Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate HSERO_RS15800 HSERO_RS15800 D-galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__HerbieS:HSERO_RS15800 Length = 522 Score = 160 bits (406), Expect = 7e-44 Identities = 133/416 (31%), Positives = 197/416 (47%), Gaps = 48/416 (11%) Query: 1 MPVAAQQP---------TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFR-EPL 50 +P+A ++P T EGY DG G RN++A+ V+C V V + R E L Sbjct: 102 LPIATKKPAPQPPLEGYTFEGYRNADGSVGTRNLLAITTTVQCVAGVVEHAVKRIRAELL 161 Query: 51 DAFDDPSAEREPPVHLIGFPGC-----YPN-GYAEKMLERLTTHPNVGA-VLFVSLGCES 103 + + E V L GC PN G + L ++ +PN G + VSLGCE Sbjct: 162 PKYPNV----EDVVALEHTYGCGVAIDAPNAGIPIRTLRNISLNPNFGGQAMVVSLGCEK 217 Query: 104 MNKHYLVDV----VRASGRPVEV-LTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMA 158 + + L+ + G P V L E G S I ++ +L +++ Sbjct: 218 LQPNRLLPENMIPIHKQGEPYVVCLQDAEHVGFNSMIDSIMNMAEARLTELNKRRRETCP 277 Query: 159 LSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAAR 218 S+LV+G CGGSD SG+TANPAVG A D L+ AGA+ +F E E+ + +R Sbjct: 278 ASDLVVGVQCGGSDAFSGVTANPAVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSR--- 334 Query: 219 PALGDEIVACVAKAARYY-SILGHG------SFAVGNADGGLTTQEEKSLGAYAKSGASP 271 A+ +E+ + + +Y + L G + GN GGL EK++G+ KSG+SP Sbjct: 335 -AVNEEVAQAMIREMDWYDNYLKQGGVDRSANTTPGNKKGGLANIVEKAMGSIVKSGSSP 393 Query: 272 IVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSV 331 I G++ PGD GL + SD +A G ++ +FTTGRG+ Sbjct: 394 ISGVLSPGDKLQQKGLI-----------YAATPASDFICGTLQLAAGMNLHIFTTGRGTP 442 Query: 332 VGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRG 387 G A PVIKV R MDV+AGRI G ++++VG E+F+ + V+ G Sbjct: 443 YGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEASIEDVGWELFQLMLDVASG 498 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: 581 Number of extensions: 37 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: 522 Length adjustment: 33 Effective length of query: 398 Effective length of database: 489 Effective search space: 194622 Effective search space used: 194622 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