Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate HSERO_RS19355 HSERO_RS19355 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__HerbieS:HSERO_RS19355 Length = 511 Score = 202 bits (514), Expect = 2e-56 Identities = 144/417 (34%), Positives = 201/417 (48%), Gaps = 38/417 (9%) Query: 5 AQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFRE---PLDAFDDPSAERE 61 A T G +R DGR RN + V V C+ AR I FR P D P+ + Sbjct: 105 ATPATFMGIVRPDGRVATRNYIGVLTSVNCSATAARAIADYFRRDIHPEVLADYPNIDGV 164 Query: 62 PPVHLIGFPGCYPNGYAEKM------LERLTTHPNVGAVLFVSLGCES------MNKHYL 109 V L GC + E + L THPN AVL V LGCE+ M H L Sbjct: 165 --VALTHGQGCALDSQGEPLQILRRTLAGYATHPNFAAVLVVGLGCETNQISGLMESHNL 222 Query: 110 VDVVRASGRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICG 169 + G TIQ GGT T+ G++ I+ + ++ P++ L +G CG Sbjct: 223 KE-----GEYFHTFTIQGTGGTAKTVALGIEKIKKMLPKANDIKREPVSAKHLTLGLQCG 277 Query: 170 GSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACV 229 GSDG SGITANPA+G A D L+ G T I ET E+ G E + RA P +G++++A + Sbjct: 278 GSDGYSGITANPALGAAVDLLVRHGGTAILSETPEIYGAEHLLTRRAVSPEVGEKLLARI 337 Query: 230 AKAARYYS---ILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGG 286 A Y + + + + GN GGLTT EKSLGA AK G + +V + K + G Sbjct: 338 AWWEEYCAKNDAEMNNNPSAGNKAGGLTTILEKSLGAVAKGGTTNLVDVYKYAEAVTARG 397 Query: 287 LYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANP 346 +D G+ IS + +A GA++I FTTGRGS G A +P +K+ N Sbjct: 398 FVFMDTP-------GYDPISATGQ----VAGGANMICFTTGRGSAYGCAPAPSLKLATNT 446 Query: 347 ATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSET--LGHQEFI 401 A ++ DMD++ G I +G T E+G F+ + + G +KSE G EF+ Sbjct: 447 ALWQRQEEDMDINCGEIADGNVTPQEIGERFFQMILDTASGKKTKSELHGYGQDEFV 503 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: 608 Number of extensions: 39 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: 511 Length adjustment: 33 Effective length of query: 398 Effective length of database: 478 Effective search space: 190244 Effective search space used: 190244 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