Align Phosphoribosyl-AMP cyclohydrolase; PRA-CH; EC 3.5.4.19 (characterized)
to candidate RR42_RS18880 RR42_RS18880 phosphoribosyl-AMP cyclohydrolase
Query= SwissProt::O26347 (138 letters) >FitnessBrowser__Cup4G11:RR42_RS18880 Length = 135 Score = 111 bits (278), Expect = 4e-30 Identities = 58/118 (49%), Positives = 78/118 (66%), Gaps = 7/118 (5%) Query: 23 LIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSGHVQRVKDV 82 L+ + Q+ + +VLM A+MNREAL+RT E G A +WS SR +LW KGE SGHVQ+V ++ Sbjct: 16 LVPVIVQEVGSNDVLMFAFMNREALQRTAEIGEAVFWSRSRKRLWHKGEESGHVQKVHEM 75 Query: 83 LVDCDGDAVVLKVEQEGG-ACHTGYRSCFYRSIDGD----ELKVREDAVKVFDPEEIY 135 +DCD D V+LKV Q G ACHTG SCF++ +GD + + E +K DP IY Sbjct: 76 RLDCDEDVVLLKVTQNDGIACHTGRHSCFFQKFEGDAESGDWQTVEPVLK--DPSTIY 131 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: 84 Number of extensions: 8 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: 135 Length adjustment: 15 Effective length of query: 123 Effective length of database: 120 Effective search space: 14760 Effective search space used: 14760 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 RR42_RS18880 RR42_RS18880 (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.4872.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-40 122.3 0.3 7.7e-40 121.0 0.4 1.6 2 lcl|FitnessBrowser__Cup4G11:RR42_RS18880 RR42_RS18880 phosphoribosyl-AMP Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS18880 RR42_RS18880 phosphoribosyl-AMP cyclohydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 121.0 0.4 7.7e-40 7.7e-40 1 74 [] 31 105 .. 31 105 .. 0.98 2 ? -2.3 0.0 0.23 0.23 35 46 .. 113 124 .. 109 127 .. 0.78 Alignments for each domain: == domain 1 score: 121.0 bits; conditional E-value: 7.7e-40 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqk.gaaCHtg 68 m+a+mn+eal++t e g+av++Srsr++lw+kGe+sg+vqkv+e+rldcDeD++llkv+q+ g aCHtg lcl|FitnessBrowser__Cup4G11:RR42_RS18880 31 MFAFMNREALQRTAEIGEAVFWSRSRKRLWHKGEESGHVQKVHEMRLDCDEDVVLLKVTQNdGIACHTG 99 99**********************************************************9679***** PP PRA-CH 69 ersCFy 74 ++sCF+ lcl|FitnessBrowser__Cup4G11:RR42_RS18880 100 RHSCFF 105 *****6 PP == domain 2 score: -2.3 bits; conditional E-value: 0.23 PRA-CH 35 tsgnvqkvkeir 46 +sg+ q+v+ + lcl|FitnessBrowser__Cup4G11:RR42_RS18880 113 ESGDWQTVEPVL 124 799999998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (135 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 3.74 // [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