Align UTP--glucose-1-phosphate uridylyltransferase AglF; Archaeal glycosylation protein F; EC 2.7.7.9 (characterized)
to candidate WP_109968440.1 DK846_RS08095 sugar phosphate nucleotidyltransferase
Query= SwissProt::D4GYH1 (243 letters) >NCBI__GCF_003173355.1:WP_109968440.1 Length = 388 Score = 107 bits (266), Expect = 5e-28 Identities = 76/235 (32%), Positives = 121/235 (51%), Gaps = 21/235 (8%) Query: 1 MQAVVLAAGKGTRLRPLTEDKPKGMVEVDGKPILTHCFDQLVDLGAEKLVVVVGYKKEII 60 +QAV+LAAG+GTR+RPLT+++PK ++ V +PIL H + L+ G ++VVVGY+KE + Sbjct: 3 VQAVILAAGEGTRIRPLTQNRPKALIPVANRPILEHLIESLLSCGVRDIIVVVGYRKEQV 62 Query: 61 IQHYDDEYRGVPITYAHQREQKGLAHALLTVEDHIDEDFMLMLGDNIFN-ANLGDVVKRQ 119 ++H + V + Q+ Q G HAL D I D +++ GDN + A+L +V+K + Sbjct: 63 MRHL--IHLPVEVRIVEQQHQIGTGHALNCALDLITGDLLVLPGDNYIDPASLKEVLKIK 120 Query: 120 REDRADAAFLVEEVDWDEASRYGVCVTNDYGEITEVIEKPEEPPSNLVMTGFYTFTPAIF 179 + L+ S +GV D G + ++EKP V G Y + Sbjct: 121 N------SMLI--TTHQHPSNFGVVDVED-GVVLGIVEKPVHAKRMTVSCGVYYLEQDLL 171 Query: 180 HACHLVQPSNRGEYEISEAIDLLIRSGRTIDAIRIDGWRLDIGYPEDRDEAEQRL 234 S + ++S+AI+ LI G +I A+ W+ D YP D +RL Sbjct: 172 --------SGMIDNQLSDAINELIVRGTSISAVYAHEWQ-DAIYPWDLICMNERL 217 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: 211 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: 388 Length adjustment: 27 Effective length of query: 216 Effective length of database: 361 Effective search space: 77976 Effective search space used: 77976 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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