Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate PP_2834 PP_2834 Putative D-galactarate dehydratase/Altronate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Putida:PP_2834 Length = 513 Score = 212 bits (540), Expect = 2e-59 Identities = 148/417 (35%), Positives = 216/417 (51%), Gaps = 32/417 (7%) Query: 1 MPVAAQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFRE---PLDAFDDPS 57 +P +A Q +G +R DGR RN + + V C+ VAR + FR P D P+ Sbjct: 105 LPGSAAQ--FQGIVRADGRVATRNYIGILTSVNCSATVARAVADHFRRDIHPEVLADYPN 162 Query: 58 AEREPPVHLIGFPGCY--PNGYAEKMLERL----TTHPNVGAVLFVSLGCESMNKHYLVD 111 + V L GC P+G A +L R HPN AVL + LGCE+ L++ Sbjct: 163 VDGV--VALSHSAGCAVDPSGEALGLLRRTLAGYAVHPNFAAVLIIGLGCETNQIETLLE 220 Query: 112 V--VRASGRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICG 169 ++AS + + TIQ GGT TI G+ ++ + ++ P++ LV+G CG Sbjct: 221 TQGLQASAQ-LRAFTIQGIGGTSKTIAAGIAQVKALLAEANQVRRQPVSARHLVVGLQCG 279 Query: 170 GSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACV 229 GSDG SGITANPA+G A D L+ AG T I ET E+ G E + RA +G+++VA + Sbjct: 280 GSDGYSGITANPALGNAVDRLVAAGGTAILSETPEIYGAEHLLTRRAVSREVGEKLVARI 339 Query: 230 AKAARYYSILG---HGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGG 286 Y + + + + GN GGLTT EKSLGA AK+G+S +V + + G Sbjct: 340 RWWEDYCQRMNAELNNNPSAGNKAGGLTTILEKSLGAVAKAGSSNLVDVYQYAQAVRAQG 399 Query: 287 LYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANP 346 L +D G+ +S + +A GA++I FTTGRGS G A +P IK+ N Sbjct: 400 LVFMDTP-------GYDPVSATGQ----VAGGANLIAFTTGRGSAYGCAPAPSIKLATNN 448 Query: 347 ATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSET--LGHQEFI 401 + + DMDV+ G I +G +++E G +FEQ + ++ G SKSE G EF+ Sbjct: 449 RVFEHQQEDMDVNCGGIADGSTSIEERGAFIFEQMLRIASGERSKSEQHGYGQNEFV 505 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: 626 Number of extensions: 32 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: 513 Length adjustment: 33 Effective length of query: 398 Effective length of database: 480 Effective search space: 191040 Effective search space used: 191040 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