Align glucosamine-1-phosphate N-acetyltransferase (EC 2.3.1.157); galactosamine-1-phosphate N-acetyltransferase (EC 2.3.1.276); UDP-N-acetylglucosamine diphosphorylase (EC 2.7.7.23); glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24); aldose-1-phosphate nucleotidyltransferase (EC 2.7.7.37); UDP-N-acetylgalactosamine diphosphorylase (EC 2.7.7.83); UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate Pf1N1B4_5938 Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24)
Query= BRENDA::Q975F9 (401 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5938 Length = 292 Score = 93.6 bits (231), Expect = 7e-24 Identities = 68/225 (30%), Positives = 109/225 (48%), Gaps = 15/225 (6%) Query: 1 MKAFILAAGSGERLEPITHTRPKAFVPILSKPLIEYQIEYLRKCGIRDITVIVSSKNKEY 60 MK ILA GSG RL PIT K +P+ KP+I Y + L GIR+I +I + ++ Sbjct: 1 MKGIILAGGSGTRLHPITRGVSKQLLPVYDKPMIYYPLSVLMLAGIREILIISTPQDLPN 60 Query: 61 FEKKLK-------EISIVTQKDDIKGTGAAILSAKF---NDEALIIYGDLFFS-NEKEIC 109 F+ L E+S Q A ++ F ++ ALI+ ++F+ + Sbjct: 61 FQNLLGDGSSFGIELSYAEQPSPDGLAQAFLIGEDFIGDSNVALILGDNIFYGYGFSALL 120 Query: 110 NIITLKEN--AIIGVKVSNPKDYGVLVLDNQNNLSKIIEKPEIPPSNLINAGIYKLNSDI 167 + ++ + G +VS+P +GV+ D+ I EKP+ P S+ G+Y ++D+ Sbjct: 121 REASQRQTGATVFGYRVSDPDRFGVVEFDDNGKAISIEEKPKHPKSDHAVTGLYFYDNDV 180 Query: 168 FTYLDKISISERGELELTDAIN--LMAKDHRVKVIEYEGYWMDIG 210 + ++ S RGELE+TD N L D V V+ W+D G Sbjct: 181 VSIAKQVKPSIRGELEITDVNNAYLQRGDLHVSVLGRGFAWLDTG 225 Lambda K H 0.317 0.139 0.393 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: 272 Number of extensions: 16 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: 401 Length of database: 292 Length adjustment: 29 Effective length of query: 372 Effective length of database: 263 Effective search space: 97836 Effective search space used: 97836 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 (21.6 bits) S2: 49 (23.5 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