Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate PfGW456L13_2186 UDP-N-acetylglucosamine 4,6-dehydratase (EC 4.2.1.-)
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2186 Length = 345 Score = 421 bits (1083), Expect = e-122 Identities = 209/335 (62%), Positives = 274/335 (81%), Gaps = 7/335 (2%) Query: 2 FVDKTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNSKLKFY 61 F + TL+ITGGTGSFGNAVL RFL + DIKEIR+FSRDEKKQ+DMR N+KLKFY Sbjct: 5 FSNSTLLITGGTGSFGNAVLKRFLDT----DIKEIRVFSRDEKKQDDMRKKYANTKLKFY 60 Query: 62 IGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINNKVT 121 IGDVR++QS+ +A GVDY+FHAAALKQVP+CEF+PMEA+ TNVLG +NVL AAI N V Sbjct: 61 IGDVRDFQSVLNATRGVDYIFHAAALKQVPSCEFHPMEAVKTNVLGTDNVLEAAIQNNVK 120 Query: 122 KVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGSVIPL 181 +V+ LSTDKAVYPINAMG+SKA+MEK+ +AK+ R+ T++C TRYGNVMASRGSVIPL Sbjct: 121 RVVCLSTDKAVYPINAMGISKAMMEKVMVAKS--RNDNNTVICGTRYGNVMASRGSVIPL 178 Query: 182 FIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTIEVLAKA 241 F+ QI+ G L++T+P+MTRF+M+L D+VDLVLYAFEHG GD+FVQK+PA+T+EVLAKA Sbjct: 179 FVDQIRSGIPLSLTDPNMTRFMMTLADAVDLVLYAFEHGTNGDMFVQKAPAATVEVLAKA 238 Query: 242 LQEIFG-SKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIPMDGRDLNYAKYFVT 300 L + + ++ IGTRHGEK +E+L+S E+MA A+D G Y+R+P D RDLNY+K+ Sbjct: 239 LINMLNVPDHPVQVIGTRHGEKLFEALLSREEMACAEDRGDYFRVPPDLRDLNYSKFVEQ 298 Query: 301 GEKKVALLDDYTSHNTKRLNLKEVKELLLTLDYVQ 335 GE K++ +DY SHNT+RL+++ +++LLL L++++ Sbjct: 299 GETKISRTEDYNSHNTERLDVEGMQKLLLKLNFMR 333 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: 400 Number of extensions: 16 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