Align ATP phosphoribosyltransferase; ATP-PRT; ATP-PRTase; EC 2.4.2.17 (uncharacterized)
to candidate Synpcc7942_0783 Synpcc7942_0783 ATP phosphoribosyltransferase catalytic subunit
Query= curated2:B0JK88 (216 letters) >FitnessBrowser__SynE:Synpcc7942_0783 Length = 218 Score = 293 bits (749), Expect = 2e-84 Identities = 148/211 (70%), Positives = 177/211 (83%) Query: 1 MLTIALPKGALLNESIQIFQKIGLDFSAFLDSKNRQLQITDPTNQAKALLVRATDVPVYV 60 MLTIALPKGALL +SI++ Q GLDFSAFL+ NRQLQI D +AKALLVR +DVPVYV Sbjct: 1 MLTIALPKGALLKDSIRLLQSAGLDFSAFLEPGNRQLQILDRQERAKALLVRNSDVPVYV 60 Query: 61 EYGQAQLGIAGYDVLLEKSPDVANLIDLKFGYCRMSVAVPADSPYQSPLDIPHHGKVASK 120 EYGQAQLG+ GYDVL EK+ VA LIDL+FG CRMS+AV A SPY+S LD+P H ++ASK Sbjct: 61 EYGQAQLGVVGYDVLREKTARVAQLIDLRFGGCRMSIAVKASSPYRSVLDLPAHCRIASK 120 Query: 121 FVNCAKDYFRRLDIPVEIIPLYGSVELGPITGMSEAIVDLVSTGRTLRENGLVEIDELFA 180 FV+CA+DYF LD+PVEI+PL GSVELGPITGMSEAIVDLV+TG+TLRENGLVEI+ LF Sbjct: 121 FVHCARDYFHNLDLPVEIVPLSGSVELGPITGMSEAIVDLVATGQTLRENGLVEIETLFD 180 Query: 181 SSARLIAHPLSYRLDRDQIYNWVEKLREPTT 211 S+ARLIA+PL+YR++ D I +E+LR+ T Sbjct: 181 STARLIANPLAYRINADGISELIEELRQSVT 211 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: 201 Number of extensions: 5 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: 218 Length adjustment: 22 Effective length of query: 194 Effective length of database: 196 Effective search space: 38024 Effective search space used: 38024 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 Synpcc7942_0783 Synpcc7942_0783 (ATP phosphoribosyltransferase catalytic subunit)
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.4264.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-66 209.2 0.0 2.7e-66 209.0 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0783 Synpcc7942_0783 ATP phosphoribos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0783 Synpcc7942_0783 ATP phosphoribosyltransferase catalytic subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 209.0 0.0 2.7e-66 2.7e-66 1 183 [] 2 187 .. 2 187 .. 0.98 Alignments for each domain: == domain 1 score: 209.0 bits; conditional E-value: 2.7e-66 TIGR00070 1 lriAlpKGrleeetlkllekaglklskke...erkliasaedeevevlllrakdiptyvekgaadlGit 66 l+iAlpKG+l++++++ll++agl++s+ +r+l + + +e+ ++ll+r++d+p+yve+g+a+lG++ lcl|FitnessBrowser__SynE:Synpcc7942_0783 2 LTIALPKGALLKDSIRLLQSAGLDFSAFLepgNRQLQILDRQERAKALLVRNSDVPVYVEYGQAQLGVV 70 79**********************998766679************************************ PP TIGR00070 67 GkDlleEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveiv 135 G+D+l+E+ a v++l+dl+fg c++++Av+ +s+++s+ dl ++ riA+k+++++r+y+++ ++veiv lcl|FitnessBrowser__SynE:Synpcc7942_0783 71 GYDVLREKTARVAQLIDLRFGGCRMSIAVKASSPYRSVLDLPAHCRIASKFVHCARDYFHNLDLPVEIV 139 ******************************************999************************ PP TIGR00070 136 kleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 +l+G+vEl p++g+++aIvD+v tG+tLrengL++ie++++s+arlia lcl|FitnessBrowser__SynE:Synpcc7942_0783 140 PLSGSVELGPITGMSEAIVDLVATGQTLRENGLVEIETLFDSTARLIA 187 **********************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (218 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: 8.81 // [ok]
This GapMind analysis is from Apr 09 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