Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate 350905 BT1377 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (NCBI ptt file)
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >FitnessBrowser__Btheta:350905 Length = 203 Score = 207 bits (528), Expect = 8e-59 Identities = 103/195 (52%), Positives = 137/195 (70%), Gaps = 1/195 (0%) Query: 9 ELDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETS 68 ELD++K +GL+P I+Q + +VLMLG+MN EA DKT+E+GKVTFFSRTK RLWTKGE S Sbjct: 2 ELDFDKMNGLVPAIIQDNETRKVLMLGFMNKEAYDKTVETGKVTFFSRTKNRLWTKGEES 61 Query: 69 GNFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGDTAHQ-WLFLYQLEQLLAERKS 127 GNFL+VVSI DCDNDTLL+ A+P GP CH GT +C+G+ + +FL L+ + +R Sbjct: 62 GNFLHVVSIKADCDNDTLLIQADPAGPVCHTGTDTCWGEKNEEPVMFLKALQDFIDKRHE 121 Query: 128 ADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLLQDQ 187 P+ SYT L+ SG +IAQKVGEE VET + AT L E +DL+YH++VLL + Sbjct: 122 EMPQGSYTTSLFESGINKIAQKVGEEAVETVIEATNGTNERLIYEGADLIYHMIVLLTSK 181 Query: 188 GLDLTTVIENLRKRH 202 G + + L++RH Sbjct: 182 GYRIEDLARELQERH 196 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: 130 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: 203 Length adjustment: 21 Effective length of query: 182 Effective length of database: 182 Effective search space: 33124 Effective search space used: 33124 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 350905 BT1377 (phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (NCBI ptt file))
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.10124.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-37 114.0 0.0 1.8e-37 113.4 0.0 1.3 1 lcl|FitnessBrowser__Btheta:350905 BT1377 phosphoribosyl-AMP cycloh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350905 BT1377 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase ( # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 113.4 0.0 1.8e-37 1.8e-37 1 73 [. 26 98 .. 26 99 .. 0.99 Alignments for each domain: == domain 1 score: 113.4 bits; conditional E-value: 1.8e-37 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtgersCF 73 ml++mn+ea++kt+etgk++++Sr++++lw+kGe+sgn+++v++i++dcD+D+ll++++++g++CHtg+++C+ lcl|FitnessBrowser__Btheta:350905 26 MLGFMNKEAYDKTVETGKVTFFSRTKNRLWTKGEESGNFLHVVSIKADCDNDTLLIQADPAGPVCHTGTDTCW 98 9***********************************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (203 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: 4.33 // [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