Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate WP_011386874.1 AMB_RS22920 phosphoribosyl-ATP pyrophosphatase
Query= reanno::azobra:AZOBR_RS01690 (113 letters) >NCBI__GCF_000009985.1:WP_011386874.1 Length = 109 Score = 130 bits (327), Expect = 5e-36 Identities = 63/105 (60%), Positives = 78/105 (74%) Query: 7 AATAEVLDRLYATVQARKGADPETSYTAKLFHRGTAKIAQKVGEEAVETVIEAVRGDKAA 66 A +++L+ LY + +RKG DP+ SYTAKLF RG KIAQK GEEAVETV+ A+ K Sbjct: 2 AQDSKILEELYTVIASRKGTDPDKSYTAKLFARGRGKIAQKFGEEAVETVVAALSEGKDE 61 Query: 67 VASESADLLYHLMVLWADAGLEPAAVWEKLAQREGTSGIAEKNAR 111 + ESAD LYHL+VLWAD G+EPA VW +LA+R GTSGI EK +R Sbjct: 62 LVGESADTLYHLLVLWADCGVEPAKVWAELARRTGTSGIDEKKSR 106 Lambda K H 0.311 0.124 0.337 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: 78 Number of extensions: 3 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: 113 Length of database: 109 Length adjustment: 12 Effective length of query: 101 Effective length of database: 97 Effective search space: 9797 Effective search space used: 9797 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_011386874.1 AMB_RS22920 (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.20675.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-36 109.0 0.0 6.6e-36 108.7 0.0 1.1 1 lcl|NCBI__GCF_000009985.1:WP_011386874.1 AMB_RS22920 phosphoribosyl-ATP p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386874.1 AMB_RS22920 phosphoribosyl-ATP pyrophosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 108.7 0.0 6.6e-36 6.6e-36 1 84 [] 8 91 .. 8 91 .. 0.99 Alignments for each domain: == domain 1 score: 108.7 bits; conditional E-value: 6.6e-36 TIGR03188 1 leeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVlla 71 leeL++vi++rk +dp++Sytakl+++g+ ki++K+gEEavE+++aa +e k+elv E+aD lYhllVl+a lcl|NCBI__GCF_000009985.1:WP_011386874.1 8 LEELYTVIASRKGTDPDKSYTAKLFARGRGKIAQKFGEEAVETVVAALSEGKDELVGESADTLYHLLVLWA 78 799******************************************************************** PP TIGR03188 72 ekgvsledvlaeL 84 + gv++++v+aeL lcl|NCBI__GCF_000009985.1:WP_011386874.1 79 DCGVEPAKVWAEL 91 ***********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (109 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: 3.65 // [ok]
This GapMind analysis is from Apr 09 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