Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_013722394.1 ALIDE2_RS14310 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000204645.1:WP_013722394.1 Length = 526 Score = 159 bits (401), Expect = 3e-43 Identities = 131/421 (31%), Positives = 197/421 (46%), Gaps = 58/421 (13%) Query: 4 AAQQP----TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAE 59 A Q+P T EGY DG G RN++A+ V+C V V + + L Sbjct: 103 APQEPLAGYTFEGYRNADGSVGTRNILAITQTVQCVAGVTAFAVQRIKAEL-------LP 155 Query: 60 REPPVH-LIGFPGCYPNGYAE---------KMLERLTTHPNVGAVLFV-SLGCESMNKHY 108 R P V ++ Y G A + L ++ +PN G L V SLGCE + Sbjct: 156 RYPHVDDVVALEHGYGCGVAIDAPDAAVPIRTLRNISLNPNFGGELMVVSLGCEKLQPER 215 Query: 109 LV--------------DVVRASGRPVEVLTIQEKG--GTRSTIQYGVDWIRGAREQLAAQ 152 L+ DV ++ ++V+ +Q++ G S ++ + +L A+ Sbjct: 216 LLPPGSIPLVDERNVADVGASADSVLDVVCLQDEAHVGFMSMVESILRQAEAHLARLNAR 275 Query: 153 QKVPMALSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHM 212 ++ + S LV+G CGGSD SG+TANPAVG D L+ AGAT +F E E+ + Sbjct: 276 RRETVPASALVVGVQCGGSDAFSGVTANPAVGFCADLLVRAGATVMFSEVTEVRDGIDQL 335 Query: 213 KTRAARPALGDEIVACVAKAARYYSILGHG------SFAVGNADGGLTTQEEKSLGAYAK 266 RAA P + A + + A Y + L G + GN GGL+ EK++G+ K Sbjct: 336 TARAATPEVAQ---ALIDQMAWYDAYLARGRVDRSANTTPGNKKGGLSNIVEKAMGSIVK 392 Query: 267 SGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTT 326 SG++PI G++ PG+ GL L P + G +A G ++ +FTT Sbjct: 393 SGSAPISGVVAPGERAARKGL-LYAATPASDFICGTLQ----------LAAGMNLHVFTT 441 Query: 327 GRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSR 386 GRG+ G A PVIKV R MDV+AGRI +G ++++VG E+F + V+ Sbjct: 442 GRGTPYGLAACPVIKVATRSDLARRWHDLMDVNAGRIADGEASIEDVGWELFHLMLDVAS 501 Query: 387 G 387 G Sbjct: 502 G 502 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: 652 Number of extensions: 48 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: 526 Length adjustment: 33 Effective length of query: 398 Effective length of database: 493 Effective search space: 196214 Effective search space used: 196214 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 24 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