Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Ac3H11_1539 UDP-N-acetylglucosamine 4,6-dehydratase (EC 4.2.1.-)
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1539 Length = 606 Score = 142 bits (359), Expect = 2e-38 Identities = 103/304 (33%), Positives = 155/304 (50%), Gaps = 30/304 (9%) Query: 1 MFVDKTLMITGGTGSFGNAVLSRFLKSNIIN----DIKEIRIFSRDEKKQEDMRIALNNS 56 +F +++TG GS G+ + + + + D+ E I+ + ++++R A Sbjct: 274 LFAGTCVLVTGAGGSIGSELCRQIARFGVARLVCVDVSEFAIY----QLEQELREAHPQM 329 Query: 57 KLKFYIGDVRNYQSIDDA--MHGVDYVFHAAALKQVPTCE-FYPMEAINTNVLGAENVLS 113 + +Y +VR + + +H VFHAAA K VP E +EA+ TNVLG NV Sbjct: 330 QGMYYTANVREVERLHAIARLHQPTVVFHAAAYKHVPLMESLNEIEALRTNVLGTMNVAR 389 Query: 114 AAINNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMA 173 A + +++STDKAV P N MG SK L E++ A A PG + V R+GNV+ Sbjct: 390 VAAAIGAARFVLISTDKAVNPTNVMGASKRLAERVMQAVAS-EHPGTRFVAV-RFGNVLG 447 Query: 174 SRGSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFV--QKSP 231 S GSV+PLF QI +G +T+T P + R+ M++ ++ LVL A G+ G IFV P Sbjct: 448 SSGSVVPLFAEQIARGGPVTVTHPDIVRYFMTIPEAAQLVLQAGLMGQSGQIFVLDMGEP 507 Query: 232 ASTIEVLAKALQEIFGSKN---AIRFIGTRHGEKHYESLVSSED-----------MAKAD 277 +E LA+ L + G I F G R GEK YE L+++ + +AK D Sbjct: 508 VKIVE-LARILVRLSGKTEQEIPIVFTGLRPGEKLYEELLANGETTEPTPHPKLHVAKTD 566 Query: 278 DLGG 281 GG Sbjct: 567 ASGG 570 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: 345 Number of extensions: 24 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: 606 Length adjustment: 33 Effective length of query: 308 Effective length of database: 573 Effective search space: 176484 Effective search space used: 176484 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: 51 (24.3 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