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 GFF3919 PGA1_65p00220 glucose-1-phosphate thymidylyltransferase RfbA
Query= SwissProt::Q05852 (292 letters) >FitnessBrowser__Phaeo:GFF3919 Length = 296 Score = 85.1 bits (209), Expect = 2e-21 Identities = 70/233 (30%), Positives = 105/233 (45%), Gaps = 33/233 (14%) Query: 5 RKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKSKRAI 64 RK II A G GTR P T A+ K++LP+ DKP I Y + + AGI +I ++T Sbjct: 10 RKGIILAGGSGTRLYPITMAVSKQLLPLYDKPMIYYPLSVLMLAGIREICVITTPQD--- 66 Query: 65 EDHFDYSPELERNLEEKGKTELLEKVKKASNLADIHYIRQKEPKGLGHAVWCARNFIGDE 124 +D F T LL + + Y+ Q P GL A A +F+ Sbjct: 67 QDQF---------------TRLLGDGSQWG--ISLTYVEQPSPDGLAQAFVLAEDFLDGA 109 Query: 125 PFAVLLGDDIVQAETPGLRQLMDEYEKTLS--SIIGVQQVPEEETHRYGIIDPLTSEGRR 182 P A++LGD++ GL +L+ + S ++ G E RYG++D +EGR Sbjct: 110 PSALVLGDNVFFGH--GLPKLLAAADAQTSGGTVFGYHVADPE---RYGVVD-FDAEGR- 162 Query: 183 YQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQ 235 + +EKP PSN A+ G Y + GE+++TD +Q Sbjct: 163 --AREIIEKP--AVPPSNYAVTGLYFLDGSAPERARQVTPSPRGELEITDLLQ 211 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: 202 Number of extensions: 20 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 292 Length of database: 296 Length adjustment: 26 Effective length of query: 266 Effective length of database: 270 Effective search space: 71820 Effective search space used: 71820 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