Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_081442692.1 ALVIN_RS01105 hypothetical protein
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_000025485.1:WP_081442692.1 Length = 258 Score = 162 bits (410), Expect = 9e-45 Identities = 94/269 (34%), Positives = 152/269 (56%), Gaps = 21/269 (7%) Query: 4 DKTLMITGGTGSFGNAVLSRFLKSNIINDI-----KEIRIFSRDEKKQEDMRIALNNSKL 58 +K++++TG G+ G ++ + L+ ++++ E +F + ++ Q + + Sbjct: 6 NKSILVTGCCGTVGGELVRQLLEDYGVDELIGIDNNESELFFQQQRYQ-------HYANA 58 Query: 59 KFYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINN 118 F++ +R+ + GVD VFHAAA K V CE P +A+ TN+ G +NV+ AA+ Sbjct: 59 NFFLASIRDRSKLVRLFKGVDIVFHAAAFKHVVLCERAPFDAVQTNINGVQNVIEAALEA 118 Query: 119 KVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGSV 178 +V +VI S+DKAV P N MG SK + E+L A + +TI TR+GNV+ SRGSV Sbjct: 119 RVGRVIFTSSDKAVNPTNVMGTSKLMGERLMTAANNCQRGCDTIFASTRFGNVLGSRGSV 178 Query: 179 IPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTIEVL 238 IP+F QI+QG +T+T+P MTRF+MS+ ++ LV+ + G++FV K P I+ L Sbjct: 179 IPIFREQIRQGGPVTLTDPEMTRFIMSIREATRLVIDSSALACGGEVFVTKMPVIRIQDL 238 Query: 239 AKALQEIFGSKNAIRFIGTRHGEKHYESL 267 A+ + IR + +G Y SL Sbjct: 239 AEVM---------IRQLAPVYGIAFYTSL 258 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: 189 Number of extensions: 7 Number of successful extensions: 1 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: 258 Length adjustment: 26 Effective length of query: 315 Effective length of database: 232 Effective search space: 73080 Effective search space used: 73080 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: 48 (23.1 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