Align D-galacturonate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate GFF364 Psest_0365 NAD dependent epimerase/dehydratase family.
Query= reanno::WCS417:GFF3392 (274 letters) >FitnessBrowser__psRCH2:GFF364 Length = 271 Score = 434 bits (1115), Expect = e-126 Identities = 215/272 (79%), Positives = 232/272 (85%), Gaps = 2/272 (0%) Query: 1 MTTTPTTPVPFNRLLLTGAAGGLGKVLRERLRPYAQVLRLSDIANMAPAADASEEVQPCD 60 MTTTPT F RLLLTGAAGGLGK LRERL+PYA+++RLSDIA MAPAA A EEV PCD Sbjct: 1 MTTTPTPQ--FGRLLLTGAAGGLGKELRERLQPYARIIRLSDIAPMAPAAGAHEEVMPCD 58 Query: 61 LADKQAVHHLVEGVDAILHFGGVSVERSFEEVLGANISGIFHIYEAARRHGVKRVIFASS 120 LADK AVH L EGVDAI HFGGVSVERSFEE+L ANI G FHIYEAAR HG+KRV+FASS Sbjct: 59 LADKAAVHALCEGVDAIAHFGGVSVERSFEEILDANIRGTFHIYEAARLHGIKRVVFASS 118 Query: 121 NHVIGFYKQGEKLDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIRIGSSFPEPQ 180 NHVIGFY Q E LDAHSPRRPD YYGLSKSYGEDMA+FY+DRYGIETVSIRIGSSFPEP Sbjct: 119 NHVIGFYPQTETLDAHSPRRPDGYYGLSKSYGEDMANFYYDRYGIETVSIRIGSSFPEPA 178 Query: 181 NRRMMHTWLSFDDLTQLLERALYTPNVGHTVVYGMSDNLDTWWDNRYAAHLGFAPKDSSE 240 NRRMM TWLSF DLT+L+ AL+TP VGHTVVYGMS N D WWDN AAHLGF+ +DSSE Sbjct: 179 NRRMMSTWLSFRDLTELMRCALFTPAVGHTVVYGMSANRDVWWDNHLAAHLGFSAQDSSE 238 Query: 241 VFRAQVETQPPVSDNDPAKVYQGGAFCAAGPF 272 VFR +VE QPP S +DPA +YQGGAF AAGPF Sbjct: 239 VFRDKVEQQPPYSADDPAGIYQGGAFVAAGPF 270 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: 349 Number of extensions: 7 Number of successful extensions: 1 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: 271 Length adjustment: 25 Effective length of query: 249 Effective length of database: 246 Effective search space: 61254 Effective search space used: 61254 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