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 WP_109968441.1 DK846_RS08100 sugar phosphate nucleotidyltransferase
Query= BRENDA::Q975F9 (401 letters) >NCBI__GCF_003173355.1:WP_109968441.1 Length = 401 Score = 255 bits (652), Expect = 1e-72 Identities = 155/402 (38%), Positives = 234/402 (58%), Gaps = 27/402 (6%) Query: 1 MKAFILAAGSGERLEPITHTRPKAFVPILSKPLIEYQIEYLRKCGIRDITVIVSSKNKEY 60 ++ ILAAG G+R+ P+T +RPK +P+ ++P++E+ I +R CGI + ++V Y Sbjct: 2 VQCVILAAGEGKRMRPLTGSRPKVMIPVANRPMLEHLINAIRDCGINEFVLVVG-----Y 56 Query: 61 FEKKLKE-----------ISIVTQKDDIKGTGAAILS--AKFNDEALIIYGDLFFSNEKE 107 E ++ I VTQK +GTG A+L+ + N + L++ GD+ S E + Sbjct: 57 HEAAVRHHFGDGSDFGVSIRYVTQKRQ-RGTGDAVLNVLSHVNGDFLLLNGDMILSRE-D 114 Query: 108 ICNIITLKENAIIGVKVSNPKDYGVLVLDNQNNLSKIIEKPEIPPSNLINAGIYKLNSDI 167 I +++ A+ K +P+D+GV+ + + ++ EK E P S+LINAG+Y N D+ Sbjct: 115 IKAVLSSPSPALGICKSDHPRDFGVVTVKD-GIITGFEEKSENPKSDLINAGLYLFNYDL 173 Query: 168 FTYLDKISISERGELELTDAINLMAKDHRVKVIEYEGYWMDIGKPWNIIDVNKWALDNLV 227 F++L I+ S RGELELTDA+ K + + W D+G PW+++ N+ L +L Sbjct: 174 FSHLKLITPSPRGELELTDALLPYIKAGSLHAVMLSS-WADMGSPWDLLTANEVLLVSLS 232 Query: 228 FSQNLGNVEDNVKIKGKVIIEEDAEIKSGTYIEGPVYIGKGSEIGPNSYLRPYTILVEKN 287 S G +ED V +KG V + + +K+GTYIEGP IGK IGP++Y+R T + + Sbjct: 233 -SCIEGEIEDGVVLKGAVQVGKGTVVKAGTYIEGPCVIGKDCRIGPHAYIRGATAIGDNC 291 Query: 288 KIGASVEVKESVIMEGSKIPHLSYVGDSVIAEDVNFGAGTLIANLRFDEKEVKVNVKGKR 347 IG S+E+K S++M S IPH +YVGDSVIA NFGAGT IANLR D+K + Sbjct: 292 HIGHSIELKNSIVMNHSNIPHFNYVGDSVIASGCNFGAGTKIANLRHDKKCISAG----G 347 Query: 348 ISSGRRKLGAFIGGHVRTGINVTILPGVKIGAYARIYPGAVV 389 +++ R+K GA IG V GIN ++ G IG RI P V Sbjct: 348 VNTRRKKFGAVIGDDVLFGINCSVNVGAVIGNRCRIAPHCFV 389 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: 453 Number of extensions: 23 Number of successful extensions: 8 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: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 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: 50 (23.9 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