Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate Ga0059261_1280 Ga0059261_1280 ATP phosphoribosyltransferase
Query= reanno::Korea:Ga0059261_1280 (219 letters) >FitnessBrowser__Korea:Ga0059261_1280 Length = 219 Score = 424 bits (1091), Expect = e-124 Identities = 219/219 (100%), Positives = 219/219 (100%) Query: 1 MSEPIILAVPKGRILEEALPLLAHAGIIPEPAFADEGSRALRFKTNRPDIDLIRVRAFDV 60 MSEPIILAVPKGRILEEALPLLAHAGIIPEPAFADEGSRALRFKTNRPDIDLIRVRAFDV Sbjct: 1 MSEPIILAVPKGRILEEALPLLAHAGIIPEPAFADEGSRALRFKTNRPDIDLIRVRAFDV 60 Query: 61 ATFVAHGAAQLGIVGSDVLAEFAYSELYAPVDLGIGYCRLSVAEPAALAATDDPRGWSHV 120 ATFVAHGAAQLGIVGSDVLAEFAYSELYAPVDLGIGYCRLSVAEPAALAATDDPRGWSHV Sbjct: 61 ATFVAHGAAQLGIVGSDVLAEFAYSELYAPVDLGIGYCRLSVAEPAALAATDDPRGWSHV 120 Query: 121 RVATKYPSLTRRHFEARGVQAECIKLNGAMELAPLLDLAPRIVDLVSSGRTLKENGLVEV 180 RVATKYPSLTRRHFEARGVQAECIKLNGAMELAPLLDLAPRIVDLVSSGRTLKENGLVEV Sbjct: 121 RVATKYPSLTRRHFEARGVQAECIKLNGAMELAPLLDLAPRIVDLVSSGRTLKENGLVEV 180 Query: 181 ETIMEVSSRLVANRAAFKTRPEIVPLIDAFRRAVEAKAA 219 ETIMEVSSRLVANRAAFKTRPEIVPLIDAFRRAVEAKAA Sbjct: 181 ETIMEVSSRLVANRAAFKTRPEIVPLIDAFRRAVEAKAA 219 Lambda K H 0.321 0.137 0.390 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: 325 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: 219 Length of database: 219 Length adjustment: 22 Effective length of query: 197 Effective length of database: 197 Effective search space: 38809 Effective search space used: 38809 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 (21.9 bits) S2: 45 (21.9 bits)
Align candidate Ga0059261_1280 Ga0059261_1280 (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.11568.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-60 187.7 0.0 1e-59 187.6 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_1280 Ga0059261_1280 ATP phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_1280 Ga0059261_1280 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 187.6 0.0 1e-59 1e-59 2 183 .] 6 192 .. 5 192 .. 0.93 Alignments for each domain: == domain 1 score: 187.6 bits; conditional E-value: 1e-59 TIGR00070 2 riAlpKGrleeetlkllekaglk....lskkeerkliasaedeevevlllrakdiptyvekgaadlGit 66 +A+pKGr++ee+l ll++ag+ + ++ +r+l +++++++++++ +ra d++t+v++gaa+lGi+ lcl|FitnessBrowser__Korea:Ga0059261_1280 6 ILAVPKGRILEEALPLLAHAGIIpepaFADEGSRALRFKTNRPDIDLIRVRAFDVATFVAHGAAQLGIV 74 58******************996444356666************************************* PP TIGR00070 67 GkDlleE.seadvvelldlgfgkcklvlAvpees.dvesledlkegkriATkypnltreylekkgvkve 133 G+D+l+E +++++ +dlg+g c+l++A p + + +++ + + r+ATkyp+ltr+++e +gv++e lcl|FitnessBrowser__Korea:Ga0059261_1280 75 GSDVLAEfAYSELYAPVDLGIGYCRLSVAEPAALaATDDPRGWS-HVRVATKYPSLTRRHFEARGVQAE 142 *******88999*********************95556666666.78********************** PP TIGR00070 134 ivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 ++kl+Ga+Elapll+la IvD+v++G+tL+engL+++e+i+e+s+rl+a lcl|FitnessBrowser__Korea:Ga0059261_1280 143 CIKLNGAMELAPLLDLAPRIVDLVSSGRTLKENGLVEVETIMEVSSRLVA 192 ************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (219 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: 7.94 // [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