Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate WP_093428508.1 BM272_RS09270 phosphoribosyl-ATP diphosphatase
Query= reanno::psRCH2:GFF3874 (110 letters) >NCBI__GCF_900112605.1:WP_093428508.1 Length = 115 Score = 129 bits (323), Expect = 1e-35 Identities = 68/105 (64%), Positives = 79/105 (75%), Gaps = 4/105 (3%) Query: 3 DTLTRLAEVLEARKGAAPDSSYVASLYHKGLNKILEKVGEESVETILAAKDAAVSGDASD 62 DTL LA VLEARKGA PDSSYVA LYHKG++ I +KVGEE+ ET++AAKD GD Sbjct: 4 DTLAELARVLEARKGADPDSSYVAGLYHKGVDGIAKKVGEEATETVMAAKD----GDPDA 59 Query: 63 LIYETADLWFHSMVMLAALGQHPQAVLDELDRRFGLSGHAEKAAR 107 L++E ADLWFHS+V+LA G P+AVL EL RFGLSG EKA R Sbjct: 60 LVHEVADLWFHSLVLLAQQGLGPEAVLAELRGRFGLSGLEEKARR 104 Lambda K H 0.314 0.128 0.353 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: 72 Number of extensions: 3 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: 110 Length of database: 115 Length adjustment: 12 Effective length of query: 98 Effective length of database: 103 Effective search space: 10094 Effective search space used: 10094 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: 40 (21.1 bits) S2: 40 (20.0 bits)
Align candidate WP_093428508.1 BM272_RS09270 (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.372457.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-35 107.2 0.0 2.4e-35 106.9 0.0 1.1 1 NCBI__GCF_900112605.1:WP_093428508.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900112605.1:WP_093428508.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 106.9 0.0 2.4e-35 2.4e-35 1 84 [] 6 89 .. 6 89 .. 0.99 Alignments for each domain: == domain 1 score: 106.9 bits; conditional E-value: 2.4e-35 TIGR03188 1 leeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVllaekgv 75 l eL++v+e+rk +dp++Sy+a l++kg d i+kKvgEEa+E+++aak++d ++lv+E+aDl++h lVlla++g+ NCBI__GCF_900112605.1:WP_093428508.1 6 LAELARVLEARKGADPDSSYVAGLYHKGVDGIAKKVGEEATETVMAAKDGDPDALVHEVADLWFHSLVLLAQQGL 80 689************************************************************************ PP TIGR03188 76 sledvlaeL 84 +e+vlaeL NCBI__GCF_900112605.1:WP_093428508.1 81 GPEAVLAEL 89 *******98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (115 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: 7.90 // [ok]
This GapMind analysis is from Jul 25 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