Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_012967603.1 KVAR_RS07925 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >NCBI__GCF_000025465.1:WP_012967603.1 Length = 198 Score = 350 bits (899), Expect = e-102 Identities = 174/202 (86%), Positives = 184/202 (91%), Gaps = 4/202 (1%) Query: 1 MLTEQQRRELDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQR 60 MLTEQ LDWEKTDG+MP IVQHAVSGEVLMLGYMN EAL+KT +GKVTF+SRTKQR Sbjct: 1 MLTEQ----LDWEKTDGMMPAIVQHAVSGEVLMLGYMNKEALEKTEATGKVTFYSRTKQR 56 Query: 61 LWTKGETSGNFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGDTAHQWLFLYQLEQ 120 LWTKGETSGN LNVVSI PDCDNDTLLVL NPIGPTCHKGT+SCFG+T HQWLFLYQLEQ Sbjct: 57 LWTKGETSGNVLNVVSITPDCDNDTLLVLVNPIGPTCHKGTTSCFGETGHQWLFLYQLEQ 116 Query: 121 LLAERKSADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHL 180 LLAERK ADPE+SYTAKLYA GTKRIAQKVGEEGVETALAATV+DRFEL NEASDLMYHL Sbjct: 117 LLAERKHADPESSYTAKLYAGGTKRIAQKVGEEGVETALAATVNDRFELKNEASDLMYHL 176 Query: 181 LVLLQDQGLDLTTVIENLRKRH 202 LVLLQDQGLDL VI+NL+ RH Sbjct: 177 LVLLQDQGLDLGEVIDNLKSRH 198 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: 212 Number of extensions: 3 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: 203 Length of database: 198 Length adjustment: 21 Effective length of query: 182 Effective length of database: 177 Effective search space: 32214 Effective search space used: 32214 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_012967603.1 KVAR_RS07925 (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.12085.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-38 116.3 0.0 3.5e-38 115.7 0.0 1.3 1 lcl|NCBI__GCF_000025465.1:WP_012967603.1 KVAR_RS07925 bifunctional phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_012967603.1 KVAR_RS07925 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl- # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 115.7 0.0 3.5e-38 3.5e-38 1 73 [. 29 101 .. 29 102 .. 0.99 Alignments for each domain: == domain 1 score: 115.7 bits; conditional E-value: 3.5e-38 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtge 69 ml+ymn+ealekt +tgk+++ySr++q+lw+kGetsgnv++v++i+ dcD+D+ll+ v++ g++CH+g+ lcl|NCBI__GCF_000025465.1:WP_012967603.1 29 MLGYMNKEALEKTEATGKVTFYSRTKQRLWTKGETSGNVLNVVSITPDCDNDTLLVLVNPIGPTCHKGT 97 9******************************************************************** PP PRA-CH 70 rsCF 73 +sCF lcl|NCBI__GCF_000025465.1:WP_012967603.1 98 TSCF 101 **** PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (198 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: 5.23 // [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