Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_037570710.1 BS73_RS08290 phosphoribosyl-ATP diphosphatase
Query= BRENDA::P9WMM9 (93 letters) >NCBI__GCF_000744815.1:WP_037570710.1 Length = 89 Score = 108 bits (269), Expect = 2e-29 Identities = 54/89 (60%), Positives = 68/89 (76%) Query: 5 LAVKTFEDLFAELGDRARTRPADSTTVAALDGGVHALGKKLLEEAGEVWLAAEHESNDAL 64 +A+KTFE+LFAEL +A S T + GVHA+GKK++EEA EVW+AAEHES+D Sbjct: 1 MALKTFEELFAELQQKAAAGETGSRTAELVGLGVHAIGKKVVEEAAEVWMAAEHESDDRT 60 Query: 65 AEEISQLLYWTQVLMISRGLSLDDVYRKL 93 AEEISQLLY QV+MI+RGL L+DVY+ L Sbjct: 61 AEEISQLLYHLQVMMIARGLRLEDVYKHL 89 Lambda K H 0.316 0.131 0.366 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: 55 Number of extensions: 2 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: 93 Length of database: 89 Length adjustment: 9 Effective length of query: 84 Effective length of database: 80 Effective search space: 6720 Effective search space used: 6720 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: 39 (20.7 bits) S2: 39 (19.6 bits)
Align candidate WP_037570710.1 BS73_RS08290 (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.4122607.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-28 83.1 1.0 7.1e-28 83.0 1.0 1.0 1 NCBI__GCF_000744815.1:WP_037570710.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037570710.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 83.0 1.0 7.1e-28 7.1e-28 2 84 .] 7 89 .] 6 89 .] 0.98 Alignments for each domain: == domain 1 score: 83.0 bits; conditional E-value: 7.1e-28 TIGR03188 2 eeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVllaekgvs 76 eeL++ +++++++ +++S ta+l+ g ++i kKv EEa+Ev++aa++e++++ +eE+++llYhl+V++ ++g++ NCBI__GCF_000744815.1:WP_037570710.1 7 EELFAELQQKAAAGETGSRTAELVGLGVHAIGKKVVEEAAEVWMAAEHESDDRTAEEISQLLYHLQVMMIARGLR 81 89************************************************************************* PP TIGR03188 77 ledvlaeL 84 ledv+++L NCBI__GCF_000744815.1:WP_037570710.1 82 LEDVYKHL 89 *****987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (89 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: 6.22 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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