPSAATPELMKHRGRAVVFEDFNHYKER 426 NDEV+RPL +PL EDGG+C+LRGNLAPRGAVLKPSAA+PELM HRGRAVVFEDF+ YK R Sbjct: 363 NDEVIRPLERPLREDGGMCVLRGNLAPRGAVLKPSAASPELMIHRGRAVVFEDFDDYKAR 422 Query: 427 INDPDLDVDASCVLVMKNVGPKGYPGMAEVGNMGLPPKVLATGVKDMVRISDARMSGTAY 486 INDPDL+VDAS VLVMKN GP+GY GMAEVGNMGLP K+L GV DMVRISDARMSGTAY Sbjct: 423 INDPDLEVDASSVLVMKNCGPRGYHGMAEVGNMGLPAKLLEQGVTDMVRISDARMSGTAY 482 Query: 487 GTVILHVAPEAAAGGPLGIVQDGDFIELDAYAGKLQLDISEEEMKRRLEARAKVLAERKP 546 GTV+LHVAPE+AAGGPL V+DGD+IELD AG L L++ + E++ RL R R+ Sbjct: 483 GTVVLHVAPESAAGGPLAAVRDGDWIELDCDAGTLHLEVDDAELEARLAERDPTAESRRI 542 Query: 547 EMVGGYQSLYVDRVLQADEGCDFDFLVGCRGAAVPKHSH 585 GGY+ LY++RVLQADEGCDFDFL G RGA VP+HSH Sbjct: 543 ASDGGYRQLYIERVLQADEGCDFDFLRGSRGADVPRHSH 581 Lambda K H 0.319 0.136 0.409 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: 1272 Number of extensions: 42 Number of successful extensions: 1 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: 585 Length of database: 581 Length adjustment: 36 Effective length of query: 549 Effective length of database: 545 Effective search space: 299205 Effective search space used: 299205 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 24 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