Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate AO356_14360 AO356_14360 mannose-1-phosphate guanylyltransferase
Query= BRENDA::P74285 (388 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_14360 Length = 223 Score = 89.4 bits (220), Expect = 9e-23 Identities = 57/149 (38%), Positives = 83/149 (55%), Gaps = 16/149 (10%) Query: 1 MKAMILAAGKGTRVRPITHTIPKPMIPILQKPVMEFLLELLRQHGFDQIMVNVSHLAEEI 60 MKAMILAAGKG R+RP+T T PKP+I + P++E+ L L + GF +I++N + L ++I Sbjct: 1 MKAMILAAGKGERMRPLTLTTPKPLIRVGGVPLIEYHLRALAKAGFSEIVINHAWLGQQI 60 Query: 61 ESYFRDGQRFGVQIAYSFEGNIVD-GDLVGKALGSAGGLKKIQEFNPFFDDTFVVLCGDA 119 E + DG FGV I +S EG ++ G + +AL G DD FVV+ GD Sbjct: 61 EDHLGDGSGFGVSIRFSPEGEPLETGGGIFRALPLLG------------DDAFVVVNGDI 108 Query: 120 LIDLDLTTAVKLHREKGAIATIITKTVPQ 148 D D + L R +A ++ P+ Sbjct: 109 WTDYDFSV---LRRPLKGLAHLVLVDNPE 134 Lambda K H 0.321 0.141 0.418 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: 213 Number of extensions: 12 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: 388 Length of database: 223 Length adjustment: 26 Effective length of query: 362 Effective length of database: 197 Effective search space: 71314 Effective search space used: 71314 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 (21.8 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