Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate WP_011386795.1 AMB_RS22525 UTP--glucose-1-phosphate uridylyltransferase
Query= BRENDA::Q8PK83 (297 letters) >NCBI__GCF_000009985.1:WP_011386795.1 Length = 291 Score = 275 bits (703), Expect = 9e-79 Identities = 145/271 (53%), Positives = 178/271 (65%), Gaps = 1/271 (0%) Query: 5 IRKAVFPVAGLGTRFLPATKTVPKEMLPIIDKPLIQYAVDEAIQAGCDTLIFVTNRYKHS 64 IRKAV PVAG+GTR LPATK +PKE+LP++DKPLIQYAV+EA +AG ++ VT R K Sbjct: 2 IRKAVLPVAGMGTRVLPATKVLPKELLPVVDKPLIQYAVEEAAEAGITEIVLVTARGKEM 61 Query: 65 IADYFDKAYELEQKLERAGKLEQLELVRHALPDGVRAIFVTQAEALGLGHAVLCAKAVVG 124 +AD+FD+ ELE+ LE GK E L++ R P GV V Q LGLGHAVLCA+ V+G Sbjct: 62 LADHFDRNAELERSLETRGKTELLDIARSTCPKGVSITTVRQPAPLGLGHAVLCARPVIG 121 Query: 125 NEPFAVLLPDDLMWNRGDAALTQMANVAEASGGSVIAVEDVPHDKTASYGIVSTDAFDGR 184 +EPFAVLLPDDL+ L Q+ +V + G VIAVE+VP D+ YGI+ GR Sbjct: 122 DEPFAVLLPDDLILG-APGCLKQLVDVWNETRGHVIAVENVPADQVDRYGILDVIEEKGR 180 Query: 185 KGRINAIVEKPKPEVAPSNLAVVGRYVLSPKIFDLLEATGAGAGGEIQLTDAIAELLKEE 244 R +VEKPKP APS L+V+GRYVL +FD LE GAGGEIQLTDAIA L Sbjct: 181 LARARGLVEKPKPSEAPSTLSVIGRYVLDASVFDALERRERGAGGEIQLTDAIARTLGSV 240 Query: 245 QVDAFRFEGRRFDCGAHIGLIEATVHFALEH 275 + RF G R+DCG G + A + AL H Sbjct: 241 PLHGARFHGTRYDCGNKAGYVAAIIDAALAH 271 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: 304 Number of extensions: 6 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: 291 Length adjustment: 26 Effective length of query: 271 Effective length of database: 265 Effective search space: 71815 Effective search space used: 71815 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 WP_011386795.1 AMB_RS22525 (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.22008.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-104 334.5 0.0 2.7e-104 334.4 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386795.1 AMB_RS22525 UTP--glucose-1-phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386795.1 AMB_RS22525 UTP--glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 334.4 0.0 2.7e-104 2.7e-104 1 261 [] 2 263 .. 2 263 .. 0.99 Alignments for each domain: == domain 1 score: 334.4 bits; conditional E-value: 2.7e-104 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsy 69 irkav+P+aG+Gtr+LPatk +Pke+lp+vdkPliqy+veea eaGi+eivlvt r+k+ + dhfD+++ lcl|NCBI__GCF_000009985.1:WP_011386795.1 2 IRKAVLPVAGMGTRVLPATKVLPKELLPVVDKPLIQYAVEEAAEAGITEIVLVTARGKEMLADHFDRNA 70 89******************************************************************* PP TIGR01099 70 eleaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee 137 ele++le+++k+ell+ r+ +++ ++i+ vrq GLGhavl+a++++gdepfavll+Ddl+ lcl|NCBI__GCF_000009985.1:WP_011386795.1 71 ELERSLETRGKTELLDIARSTCPKgVSITTVRQPAPLGLGHAVLCARPVIGDEPFAVLLPDDLILGAPG 139 ***********************99******************************************** PP TIGR01099 138 alkqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvl 206 +lkql++++++t+ ++iave+vp+++v++YG++d+ e + +l + + lvekPkp eaps l ++GrYvl lcl|NCBI__GCF_000009985.1:WP_011386795.1 140 CLKQLVDVWNETRGHVIAVENVPADQVDRYGILDVIEEKGRLARARGLVEKPKPSEAPSTLSVIGRYVL 208 ********************************************************************* PP TIGR01099 207 tpeifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261 ++++f++le+ ++G+ggeiqltDa++ +l + +++ +++g+ryD+G+k gy+ a lcl|NCBI__GCF_000009985.1:WP_011386795.1 209 DASVFDALERRERGAGGEIQLTDAIARTLGSVPLHGARFHGTRYDCGNKAGYVAA 263 ****************************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (291 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: 8.46 // [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