Align D-galactonate dehydratase; EC 4.2.1.6 (characterized)
to candidate Ga0059261_1631 Ga0059261_1631 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily
Query= CharProtDB::CH_024133 (382 letters) >FitnessBrowser__Korea:Ga0059261_1631 Length = 403 Score = 172 bits (435), Expect = 2e-47 Identities = 123/393 (31%), Positives = 183/393 (46%), Gaps = 38/393 (9%) Query: 18 LKIETDEGVVGWGEPVIEGRARTVEAAVHE-LGDYLIGQDPSRINDLWQVMYRAGFYRGG 76 LK+E D+G G G+ + GR V A + + + LIG+D RI D+WQ +Y+ ++R G Sbjct: 21 LKVECDDGTTGIGDATLNGRELAVAAYLSDHVAPCLIGRDAHRIEDIWQYLYKGAYWRRG 80 Query: 77 PILMSAIAGIDQALWDIKGKVLNAPVWQLMGGLVRDKIKAYSWVGGDRPADVIDGIKTLR 136 P+ M+AIA +D ALWDIKGK+ PV+QL+GG R+ Y G + I + Sbjct: 81 PVTMTAIAAVDMALWDIKGKLAGMPVYQLLGGASREGCMVYGHANGTSIEETIKAALDYQ 140 Query: 137 EIGFDTFKLNGCEELGLI---------------------DNSRAVDAAVNTVAQI----R 171 G+ +L C G+ +N + + V ++ R Sbjct: 141 LQGYKAIRLQ-CGVPGMASTYGVSKDKYFYEPADAALPSENVWSTSKYLRIVPELFEAAR 199 Query: 172 EAFGNQIEFGLDFHGRVSAPMAKVLIKELEPYRPLFIEEPVLAEQAEYYPKLAAQTHIPL 231 EA G + D H R++ A L K+LE YRP +IE+ AE E + + T P+ Sbjct: 200 EALGWDVHLLHDVHHRLTPIEAARLGKDLERYRPFWIEDATPAEDQESFRLIRQHTTTPI 259 Query: 232 AAGERMFSRFDFKRVLEAGGISILQPDLSHAGGITECYKIAGMAEAYDVTLAPH--CPLG 289 A GE S +D K ++E I ++ + HAGGIT +IA +A+ + + H L Sbjct: 260 AVGEIFSSIWDCKALIENRLIDYIRATVLHAGGITHMRQIAALADLHQIRTGCHGATDLS 319 Query: 290 PIALAACLHIDFVSYNAVLQEQSMGIHYNKGAELLDFVKNKEDFSMVGGFFKPLTKPGLG 349 P+ +AA LH+ N +QE Y + D V +S G P PGLG Sbjct: 320 PVTMAAALHLGLAIPNFGIQE------YMRHTPETDAV-FPHAYSFADGMLHPGEVPGLG 372 Query: 350 VEIDEAKVIEFSKNAPDWRNPLWRHEDNSVAEW 382 VEIDE F + P+ R ED ++ W Sbjct: 373 VEIDETLAGTFPYDRA--YLPVNRLEDGTMWSW 403 Lambda K H 0.321 0.140 0.433 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: 377 Number of extensions: 15 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: 382 Length of database: 403 Length adjustment: 31 Effective length of query: 351 Effective length of database: 372 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 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