Align uridine phosphorylase; EC 2.4.2.3 (characterized)
to candidate 203376 SO4297 uridine phosphorylase, putative (NCBI ptt file)
Query= CharProtDB::CH_003939 (253 letters) >FitnessBrowser__MR1:203376 Length = 241 Score = 122 bits (307), Expect = 5e-33 Identities = 81/237 (34%), Positives = 115/237 (48%), Gaps = 26/237 (10%) Query: 22 AIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEEL 81 A+V G+P+RV +I A + LA +REF R V VCSTGIG PS IA+EEL Sbjct: 18 AVVCGEPNRVNRIVAHLTDVESLADNREFRLMRGRYGDTIVTVCSTGIGAPSAIIALEEL 77 Query: 82 AQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALV 141 Q G++ +RIG+ GA+QP I +GDV++ A+VR DG S + FPA A+ L Sbjct: 78 YQCGVKQLIRIGSAGALQPQIAIGDVIIAEAAVRDDGGSASYVKPGFPAYANHRLVGKLQ 137 Query: 142 EAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESAT 201 H GV S D+FY QE + + H+ W GV+ +ME+A Sbjct: 138 AYCAQHHICAHSGVVRSHDSFYTDQE-------QDLCHY------WHRQGVLGADMETAA 184 Query: 202 LLTMCASQGLRAGMVAGVIVN----------RTQQEIPNAETMKQTESHAVKIVVEA 248 L T+ LR VA ++ N + +++ Q E HA+ + A Sbjct: 185 LFTV---GRLRQLEVAAILTNVVLFDQDVKAGVNDYVASSKASAQGEQHAILAALNA 238 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: 134 Number of extensions: 4 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: 253 Length of database: 241 Length adjustment: 24 Effective length of query: 229 Effective length of database: 217 Effective search space: 49693 Effective search space used: 49693 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