Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate 8502466 DvMF_3172 UTP--glucose-1-phosphate uridylyltransferase (RefSeq)
Query= BRENDA::D3HTY9 (485 letters) >FitnessBrowser__Miya:8502466 Length = 467 Score = 340 bits (871), Expect = 8e-98 Identities = 205/467 (43%), Positives = 261/467 (55%), Gaps = 17/467 (3%) Query: 19 KMQASGVEEKCIHIFLIQHALVRKGETGYIPEKSISPV--ESLPFLQGIETKGE-NTALL 75 KM +G+ + +F + G TG IPE I PV + LP L + A L Sbjct: 12 KMARAGLPSPLVALFASYLEELACGSTGLIPESDILPVGRDDLPLLDDLAPYAAIGRARL 71 Query: 76 RQAVVLKLNGGLGTGMGLNGPKSLLQVKNGQTFLDFTALQLEHFRQVRNCNVPFMLMNSF 135 R+A +KLNGGLGT MG+ KSLL K+G TFL+ Q EH R+ P + MNSF Sbjct: 72 REAACIKLNGGLGTSMGMTHAKSLLPAKDGATFLELIVRQAEHQRRTHGGPSPLLFMNSF 131 Query: 136 STSGETKNFLRKYPTL-YEVFDSDIELMQNRVPKIRQDNFFPVTYEADPTCEWVPPGHGD 194 ST +T LR L + +Q+R PK+ + PV Y +P EW PPGHGD Sbjct: 132 STHQDT---LRALDVLGLQHAGRPGTFLQHRFPKVSRATLLPVEYPENPDLEWNPPGHGD 188 Query: 195 VYTVLYSSGKLDYLLGKGYRYMFISNGDNLGATLDVRLLDYMHEKQLGFLMEVCRRTESD 254 +Y L SG L LL G RY ISN DNLGATLD +L Y+ E+ + FLME RT SD Sbjct: 189 LYAALALSGHLARLLESGRRYALISNADNLGATLDPAILGYLMEEDIPFLMECAPRTPSD 248 Query: 255 KKGGHLAYKDVIDETTGQTRRRFVLRESAQCPKEDEDSFQNIAKHCFFNTNNIWINLMEL 314 +KGGHLA VLRE AQCP +D FQ+I ++ FNTNNIW++L L Sbjct: 249 RKGGHLA---------RSRHGGLVLRELAQCPDDDLPRFQDIVRYGLFNTNNIWLDLRAL 299 Query: 315 KKMMDEQLGVLRLPVMRNPKTVNPQDSQSTKVYQLEVAMGAAISLFDRSEAVVVPRERFA 374 ++ +DE G+LRLP++RNPKTVNP+D S KV+Q+E AMGAAISLF R+ A+V RERF Sbjct: 300 RQHIDE-YGLLRLPMIRNPKTVNPRDPDSEKVWQVETAMGAAISLFPRARAIVTRRERFL 358 Query: 375 PVKTCSDLLALRSDAYQVTEDQRLVLCEERNGKPPAIDLDGEHYKMIDGFEKLVKGGVPS 434 PVK CSDLL L SD + + ++LDG HY D G PS Sbjct: 359 PVKKCSDLLVLWSDRTLLEPGGHVRPNPACTTPGVLVELDGAHYGTWDRLMARFPHGAPS 418 Query: 435 LRQCTSLTVRGLVEFGADVSVRGNVVIKNLKEEPLIIGSGRVLDNEV 481 L C +L V G V FG +V+ RG VV++N +I G VL+ +V Sbjct: 419 LLHCDALAVHGDVLFGGNVTARGRVVVRNPSCMQAVIPHGTVLEGDV 465 Lambda K H 0.319 0.137 0.402 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: 590 Number of extensions: 25 Number of successful extensions: 6 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: 485 Length of database: 467 Length adjustment: 33 Effective length of query: 452 Effective length of database: 434 Effective search space: 196168 Effective search space used: 196168 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: 51 (24.3 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