Align D-mannonate dehydratase; ManD; EC 4.2.1.8 (characterized)
to candidate WP_007690272.1 C447_RS01785 galactonate dehydratase
Query= SwissProt::Q1NAJ2 (403 letters) >NCBI__GCF_000336675.1:WP_007690272.1 Length = 384 Score = 219 bits (558), Expect = 1e-61 Identities = 134/412 (32%), Positives = 216/412 (52%), Gaps = 37/412 (8%) Query: 1 MPKIIDAKVIITCPGRNFVTLKIMTDEGVYGLGDATLNGRELAVASYLTDHVIPCLIGRD 60 M +I+D ++ P ++ L++ T +G+ G G+ + GR VA+ + + + L+GRD Sbjct: 1 MTEIVDYELYDVPP--RWLFLELETSDGLVGWGEPVVEGRSKTVAAAVEELLDNYLLGRD 58 Query: 61 AHRIEDLWQYLYKGAYWRRGPVTMTAIAAVDMALWDIKGKIAGLPVYQLLGGASREGVMV 120 +RIED WQ +Y+G ++R GP+ M+AIA +D ALWDIKGK G PV++LLGG +R+ + V Sbjct: 59 PNRIEDHWQAMYRGGFYRGGPILMSAIAGIDQALWDIKGKRFGAPVHELLGGRARDRIRV 118 Query: 121 YGHANGTTIEDTVKVALDYQAQGYKAIRLQCGVPGMASTYGVSKDKYFYEPADADLPTEN 180 Y G D + A + G+ A+++ + + PA + E Sbjct: 119 YQWIGGDRPADVGEAAAEQVEAGFSALKMN----------ATPEIRRVDSPAAVEAAVER 168 Query: 181 IWNTSKYLRIVPELFKAARESLGWDVHLLHDIHHRLTPIEAGRLGQDLEPYRPFWLEDAT 240 + ++ RE++G +V + D H R+T A RL LEP+ P ++E+ Sbjct: 169 L--------------RSVREAVGPEVEIGVDFHGRVTKPMAKRLVAALEPHEPMFVEEPV 214 Query: 241 PAENQEAFRLIRQHTTAPLAVGEIFNSIWDAKDLIQNQLIDYIRATVVHAGGITHLRRIA 300 ++ +A I HTT P+A GE S WD K++ ++ +D I+ + HAGGIT +++IA Sbjct: 215 LPQHNDALAEIASHTTTPIATGERMFSRWDYKEVFEDGTVDVIQPDLSHAGGITEVKKIA 274 Query: 301 ALADLYQIRTGCHGATDLSPVCMAAALHFDLSVPNFGIQEYMR--HMPETDAVF-----P 353 A+A+ Y + H L PV +A+ + D PN IQE H ET V P Sbjct: 275 AMAEAYDVALAPH--CPLGPVALASCIQVDACSPNALIQEQSLNIHYNETSDVLDYLADP 332 Query: 354 HAYTFADGMMHPGDQPGLGVDIDEDL--AAGYEYKRAFLPVNRLEDGTMFNW 403 + + DG + D+PGLG+D+DE+ A E P+ R +DG++ W Sbjct: 333 SVFEYEDGFVDVLDEPGLGIDLDEEYIEAQSEEPVDWHNPIWRHDDGSVAEW 384 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: 446 Number of extensions: 17 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: 384 Length adjustment: 31 Effective length of query: 372 Effective length of database: 353 Effective search space: 131316 Effective search space used: 131316 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 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