Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_077244013.1 B1A74_RS05500 polysaccharide biosynthesis protein
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_001995255.1:WP_077244013.1 Length = 635 Score = 144 bits (362), Expect = 8e-39 Identities = 96/290 (33%), Positives = 154/290 (53%), Gaps = 22/290 (7%) Query: 3 VDKTLMITGGTGSFGNAVLSRFLKSN----IINDIKEIRIFSRDEKKQEDMRIALN-NSK 57 VD+ +M+TG GS G+ + R L+ ++ + E ++ R E + + +R L + Sbjct: 294 VDRRVMVTGAGGSIGSELCRRILRQGPAELVLFERNEFALY-RIEHEMQALRAELGLDCP 352 Query: 58 LKFYIGDVRNYQSIDD--AMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAA 115 + +G V + ++ A H + ++HAAA K VP E +E + NVLG + AA Sbjct: 353 IHAVLGSVTLPRRVESVLARHRIQTLYHAAAYKHVPIVEENAVEGVRNNVLGTRVLADAA 412 Query: 116 INNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASR 175 I V + I++STDKAV P N MG SK L E I + R T+ + R+GNV+ S Sbjct: 413 IAAGVERFILISTDKAVRPTNVMGASKRLAEM--ILQDRAAGTPATVFSMVRFGNVLGSS 470 Query: 176 GSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFV-QKSPAST 234 GSV+PLF QI++G +T+T P +TR+ MS+ ++ +LV+ A G++FV Sbjct: 471 GSVVPLFHRQIREGGPVTVTHPEITRYFMSIPEAAELVIQAGTMAGGGEVFVLDMGEPVR 530 Query: 235 IEVLAKALQEIFGSK-----------NAIRFIGTRHGEKHYESLVSSEDM 273 I+ LA+ + + G + AI+F G R GEK YE L+ +++ Sbjct: 531 IQDLARRMIRLHGRQVRDDNGDPPDGVAIQFTGLRPGEKLYEELLIGDNV 580 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: 396 Number of extensions: 23 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: 635 Length adjustment: 33 Effective length of query: 308 Effective length of database: 602 Effective search space: 185416 Effective search space used: 185416 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