Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate 199289 SO0092 purine nucleoside phosphorylase (NCBI ptt file)
Query= BRENDA::P0ABP8 (239 letters) >FitnessBrowser__MR1:199289 Length = 236 Score = 286 bits (733), Expect = 2e-82 Identities = 132/234 (56%), Positives = 178/234 (76%) Query: 1 MATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISV 60 M+TPHINA GDFA ++M GDPLRAK IAET+LED +EV NVRG+LGFTG YK + IS+ Sbjct: 1 MSTPHINANPGDFAKTIIMSGDPLRAKLIAETYLEDVKEVTNVRGILGFTGKYKSKDISI 60 Query: 61 MGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIR 120 MGHGMG PS SIY EL+ +GVK IRVGSCGA+ ++ L+D+++ MGA TDSK+NRIR Sbjct: 61 MGHGMGAPSASIYFHELMATYGVKNFIRVGSCGAISDNIHLKDLIVAMGASTDSKINRIR 120 Query: 121 FKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVE 180 F DHD AAIA++D+++ ++ K ++ +VGN+FS+DLFY P+ + +M KYG+LGVE Sbjct: 121 FLDHDLAAIANYDLLQACIEVLKTTTVNYKVGNVFSSDLFYRPNENDYTLMAKYGVLGVE 180 Query: 181 MEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVL 234 ME +Y +AAE +AL +CTV+DHI HE TA ER+T ++M+K+ALE+ + Sbjct: 181 MEVNALYALAAEHQCRALALCTVTDHIVQHEHLTADERRTDLHEMVKVALETAI 234 Lambda K H 0.322 0.138 0.401 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: 218 Number of extensions: 5 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: 239 Length of database: 236 Length adjustment: 23 Effective length of query: 216 Effective length of database: 213 Effective search space: 46008 Effective search space used: 46008 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 (21.9 bits) S2: 46 (22.3 bits)
Align candidate 199289 SO0092 (purine nucleoside phosphorylase (NCBI ptt file))
to HMM TIGR00107 (deoD: purine nucleoside 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/TIGR00107.hmm # target sequence database: /tmp/gapView.2010919.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00107 [M=232] Accession: TIGR00107 Description: deoD: purine nucleoside 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-103 330.8 1.5 2.4e-103 330.7 1.5 1.0 1 lcl|FitnessBrowser__MR1:199289 SO0092 purine nucleoside phospho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:199289 SO0092 purine nucleoside phosphorylase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 330.7 1.5 2.4e-103 2.4e-103 1 230 [. 5 234 .. 5 236 .] 0.99 Alignments for each domain: == domain 1 score: 330.7 bits; conditional E-value: 2.4e-103 TIGR00107 1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiyskelikeyev 79 hina+ gd+a++++++GdPlrak iae++led+kev++vrg+lgftGkyk+k is+mGhGmG ps siy +el+ +y+v lcl|FitnessBrowser__MR1:199289 5 HINANPGDFAKTIIMSGDPLRAKLIAETYLEDVKEVTNVRGILGFTGKYKSKDISIMGHGMGAPSASIYFHELMATYGV 83 9****************************************************************************** PP TIGR00107 80 kkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaakkkgldvkvGnvfsadlfys 158 k+ irvGsCGai+ +++lkd+i+a++astdsk+nr+rf ++dlaaia+++l+++ e k+ ++ kvGnvfs+dlfy+ lcl|FitnessBrowser__MR1:199289 84 KNFIRVGSCGAISDNIHLKDLIVAMGASTDSKINRIRFLDHDLAAIANYDLLQACIEVLKTTTVNYKVGNVFSSDLFYR 162 ******************************************************************************* PP TIGR00107 159 tdkevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthealtaeerqktfkdmielalesvs 230 ++++ l++kygvl+veme +alya+aae++ +al+l+tv+dh+v he+lta+er++ +++m+++ale++ lcl|FitnessBrowser__MR1:199289 163 PNENDYTLMAKYGVLGVEMEVNALYALAAEHQCRALALCTVTDHIVQHEHLTADERRTDLHEMVKVALETAI 234 ********************************************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (232 nodes) Target sequences: 1 (236 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: 18.15 // [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