Align Galactose-1-phosphate uridylyltransferase; Gal-1-P uridylyltransferase; EC 2.7.7.12; UDP-glucose--hexose-1-phosphate uridylyltransferase (uncharacterized)
to candidate WP_083790008.1 TCUR_RS15505 galactose-1-phosphate uridylyltransferase
Query= curated2:P13212 (354 letters) >NCBI__GCF_000024385.1:WP_083790008.1 Length = 426 Score = 328 bits (841), Expect = 2e-94 Identities = 180/354 (50%), Positives = 216/354 (61%), Gaps = 15/354 (4%) Query: 1 MKKTSTRLADGRELVYYDLRDDTVRDAVDRRPLERTVTTSEVRRDPLLGDSAPSRLAPQG 60 +++T TRLADGREL+Y+D + RDAVD RP SE+R DPLL + QG Sbjct: 83 VRRTVTRLADGRELIYFDRCERPGRDAVDTRPAGGPPPVSELRYDPLLEEWVTIAAHRQG 142 Query: 61 RTYHPPADQCPLCPSGRGTAERDPA--YDVVVFENRFPSL--AGDSGRCEVVCFTSDHDA 116 RT+ P D CPLCPS G PA Y+VVV ENRFP+ GRCEVVCF+ DH A Sbjct: 143 RTFLPGEDACPLCPSAPGRPTEIPAADYEVVVLENRFPTFQPGATGGRCEVVCFSPDHHA 202 Query: 117 SFADLSEEQARLVVDAWTDRTSELSHLPSVEQVFCFENRGAEIGVTLGHPHGQIYAYPFT 176 SFADL +Q R V++AW DRT+ELS LP VEQVFCFENRG EIGVTL HPHGQIYAYPF Sbjct: 203 SFADLPPQQVRTVIEAWADRTAELSALPGVEQVFCFENRGEEIGVTLRHPHGQIYAYPFV 262 Query: 177 TPRTALMLRSLAAHKDATGGGNLFDSVLEEELAGERVVLEGEHWAAFVAYGAHWPYEVHL 236 PRT ML ++ H + TGG + + E AG RVV E W AFV + A WP+EVHL Sbjct: 263 PPRTRQMLAAVRRHAERTGGDLFAELLAAEREAGTRVVAANELWTAFVPHAARWPFEVHL 322 Query: 237 YPKRRVPDLLGLDEAARTEFPKVYLELLRRFDRIFGEGEPPTPYIAAWHQAPF-GQLEFE 295 YP RRVPD+ L+EA R F +YL++L RFDR+FG P PY+AAWHQAP + E Sbjct: 323 YPHRRVPDICALEEAERDAFAALYLDVLGRFDRLFGR---PMPYVAAWHQAPVRHERELA 379 Query: 296 GVTRDDFALHLNFSLPPYVRQAEVPRGLRIRHERVHQRDVPPERAAERLREVAD 349 + F++ Y+ +E G I DV PE AA LR D Sbjct: 380 YLHLRLFSIRRAADRLKYLAGSESAMGAFI-------NDVRPEEAARLLRAAGD 426 Lambda K H 0.320 0.138 0.425 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: 564 Number of extensions: 26 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: 354 Length of database: 426 Length adjustment: 30 Effective length of query: 324 Effective length of database: 396 Effective search space: 128304 Effective search space used: 128304 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: 50 (23.9 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