Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate PfGW456L13_3725 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 Length = 560 Score = 336 bits (861), Expect = 2e-96 Identities = 209/552 (37%), Positives = 312/552 (56%), Gaps = 19/552 (3%) Query: 21 GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80 G A R+ ++ G F +P IGI +TW+ +TPCN H+ LA ++G AG Sbjct: 17 GVEAAPARAMLRAVGFTDADFT-KPQIGIASTWAMVTPCNMHIDKLALEAEKGANAAGAK 75 Query: 81 PVEFPVFSTGESTLRPT-----AMMFRNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLL 135 V F + + T +++ R + A +E DG+V +GGCDK P L Sbjct: 76 GVIFNTITISDGIANGTEGMKYSLVSREVIADSIEVVTGCEGFDGLVTIGGCDKNMPGCL 135 Query: 136 MGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMAR 195 +G A ++ P+I V GG + G + A+ Q + G++S + E+ Sbjct: 136 IGMARLNRPSIFVYGGTIQPGAGHTDIISVFEAVGQHAR----GDISEIQVKQIEEVAIP 191 Query: 196 SAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPS 255 GSC M TA+TMAS EALGM+L G+++ A+ A + S G++++E++K DLKP Sbjct: 192 GPGSCGGMYTANTMASAIEALGMSLPGSSSQDAIGADKASDSFRAGQQVMELLKLDLKPR 251 Query: 256 DILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQPS 315 DI+T++AFENAIRV A+ GSTNAVLHLLA+A V V+L+LDD+ LG+ P + +L+PS Sbjct: 252 DIMTRKAFENAIRVVIALAGSTNAVLHLLAMANAVDVELTLDDFVELGKVSPVVADLRPS 311 Query: 316 GKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKGVVNY--NEDVILPRE 373 GKY+M E GG+ ++K + + G+LH D +TV+G T+ ++ V +Y +DVI P + Sbjct: 312 GKYMMSELVAIGGIQPLMKRMLDAGMLHGDVLTVTGQTLAENLASVPDYPAGQDVIRPFD 371 Query: 374 KALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDID 433 + + K + +LRGNL+P GAV K + ++ +G A V+ E A I ++ Sbjct: 372 QPIKKDSHLVILRGNLSPTGAVAKITGKEG--LRFEGTARVYHGEEGALAGILNGEVQPG 429 Query: 434 ETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGI-TDMIRISDARMSGTAYGTVILHTA 492 E ++V++Y GPKG PGM E+ + V+ KG+ ++ I+D R SG ++G V+ H Sbjct: 430 E--VIVIRYEGPKGGPGMREM--LSPTSAVMGKGLGKEVALITDGRFSGGSHGFVVGHIT 485 Query: 493 PEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYIK 552 PEA EGGP+ALVENGD I +D R + + VSD LA R++ WV P G Y K Sbjct: 486 PEAFEGGPIALVENGDRIIIDAETRLITVDVSDAVLAERKSRWVRPESKYKRGVLAKYAK 545 Query: 553 TVMQADAGADLD 564 TV A GA D Sbjct: 546 TVSSASEGAVTD 557 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: 889 Number of extensions: 40 Number of successful extensions: 6 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: 579 Length of database: 560 Length adjustment: 36 Effective length of query: 543 Effective length of database: 524 Effective search space: 284532 Effective search space used: 284532 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