Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate Echvi_2517 Echvi_2517 phosphoribosyl-ATP pyrophosphohydrolase
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >FitnessBrowser__Cola:Echvi_2517 Length = 201 Score = 211 bits (536), Expect = 9e-60 Identities = 103/196 (52%), Positives = 140/196 (71%), Gaps = 1/196 (0%) Query: 9 ELDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETS 68 ++D++K +GL+P I+Q A + VLMLGYMN EAL KT ESGKVTFFSRTKQRLWTKGETS Sbjct: 5 KIDFDKVNGLVPAIIQDATTNAVLMLGYMNEEALQKTQESGKVTFFSRTKQRLWTKGETS 64 Query: 69 GNFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGD-TAHQWLFLYQLEQLLAERKS 127 GNF++V SI DCDNDTLL+ A+P+GP CH G +CF + + F+ QL ++ +RK+ Sbjct: 65 GNFMHVQSIKVDCDNDTLLIKADPVGPVCHTGADTCFDEKNTSKTAFIDQLRSIIKDRKN 124 Query: 128 ADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLLQDQ 187 + SYTA L+A G ++AQKVGEE VE + A + EA+DL++H LVLL+ + Sbjct: 125 NPTDKSYTASLFAKGINKVAQKVGEEAVEIVIEAKDDHKDLFMGEAADLLFHYLVLLEAK 184 Query: 188 GLDLTTVIENLRKRHQ 203 G +L V++ L +RH+ Sbjct: 185 GYELDEVMDVLIQRHK 200 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: 131 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: 201 Length adjustment: 21 Effective length of query: 182 Effective length of database: 180 Effective search space: 32760 Effective search space used: 32760 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 Echvi_2517 Echvi_2517 (phosphoribosyl-ATP pyrophosphohydrolase)
to HMM TIGR03188 (hisE: phosphoribosyl-ATP diphosphatase (EC 3.6.1.31))
# 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/TIGR03188.hmm # target sequence database: /tmp/gapView.4850.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03188 [M=84] Accession: TIGR03188 Description: histidine_hisI: phosphoribosyl-ATP diphosphatase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-34 101.9 0.3 1.5e-33 101.2 0.3 1.4 1 lcl|FitnessBrowser__Cola:Echvi_2517 Echvi_2517 phosphoribosyl-ATP py Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2517 Echvi_2517 phosphoribosyl-ATP pyrophosphohydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 101.2 0.3 1.5e-33 1.5e-33 2 84 .] 113 195 .. 112 195 .. 0.98 Alignments for each domain: == domain 1 score: 101.2 bits; conditional E-value: 1.5e-33 TIGR03188 2 eeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVllaekgv 75 ++L ++i++rk+++ ++Syta+l++kg++k+++KvgEEavE++i+ak+++k+ + EaaDll+h lVll++kg lcl|FitnessBrowser__Cola:Echvi_2517 113 DQLRSIIKDRKNNPTDKSYTASLFAKGINKVAQKVGEEAVEIVIEAKDDHKDLFMGEAADLLFHYLVLLEAKGY 186 799*********************************************************************** PP TIGR03188 76 sledvlaeL 84 +l++v+++L lcl|FitnessBrowser__Cola:Echvi_2517 187 ELDEVMDVL 195 ******987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (201 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: 8.57 // [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