Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate BPHYT_RS09795 BPHYT_RS09795 UTP--glucose-1-phosphate uridylyltransferase
Query= BRENDA::Q8PK83 (297 letters) >FitnessBrowser__BFirm:BPHYT_RS09795 Length = 305 Score = 293 bits (749), Expect = 4e-84 Identities = 157/294 (53%), Positives = 201/294 (68%), Gaps = 6/294 (2%) Query: 4 RIRKAVFPVAGLGTRFLPATKTVPKEMLPIIDKPLIQYAVDEAIQAGCDTLIFVTNRYKH 63 ++ KAVFPVAGLGTRFLPATK PKEMLPI+DKPLIQYAV+EAI AG +IFVT R K Sbjct: 3 KVTKAVFPVAGLGTRFLPATKASPKEMLPIVDKPLIQYAVEEAIAAGITEMIFVTGRSKR 62 Query: 64 SIADYFDKAYELEQKLERAGKLEQLELVRHALPDGVRAIFVTQAEALGLGHAVLCAKAVV 123 +I D+FDK+YE+E +LE K + L+LVR P V +V QAEALGLGHAVLCA+ +V Sbjct: 63 AIEDHFDKSYEIEAELEARNKQKLLDLVRSIKPANVDCFYVRQAEALGLGHAVLCAEKLV 122 Query: 124 GNEPFAVLLPDDLMWNRGDAALTQMANVAEASGGSVIAVEDVPHDKTASYGIVSTDAFDG 183 G PFAV+L DDL+ + ++Q+ + SVI VE + + + SYG+V ++ Sbjct: 123 GESPFAVILADDLL-HSSKPVMSQLVDTFNHYHSSVIGVETIAREDSRSYGVVDGREWED 181 Query: 184 RKGRINAIVEKPKPEVAPSNLAVVGRYVLSPKIFDLLEATGAGAGGEIQLTDAIAELLKE 243 +++ IVEKP P+ APSNL VVGRYVL P IF + A GAGGE+QLTDA+ LL E Sbjct: 182 NVIKLSGIVEKPAPDKAPSNLGVVGRYVLMPTIFKHIRALKPGAGGELQLTDAVQSLLTE 241 Query: 244 EQVDAFRFEGRRFDCGAHIGLIEATVHFALEHEKHGGPAKEILREALAQADVRG 297 EQV A+R+ G RFDCG+ +G ++ATV FAL H P + EA QA ++G Sbjct: 242 EQVLAYRYFGTRFDCGSKLGYLKATVEFALRH-----PEVKADFEAYLQAYMQG 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: 281 Number of extensions: 7 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: 305 Length adjustment: 27 Effective length of query: 270 Effective length of database: 278 Effective search space: 75060 Effective search space used: 75060 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 BPHYT_RS09795 BPHYT_RS09795 (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.21022.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-119 381.9 0.0 9.7e-119 381.7 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS09795 BPHYT_RS09795 UTP--glucose-1-pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS09795 BPHYT_RS09795 UTP--glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 381.7 0.0 9.7e-119 9.7e-119 1 261 [] 4 265 .. 4 265 .. 0.99 Alignments for each domain: == domain 1 score: 381.7 bits; conditional E-value: 9.7e-119 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsye 70 + kav+P+aGlGtr+LPatka PkemlpivdkPliqy+veea++aGi+e+++vtgrskraiedhfD+sye lcl|FitnessBrowser__BFirm:BPHYT_RS09795 4 VTKAVFPVAGLGTRFLPATKASPKEMLPIVDKPLIQYAVEEAIAAGITEMIFVTGRSKRAIEDHFDKSYE 73 679******************************************************************* PP TIGR01099 71 leaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeeeal 139 +ea+le +nk++ll+ vr+i + ++++yvrq ea GLGhavl+ae+lvg+ pfav+l+Ddl++++++++ lcl|FitnessBrowser__BFirm:BPHYT_RS09795 74 IEAELEARNKQKLLDLVRSIKPAnVDCFYVRQAEALGLGHAVLCAEKLVGESPFAVILADDLLHSSKPVM 143 *********************988********************************************** PP TIGR01099 140 kqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpe 209 ql+++++++++s+i+ve++++e+ ++YGv+dg+e e+++++++ +vekP p++apsnl +vGrYvl p+ lcl|FitnessBrowser__BFirm:BPHYT_RS09795 144 SQLVDTFNHYHSSVIGVETIAREDSRSYGVVDGREWEDNVIKLSGIVEKPAPDKAPSNLGVVGRYVLMPT 213 ********************************************************************** PP TIGR01099 210 ifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261 if++++ +k+G+gge+qltDa++ ll++e+vla++ g+r+D+G+klgylka lcl|FitnessBrowser__BFirm:BPHYT_RS09795 214 IFKHIRALKPGAGGELQLTDAVQSLLTEEQVLAYRYFGTRFDCGSKLGYLKA 265 **************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (305 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: 9.73 // [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