Align ATP phosphoribosyltransferase; ATP-PRT; ATP-PRTase; EC 2.4.2.17 (characterized)
to candidate WP_017601183.1 D471_RS0125195 ATP phosphoribosyltransferase
Query= SwissProt::P9WMN1 (284 letters) >NCBI__GCF_000341125.1:WP_017601183.1 Length = 284 Score = 306 bits (785), Expect = 3e-88 Identities = 157/283 (55%), Positives = 206/283 (72%), Gaps = 3/283 (1%) Query: 1 MLRVAVPNKGALSEPATEILAEAGYRRRTDSKDLTVIDPVNNVEFFFLRPKDIAIYVGSG 60 +LR+AVPNKG LSEPA E+L EAGYR+R S+DL ++DP N+ EFFFLRPKDIA+YVG G Sbjct: 4 LLRIAVPNKGQLSEPAVEMLREAGYRQRKSSRDLVMVDPDNDTEFFFLRPKDIAVYVGEG 63 Query: 61 ELDFGITGRDLVCDSGAQVRERLALGFGSSSFRYAAPAGRNWTTADLAGMRIATAYPNLV 120 L GITGRD++ DSGA V E LALGFG+S+FR+AAP G + DL G RIAT++ L+ Sbjct: 64 ILQAGITGRDMLLDSGAAVDEVLALGFGASTFRFAAPNGASMKVCDLNGKRIATSFDGLL 123 Query: 121 RKDLATKGIEATVIRLDGAVEISVQLGVADAIADVVGSGRTLSQHDLVAFGEPLCDSEAV 180 R L +G++A VI LDGAVE SVQLGVADA+ADVV +G TL Q + FGEP+ SEAV Sbjct: 124 RSYLDEQGVDARVIHLDGAVESSVQLGVADAVADVVSTGTTLRQAGMETFGEPILVSEAV 183 Query: 181 LIERAGTDGQDQTEARDQLVARVQGVVFGQQYLMLDYDCPRSALKKATAITPGLESPTIA 240 +I +G + E QL+ R++GV+ + Y+M++YD L+ A A+TPG+E PT++ Sbjct: 184 VIRPSGAGEDPKIE---QLLRRLRGVLVARDYVMMEYDVHAEHLEPAVALTPGMEGPTVS 240 Query: 241 PLADPDWVAIRALVPRRDVNGIMDELAAIGAKAILASDIRFCR 283 PL WVA+R++VPR+D IMD+L +GA+AIL +DI CR Sbjct: 241 PLHREGWVAVRSMVPRQDAQRIMDDLWHLGARAILVTDIYACR 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: 14 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: 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_017601183.1 D471_RS0125195 (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.10568.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-57 179.2 0.0 4.6e-57 178.9 0.0 1.1 1 lcl|NCBI__GCF_000341125.1:WP_017601183.1 D471_RS0125195 ATP phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_017601183.1 D471_RS0125195 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.9 0.0 4.6e-57 4.6e-57 1 182 [. 5 185 .. 5 186 .. 0.97 Alignments for each domain: == domain 1 score: 178.9 bits; conditional E-value: 4.6e-57 TIGR00070 1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGk 68 lriA+p KG+l+e+++++l++ag++ +k++ r+l++ ++d++ e+++lr+kdi++yv +g++++GitG lcl|NCBI__GCF_000341125.1:WP_017601183.1 5 LRIAVPnKGQLSEPAVEMLREAGYRQRKSS-RDLVMVDPDNDTEFFFLRPKDIAVYVGEGILQAGITGR 72 89**********************999999.************************************** PP TIGR00070 69 DlleEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkl 137 D+l +s+a+v e+l lgfg++++ +A+p+ ++ ++ dl+ gkriAT+++ l r+yl+++gv++++++l lcl|NCBI__GCF_000341125.1:WP_017601183.1 73 DMLLDSGAAVDEVLALGFGASTFRFAAPNGASM-KVCDLN-GKRIATSFDGLLRSYLDEQGVDARVIHL 139 *******************************87.5699**.9*************************** PP TIGR00070 138 eGavElapllgladaIvDivetGttLrengLkii.eeilessarli 182 +GavE +++lg+ada++D+v+tGttLr+ g++++ e il s+a++i lcl|NCBI__GCF_000341125.1:WP_017601183.1 140 DGAVESSVQLGVADAVADVVSTGTTLRQAGMETFgEPILVSEAVVI 185 **********************************457******998 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 7.12 // [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