Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 3607836 Dshi_1244 Dihydroxy-acid dehydratase (RefSeq)
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >FitnessBrowser__Dino:3607836 Length = 569 Score = 717 bits (1850), Expect = 0.0 Identities = 361/568 (63%), Positives = 437/568 (76%), Gaps = 6/568 (1%) Query: 12 RSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRELAEYVK 71 R++AW+G D+DGF+HRSWMKNQG P FDGRPVIGICNTWSELTPCN R LAE VK Sbjct: 6 RNRAWYGKLDKDGFIHRSWMKNQGFPDHVFDGRPVIGICNTWSELTPCNHGLRTLAEGVK 65 Query: 72 KGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGCDKTT 131 +GV EAGG P+EFPVMSLGET ++PTAMLFRNL +MDVEESIR MDGV+LL GCDKTT Sbjct: 66 RGVWEAGGFPVEFPVMSLGETQMKPTAMLFRNLLAMDVEESIRAYGMDGVVLLGGCDKTT 125 Query: 132 PALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEFTEAES 191 P LMGAAS +LP++ VS GPMLNG++RG++IGSGT VW+ SE VRAG MT +F AE+ Sbjct: 126 PGQLMGAASVDLPSIVVSAGPMLNGKYRGQDIGSGTDVWKFSEAVRAGEMTLADFMNAEA 185 Query: 192 CMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMVRED 251 M+RS G CMTMGTASTMAS+VE++GM LP NAA+PAVDARR LAHL G+RIV+MV ED Sbjct: 186 GMSRSAGVCMTMGTASTMASLVEAMGMSLPLNAALPAVDARRMALAHLTGKRIVEMVEED 245 Query: 252 LTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWELGSNVPCLVNL 311 L ILT+ AFENAI NAA+GGSTNAV+HL+ALA R GV+L+L+D+E+G +P LVN Sbjct: 246 LRPSAILTKPAFENAILANAAVGGSTNAVMHLLALAGRAGVDLTLKDFEIGGEIPLLVNC 305 Query: 312 QPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDEKVITTF 371 PSG+YLMEDF YAGG+P VL +L + + A TV GK + A ++ VI + Sbjct: 306 MPSGKYLMEDFAYAGGMPVVLSELRDH---LRPATTVLGKDIAAYTEGAECFNRDVIHAY 362 Query: 372 AEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKIDDESLDI 431 P KP AG+ VL+G+LAP+GA++KPSAAT +LL+H G A VFENIE++ A ID + L I Sbjct: 363 DAPVKPAAGLRVLRGSLAPDGAIVKPSAATDALLEHEGPAFVFENIEDMKANIDRDDLPI 422 Query: 432 DEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTAYGAVVLHVS 491 I+VLKG GPKGYPG EVGNMP+P K++++G+ DM+R+SD RMSGTAYG V+LHV+ Sbjct: 423 TPDTILVLKGCGPKGYPGMPEVGNMPIPAKLVREGVRDMIRVSDARMSGTAYGTVILHVA 482 Query: 492 PEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAP--KRGYYKLYV 549 PEA AGGPLA V+TGD I + E L L V ELA RRAAWQ P+ P RGY KLY+ Sbjct: 483 PEAQAGGPLALVKTGDRIRVSAREGVLDLLVDATELAARRAAWQ-PDPPHYTRGYAKLYI 541 Query: 550 EHVLQADQGADLDFLVGSSGAPVPRDSH 577 +HVLQAD+GADLDFLVG PV R+SH Sbjct: 542 DHVLQADRGADLDFLVGKDTRPVTRESH 569 Lambda K H 0.318 0.135 0.401 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: 1007 Number of extensions: 41 Number of successful extensions: 3 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: 577 Length of database: 569 Length adjustment: 36 Effective length of query: 541 Effective length of database: 533 Effective search space: 288353 Effective search space used: 288353 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