Align UTP--glucose-1-phosphate uridylyltransferase; Alpha-D-glucosyl-1-phosphate uridylyltransferase; General stress protein 33; GSP33; UDP-glucose pyrophosphorylase; UDPGP; Uridine diphosphoglucose pyrophosphorylase; EC 2.7.7.9 (characterized)
to candidate SM_b20960 SM_b20960 UDP-glucose pyrophosphorylase
Query= SwissProt::Q05852 (292 letters) >FitnessBrowser__Smeli:SM_b20960 Length = 301 Score = 252 bits (643), Expect = 8e-72 Identities = 129/278 (46%), Positives = 178/278 (64%), Gaps = 1/278 (0%) Query: 1 MKKVRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKS 60 ++ VRKA+IP AG GTRFLPATKA+PKEML IVD+P +QY ++EA +AGIE I+ VT ++ Sbjct: 4 VRTVRKAVIPVAGNGTRFLPATKAVPKEMLTIVDRPVVQYAVDEARQAGIEHIVFVTSRN 63 Query: 61 KRAIEDHFDYSPELERNLEEKGKTELLEKVKKASNLA-DIHYIRQKEPKGLGHAVWCARN 119 K+ IEDHFD +PEL +L GK+ + +++ A + + RQ+ P GLGHAVWCAR+ Sbjct: 64 KQVIEDHFDDAPELISSLSRSGKSAQISELEAMLPAAGSVSFTRQQAPLGLGHAVWCARD 123 Query: 120 FIGDEPFAVLLGDDIVQAETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPLTSE 179 IGDEPFA+LL D + + LMD Y + +++GV+Q EE +YGI+ + Sbjct: 124 LIGDEPFALLLPDMVSFGARGCVAGLMDLYHEVGGNVVGVEQCAPEEASKYGIVGKGETV 183 Query: 180 GRRYQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQKLNE 239 + V VEKP G APSN + GRY+ PEIF L Q GAG EIQLTD + L++ Sbjct: 184 RHGFSVTEMVEKPAAGKAPSNYYLNGRYILQPEIFSILAHQTRGAGNEIQLTDGMLTLSQ 243 Query: 240 IQRVFAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRD 277 Q A+ +EG+ +D G K GFI + FA+ ++ D Sbjct: 244 SQSFHAHPYEGRTFDCGSKQGFIEANVAFALARADIGD 281 Lambda K H 0.317 0.138 0.389 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: 236 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: 292 Length of database: 301 Length adjustment: 26 Effective length of query: 266 Effective length of database: 275 Effective search space: 73150 Effective search space used: 73150 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