Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_011321574.1 AVA_RS24950 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >NCBI__GCF_000204075.1:WP_011321574.1 Length = 216 Score = 147 bits (370), Expect = 2e-40 Identities = 82/199 (41%), Positives = 117/199 (58%), Gaps = 18/199 (9%) Query: 17 GLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSGNFLNVVS 76 GL+P IVQ + G VLM+ +MN E+L KTL++G+ F+SR++Q LW KG TSG+ V S Sbjct: 24 GLVPAIVQDYLDGTVLMMAWMNRESLQKTLDTGETWFWSRSRQELWHKGGTSGHTQKVQS 83 Query: 77 IAPDCDNDTLLVLANPIGP-TCHKGTSSCF-----------GDTAHQWLFLYQLEQLLAE 124 I DCD+D LLV IG CH G SCF GDT L Q+ Q++ + Sbjct: 84 IRYDCDSDALLVGVEQIGDIACHTGERSCFHQVEGKIVAPPGDT------LSQVFQVICD 137 Query: 125 RKSADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLL 184 R++ E+SYT+KL+A G +I +K+GEE E +A D+ + E +DL+YH LV L Sbjct: 138 RQNHPSESSYTSKLFAGGDNKILKKIGEESAEVVMACKDDDQEAIAGEVADLLYHTLVAL 197 Query: 185 QDQGLDLTTVIENLRKRHQ 203 +D+ V L++R + Sbjct: 198 AHHQVDIKAVYRKLQERRR 216 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: 119 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: 216 Length adjustment: 21 Effective length of query: 182 Effective length of database: 195 Effective search space: 35490 Effective search space used: 35490 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_011321574.1 AVA_RS24950 (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.18359.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-40 122.4 1.0 2.8e-40 122.4 1.0 1.8 2 lcl|NCBI__GCF_000204075.1:WP_011321574.1 AVA_RS24950 bifunctional phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204075.1:WP_011321574.1 AVA_RS24950 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 122.4 1.0 2.8e-40 2.8e-40 1 74 [] 40 114 .. 40 114 .. 0.98 2 ? -1.9 0.0 0.17 0.17 34 57 .. 165 185 .. 155 189 .. 0.63 Alignments for each domain: == domain 1 score: 122.4 bits; conditional E-value: 2.8e-40 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkg.aaCHtg 68 m+a+mn+e+l+ktl+tg+++++Srsrq+lw+kG tsg++qkv++ir+dcD+Dall+ veq g aCHtg lcl|NCBI__GCF_000204075.1:WP_011321574.1 40 MMAWMNRESLQKTLDTGETWFWSRSRQELWHKGGTSGHTQKVQSIRYDCDSDALLVGVEQIGdIACHTG 108 9************************************************************868***** PP PRA-CH 69 ersCFy 74 ersCF+ lcl|NCBI__GCF_000204075.1:WP_011321574.1 109 ERSCFH 114 *****6 PP == domain 2 score: -1.9 bits; conditional E-value: 0.17 PRA-CH 34 etsgnvqkvkeirldcDeDalllk 57 e+s +v+ d D++a+ + lcl|NCBI__GCF_000204075.1:WP_011321574.1 165 EESA---EVVMACKDDDQEAIAGE 185 5544...45555667777777655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (216 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: 6.59 // [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