Align UTP--glucose-1-phosphate uridylyltransferase AglF; Archaeal glycosylation protein F; EC 2.7.7.9 (characterized)
to candidate WP_047006779.1 AAW01_RS07470 glucose-1-phosphate thymidylyltransferase RfbA
Query= SwissProt::D4GYH1 (243 letters) >NCBI__GCF_001010925.1:WP_047006779.1 Length = 293 Score = 90.9 bits (224), Expect = 3e-23 Identities = 66/215 (30%), Positives = 104/215 (48%), Gaps = 16/215 (7%) Query: 2 QAVVLAAGKGTRLRPLTEDKPKGMVEVDGKPILTHCFDQLVDLGAEKLVVVVGYKKEIII 61 + ++LA G GTRL PLT K ++ V KP++ + L+ G ++++ + + Sbjct: 4 KGIILAGGSGTRLYPLTRGVSKQLMPVYDKPMIYYPLSTLMLAGIRDILIITTPEDQPQF 63 Query: 62 QHY--DDEYRGVPITYAHQREQKGLAHALLTVEDHIDEDFM------LMLGDNIFNAN-L 112 Q D GV ++YA Q GLA A HI DF+ L+LGDNIF + L Sbjct: 64 QRVLGDGSDFGVALSYAVQPNPDGLAQAF-----HIGADFIGGDASALVLGDNIFYGHGL 118 Query: 113 GDVVKRQREDRADAAFLVEEVDWDEASRYGVCVTNDYGEITEVIEKPEEPPSNLVMTGFY 172 +V+ A A+ V + + YGV + G + + EKPE+P SN +TG Y Sbjct: 119 PEVLHSAHARDAGASVFAYRVK--DPTAYGVVAFDANGRASSIEEKPEKPKSNYAVTGLY 176 Query: 173 TFTPAIFHACHLVQPSNRGEYEISEAIDLLIRSGR 207 + + ++PS RGE EI++ L + G+ Sbjct: 177 FYDDTVVERARALKPSARGELEITDLNRLYMDHGQ 211 Lambda K H 0.318 0.138 0.404 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: 216 Number of extensions: 12 Number of successful extensions: 3 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: 243 Length of database: 293 Length adjustment: 25 Effective length of query: 218 Effective length of database: 268 Effective search space: 58424 Effective search space used: 58424 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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