Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate Dsui_2700 Dsui_2700 UTP-glucose-1-phosphate uridylyltransferase
Query= BRENDA::Q8PK83 (297 letters) >FitnessBrowser__PS:Dsui_2700 Length = 288 Score = 305 bits (781), Expect = 8e-88 Identities = 160/277 (57%), Positives = 197/277 (71%), Gaps = 1/277 (0%) Query: 3 QRIRKAVFPVAGLGTRFLPATKTVPKEMLPIIDKPLIQYAVDEAIQAGCDTLIFVTNRYK 62 +++RKAVFPVAGLGTRFLPATK PKEMLPI+DKPLIQYAV+EA AG +IFVT R K Sbjct: 2 KKVRKAVFPVAGLGTRFLPATKASPKEMLPIVDKPLIQYAVEEACAAGITDMIFVTGRSK 61 Query: 63 HSIADYFDKAYELEQKLERAGKLEQLELVRHALPDGVRAIFVTQAEALGLGHAVLCAKAV 122 +I D+FDKAYELE++L GK E L+ V+ LP + I++ Q EALGLGHAVLCA V Sbjct: 62 RAIEDHFDKAYELEKELAERGKTEMLKFVQDMLPKSMNCIYIRQPEALGLGHAVLCAAPV 121 Query: 123 VGNEPFAVLLPDDLMWNRGDAALTQMANVAEASGGSVIAVEDVPHDKTASYGIVSTDAFD 182 V +EPFAV+L DDL+ + + QM + + SV+ V+DVP T SYGIV Sbjct: 122 VQDEPFAVILADDLL-DGETPVMKQMVDTYDYYHCSVLGVQDVPRADTKSYGIVDAKPVA 180 Query: 183 GRKGRINAIVEKPKPEVAPSNLAVVGRYVLSPKIFDLLEATGAGAGGEIQLTDAIAELLK 242 R +I AIVEKPKPE APS LAVVGRY+L+P+IF LE G G+GGEIQLTD IA LL Sbjct: 181 ERLEQIAAIVEKPKPEEAPSTLAVVGRYILTPRIFHHLERIGKGSGGEIQLTDGIASLLS 240 Query: 243 EEQVDAFRFEGRRFDCGAHIGLIEATVHFALEHEKHG 279 EEQV A+R+ G R+DCG+ +G ++ATV H + G Sbjct: 241 EEQVLAYRYAGTRYDCGSKLGYLQATVDLGRRHPEVG 277 Lambda K H 0.319 0.137 0.393 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: 283 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: 297 Length of database: 288 Length adjustment: 26 Effective length of query: 271 Effective length of database: 262 Effective search space: 71002 Effective search space used: 71002 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: 48 (23.1 bits)
Align candidate Dsui_2700 Dsui_2700 (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.3899.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-119 383.7 0.0 2.6e-119 383.6 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_2700 Dsui_2700 UTP-glucose-1-phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_2700 Dsui_2700 UTP-glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.6 0.0 2.6e-119 2.6e-119 1 261 [] 4 265 .. 4 265 .. 0.99 Alignments for each domain: == domain 1 score: 383.6 bits; conditional E-value: 2.6e-119 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleaklek 77 +rkav+P+aGlGtr+LPatka PkemlpivdkPliqy+veea +aGi+++++vtgrskraiedhfD++yele++l + lcl|FitnessBrowser__PS:Dsui_2700 4 VRKAVFPVAGLGTRFLPATKASPKEMLPIVDKPLIQYAVEEACAAGITDMIFVTGRSKRAIEDHFDKAYELEKELAE 80 79*************************************************************************** PP TIGR01099 78 knkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeeealkqlielyektgasi 153 ++k+e+lk v+++ ++ ++++y+rq ea GLGhavl+a ++v depfav+l+Ddl++ e++++kq++++y+ +++s+ lcl|FitnessBrowser__PS:Dsui_2700 81 RGKTEMLKFVQDMLPKsMNCIYIRQPEALGLGHAVLCAAPVVQDEPFAVILADDLLDGETPVMKQMVDTYDYYHCSV 157 *************99989*********************************************************** PP TIGR01099 154 iaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkggeiqltDa 230 ++v++vp+ ++++YG++d++ v e+l ++ ++vekPkpeeaps la+vGrY+ltp+if++le++ +G ggeiqltD+ lcl|FitnessBrowser__PS:Dsui_2700 158 LGVQDVPRADTKSYGIVDAKPVAERLEQIAAIVEKPKPEEAPSTLAVVGRYILTPRIFHHLERIGKGSGGEIQLTDG 234 ***************************************************************************** PP TIGR01099 231 lrlllekeevlavklkgkryDvGdklgylka 261 ++ ll++e+vla++ g+ryD+G+klgyl+a lcl|FitnessBrowser__PS:Dsui_2700 235 IASLLSEEQVLAYRYAGTRYDCGSKLGYLQA 265 *****************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (288 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: 10.69 // [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