Align D-galacturonate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate SMc04145 SMc04145 hypothetical protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_4511 (270 letters) >FitnessBrowser__Smeli:SMc04145 Length = 261 Score = 285 bits (729), Expect = 7e-82 Identities = 143/259 (55%), Positives = 189/259 (72%), Gaps = 7/259 (2%) Query: 9 RLLLTGAAGGLGKVLRERLRPYANVLRLSDIANMAPAIDDREEVVPCDLADKQAVHQLVE 68 RLL+TGAAGGLG+ RE L+ A+VLRLSD+A ++PA + EE+V CDLA+++AV QLV Sbjct: 4 RLLITGAAGGLGRYAREGLKGCADVLRLSDVATLSPA-GEGEEIVRCDLAEREAVDQLVR 62 Query: 69 GVDAILHFGGVSVERPFEEILGANICGVFHIYEAARRHGVKRVIFASSNHVIGFYKQDKT 128 G DAILH G +SVE F+ +L ANI G +++YEAAR+ GV R++FAS+NHV GF+ +T Sbjct: 63 GCDAILHLGAISVESDFDALLQANILGTYNLYEAARKAGVNRILFASTNHVTGFHPIGET 122 Query: 129 LDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIRIGSSFPEPQNRRMMSTWLSFD 188 LD SPRRPDS YG+SK +GED++ YFD+YG+ET +RIGS F EP NRRM+STWLS Sbjct: 123 LDHLSPRRPDSLYGVSKCFGEDLSRLYFDKYGMETACLRIGSCFAEPTNRRMLSTWLSPR 182 Query: 189 DMTQLLERALYTPNVGHTVVYGMSANKSVWWDNRFAAHLGFAPQDTSEVFREKVEAQPMP 248 D L+ R L P +GH V+YG+SAN+ VWW N A LG+ PQD+SE +R ++E + Sbjct: 183 DFLALVRRLLDAPKIGHLVLYGVSANRDVWWSNGHADFLGWRPQDSSEPYRHEIEKR--- 239 Query: 249 AEDDPAR--VYQGGAFVAA 265 E++P+ YQGG AA Sbjct: 240 -EEEPSDGVRYQGGRHAAA 257 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: 229 Number of extensions: 5 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: 261 Length adjustment: 25 Effective length of query: 245 Effective length of database: 236 Effective search space: 57820 Effective search space used: 57820 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