Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate WP_086509319.1 BZY95_RS07450 phosphoribosyl-ATP diphosphatase
Query= reanno::Marino:GFF3253 (109 letters) >NCBI__GCF_002151265.1:WP_086509319.1 Length = 111 Score = 141 bits (356), Expect = 2e-39 Identities = 75/111 (67%), Positives = 87/111 (78%), Gaps = 2/111 (1%) Query: 1 MSDVLENLARVLEARKEADPETSYVASLHAKGLNKILEKVGEECTETLLAAKDAEHSG-- 58 M D+L+ L VL R+ ADP SYVA+LH KGLNKILEKVGEE TETLLAAKDAE G Sbjct: 1 MRDILDELFDVLSQRRSADPAESYVAALHDKGLNKILEKVGEEATETLLAAKDAETGGDD 60 Query: 59 ETRDVVYETADLWFHSMVMLSRLGLGPKDILDELASRFDLSGLEEKASRNK 109 E + +V ETADLWFHS+VMLS LGL +D+LDELA RF +SG EEKA+R+K Sbjct: 61 ERQALVAETADLWFHSLVMLSHLGLDHRDVLDELARRFGISGHEEKAARSK 111 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: 76 Number of extensions: 4 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: 111 Length adjustment: 12 Effective length of query: 97 Effective length of database: 99 Effective search space: 9603 Effective search space used: 9603 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_086509319.1 BZY95_RS07450 (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.29556.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-32 96.3 0.2 6.9e-32 95.8 0.2 1.2 1 lcl|NCBI__GCF_002151265.1:WP_086509319.1 BZY95_RS07450 phosphoribosyl-ATP Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086509319.1 BZY95_RS07450 phosphoribosyl-ATP diphosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 95.8 0.2 6.9e-32 6.9e-32 1 84 [] 5 94 .. 5 94 .. 0.90 Alignments for each domain: == domain 1 score: 95.8 bits; conditional E-value: 6.9e-32 TIGR03188 1 leeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkee......lveEaaDllYh 65 l+eL++v+++r+++dp eSy+a l++kg +kil+KvgEEa+E+++aak++++ lv E+aDl++h lcl|NCBI__GCF_002151265.1:WP_086509319.1 5 LDELFDVLSQRRSADPAESYVAALHDKGLNKILEKVGEEATETLLAAKDAETGGdderqaLVAETADLWFH 75 789*********************************************864322222356*********** PP TIGR03188 66 llVllaekgvsledvlaeL 84 lV+l++ g++ +dvl+eL lcl|NCBI__GCF_002151265.1:WP_086509319.1 76 SLVMLSHLGLDHRDVLDEL 94 ****************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (111 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: 4.62 // [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