Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Dsui_0083 Dsui_0083 UDP-N-acetylglucosamine 4,6-dehydratase
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__PS:Dsui_0083 Length = 332 Score = 205 bits (522), Expect = 1e-57 Identities = 125/327 (38%), Positives = 193/327 (59%), Gaps = 10/327 (3%) Query: 1 MFVDKTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALN-NSKLK 59 M + +++ITGGTGSFGN + L + K+I IFSRDE KQ +M + +++ Sbjct: 1 MLTNTSILITGGTGSFGNTFVPMTLAKF---NPKKIVIFSRDEMKQWEMAKKFGGDERVR 57 Query: 60 FYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINNK 119 F+IGDVR+ + + A+ G+DYV HAAA K VPT E+ P E + TN+ GA N++ A I+ Sbjct: 58 FFIGDVRDRERLYRALDGIDYVVHAAATKIVPTAEYNPFECVKTNINGAMNLIDACIDKG 117 Query: 120 VTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGSVI 179 V +V+ LSTDKA P+N G +K +KL +A +T V RYGNVM SRGSVI Sbjct: 118 VKRVVALSTDKASSPVNLYGATKLASDKLFVAGNSYAGGHDTRFAVVRYGNVMGSRGSVI 177 Query: 180 PLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTIEVLA 239 P F+ IK L IT+ MTRF++SL V+LV +AF G+I+V+K P+ + LA Sbjct: 178 PFFM-SIKDKGVLPITDERMTRFMISLEQGVELVWHAFGDMEGGEIYVKKIPSMKVTDLA 236 Query: 240 KALQEIFGSKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIPMDGRDLNYAKYFV 299 +A+ ++ ++G R GEK +E ++S ED + + +++I + + + + Sbjct: 237 RAI----APNASLEYVGIRPGEKLHEQMISEEDALYSYEYPEHFKILPAIHNWHLSPGRI 292 Query: 300 TGEKKVALLDDYTS-HNTKRLNLKEVK 325 KKV YTS +N++ + ++E++ Sbjct: 293 KDGKKVPEGFSYTSDNNSEWMGIEELQ 319 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: 299 Number of extensions: 21 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: 332 Length adjustment: 28 Effective length of query: 313 Effective length of database: 304 Effective search space: 95152 Effective search space used: 95152 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