Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Synpcc7942_1149 Synpcc7942_1149 dTDP-glucose 46-dehydratase
Query= SwissProt::A0R5C5 (313 letters) >FitnessBrowser__SynE:Synpcc7942_1149 Length = 325 Score = 141 bits (355), Expect = 2e-38 Identities = 100/318 (31%), Positives = 153/318 (48%), Gaps = 15/318 (4%) Query: 1 MRTLVTGAAGFIGSTLVDRLLADGHGVVGLDDLSSGRAENLHSAENSDKFEFVKADIVDA 60 MR LVTG AGFIGS L+DRL++ GH V+ LD+ +GR N+ +FE ++ DI D Sbjct: 2 MRILVTGGAGFIGSHLIDRLMSAGHEVICLDNYFTGRKHNVAQWYGHPRFELIRHDITDP 61 Query: 61 DLTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARLAGVRKVVHTS 120 + + I+HLA S +P A + +GTV + A+ R ++ ++ Sbjct: 62 ------IRLEVDQIYHLACPASPVHYQYNPIKTAKTSFLGTVNMLGLAKRVKARLLMAST 115 Query: 121 SGGSVYGTPPAYPTSEDM-----PVNPASPYAAGKVAGEVYLNMYRNLYDLDCSHIAPAN 175 S VYG P +P +ED P+ S Y GK E Y ++L+ N Sbjct: 116 S--EVYGDPHVHPQTEDYWGNVNPIGIRSCYDEGKRVAETLCFDYHRQHNLEIRVARIFN 173 Query: 176 VYGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVRAGGPAGGG 235 YGPR + VV+ F L G+ ++G G TR + +V D+VD +R G Sbjct: 174 TYGPRM-LENDGRVVSNFIVQALQGQPLTVYGRGEQTRSFCYVSDLVDGLIRLMNGDHLG 232 Query: 236 QRFNVGTGVETSTRELHTAIAGAVGAPDEPEFHPPRLGDLRRSRLDNTRAREVLGWQPQV 295 N+G E + +L I + EF P D ++ R D +RA+ L WQP V Sbjct: 233 P-VNLGNPSEYTILQLAELIRDRIDPALPIEFRPLPQDDPQQRRPDISRAQAWLKWQPLV 291 Query: 296 ALAEGIAKTVEFFRNKSQ 313 ++ +G+ +T+ FR++ Q Sbjct: 292 SVQDGLDRTIADFRDRQQ 309 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: 253 Number of extensions: 14 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: 313 Length of database: 325 Length adjustment: 28 Effective length of query: 285 Effective length of database: 297 Effective search space: 84645 Effective search space used: 84645 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