Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_011157024.1 TX73_RS07465 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >NCBI__GCF_000195775.1:WP_011157024.1 Length = 618 Score = 269 bits (688), Expect = 2e-76 Identities = 194/565 (34%), Positives = 288/565 (50%), Gaps = 62/565 (10%) Query: 21 GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80 G+N R + G+ F G+PII + N++++ P + HL+DL + V R + AGG Sbjct: 12 GRNMAGARGLWRATGMKDSDF-GKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGV 70 Query: 81 PVEFPVFSTGES-TLRPTAMMF----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLL 135 EF + + + M++ R L A VE + + D +V + CDK TP +L Sbjct: 71 AKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGML 130 Query: 136 MGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGE--MSLEEFMDAEQGM 193 M A ++IPA+ VSGGPM GK K G A+ MV + + MS E+ E+ Sbjct: 131 MAAMRLNIPAVFVSGGPMEAGKVVLK--GKTHAVDLIDAMVAAADSAMSDEDVQTMERSA 188 Query: 194 ARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKE--- 250 + GSC M TA++M + EALG++L GN ++ A A R+ + G IV++ + Sbjct: 189 CPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADRKRLFVEAGHTIVDLARRYYE 248 Query: 251 ----DLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDV 306 + P +I +AFENA+ ++ A+GGSTN VLHLLA A +D S+ D DRL R V Sbjct: 249 GDDASVLPRNIANFKAFENAMTLDIAMGGSTNTVLHLLAAAREAELDFSMKDIDRLSRRV 308 Query: 307 PTIVNLQPS-GKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTI------WN--- 356 P + + PS ME+ + AGG+ ++ + GLL TV +T+ W+ Sbjct: 309 PCLSKIAPSVSDVHMEDVHRAGGIMAILGELDRAGLLDTSCTTVHSETLGAALARWDIRQ 368 Query: 357 ---------------DVKGVVNYNED-----VILPREK--------ALTKSGGIAVLRGN 388 V +++D + L REK A +K GG+AVL GN Sbjct: 369 SNSESVRTFFRAAPGGVPSQTAFSQDRRYDELDLDREKGVIRDAAHAFSKDGGLAVLYGN 428 Query: 389 LAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVLKYCGPKGY 448 +A G ++K + ++ G VFES +D + I + + ++V++Y GP+G Sbjct: 429 IALDGCIVKTAGVDASILTFSGPVKVFESQDDAVSAILTNKIVAGD--VVVIRYEGPRGG 486 Query: 449 PGMAEVGNMGLPPKVLK-KGITDMIR-ISDARMSGTAYGTVILHTAPEAAEGGPLALVEN 506 PGM E M P LK KG+ I+D R SG G I H +PEAAEGG + LV + Sbjct: 487 PGMQE---MLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIGLVRD 543 Query: 507 GDLIEVDIPNRTLHLHVSDEELARR 531 GD I +DIPNRT+ L VS+ ELA+R Sbjct: 544 GDRISIDIPNRTISLDVSEAELAKR 568 Lambda K H 0.318 0.135 0.402 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: 845 Number of extensions: 39 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 579 Length of database: 618 Length adjustment: 37 Effective length of query: 542 Effective length of database: 581 Effective search space: 314902 Effective search space used: 314902 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 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