Align UDP-glucose-hexose-1-phosphate uridylyltransferase (EC 2.7.7.12) (characterized)
to candidate WP_015820454.1 TERTU_RS10215 UDP-glucose--hexose-1-phosphate uridylyltransferase
Query= BRENDA::P09148 (348 letters) >NCBI__GCF_000023025.1:WP_015820454.1 Length = 354 Score = 447 bits (1149), Expect = e-130 Identities = 203/341 (59%), Positives = 256/341 (75%), Gaps = 1/341 (0%) Query: 4 FNPVDHPHRRYNPLTGQWILVSPHRAKRPWQGAQETPAKQVLPAHDPDCFLCAGNVRVTG 63 F+P DHPHRR+N LTG+W+LVSPHRAKRPWQG ET P++DPDC+LC GN R+TG Sbjct: 5 FDPKDHPHRRFNALTGEWVLVSPHRAKRPWQGQSETLDVTERPSYDPDCYLCPGNKRITG 64 Query: 64 DKNPDYTGTYVFTNDFAALMSDTPDAPESHDPLMRCQSARGTSRVICFSPDHSKTLPELS 123 D+NP+Y T+VF+NDFAAL ++TP+ S D L R ++ +G +RVICFSPDHSKTLPEL Sbjct: 65 DENPNYLNTFVFSNDFAALQANTPNM-YSDDELFRLEAEQGEARVICFSPDHSKTLPELE 123 Query: 124 VAALTEIVKTWQEQTAELGKTYPWVQVFENKGAAMGCSNPHPHGQIWANSFLPNEAERED 183 + +T+IV+ W EQT EL Y +QVFENKG+ MGCS PHPHGQ+WA +P +E Sbjct: 124 LTQITKIVECWVEQTKELSGRYAHIQVFENKGSMMGCSMPHPHGQVWAQKNMPTLVAKEH 183 Query: 184 RLQKEYFAEQKSPMLVDYVQRELADGSRTVVETEHWLAVVPYWAAWPFETLLLPKAHVLR 243 Q YF +L+DY +REL DG R VV + W+ VVP+WAAWPFETL+LP+ V + Sbjct: 184 EHQGTYFENNNRALLLDYAERELKDGQRLVVSNDDWIVVVPWWAAWPFETLVLPRFSVQK 243 Query: 244 ITDLTDAQRSDLALALKKLTSRYDNLFQCSFPYSMGWHGAPFNGEENQHWQLHAHFYPPL 303 + DL +QR LA ++++ RYDNLF SFPYSMGWHGAP +GEE+ WQLH HF+PPL Sbjct: 244 MVDLNSSQRLSLADVVRQIAIRYDNLFNMSFPYSMGWHGAPIDGEEHSAWQLHGHFFPPL 303 Query: 304 LRSATVRKFMVGYEMLAETQRDLTAEQAAERLRAVSDIHFR 344 LRSATVRKFMVGYEMLAE+QRDLT EQAA++LR++ H++ Sbjct: 304 LRSATVRKFMVGYEMLAESQRDLTPEQAADKLRSLPASHYK 344 Lambda K H 0.319 0.133 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: 495 Number of extensions: 16 Number of successful extensions: 2 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: 348 Length of database: 354 Length adjustment: 29 Effective length of query: 319 Effective length of database: 325 Effective search space: 103675 Effective search space used: 103675 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