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 WP_109969550.1 DK846_RS13790 UTP--glucose-1-phosphate uridylyltransferase GalU
Query= SwissProt::Q05852 (292 letters) >NCBI__GCF_003173355.1:WP_109969550.1 Length = 294 Score = 266 bits (680), Expect = 4e-76 Identities = 143/287 (49%), Positives = 187/287 (65%), Gaps = 6/287 (2%) Query: 1 MKKVRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKS 60 ++KVRK +IPAAGLGTRFLP TKA PKEMLP+VDKP IQY++EEAV +GI+DIIIVTG++ Sbjct: 2 VQKVRKVVIPAAGLGTRFLPITKAQPKEMLPVVDKPVIQYVVEEAVASGIDDIIIVTGRN 61 Query: 61 KRAIEDHFDYSPELERNLEEKGKTELLEKVKKASNLADIHYIRQKEPKGLGHAVWCARNF 120 KRAIEDHFD ELE + + S++ +IHYIRQ+EP+GLG A+ + Sbjct: 62 KRAIEDHFDRCIELEHVFPSNQGSGASDAYVDLSDIPNIHYIRQREPRGLGDAILLSEKH 121 Query: 121 IGDEPFAVLLGDDIVQA---ETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPLT 177 DEPF VLLGD I A E Q++ Y K SII V+ VPE++ YGIID Sbjct: 122 CNDEPFVVLLGDTITIAPENEKTCTSQMIHAYTKYGQSIIAVEPVPEKKIPDYGIIDGNL 181 Query: 178 SEGRRYQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQKL 237 + Y++KN VEKP APSNL +G Y+FTPEIF L++ G GGEIQLTDAI+KL Sbjct: 182 IDKNFYEIKNIVEKPTISDAPSNLGAIGCYLFTPEIFSCLKQTTPGKGGEIQLTDAIKKL 241 Query: 238 NEIQRVFAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRDQLVPFME 284 + + +RYD+G+K+G++ E A+ KE D L+ ++ Sbjct: 242 SHSIGMIT---NCRRYDIGDKIGWMKAFFELALSRKEFHDDLMSILQ 285 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: 278 Number of extensions: 14 Number of successful extensions: 4 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: 294 Length adjustment: 26 Effective length of query: 266 Effective length of database: 268 Effective search space: 71288 Effective search space used: 71288 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 WP_109969550.1 DK846_RS13790 (UTP--glucose-1-phosphate uridylyltransferase GalU)
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.1601190.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-106 340.4 0.0 4.6e-106 340.1 0.0 1.0 1 NCBI__GCF_003173355.1:WP_109969550.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003173355.1:WP_109969550.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 340.1 0.0 4.6e-106 4.6e-106 1 261 [] 5 265 .. 5 265 .. 0.97 Alignments for each domain: == domain 1 score: 340.1 bits; conditional E-value: 4.6e-106 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyelea 73 +rk+viPaaGlGtr+LP+tka+Pkemlp+vdkP+iqyvveeav++Gi++i++vtgr+kraiedhfD+ +ele+ NCBI__GCF_003173355.1:WP_109969550.1 5 VRKVVIPAAGLGTRFLPITKAQPKEMLPVVDKPVIQYVVEEAVASGIDDIIIVTGRNKRAIEDHFDRCIELEH 77 79*********************************************************************** PP TIGR01099 74 klekknkeellkevrkiaelatilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee...alkqli 143 + +++ + + + ++++ +i+y+rq+e +GLG+a+ll+e++ depf+vllgD+++ + e+ ++ q+i NCBI__GCF_003173355.1:WP_109969550.1 78 VFPSNQGSGASDAYVDLSDIPNIHYIRQREPRGLGDAILLSEKHCNDEPFVVLLGDTITIAPENektCTSQMI 150 **********************************************************9766555569***** PP TIGR01099 144 elyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifellee 216 ++y+k+g+siiave vp++++ YG+idg+ ++++ ye+k++vekP+ +apsnl +G Y++tpeif+ l++ NCBI__GCF_003173355.1:WP_109969550.1 151 HAYTKYGQSIIAVEPVPEKKIPDYGIIDGNLIDKNFYEIKNIVEKPTISDAPSNLGAIGCYLFTPEIFSCLKQ 223 ************************************************************************* PP TIGR01099 217 tkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261 t +GkggeiqltDa+++l + +++ +++ryD+Gdk+g++ka NCBI__GCF_003173355.1:WP_109969550.1 224 TTPGKGGEIQLTDAIKKLS---HSIGMITNCRRYDIGDKIGWMKA 265 *****************94...45788899*************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (294 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.80 // [ok]
This GapMind analysis is from Apr 09 2024. 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