Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_041530984.1 PERMA_RS01820 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >NCBI__GCF_000021565.1:WP_041530984.1 Length = 206 Score = 166 bits (419), Expect = 4e-46 Identities = 89/195 (45%), Positives = 119/195 (61%), Gaps = 8/195 (4%) Query: 17 GLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSGNFLNVVS 76 GL+PVI Q SG+VLM Y N EA+ KT+E+G T++SR++ LW KGETSGN VV Sbjct: 12 GLVPVITQSYYSGKVLMQAYANREAILKTVETGFATYYSRSRNELWIKGETSGNKQRVVD 71 Query: 77 IAPDCDNDTLLVLANPIGPTCHKGTSSCF--------GDTAHQWLFLYQLEQLLAERKSA 128 I DCD D++L L G CH G SCF + + L+ L + + ERK Sbjct: 72 IRVDCDGDSVLYLVVDYGVACHTGKESCFYRDIDFKEKEKPDPYEILHALYKKIEERKEK 131 Query: 129 DPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLLQDQG 188 PE SY AKL++ G+ +I QKVGEE VET +A D+ E+ EASDL++HLL+ L D G Sbjct: 132 RPEGSYVAKLFSKGSDKIIQKVGEEAVETVIALKNRDKNEIVYEASDLVFHLLIALVDSG 191 Query: 189 LDLTTVIENLRKRHQ 203 + L + E L KR++ Sbjct: 192 VKLEDIQEELLKRYK 206 Lambda K H 0.317 0.132 0.384 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: 100 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: 203 Length of database: 206 Length adjustment: 21 Effective length of query: 182 Effective length of database: 185 Effective search space: 33670 Effective search space used: 33670 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: 45 (21.9 bits)
Align candidate WP_041530984.1 PERMA_RS01820 (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.24472.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-37 112.4 0.2 6.6e-37 111.6 0.2 1.4 1 lcl|NCBI__GCF_000021565.1:WP_041530984.1 PERMA_RS01820 bifunctional phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021565.1:WP_041530984.1 PERMA_RS01820 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 111.6 0.2 6.6e-37 6.6e-37 1 74 [] 28 101 .. 28 101 .. 0.99 Alignments for each domain: == domain 1 score: 111.6 bits; conditional E-value: 6.6e-37 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtge 69 m ay+n+ea+ kt+etg a+yySrsr++lw kGetsgn q+v++ir+dcD+D++l+ v g aCHtg+ lcl|NCBI__GCF_000021565.1:WP_041530984.1 28 MQAYANREAILKTVETGFATYYSRSRNELWIKGETSGNKQRVVDIRVDCDGDSVLYLVVDYGVACHTGK 96 99******************************************************************* PP PRA-CH 70 rsCFy 74 +sCFy lcl|NCBI__GCF_000021565.1:WP_041530984.1 97 ESCFY 101 ****7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (206 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: 5.74 // [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