Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate CA265_RS03605 CA265_RS03605 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >FitnessBrowser__Pedo557:CA265_RS03605 Length = 200 Score = 214 bits (545), Expect = 8e-61 Identities = 107/194 (55%), Positives = 138/194 (71%), Gaps = 1/194 (0%) Query: 10 LDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSG 69 LDW+KT GL+PVI+Q + EVLMLGYMN EAL+KT GKVTFFSR+K RLWTKGETS Sbjct: 8 LDWDKTAGLLPVIIQDYKTLEVLMLGYMNAEALEKTQAEGKVTFFSRSKNRLWTKGETSN 67 Query: 70 NFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGDTAHQWLFLYQLEQLLAERKSAD 129 NFL V + DCD+DT+L+ A+ +GPTCH G+ SCF T + F+++LE ++ +R Sbjct: 68 NFLYVKELFVDCDHDTILIKADAVGPTCHTGSRSCF-KTDYNQNFIFELENIINDRYENP 126 Query: 130 PETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLLQDQGL 189 E SY K+ G +IAQKVGEEGVET +AA EL EASDL++HLL LL+++GL Sbjct: 127 VEGSYINKMRNKGLNKIAQKVGEEGVETVIAALAETEEELIGEASDLVFHLLFLLKEKGL 186 Query: 190 DLTTVIENLRKRHQ 203 + + +NL KRHQ Sbjct: 187 SIQDIAKNLEKRHQ 200 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: 140 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: 203 Length of database: 200 Length adjustment: 21 Effective length of query: 182 Effective length of database: 179 Effective search space: 32578 Effective search space used: 32578 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 CA265_RS03605 CA265_RS03605 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase)
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.25832.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-37 111.8 0.1 8.6e-37 111.2 0.1 1.3 1 lcl|FitnessBrowser__Pedo557:CA265_RS03605 CA265_RS03605 bifunctional phosp Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS03605 CA265_RS03605 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosy # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 111.2 0.1 8.6e-37 8.6e-37 1 74 [] 31 104 .. 31 104 .. 0.99 Alignments for each domain: == domain 1 score: 111.2 bits; conditional E-value: 8.6e-37 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtg 68 ml+ymn+ealekt ++gk++++Srs+++lw+kGets+n++ vke+ +dcD+D++l+k++ g++CHtg lcl|FitnessBrowser__Pedo557:CA265_RS03605 31 MLGYMNAEALEKTQAEGKVTFFSRSKNRLWTKGETSNNFLYVKELFVDCDHDTILIKADAVGPTCHTG 98 9******************************************************************* PP PRA-CH 69 ersCFy 74 +rsCF+ lcl|FitnessBrowser__Pedo557:CA265_RS03605 99 SRSCFK 104 *****5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (200 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: 5.25 // [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