Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate BWI76_RS00975 BWI76_RS00975 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__Koxy:BWI76_RS00975 Length = 616 Score = 261 bits (666), Expect = 8e-74 Identities = 188/568 (33%), Positives = 280/568 (49%), Gaps = 62/568 (10%) Query: 21 GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80 G+N R+ + G+ D F G+PII + N++++ P + HLRDL + V + AGG Sbjct: 12 GRNMAGARALWRATGMTDDDF-GKPIIAVVNSFTQFVPGHVHLRDLGKLVAEQIEAAGGV 70 Query: 81 PVEFPVFSTGESTLRPTAMMF-----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLL 135 EF + + M R L A VE + + D +V + CDK TP +L Sbjct: 71 AKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGML 130 Query: 136 MGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMAR 195 M + ++IP I VSGGPM GK + D + ++S ++ E+ Sbjct: 131 MASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDDQSDQVERSACP 190 Query: 196 SAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLK-- 253 + GSC M TA++M + EALG++ GN ++ A A R+ + G RIVE+ K + Sbjct: 191 TCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGSRIVELTKRYYEQD 250 Query: 254 -----PSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPT 308 P +I K AFENA+ ++ A+GGSTN VLHLLA A +D ++ D D+L R VP Sbjct: 251 DASALPRNIANKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSDIDKLSRKVPQ 310 Query: 309 IVNLQPS-GKYLMEEFYYAGGLPVVIKAVAEMGLLHNDA----------------ITVSG 351 + + PS KY ME+ + AGG+ ++ + GLL+ D ITV+ Sbjct: 311 LCKVAPSTQKYHMEDVHRAGGVLGILGELERAGLLNRDVKNVLGLSLPQTLEQYDITVTQ 370 Query: 352 DTI-----------------------WNDVKGVVNYNEDVILPREKALTKSGGIAVLRGN 388 D W+ + + E I E A +K GG+AVL GN Sbjct: 371 DEAVKKMFRAGPAGIRTTQAFSQNCRWDTLDD--DRAEGCIRSLEHAYSKDGGLAVLYGN 428 Query: 389 LAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVLKYCGPKGY 448 A G ++K + +++ G A V+ES + I + + ++V++Y GPKG Sbjct: 429 FAENGCIVKTAGVDDSILKFTGPAKVYESQDAAVDAILGGKIVAGD--VVVIRYEGPKGG 486 Query: 449 PGMAEVGNMGLPPKVLKK-GITDMIR-ISDARMSGTAYGTVILHTAPEAAEGGPLALVEN 506 PGM E M P LK G+ I+D R SG G I H +PEAA GG +A++E+ Sbjct: 487 PGMQE---MLYPTTFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGNIAIIED 543 Query: 507 GDLIEVDIPNRTLHLHVSDEELARRRAA 534 GD+I +DIPNR + L +SD E+A RR A Sbjct: 544 GDMIAIDIPNRGIQLQLSDAEIAARREA 571 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: 834 Number of extensions: 42 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: 616 Length adjustment: 37 Effective length of query: 542 Effective length of database: 579 Effective search space: 313818 Effective search space used: 313818 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 Apr 09 2024. 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