Align UDP-glucose-hexose-1-phosphate uridylyltransferase (EC 2.7.7.12) (characterized)
to candidate WP_011444204.1 SARO_RS02705 UDP-glucose--hexose-1-phosphate uridylyltransferase
Query= BRENDA::P09148 (348 letters) >NCBI__GCF_000013325.1:WP_011444204.1 Length = 341 Score = 420 bits (1080), Expect = e-122 Identities = 197/338 (58%), Positives = 241/338 (71%), Gaps = 1/338 (0%) Query: 1 MTQFNPVDHPHRRYNPLTGQWILVSPHRAKRPWQGAQETPAKQVLPAHDPDCFLCAGNVR 60 MT+F+ DHPHRR N LTG+W+LVSPHRAKRPWQG PA P+HDP C+LC GN R Sbjct: 1 MTRFSTDDHPHRRQNLLTGKWVLVSPHRAKRPWQGETGDPAPTGGPSHDPGCYLCPGNAR 60 Query: 61 VTGDKNPDYTGTYVFTNDFAALMSDTPDAPESHDPLMRCQSARGTSRVICFSPDHSKTLP 120 +G++NPDY G + F NDF ALM D P APE DP+ R ARGT+RVIC+SPDHSKT+P Sbjct: 61 TSGERNPDYPGAFAFDNDFPALMPDNP-APEGGDPVFRVAEARGTARVICYSPDHSKTMP 119 Query: 121 ELSVAALTEIVKTWQEQTAELGKTYPWVQVFENKGAAMGCSNPHPHGQIWANSFLPNEAE 180 ++ VAA+ +V W +++ LG + VQ+FENKGA MGCS+PHPHGQIWA+ F+P E Sbjct: 120 DMDVAAIRSLVNCWAQESETLGAHFANVQIFENKGAMMGCSSPHPHGQIWASDFIPTEVA 179 Query: 181 REDRLQKEYFAEQKSPMLVDYVQRELADGSRTVVETEHWLAVVPYWAAWPFETLLLPKAH 240 EDR Q + A + +L + +RELA G R V EHWLAVVP+WA WPFE LL+ + Sbjct: 180 DEDREQAAWHASRGRVLLDEVAERELASGERVVEANEHWLAVVPWWATWPFEILLVARDG 239 Query: 241 VLRITDLTDAQRSDLALALKKLTSRYDNLFQCSFPYSMGWHGAPFNGEENQHWQLHAHFY 300 V RI +L+DA R LA L+ +T RYD LF SFPYSMGWH P + W+LHAHF Sbjct: 240 VGRIEELSDASRDALASILRAVTRRYDALFNASFPYSMGWHQRPAGSSDPAAWRLHAHFN 299 Query: 301 PPLLRSATVRKFMVGYEMLAETQRDLTAEQAAERLRAV 338 PPLLRSATVRKFMVG+EM E+QRD+T E AA RLRA+ Sbjct: 300 PPLLRSATVRKFMVGFEMFGESQRDITPETAAARLRAL 337 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: 493 Number of extensions: 17 Number of successful extensions: 3 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: 341 Length adjustment: 29 Effective length of query: 319 Effective length of database: 312 Effective search space: 99528 Effective search space used: 99528 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