Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate 1937129 b3788 dTDP-glucose 4,6-dehydratase (NCBI)
Query= BRENDA::F2NQX6 (314 letters) >FitnessBrowser__Keio:1937129 Length = 355 Score = 121 bits (304), Expect = 2e-32 Identities = 102/337 (30%), Positives = 154/337 (45%), Gaps = 38/337 (11%) Query: 2 RVLVTGGAGFIGSHLV-HALHQKGIPVAVLDDLS-TGKRAHIPPDVP-----LYQTDIRD 54 ++L+TGGAGFIGS LV + +++ V V+D L+ G + P + DI D Sbjct: 3 KILITGGAGFIGSALVRYIINETSDAVVVVDKLTYAGNLMSLAPVAQSERFAFEKVDICD 62 Query: 55 LNAVLHAFQDFQPTHVAHQAAQASVKHSVQNPCKDAEINLLGGLNILEAMRA-----TGT 109 + F + QP V H AA++ V S+ P E N++G +LEA RA T Sbjct: 63 RAELARVFTEHQPDCVMHLAAESHVDRSIDGPAAFIETNIVGTYTLLEAARAYWNALTED 122 Query: 110 QKIVFAS---TGGAIYGEVPEGRRA-PETWPPKPKSPYAASKAAFEHYLEVYRQTHGLTY 165 +K F + +YG++ ET P P SPY+ASKA+ +H + + +T+GL Sbjct: 123 KKSAFRFHHISTDEVYGDLHSTDDFFTETTPYAPSSPYSASKASSDHLVRAWLRTYGLPT 182 Query: 166 TTLRYANVYGPRQDPHGEAGVVAIFTNRLLHAQPVTLYARKEPGDPGCIRDYIHVEDVTR 225 +N YGP P ++ + L + + +Y G+ IRD+++VED R Sbjct: 183 LITNCSNNYGPYHFPE---KLIPLMILNALAGKSLPVY-----GNGQQIRDWLYVEDHAR 234 Query: 226 ANLLALETNLEG-TYNVSTGQGRTTEDVLYTIARALGT------------TPRVTYAPPR 272 A T G TYN+ R DV+ TI L +T+ R Sbjct: 235 ALYCVATTGKVGETYNIGGHNERKNLDVVETICELLEELAPNKPHGVAHYRDLITFVADR 294 Query: 273 DG-DLEVSVLDPTQLQAHGWRPQVPFEEGIRRTVAWF 308 G DL ++ + GW PQ FE G+R+TV W+ Sbjct: 295 PGHDLRYAIDASKIARELGWLPQETFESGMRKTVQWY 331 Lambda K H 0.318 0.135 0.411 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: 270 Number of extensions: 19 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: 314 Length of database: 355 Length adjustment: 28 Effective length of query: 286 Effective length of database: 327 Effective search space: 93522 Effective search space used: 93522 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 (21.7 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