Align Altronate oxidoreductase; EC 1.1.1.58; Tagaturonate dehydrogenase; Tagaturonate reductase (uncharacterized)
to candidate H281DRAFT_00668 H281DRAFT_00668 tagaturonate reductase
Query= curated2:Q9KFI7 (512 letters) >FitnessBrowser__Burk376:H281DRAFT_00668 Length = 377 Score = 140 bits (353), Expect = 8e-38 Identities = 112/372 (30%), Positives = 178/372 (47%), Gaps = 37/372 (9%) Query: 23 PERVLQFGEGNFLRGFIDWMIQQMNKQNVFN--GRVVAIQPTPHGKVVPKLQ--EQDSLY 78 P +LQFG FL+ +D + + ++N + G++ +Q T + ++ ++ Y Sbjct: 5 PCPILQFGTSRFLQAHVDLFVCEAARRNPDDALGKIAMVQTTASTQSRARIDAIRANARY 64 Query: 79 TVWLRGIADGETVDHHEVITSISRGLNPYTNWQDVLEVAASPDISVVFSNTTEAGLTYLE 138 V +RG+ ETVD S+++ L+ +W +LE ++ V+ SNT + G Sbjct: 65 PVRIRGLHRKETVDLTIECDSVAQALHADDDWPLLLEYIRD-EVKVIVSNTADNGYALFA 123 Query: 139 EG----YDKEKAPLSFPGKLAACLWHRYETLGWGEGSGLVIIPCELVEQNGKVLKELVCR 194 E D AP F KLA L RY G + ++PCELV +NG VL++LV Sbjct: 124 EDTASVLDGRTAPRGFAAKLAVLLHERYRA----GGKAITLLPCELVSRNGDVLRDLVLS 179 Query: 195 YAKAWNFPQEFFTWLERENEFCHTLVDRIVPGFPSDTADECFERLGYEDILLTVAEPYHL 254 A+ W +F +L + + ++LVDRIV E E +G VAEPY L Sbjct: 180 VARGWQMDADFLRYLTNDCIWVNSLVDRIV--------SEAIEPVG------AVAEPYAL 225 Query: 255 FIIEGSERVRKLLPFNEAGLHVRWNHLEKHRNMKVRVLNGTHTFMFALSYLSG----VDT 310 + IE + + +LP + V ++L + +K+ +LN HT M A +L T Sbjct: 226 WAIEQQDGM--VLPCRHESIVVT-DNLAHYERLKLFLLNLGHT-MLAQCWLDSQGDPATT 281 Query: 311 VGEAMADEQLCSFIRKGLFEEIIPCVDAPEQE--VTAFAETVLERFENPFLQHRLTDIGL 368 V + M +E + + +E++P +A Q T + + V +RF NPFL HRL DI Sbjct: 282 VLDGMRNESWRATLESTWKDEVLPVFEALGQSEIATKYLDDVRDRFSNPFLAHRLADIAN 341 Query: 369 NAVNKFRTRLMP 380 N K + RL P Sbjct: 342 NHQEKKQRRLKP 353 Lambda K H 0.321 0.138 0.419 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: 425 Number of extensions: 26 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: 512 Length of database: 377 Length adjustment: 32 Effective length of query: 480 Effective length of database: 345 Effective search space: 165600 Effective search space used: 165600 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 (21.8 bits) S2: 51 (24.3 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