Align D-mannonate dehydratase; ManD; EC 4.2.1.8 (characterized)
to candidate Echvi_3769 Echvi_3769 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily
Query= SwissProt::Q1NAJ2 (403 letters) >FitnessBrowser__Cola:Echvi_3769 Length = 386 Score = 197 bits (502), Expect = 3e-55 Identities = 130/393 (33%), Positives = 202/393 (51%), Gaps = 38/393 (9%) Query: 21 LKIMTDEGVYGLGDATLNGRELAVASYLTDHVIPCLIGRDAHRIEDLWQYLYKGAYWRRG 80 +KI T G+ G G+ + G+ VA+ + + + LIGR AH IED+WQ LY+G ++R G Sbjct: 22 VKITTKSGLVGWGEPVIEGKADTVAACVRE-MEQYLIGRGAHEIEDIWQVLYRGGFYRGG 80 Query: 81 PVTMTAIAAVDMALWDIKGKIAGLPVYQLLGGASREGVMVYGHANGTTIEDTVKVALDYQ 140 P+ M+A++ +D ALWDIKGK +PVY+LLGGA R+ + +Y G E ++ A + Sbjct: 81 PILMSALSGIDQALWDIKGKHLNVPVYELLGGAVRQKMKMYCWIGGDHPEVVLEQAQEKV 140 Query: 141 AQGYKAIRLQCGVPGMASTYGVSKDKYFYEPADADLPTENIWNTS-KYLRIVPELFKAAR 199 GY A+++ E W +S K ++ V E K R Sbjct: 141 DAGYTAVKMNA-------------------------TGEMDWVSSVKEVKKVVENIKLIR 175 Query: 200 ESLGWDVHLLHDIHHRLTPIEAGRLGQDLEPYRPFWLEDATPAENQEAFRLIRQHTTAPL 259 + G + + D H R+ RL +L P+ P ++E+ AEN +A I +++ P+ Sbjct: 176 QHFGDSLDVGLDFHGRVHKPMVKRLIDELSPFDPLFIEEPVLAENNDALGHIYRYSAIPI 235 Query: 260 AVGEIFNSIWDAKDLIQNQLIDYIRATVVHAGGITHLRRIAALADLYQIRTGCHGATDLS 319 A GE S WD K+++ ++D I+ + HAGGI+ +RRIA +A+ Y I H L Sbjct: 236 ATGERMFSRWDFKEILHQGVVDIIQPDLSHAGGISEVRRIATMAEAYDITIAPH--CPLG 293 Query: 320 PVCMAAALHFDLSVPNFGIQE------YMRHMPETDAV-FPHAYTFADGMMHPGDQPGLG 372 P+ +A+ALH D N IQE Y + D V P + +G + D+PGLG Sbjct: 294 PISLASALHVDFVSANAFIQESSLGIHYNQGFDLLDYVKNPEVFDLKEGYIDLFDRPGLG 353 Query: 373 VDIDED-LAAGYEYKRAFL-PVNRLEDGTMFNW 403 V++DE+ L G + + P+ R DG+ W Sbjct: 354 VEMDEERLKEGQKIGHHWANPIWRNADGSFAEW 386 Lambda K H 0.322 0.139 0.438 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: 413 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 403 Length of database: 386 Length adjustment: 31 Effective length of query: 372 Effective length of database: 355 Effective search space: 132060 Effective search space used: 132060 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 (21.9 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