Align UTP--glucose-1-phosphate uridylyltransferase; Alpha-D-glucosyl-1-phosphate uridylyltransferase; General stress protein 33; GSP33; UDP-glucose pyrophosphorylase; UDPGP; Uridine diphosphoglucose pyrophosphorylase; EC 2.7.7.9 (characterized)
to candidate WP_028586084.1 G494_RS0120995 UTP--glucose-1-phosphate uridylyltransferase
Query= SwissProt::Q05852 (292 letters) >NCBI__GCF_000429965.1:WP_028586084.1 Length = 295 Score = 313 bits (802), Expect = 3e-90 Identities = 153/287 (53%), Positives = 207/287 (72%), Gaps = 1/287 (0%) Query: 3 KVRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKSKR 62 +++KA+ P AGLGTRFLPATKAMPKEMLP+VDKP IQY +EEA+ AGIE II VTG K Sbjct: 2 RIKKAVFPVAGLGTRFLPATKAMPKEMLPVVDKPIIQYAVEEALAAGIEQIIFVTGSGKS 61 Query: 63 AIEDHFDYSPELERNLEEKGKTELLEKVKK-ASNLADIHYIRQKEPKGLGHAVWCARNFI 121 A+EDHFD + +LE L+E+GKT+LL V+ A + ++ Y RQ EP GLGHA+WCAR+ + Sbjct: 62 ALEDHFDTNLQLENTLKERGKTDLLRTVESVAPHASNFVYTRQSEPLGLGHAIWCARDIV 121 Query: 122 GDEPFAVLLGDDIVQAETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPLTSEGR 181 GDEPFAVLL DD++Q+E P L Q+++E+++ +S++ + V +EET RYGII+ Sbjct: 122 GDEPFAVLLADDLIQSEVPVLHQMINEFDRLRASMMAIIVVEQEETSRYGIIEAEQGFNG 181 Query: 182 RYQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQKLNEIQ 241 QV++ VEKP APSNLA++GRY+ TP IF +L Q GAG EIQLTDA+ L Q Sbjct: 182 TVQVRSMVEKPAPEEAPSNLAVIGRYILTPRIFDHLGRQDRGAGNEIQLTDAMSSLLTEQ 241 Query: 242 RVFAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRDQLVPFMEGLLN 288 +F Y F+G+R+D G+K GF + FA++ ELR QL+P + L++ Sbjct: 242 PIFGYKFKGRRFDCGDKAGFQMANIAFALERPELRKQLLPGLAKLVS 288 Lambda K H 0.317 0.138 0.389 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: 285 Number of extensions: 7 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: 292 Length of database: 295 Length adjustment: 26 Effective length of query: 266 Effective length of database: 269 Effective search space: 71554 Effective search space used: 71554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
Align candidate WP_028586084.1 G494_RS0120995 (UTP--glucose-1-phosphate uridylyltransferase)
to HMM TIGR01099 (galU: UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01099.hmm # target sequence database: /tmp/gapView.16287.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01099 [M=261] Accession: TIGR01099 Description: galU: UTP--glucose-1-phosphate uridylyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-117 378.4 0.0 1.2e-117 378.2 0.0 1.0 1 lcl|NCBI__GCF_000429965.1:WP_028586084.1 G494_RS0120995 UTP--glucose-1-ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429965.1:WP_028586084.1 G494_RS0120995 UTP--glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.2 0.0 1.2e-117 1.2e-117 1 259 [. 3 262 .. 3 264 .. 0.99 Alignments for each domain: == domain 1 score: 378.2 bits; conditional E-value: 1.2e-117 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsy 69 i+kav+P+aGlGtr+LPatka+Pkemlp+vdkP+iqy+veea++aGie+i++vtg++k a+edhfDt++ lcl|NCBI__GCF_000429965.1:WP_028586084.1 3 IKKAVFPVAGLGTRFLPATKAMPKEMLPVVDKPIIQYAVEEALAAGIEQIIFVTGSGKSALEDHFDTNL 71 89******************************************************************* PP TIGR01099 70 eleaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee 137 +le++l++++k++ll++v+++a++ +++y+rq e GLGha+++a+++vgdepfavll+Ddl+++e + lcl|NCBI__GCF_000429965.1:WP_028586084.1 72 QLENTLKERGKTDLLRTVESVAPHaSNFVYTRQSEPLGLGHAIWCARDIVGDEPFAVLLADDLIQSEVP 140 **********************99789****************************************** PP TIGR01099 138 alkqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvl 206 +l+q+i+ +++ +as++a+ v++ee+s+YG+i++e+ + +++v+++vekP peeapsnla++GrY+l lcl|NCBI__GCF_000429965.1:WP_028586084.1 141 VLHQMINEFDRLRASMMAIIVVEQEETSRYGIIEAEQGFNGTVQVRSMVEKPAPEEAPSNLAVIGRYIL 209 ********************************************************************* PP TIGR01099 207 tpeifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgyl 259 tp+if++l ++++G+g+eiqltDa++ ll+++ ++++k+kg+r+D+Gdk g+ lcl|NCBI__GCF_000429965.1:WP_028586084.1 210 TPRIFDHLGRQDRGAGNEIQLTDAMSSLLTEQPIFGYKFKGRRFDCGDKAGFQ 262 **************************************************995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (295 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.52 // [ok]
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