Align UTP--glucose-1-phosphate uridylyltransferase; Alpha-D-glucosyl-1-phosphate uridylyltransferase; UDP-glucose pyrophosphorylase; UDPGP; Uridine diphosphoglucose pyrophosphorylase; EC 2.7.7.9 (characterized)
to candidate 16147 b2039 glucose-1-phosphate thymidylyltransferase (NCBI)
Query= SwissProt::Q2G1T6 (288 letters) >FitnessBrowser__Keio:16147 Length = 293 Score = 85.9 bits (211), Expect = 1e-21 Identities = 73/236 (30%), Positives = 109/236 (46%), Gaps = 41/236 (17%) Query: 3 KIKKAIIPAAGLGTRFLPATKAMPKEMLPILDKPTIQYIVEEAARAGIEDIIIV-----T 57 K++K II A G GTR P T A+ K++LPI DKP I Y + AGI DI+I+ T Sbjct: 2 KMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDT 61 Query: 58 GRHKRAIEDHFDSQKELEMVLKEKGKSELLEKVQYSTELANIFYVRQKEQKGLGHAISSA 117 R ++ + D SQ L N+ Y Q GL A Sbjct: 62 PRFQQLLGD--GSQWGL-----------------------NLQYKVQPSPDGLAQAFIIG 96 Query: 118 RQFIGNEPFAVLLGDDIVES-EVPAVKQLIDVYEETGHSVIGVQEVPEADTHRYGIIDPL 176 +FIG + A++LGD+I ++P + + V +E+G +V D RYG+++ Sbjct: 97 EEFIGGDDCALVLGDNIFYGHDLPKLMEAA-VNKESGATVFAYH---VNDPERYGVVE-F 151 Query: 177 TKNGRQYEVKKFVEKPAQGTAPSNLAIMGRYVLTPEIFDYLKTQKEGAGNEIQLTD 232 KNG ++ EKP + SN A+ G Y ++ K K A E+++TD Sbjct: 152 DKNGTAISLE---EKPLE--PKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITD 202 Lambda K H 0.316 0.136 0.374 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: 178 Number of extensions: 14 Number of successful extensions: 3 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: 288 Length of database: 293 Length adjustment: 26 Effective length of query: 262 Effective length of database: 267 Effective search space: 69954 Effective search space used: 69954 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 (21.6 bits) S2: 48 (23.1 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