Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate BPHYT_RS27220 BPHYT_RS27220 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__BFirm:BPHYT_RS27220 Length = 508 Score = 191 bits (485), Expect = 4e-53 Identities = 133/404 (32%), Positives = 205/404 (50%), Gaps = 28/404 (6%) Query: 11 EGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVHLIGFP 70 +G++R DG+ G RN + V V C+ V I F+ DA D P + + V + Sbjct: 112 QGFVRADGQVGTRNYIGVIASVNCSASVCHAIADAFKG--DAMD-PFSTVDGVVAITHQS 168 Query: 71 GCYPNGYAEKM--LERLTT----HPNVGAVLFVSLGCESMNKHYLVDVVRASGRP--VEV 122 GC + + M L R T +PN VL V LGCE L + A G P VE Sbjct: 169 GCGMSATGDGMALLRRTLTGYACNPNFAGVLLVGLGCEVNQVSGLTRSLEA-GSPALVET 227 Query: 123 LTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPA 182 L IQ++GG R T+ G+ +R + +++ + + L +G CGGSDG SGITANPA Sbjct: 228 LVIQDEGGVRETVARGIAIVREMLSAASRIRRIEVPAARLKVGLQCGGSDGYSGITANPA 287 Query: 183 VGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILG-- 240 +G A D L+ G T I ET E+ G E + RA + ++ + RY + G Sbjct: 288 LGAAVDLLVRHGGTAILSETPEIYGAEHLLTARAVSSDVAGRLLDKLRWWERYAAEAGGD 347 Query: 241 -HGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPR 299 + + + GN GG+TT EKSLGA +K G++ + + + + GL +D Sbjct: 348 MNNNPSPGNKAGGITTILEKSLGAVSKGGSTALNAVYEYAERASESGLVFMDTP------ 401 Query: 300 FGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVD 359 G+ +S + IA GA+++ FTTGRGSV GS P IK+ + + DMD + Sbjct: 402 -GYDPVSATGQ----IAGGANLVCFTTGRGSVFGSKPVPTIKLATTTGLFERMRADMDFN 456 Query: 360 AGRILEGRGTLDEVGREVFEQTVAVSRGAASKSET--LGHQEFI 401 G+I++G T+++ G +VF+ + ++ G + SE +G +EF+ Sbjct: 457 CGQIVDGSLTVEQAGAQVFQLMLDIASGTKTHSEQNGMGDREFV 500 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: 617 Number of extensions: 35 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: 508 Length adjustment: 33 Effective length of query: 398 Effective length of database: 475 Effective search space: 189050 Effective search space used: 189050 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