Align ATP phosphoribosyltransferase; ATP-PRT; ATP-PRTase; EC 2.4.2.17 (uncharacterized)
to candidate WP_017550011.1 C792_RS0113590 ATP phosphoribosyltransferase
Query= curated2:B9DQ89 (205 letters) >NCBI__GCF_000330705.1:WP_017550011.1 Length = 200 Score = 196 bits (498), Expect = 2e-55 Identities = 100/200 (50%), Positives = 135/200 (67%), Gaps = 1/200 (0%) Query: 1 MLTVALSKGRLLKDFIKFLERNNNHVWADAIIHRERKLQITADSIKFILVKGSDVPTYVE 60 M+TVAL+KGRL KDFI+++E N + + A+ R L D +KFI KG DVPTYVE Sbjct: 1 MITVALTKGRLFKDFIEYMEENGLNDYIGALTGETRSLYTVVDDVKFIFAKGPDVPTYVE 60 Query: 61 EGIADIGITGSDILKERPNRNINNYIDLPFGECHFSVAAKPNVTNIQRVATTYVKTTRDY 120 G+AD+GI GSDI+ E NI N LPFG+CHFSVAA P +AT Y ++ Sbjct: 61 SGVADLGIVGSDIIAE-DEFNILNVSQLPFGDCHFSVAALPGQEAFGTIATKYTNVAFEH 119 Query: 121 FNQKGTDISIIQLSGSVELAAVVDMVDAIVDIVQTGTTLKSNGLEEREQIGEINARLITN 180 F + D+S++ L+GSVELA ++ + DAIVDIVQTG TL+ NGL E E+I +I+ARLI N Sbjct: 120 FKNRKMDVSLVHLNGSVELAPLLGLSDAIVDIVQTGGTLRDNGLIEYEKIMDIHARLIAN 179 Query: 181 KHSFFSKSKAIENFIQQLGV 200 K +F++K I F++++GV Sbjct: 180 KRTFYTKEDGIYAFLKEIGV 199 Lambda K H 0.319 0.135 0.374 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: 138 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: 205 Length of database: 200 Length adjustment: 21 Effective length of query: 184 Effective length of database: 179 Effective search space: 32936 Effective search space used: 32936 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 (21.7 bits) S2: 45 (21.9 bits)
Align candidate WP_017550011.1 C792_RS0113590 (ATP phosphoribosyltransferase)
to HMM TIGR00070 (hisG: ATP phosphoribosyltransferase (EC 2.4.2.17))
# 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.aa/TIGR00070.hmm # target sequence database: /tmp/gapView.2116067.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00070 [M=183] Accession: TIGR00070 Description: hisG: ATP phosphoribosyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-56 176.5 0.0 3.1e-56 176.2 0.0 1.1 1 NCBI__GCF_000330705.1:WP_017550011.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_017550011.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 176.2 0.0 3.1e-56 3.1e-56 1 183 [] 2 178 .. 2 178 .. 0.91 Alignments for each domain: == domain 1 score: 176.2 bits; conditional E-value: 3.1e-56 TIGR00070 1 lriAlpKGrleeetlkllekaglk..lskke....erkliasaedeevevlllrakdiptyvekgaadlGitG 67 +++Al+KGrl+++ ++++e++gl+ + + +r+l+ + ++v++++++ d+ptyve+g+adlGi+G NCBI__GCF_000330705.1:WP_017550011.1 2 ITVALTKGRLFKDFIEYMEENGLNdyI--GAltgeTRSLY--TVVDDVKFIFAKGPDVPTYVESGVADLGIVG 70 79*********************9553..33333245555..55568************************** PP TIGR00070 68 kDlleEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGa 140 +D+++E+e ++ ++ +l fg c++++A+ ++ iATky+n++ e++++++++v++v+l+G+ NCBI__GCF_000330705.1:WP_017550011.1 71 SDIIAEDEFNILNVSQLPFGDCHFSVAALPGQEAFG--------TIATKYTNVAFEHFKNRKMDVSLVHLNGS 135 ****************************99995544........6**************************** PP TIGR00070 141 vElapllgladaIvDivetGttLrengLkiieeilessarlia 183 vElapllgl+daIvDiv+tG tLr ngL ++e+i++++arlia NCBI__GCF_000330705.1:WP_017550011.1 136 VELAPLLGLSDAIVDIVQTGGTLRDNGLIEYEKIMDIHARLIA 178 *****************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (200 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.52 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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