Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate HSERO_RS10830 HSERO_RS10830 UTP--glucose-1-phosphate uridylyltransferase
Query= BRENDA::Q8PK83 (297 letters) >FitnessBrowser__HerbieS:HSERO_RS10830 Length = 296 Score = 321 bits (822), Expect = 1e-92 Identities = 162/290 (55%), Positives = 209/290 (72%), Gaps = 2/290 (0%) Query: 1 MSQRIRKAVFPVAGLGTRFLPATKTVPKEMLPIIDKPLIQYAVDEAIQAGCDTLIFVTNR 60 M ++I+KAVFPVAGLG+RFLPATK PKEMLPI+DKPLI YAV+EA+ AG ++F+T R Sbjct: 1 MIKKIKKAVFPVAGLGSRFLPATKAQPKEMLPIVDKPLIHYAVEEAVAAGITEMVFITGR 60 Query: 61 YKHSIADYFDKAYELEQKLERAGKLEQLELVRHALPDGVRAIFVTQAEALGLGHAVLCAK 120 K +I D+FDKAYELE +LE AGK + LE+V++ +P V IF+ Q+ LGLGHAVLCA+ Sbjct: 61 NKRAIEDHFDKAYELESELEAAGKKKLLEIVQNVVPKSVNCIFIRQSVPLGLGHAVLCAR 120 Query: 121 AVVGNEPFAVLLPDDLMWNRGDA--ALTQMANVAEASGGSVIAVEDVPHDKTASYGIVST 178 VVG EPFAVLL DD M L QM + E G S++AV++VP T YGIVS Sbjct: 121 PVVGEEPFAVLLADDFMDTDAGVKPVLAQMTEIYEREGMSMLAVQEVPQSDTKQYGIVSA 180 Query: 179 DAFDGRKGRINAIVEKPKPEVAPSNLAVVGRYVLSPKIFDLLEATGAGAGGEIQLTDAIA 238 + R+NAIVEKP PE APS LAVVGRYVL+ +IFD LE G GAGGEIQLTD IA Sbjct: 181 TPYQPNLERVNAIVEKPAPEEAPSTLAVVGRYVLNNRIFDYLENIGRGAGGEIQLTDGIA 240 Query: 239 ELLKEEQVDAFRFEGRRFDCGAHIGLIEATVHFALEHEKHGGPAKEILRE 288 +L++ E V A+R++G+R+DCG+ +G ++ATV ++H + G E L++ Sbjct: 241 KLMQAESVLAYRYQGQRYDCGSKLGYLKATVAMGMKHPETGAAFSEFLKD 290 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: 264 Number of extensions: 4 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: 296 Length adjustment: 26 Effective length of query: 271 Effective length of database: 270 Effective search space: 73170 Effective search space used: 73170 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 HSERO_RS10830 HSERO_RS10830 (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.20183.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-116 374.8 0.1 1.5e-116 374.6 0.1 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS10830 HSERO_RS10830 UTP--glucose-1-pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS10830 HSERO_RS10830 UTP--glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 374.6 0.1 1.5e-116 1.5e-116 1 261 [] 5 269 .. 5 269 .. 0.99 Alignments for each domain: == domain 1 score: 374.6 bits; conditional E-value: 1.5e-116 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDts 68 i+kav+P+aGlG r+LPatka+PkemlpivdkPli+y+veeav+aGi+e+v++tgr+kraiedhfD++ lcl|FitnessBrowser__HerbieS:HSERO_RS10830 5 IKKAVFPVAGLGSRFLPATKAQPKEMLPIVDKPLIHYAVEEAVAAGITEMVFITGRNKRAIEDHFDKA 72 89****************************************************************** PP TIGR01099 69 yeleaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvsee 135 yele++le ++k++ll+ v++++++ ++++++rq GLGhavl+a+++vg+epfavll+Dd ++ + lcl|FitnessBrowser__HerbieS:HSERO_RS10830 73 YELESELEAAGKKKLLEIVQNVVPKsVNCIFIRQSVPLGLGHAVLCARPVVGEEPFAVLLADDFMDTD 140 ***********************998***************************************998 PP TIGR01099 136 ee...alkqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlai 200 +l+q++e+ye+ g+s++av+evp++++++YG+++++ + +l +v+++vekP peeaps la+ lcl|FitnessBrowser__HerbieS:HSERO_RS10830 141 AGvkpVLAQMTEIYEREGMSMLAVQEVPQSDTKQYGIVSATPYQPNLERVNAIVEKPAPEEAPSTLAV 208 76667*************************************************************** PP TIGR01099 201 vGrYvltpeifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261 vGrYvl+ +if++le++ +G+ggeiqltD++++l+++e+vla++ +g+ryD+G+klgylka lcl|FitnessBrowser__HerbieS:HSERO_RS10830 209 VGRYVLNNRIFDYLENIGRGAGGEIQLTDGIAKLMQAESVLAYRYQGQRYDCGSKLGYLKA 269 ***********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (296 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: 8.48 // [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