Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_013841341.1 DESRU_RS06620 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >NCBI__GCF_000215085.1:WP_013841341.1 Length = 229 Score = 147 bits (370), Expect = 2e-40 Identities = 86/216 (39%), Positives = 120/216 (55%), Gaps = 29/216 (13%) Query: 17 GLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSGNFLNVVS 76 GL+P IVQ S EVLM+ +MN EA++KTL +G+ F+SR++Q +W KGETSG+ V Sbjct: 14 GLIPAIVQEVRSREVLMMAWMNQEAVEKTLATGETWFYSRSRQAMWKKGETSGHVQRVKG 73 Query: 77 IAPDCDNDTLLVLANPI-GPTCHKGTSSCFGD---------------------------- 107 + DCD DTLLVLA G CH+G +SCF + Sbjct: 74 LYYDCDADTLLVLAEQEGGAACHEGYTSCFHNRVNPDRSVSIEGEKKFEPAQVYGGQEAR 133 Query: 108 TAHQWLFLYQLEQLLAERKSADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRF 167 T+ + L +++ RK+ PE +YT L+ G +I +KVGEE E + A + + Sbjct: 134 TSADPEIINDLFRVILSRKAERPEGAYTTYLFDQGVDKICKKVGEECAEVIIGAKNNSKE 193 Query: 168 ELTNEASDLMYHLLVLLQDQGLDLTTVIENLRKRHQ 203 ELT EA+DLMYHLLVLL +QG+ + L KR + Sbjct: 194 ELTYEAADLMYHLLVLLANQGISPEEIYRELAKRRK 229 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: 138 Number of extensions: 6 Number of successful extensions: 3 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: 229 Length adjustment: 22 Effective length of query: 181 Effective length of database: 207 Effective search space: 37467 Effective search space used: 37467 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_013841341.1 DESRU_RS06620 (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.3129053.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-38 116.9 1.2 2.2e-38 116.3 1.2 1.3 1 NCBI__GCF_000215085.1:WP_013841341.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013841341.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 116.3 1.2 2.2e-38 2.2e-38 1 74 [] 30 104 .. 30 104 .. 0.98 Alignments for each domain: == domain 1 score: 116.3 bits; conditional E-value: 2.2e-38 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkg.aaCHtgersC 72 m+a+mn+ea+ektl+tg++++ySrsrq +wkkGetsg+vq+vk +++dcD+D+ll+ +eq+g aaCH+g++sC NCBI__GCF_000215085.1:WP_013841341.1 30 MMAWMNQEAVEKTLATGETWFYSRSRQAMWKKGETSGHVQRVKGLYYDCDADTLLVLAEQEGgAACHEGYTSC 102 9************************************************************649********* PP PRA-CH 73 Fy 74 F+ NCBI__GCF_000215085.1:WP_013841341.1 103 FH 104 *6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (229 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: 16.04 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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