Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate GFF1978 HP15_1935 UTP-glucose-1-phosphate uridylyltransferase
Query= BRENDA::O25363 (273 letters) >FitnessBrowser__Marino:GFF1978 Length = 278 Score = 356 bits (914), Expect = e-103 Identities = 171/271 (63%), Positives = 211/271 (77%), Gaps = 1/271 (0%) Query: 1 MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKR 60 MIKKCLFP AGYGTRFLP TK +PKE+LP+V+KPL+QY VEEA EAG VTGR KR Sbjct: 1 MIKKCLFPVAGYGTRFLPATKAMPKEILPVVNKPLVQYGVEEAAEAGIHEFGFVTGRGKR 60 Query: 61 SLEDYFDTSYEIEHQIQGTNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIG 120 ++ED+FD SYE+E QI G+ KE L SIR +I+ F++ RQ +MKGLGHAILTG L+G Sbjct: 61 AIEDHFDISYELEQQIAGSGKEELLTSIRELIDHNSFAFTRQNEMKGLGHAILTGRNLVG 120 Query: 121 NEPFAVILADDLCISHD-HPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLE 179 + PFAV+LADD CI D VL QM LY +++CSIVAIEEV +E KYGVI GE ++ Sbjct: 121 DNPFAVVLADDFCIGPDGEDGVLAQMVKLYNQFRCSIVAIEEVPADETHKYGVIAGESMK 180 Query: 180 EGVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAK 239 +G+Y I DMVEKP EDAPSNLA+IGRYILTPDIFEI+ +T GKN E+QITDAL QAK Sbjct: 181 DGLYRITDMVEKPAPEDAPSNLAIIGRYILTPDIFEIIEKTPAGKNGEVQITDALLEQAK 240 Query: 240 RKRIIAYQFKGKRYDCGSVEGYIEASNAYYK 270 ++AYQFKG+R+DCGS++G++EA+N Y+ Sbjct: 241 NGCVLAYQFKGRRFDCGSIDGFVEATNYVYE 271 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: 295 Number of extensions: 8 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: 273 Length of database: 278 Length adjustment: 25 Effective length of query: 248 Effective length of database: 253 Effective search space: 62744 Effective search space used: 62744 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 GFF1978 HP15_1935 (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.20072.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-120 387.7 0.0 1.7e-120 387.5 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF1978 HP15_1935 UTP-glucose-1-phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1978 HP15_1935 UTP-glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 387.5 0.0 1.7e-120 1.7e-120 1 261 [] 2 265 .. 2 265 .. 0.98 Alignments for each domain: == domain 1 score: 387.5 bits; conditional E-value: 1.7e-120 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleakl 75 i+k+++P+aG+Gtr+LPatka+Pke+lp+v+kPl+qy veea eaGi+e +vtgr+kraiedhfD+syele+++ lcl|FitnessBrowser__Marino:GFF1978 2 IKKCLFPVAGYGTRFLPATKAMPKEILPVVNKPLVQYGVEEAAEAGIHEFGFVTGRGKRAIEDHFDISYELEQQI 76 89************************************************************************* PP TIGR01099 76 ekknkeellkevrkiaelatilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee...alkqlielye 147 ++keell ++r+++++ ++ ++rq+e+kGLGha+l++++lvgd+pfav+l+Dd + + +l+q+++ly+ lcl|FitnessBrowser__Marino:GFF1978 77 AGSGKEELLTSIRELIDHNSFAFTRQNEMKGLGHAILTGRNLVGDNPFAVVLADDFCIGPDGedgVLAQMVKLYN 151 *********************************************************87655556********** PP TIGR01099 148 ktgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkg 222 ++++si+a+eevp++e++kYGvi+ge++++ ly+++d+vekP pe+apsnlai+GrY+ltp+ife++e+t+aGk+ lcl|FitnessBrowser__Marino:GFF1978 152 QFRCSIVAIEEVPADETHKYGVIAGESMKDGLYRITDMVEKPAPEDAPSNLAIIGRYILTPDIFEIIEKTPAGKN 226 *************************************************************************** PP TIGR01099 223 geiqltDalrlllekeevlavklkgkryDvGdklgylka 261 ge+q+tDal ++++ +vla+++kg+r+D+G+ g+++a lcl|FitnessBrowser__Marino:GFF1978 227 GEVQITDALLEQAKNGCVLAYQFKGRRFDCGSIDGFVEA 265 ************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (278 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.01 // [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