Align Purine nucleoside phosphorylase 1; PNP 1; Inosine phosphorylase; Inosine-guanosine phosphorylase; Purine nucleoside phosphorylase I; PNP I; Pu-NPase I; EC 2.4.2.1 (characterized)
to candidate SMc04123 SMc04123 purine nucleoside phosphorylase
Query= SwissProt::P77834 (274 letters) >FitnessBrowser__Smeli:SMc04123 Length = 265 Score = 217 bits (553), Expect = 2e-61 Identities = 111/241 (46%), Positives = 156/241 (64%), Gaps = 4/241 (1%) Query: 9 AAQFLKEKFPT-SPQIGLILGSGLGVLADEIEQAIKIPYSDIPNFPVSTVEGHAGQLVYG 67 AA FLK + +P+ G++LGSGLG L D + + ++IPY++IP FPVS+V GHAG+ V G Sbjct: 4 AADFLKGRLGAHAPRYGIVLGSGLGSLVDAVAEPLRIPYAEIPGFPVSSVSGHAGEFVAG 63 Query: 68 QLEGATVVVMQGRFHYYEGYSFDKVTFPVRVMKALGVEQLIVTNAAGGVNESFEPGDLMI 127 ++ V V+ GR HYYE + P+ +K +GVE LI+TN+AG + E PG +M Sbjct: 64 RIGDTPVAVLSGRAHYYERGDAKAMRVPIETLKRIGVENLILTNSAGSLREDMPPGSVMR 123 Query: 128 ISDHINNMGGNPLIGPNDSALGVRFPDMSEAYSKRLRQLAKDVANDIGLRVREGVYVANT 187 I+DHI G NPLIG RF M+ AY L ++ A +G+ + GVY+ + Sbjct: 124 IADHIAFAGANPLIGLESDE---RFVGMTNAYDAALAIGMEEAAERLGIPLARGVYMWFS 180 Query: 188 GPAYETPAEIRMIRVMGGDAVGMSTVPEVIVARHAGMEVLGISCISNMAAGILDQPLTHD 247 GP++ETPAEIRM R++G DAVGMSTVPEVI+AR G++V S ++N AAG+ L+H+ Sbjct: 181 GPSFETPAEIRMARILGADAVGMSTVPEVILARFFGLKVAAASVVTNFAAGMTGSELSHE 240 Query: 248 E 248 E Sbjct: 241 E 241 Lambda K H 0.319 0.137 0.388 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: 201 Number of extensions: 6 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: 274 Length of database: 265 Length adjustment: 25 Effective length of query: 249 Effective length of database: 240 Effective search space: 59760 Effective search space used: 59760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate SMc04123 SMc04123 (purine nucleoside phosphorylase)
to HMM TIGR01698 (purine nucleotide phosphorylase (EC 2.4.2.1))
# 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.carbon/TIGR01698.hmm # target sequence database: /tmp/gapView.27179.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01698 [M=245] Accession: TIGR01698 Description: PUNP: purine nucleotide phosphorylase 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-133 429.2 4.3 2.5e-133 429.0 4.3 1.0 1 lcl|FitnessBrowser__Smeli:SMc04123 SMc04123 purine nucleoside phosp Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc04123 SMc04123 purine nucleoside phosphorylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 429.0 4.3 2.5e-133 2.5e-133 2 245 .] 19 262 .. 18 262 .. 0.99 Alignments for each domain: == domain 1 score: 429.0 bits; conditional E-value: 2.5e-133 TIGR01698 2 laivlGsGlgalvealaetvelpyaeiPGfsapavaGhagrllrvrigdrsvlvlegrthayegkdvravvvpvr 76 ++ivlGsGlg+lv+a+ae++++pyaeiPGf++++v+Ghag+++++rigd++v+vl+gr+h+ye++d++a++vp++ lcl|FitnessBrowser__Smeli:SMc04123 19 YGIVLGSGLGSLVDAVAEPLRIPYAEIPGFPVSSVSGHAGEFVAGRIGDTPVAVLSGRAHYYERGDAKAMRVPIE 93 89************************************************************************* PP TIGR01698 77 aaraiGaelliltnaaGslreelgaGslvlladhinltarsPliGlesderfvdltdaydprlrigleelaervd 151 ++++iG+e+liltn+aGslre++++Gs++++adhi++++++PliGlesderfv++t+ayd++l+ig+ee+aer++ lcl|FitnessBrowser__Smeli:SMc04123 94 TLKRIGVENLILTNSAGSLREDMPPGSVMRIADHIAFAGANPLIGLESDERFVGMTNAYDAALAIGMEEAAERLG 168 *************************************************************************** PP TIGR01698 152 lplaeGvyaqfsGPsyetPaevrmarilGadlvGmstvletilarflGlevlavslvtnlaaGitgeelshaevk 226 +pla+Gvy++fsGPs+etPae+rmarilGad+vGmstv+e+ilarf+Gl+v+a+s+vtn+aaG+tg+elsh+e+k lcl|FitnessBrowser__Smeli:SMc04123 169 IPLARGVYMWFSGPSFETPAEIRMARILGADAVGMSTVPEVILARFFGLKVAAASVVTNFAAGMTGSELSHEETK 243 *************************************************************************** PP TIGR01698 227 avaaaagtrlaalladlia 245 ++a+++gtrlaa+l+++i+ lcl|FitnessBrowser__Smeli:SMc04123 244 QMAPLGGTRLAAILKEMIS 262 *****************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (245 nodes) Target sequences: 1 (265 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.58 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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