Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate NP_348811.1 CA_C2194 nucleoside-diphosphate sugar epimerase
Query= curated2:A8GWP0 (341 letters) >NCBI__GCF_000008765.1:NP_348811.1 Length = 340 Score = 231 bits (590), Expect = 2e-65 Identities = 140/339 (41%), Positives = 203/339 (59%), Gaps = 16/339 (4%) Query: 2 FVDKTLLITGGTGSFGNAVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNN--PKIK 59 F K +LI GGTG+ G+ +++ LK ++ K IRIFSRDE KQ M+ K + Sbjct: 4 FTGKNVLIVGGTGTIGHGLINELLK----ENPKVIRIFSRDEYKQFLMQNEFRGIAEKFR 59 Query: 60 FYIGDVRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATINK 119 F IGDVR+Y+ ++ AM +D VF+ AA+K VP CE+ P EAI TNI G ENV++AAT + Sbjct: 60 FLIGDVRDYDRVERAMNGIDVVFNLAAMKHVPACEYNPEEAIRTNITGMENVIKAATYHN 119 Query: 120 VAKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSVI 179 V V+ S+DKA+ P N+ G +K L EKL A +T F R+GNVM SRGSVI Sbjct: 120 VECVVFTSSDKAINPTNSYGATKLLAEKLVQAANYSKGNVRTKFVAVRFGNVMGSRGSVI 179 Query: 180 PLFINQIKQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTIEVLA 239 PLF QI++N +T+T+P+M+RF+M+L +V L++ A + G++F+ K P + LA Sbjct: 180 PLFKKQIEENAVITVTDPTMSRFMMTLSQAVKLIMTAAKEATGGEVFILKMPVIKLIDLA 239 Query: 240 KAL-------QGIFNSKNKIRFIGTRHGEKHYESLVSSEEMAKAEDLG-NYYRIPMDGRD 291 K + I + KI+ IG R GE+ YE L++ EE A DLG +Y IP Sbjct: 240 KVVVEETSRKLDINPERIKIKEIGLRAGERCYEELMTREESVNAYDLGHSYVVIPSSFYI 299 Query: 292 LNYAKYFVEGEKKIALLEDYTSHNTKRLNLEEVKELLLN 330 +Y + + +K A + Y S + + + L+EV++LL N Sbjct: 300 TDYKSKYSKYKK--AEIGSYNSSSIEPITLDEVRQLLKN 336 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: 276 Number of extensions: 12 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: 340 Length adjustment: 28 Effective length of query: 313 Effective length of database: 312 Effective search space: 97656 Effective search space used: 97656 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