Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate WP_013134065.1 ARNIT_RS01265 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= reanno::Korea:Ga0059261_1051 (107 letters) >NCBI__GCF_000092245.1:WP_013134065.1 Length = 227 Score = 81.3 bits (199), Expect = 7e-21 Identities = 44/100 (44%), Positives = 62/100 (62%) Query: 5 ILDTLEAVIRERRTGDPATSYVAKLTAKGRAKIAQKLGEEAVEAAIAAVQDDRDGLTGEA 64 +LD L VI++R+ DP SY +KL + +K+ EEA E A D+ + + EA Sbjct: 125 VLDNLFHVIQDRKNDDPKKSYTSKLLNGKENSMLKKIVEEAGEFTFAVKDDNSEEMIYEA 184 Query: 65 ADLIFHLLVLLADTGLSLDDVRAELARREGISGIDEKASR 104 ADL++H +V LA +S D ++ ELARR G+SGIDEK SR Sbjct: 185 ADLVYHTMVALASKDISPDRIKQELARRFGMSGIDEKNSR 224 Lambda K H 0.315 0.132 0.347 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: 49 Number of extensions: 1 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: 107 Length of database: 227 Length adjustment: 17 Effective length of query: 90 Effective length of database: 210 Effective search space: 18900 Effective search space used: 18900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 43 (21.2 bits)
Align candidate WP_013134065.1 ARNIT_RS01265 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE)
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.27306.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-34 101.9 1.3 2.7e-33 100.3 0.3 2.1 2 lcl|NCBI__GCF_000092245.1:WP_013134065.1 ARNIT_RS01265 bifunctional phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013134065.1 ARNIT_RS01265 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.6 0.0 0.087 0.087 25 40 .. 51 65 .. 44 90 .. 0.59 2 ! 100.3 0.3 2.7e-33 2.7e-33 1 84 [] 126 209 .. 126 209 .. 0.98 Alignments for each domain: == domain 1 score: -0.6 bits; conditional E-value: 0.087 TIGR03188 25 lekgedkilkKvgEEa 40 +++ +++i kK gEE+ lcl|NCBI__GCF_000092245.1:WP_013134065.1 51 FSRSKQRIWKK-GEES 65 56666677766.4443 PP == domain 2 score: 100.3 bits; conditional E-value: 2.7e-33 TIGR03188 1 leeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVl 69 l++L++vi++rk++dp++Syt+kll+ e+ +lkK+ EEa E+ +a+k++++ee+++EaaDl+Yh++V+ lcl|NCBI__GCF_000092245.1:WP_013134065.1 126 LDNLFHVIQDRKNDDPKKSYTSKLLNGKENSMLKKIVEEAGEFTFAVKDDNSEEMIYEAADLVYHTMVA 194 789****************************************************************** PP TIGR03188 70 laekgvsledvlaeL 84 la+k++s++++ +eL lcl|NCBI__GCF_000092245.1:WP_013134065.1 195 LASKDISPDRIKQEL 209 ************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (227 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: 3.30 // [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