Align galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (characterized)
to candidate WP_011937787.1 GURA_RS04350 galactose-1-phosphate uridylyltransferase
Query= metacyc::MONOMER-15710 (344 letters) >NCBI__GCF_000016745.1:WP_011937787.1 Length = 341 Score = 239 bits (611), Expect = 6e-68 Identities = 132/349 (37%), Positives = 189/349 (54%), Gaps = 27/349 (7%) Query: 11 ELRKDSVTNRWVIFSPARAKRPSDFKSKSPAPSSTDSPQTCPFCIGQEHHCAPEIFRF-- 68 ELR D + WVI + R +RP DF+ + T +CPFC G E EIF Sbjct: 3 ELRWDPLKLHWVIIATERGRRPRDFQVEQQEAEMT----SCPFCYGNEDKTPAEIFAIRP 58 Query: 69 --PPQNPDWKVRVIQNLYPALSRDKDLDSSTSLSSGSLLWGCLLDGYGFHDVIIESPVHS 126 P +P+WKVRVI N YP L + ++ S G L+ ++ G G H+VIIE+P H Sbjct: 59 SGPANSPNWKVRVIPNKYPVLRIEGEIKSK-----GYGLYD-VMTGIGAHEVIIETPQHE 112 Query: 127 VHLSDLTPEDVAQVLFAYKKRILQLASDDSIKYVQVFKNHGASAGASMTHPHSQMVGLPV 186 L+DL+ +V VL AY+ R L L D +Y+ +FKNHG AGA++ H HSQ++ +P+ Sbjct: 113 KGLADLSVAEVTDVLIAYRARFLDLRRDSRFRYMVLFKNHGVRAGATLAHSHSQLIAVPL 172 Query: 187 IPPSVTTRLDSMKQYFNETGKCSIC-----HVPTKDLLVDESVHFISVVPYAASFPFELW 241 PP T L + ++ +C C + D +V E +F+SV PYA+ FPFEL Sbjct: 173 TPPVAATELKICRDFYANKERCIFCDLIDFELTCGDRVVKEFPNFVSVTPYASCFPFELR 232 Query: 242 IVPRDHVSHFHELDQEKAVDLGGLLKVTLIKMSLQLNKPPFNFMIHTSPLQASD------ 295 + P+ H F +D + +L +K L+++ L PP+NF++H++P Q Sbjct: 233 LYPKKHSHDFAMMDDGQLAELAVAMKDMLLRLKTVLKDPPYNFILHSAPPQQQRLGKPEY 292 Query: 296 -SDLAYS-HWFFQIVPHLSGVGGFELGTGCYINPVFPEDAAKVMREVNI 342 L Y HW ++VP L+ + GFE GTG YINP PEDAA +RE I Sbjct: 293 WGSLEYDYHWHIELVPRLTQIAGFEWGTGFYINPTSPEDAALFLREAEI 341 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: 336 Number of extensions: 19 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: 341 Length adjustment: 29 Effective length of query: 315 Effective length of database: 312 Effective search space: 98280 Effective search space used: 98280 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