Align UTP--glucose-1-phosphate uridylyltransferase AglF; Archaeal glycosylation protein F; EC 2.7.7.9 (characterized)
to candidate GFF260 PS417_01325 glucose-1-phosphate thymidylyltransferase
Query= SwissProt::D4GYH1 (243 letters) >FitnessBrowser__WCS417:GFF260 Length = 291 Score = 90.1 bits (222), Expect = 4e-23 Identities = 64/213 (30%), Positives = 105/213 (49%), Gaps = 12/213 (5%) Query: 1 MQAVVLAAGKGTRLRPLTEDKPKGMVEVDGKPILTHCFDQLVDLGAEKLVVVVGYKKEII 60 M+ +VLA G GTRL P+T K ++ V KP++ + L+ G + ++V+ + Sbjct: 2 MKGIVLAGGSGTRLHPITLGVSKQLLPVYDKPMIYYPISVLMLAGIKDILVI---STPVD 58 Query: 61 IQHY-----DDEYRGVPITYAHQREQKGLAHALLTVEDHIDED-FMLMLGDNIFNA-NLG 113 + Y D GV +YA Q GLA A + E+ I +D L+LGDNIF+ + G Sbjct: 59 LPQYRNLLGDGSQFGVRFSYAEQPTPDGLAQAFIIGEEFIGDDPVCLILGDNIFHGQHFG 118 Query: 114 DVVKRQREDRADAAFLVEEVDWDEASRYGVCVTNDYGEITEVIEKPEEPPSNLVMTGFYT 173 + + + + A V + R+GV + G + EKP +P S+ +TG Y Sbjct: 119 EQLLGAAKRASGATVFGYWVK--DPERFGVIDFDSEGRALSIEEKPAKPKSSYAVTGLYF 176 Query: 174 FTPAIFHACHLVQPSNRGEYEISEAIDLLIRSG 206 + + V+PS RGEYEI++ + ++ G Sbjct: 177 YDNDVIKIAKAVKPSPRGEYEITDVNNAYLKRG 209 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: 192 Number of extensions: 13 Number of successful extensions: 4 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: 291 Length adjustment: 25 Effective length of query: 218 Effective length of database: 266 Effective search space: 57988 Effective search space used: 57988 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 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