Align D-galacturonate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate AO356_23065 AO356_23065 NAD-dependent dehydratase
Query= reanno::pseudo1_N1B4:Pf1N1B4_4511 (270 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23065 Length = 273 Score = 477 bits (1227), Expect = e-139 Identities = 232/273 (84%), Positives = 250/273 (91%), Gaps = 3/273 (1%) Query: 1 MTNT---SPFNRLLLTGAAGGLGKVLRERLRPYANVLRLSDIANMAPAIDDREEVVPCDL 57 MT T P NRLLLTGAAGGLGKVLRERL+P+A +RLSDIANMAPAID+ EEVVPCDL Sbjct: 1 MTTTPIRQPLNRLLLTGAAGGLGKVLRERLKPFARHIRLSDIANMAPAIDESEEVVPCDL 60 Query: 58 ADKQAVHQLVEGVDAILHFGGVSVERPFEEILGANICGVFHIYEAARRHGVKRVIFASSN 117 +DK AVHQLVEGVDAILHFGGVSVERPFEEILGANI GVFHIYEAAR+HGVKRVIFASSN Sbjct: 61 SDKHAVHQLVEGVDAILHFGGVSVERPFEEILGANISGVFHIYEAARKHGVKRVIFASSN 120 Query: 118 HVIGFYKQDKTLDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIRIGSSFPEPQN 177 HVIGFYKQD+ LDA SPRRPD YYGLSKSYGED+ASFYFDRYGIETVSIRIGSSF EPQN Sbjct: 121 HVIGFYKQDEALDALSPRRPDGYYGLSKSYGEDVASFYFDRYGIETVSIRIGSSFAEPQN 180 Query: 178 RRMMSTWLSFDDMTQLLERALYTPNVGHTVVYGMSANKSVWWDNRFAAHLGFAPQDTSEV 237 RRMMSTWLSFDD+TQLLE +LYTP VGHTVVYG+SAN+ VWWDN AAHLG+ P+DTSE+ Sbjct: 181 RRMMSTWLSFDDLTQLLECSLYTPKVGHTVVYGVSANRDVWWDNSHAAHLGYQPKDTSEI 240 Query: 238 FREKVEAQPMPAEDDPARVYQGGAFVAAGPFGD 270 FR+K+EAQPMPA DDPAR+YQGGAFVAAGPF D Sbjct: 241 FRDKIEAQPMPAADDPARIYQGGAFVAAGPFDD 273 Lambda K H 0.321 0.137 0.415 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: 370 Number of extensions: 8 Number of successful extensions: 2 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: 270 Length of database: 273 Length adjustment: 25 Effective length of query: 245 Effective length of database: 248 Effective search space: 60760 Effective search space used: 60760 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