Align UTP--glucose-1-phosphate uridylyltransferase; EC 2.7.7.9; Alpha-D-glucosyl-1-phosphate uridylyltransferase; UDP-glucose pyrophosphorylase; UDPGP; Uridine diphosphoglucose pyrophosphorylase (uncharacterized)
to candidate Echvi_2361 Echvi_2361 glucose-1-phosphate thymidylyltransferase, short form
Query= curated2:Q59633 (279 letters) >FitnessBrowser__Cola:Echvi_2361 Length = 285 Score = 84.0 bits (206), Expect = 3e-21 Identities = 72/240 (30%), Positives = 115/240 (47%), Gaps = 37/240 (15%) Query: 4 KYLFPAAGYGTRFLPATKAMPKEMLPVVNKPLIQYGVEEALDAGLNEISIVTGRGKRALE 63 K + A G GTR P T A+ K+++PV +KP+I Y + + AG+ EI I+T E Sbjct: 2 KGIILAGGSGTRLYPLTIAVSKQLMPVYDKPMIYYPLSVLMMAGIREIMIIT-----TPE 56 Query: 64 DHFDISYELENQIKGTDKEKYLVGIRKLLDECSFSYTRQTQMKGLGHAILTGRPLIGDEP 123 D D K L+G L C F++ Q + +GL A + G IGD+ Sbjct: 57 D--------------ADAFKKLLGDGSHLG-CEFTFAIQPKPEGLAQAFVIGEEFIGDDK 101 Query: 124 FAVVLADDLCVNLEGDGVLTQMVKLYQKYRCTIVAVMEVNPTETNKYGVIAGDDIGDGLI 183 A++L D++ G G+ ++K + +V VN + +YGV+ D + Sbjct: 102 VALILGDNI---FYGSGLQETLLK-HTDPEGGVVFAYHVN--DPQRYGVVEFDQNKKAI- 154 Query: 184 RVRDMVEKP-APEDAPSNLAIIGRYILTPDIFKLIEETEPGKGGEIQITD---ALLKQAK 239 + EKP AP+ SN A+ G Y + ++ ++ +P GE++ITD A LK+ K Sbjct: 155 ---SIEEKPQAPK---SNFAVPGLYFYDNRVVEIAKQIKPSARGELEITDVNNAYLKEGK 208 Lambda K H 0.319 0.141 0.413 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: 227 Number of extensions: 14 Number of successful extensions: 3 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: 279 Length of database: 285 Length adjustment: 26 Effective length of query: 253 Effective length of database: 259 Effective search space: 65527 Effective search space used: 65527 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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