Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate Pf1N1B4_2303 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 Length = 613 Score = 271 bits (694), Expect = 4e-77 Identities = 191/567 (33%), Positives = 284/567 (50%), Gaps = 64/567 (11%) Query: 21 GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80 G+N R+ + G+ D F +PII I N++++ P + HL+DL + V R + AGG Sbjct: 12 GRNMAGARALWRATGMKDDDFK-KPIIAIANSFTQFVPGHVHLKDLGQLVAREIERAGGV 70 Query: 81 PVEFPVFSTGES-TLRPTAMMF----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLL 135 EF + + + M++ R + A VE + + D +V + CDK TP +L Sbjct: 71 AKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCISNCDKITPGML 130 Query: 136 MGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMAR 195 M + ++IP I VSGGPM GK K G + + S E+ + E+ Sbjct: 131 MASLRLNIPVIFVSGGPMEAGKT--KLASHGLDLVDAMVIAADSSASDEKVAEYERSACP 188 Query: 196 SAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVK------ 249 + GSC M TA++M + EALG+ L GN + A + R + GR IVE+ K Sbjct: 189 TCGSCSGMFTANSMNCLVEALGLALPGNGSTLATHSDREQLFLQAGRTIVELCKRYYGEN 248 Query: 250 -EDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPT 308 E + P +I +AFENA+ ++ A+GGSTN +LHLLA A +D L D DRL R VP Sbjct: 249 DESVLPRNIANFKAFENAMTLDIAMGGSTNTILHLLAAAQEAEIDFDLRDIDRLSRHVPQ 308 Query: 309 IVNLQPS-GKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITV------------------ 349 + + P+ KY ME+ + AGG+ ++ ++A GLLH D TV Sbjct: 309 LCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSKSMAEGIAKWDITQTT 368 Query: 350 ---------------------SGDTIWNDVKGVVNYNEDVILPREKALTKSGGIAVLRGN 388 S T W + + I E A +K GG+AVL GN Sbjct: 369 DEAVHHFFKAGPAGIPTQTAFSQSTRWETLDD--DRENGCIRSVEHAYSKEGGLAVLYGN 426 Query: 389 LAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVLKYCGPKGY 448 +A G V+K + + +G A +FES + I +++ + I++++Y GPKG Sbjct: 427 IALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGILADEVKAGD--IVIIRYEGPKGG 484 Query: 449 PGMAEVGNMGLPPKVLK-KGITDMIR-ISDARMSGTAYGTVILHTAPEAAEGGPLALVEN 506 PGM E M P LK KG+ ++D R SG G I H +PEAA GG + LV++ Sbjct: 485 PGMQE---MLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVQD 541 Query: 507 GDLIEVDIPNRTLHLHVSDEELARRRA 533 GD + +DIPNR+++L +SDEE+A RRA Sbjct: 542 GDKVLIDIPNRSINLLISDEEMAARRA 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: 859 Number of extensions: 33 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: 613 Length adjustment: 37 Effective length of query: 542 Effective length of database: 576 Effective search space: 312192 Effective search space used: 312192 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