Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate Ga0059261_4216 Ga0059261_4216 Dihydroxyacid dehydratase/phosphogluconate dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__Korea:Ga0059261_4216 Length = 573 Score = 301 bits (771), Expect = 5e-86 Identities = 187/550 (34%), Positives = 298/550 (54%), Gaps = 19/550 (3%) Query: 21 GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80 G HRS+ G+ + RP + + + ++ PCN L A+ ++GV + GG Sbjct: 18 GPERAPHRSYYYAMGISEEEI-ARPFVALASAGNDSAPCNTTLDAQADAARKGVADNGGL 76 Query: 81 PVEFPVFSTGESTLR-----PTAMMFRNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLL 135 P F + + ++++ R + A VE S+RG+ D +V GCDK+ P ++ Sbjct: 77 PRRFNTITVTDGIAMGHQGMKSSLVSREVIADSVELSVRGHCYDALVGFAGCDKSLPGMM 136 Query: 136 MGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVK--SGEMSLEEFMDAEQGM 193 M ++IP+I V GG +L G+++ +DV T + F + K +G + E E+ Sbjct: 137 MAMLRLNIPSIFVYGGSILPGRYQDRDV---TVVDVFEVVGKFAAGTCPISEVHALEKVA 193 Query: 194 ARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLK 253 G+C TA+TMA + EA+G++L + +PA R I+ G +++E+++ +++ Sbjct: 194 CPGHGACGGQYTANTMACVGEAIGLSLPNSNMVPAPYTSREQIAVAAGYQVMELLERNIR 253 Query: 254 PSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQ 313 P DI T+EAF NA R+ A GGSTN LHL A+A G+D L D + + P +L+ Sbjct: 254 PRDICTREAFINAARIVAATGGSTNGALHLPAMASEAGIDFDLFDVAEVFKSTPYAADLK 313 Query: 314 PSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKGVV-NYNEDVILPR 372 P GKY+ ++ Y AGG+ +++K++ E GLL+ D +TV+G T+ ++ V N ++ VI Sbjct: 314 PGGKYVAKDMYEAGGVYMLMKSMLENGLLYGDCMTVTGKTLGENIDQVTWNPDQKVIYDV 373 Query: 373 EKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDI 432 +T +GG+ LRG LAP GA++K + S + +G A F+ ED A + E +I Sbjct: 374 RTPITPTGGVVGLRGTLAPNGAIVKVAGMS--RLVFEGPARCFDCEEDAFAAV--EKREI 429 Query: 433 DETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIR-ISDARMSGTAYGTVILHT 491 E ++V++Y GPKG PGM E+ + + G+ + + I+D R SG G I H Sbjct: 430 REGEVVVIRYEGPKGGPGMREM--LSTTAALYGLGMGEKVALITDGRFSGATRGFCIGHV 487 Query: 492 APEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYI 551 PEAAE GP+ALVE+GD I +D T+ LHV+++ LA RRA W G Y Sbjct: 488 GPEAAECGPIALVEDGDTIRIDAEAGTIDLHVAEDVLAERRARWQPRENAYQSGALWRYA 547 Query: 552 KTVMQADAGA 561 + V A GA Sbjct: 548 QNVGPAYKGA 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: 805 Number of extensions: 46 Number of successful extensions: 7 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: 573 Length adjustment: 36 Effective length of query: 543 Effective length of database: 537 Effective search space: 291591 Effective search space used: 291591 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