Align D-galacturonate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate Ac3H11_3958 UDP-glucose 4-epimerase (EC 5.1.3.2)
Query= reanno::WCS417:GFF3392 (274 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3958 Length = 299 Score = 329 bits (843), Expect = 5e-95 Identities = 159/267 (59%), Positives = 200/267 (74%), Gaps = 2/267 (0%) Query: 7 TPVPFNRLLLTGAAGGLGKVLRERLRPYAQVLRLSDIANMAPAADASEEVQPCDLADKQA 66 TP+ F RLLLTGAAGGLG+ LR RL+ Y LRLSDIAN+ A EE++P L D A Sbjct: 33 TPLRFQRLLLTGAAGGLGQELRTRLKAYCTTLRLSDIANLGDEG-AGEELRPARLEDAGA 91 Query: 67 VHHLVEGVDAILHFGGVSVERSFEEVLGANISGIFHIYEAARRHGVKRVIFASSNHVIGF 126 V L+EGVDA++H GGVS E+ +E +L ANI G++++YEAAR+ GVKRV+FASSNHV GF Sbjct: 92 VLGLLEGVDAVVHLGGVSTEQPWEPILQANIVGVYNLYEAARKQGVKRVVFASSNHVTGF 151 Query: 127 YKQGEKLDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIRIGSSFPEPQNRRMMH 186 Y+Q E + P RPD YG+SK++GED++ FYFDRYGIETV +RIGSSFPEP+NRRM+ Sbjct: 152 YRQDEVVGLRDPARPDGLYGVSKAFGEDLSRFYFDRYGIETVCLRIGSSFPEPRNRRMLA 211 Query: 187 TWLSFDDLTQLLERALYTPNVGHTVVYGMSDNLDTWWDNRYAAHLGFAPKDSSEVFRAQV 246 TW+S+DDL +L+ +L P VGH+++YGM DN TWWDN A H+G+ P+DSSE FRA+V Sbjct: 212 TWMSYDDLERLVVASLTAPVVGHSIIYGMGDNTTTWWDNTLARHIGYRPEDSSEPFRAKV 271 Query: 247 ETQPPVSD-NDPAKVYQGGAFCAAGPF 272 E P D DPA +YQGG F GPF Sbjct: 272 EVADPHPDLTDPAVIYQGGPFVHTGPF 298 Lambda K H 0.319 0.136 0.413 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: 308 Number of extensions: 8 Number of successful extensions: 3 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: 274 Length of database: 299 Length adjustment: 26 Effective length of query: 248 Effective length of database: 273 Effective search space: 67704 Effective search space used: 67704 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: 47 (22.7 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