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 Ga0059261_3133 Ga0059261_3133 UTP--glucose-1-phosphate uridylyltransferase
Query= SwissProt::Q05852 (292 letters) >FitnessBrowser__Korea:Ga0059261_3133 Length = 292 Score = 291 bits (745), Expect = 1e-83 Identities = 148/291 (50%), Positives = 199/291 (68%), Gaps = 6/291 (2%) Query: 1 MKKVRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKS 60 +K +RKA+ P GLGTRFLPATKA+PKEMLP+VD+P IQY ++EA+EAGIE II VTG+ Sbjct: 3 IKPLRKAVFPVGGLGTRFLPATKALPKEMLPVVDRPLIQYAVDEALEAGIEQIIFVTGRG 62 Query: 61 KRAIEDHFDYSPELERNLEEKGKT-ELLEKVKKASNLADIHYIRQKEPKGLGHAVWCARN 119 K AIEDHFD S ELE + +GK ++L+ + I Y+RQ+EP GLGHAVWCAR+ Sbjct: 63 KSAIEDHFDISYELETTMAARGKPLDVLDGTRLKPGA--IAYVRQQEPMGLGHAVWCARD 120 Query: 120 FIGDEPFAVLLGDDIV---QAETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPL 176 +GDEPFAVLL DD + Q + LRQ+++ Y K +++ QQV E++T +YG+I P Sbjct: 121 IVGDEPFAVLLADDFMVSAQGQRGCLRQMVEAYNKVGGNLLCAQQVAEDQTDKYGVITPG 180 Query: 177 TSEGRRYQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQK 236 T +G +VK VEKP GTAPSNLA++GRY+ PE+ LE Q+ GAGGEIQLTDA+ + Sbjct: 181 TRDGTLTEVKGLVEKPKAGTAPSNLAVIGRYILQPEVMRVLEGQEKGAGGEIQLTDAMAR 240 Query: 237 LNEIQRVFAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRDQLVPFMEGLL 287 + Q F+G RYD G+K G+ L A+ +++ + F +GLL Sbjct: 241 MIGGQPFHGVTFQGVRYDCGDKAGYAQANLALALSREDIGPAVREFAKGLL 291 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: 280 Number of extensions: 5 Number of successful extensions: 3 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: 292 Length adjustment: 26 Effective length of query: 266 Effective length of database: 266 Effective search space: 70756 Effective search space used: 70756 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 Ga0059261_3133 Ga0059261_3133 (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.6590.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-105 338.3 0.0 2e-105 338.1 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_3133 Ga0059261_3133 UTP--glucose-1-ph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_3133 Ga0059261_3133 UTP--glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 338.1 0.0 2e-105 2e-105 1 261 [] 6 268 .. 6 268 .. 0.96 Alignments for each domain: == domain 1 score: 338.1 bits; conditional E-value: 2e-105 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsy 69 +rkav+P+ GlGtr+LPatka+Pkemlp+vd+Pliqy+v+ea+eaGie+i++vtgr+k aiedhfD+sy lcl|FitnessBrowser__Korea:Ga0059261_3133 6 LRKAVFPVGGLGTRFLPATKALPKEMLPVVDRPLIQYAVDEALEAGIEQIIFVTGRGKSAIEDHFDISY 74 59******************************************************************* PP TIGR01099 70 eleaklekknke.ellkevrkiaelatilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee 137 ele+++ ++k ++l+ r + i yvrq+e GLGhav++a+++vgdepfavll+Dd +++ + lcl|FitnessBrowser__Korea:Ga0059261_3133 75 ELETTMAARGKPlDVLDGTR--LKPGAIAYVRQQEPMGLGHAVWCARDIVGDEPFAVLLADDFMVSAQG 141 ********999613444433..46689************************************999887 PP TIGR01099 138 ...alkqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGr 203 +l+q++e+y+k+g + + ++v++++++kYGvi++ + + +l+evk lvekPk+ +apsnla++Gr lcl|FitnessBrowser__Korea:Ga0059261_3133 142 qrgCLRQMVEAYNKVGGNLLCAQQVAEDQTDKYGVITPGTRDGTLTEVKGLVEKPKAGTAPSNLAVIGR 210 788****************************************************************** PP TIGR01099 204 YvltpeifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261 Y+l+pe+ ++le +++G+ggeiqltDa++ ++ + +++v+++g ryD+Gdk gy +a lcl|FitnessBrowser__Korea:Ga0059261_3133 211 YILQPEVMRVLEGQEKGAGGEIQLTDAMARMIGGQPFHGVTFQGVRYDCGDKAGYAQA 268 *******************************************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (292 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: 10.65 // [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