Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_012102426.1 CKL_RS10240 NAD-dependent dehydratase
Query= SwissProt::A0R5C5 (313 letters) >NCBI__GCF_000016505.1:WP_012102426.1 Length = 335 Score = 177 bits (450), Expect = 2e-49 Identities = 117/327 (35%), Positives = 165/327 (50%), Gaps = 26/327 (7%) Query: 1 MRTLVTGAAGFIGSTLVDRLLADGHGVVGLDDLSSGRAENLHSAENSDKFEFVKADIVDA 60 M TLVTG AGFIG + RLL + V LD+LS+G EN+ +N+ F+F+ DI D Sbjct: 1 MNTLVTGGAGFIGRWVTKRLLNENDSVTVLDNLSNGTLENIEEFKNNTHFKFIGGDIKDK 60 Query: 61 DLTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAAR--LAGVR---- 114 + + + K ++I+HLAA I+V+ S+DDP + +GT + E AR + G R Sbjct: 61 NKLDEVFKNKFDIIYHLAASINVQDSIDDPETTFFNDTLGTFNILEKARYQMFGKRGRMD 120 Query: 115 ---------------KVVHTSSGGSVYGTPPAYPTSEDMPVNPASPYAAGKVAGEVYLNM 159 K+V S+ VY SE PV P SPY K+A E + Sbjct: 121 GNSWVLDPNEDTYPCKIVFMST-CMVYDVSKDEGISETHPVKPVSPYGGSKIAAENMVLS 179 Query: 160 YRNLYDLDCSHIAPANVYGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVD 219 Y N Y L I P N YG Q GE GVVAIF +L GR I+G G TRD ++V Sbjct: 180 YYNAYKLPAVVIRPFNTYGSFQKTGGEGGVVAIFINNVLHGRDINIYGSGEQTRDLLYVK 239 Query: 220 DVVDAFVRAG-GPAGGGQRFNVGTGVETSTRELHTAIAGA-VGAPDEPEFHPPRLGDLRR 277 D D V +G GQ N GTG + + EL I G+ + HP ++ + Sbjct: 240 DCADFVVESGYSEKVNGQIVNAGTGRDVTINELADIICGSKIKINHVKHIHPQ--SEIMK 297 Query: 278 SRLDNTRAREVLGWQPQVALAEGIAKT 304 + D ++A++++GWQP+ L +GI +T Sbjct: 298 LKCDYSKAKKLIGWQPKYTLEQGIEET 324 Lambda K H 0.317 0.136 0.396 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: 251 Number of extensions: 8 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: 313 Length of database: 335 Length adjustment: 28 Effective length of query: 285 Effective length of database: 307 Effective search space: 87495 Effective search space used: 87495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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