Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate 6937807 Sama_1948 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein (RefSeq)
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >FitnessBrowser__SB2B:6937807 Length = 208 Score = 249 bits (637), Expect = 2e-71 Identities = 127/207 (61%), Positives = 158/207 (76%), Gaps = 6/207 (2%) Query: 1 MLTEQQRRELDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQR 60 M E LDW+K DGL+P IVQ+ +SG+VLM GYM+ AL+KTL++G VTFFSR+KQR Sbjct: 1 MADETLLNRLDWDKQDGLIPAIVQNHLSGKVLMQGYMDKAALEKTLQTGMVTFFSRSKQR 60 Query: 61 LWTKGETSGNFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGDTAHQWLFLYQLEQ 120 LWTKGE+SGN L+++SIA DCDND+LLV P GPTCH GT SC+ D +H F+ LE Sbjct: 61 LWTKGESSGNVLSLISIAADCDNDSLLVQVLPKGPTCHTGTESCWQDGSHS--FIAGLES 118 Query: 121 LLAERKSA----DPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDL 176 L+ RK A + +SYTA L+ASGTKR+AQKVGEEG+ETALAA HD+ EL +EASDL Sbjct: 119 LIQGRKKACGAGEGGSSYTASLFASGTKRMAQKVGEEGLETALAAATHDKEELVDEASDL 178 Query: 177 MYHLLVLLQDQGLDLTTVIENLRKRHQ 203 ++HL+VLL+DQGL L + ENL KRHQ Sbjct: 179 LFHLMVLLEDQGLSLADITENLYKRHQ 205 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: 137 Number of extensions: 2 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: 208 Length adjustment: 21 Effective length of query: 182 Effective length of database: 187 Effective search space: 34034 Effective search space used: 34034 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 6937807 Sama_1948 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein (RefSeq))
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.23639.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-37 111.4 0.0 1.3e-36 110.7 0.0 1.3 1 lcl|FitnessBrowser__SB2B:6937807 Sama_1948 bifunctional phosphori Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937807 Sama_1948 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyropho # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 110.7 0.0 1.3e-36 1.3e-36 1 74 [] 33 106 .. 33 106 .. 0.99 Alignments for each domain: == domain 1 score: 110.7 bits; conditional E-value: 1.3e-36 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtgersCFy 74 m +ym++ alektl+tg ++++Srs+q+lw+kGe+sgnv+++ +i++dcD+D+ll++v +kg++CHtg++sC++ lcl|FitnessBrowser__SB2B:6937807 33 MQGYMDKAALEKTLQTGMVTFFSRSKQRLWTKGESSGNVLSLISIAADCDNDSLLVQVLPKGPTCHTGTESCWQ 106 99**********************************************************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (208 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: 4.90 // [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