Align Galactose-1-phosphate uridylyltransferase; Gal-1-P uridylyltransferase; EC 2.7.7.12; UDP-glucose--hexose-1-phosphate uridylyltransferase (uncharacterized)
to candidate WP_076476050.1 BW971_RS02200 galactose-1-phosphate uridylyltransferase
Query= curated2:P13212 (354 letters) >NCBI__GCF_900156495.1:WP_076476050.1 Length = 365 Score = 276 bits (705), Expect = 8e-79 Identities = 164/364 (45%), Positives = 200/364 (54%), Gaps = 36/364 (9%) Query: 8 LADGRELVYYDLRDDTVRDAVDRRPLE-RTVTTSEVRRDPLLGDSAPSRLAPQGRTYHPP 66 LADGR+ +++ L VDRRPL RT SE+R D G Q RTY PP Sbjct: 12 LADGRQELFFSLPGHVPEPVVDRRPLPPRTDQQSEIRYDRQTGQWVIVAALRQDRTYKPP 71 Query: 67 ADQCPLCPSGRGTAERDPA--YDVVVFENRFPSLAGDS--------------------GR 104 ADQCPLCP GT PA YDVVVFENRFPSL+G + GR Sbjct: 72 ADQCPLCPGPTGTLSEIPAASYDVVVFENRFPSLSGAATADVALPSLDGTDFVTAPGHGR 131 Query: 105 CEVVCFTSDHDASFADLSEEQARLVVDAWTDRTSELSHLPSVEQVFCFENRGAEIGVTLG 164 CEV+CF+SDH ASFA L QARLVVDAW RT++L P +EQVFCFENRG EIGVTL Sbjct: 132 CEVICFSSDHRASFAQLPPAQARLVVDAWRHRTADLMSRPGIEQVFCFENRGEEIGVTLT 191 Query: 165 HPHGQIYAYPFTTPRTALMLRSLAAHKDATGGGNLFDSVLEEELAGERVVLEGEHWAAFV 224 HPHGQIY YP+ TPRTA ML+ A+ + G D + +E + G RV+ EH+ AFV Sbjct: 192 HPHGQIYGYPYLTPRTAQMLQQADAYAERHGRNMFTDLLADEVVDGSRVIARTEHFTAFV 251 Query: 225 AYGAHWPYEVHLYPKRRVPDLLGLDEAARTEFPKVYLELLRRFDRIFGEGEPPTPYIAAW 284 + A WP EVH+YP R +L LD ++YL++L RFDR++ P PYI+A Sbjct: 252 PFAARWPVEVHIYPNRFAHNLTELDSIELDGLAEIYLDVLGRFDRLY---PTPLPYISAL 308 Query: 285 HQAPFGQLEFEGVTRDDFALHLNFSLPPYVRQAEVPRGLRIRHERVHQ--RDVPPERAAE 342 HQ + EG + + L R A + L + DV PE A Sbjct: 309 HQYRDVPTQREG--------YFHIELMSVRRSANKLKFLAGSESAMDAFISDVTPESVAL 360 Query: 343 RLRE 346 RLRE Sbjct: 361 RLRE 364 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: 442 Number of extensions: 23 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: 365 Length adjustment: 29 Effective length of query: 325 Effective length of database: 336 Effective search space: 109200 Effective search space used: 109200 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