Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate WP_011736885.1 PPRO_RS15165 phosphoribosyl-ATP pyrophosphatase
Query= reanno::Marino:GFF3253 (109 letters) >NCBI__GCF_000015045.1:WP_011736885.1 Length = 108 Score = 84.7 bits (208), Expect = 3e-22 Identities = 46/104 (44%), Positives = 67/104 (64%), Gaps = 4/104 (3%) Query: 4 VLENLARVLEARKEADPETSYVASLHAKGLNKILEKVGEECTETLLAAKDAEHSGETRDV 63 +L+ + V+ ARK E SY ASL KGL+ +L+KVGEE TE ++A K G +V Sbjct: 7 ILDAVYGVILARKATQTENSYTASLMRKGLDSVLKKVGEEATELVIAGK----GGVADEV 62 Query: 64 VYETADLWFHSMVMLSRLGLGPKDILDELASRFDLSGLEEKASR 107 VYE ADL+FH++++LS + + + EL RF +SG++EK SR Sbjct: 63 VYEAADLFFHTLLLLSYQDIPLERVYTELRRRFGISGIDEKNSR 106 Lambda K H 0.312 0.129 0.352 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: 35 Number of extensions: 2 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: 109 Length of database: 108 Length adjustment: 12 Effective length of query: 97 Effective length of database: 96 Effective search space: 9312 Effective search space used: 9312 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 (20.9 bits) S2: 40 (20.0 bits)
Align candidate WP_011736885.1 PPRO_RS15165 (phosphoribosyl-ATP pyrophosphatase)
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.24269.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-32 97.0 0.1 3.4e-32 96.8 0.1 1.1 1 lcl|NCBI__GCF_000015045.1:WP_011736885.1 PPRO_RS15165 phosphoribosyl-ATP Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011736885.1 PPRO_RS15165 phosphoribosyl-ATP pyrophosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 96.8 0.1 3.4e-32 3.4e-32 1 84 [] 8 91 .. 8 91 .. 0.98 Alignments for each domain: == domain 1 score: 96.8 bits; conditional E-value: 3.4e-32 TIGR03188 1 leeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVlla 71 l++++ vi +rk+++ e+Syta+l++kg d +lkKvgEEa+E++ia k + +e+v+EaaDl++h+l ll+ lcl|NCBI__GCF_000015045.1:WP_011736885.1 8 LDAVYGVILARKATQTENSYTASLMRKGLDSVLKKVGEEATELVIAGKGGVADEVVYEAADLFFHTLLLLS 78 678999***************************************************************** PP TIGR03188 72 ekgvsledvlaeL 84 ++++ le+v++eL lcl|NCBI__GCF_000015045.1:WP_011736885.1 79 YQDIPLERVYTEL 91 **********998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (108 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: 4.38 // [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