Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate CCNA_01204 CCNA_01204 dTDP-glucose 4,6-dehydratase
Query= SwissProt::A0R5C5 (313 letters) >FitnessBrowser__Caulo:CCNA_01204 Length = 315 Score = 125 bits (313), Expect = 2e-33 Identities = 94/315 (29%), Positives = 144/315 (45%), Gaps = 19/315 (6%) Query: 2 RTLVTGAAGFIGSTLVDRLLADGHGVVGLDDLSSGRAENLHSAENSDKFEFVKADIVDAD 61 R LVTG AGF+GS L DRLL G V+ +D+ +G N+ ++ +FE ++ D+ Sbjct: 5 RILVTGGAGFVGSHLCDRLLETGAEVLCVDNYYTGSRLNVAQNLSNPRFELLRHDVT--- 61 Query: 62 LTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARLAGVRKVVHTSS 121 + + + I++LA S DP +V G + + A+ V+ + +S Sbjct: 62 ---MPLYVEVDQIYNLACPASPVHYQFDPVQTTKTSVHGAINMLGLAK--RVKAKILQAS 116 Query: 122 GGSVYGTPPAYPTSEDM-----PVNPASPYAAGKVAGEVYLNMYRNLYDLDCSHIAPANV 176 VYG P +P E P+ S Y GK E Y + L N Sbjct: 117 TSEVYGDPTIHPQVESYWGNVNPIGLRSCYDEGKRCAETLFFDYWRQHKLRIKVARIFNT 176 Query: 177 YGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVR---AGGPAG 233 YGPR P+ + VV+ F L G ++GDG+ TR + +VDD+VD +R G Sbjct: 177 YGPRMHPN-DGRVVSNFIVQALKGEDITLYGDGNQTRSFCYVDDLVDGLIRLMKTGDEVT 235 Query: 234 GGQRFNVGTGVETSTRELHTAIAGAVGAPDEPEFHPPRLGDLRRSRLDNTRAREVLGWQP 293 G N+G VE + ++L + G+ P D R+ + D T A++VL W P Sbjct: 236 G--PINLGNPVEFTMKQLAELVLELTGSQSTIVHRPLPSDDPRQRQPDITLAKQVLDWTP 293 Query: 294 QVALAEGIAKTVEFF 308 L G+ KT+E+F Sbjct: 294 TAPLKVGLMKTIEYF 308 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: 258 Number of extensions: 13 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: 315 Length adjustment: 27 Effective length of query: 286 Effective length of database: 288 Effective search space: 82368 Effective search space used: 82368 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 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