Align phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19) (characterized)
to candidate WP_012284026.1 HM1_RS13850 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= reanno::HerbieS:HSERO_RS20310 (166 letters) >NCBI__GCF_000019165.1:WP_012284026.1 Length = 225 Score = 119 bits (298), Expect = 3e-32 Identities = 62/139 (44%), Positives = 91/139 (65%), Gaps = 11/139 (7%) Query: 1 MSISAKWLNKVKWDEVGLVPVIAQEVGSNDVLMFAWMNREALARTVEIGQAVYWSRSRKK 60 ++++ +++++K+D GL+P + Q+ S VLM A+MNRE++A+T+E GQ ++SRSRK+ Sbjct: 4 LNVAPSFIDELKFDAHGLIPAVIQDAASGRVLMVAYMNRESIAKTLETGQTHFYSRSRKE 63 Query: 61 LWHKGEESGHFQKVHEIRLDCDEDVVLLKVEQVAGIACHTGRHSCFFQKFE----GSADS 116 LWHKG SGHFQ+V + DCD D +L +VEQV G ACH G SCF E G+ DS Sbjct: 64 LWHKGATSGHFQQVTAVEYDCDRDCLLWQVEQV-GAACHEGSFSCFRGIGEVAGKGAVDS 122 Query: 117 GEWVT------VEPVLKDL 129 E V + +L+DL Sbjct: 123 AESVAGAGGSRIGAILEDL 141 Lambda K H 0.316 0.132 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: 109 Number of extensions: 6 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: 166 Length of database: 225 Length adjustment: 20 Effective length of query: 146 Effective length of database: 205 Effective search space: 29930 Effective search space used: 29930 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: 44 (21.6 bits)
Align candidate WP_012284026.1 HM1_RS13850 (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.9311.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-39 119.2 2.0 4.7e-39 118.5 2.0 1.4 1 lcl|NCBI__GCF_000019165.1:WP_012284026.1 HM1_RS13850 bifunctional phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_012284026.1 HM1_RS13850 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 118.5 2.0 4.7e-39 4.7e-39 1 73 [. 36 108 .. 36 109 .. 0.99 Alignments for each domain: == domain 1 score: 118.5 bits; conditional E-value: 4.7e-39 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtge 69 m+aymn+e+++ktletg++++ySrsr++lw+kG+tsg++q+v+ +++dcD+D+ll +veq gaaCH+g+ lcl|NCBI__GCF_000019165.1:WP_012284026.1 36 MVAYMNRESIAKTLETGQTHFYSRSRKELWHKGATSGHFQQVTAVEYDCDRDCLLWQVEQVGAACHEGS 104 9******************************************************************** PP PRA-CH 70 rsCF 73 sCF lcl|NCBI__GCF_000019165.1:WP_012284026.1 105 FSCF 108 **** PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (225 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 5.08 // [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