Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate 349909 BT0381 capsular polysaccharide biosynthesis protein capD (NCBI ptt file)
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__Btheta:349909 Length = 349 Score = 404 bits (1039), Expect = e-117 Identities = 209/345 (60%), Positives = 266/345 (77%), Gaps = 13/345 (3%) Query: 1 MFVDKTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNS---- 56 +F KTLMITGGTGSFGNAVL+RFL++ DI EIRIFSRDEKKQ+DMR Sbjct: 3 IFAGKTLMITGGTGSFGNAVLNRFLRT----DIGEIRIFSRDEKKQDDMRHEYQVKYPDV 58 Query: 57 --KLKFYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSA 114 K+KF+IGDVRN QS +AM GVDY+FHAAALKQVP+CEF+PMEA+ TNV+G +NVL+A Sbjct: 59 AHKIKFFIGDVRNLQSCKNAMPGVDYIFHAAALKQVPSCEFFPMEAVKTNVIGTDNVLTA 118 Query: 115 AINNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMAS 174 AI V VI LSTDKA YPINAMG++KA+ EK+A+AK+R G+T +C TRYGNVM S Sbjct: 119 AIEAGVGAVICLSTDKAAYPINAMGITKAVEEKIAVAKSRY--SGKTKICCTRYGNVMCS 176 Query: 175 RGSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPAST 234 RGSVIPL+I QI+ G +T+TEP+MTRF+MSL ++VDLVL+AFEHG+ GDI VQK+PA T Sbjct: 177 RGSVIPLWIEQIRNGNPVTLTEPTMTRFIMSLEEAVDLVLFAFEHGQNGDILVQKAPACT 236 Query: 235 IEVLAKALQEIFGSKNA-IRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIPMDGRDLN 293 I+ A+A+ E+FG K I+ IG RHGEK YE+L+++E+ AKA+D+G +YR+P D R LN Sbjct: 237 IQTQAEAVCELFGGKKEDIKVIGIRHGEKMYETLLTNEECAKAEDMGNFYRVPADNRGLN 296 Query: 294 YAKYFVTGEKKVALLDDYTSHNTKRLNLKEVKELLLTLDYVQKEL 338 Y K+F GE + L ++ S+NT LN++E K + LDY+QKEL Sbjct: 297 YDKFFKEGETERNTLTEFNSNNTYILNVEETKVKIAALDYIQKEL 341 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: 393 Number of extensions: 19 Number of successful extensions: 5 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: 349 Length adjustment: 29 Effective length of query: 312 Effective length of database: 320 Effective search space: 99840 Effective search space used: 99840 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 17 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