Align Phosphoribosyl-AMP cyclohydrolase; PRA-CH; EC 3.5.4.19 (characterized)
to candidate GFF3873 Psest_3943 Phosphoribosyl-AMP cyclohydrolase
Query= SwissProt::O26347 (138 letters) >FitnessBrowser__psRCH2:GFF3873 Length = 131 Score = 135 bits (339), Expect = 3e-37 Identities = 66/122 (54%), Positives = 85/122 (69%), Gaps = 3/122 (2%) Query: 17 NINGEDLIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSGHV 76 N N + ++ A+AQD+++G VLM+A+MNREAL T + G A YWS SRGKLW KGE SGHV Sbjct: 8 NWNADGMVPAIAQDYQSGRVLMMAWMNREALALTAQEGRAIYWSRSRGKLWRKGEESGHV 67 Query: 77 QRVKDVLVDCDGDAVVLKVEQEGG-ACHTGYRSCFYRSIDGDELKVREDAVKVFDPEEIY 135 QR+ ++ +DCD D ++L VEQ GG ACHTG SCFYR + KV E +K DP IY Sbjct: 68 QRLHELRLDCDADVIILMVEQIGGIACHTGRESCFYRVFENGSWKVVEPVLK--DPHAIY 125 Query: 136 GD 137 + Sbjct: 126 AE 127 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: 91 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: 138 Length of database: 131 Length adjustment: 15 Effective length of query: 123 Effective length of database: 116 Effective search space: 14268 Effective search space used: 14268 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: 42 (20.8 bits)
Align candidate GFF3873 Psest_3943 (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.681.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-39 118.5 0.1 6.1e-39 118.1 0.1 1.2 1 lcl|FitnessBrowser__psRCH2:GFF3873 Psest_3943 Phosphoribosyl-AMP cy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF3873 Psest_3943 Phosphoribosyl-AMP cyclohydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 118.1 0.1 6.1e-39 6.1e-39 1 74 [] 29 103 .. 29 103 .. 0.98 Alignments for each domain: == domain 1 score: 118.1 bits; conditional E-value: 6.1e-39 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkg.aaCHtgersCFy 74 m+a+mn+eal+ t ++g+a+y+Srsr klw+kGe+sg+vq+++e+rldcD+D+++l+veq g aCHtg++sCFy lcl|FitnessBrowser__psRCH2:GFF3873 29 MMAWMNREALALTAQEGRAIYWSRSRGKLWRKGEESGHVQRLHELRLDCDADVIILMVEQIGgIACHTGRESCFY 103 9************************************************************648**********7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (131 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: 4.27 // [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