Align galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (characterized)
to candidate WP_014450362.1 LFE_RS11335 galactose-1-phosphate uridylyltransferase
Query= metacyc::MONOMER-15710 (344 letters) >NCBI__GCF_000284315.1:WP_014450362.1 Length = 340 Score = 262 bits (670), Expect = 8e-75 Identities = 133/345 (38%), Positives = 204/345 (59%), Gaps = 22/345 (6%) Query: 10 PELRKDSVTNRWVIFSPARAKRPSDFKSKSPAPSSTDSPQTCPFCIGQEHHCAPEIFRFP 69 PELRKD + RWVI + +R RP D++++ Q+CP C GQE PE+ + Sbjct: 2 PELRKDPIIGRWVIIATSRGLRPKDYQAEKVRYLY----QSCPLCPGQEEKTPPEVLAYR 57 Query: 70 -----PQNPDWKVRVIQNLYPALSRDKDLDSSTSLSSGSLLWGCLLDGYGFHDVIIESPV 124 P P W +RV+ N +PAL + LD G L+ ++G G H+V+IE+P Sbjct: 58 QSGSLPNTPGWTLRVVPNKFPALEVEGTLDRE-----GVGLYD-RMNGIGAHEVVIETPE 111 Query: 125 HSVHLSDLTPEDVAQVLFAYKKRILQLASDDSIKYVQVFKNHGASAGASMTHPHSQMVGL 184 H LS T ++ +L+AY+ RIL L D +Y+ +FKN+G +AGAS+ H HSQ++ L Sbjct: 112 HKKALSKFTEKEFENLLWAYRDRILDLRKDTRFRYIMIFKNYGEAAGASLEHSHSQLIAL 171 Query: 185 PVIPPSVTTRLDSMKQYFNETGKCSICHVPTKDL-----LVDESVHFISVVPYAASFPFE 239 P+IP +V L K ++ E +C C + ++L +V E+ F+++ P+A FPFE Sbjct: 172 PIIPTAVVEELVGAKSHYEEKERCIFCDIIRQELSDGSRIVQENQEFLAITPFAPKFPFE 231 Query: 240 LWIVPRDHVSHFHELDQEKAVDLGGLLKVTLIKMSLQLNKPPFNFMIHTSPLQASDSDLA 299 +WI+P+ H S F + + + L + L ++++ L PP+NF++H+SPLQ D Sbjct: 232 VWILPKKHASSFDQGQKSQYEALSRIFLDVLRRLNVALKDPPYNFILHSSPLQERAED-- 289 Query: 300 YSHWFFQIVPHLSGVGGFELGTGCYINPVFPEDAAKVMREVNISI 344 Y HW F+I+P L+ V GFE GTG YINP PEDAA+ +RE++++I Sbjct: 290 YYHWHFEIMPTLTRVAGFEWGTGFYINPTPPEDAARFLREIDLTI 334 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: 329 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: 340 Length adjustment: 29 Effective length of query: 315 Effective length of database: 311 Effective search space: 97965 Effective search space used: 97965 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