Align D-mannonate dehydratase; ManD; EC 4.2.1.8 (characterized)
to candidate Ga0059261_1631 Ga0059261_1631 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily
Query= SwissProt::Q1NAJ2 (403 letters) >FitnessBrowser__Korea:Ga0059261_1631 Length = 403 Score = 720 bits (1859), Expect = 0.0 Identities = 335/403 (83%), Positives = 377/403 (93%) Query: 1 MPKIIDAKVIITCPGRNFVTLKIMTDEGVYGLGDATLNGRELAVASYLTDHVIPCLIGRD 60 MPKI+ A+VI+T PGRNFVTLK+ D+G G+GDATLNGRELAVA+YL+DHV PCLIGRD Sbjct: 1 MPKIVSARVIVTSPGRNFVTLKVECDDGTTGIGDATLNGRELAVAAYLSDHVAPCLIGRD 60 Query: 61 AHRIEDLWQYLYKGAYWRRGPVTMTAIAAVDMALWDIKGKIAGLPVYQLLGGASREGVMV 120 AHRIED+WQYLYKGAYWRRGPVTMTAIAAVDMALWDIKGK+AG+PVYQLLGGASREG MV Sbjct: 61 AHRIEDIWQYLYKGAYWRRGPVTMTAIAAVDMALWDIKGKLAGMPVYQLLGGASREGCMV 120 Query: 121 YGHANGTTIEDTVKVALDYQAQGYKAIRLQCGVPGMASTYGVSKDKYFYEPADADLPTEN 180 YGHANGT+IE+T+K ALDYQ QGYKAIRLQCGVPGMASTYGVSKDKYFYEPADA LP+EN Sbjct: 121 YGHANGTSIEETIKAALDYQLQGYKAIRLQCGVPGMASTYGVSKDKYFYEPADAALPSEN 180 Query: 181 IWNTSKYLRIVPELFKAARESLGWDVHLLHDIHHRLTPIEAGRLGQDLEPYRPFWLEDAT 240 +W+TSKYLRIVPELF+AARE+LGWDVHLLHD+HHRLTPIEA RLG+DLE YRPFW+EDAT Sbjct: 181 VWSTSKYLRIVPELFEAAREALGWDVHLLHDVHHRLTPIEAARLGKDLERYRPFWIEDAT 240 Query: 241 PAENQEAFRLIRQHTTAPLAVGEIFNSIWDAKDLIQNQLIDYIRATVVHAGGITHLRRIA 300 PAE+QE+FRLIRQHTT P+AVGEIF+SIWD K LI+N+LIDYIRATV+HAGGITH+R+IA Sbjct: 241 PAEDQESFRLIRQHTTTPIAVGEIFSSIWDCKALIENRLIDYIRATVLHAGGITHMRQIA 300 Query: 301 ALADLYQIRTGCHGATDLSPVCMAAALHFDLSVPNFGIQEYMRHMPETDAVFPHAYTFAD 360 ALADL+QIRTGCHGATDLSPV MAAALH L++PNFGIQEYMRH PETDAVFPHAY+FAD Sbjct: 301 ALADLHQIRTGCHGATDLSPVTMAAALHLGLAIPNFGIQEYMRHTPETDAVFPHAYSFAD 360 Query: 361 GMMHPGDQPGLGVDIDEDLAAGYEYKRAFLPVNRLEDGTMFNW 403 GM+HPG+ PGLGV+IDE LA + Y RA+LPVNRLEDGTM++W Sbjct: 361 GMLHPGEVPGLGVEIDETLAGTFPYDRAYLPVNRLEDGTMWSW 403 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: 716 Number of extensions: 23 Number of successful extensions: 1 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: 403 Length adjustment: 31 Effective length of query: 372 Effective length of database: 372 Effective search space: 138384 Effective search space used: 138384 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 Apr 09 2024. 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