Align Galactose-1-phosphate uridylyltransferase; Gal-1-P uridylyltransferase; EC 2.7.7.12; UDP-glucose--hexose-1-phosphate uridylyltransferase (uncharacterized)
to candidate WP_005459317.1 SACCYDRAFT_RS21270 galactose-1-phosphate uridylyltransferase
Query= curated2:P13212 (354 letters) >NCBI__GCF_000244975.1:WP_005459317.1 Length = 351 Score = 284 bits (727), Expect = 2e-81 Identities = 172/352 (48%), Positives = 200/352 (56%), Gaps = 20/352 (5%) Query: 1 MKKTSTRLADGRELVYYDLRD-DTVRDAVDRRPLERTVTTSEVRRDPLLGDSAPSRLAPQ 59 M KT RL+DGR + YYD + R AVD R L SEVRRDPL G+ Q Sbjct: 1 MNKTVRRLSDGRRITYYDEGERPRPRTAVDTRELPEVTAVSEVRRDPLTGELVVIAAHRQ 60 Query: 60 GRTYHPPADQCPLCPSGRGTAERDPA--YDVVVFENRFPSLAGDSGRCEVVCFTSDHDAS 117 RTY P D CPLCPS G+ P YDVVVF+NRFP+ +G +G +VVCFTSDH +S Sbjct: 61 TRTYKPAVDLCPLCPSVPGSPTEVPEADYDVVVFDNRFPAFSGGTGHADVVCFTSDHHSS 120 Query: 118 FADLSEEQARLVVDAWTDRTSELSHLPSVEQVFCFENRGAEIGVTLGHPHGQIYAYPFTT 177 FA+L + R V++A DRT+ELS VE VF FENRG EIGVTL HPHGQIYAYPF Sbjct: 121 FAELEPRRVRTVLEALADRTAELSVQEGVELVFPFENRGEEIGVTLHHPHGQIYAYPFVP 180 Query: 178 PRTALMLRSLAAHKDATGGGNLFDSVLEEELAGERVVLEGEHWAAFVAYGAHWPYEVHLY 237 PRT ML + AH D G L D + E R+V EG HW AFV A WP +V + Sbjct: 181 PRTERMLAAARAHHDERGTPLLGDVLASERADRRRIVAEGRHWTAFVPPAAKWPVQVLVV 240 Query: 238 PKRRVPDLLGLDEAARTEFPKVYLELLRRFDRIFGEGEPPTPYIAAWHQAPFGQLEFEGV 297 P R+VPDL+ L A R +F VYL LLR D ++ P PY+A WHQAP Sbjct: 241 PHRQVPDLVELTTAEREDFAAVYLSLLRGCDALY---HRPLPYVAGWHQAPVHH------ 291 Query: 298 TRDDFALHLN-FSLPPYVRQAEVPRGLRIRHE---RVHQRDVPPERAAERLR 345 RD LHL FS VR+AE E V D PER AERLR Sbjct: 292 DRDLAWLHLELFS----VRRAEDKLKYLAGSESGMAVWINDSTPERIAERLR 339 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: 476 Number of extensions: 29 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: 354 Length of database: 351 Length adjustment: 29 Effective length of query: 325 Effective length of database: 322 Effective search space: 104650 Effective search space used: 104650 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