Align D-mannonate dehydratase; ManD; EC 4.2.1.8 (characterized)
to candidate AZOBR_RS25270 AZOBR_RS25270 mandelate racemase
Query= SwissProt::Q1NAJ2 (403 letters) >FitnessBrowser__azobra:AZOBR_RS25270 Length = 397 Score = 175 bits (443), Expect = 2e-48 Identities = 132/382 (34%), Positives = 191/382 (50%), Gaps = 35/382 (9%) Query: 14 PGR--NFVTLKIMTDEGVYGLGDATLN-GRELAVASYLTDHVIPCLIGRDAHRIEDLWQY 70 PGR N + ++I T+ G+YG G+ + G+E VA+Y+ D + P LIGR+ I L Q Sbjct: 13 PGRAKNLLFVRIETESGIYGWGEGYVTAGKEKVVAAYV-DAIAPLLIGREIWNIRQLAQT 71 Query: 71 LYKGAYWRRGPVT-MTAIAAVDMALWDIKGKIAGLPVYQLLGGASREGVMVYGHA---NG 126 L RR V + A++AV++A WDI GK AGLPV++LLGGA RE + VY + Sbjct: 72 LLDDFSIRRTSVDFLCALSAVEIASWDIVGKRAGLPVHKLLGGAVREKIRVYANGWWFGA 131 Query: 127 TTIEDTVKVALDYQAQGYKAIRLQCGVPGMASTYGVSKDKYFYEPADADLPTENIWNTSK 186 ++I+DT A AQGY A++ +PG Y +P D D EN+ Sbjct: 132 SSIDDTANRAAAVVAQGYDALKWD-PIPGPWRNY--------VDPKDLDHAVENV----- 177 Query: 187 YLRIVPELFKAARESLGWDVHLLHDIHHRLTPIEAGRLGQDLEPYRPFWLEDATPAENQE 246 +A RE++G +V LL D H RL+P A RL + L + W E+ P EN + Sbjct: 178 ---------RAVREAVGPNVELLIDGHRRLSPNHAIRLIERLREFGIAWYEEPCPPENLD 228 Query: 247 AFRLIRQHTTAPLAVGEIFNSIWDAKDLIQNQLIDYIRATVVHAGGITHLRRIAALADLY 306 +R+ T P+ GE + L + + D I + GGI + IAALA + Sbjct: 229 LTAEVRRTTNVPIVSGEALYTKEQYLPLFEKRAADIINPDISAVGGILAMLDIAALAQPH 288 Query: 307 QIRTGCHGATDLSPVC-MAAALHFDLSVPNFGIQEYMRHMPE-TDAVFPHAYTFADGMMH 364 I H SP+ +AA +H V NF I E ++ E T + T ADG + Sbjct: 289 SIAVSPHNFN--SPIVGLAATVHLSALVTNFTIAELFVNLVEPTRELALQGLTIADGYVD 346 Query: 365 PGDQPGLGVDIDEDLAAGYEYK 386 D PGLGVD+D ++ + Y+ Sbjct: 347 IPDTPGLGVDLDVEVLRRHPYQ 368 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: 406 Number of extensions: 25 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: 403 Length of database: 397 Length adjustment: 31 Effective length of query: 372 Effective length of database: 366 Effective search space: 136152 Effective search space used: 136152 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