Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate GFF2455 HP15_2399 polysaccharide biosynthesis protein CapD
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__Marino:GFF2455 Length = 310 Score = 189 bits (480), Expect = 8e-53 Identities = 117/283 (41%), Positives = 168/283 (59%), Gaps = 6/283 (2%) Query: 34 KEIRIFSRDEKKQEDM-RIALNNSKLKFYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPT 92 K+I +FSRDE KQ +M ++ + +L+F+IGDVR+ + A+ GVDYV HAAA K VPT Sbjct: 9 KKIIVFSRDEMKQWEMAKLFQGDDRLRFFIGDVRDRDRLYRALDGVDYVVHAAATKIVPT 68 Query: 93 CEFYPMEAINTNVLGAENVLSAAINNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAK 152 E+ P E + TN+ GA N++ AAI+ V V+ LSTDKA PIN G +K +KL +A Sbjct: 69 AEYNPFECVKTNIHGAMNLIDAAIDKGVKGVVALSTDKASSPINLYGATKLASDKLFVAG 128 Query: 153 ARMRSPGETILCVTRYGNVMASRGSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDL 212 ET V RYGNVM SRGSVIP F+ IK+ L IT+P MTRF++SL V+L Sbjct: 129 NSYSGGHETKFSVVRYGNVMGSRGSVIPFFM-SIKEKGVLPITDPRMTRFMISLEQGVEL 187 Query: 213 VLYAFEHGRQGDIFVQKSPASTIEVLAKALQEIFGSKNAIRFIGTRHGEKHYESLVSSED 272 V +AFE G+I+V+K P+ + LA+ + +K + +G R GEK +E ++ +ED Sbjct: 188 VWHAFEDMVGGEIYVKKIPSMKVTDLAQVVAP--DAKQEV--VGIRPGEKLHEQMIGAED 243 Query: 273 MAKADDLGGYYRIPMDGRDLNYAKYFVTGEKKVALLDDYTSHN 315 + +++I + D + + KKV Y+S N Sbjct: 244 SYFTYEYPEHFKILPNINDWGTCESRIKDGKKVPEGFVYSSDN 286 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: 261 Number of extensions: 9 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: 310 Length adjustment: 28 Effective length of query: 313 Effective length of database: 282 Effective search space: 88266 Effective search space used: 88266 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: 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