Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_011995749.1 XAUT_RS00355 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >NCBI__GCF_000017645.1:WP_011995749.1 Length = 617 Score = 256 bits (655), Expect = 1e-72 Identities = 192/573 (33%), Positives = 293/573 (51%), Gaps = 71/573 (12%) Query: 21 GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80 G+N R + G+ F G+PII + N++++ P + HL+DL + V R + +AGG Sbjct: 12 GRNMAGARGLWRATGMKDGDF-GKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEKAGGV 70 Query: 81 PVEFPVFSTGES-TLRPTAMMF----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLL 135 EF + + + M++ R + A VE + + D +V + CDK TP +L Sbjct: 71 AKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAMVCISNCDKITPGML 130 Query: 136 MGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTA-IWQFSEMVKSGEMSLEEFMDAE-QGM 193 M A ++IPA+ VSGGPM GK + +G + M+ + + ++ DA+ Q M Sbjct: 131 MAAMRLNIPAVFVSGGPMEAGKVL---LSTGEKKVDLIDAMIAAAD---DKVTDADVQVM 184 Query: 194 ARSA----GSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVK 249 RSA GSC M TA++M + EALG+ L GN + A A R + G IV++ + Sbjct: 185 ERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSTLATHADRERLFVEAGHLIVDLAR 244 Query: 250 E-------DLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRL 302 + P + + +AFENA+ ++ ++GGSTN VLHLLA A V ++ D DRL Sbjct: 245 RYYEQDDASVLPRSVASFKAFENAMTLDISMGGSTNTVLHLLAAANEGEVPFTMADIDRL 304 Query: 303 GRDVPTIVNLQPS-GKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTI------W 355 R VP + + P+ ME+ + AGG+ ++ + GL+H D TV T+ W Sbjct: 305 SRRVPVLCKVAPAVANIHMEDVHRAGGIMAILGELDRGGLIHTDLPTVHAATMADALDRW 364 Query: 356 NDVKGVVNYN------------------------EDVILPRE--------KALTKSGGIA 383 DVK + + +D+ L RE A +K GG+A Sbjct: 365 -DVKRTKSESVATFFRAAPGGVPTQVAFSQSRRWDDLDLDRETGVIRDVAHAYSKDGGLA 423 Query: 384 VLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVLKYC 443 VL GN+A G ++K + +++ G+A +FES +D I +++++Y Sbjct: 424 VLYGNIALDGCIVKTAGVDASILKFTGKARIFES-QDAAVEAILSTGRIQAGDVVLIRYE 482 Query: 444 GPKGYPGMAEVGNMGLPPKVLK-KGITDMIR-ISDARMSGTAYGTVILHTAPEAAEGGPL 501 GP+G PGM E M P LK KG+ ++D R SG + G I H +PEAAEGG + Sbjct: 483 GPRGGPGMQE---MLYPTSYLKSKGLGKACALVTDGRFSGGSSGLSIGHVSPEAAEGGAI 539 Query: 502 ALVENGDLIEVDIPNRTLHLHVSDEELARRRAA 534 LVE GD IE+DIPNR + + VSDE L++RRAA Sbjct: 540 GLVEEGDTIEIDIPNRIIRVAVSDEVLSQRRAA 572 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: 883 Number of extensions: 52 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: 617 Length adjustment: 37 Effective length of query: 542 Effective length of database: 580 Effective search space: 314360 Effective search space used: 314360 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