Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate CCNA_00233 CCNA_00233 UDP-N-acetylglucosamine 4,6-dehydratase
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__Caulo:CCNA_00233 Length = 345 Score = 220 bits (560), Expect = 5e-62 Identities = 131/320 (40%), Positives = 188/320 (58%), Gaps = 16/320 (5%) Query: 5 KTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNN-------SK 57 K +++TGGTGSFG + L+ D +++ ++SRDE KQ DM+I L +K Sbjct: 14 KVILVTGGTGSFGRRFIETVLRRY---DPRKVIVYSRDELKQSDMQIELREQFDEATVAK 70 Query: 58 LKFYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAIN 117 ++F++GDVR+ + + A+ GVD V HAAALKQVP E+ P E I+TNVLGAENV+ A++ Sbjct: 71 MRFFLGDVRDRERLTLALRGVDIVIHAAALKQVPAAEYNPSECIHTNVLGAENVVWASLA 130 Query: 118 NKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGS 177 N V +V+ LSTDKA P N G +K +K +A + T CV RYGNV+ SRGS Sbjct: 131 NAVKQVVALSTDKACNPTNLYGATKLASDKTFVAANNLSGDIGTRFCVVRYGNVVGSRGS 190 Query: 178 VIPLFIHQIKQG-KELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTIE 236 V+PL+ + QG EL +T+P MTRF ++L + VD VL + R G+IFV K P+ + Sbjct: 191 VVPLYRRLLSQGATELPVTDPRMTRFWITLNEGVDFVLSSLTMMRGGEIFVPKIPSMAMP 250 Query: 237 VLAKALQEIFGSKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIPMDGRDLNYAK 296 L KA+ S A++ IG R GEK +E ++S++D + Y I + + Sbjct: 251 DLVKAM----SSTAAMKVIGIRPGEKLHEIMISADDARSTVEFDDRYAIEPNFAEFGREP 306 Query: 297 YFVT-GEKKVALLDDYTSHN 315 Y + G K VA Y+S N Sbjct: 307 YAASDGAKPVAEDFSYSSDN 326 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: 293 Number of extensions: 13 Number of successful extensions: 4 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: 345 Length adjustment: 29 Effective length of query: 312 Effective length of database: 316 Effective search space: 98592 Effective search space used: 98592 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 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