Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_012402130.1 BPHY_RS14035 ATP phosphoribosyltransferase
Query= reanno::BFirm:BPHYT_RS17715 (232 letters) >NCBI__GCF_000020045.1:WP_012402130.1 Length = 232 Score = 405 bits (1041), Expect = e-118 Identities = 210/232 (90%), Positives = 219/232 (94%) Query: 1 MSAMPQTSSSPAVSAPLTLALSKGRIFEETLPLLAAAGIEVAEDPETSRKLILPTTDANL 60 MS +PQTSSSPA PLTLALSKGRIFEET+PLLAAAGIEV EDPETSRKLILPT D N+ Sbjct: 1 MSELPQTSSSPAAGKPLTLALSKGRIFEETVPLLAAAGIEVTEDPETSRKLILPTNDPNV 60 Query: 61 RVIIVRATDVPTYVEYGAADFGVAGKDVLLEHGGSGLYQPVDLDIARCRMSVAVAAGFDY 120 RVIIVRATDVPTYVEYGAADFGVAGKDVL+EHGG GLYQP+DLDIARCRMSVAVAAGFDY Sbjct: 61 RVIIVRATDVPTYVEYGAADFGVAGKDVLIEHGGGGLYQPIDLDIARCRMSVAVAAGFDY 120 Query: 121 ANAVRQGARLRVATKYVETAREHFAAKGVHVDLIKLYGSMELAPLVGLADAIVDLVSSGN 180 ANAVRQGARLR+ATKYVETAREHFA+KGVHVDLIKLYGSMELAPLVGLADAIVDLVSSG Sbjct: 121 ANAVRQGARLRIATKYVETAREHFASKGVHVDLIKLYGSMELAPLVGLADAIVDLVSSGG 180 Query: 181 TLRANNLVEVEEIMQISSRLVVNQAALKLKRAALRPILDAFERASKAGAATA 232 TLRANNLVEVEEIMQISSRLVVNQAALKLKRAAL PILDAF+RAS+ ATA Sbjct: 181 TLRANNLVEVEEIMQISSRLVVNQAALKLKRAALAPILDAFQRASQRTGATA 232 Lambda K H 0.318 0.132 0.357 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: 266 Number of extensions: 1 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: 232 Length of database: 232 Length adjustment: 23 Effective length of query: 209 Effective length of database: 209 Effective search space: 43681 Effective search space used: 43681 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_012402130.1 BPHY_RS14035 (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.2279.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-63 199.9 0.1 2e-63 199.7 0.1 1.0 1 lcl|NCBI__GCF_000020045.1:WP_012402130.1 BPHY_RS14035 ATP phosphoribosylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020045.1:WP_012402130.1 BPHY_RS14035 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.7 0.1 2e-63 2e-63 1 183 [] 17 202 .. 17 202 .. 0.95 Alignments for each domain: == domain 1 score: 199.7 bits; conditional E-value: 2e-63 TIGR00070 1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitG 67 l++Al KGr++eet+ ll++ag+++++ +rkli ++d++v+v+++ra+d+ptyve+gaad+G+ G lcl|NCBI__GCF_000020045.1:WP_012402130.1 17 LTLALSKGRIFEETVPLLAAAGIEVTEDPetSRKLILPTNDPNVRVIIVRATDVPTYVEYGAADFGVAG 85 79**********************99877789************************************* PP TIGR00070 68 kDlleEsead.vvelldlgfgkcklvlAvpeesdvesledlkegk..riATkypnltreylekkgvkve 133 kD+l E++ +++ +dl++ +c++++Av d+ + ++++g+ riATky++++re++++kgv+v+ lcl|NCBI__GCF_000020045.1:WP_012402130.1 86 KDVLIEHGGGgLYQPIDLDIARCRMSVAVAAGFDYAN--AVRQGArlRIATKYVETAREHFASKGVHVD 152 ******77766**********************9988..44444346********************** PP TIGR00070 134 ivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 ++kl+G++Elapl+gladaIvD+v++G tLr+n+L+++eei+++s+rl++ lcl|NCBI__GCF_000020045.1:WP_012402130.1 153 LIKLYGSMELAPLVGLADAIVDLVSSGGTLRANNLVEVEEIMQISSRLVV 202 ***********************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (232 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: 9.99 // [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