Align D-xylonate dehydratase YagF; EC 4.2.1.82 (characterized)
to candidate GFF612 HP15_595 dihydroxy-acid dehydratase
Query= SwissProt::P77596 (655 letters) >FitnessBrowser__Marino:GFF612 Length = 597 Score = 197 bits (502), Expect = 9e-55 Identities = 182/614 (29%), Positives = 277/614 (45%), Gaps = 72/614 (11%) Query: 72 GIRAGD-GRPIALGYHT------GHWEIGMQMQAAAKEITRNGGIPFAAFVSDPCDGRSQ 124 G++ GD G+PI ++ GH + Q +EI GG+ DG + Sbjct: 12 GMKDGDFGKPIIAVANSFTQFVPGHVHLKDLGQLVCREIESAGGVAKEFNTIAVDDGIAM 71 Query: 125 GTHGMFDSLPYRNDAAIVFRRLIRSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILV 184 G GM SLP R A ++ + A++ ++ CDK P ++A ++ +PTI V Sbjct: 72 GHDGMLYSLPSREIIADSVEYMVNA-HCADALVCISNCDKITPGMLMAAMRLN-IPTIFV 129 Query: 185 PGGATLPPTVGEDAGKVQTIGARF--ANHELSLQEAAELGCRACASPGGGCQFLGTAGTS 242 GG K+ + A A+ S ++ E AC + G C + TA + Sbjct: 130 SGGPMEAGKTKLSEHKLDLVDAMVIAADPNASDEQVEEYERNACPTCGS-CSGMFTANSM 188 Query: 243 QVVAEALGLALPHS----ALAPSGQAVWLEIARQ---SARAVSELDSRGITTRDILSDKA 295 + EA+GLALP + A + ++L+ RQ +AR E D + I S A Sbjct: 189 NCLTEAIGLALPGNGSLLATHADREQLFLKAGRQIVENARRYYEEDDASVLPLSIASMAA 248 Query: 296 IENAMVIHAAFGGSTNLLLHIPAIAHAAGC--TIPDVEHWTRINRKVPRLVSVLPNGPDY 353 ENAMV+ A GGSTN +LH+ A A G T+ +++ +++R+VP+L V PN P Y Sbjct: 249 FENAMVMDIAMGGSTNTILHLLAAAQEGGVPFTLNEID---QLSRRVPQLCKVAPNSPKY 305 Query: 354 HPTVRAFLAGGVPEVMLHLRDLGLLHLDAMTVTGQTVGENLEWWQASER----------- 402 H AGG+ ++ L GL++ D TV +T+ E LE W Sbjct: 306 HME-DVHRAGGIMGILGELERGGLINTDLPTVHSKTMREALETWDIMRSPPTEVVEFYKA 364 Query: 403 -------RARFRQCLR--EQDGVEPDDVILPPEKAKAKGLTSTVCFPTGNIAPEGSVIKA 453 + F Q R DG I E A + V + GNIA +G V+K Sbjct: 365 GPAGIPTQTAFSQSTRWPTLDGDRETGCIRSVENAYSSEGGLAVLY--GNIALDGCVVKT 422 Query: 454 TAIDPSVVGEDGVYHHTGRVRVFVSEAQAIKAIKREEIVQGDIMVVIGGGP-SGTGMEET 512 +D S+ + G+ RVF S+ A+ I +E+ G+++++ GP G GM+E Sbjct: 423 AGVDESI------FVFEGKARVFESQDSAVAGILSDEVKPGEVVIIRYEGPRGGPGMQEM 476 Query: 513 YQLTSALKHISWGKTVSLITDARFSGVSTGACFGHVSPEALAGGPIGKLRDNDIIEIAVD 572 TS LK GK +L+TD RFSG ++G GH SPEA AGG IG + + D I I + Sbjct: 477 LYPTSYLKSKGLGKDCALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLIENGDTIRIDI- 535 Query: 573 RLTLTGSVNFIGTADNPLTPEEGARELARRQTHPDLHA-HDFLPDDTRLWAALQS---VS 628 + + E EL RR+ D LP D ++ AAL++ ++ Sbjct: 536 -------------PNRSINVELDQHELDRRREARDAKGWKPELPRDRKVSAALKAYALLA 582 Query: 629 GGTWKGCIYDTDKI 642 KG + D +K+ Sbjct: 583 TSADKGAVRDLEKL 596 Lambda K H 0.319 0.136 0.411 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: 975 Number of extensions: 60 Number of successful extensions: 8 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: 655 Length of database: 597 Length adjustment: 38 Effective length of query: 617 Effective length of database: 559 Effective search space: 344903 Effective search space used: 344903 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: 54 (25.4 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