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 CA265_RS19325 CA265_RS19325 glucose-1-phosphate thymidylyltransferase
Query= SwissProt::Q2G1T6 (288 letters) >FitnessBrowser__Pedo557:CA265_RS19325 Length = 286 Score = 82.0 bits (201), Expect = 1e-20 Identities = 67/227 (29%), Positives = 99/227 (43%), Gaps = 30/227 (13%) Query: 6 KAIIPAAGLGTRFLPATKAMPKEMLPILDKPTIQYIVEEAARAGIEDIIIVTGRHKRAIE 65 K II A G GTR P T A K+M+P+ DKP I Y + AGI++I+I++ H Sbjct: 2 KGIILAGGSGTRLHPLTLACSKQMMPVYDKPMIYYPLSTLMLAGIKEILIISTPH----- 56 Query: 66 DHFDSQKELEMVLKEKGKSELLEKVQYSTELANIFYVRQKEQKGLGHAISSARQFIGNEP 125 +L K G L Y Q E GL A +FIG + Sbjct: 57 -------DLPNFQKLLGDGTSLG--------CKFSYAVQAEPNGLAQAFVIGEEFIGKDK 101 Query: 126 FAVLLGDDIVESEVPAVKQLIDVYEETGHSVIGVQEVPEADTHRYGIIDPLTKNGRQYEV 185 A++LGD+I S+ + +L+ + V+ +V AD RYG+++ N + Sbjct: 102 VALVLGDNIFHSD--GLAKLLQASSDPDGGVVFAYQV--ADPERYGVVEFDGSN----KA 153 Query: 186 KKFVEKPAQGTAPSNLAIMGRYVLTPEIFDYLKTQKEGAGNEIQLTD 232 EKP Q S+ A+ G Y E+ + K K E ++TD Sbjct: 154 ISIEEKPVQ--PKSSYAVPGLYFYDNEVVEIAKNIKPSPRGEYEITD 198 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: 174 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: 286 Length adjustment: 26 Effective length of query: 262 Effective length of database: 260 Effective search space: 68120 Effective search space used: 68120 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: 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