Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Ga0059261_4092 Ga0059261_4092 Predicted nucleoside-diphosphate sugar epimerases
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__Korea:Ga0059261_4092 Length = 661 Score = 131 bits (329), Expect = 6e-35 Identities = 100/313 (31%), Positives = 151/313 (48%), Gaps = 23/313 (7%) Query: 1 MFVDKTLMITGGTGSFGNAVLSRFLKSN----IINDIKEIRIFSRDEKKQEDMRIALNNS 56 M + +++TG G+ G + + + I+ D E ++ D + +E ++ + Sbjct: 301 MIGGRRILVTGAGGTIGRELARQIAEHGPARLILLDANEFNLYDADLEMRES-HPQVSCT 359 Query: 57 KLKFYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAI 116 + I R + A H + VFHAAALK VP E +P + TNVLG NV AA Sbjct: 360 PVLCSIRQRRQLMQVF-AEHRPELVFHAAALKHVPLVEMHPAAGVQTNVLGTRNVADAAR 418 Query: 117 NNKVTKVIVLSTDKAVYPINAMGLSKALMEKL--AIAKARMRSPGETILCVTRYGNVMAS 174 ++ +STDKAV P+ MG++K L E A+ A PG R+GNV+ S Sbjct: 419 FYGALAMVQVSTDKAVNPVGFMGVTKRLGEFYCQALDLAGSDDPGAPRFITVRFGNVLGS 478 Query: 175 RGSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHG-----RQGDIFV-- 227 GS+IPLF Q+ +G LT+T P + RF M++ ++V L+L + G R G IFV Sbjct: 479 SGSLIPLFQRQLSRGGPLTVTHPEIERFFMTVHEAVQLILQSASRGLRDGMRHGRIFVLD 538 Query: 228 QKSPASTIEVLAKALQEIFGSKN----AIRFIGTRHGEKHYESLVSSEDMAKADDLGGYY 283 P I++ A+ + + G I IG R GEK YE L +E+ + G + Sbjct: 539 MGEPIRVIDI-ARRMIRLAGLDPEIDVGIDIIGLRPGEKLYEELFDAEESRLPSSIPGVF 597 Query: 284 RI---PMDGRDLN 293 P+ R LN Sbjct: 598 EAEPRPIPLRTLN 610 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: 371 Number of extensions: 13 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: 661 Length adjustment: 33 Effective length of query: 308 Effective length of database: 628 Effective search space: 193424 Effective search space used: 193424 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