Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_010529312.1 ON01_RS01875 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >NCBI__GCF_000224785.1:WP_010529312.1 Length = 214 Score = 165 bits (417), Expect = 6e-46 Identities = 88/204 (43%), Positives = 126/204 (61%), Gaps = 6/204 (2%) Query: 4 EQQRRELDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWT 63 ++Q +L +++ GL+P I+Q A + EVL L YMN E+L++TLE+G+ F+SR +Q LW Sbjct: 3 DEQLNKLTFDQ-QGLIPAIIQDAETAEVLTLAYMNKESLNRTLETGETWFYSRKRQELWH 61 Query: 64 KGETSGNFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGDTAHQ-----WLFLYQL 118 KG TSGN +V +I DCD DTLLVL P+GP CH G SCF T + + L +L Sbjct: 62 KGATSGNKQHVKTIRYDCDADTLLVLVEPLGPVCHTGEKSCFYSTLQKIESPDQMGLNEL 121 Query: 119 EQLLAERKSADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMY 178 L+ +R+ E SYT L+ G +I +KVGEE E + A +D E+T E +DL Y Sbjct: 122 AALIRQRRKEANEGSYTTYLFEEGIDKILKKVGEETSEVIIGAKNNDHSEMTWEIADLTY 181 Query: 179 HLLVLLQDQGLDLTTVIENLRKRH 202 H LVL+ G+ ++ + + L KRH Sbjct: 182 HTLVLMDLMGVSISDIKQELAKRH 205 Lambda K H 0.317 0.132 0.384 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: 136 Number of extensions: 7 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: 203 Length of database: 214 Length adjustment: 21 Effective length of query: 182 Effective length of database: 193 Effective search space: 35126 Effective search space used: 35126 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: 45 (21.9 bits)
Align candidate WP_010529312.1 ON01_RS01875 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE)
to HMM PF01502 (PRA-CH)
# 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/PF01502.22.hmm # target sequence database: /tmp/gapView.3411270.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PRA-CH [M=74] Accession: PF01502.22 Description: Phosphoribosyl-AMP cyclohydrolase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-39 119.5 0.1 3.5e-39 118.9 0.1 1.3 1 NCBI__GCF_000224785.1:WP_010529312.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010529312.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 118.9 0.1 3.5e-39 3.5e-39 2 74 .] 32 104 .. 31 104 .. 0.99 Alignments for each domain: == domain 1 score: 118.9 bits; conditional E-value: 3.5e-39 PRA-CH 2 laymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtgersCFy 74 laymn+e+l++tletg++++ySr+rq+lw+kG+tsgn q+vk+ir+dcD+D+ll+ ve+ g++CHtge+sCFy NCBI__GCF_000224785.1:WP_010529312.1 32 LAYMNKESLNRTLETGETWFYSRKRQELWHKGATSGNKQHVKTIRYDCDADTLLVLVEPLGPVCHTGEKSCFY 104 79**********************************************************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (214 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.27 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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