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 AZOBR_RS31075 AZOBR_RS31075 UTP--glucose-1-phosphate uridylyltransferase
Query= SwissProt::Q05852 (292 letters) >FitnessBrowser__azobra:AZOBR_RS31075 Length = 289 Score = 296 bits (758), Expect = 4e-85 Identities = 151/280 (53%), Positives = 195/280 (69%), Gaps = 3/280 (1%) Query: 2 KKVRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKSK 61 K VRK + P AGLGTRFLPATKA+PKEMLP+VD+P +Q+ +EEA AGIED + VTG+SK Sbjct: 3 KPVRKVVFPVAGLGTRFLPATKAIPKEMLPLVDRPLLQHAVEEARAAGIEDFVFVTGRSK 62 Query: 62 RAIEDHFDYSPELERNLEEKGKTELLEKVKKASNLAD--IHYIRQKEPKGLGHAVWCARN 119 RAIEDHFD EL R LEE+GK + LE V+ S +A Y RQ+ P GLGHAVWCAR Sbjct: 63 RAIEDHFDTDTELNRTLEERGKQDALEVVRD-SEIAPGRCFYTRQQVPLGLGHAVWCARA 121 Query: 120 FIGDEPFAVLLGDDIVQAETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPLTSE 179 IG++PFA++L DD VQ +TP L+Q+++ Y + +I+ V VP E T YGI+D + Sbjct: 122 VIGNDPFAIVLPDDFVQGDTPCLKQMVEAYNEVGGNIVAVVDVPRERTSSYGILDVEKDD 181 Query: 180 GRRYQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQKLNE 239 GR V+ VEKP APS L+I+GRY+ PE+F +LE+QQ GAG EIQLTDA+ KL Sbjct: 182 GRLATVRGLVEKPKPEEAPSTLSIIGRYILQPEVFDHLEKQQRGAGNEIQLTDAMAKLIG 241 Query: 240 IQRVFAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRDQL 279 Q FEG RYD G+K+GFI TL A++ ++ D++ Sbjct: 242 TQPFHGLRFEGTRYDCGDKVGFIEATLAHALRRPDMADKV 281 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: 289 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: 292 Length of database: 289 Length adjustment: 26 Effective length of query: 266 Effective length of database: 263 Effective search space: 69958 Effective search space used: 69958 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 AZOBR_RS31075 AZOBR_RS31075 (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.28732.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-109 351.0 0.0 2.6e-109 350.8 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS31075 AZOBR_RS31075 UTP--glucose-1-pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS31075 AZOBR_RS31075 UTP--glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 350.8 0.0 2.6e-109 2.6e-109 1 261 [] 5 266 .. 5 266 .. 0.98 Alignments for each domain: == domain 1 score: 350.8 bits; conditional E-value: 2.6e-109 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsy 69 +rk+v+P+aGlGtr+LPatkaiPkemlp+vd+Pl+q++veea +aGie+ v+vtgrskraiedhfDt++ lcl|FitnessBrowser__azobra:AZOBR_RS31075 5 VRKVVFPVAGLGTRFLPATKAIPKEMLPLVDRPLLQHAVEEARAAGIEDFVFVTGRSKRAIEDHFDTDT 73 79******************************************************************* PP TIGR01099 70 eleaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee 137 el+++le+++k+++l+ vr+ +++y+rq+ GLGhav++a++++g++pfa++l+Dd v+ +++ lcl|FitnessBrowser__azobra:AZOBR_RS31075 74 ELNRTLEERGKQDALEVVRDSEIApGRCFYTRQQVPLGLGHAVWCARAVIGNDPFAIVLPDDFVQGDTP 142 ******************98654449******************************************* PP TIGR01099 138 alkqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvl 206 +lkq++e+y+++g +i+av +vp+e +s+YG++d+e+ + +l +v+ lvekPkpeeaps l i+GrY+l lcl|FitnessBrowser__azobra:AZOBR_RS31075 143 CLKQMVEAYNEVGGNIVAVVDVPRERTSSYGILDVEKDDGRLATVRGLVEKPKPEEAPSTLSIIGRYIL 211 ********************************************************************* PP TIGR01099 207 tpeifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261 +pe+f++le++++G+g+eiqltDa+++l+ ++ +++ +++g+ryD+Gdk+g+++a lcl|FitnessBrowser__azobra:AZOBR_RS31075 212 QPEVFDHLEKQQRGAGNEIQLTDAMAKLIGTQPFHGLRFEGTRYDCGDKVGFIEA 266 *****************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (289 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: 11.25 // [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