Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate WP_029936328.1 N746_RS0110280 phosphoribosyl-ATP diphosphatase
Query= reanno::pseudo5_N2C3_1:AO356_09525 (110 letters) >NCBI__GCF_000711195.1:WP_029936328.1 Length = 50 Score = 67.0 bits (162), Expect = 3e-17 Identities = 32/50 (64%), Positives = 44/50 (88%) Query: 1 MSDTLTRLAQVLEERKGAAADSSYVASLYHKGLNKILEKVGEESVETIIA 50 MS+ LT+L Q+LE RK +ADSSYVASLY KGL++IL+K+GEE++ET++A Sbjct: 1 MSEILTQLDQLLETRKSESADSSYVASLYAKGLDQILKKLGEEAIETVMA 50 Lambda K H 0.314 0.129 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: 30 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: 110 Length of database: 50 Length adjustment: 7 Effective length of query: 103 Effective length of database: 43 Effective search space: 4429 Effective search space used: 4429 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: 37 (19.7 bits) S2: 37 (18.9 bits)
Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate WP_081836020.1 N746_RS0100005 hypothetical protein
Query= reanno::pseudo5_N2C3_1:AO356_09525 (110 letters) >NCBI__GCF_000711195.1:WP_081836020.1 Length = 46 Score = 56.6 bits (135), Expect = 4e-14 Identities = 28/44 (63%), Positives = 31/44 (70%) Query: 64 IYETADLWFHSLVMLAQLGQHPQAVLDELDRRFGLSGHVEKASR 107 +YE DLWFHSLV+LA VL EL+RRFGLSG VEKA R Sbjct: 1 MYEVTDLWFHSLVLLAHQNLSSADVLKELERRFGLSGLVEKAQR 44 Lambda K H 0.314 0.129 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: 29 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: 110 Length of database: 46 Length adjustment: 6 Effective length of query: 104 Effective length of database: 40 Effective search space: 4160 Effective search space used: 4160 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: 37 (19.7 bits) S2: 37 (18.9 bits)
Align candidate WP_029936328.1 N746_RS0110280 (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.18838.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-18 53.0 0.2 1.7e-18 52.9 0.2 1.0 1 lcl|NCBI__GCF_000711195.1:WP_029936328.1 N746_RS0110280 phosphoribosyl-AT Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711195.1:WP_029936328.1 N746_RS0110280 phosphoribosyl-ATP diphosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 52.9 0.2 1.7e-18 1.7e-18 1 46 [. 5 50 .] 5 50 .] 0.98 Alignments for each domain: == domain 1 score: 52.9 bits; conditional E-value: 1.7e-18 TIGR03188 1 leeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviia 46 l +L++++e rk+e+ ++Sy+a+l++kg d+ilkK+gEEa+E+++a lcl|NCBI__GCF_000711195.1:WP_029936328.1 5 LTQLDQLLETRKSESADSSYVASLYAKGLDQILKKLGEEAIETVMA 50 689*****************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (50 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: 1.59 // [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