Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_090444680.1 BLS63_RS12555 dTDP-glucose 4,6-dehydratase
Query= BRENDA::F6DEY6 (311 letters) >NCBI__GCF_900100495.1:WP_090444680.1 Length = 364 Score = 139 bits (349), Expect = 1e-37 Identities = 113/351 (32%), Positives = 172/351 (49%), Gaps = 57/351 (16%) Query: 1 MRVLVTGGAGFIGSHIVEDLLARGLEVAV-LDNLA-TGKRENV-----PKGVPFFQVDLR 53 M++LVTGGAGFIGS ++ ++ + V LD L G E++ + F +VD+ Sbjct: 1 MKILVTGGAGFIGSAVIRHIIGSTTDSVVNLDKLTYAGNLESLVEVSASERYAFERVDIC 60 Query: 54 DKEEVERAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQY--GVE- 110 D+ EVER FRE +P V H AA++ V S++ P E N++G LLEA RQY G++ Sbjct: 61 DRIEVERVFREHQPDAVMHLAAESHVDRSIDGPAAFIETNIVGTYTLLEAARQYWQGLDE 120 Query: 111 --KLVFA---STGGAIYGEVPEGERA-EETWPPRPKSPYAASKAAFEHYLSVYGQSYGLK 164 K F + +YG++ + E E P P SPY+ASKA+ +H + + ++YGL Sbjct: 121 SRKTAFRFHHISTDEVYGDLDDPEELFTEATPYAPSSPYSASKASSDHLVRAWRRTYGLP 180 Query: 165 WVSLRYGNVYGPRQDPHGEAGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGDVA 224 + N YGP P ++ + L G P+ +Y + GD+ VRD++YV D Sbjct: 181 TLVTNCSNNYGPYHFPE---KLIPLIILNALEGKPLPVYGK---GDQ--VRDWLYVED-- 230 Query: 225 EAHALALFSL--EG----IYNVGTGEGHTTREVLEAVAEAAGKAPQVQP----------- 267 HA AL+ + EG YN+G GH ++ +E V +++P Sbjct: 231 --HARALYKVVTEGQIGETYNIG---GHNEKQNIEVVHALCVLLDELRPVRANSFASHLT 285 Query: 268 --------APPRPGDLERSVLSPLKLMAH-GWRPKVGFQEGIRLTVDHFRG 309 RPG R + K+ GW P+ F+ GIR TV+ + G Sbjct: 286 CYKDLITHVQDRPGHDLRYAIDASKIQRELGWTPEETFESGIRKTVEWYLG 336 Lambda K H 0.318 0.138 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: 298 Number of extensions: 22 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: 311 Length of database: 364 Length adjustment: 28 Effective length of query: 283 Effective length of database: 336 Effective search space: 95088 Effective search space used: 95088 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 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