Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_028313359.1 G491_RS0101780 capsule biosynthesis protein CapD
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_000429905.1:WP_028313359.1 Length = 359 Score = 189 bits (481), Expect = 7e-53 Identities = 111/293 (37%), Positives = 170/293 (58%), Gaps = 19/293 (6%) Query: 5 KTLMITGGTGSFGNAVLSRFLKSNIINDI-----KEIRIFSRDEKKQEDMRIALNNSKLK 59 K +++TG G+ G+ ++ + L+ + + ++ E +F +++ Q+ N+ + Sbjct: 8 KRVLVTGACGTVGSELVRQLLEEHQVEELIGLDNNESELFFLEQRFQK-------NANGR 60 Query: 60 FYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINNK 119 F++ DVR+ + M GV VFHAAA K V CE P EA+ TN++G +N+++AA +NK Sbjct: 61 FFLADVRDEHKLARKMRGVHAVFHAAAFKHVILCEKSPFEAVRTNIMGVQNIITAAADNK 120 Query: 120 VTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGSVI 179 V +VI S+DKAV P N MG SK + E+L A G I TR+GNV+ SRGSVI Sbjct: 121 VERVIFTSSDKAVNPTNVMGTSKLMGERLMTAADSNSRDGGPIYASTRFGNVLGSRGSVI 180 Query: 180 PLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTIEVLA 239 P+F QI++G +T+T+P MTRF+MSL +V LV+ + G++FV K P+ I LA Sbjct: 181 PIFREQIRKGGPVTLTDPGMTRFIMSLPQAVQLVIDSASLACGGEVFVTKMPSIKISDLA 240 Query: 240 KA----LQEIFG---SKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRI 285 + L E FG I IG + GEK YE L+S E+ + +L Y+ + Sbjct: 241 QVMIDELAEEFGRDPKSIEIENIGIKPGEKMYEELMSHEETRRVWELPKYFAV 293 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: 286 Number of extensions: 10 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: 359 Length adjustment: 29 Effective length of query: 312 Effective length of database: 330 Effective search space: 102960 Effective search space used: 102960 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: 49 (23.5 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