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 351409 BT1881 purine nucleoside phosphorylase I (NCBI ptt file)
Query= SwissProt::P77834 (274 letters) >FitnessBrowser__Btheta:351409 Length = 269 Score = 280 bits (717), Expect = 2e-80 Identities = 136/263 (51%), Positives = 188/263 (71%), Gaps = 1/263 (0%) Query: 6 IEQAAQFLKEKFPTSPQIGLILGSGLGVLADEIEQAIKIPYSDIPNFPVSTVEGHAGQLV 65 I++ A FLK K TSP+ +ILG+GLG LADEI + +I YSDIPNFPVSTVEGH+G+L+ Sbjct: 5 IQETAAFLKGKMHTSPETAIILGTGLGSLADEITEKYEIKYSDIPNFPVSTVEGHSGKLI 64 Query: 66 YGQLEGATVVVMQGRFHYYEGYSFDKVTFPVRVMKALGVEQLIVTNAAGGVNESFEPGDL 125 +G+L ++ MQGRFHYYEGYS +VTFPVRVM+ LG++ L V+NA+GG NE+FE GDL Sbjct: 65 FGKLGNKDIMAMQGRFHYYEGYSMKEVTFPVRVMRELGIKTLFVSNASGGTNEAFEIGDL 124 Query: 126 MIISDHINNMGGNPLIGPNDSALGVRFPDMSEAYSKRLRQLAKDVANDIGLRVREGVYVA 185 MII+DHIN +PL G N G RFPDMSEAY K L + A ++A + G++V+ G+Y+ Sbjct: 125 MIITDHINYFPEHPLRGKN-IPYGPRFPDMSEAYDKELIRKADEIAQEKGIKVQHGIYIG 183 Query: 186 NTGPAYETPAEIRMIRVMGGDAVGMSTVPEVIVARHAGMEVLGISCISNMAAGILDQPLT 245 GP +ETPAE ++ ++G DAVGMSTVPEVIVA H G++V GIS I+++ ++ Sbjct: 184 TQGPTFETPAEYKLFHILGADAVGMSTVPEVIVANHCGIKVFGISVITDLGVEGKIVEVS 243 Query: 246 HDEVIETTEKVKADFLRFVKAIV 268 H+EV + + + ++ ++ Sbjct: 244 HEEVQKAADAAQPKMTTIMRELI 266 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: 252 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: 269 Length adjustment: 25 Effective length of query: 249 Effective length of database: 244 Effective search space: 60756 Effective search space used: 60756 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 351409 BT1881 (purine nucleoside phosphorylase I (NCBI ptt file))
to HMM TIGR01700 (purine nucleoside phosphorylase I, inosine and guanosine-specific (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/TIGR01700.hmm # target sequence database: /tmp/gapView.28942.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01700 [M=249] Accession: TIGR01700 Description: PNPH: purine nucleoside phosphorylase I, inosine and guanosine-specific 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-110 353.4 0.8 3.7e-110 353.2 0.8 1.0 1 lcl|FitnessBrowser__Btheta:351409 BT1881 purine nucleoside phospho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:351409 BT1881 purine nucleoside phosphorylase I (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 353.2 0.8 3.7e-110 3.7e-110 2 248 .. 22 266 .. 21 267 .. 0.97 Alignments for each domain: == domain 1 score: 353.2 bits; conditional E-value: 3.7e-110 TIGR01700 2 iaiilGsGlGelaekvedavildyseiPefpestveGhkGklvfGklegkkvvilqGrfhlyegydlakvtfPvrv 77 +aiilG+GlG+la++++++ ++ys+iP+fp stveGh+Gkl+fGkl++k ++++qGrfh+yegy++++vtfPvrv lcl|FitnessBrowser__Btheta:351409 22 TAIILGTGLGSLADEITEKYEIKYSDIPNFPVSTVEGHSGKLIFGKLGNKDIMAMQGRFHYYEGYSMKEVTFPVRV 97 79************************************************************************** PP TIGR01700 78 lkllGvealvvtnaaGgintefkvGdlmlikdhinllalnPliGpneekfGarfpdmsdaydkelrqkakeiakel 153 ++ lG+++l+v+na+Gg n f+ Gdlm+i+dhin+ + Pl+G n + +G+rfpdms+aydkel++ka eia+e lcl|FitnessBrowser__Btheta:351409 98 MRELGIKTLFVSNASGGTNEAFEIGDLMIITDHINYFPEHPLRGKNIP-YGPRFPDMSEAYDKELIRKADEIAQEK 172 *********************************************986.8************************** PP TIGR01700 154 ditlkeGvyvavtGPsyetpaevrllkklGadavGmstvpevivarhcGlrvlglslitnkaagildaelsdheev 229 +i++++G+y++ +GP +etpae++l++ lGadavGmstvpeviva+hcG++v+g+s+it+ +++ e+s heev lcl|FitnessBrowser__Btheta:351409 173 GIKVQHGIYIGTQGPTFETPAEYKLFHILGADAVGMSTVPEVIVANHCGIKVFGISVITDLGVEGKIVEVS-HEEV 247 *************************************************************9976666776.**** PP TIGR01700 230 levakkakekleklvsalv 248 ++a++a+ k++ ++ +l+ lcl|FitnessBrowser__Btheta:351409 248 QKAADAAQPKMTTIMRELI 266 **************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (249 nodes) Target sequences: 1 (269 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: 7.39 // [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