Align ATP phosphoribosyltransferase; ATP-PRT; ATP-PRTase; EC 2.4.2.17 (characterized)
to candidate WP_089301410.1 CHB84_RS10830 ATP phosphoribosyltransferase
Query= SwissProt::P9WMN1 (284 letters) >NCBI__GCF_900188115.1:WP_089301410.1 Length = 284 Score = 405 bits (1040), Expect = e-118 Identities = 201/283 (71%), Positives = 234/283 (82%) Query: 1 MLRVAVPNKGALSEPATEILAEAGYRRRTDSKDLTVIDPVNNVEFFFLRPKDIAIYVGSG 60 MLRVAVPNKG LS PA+E+LAEAGYR+R +++DL +IDPVN VEFFFLRPKDI IYVGSG Sbjct: 1 MLRVAVPNKGTLSGPASEMLAEAGYRQRHEARDLILIDPVNEVEFFFLRPKDIPIYVGSG 60 Query: 61 ELDFGITGRDLVCDSGAQVRERLALGFGSSSFRYAAPAGRNWTTADLAGMRIATAYPNLV 120 ELD GITGRDL DSGA V +RL LGFG S+FRYAAPA R WT DL G R+AT+YP LV Sbjct: 61 ELDLGITGRDLALDSGAPVEDRLGLGFGGSTFRYAAPADREWTIGDLEGKRVATSYPRLV 120 Query: 121 RKDLATKGIEATVIRLDGAVEISVQLGVADAIADVVGSGRTLSQHDLVAFGEPLCDSEAV 180 + DLA G+EA VIRLDGAVEIS+QLGVADAI DVVGSGRTL Q++LVAFGEP+C SEAV Sbjct: 121 QDDLAGHGVEAEVIRLDGAVEISIQLGVADAIGDVVGSGRTLRQNNLVAFGEPICQSEAV 180 Query: 181 LIERAGTDGQDQTEARDQLVARVQGVVFGQQYLMLDYDCPRSALKKATAITPGLESPTIA 240 LI+RA + G D + + QL AR+QGVVF QQY+M+DYDCPRS L A +TPGLESPT+A Sbjct: 181 LIQRAASTGSDNEKWKAQLTARLQGVVFAQQYMMIDYDCPRSLLDAAVDLTPGLESPTVA 240 Query: 241 PLADPDWVAIRALVPRRDVNGIMDELAAIGAKAILASDIRFCR 283 PLA+ WVA+RA+V R++VN MD LA +GAKA+LASDIR CR Sbjct: 241 PLAEDGWVAVRAMVARKEVNHTMDALAELGAKAVLASDIRSCR 283 Lambda K H 0.321 0.137 0.397 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: 292 Number of extensions: 4 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: 284 Length of database: 284 Length adjustment: 26 Effective length of query: 258 Effective length of database: 258 Effective search space: 66564 Effective search space used: 66564 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: 47 (22.7 bits)
Align candidate WP_089301410.1 CHB84_RS10830 (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.8455.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-54 169.7 0.0 4.2e-54 169.3 0.0 1.2 1 lcl|NCBI__GCF_900188115.1:WP_089301410.1 CHB84_RS10830 ATP phosphoribosyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188115.1:WP_089301410.1 CHB84_RS10830 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 169.3 0.0 4.2e-54 4.2e-54 1 183 [] 2 183 .. 2 183 .. 0.97 Alignments for each domain: == domain 1 score: 169.3 bits; conditional E-value: 4.2e-54 TIGR00070 1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGk 68 lr+A+p KG l+ ++ ++l++ag++ ++++ r+li ++ +eve+++lr+kdip yv +g +dlGitG lcl|NCBI__GCF_900188115.1:WP_089301410.1 2 LRVAVPnKGTLSGPASEMLAEAGYRQRHEA-RDLILIDPVNEVEFFFLRPKDIPIYVGSGELDLGITGR 69 89***********************99999.************************************** PP TIGR00070 69 DlleEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkl 137 Dl +s+a v+ l lgfg +++ +A+p + +++ + dl+ gkr+AT+yp+l+++ l+ +gv++e+++l lcl|NCBI__GCF_900188115.1:WP_089301410.1 70 DLALDSGAPVEDRLGLGFGGSTFRYAAPADREWT-IGDLE-GKRVATSYPRLVQDDLAGHGVEAEVIRL 136 *******************************995.59***.9*************************** PP TIGR00070 138 eGavElapllgladaIvDivetGttLrengLkii.eeilessarlia 183 +GavE++++lg+adaI D+v +G+tLr+n+L+ + e i++s+a+li+ lcl|NCBI__GCF_900188115.1:WP_089301410.1 137 DGAVEISIQLGVADAIGDVVGSGRTLRQNNLVAFgEPICQSEAVLIQ 183 **********************************457********95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (284 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: 12.25 // [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