Align uronate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate H281DRAFT_03826 H281DRAFT_03826 uronate dehydrogenase
Query= BRENDA::Q88NN6 (268 letters) >FitnessBrowser__Burk376:H281DRAFT_03826 Length = 283 Score = 295 bits (756), Expect = 6e-85 Identities = 145/263 (55%), Positives = 190/263 (72%), Gaps = 2/263 (0%) Query: 5 PFNRLLLTGAAGGLGKVLRERLKGYAEVLRLSDISPMAPAAGPHEEVITCDLADKAAVHT 64 PF RLLLTGAAG LG+ LR L +A+V+R++DI+ + A PHEE DLAD+ AV Sbjct: 15 PFRRLLLTGAAGNLGRQLRGVLAQWADVVRVTDIASLGEPA-PHEEASVVDLADREAVMQ 73 Query: 65 LVEGVDAIIHFGGVSTEHAFEEILGPNICGVFHVYEAARKHGVKRIIFASSNHTIGFYRQ 124 LVEGVDAI+H GG+S + F+++LG NI G +++YEAARKHGVKRI FASSNH IGF+ Sbjct: 74 LVEGVDAIVHLGGISIDAPFDDLLGANIAGTYNLYEAARKHGVKRIAFASSNHVIGFHPV 133 Query: 125 DERIDAHAPRRPDSYYGLSKCYGEDVASFYFDRYGIETVSIRIGSSFPQPQNLRMLCTWL 184 E +DA AP+RPD+ YG++KC+GE ++ +Y+DR+GIETV +RIGSSF +P+N RML T+L Sbjct: 134 TEVLDADAPQRPDTLYGVTKCFGEALSRYYYDRFGIETVCMRIGSSFDEPKNSRMLVTYL 193 Query: 185 SYDDLVQLIERGLFTPGVGHTIVYGASDNRTVWWDNRHAAHLGYVPKDSSETFRAAVEA- 243 SY D ++L+ LFT VGH +VYGASDN WWDN + LG+ P+DSS F A A Sbjct: 194 SYRDFIELVRCSLFTNRVGHVVVYGASDNPVKWWDNTKVSFLGFNPRDSSAPFAARFPAT 253 Query: 244 QPAPAADDPSMVYQGGAFAVAGP 266 P + DDP+ +QGG F + P Sbjct: 254 APDASRDDPAQRFQGGPFVLGEP 276 Lambda K H 0.321 0.138 0.427 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: 235 Number of extensions: 9 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: 268 Length of database: 283 Length adjustment: 25 Effective length of query: 243 Effective length of database: 258 Effective search space: 62694 Effective search space used: 62694 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