Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate PfGW456L13_3478 Altronate dehydratase (EC 4.2.1.7)
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3478 Length = 510 Score = 202 bits (513), Expect = 3e-56 Identities = 138/409 (33%), Positives = 210/409 (51%), Gaps = 26/409 (6%) Query: 4 AAQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQF-REPLDAFDDPSAEREP 62 A ++ T +G +R DGR RN + + + C VAR+I F E L AF P+ + Sbjct: 107 ADKRATFQGIIREDGRVATRNYLGIFVVGNCGATVARKIANHFDEERLAAF--PNIDGVV 164 Query: 63 P-VHLIGFPGCYPNGYAEKMLERLT----THPNVGAVLFVSLGCESMNKHYLVDVVR-AS 116 P VH IG G G +L R H N L ++LGCE N + ++ + Sbjct: 165 PFVHEIGC-GMEMTGEPMNLLRRTIGGHIKHANTAGGLLIALGCERNNIYGFIEQEQLVL 223 Query: 117 GRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSG 176 G ++ L IQ+ GG ++ + G+ I+ Q A Q+ ++ L+IG CGGSDG SG Sbjct: 224 GDMLKSLVIQDVGGVKTAVDQGIKMIQAMLPQANAVQRETVSAEHLIIGMQCGGSDGFSG 283 Query: 177 ITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARY- 235 ++ANPA+G A D L+ G T I ET E+ G E + RAA P +G +++ + Y Sbjct: 284 LSANPALGAAVDILVRHGGTAILSETSEIFGVEHTLTARAATPEVGRKLIDRIDWWLEYN 343 Query: 236 --YSILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVV 293 +G + GN GGL EKSLG K G +P++ + + T GL +D Sbjct: 344 KGRDTQINGRVSPGNNAGGLANVLEKSLGGAKKGGNAPLMDVYEYAYPVTTHGLVFMDTP 403 Query: 294 PDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLS 353 G+ +S + IA GA++I FTTGRGS GS +P K+ +N + +S Sbjct: 404 -------GYDPVSATGQ----IAGGANMIAFTTGRGSCFGSVPAPTFKLASNSPMFNRMS 452 Query: 354 GDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSET--LGHQEF 400 DMD++ G+I++G T+ ++G+E+FE+ + + G +KSE LG EF Sbjct: 453 DDMDINCGQIIDGDKTIQQMGQEIFERLLTHASGDKTKSELNGLGEDEF 501 Lambda K H 0.318 0.137 0.408 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: 584 Number of extensions: 38 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: 431 Length of database: 510 Length adjustment: 33 Effective length of query: 398 Effective length of database: 477 Effective search space: 189846 Effective search space used: 189846 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: 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