Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_077244485.1 B1A74_RS09465 NAD-dependent epimerase
Query= BRENDA::F6DEY6 (311 letters) >NCBI__GCF_001995255.1:WP_077244485.1 Length = 335 Score = 130 bits (327), Expect = 4e-35 Identities = 104/339 (30%), Positives = 155/339 (45%), Gaps = 40/339 (11%) Query: 1 MRVLVTGGAGFIGSHIVEDLLARGLEVAVLDNLATGKRENVPKG----------VPFFQV 50 M++L+TG AGFIG+ + LL RG EV +DNL ++ K +V Sbjct: 1 MKILITGTAGFIGNALALRLLERGDEVVGVDNLNDYYDVSLKKARLARIQDHERFTEERV 60 Query: 51 DLRDKEEVERAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVE 110 D+ D+E ++R FRE +P V + AAQA V+ S+E+P + NL+G N+LE CR GVE Sbjct: 61 DIADREAMQRVFREHQPQRVVNLAAQAGVRYSLENPAAYIDTNLVGFGNILEGCRHNGVE 120 Query: 111 KLVFASTGGAIYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRY 170 LV+AS+ ++YG E + P S YAASK A E Y Y L LR+ Sbjct: 121 HLVYASSS-SVYGANEEMPFSVHHNVDHPLSLYAASKKANELMAHTYSHLYQLPTTGLRF 179 Query: 171 GNVYGPRQDPHGEAGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGDVAEAHALA 230 VYGP P + +F ++L G P+ ++ G+ RD+ Y+ D+ E Sbjct: 180 FTVYGPWGRPDM---ALFMFTRKILAGEPIDVF---NYGNHR--RDFTYIDDIVEGVIRT 231 Query: 231 L--------------------FSLEGIYNVGTGEGHTTREVLEAVAEAAGKAPQVQPAPP 270 L + +YN+G +E + E GK + P Sbjct: 232 LDRPAQPNPEWSGAQPDSATSAAPYRLYNIGAHRPVELMHYIEVLEENLGKKAEKNLLPL 291 Query: 271 RPGDLERSVLSPLKLMAH-GWRPKVGFQEGIRLTVDHFR 308 +PGD+ + L A G+ P +EG+ V +R Sbjct: 292 QPGDVPDTYADVEDLRADTGYEPTTSVEEGVASFVAWYR 330 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: 286 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 311 Length of database: 335 Length adjustment: 28 Effective length of query: 283 Effective length of database: 307 Effective search space: 86881 Effective search space used: 86881 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