Align UTP--glucose-1-phosphate uridylyltransferase AglF; Archaeal glycosylation protein F; EC 2.7.7.9 (characterized)
to candidate Ac3H11_1882 Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24)
Query= SwissProt::D4GYH1 (243 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1882 Length = 294 Score = 87.0 bits (214), Expect = 4e-22 Identities = 76/242 (31%), Positives = 121/242 (50%), Gaps = 19/242 (7%) Query: 2 QAVVLAAGKGTRLRPLTEDKPKGMVEVDGKPILTHCFDQLVDLGAEKLVVVVGYKKEI-- 59 + ++LA G GTRL P T K ++ V KP++ + L+ LG + ++++ ++ Sbjct: 5 KGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLM-LGGIRDILIISTPQDTPR 63 Query: 60 IIQHYDDEYR-GVPITYAHQREQKGLAHALLTVEDHI-DEDFMLMLGDNIFNAN-----L 112 Q D + G+ + YA Q GLA A + ED + L+LGDNIF + L Sbjct: 64 FAQLLGDGSQWGLNLQYAVQPSPDGLAQAFVIGEDFLAGAPSALVLGDNIFYGHDFHELL 123 Query: 113 GDVVKRQREDRADA-AFLVEEVDWDEASRYGVCVTNDYGEITEVIEKPEEPPSNLVMTGF 171 G+ RQR D A A+ V++ + RYGV +D G++ + EKP++P S+ +TG Sbjct: 124 GNA--RQRTDGASVFAYHVQDPE-----RYGVAEFDDQGKVLSLEEKPKQPKSSYAVTGL 176 Query: 172 YTFTPAIFHACHLVQPSNRGEYEISEAIDLLIRSGRTIDAIRIDGWR-LDIGYPEDRDEA 230 Y + + ++PS RGE EI++ L + G+ I G+ LD G E EA Sbjct: 177 YFYDGQVVQMAKDLKPSPRGELEITDLNRLYLEQGQLNVEIMGRGYAWLDTGTHESLLEA 236 Query: 231 EQ 232 Q Sbjct: 237 GQ 238 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: 178 Number of extensions: 11 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: 243 Length of database: 294 Length adjustment: 25 Effective length of query: 218 Effective length of database: 269 Effective search space: 58642 Effective search space used: 58642 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