Align uridine phosphorylase; EC 2.4.2.3 (characterized)
to candidate 6936223 Sama_0412 uridine phosphorylase (RefSeq)
Query= CharProtDB::CH_003939 (253 letters) >FitnessBrowser__SB2B:6936223 Length = 252 Score = 397 bits (1021), Expect = e-116 Identities = 198/250 (79%), Positives = 219/250 (87%) Query: 4 SDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVI 63 +DVFHLGLTKN L GATLAIVPGDP+RV++IA LMDKP LASHREFT++ A LDGKPV+ Sbjct: 2 ADVFHLGLTKNMLDGATLAIVPGDPERVKRIAELMDKPTFLASHREFTSYLAYLDGKPVV 61 Query: 64 VCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHF 123 VCSTGIGGPSTSIAVEELAQLGI TFLR+GTTGAIQPH+NVGD++VT ASVRLDGASLHF Sbjct: 62 VCSTGIGGPSTSIAVEELAQLGINTFLRVGTTGAIQPHVNVGDLIVTQASVRLDGASLHF 121 Query: 124 APLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGS 183 AP+EFPAVA+FECTTA+V A + G HVGVTASSDTFYPGQERYDT SGRV R F+GS Sbjct: 122 APMEFPAVANFECTTAMVAACRDAGVEPHVGVTASSDTFYPGQERYDTVSGRVTRRFEGS 181 Query: 184 MEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVK 243 M+EWQ MGV+NYEMESATL TMCASQG RA VAGVIVNRTQQEIP+ TMK TE AV Sbjct: 182 MKEWQEMGVLNYEMESATLFTMCASQGWRAACVAGVIVNRTQQEIPDEATMKNTEVSAVS 241 Query: 244 IVVEAARRLL 253 +VV AAR+LL Sbjct: 242 VVVAAARKLL 251 Lambda K H 0.318 0.131 0.375 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: 283 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: 253 Length of database: 252 Length adjustment: 24 Effective length of query: 229 Effective length of database: 228 Effective search space: 52212 Effective search space used: 52212 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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