Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate WP_038209771.1 Q392_RS15555 phosphoribosyl-ATP diphosphatase
Query= reanno::BFirm:BPHYT_RS17670 (131 letters) >NCBI__GCF_000745855.1:WP_038209771.1 Length = 126 Score = 164 bits (416), Expect = 3e-46 Identities = 83/124 (66%), Positives = 99/124 (79%), Gaps = 3/124 (2%) Query: 11 DSASTTDTLMRLAAIIDSR---KGGDPDVSYVSRLFHKGDDAVLKKIGEEATEVVLAAKD 67 + ASTTD L RLAA+IDSR +GGDP+ SYV+RL H+G DA LKKIGEEATEVV+AAKD Sbjct: 3 EPASTTDVLDRLAAVIDSRLPGRGGDPEASYVARLLHRGPDAFLKKIGEEATEVVMAAKD 62 Query: 68 ARHGGAPKALVGEVADLWFHCLVMLSHFDLSPADVLAELERREGMSGIEEKALRKSRDRE 127 A HGG + +V EVADLWFH ++ L+H+ L+P DV AEL RREG SGIEEKALRK++ RE Sbjct: 63 ADHGGERQKIVNEVADLWFHSMIALAHYGLAPRDVAAELARREGTSGIEEKALRKAQGRE 122 Query: 128 QNGD 131 GD Sbjct: 123 AAGD 126 Lambda K H 0.313 0.129 0.359 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: 100 Number of extensions: 7 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: 131 Length of database: 126 Length adjustment: 14 Effective length of query: 117 Effective length of database: 112 Effective search space: 13104 Effective search space used: 13104 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 bits) S2: 41 (20.4 bits)
Align candidate WP_038209771.1 Q392_RS15555 (phosphoribosyl-ATP diphosphatase)
to HMM TIGR03188 (hisE: phosphoribosyl-ATP diphosphatase (EC 3.6.1.31))
# 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/TIGR03188.hmm # target sequence database: /tmp/gapView.23738.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03188 [M=84] Accession: TIGR03188 Description: histidine_hisI: phosphoribosyl-ATP diphosphatase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-30 90.6 0.0 3.7e-30 90.3 0.0 1.2 1 lcl|NCBI__GCF_000745855.1:WP_038209771.1 Q392_RS15555 phosphoribosyl-ATP Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745855.1:WP_038209771.1 Q392_RS15555 phosphoribosyl-ATP diphosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 90.3 0.0 3.7e-30 3.7e-30 1 84 [] 11 101 .. 11 101 .. 0.91 Alignments for each domain: == domain 1 score: 90.3 bits; conditional E-value: 3.7e-30 TIGR03188 1 leeLeevieerke...edpeeSytakllekgedkilkKvgEEavEviiaaknedkee....lveEaaDl 62 l++L++vi++r dpe Sy+a+ll++g d+ lkK+gEEa+Ev++aak++d+ +v+E+aDl lcl|NCBI__GCF_000745855.1:WP_038209771.1 11 LDRLAAVIDSRLPgrgGDPEASYVARLLHRGPDAFLKKIGEEATEVVMAAKDADHGGerqkIVNEVADL 79 7899*******766669**********************************9875433445******** PP TIGR03188 63 lYhllVllaekgvsledvlaeL 84 ++h +++la+ g+ ++dv+aeL lcl|NCBI__GCF_000745855.1:WP_038209771.1 80 WFHSMIALAHYGLAPRDVAAEL 101 ********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (126 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 3.26 // [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