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_026596765.1 H035_RS0117045 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase
Query= BRENDA::Q975F9 (401 letters) >NCBI__GCF_000421465.1:WP_026596765.1 Length = 457 Score = 100 bits (248), Expect = 1e-25 Identities = 116/453 (25%), Positives = 193/453 (42%), Gaps = 96/453 (21%) Query: 5 ILAAGSGERLEPITHTRPKAFVPILSKPLIEYQIEYLRKCGIRDITVIVSSKNKEYFEKK 64 ILAAG G R+ RPK + KPL+++ E R+ + T IV E ++ Sbjct: 10 ILAAGQGTRMRS---DRPKILHTVGGKPLLQHVYERARELN-PETTAIVYGHGGEQVRQR 65 Query: 65 LKEISI--VTQKDDIKGTGAAILSAK--FNDEALII--YGDLFFSNEKEICNIITLKEN- 117 + S V Q + GTG A+ A D+ALI+ YGD+ + ++++ Sbjct: 66 FPDWSAHWVEQSPQL-GTGHAVQQALPVLRDDALILVLYGDVPLLQRPPLERLLSVAATD 124 Query: 118 --AIIGVKVSNPKDYGVLVLDNQNNLSKIIEKPEIPPSNL----INAGIYKLNS-DIFTY 170 A++ V +++P YG +V D + +I+E+ + +N GI + + T+ Sbjct: 125 TLALLTVDMNDPTGYGRIVRDADGRVVRIVEEKDAAAEEKRITEVNTGILAVPGFKLKTW 184 Query: 171 LDKI-SISERGELELTDAINLMAKDHRVKVIEYEGYWMDI--GKPWNIIDVNKW----AL 223 LD++ + + +GE LTD I + A EG ++ P ++ VN AL Sbjct: 185 LDRLDNDNAQGEYYLTDVIAMAAT---------EGMMIETVSAPPNDVAGVNNKRQLAAL 235 Query: 224 DNLVFSQNLGNVEDN---------VKIKGKV-IIEEDAEIKSGTYIEGPVYIGKG----- 268 + + S+ ++ D ++G + + D EI +EG V +G Sbjct: 236 ERIYQSRQAEDLLDRGVTLRDPARFDLRGDLEAVGRDVEIDVNVLLEGTVRLGHRVKIGP 295 Query: 269 -----------------------------SEIGPNSYLRPYTILVEKNKIGASVEVKESV 299 S +GP + +RP T+L E+ +G VE+K+S Sbjct: 296 QVVIRDAVIGDDVEIMSHSVIEQAEIGARSRVGPFARIRPETVLAEEAHVGNFVEIKKST 355 Query: 300 IMEGSKIPHLSYVGDSVIAEDVNFGAGTLIANLRFDEKEVKVNVKGKRISSGRRKLGAFI 359 + G+K+ HLSY+GDS + VN GAGT+ N K V + GAFI Sbjct: 356 LGGGTKVNHLSYIGDSEVGAGVNVGAGTITCNYDGANKHKTV-----------IEDGAFI 404 Query: 360 GGHVRTGINVTILPGVKIGAYARIYPGAVVNRD 392 G + ++ VK+G A I G+ + D Sbjct: 405 GS------DTQLVAPVKVGRDATIGAGSTITHD 431 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: 465 Number of extensions: 33 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 2 Length of query: 401 Length of database: 457 Length adjustment: 32 Effective length of query: 369 Effective length of database: 425 Effective search space: 156825 Effective search space used: 156825 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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