Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate RR42_RS18875 RR42_RS18875 phosphoribosyl-ATP pyrophosphatase
Query= reanno::BFirm:BPHYT_RS17670 (131 letters) >FitnessBrowser__Cup4G11:RR42_RS18875 Length = 126 Score = 150 bits (378), Expect = 8e-42 Identities = 79/122 (64%), Positives = 93/122 (76%), Gaps = 7/122 (5%) Query: 9 SSDSASTTDTLMRLAAIIDSRK---GGDPDVSYVSRLFHKGDDAVLKKIGEEATEVVLAA 65 S S+TD L RLAA+++SRK GGDPD SYV+RLFHKGDDA+LKKIGEEATE V+AA Sbjct: 2 SEQHLSSTDVLARLAAVLESRKPENGGDPDKSYVARLFHKGDDAILKKIGEEATETVMAA 61 Query: 66 KDARHGGAPKALVG----EVADLWFHCLVMLSHFDLSPADVLAELERREGMSGIEEKALR 121 KDAR G VG EVADLWFH +V+L+ F L PADV+ EL RREG+SG+EEKA R Sbjct: 62 KDARAAGLGPEAVGKVVYEVADLWFHSMVLLARFGLKPADVVNELARREGLSGLEEKAQR 121 Query: 122 KS 123 K+ Sbjct: 122 KA 123 Lambda K H 0.313 0.129 0.359 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: 94 Number of extensions: 4 Number of successful extensions: 3 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: 131 Length of database: 126 Length adjustment: 14 Effective length of query: 117 Effective length of database: 112 Effective search space: 13104 Effective search space used: 13104 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: 41 (21.5 bits) S2: 41 (20.4 bits)
Align candidate RR42_RS18875 RR42_RS18875 (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.25613.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-31 93.3 0.0 8.5e-31 92.3 0.0 1.5 1 lcl|FitnessBrowser__Cup4G11:RR42_RS18875 RR42_RS18875 phosphoribosyl-ATP Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS18875 RR42_RS18875 phosphoribosyl-ATP pyrophosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 92.3 0.0 8.5e-31 8.5e-31 1 84 [] 12 106 .. 12 106 .. 0.92 Alignments for each domain: == domain 1 score: 92.3 bits; conditional E-value: 8.5e-31 TIGR03188 1 leeLeevieerke...edpeeSytakllekgedkilkKvgEEavEviiaaknedkee........lveE 58 l +L++v+e+rk dp++Sy+a+l++kg+d+ilkK+gEEa+E+++aak+++ +v+E lcl|FitnessBrowser__Cup4G11:RR42_RS18875 12 LARLAAVLESRKPengGDPDKSYVARLFHKGDDAILKKIGEEATETVMAAKDARAAGlgpeavgkVVYE 80 679********9866689**********************************98765666677889*** PP TIGR03188 59 aaDllYhllVllaekgvsledvlaeL 84 +aDl++h +Vlla+ g++++dv++eL lcl|FitnessBrowser__Cup4G11:RR42_RS18875 81 VADLWFHSMVLLARFGLKPADVVNEL 106 ************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (126 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: 1.41 // [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