Align UTP--hexose-1-phosphate uridylyltransferase (EC 2.7.7.10) (characterized)
to candidate WP_101446337.1 BD749_RS16425 UDP-glucose--hexose-1-phosphate uridylyltransferase
Query= reanno::Cola:Echvi_0695 (347 letters) >NCBI__GCF_002846395.1:WP_101446337.1 Length = 344 Score = 457 bits (1175), Expect = e-133 Identities = 201/338 (59%), Positives = 253/338 (74%) Query: 1 MTDFNFEDHSHRRYNPFTGDWLQVSPHRGKRPWQGQEEDTAEAQKPAYDEKCYLCPGNTR 60 M F+ +H HRR+NP TG+W+ VSPHR KRPWQGQ+E+ +PAYD CYLCPGNTR Sbjct: 1 MATFDLAEHPHRRFNPLTGEWVLVSPHRSKRPWQGQQEEQPHDSRPAYDPTCYLCPGNTR 60 Query: 61 INGEKNPDYTGAYVFQNDFGALTSDIPQGEMSEGEFFRAKSERGICKVICFSPRHDLTIP 120 +GE+NP Y +VF NDFGAL IP+G G+ RA+SERGIC+VICFSPRHDLT+ Sbjct: 61 ASGEQNPAYATTFVFNNDFGALQDGIPEGAYVAGDLIRAESERGICRVICFSPRHDLTLA 120 Query: 121 ELDVQAITKVVELWKKEYQELGGKDFINHVQIFENKGSVMGCSNPHPHGQIWAQESIPVE 180 E+ I KVV+LW+KEY EL D+IN+VQIFENKGS+MGCSNPHPHGQ+WAQ ++PVE Sbjct: 121 EMSTADIRKVVDLWQKEYAELSSLDYINYVQIFENKGSIMGCSNPHPHGQVWAQSTVPVE 180 Query: 181 PAKKQVKFGEYYQKYGRSMVLDYVYEELKKGERILFENDYFVGLVPFWAVWPFEAMIAPK 240 PAK+ + +Y+ + RS++ DY+ ELK ER++ EN++FV LVPFWAVWPFE ++ K Sbjct: 181 PAKETTQQAQYFAHHSRSLLADYLQLELKLQERVVVENEHFVVLVPFWAVWPFETIVISK 240 Query: 241 THIASLSEMDAAQMEALADAYRQLAIMYDNVFKVSFPYSAGIHQAPTDGQNHPEWDLHMV 300 H + +M A+ + + + L + YD VF VSFPYS GIHQ+PTDGQ HP W HM Sbjct: 241 RHFQHIGQMTDAEKDGFSKVLQALTVTYDRVFGVSFPYSCGIHQSPTDGQEHPGWHFHMH 300 Query: 301 FYPPLLRSATVKKFMVGYEMLANPQRDITAESAVKILK 338 FYPPLLRSATVKKFMVGYEM+ NPQRDIT E+A ++L+ Sbjct: 301 FYPPLLRSATVKKFMVGYEMMGNPQRDITPEAAARVLR 338 Lambda K H 0.319 0.136 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: 452 Number of extensions: 10 Number of successful extensions: 1 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: 347 Length of database: 344 Length adjustment: 29 Effective length of query: 318 Effective length of database: 315 Effective search space: 100170 Effective search space used: 100170 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 (21.7 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