Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate PP_0406 PP_0406 Nucleotidyltransferase family protein
Query= BRENDA::P74285 (388 letters) >FitnessBrowser__Putida:PP_0406 Length = 223 Score = 86.3 bits (212), Expect = 8e-22 Identities = 66/209 (31%), Positives = 100/209 (47%), Gaps = 24/209 (11%) Query: 1 MKAMILAAGKGTRVRPITHTIPKPMIPILQKPVMEFLLELLRQHGFDQIMVNVSHLAEEI 60 MKAMILAAGKG R+RP+T PKP++P+ +P++E+ L L G ++++N + L ++I Sbjct: 1 MKAMILAAGKGERMRPLTLHTPKPLVPVAGQPLIEYHLRALAAAGVTEVVINHAWLGQQI 60 Query: 61 ESYFRDGQRFGVQIAYSFEGNIVD-GDLVGKALGSAGGLKKIQEFNPFFDDTFVVLCGDA 119 E + DG RFG+ I YS EG ++ G + KAL G D F+++ GD Sbjct: 61 EDHLGDGSRFGLSIRYSPEGEPLETGGGIFKALPLLG------------DAPFLLVNGDV 108 Query: 120 LIDLDLTTAVKLHREKGAIATIITKTVPQ-------ELVSSYGVVVTDDNGKILTFQEKP 172 D D +L +A ++ P LV VV DD LTF Sbjct: 109 WTDYDF---ARLQAPLQGLAHLVLVDNPGHHGRGDFRLVGEQ-VVDGDDAPGTLTFSGIS 164 Query: 173 AVEEALSTEINTGIYIFEPEVIDYIPSGQ 201 + AL G + P + + +G+ Sbjct: 165 VLHPALFEGCQAGAFKLAPLLRQAMAAGK 193 Score = 25.8 bits (55), Expect = 0.001 Identities = 16/39 (41%), Positives = 19/39 (48%), Gaps = 2/39 (5%) Query: 194 IDYIPSGQEYDLGGDLFPKLVDSG-LPFYAVNMDFEWVD 231 I Y P G+ + GG +F L G PF VN D W D Sbjct: 74 IRYSPEGEPLETGGGIFKALPLLGDAPFLLVNGDV-WTD 111 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: 224 Number of extensions: 15 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: 2 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