Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_101446957.1 BD749_RS17655 UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_002846395.1:WP_101446957.1 Length = 341 Score = 214 bits (545), Expect = 3e-60 Identities = 124/289 (42%), Positives = 175/289 (60%), Gaps = 18/289 (6%) Query: 4 DKTLMITGGTGSFGNA----VLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNSK-- 57 +K +++TGGTGSFG V +RF D+K + I+SRDE KQ +M +SK Sbjct: 7 NKAILVTGGTGSFGKKFVEMVYARF------PDVKRVVIYSRDELKQFEMSQVFPHSKYN 60 Query: 58 -LKFYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAI 116 ++++IGDVR+ + A G+D + HAAA+KQVP E+ PME I TNVLGAEN+++AA+ Sbjct: 61 SVRYFIGDVRDGERFKRACEGIDIIVHAAAMKQVPAAEYNPMECIKTNVLGAENIINAAL 120 Query: 117 NNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRG 176 + V V+ LSTDKA PIN G +K +KL +A M+ + V RYGNV+ SRG Sbjct: 121 DTGVKHVVALSTDKAAAPINLYGATKLCSDKLFVAANNMKGKRDIKFSVVRYGNVIGSRG 180 Query: 177 SVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTIE 236 SV+P F+ + ++G L IT P MTRF +SL + V+LV +A EH G+IFV K P+ I Sbjct: 181 SVVPFFLKKREEG-ILPITHPEMTRFNISLEEGVELVFHALEHHWGGEIFVPKIPSYVIT 239 Query: 237 VLAKALQEIFGSKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRI 285 LA+A+ G +G R GEK +E +++ D +L YY I Sbjct: 240 DLAEAI----GPNCKQEVVGIRPGEKLHEEMITETDSLNTVELDKYYVI 284 Lambda K H 0.319 0.135 0.373 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: 298 Number of extensions: 13 Number of successful extensions: 5 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: 341 Length of database: 341 Length adjustment: 29 Effective length of query: 312 Effective length of database: 312 Effective search space: 97344 Effective search space used: 97344 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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