Align Galactose-1-phosphate uridylyltransferase; Gal-1-P uridylyltransferase; EC 2.7.7.12; UDP-glucose--hexose-1-phosphate uridylyltransferase (uncharacterized)
to candidate WP_012407023.1 NPUN_RS01080 galactose-1-phosphate uridylyltransferase
Query= curated2:O33836 (318 letters) >NCBI__GCF_000020025.1:WP_012407023.1 Length = 366 Score = 224 bits (572), Expect = 2e-63 Identities = 125/326 (38%), Positives = 191/326 (58%), Gaps = 18/326 (5%) Query: 4 LRYNPLTDEWVIVSAATQKRPVQPSKTECPICVGG-----LELPE-EYDLVTFENRYPSL 57 LR++PL EWV ++ Q R P P+ ELP+ +YD+ F+NR+PS+ Sbjct: 42 LRWHPLRGEWVAYASHRQGRTFMPPPEYNPLAPTTNPEFPTELPQGKYDVAVFDNRFPSM 101 Query: 58 KK--DPPPVNWKEKGPFRKEESRGVCEVVVYTSDHNTALPGMPLKQIEKLVEMWVDRTRD 115 + PP E P + G CEVVV+T D +L + L ++ L+E+W DRTR+ Sbjct: 102 TPTANNPPDTIVETLP-----ANGACEVVVFTQDARASLSSLELDHLDLLLEVWGDRTRE 156 Query: 116 LSQHDFVKYIFIFENRGKEVGASLPHPHGQIYAFPFLPKRIEVKIGAMRKWYEEKRKCPI 175 L + ++Y+ FEN+G EVG +L HPHGQIYA+PF+P + +++YE+ R+ + Sbjct: 157 LGLNPQIQYVLPFENKGVEVGVTLHHPHGQIYAYPFIPPVPARMLSMQQEYYEKHRRGLL 216 Query: 176 CEVLESE--GEERKVYETEHFLALVPFYARFPYEVHIYPKRHVSTLLEFSKEEKKEFAKV 233 ++++ E R +Y+ E+ +A VP AR+PYEV I PK VST ++ + E++ AK Sbjct: 217 QDLIQKEIADNRRIIYQDEYAIAFVPVCARYPYEVWIAPKEPVSTFMDLTPEQRWGLAKA 276 Query: 234 LKVVTAKYDKLFDQEFPYMMMFFQAPFNEEDVSH-FFHFHVEFNPPKRDRDKLKWMASVE 292 LK VT KYD L+++ FPY+M +FQAP + ++H H H EF PP R ++LK++A E Sbjct: 277 LKTVTLKYDGLWNRPFPYLMAWFQAP--TDGLAHPEAHLHAEFFPPYRTSERLKYLAGTE 334 Query: 293 TGTWAFINPVVPEEAARQLRETEVEI 318 F N +PEE A++L+ V I Sbjct: 335 LAAGMFANDALPEEKAKELQAVVVNI 360 Lambda K H 0.320 0.138 0.429 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: 436 Number of extensions: 26 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: 318 Length of database: 366 Length adjustment: 29 Effective length of query: 289 Effective length of database: 337 Effective search space: 97393 Effective search space used: 97393 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