Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_067476622.1 BJL86_RS12805 dTDP-glucose 4,6-dehydratase
Query= BRENDA::F6DEY6 (311 letters) >NCBI__GCF_001659785.1:WP_067476622.1 Length = 334 Score = 95.1 bits (235), Expect = 2e-24 Identities = 97/321 (30%), Positives = 143/321 (44%), Gaps = 24/321 (7%) Query: 1 MRVLVTGGAGFIGSHIVEDLLAR---GLEVAVLDNLATGKRENVPKGVP--FFQVDLRDK 55 MR+LVTGGAGFIGS+ V L R + VLD E P + D+ D Sbjct: 1 MRLLVTGGAGFIGSNFVR-LTGRVRPDTHITVLDAFTYAANEASVADAPCDVIRGDVADP 59 Query: 56 EEVERAFREFRPTH-VSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVEKLVF 114 ++ F P + H AA++ S+ P N+ G +LEA R++ V +L Sbjct: 60 GVLDEILAGFGPDDAIVHFAAESHNDNSIASPGQFVHTNITGTFEILEAARRHDV-RLHH 118 Query: 115 ASTGGAIYGEVPEG--ERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRYGN 172 ST +YG++P G E E RP SPY+ASKA+ + + + ++YGL+ N Sbjct: 119 VSTD-EVYGDLPLGTPEAFTEDTAYRPSSPYSASKASADMLVRAWIRTYGLRATLSNCSN 177 Query: 173 VYGPRQDPHGEAGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGD--VAEAHALA 230 YGPRQ H E + + G P LY G VRD+++V D A L Sbjct: 178 NYGPRQ--HVEKFIPRQITTLIDGGRP-RLY-----GSGENVRDWIHVDDHNAAVWEILE 229 Query: 231 LFSLEGIYNVGTGEGHTTREVLEAVAEAAGKAP-QVQPAPPRPGDLERSVLSPLKLMAH- 288 + Y +G + RE++ + + P +V RPG R + KL Sbjct: 230 RGRMGETYLIGADGQASNREIVRELCLLCDRDPDEVDFVTDRPGHDRRYAIDATKLRREL 289 Query: 289 GWRPK-VGFQEGIRLTVDHFR 308 GW P+ + G+ TV+ +R Sbjct: 290 GWAPEHTDLRSGLADTVEWYR 310 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: 290 Number of extensions: 16 Number of successful extensions: 2 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: 334 Length adjustment: 28 Effective length of query: 283 Effective length of database: 306 Effective search space: 86598 Effective search space used: 86598 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: 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