Align galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (characterized)
to candidate WP_072908934.1 BUB13_RS11630 galactose-1-phosphate uridylyltransferase
Query= metacyc::MONOMER-15710 (344 letters) >NCBI__GCF_900142125.1:WP_072908934.1 Length = 348 Score = 224 bits (572), Expect = 2e-63 Identities = 126/352 (35%), Positives = 190/352 (53%), Gaps = 28/352 (7%) Query: 11 ELRKDSVTNRWVIFSPARAKRPSDFKSKSPAPSSTDSPQTCPFCIGQEHHCAPEIFRFPP 70 ELR D + N W I + R +RP DF K CPFC G E PEI+ + P Sbjct: 3 ELRWDPLKNNWTIMTKGRGRRPQDFLQKREQVKMA----ACPFCNGNETKTPPEIYAYRP 58 Query: 71 QN-----PDWKVRVIQNLYPALSRDKDLDSSTSLSSGSLLWGCLLDGYGFHDVIIESPVH 125 P W+VRVI N +PAL + +LD+ + +G G H+VIIE P H Sbjct: 59 DGSRANQPGWQVRVIPNKFPALGIEGELDNRAEGLYDRM------NGIGAHEVIIEHPDH 112 Query: 126 SVHLSDLTPEDVAQVLFAYKKRILQLASDDSIKYVQVFKNHGASAGASMTHPHSQMVGLP 185 ++DLT +++A+VL AY+ R+L L D +Y+ VFKN G A A++ H HSQ++ +P Sbjct: 113 DKSMADLTTDELAEVLKAYRARMLDLHRDGRFRYIFVFKNFGIEAAANVPHSHSQLIAVP 172 Query: 186 VIPPSVTTRLDSMKQYFNETGKCSICHV-----PTKDLLVDESVHFISVVPYAASFPFEL 240 ++PP + T L+S +++F +C IC + TK +V + +FIS PYA+ FPFEL Sbjct: 173 LVPPLIATELESCREHFARKERCLICDLIRQERETKTRVVRDDGNFISYAPYASKFPFEL 232 Query: 241 WIVPRDHVSHFHELDQEKAVDLGGLLKVTLIKMSLQLNKPPFNFMIHTSP---LQASDSD 297 I P H F ++ + L L +L ++ L PP++F++H +P L+ D Sbjct: 233 MIAPLQHSHDFTLCTDQQLLLLADTLGDSLRRLRSILRDPPYSFILHNAPPLHLRRGRPD 292 Query: 298 LAYS-----HWFFQIVPHLSGVGGFELGTGCYINPVFPEDAAKVMREVNISI 344 S HW +I P L+ V GFE G+G +NP PE+AA+ +R+ + ++ Sbjct: 293 YWGSLPVDYHWHIEIAPKLTNVAGFEWGSGFQMNPTPPEEAAEFLRQADPTV 344 Lambda K H 0.320 0.135 0.421 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: 317 Number of extensions: 17 Number of successful extensions: 6 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: 344 Length of database: 348 Length adjustment: 29 Effective length of query: 315 Effective length of database: 319 Effective search space: 100485 Effective search space used: 100485 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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