Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_083772003.1 ARNIT_RS12680 polysaccharide biosynthesis protein
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_000092245.1:WP_083772003.1 Length = 577 Score = 145 bits (366), Expect = 3e-39 Identities = 98/283 (34%), Positives = 152/283 (53%), Gaps = 22/283 (7%) Query: 4 DKTLMITGGTGSFGNAVLSRFLKSN----IINDIKEIRIFSRDEKKQEDMRIALNNSKLK 59 DK ++ITG GS G+ + + K I+ D E ++ E+ D+ I + + Sbjct: 262 DKVVLITGAGGSIGSEISRQCKKFGAKQLILLDHSEFNLYQITEELNSDIVIPVMQT--- 318 Query: 60 FYIGDVRNYQSIDDAM--HGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAIN 117 VRN+ I++ + V HAAA K VP E +E I+ N++G +N + +I Sbjct: 319 -----VRNFGFIENTFKKYKPQIVIHAAAYKHVPLVEDNILEGISNNIIGTKNCIDLSIK 373 Query: 118 NKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGS 177 +V K +++STDKAV P N MG +K + E A ++S I+ V R+GNV+ S GS Sbjct: 374 YEVEKFVLISTDKAVRPTNVMGTTKRICELYA---QNVKSDSTEIVAV-RFGNVLGSSGS 429 Query: 178 VIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFV--QKSPASTI 235 VIP F QI+ G +T+T P +TR+ M + ++ +LVL A G+ G+IF+ P + Sbjct: 430 VIPKFKSQIESGGPITVTHPDITRYFMLIPEACELVLQAASIGKGGEIFILDMGEPIKIV 489 Query: 236 EVLAKALQEIFGSKNA-IRFIGTRHGEKHYESLVSSEDMAKAD 277 + LAK + E+ G +N I F G R GEK YE L+ ++ D Sbjct: 490 D-LAKKMIELSGRENVQIEFCGLRPGEKLYEELLINDSDKNTD 531 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: 412 Number of extensions: 22 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: 577 Length adjustment: 32 Effective length of query: 309 Effective length of database: 545 Effective search space: 168405 Effective search space used: 168405 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 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