Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate 6938128 Sama_2249 hypothetical protein (RefSeq)
Query= curated2:Q56623 (328 letters) >FitnessBrowser__SB2B:6938128 Length = 307 Score = 162 bits (411), Expect = 8e-45 Identities = 96/297 (32%), Positives = 158/297 (53%), Gaps = 3/297 (1%) Query: 12 ILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNKDDGLLFEVGDINASTDFELPLKNT 71 +L+TG +GFVG L + +Y V R N D ++ + I+ TD++ LKN Sbjct: 3 VLITGGSGFVGRYL-QGYFNSDEYDVAITSRCKSNISDFPVYTIPAIDQHTDWKHALKNV 61 Query: 72 TVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVNGEGT 131 VVVH A+RAH D+ + + N G L I GVKR I++SSIK GE T Sbjct: 62 DVVVHLASRAHSSDNHSEAAKEDFTKTNVLGLSKLLDDCIFLGVKRIIYLSSIKALGEST 121 Query: 132 LVGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKANFASL 191 F D + P D YG++K+ AE+ +V K S ++ IIRP +VYG KAN S+ Sbjct: 122 DGRDAFSESDKYNPADYYGITKARAEQLVVEKCKHSGLDYTIIRPPLVYGKSAKANLQSI 181 Query: 192 MRLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDVSTAEMV 251 R +S +P P+ + + N+RSL+S+++L IV + P NQ++ V+D + +ST ++ Sbjct: 182 ARGLSYSLPFPYFT-SSNRRSLISVHSLCRFIVAVANDPNTNNQIYNVADNYVLSTKDIF 240 Query: 252 RELAIALDKPTWQLPVPIWCYKLFGKLFGK-SDIVDRLTGTLQVDISHTKETLGWKP 307 + + ++ P+P + + + K D+ +L G+L+++ + + + WKP Sbjct: 241 SLIKSCSNSKSFIFPIPKFIFTFLAFFWSKFGDVSTKLYGSLEINNTKATKVISWKP 297 Lambda K H 0.318 0.134 0.388 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: 239 Number of extensions: 10 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: 328 Length of database: 307 Length adjustment: 27 Effective length of query: 301 Effective length of database: 280 Effective search space: 84280 Effective search space used: 84280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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