Align ATP phosphoribosyltransferase; ATP-PRT; ATP-PRTase; EC 2.4.2.17 (uncharacterized)
to candidate WP_009543681.1 CCE_RS20025 ATP phosphoribosyltransferase
Query= curated2:B0JK88 (216 letters) >NCBI__GCF_000017845.1:WP_009543681.1 Length = 213 Score = 324 bits (831), Expect = 7e-94 Identities = 160/207 (77%), Positives = 188/207 (90%) Query: 1 MLTIALPKGALLNESIQIFQKIGLDFSAFLDSKNRQLQITDPTNQAKALLVRATDVPVYV 60 M+TIALPKGALL++SI++F++IGLDFS+FLDSKNRQLQI DPTN A+ LLVRATDVPVYV Sbjct: 1 MITIALPKGALLSDSIELFKRIGLDFSSFLDSKNRQLQIIDPTNTAQGLLVRATDVPVYV 60 Query: 61 EYGQAQLGIAGYDVLLEKSPDVANLIDLKFGYCRMSVAVPADSPYQSPLDIPHHGKVASK 120 EYGQAQLGI GYD+LLEKSPDVA+L DL FG CRMSVAVP SPYQ+P ++P +GKVASK Sbjct: 61 EYGQAQLGIVGYDLLLEKSPDVAHLADLNFGGCRMSVAVPKTSPYQTPAELPPNGKVASK 120 Query: 121 FVNCAKDYFRRLDIPVEIIPLYGSVELGPITGMSEAIVDLVSTGRTLRENGLVEIDELFA 180 FVNCAK YF++LD+PVEIIPLYGSVELGPITGMSEAIVDLVSTGRTL+ENGLVE++ LF Sbjct: 121 FVNCAKTYFQQLDLPVEIIPLYGSVELGPITGMSEAIVDLVSTGRTLKENGLVEVETLFH 180 Query: 181 SSARLIAHPLSYRLDRDQIYNWVEKLR 207 S+ARLIAHPLSYRL+ D + + E+++ Sbjct: 181 STARLIAHPLSYRLNLDNLNDLSEQIK 207 Lambda K H 0.320 0.138 0.395 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: 214 Number of extensions: 3 Number of successful extensions: 1 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: 216 Length of database: 213 Length adjustment: 22 Effective length of query: 194 Effective length of database: 191 Effective search space: 37054 Effective search space used: 37054 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: 45 (21.9 bits)
Align candidate WP_009543681.1 CCE_RS20025 (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.11686.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-66 208.5 0.0 4.4e-66 208.3 0.0 1.0 1 lcl|NCBI__GCF_000017845.1:WP_009543681.1 CCE_RS20025 ATP phosphoribosyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017845.1:WP_009543681.1 CCE_RS20025 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 208.3 0.0 4.4e-66 4.4e-66 1 183 [] 2 187 .. 2 187 .. 0.97 Alignments for each domain: == domain 1 score: 208.3 bits; conditional E-value: 4.4e-66 TIGR00070 1 lriAlpKGrleeetlkllekaglklskke...erkliasaedeevevlllrakdiptyvekgaadlGit 66 ++iAlpKG+l+ ++++l++++gl++s+ +r+l + +++++ + ll+ra+d+p+yve+g+a+lGi+ lcl|NCBI__GCF_000017845.1:WP_009543681.1 2 ITIALPKGALLSDSIELFKRIGLDFSSFLdskNRQLQIIDPTNTAQGLLVRATDVPVYVEYGQAQLGIV 70 79**********************886544559************************************ PP TIGR00070 67 GkDlleEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveiv 135 G+Dll E+++dv++l+dl+fg c++++Avp++s+++++++l ++ ++A+k++n+++ y+++ ++vei+ lcl|NCBI__GCF_000017845.1:WP_009543681.1 71 GYDLLLEKSPDVAHLADLNFGGCRMSVAVPKTSPYQTPAELPPNGKVASKFVNCAKTYFQQLDLPVEII 139 ******************************************999************************ PP TIGR00070 136 kleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 +l+G+vEl p++g+++aIvD+v+tG+tL+engL+++e++++s+arlia lcl|NCBI__GCF_000017845.1:WP_009543681.1 140 PLYGSVELGPITGMSEAIVDLVSTGRTLKENGLVEVETLFHSTARLIA 187 **********************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (213 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: 6.74 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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