Align Phosphoribosyl-AMP cyclohydrolase; PRA-CH; EC 3.5.4.19 (uncharacterized)
to candidate GFF5534 PS417_28325 phosphoribosyl-AMP cyclohydrolase
Query= curated2:Q1QWC3 (146 letters) >FitnessBrowser__WCS417:GFF5534 Length = 137 Score = 175 bits (443), Expect = 3e-49 Identities = 88/136 (64%), Positives = 99/136 (72%) Query: 1 MTQRFKQLETAAQGTREATRDLLDAARWNDAGLIPAIAQQHDSGEVLMMAWMNRAALEET 60 MT LE AA G+R +LDA WN GLI AIAQQH SGEVLM+AWMNR AL+ET Sbjct: 1 MTLSMLDLEGAAVGSRFPLEPVLDALPWNRDGLIAAIAQQHGSGEVLMLAWMNRQALKET 60 Query: 61 LATGRVCYWSRSRGKPWRKGESSGQVQQLVTAHLDCDGDTLLLGVDQQGPACHTGRRSCF 120 L TG+VCYWSRSR + WRKGESSG QQLV A LDCDGD +LL VDQQG ACHTGR +CF Sbjct: 61 LDTGQVCYWSRSRQQLWRKGESSGHWQQLVEARLDCDGDAVLLIVDQQGTACHTGRPTCF 120 Query: 121 YVALGADTAHVDSAPL 136 Y A+ D H+ + PL Sbjct: 121 YNAIDGDYVHIITEPL 136 Lambda K H 0.319 0.132 0.414 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: 106 Number of extensions: 2 Number of successful extensions: 1 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: 146 Length of database: 137 Length adjustment: 16 Effective length of query: 130 Effective length of database: 121 Effective search space: 15730 Effective search space used: 15730 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 42 (20.8 bits)
Align candidate GFF5534 PS417_28325 (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.31181.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-40 122.2 0.4 4.6e-40 121.7 0.4 1.2 1 lcl|FitnessBrowser__WCS417:GFF5534 PS417_28325 phosphoribosyl-AMP c Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF5534 PS417_28325 phosphoribosyl-AMP cyclohydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 121.7 0.4 4.6e-40 4.6e-40 1 74 [] 48 121 .. 48 121 .. 0.99 Alignments for each domain: == domain 1 score: 121.7 bits; conditional E-value: 4.6e-40 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtgersCFy 74 mla+mn++al++tl+tg+++y+Srsrq+lw+kGe+sg+ q+++e rldcD+Da+ll v+q+g+aCHtg+ +CFy lcl|FitnessBrowser__WCS417:GFF5534 48 MLAWMNRQALKETLDTGQVCYWSRSRQQLWRKGESSGHWQQLVEARLDCDGDAVLLIVDQQGTACHTGRPTCFY 121 9************************************************************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (137 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: 4.87 // [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