Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate PfGW456L13_3725 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 Length = 560 Score = 248 bits (632), Expect = 6e-70 Identities = 167/510 (32%), Positives = 265/510 (51%), Gaps = 28/510 (5%) Query: 45 RPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRN 104 +P IGIA T + +TPCN H +LA + G AG + F I++ T + + Sbjct: 39 KPQIGIASTWAMVTPCNMHIDKLALEAEKGANAAGAKGVIFNTITISDGIANGTEGMKYS 98 Query: 105 LAYLGLV----EILHGYP-LDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHH 159 L ++ E++ G DG+V GCDK P CL+ A + P+I + GG + G Sbjct: 99 LVSREVIADSIEVVTGCEGFDGLVTIGGCDKNMPGCLIGMARLNRPSIFVYGGTIQPGAG 158 Query: 160 KGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGM 219 ++I ++ A A G+I ++ A P G C M TA +M + EALGM Sbjct: 159 HTDIIS----VFEAVGQHARGDISEIQVKQIEEVAIPGPGSCGGMYTANTMASAIEALGM 214 Query: 220 SLPGCASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQAFENAIAVASALGASSN 279 SLPG +S A ++ ++ G+++ EL+ D++P IMTR+AFENAI V AL S+N Sbjct: 215 SLPGSSSQDAIGADKASDSFRAGQQVMELLKLDLKPRDIMTRKAFENAIRVVIALAGSTN 274 Query: 280 CPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQK 339 HL+A+A + VEL+LDD+ +G+ P++ + P+GKY+ GG+ +M + Sbjct: 275 AVLHLLAMANAVDVELTLDDFVELGKVSPVVADLRPSGKYMMSELVAIGGIQPLMKRMLD 334 Query: 340 AGRLHEDCATVSGRTIGEIVSS--SLTSNADVIHPFDTPLKHRAGFIVLSGNFFDSAIMK 397 AG LH D TV+G+T+ E ++S + DVI PFD P+K + ++L GN + + Sbjct: 335 AGMLHGDVLTVTGQTLAENLASVPDYPAGQDVIRPFDQPIKKDSHLVILRGNLSPTGAVA 394 Query: 398 MSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTV 457 E R FE A V+ G E A I + + E ++VIR G Sbjct: 395 KITGKEGLR------------FEGTARVYHGEEGALAGILNGEVQPGE--VIVIRYEGPK 440 Query: 458 GYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQ 516 G PG E+ ++P +A++ +G+ + + DGR SG S + +++PEA GG +AL++ Sbjct: 441 GGPGMREM--LSPTSAVMGKGLGKEVALITDGRFSGGSHGFVVGHITPEAFEGGPIALVE 498 Query: 517 TNDRLKVDLNTRTVNLLIDDEEMARRRLEW 546 DR+ +D TR + + + D +A R+ W Sbjct: 499 NGDRIIIDAETRLITVDVSDAVLAERKSRW 528 Lambda K H 0.319 0.135 0.407 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: 794 Number of extensions: 31 Number of successful extensions: 5 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: 594 Length of database: 560 Length adjustment: 36 Effective length of query: 558 Effective length of database: 524 Effective search space: 292392 Effective search space used: 292392 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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