Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_057506692.1 ABB28_RS00220 polysaccharide biosynthesis protein
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_001431535.1:WP_057506692.1 Length = 634 Score = 133 bits (334), Expect = 1e-35 Identities = 87/279 (31%), Positives = 151/279 (54%), Gaps = 17/279 (6%) Query: 5 KTLMITGGTGSFGNAVLSRFLKSN----IINDIKEIRIFSRDEKKQEDMRIALNNSKLKF 60 +T+++TG GS G+ + + + ++ ++ E+ + + + ++ + + +++ Sbjct: 285 RTVLVTGAGGSIGSELCRQCARHGAGRIVLLEMSELLLLTIEA----ELCRSFPDIEVEA 340 Query: 61 YIGDVRNYQSIDDAM--HGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINN 118 +GD + I A+ H ++ FHAAA KQVP E EA+ N+L ENV A + Sbjct: 341 VLGDCGDPAVIRHALSLHRIEAAFHAAAYKQVPVLERQLREAVRNNILATENVARACMEA 400 Query: 119 KVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGSV 178 KV + +STDKAV P+N++G SK E I ++ + T R+GNV+AS GSV Sbjct: 401 KVEHFVFISTDKAVDPVNSLGASKRYAE--MICQSLDQKSTHTRFVTVRFGNVLASAGSV 458 Query: 179 IPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIF-VQKSPASTIEV 237 +PLF QI +G +T+T+P +TR+ M++ ++ L+L A G I+ + I V Sbjct: 459 VPLFRDQIMKGGPVTVTDPEVTRYFMTIPEACQLILQAAASASHGAIYTLDMGEPVPIRV 518 Query: 238 LAKALQEIFGSKN----AIRFIGTRHGEKHYESLVSSED 272 LA+ + + G + AI + G R GEK +E+L S++ Sbjct: 519 LAEQMIRLAGKQPYKDIAIIYTGLRPGEKLHETLFYSDE 557 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: 387 Number of extensions: 11 Number of successful extensions: 2 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: 634 Length adjustment: 33 Effective length of query: 308 Effective length of database: 601 Effective search space: 185108 Effective search space used: 185108 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