Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate 3610476 Dshi_3857 polysaccharide biosynthesis protein CapD (RefSeq)
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__Dino:3610476 Length = 630 Score = 135 bits (341), Expect = 2e-36 Identities = 90/289 (31%), Positives = 151/289 (52%), Gaps = 23/289 (7%) Query: 2 FVDKTLMITGGTGSFGNAVLSRFLKSN----IINDIKEIRIFSRDEKKQEDMRIALNNSK 57 + D+ ++I+G GS G+ + + L ++ ++ E+ +++ D + + + ++ Sbjct: 286 YADRVVLISGAGGSIGSELCRQVLACRPAKLVLYELNELALYNVDMELRSLAEVT--GTE 343 Query: 58 LKFYIGDVRNYQSIDDAM--HGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAA 115 L +G V + + + + H V V HAAA K VP E P+ + NV G + + A Sbjct: 344 LVPVLGSVTDPRQVRGVLAEHKVQVVLHAAAYKHVPLVEANPLAGLANNVFGTQTLAREA 403 Query: 116 INNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASR 175 + + I++S+DKAV P N MG SK L E L I R G T+ + R+GNV+ S Sbjct: 404 AEYGIERFILISSDKAVRPTNVMGASKRLAE-LVIQDLETRYTG-TVFTMVRFGNVLGSS 461 Query: 176 GSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTI 235 GSV+PLF QI++G +T+T+P +TR+ M++ ++V LVL A R G++FV A + Sbjct: 462 GSVVPLFQEQIRRGGPVTVTDPKVTRYFMTVQEAVRLVLTAGSMARGGEVFVLDMGA-PV 520 Query: 236 EVLAKALQEIFGSKNAIR------------FIGTRHGEKHYESLVSSED 272 ++ A Q I + +R F G R GEK +E L ++D Sbjct: 521 PIVQLARQVIESAGYTVRDDATPDGDIEIVFTGLRPGEKMFEELTITDD 569 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: 390 Number of extensions: 22 Number of successful extensions: 3 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: 630 Length adjustment: 33 Effective length of query: 308 Effective length of database: 597 Effective search space: 183876 Effective search space used: 183876 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 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