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 Echvi_0304 Echvi_0304 purine nucleoside phosphorylase I, inosine and guanosine-specific
Query= SwissProt::P77834 (274 letters) >FitnessBrowser__Cola:Echvi_0304 Length = 282 Score = 252 bits (644), Expect = 6e-72 Identities = 129/264 (48%), Positives = 174/264 (65%) Query: 6 IEQAAQFLKEKFPTSPQIGLILGSGLGVLADEIEQAIKIPYSDIPNFPVSTVEGHAGQLV 65 I A ++ E+ P P++G+ILG+GLG L D+IE + Y DIP FP+STVE HAG+LV Sbjct: 14 ITAAVTYISEQHPFIPEVGIILGTGLGQLIDKIEVEASLSYKDIPCFPISTVETHAGELV 73 Query: 66 YGQLEGATVVVMQGRFHYYEGYSFDKVTFPVRVMKALGVEQLIVTNAAGGVNESFEPGDL 125 G L G +V M+GRFHYYEGY VTFPVRVM+ LG++QLIV+NAAGG++ +FE GD+ Sbjct: 74 LGTLHGVPIVAMKGRFHYYEGYDMKAVTFPVRVMRQLGIKQLIVSNAAGGLDPAFEVGDV 133 Query: 126 MIISDHINNMGGNPLIGPNDSALGVRFPDMSEAYSKRLRQLAKDVANDIGLRVREGVYVA 185 M+I+DHI+ NPL G N GVRFPDMSE Y + + A VA G++V +GVY Sbjct: 134 MLINDHIDLFPENPLRGKNLDDFGVRFPDMSEPYDQGWLEAAVRVAKQEGIKVHQGVYAG 193 Query: 186 NTGPAYETPAEIRMIRVMGGDAVGMSTVPEVIVARHAGMEVLGISCISNMAAGILDQPLT 245 GP ET AE R +R +G DAVGMSTVPEVIVAR + VL +S I+++ + + ++ Sbjct: 194 VQGPNLETKAEYRYLRTIGADAVGMSTVPEVIVARQMELPVLAMSAITDLCSPGKVKKIS 253 Query: 246 HDEVIETTEKVKADFLRFVKAIVR 269 EVI + R + +++R Sbjct: 254 IQEVIAAAAIAEPKMTRIIASLIR 277 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: 238 Number of extensions: 8 Number of successful extensions: 1 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: 282 Length adjustment: 25 Effective length of query: 249 Effective length of database: 257 Effective search space: 63993 Effective search space used: 63993 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 Echvi_0304 Echvi_0304 (purine nucleoside phosphorylase I, inosine and guanosine-specific)
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.26602.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-101 322.5 0.2 9.8e-101 322.3 0.2 1.0 1 lcl|FitnessBrowser__Cola:Echvi_0304 Echvi_0304 purine nucleoside pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_0304 Echvi_0304 purine nucleoside phosphorylase I, inosine and guanosine-specific # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 322.3 0.2 9.8e-101 9.8e-101 2 248 .. 31 276 .. 30 277 .. 0.98 Alignments for each domain: == domain 1 score: 322.3 bits; conditional E-value: 9.8e-101 TIGR01700 2 iaiilGsGlGelaekvedavildyseiPefpestveGhkGklvfGklegkkvvilqGrfhlyegydlakvtfPv 75 ++iilG+GlG+l++k+e + l y++iP fp stve h+G+lv+G+l+g+++v+++Grfh+yegyd++ vtfPv lcl|FitnessBrowser__Cola:Echvi_0304 31 VGIILGTGLGQLIDKIEVEASLSYKDIPCFPISTVETHAGELVLGTLHGVPIVAMKGRFHYYEGYDMKAVTFPV 104 89************************************************************************ PP TIGR01700 76 rvlkllGvealvvtnaaGgintefkvGdlmlikdhinllalnPliGpneekfGarfpdmsdaydkelrqkakei 149 rv+++lG+++l+v+naaGg+++ f+vGd+mli+dhi l + nPl+G n ++fG+rfpdms+ yd+ + + a + lcl|FitnessBrowser__Cola:Echvi_0304 105 RVMRQLGIKQLIVSNAAGGLDPAFEVGDVMLINDHIDLFPENPLRGKNLDDFGVRFPDMSEPYDQGWLEAAVRV 178 ************************************************************************** PP TIGR01700 150 akelditlkeGvyvavtGPsyetpaevrllkklGadavGmstvpevivarhcGlrvlglslitnkaagildael 223 ak+ +i++++Gvy +v+GP+ et ae+r l+++GadavGmstvpevivar+ l vl++s it+ + +++ lcl|FitnessBrowser__Cola:Echvi_0304 179 AKQEGIKVHQGVYAGVQGPNLETKAEYRYLRTIGADAVGMSTVPEVIVARQMELPVLAMSAITDLCSPGKVKKI 252 *****************************************************************996666666 PP TIGR01700 224 sdheevlevakkakekleklvsalv 248 s +ev+ +a a+ k+++++++l+ lcl|FitnessBrowser__Cola:Echvi_0304 253 S-IQEVIAAAAIAEPKMTRIIASLI 276 6.9******************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (249 nodes) Target sequences: 1 (282 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: 00:00:00.01 # Mc/sec: 6.62 // [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