Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate GFF2758 PS417_14065 UTP--glucose-1-phosphate uridylyltransferase
Query= BRENDA::O25363 (273 letters) >FitnessBrowser__WCS417:GFF2758 Length = 279 Score = 371 bits (953), Expect = e-108 Identities = 178/270 (65%), Positives = 221/270 (81%) Query: 1 MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKR 60 MIKKCLFPAAGYGTRFLP TK +PKEMLP+V+KPLIQY VEEA++AG ++IVTGR KR Sbjct: 1 MIKKCLFPAAGYGTRFLPATKAMPKEMLPVVNKPLIQYGVEEALDAGLNEISIVTGRGKR 60 Query: 61 SLEDYFDTSYEIEHQIQGTNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIG 120 +LED+FD SYE+E+QI+GT+KE L IR ++++C FSY RQ QMKGLGHAILTG LIG Sbjct: 61 ALEDHFDISYELENQIKGTDKEKYLVGIRKLLDECSFSYTRQTQMKGLGHAILTGRPLIG 120 Query: 121 NEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEE 180 +EPFAV+LADDLC++ + VL QM LYQKY+C+IVA+ EV E +KYGVI G+ + + Sbjct: 121 DEPFAVVLADDLCVNLEGDGVLTQMVKLYQKYRCTIVAVMEVNPTETNKYGVIAGDDIGD 180 Query: 181 GVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKR 240 G+ ++DMVEKP EDAPSNLA+IGRYILTPDIF+++ ET+PGK EIQITDAL QAK Sbjct: 181 GLIRVRDMVEKPAPEDAPSNLAIIGRYILTPDIFKLIEETEPGKGGEIQITDALLKQAKD 240 Query: 241 KRIIAYQFKGKRYDCGSVEGYIEASNAYYK 270 +IAY+FKG+R+DCG EGYIEA+N Y+ Sbjct: 241 GCVIAYKFKGQRFDCGGAEGYIEATNFCYE 270 Lambda K H 0.318 0.136 0.391 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: 310 Number of extensions: 8 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: 273 Length of database: 279 Length adjustment: 25 Effective length of query: 248 Effective length of database: 254 Effective search space: 62992 Effective search space used: 62992 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate GFF2758 PS417_14065 (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.23762.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-123 395.6 0.0 6.2e-123 395.4 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF2758 PS417_14065 UTP--glucose-1-phosp Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF2758 PS417_14065 UTP--glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 395.4 0.0 6.2e-123 6.2e-123 1 261 [] 2 264 .. 2 264 .. 0.99 Alignments for each domain: == domain 1 score: 395.4 bits; conditional E-value: 6.2e-123 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleakl 75 i+k+++PaaG+Gtr+LPatka+Pkemlp+v+kPliqy veea++aG++ei +vtgr+kra+edhfD+syele+++ lcl|FitnessBrowser__WCS417:GFF2758 2 IKKCLFPAAGYGTRFLPATKAMPKEMLPVVNKPLIQYGVEEALDAGLNEISIVTGRGKRALEDHFDISYELENQI 76 89************************************************************************* PP TIGR01099 76 ekknkeellkevrkiaelatilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee..alkqlielyek 148 + ++ke++l +rk+ +++++ y+rq ++kGLGha+l++++l+gdepfav+l+Ddl+++ e +l q+++ly+k lcl|FitnessBrowser__WCS417:GFF2758 77 KGTDKEKYLVGIRKLLDECSFSYTRQTQMKGLGHAILTGRPLIGDEPFAVVLADDLCVNLEGdgVLTQMVKLYQK 151 **********************************************************998888*********** PP TIGR01099 149 tgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkgg 223 ++++i+av+ev+ +e++kYGvi+g+ + + l++v+d+vekP pe+apsnlai+GrY+ltp+if+l+eet++Gkgg lcl|FitnessBrowser__WCS417:GFF2758 152 YRCTIVAVMEVNPTETNKYGVIAGDDIGDGLIRVRDMVEKPAPEDAPSNLAIIGRYILTPDIFKLIEETEPGKGG 226 *************************************************************************** PP TIGR01099 224 eiqltDalrlllekeevlavklkgkryDvGdklgylka 261 eiq+tDal +++++ +v+a+k+kg+r+D+G ++gy++a lcl|FitnessBrowser__WCS417:GFF2758 227 EIQITDALLKQAKDGCVIAYKFKGQRFDCGGAEGYIEA 264 ************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (279 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: 9.06 // [ok]
This GapMind analysis is from Sep 17 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