Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate HSERO_RS05150 HSERO_RS05150 galactonate dehydratase
Query= BRENDA::A0A0H3C643 (403 letters) >FitnessBrowser__HerbieS:HSERO_RS05150 Length = 382 Score = 205 bits (521), Expect = 2e-57 Identities = 130/393 (33%), Positives = 203/393 (51%), Gaps = 38/393 (9%) Query: 21 LKITTEDGITGVGDATLNGRELSVVSFLQDHMVPSLIGRDAHQIEDIWQFFYRGSYWRGG 80 LKI T++G+ G G+ + GR SV + +++ + LIG+D IED W YRG ++RGG Sbjct: 18 LKIETDEGVVGWGEPIVEGRAHSVAAAVEE-LSDYLIGKDPRNIEDHWTVLYRGGFYRGG 76 Query: 81 PVAMTALAAVDMALWDIKGKVAGLPVYQLLGGACRTGVTVYGHANGETIEDTIAEAVKYK 140 + M+ALA +D ALWDIKGK G+PV+QLLGGA R + VY G+ DT A A Sbjct: 77 AIHMSALAGIDQALWDIKGKDLGVPVHQLLGGAVRNSIRVYSWIGGDRPADTAAAAKSAV 136 Query: 141 AMGYKAIRLQTGVPGLASTYGVSKDKMFYEPADN-DLPTENIWSTAKYLNSVPKLFERAR 199 A G+ A+++ +++ F + D +L N+ + R Sbjct: 137 ARGFTAVKMNG-----------TEELQFIDSHDKIELTLANV--------------QAVR 171 Query: 200 EVLGWDVHLLHDVHHRLTPIEAARLGKDLEPYRLFWLEDSVPAENQAGFRLIRQHTTTPL 259 E +G +V + D H R+ A L K+LEPY+L ++E+ V +EN + I T+TP+ Sbjct: 172 EAVGPNVGIGVDFHGRVHKPMAKALIKELEPYKLMFIEEPVLSENAEALKEIAHLTSTPI 231 Query: 260 AVGEIFAHVWDAKQLIEEQLIDYLRATVLHAGGITNLKKIAAFADLHHVKTGCHGATDLS 319 A+GE WD K+++ E +D ++ V HAGGIT +KIA A+ + V H L Sbjct: 232 ALGERLYSRWDFKRILSEGYVDIIQPDVSHAGGITETRKIAMMAEAYDVALALH--CPLG 289 Query: 320 PVTMAAALHFDMSITNFGLQEYMR--HTPETDAVFPH-----AYTFSDGMLHPGDKPGLG 372 P+ +A+ L D N +QE H E++ + + + + DG + PGLG Sbjct: 290 PIALASCLQVDAGSYNAFIQEQSLGIHYNESNDLLDYIRDKNVFAYEDGYVKIPQGPGLG 349 Query: 373 VDIDEDLAAKHPY--KRAYLPVNRLEDGTMFNW 403 ++I+E+ + R P+ R +DG+ W Sbjct: 350 IEINEEYVRQRAEVGHRWRNPIWRHKDGSFAEW 382 Lambda K H 0.321 0.138 0.427 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: 390 Number of extensions: 24 Number of successful extensions: 4 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: 403 Length of database: 382 Length adjustment: 31 Effective length of query: 372 Effective length of database: 351 Effective search space: 130572 Effective search space used: 130572 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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