Align Phosphoribosyl-AMP cyclohydrolase; PRA-CH; EC 3.5.4.19 (characterized)
to candidate WP_011189880.1 DP_RS13395 phosphoribosyl-AMP cyclohydrolase
Query= SwissProt::O26347 (138 letters) >NCBI__GCF_000025945.1:WP_011189880.1 Length = 127 Score = 143 bits (360), Expect = 1e-39 Identities = 71/126 (56%), Positives = 93/126 (73%), Gaps = 5/126 (3%) Query: 12 LNFRHNINGEDLIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGE 71 LNF +++G L+ AV QD+ +GEVLM+AY+N+ + +TLETG AHYWS SR LWLKGE Sbjct: 4 LNFEKSVDG--LLPAVVQDYVSGEVLMLAYINKLSWEKTLETGQAHYWSRSRNSLWLKGE 61 Query: 72 SSGHVQRVKDVLVDCDGDAVVLKVEQEG-GACHTGYRSCFYRSIDGDELKVREDAVKVFD 130 SSG+VQ + D+LVDCD D VV KV+Q G ACHTG+RSCF+R + EL V + +FD Sbjct: 62 SSGNVQVIHDILVDCDSDTVVFKVDQIGDAACHTGHRSCFFRRVHQGELVV--EGKPLFD 119 Query: 131 PEEIYG 136 P ++YG Sbjct: 120 PAQVYG 125 Lambda K H 0.318 0.137 0.410 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: 97 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: 138 Length of database: 127 Length adjustment: 15 Effective length of query: 123 Effective length of database: 112 Effective search space: 13776 Effective search space used: 13776 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 (21.7 bits) S2: 41 (20.4 bits)
Align candidate WP_011189880.1 DP_RS13395 (phosphoribosyl-AMP cyclohydrolase)
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.20685.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-38 115.6 0.4 4.8e-38 115.2 0.4 1.1 1 lcl|NCBI__GCF_000025945.1:WP_011189880.1 DP_RS13395 phosphoribosyl-AMP cy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025945.1:WP_011189880.1 DP_RS13395 phosphoribosyl-AMP cyclohydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 115.2 0.4 4.8e-38 4.8e-38 1 74 [] 28 102 .. 28 102 .. 0.98 Alignments for each domain: == domain 1 score: 115.2 bits; conditional E-value: 4.8e-38 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkg.aaCHtg 68 mlay+n+ ++ektletg+a+y+Srsr++lw kGe+sgnvq +++i +dcD+D++++kv+q g aaCHtg lcl|NCBI__GCF_000025945.1:WP_011189880.1 28 MLAYINKLSWEKTLETGQAHYWSRSRNSLWLKGESSGNVQVIHDILVDCDSDTVVFKVDQIGdAACHTG 96 9************************************************************868***** PP PRA-CH 69 ersCFy 74 +rsCF+ lcl|NCBI__GCF_000025945.1:WP_011189880.1 97 HRSCFF 102 *****6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (127 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: 3.40 // [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