Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_013450833.1 CALNI_RS03545 UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_000183405.1:WP_013450833.1 Length = 330 Score = 228 bits (582), Expect = 1e-64 Identities = 142/333 (42%), Positives = 194/333 (58%), Gaps = 14/333 (4%) Query: 1 MFVDKTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNSK-LK 59 MF DK ++ITGGTGSFG + LK+ D K + IFSRDE KQ +M + L+ Sbjct: 1 MFKDKNILITGGTGSFGKEFVKYLLKNC---DPKRVVIFSRDEFKQYEMAQEFGGDRRLR 57 Query: 60 FYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINNK 119 F++GDVR+ + A +G+DYV HAAALKQVP E+ P E I TN+LGA+NV+ A I+N Sbjct: 58 FFLGDVRDKDRLYRAFYGIDYVVHAAALKQVPAAEYNPFEVIKTNILGAQNVIEACIDNN 117 Query: 120 VTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGSVI 179 V KV+ LSTDKA PIN G +K +KL +A T V RYGNV+ SRGSV+ Sbjct: 118 VKKVVALSTDKAAIPINLYGATKLCSDKLFVAGNSYAGGRVTRFGVVRYGNVLGSRGSVL 177 Query: 180 PLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTIEVLA 239 PLF+ Q K+G +TIT MTRF ++L +V+LV+ AF++ G+IFV K P+ + A Sbjct: 178 PLFLKQKKEG-VVTITHKDMTRFWITLPQAVELVVKAFKYMTGGEIFVPKIPSMKMIDFA 236 Query: 240 KALQEIFGSKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIPMDGRDLNYAKYFV 299 KA+ + IR +G R GEK +E ++ +D + +YRI + D K F Sbjct: 237 KAI----APEAEIREMGIRPGEKMHEVMIPEDDARHTREYDDHYRIIPEFLDWKAPKEFG 292 Query: 300 TGEKKVALLDDYTSHN-----TKRLNLKEVKEL 327 G K + Y S N T++ LK + EL Sbjct: 293 NGGKPLPEGFSYRSDNNSWWLTEQELLKIIDEL 325 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: 313 Number of extensions: 18 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: 330 Length adjustment: 28 Effective length of query: 313 Effective length of database: 302 Effective search space: 94526 Effective search space used: 94526 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 24 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