Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate 3609474 Dshi_2858 purine nucleoside phosphorylase (RefSeq)
Query= BRENDA::O34925 (233 letters) >FitnessBrowser__Dino:3609474 Length = 234 Score = 254 bits (650), Expect = 8e-73 Identities = 126/231 (54%), Positives = 174/231 (75%), Gaps = 1/231 (0%) Query: 1 MSVHIGAEKGQIADTVLLPGDPLRAKFIAETYLENVECYNEVRGMYGFTGTYKGKKISVQ 60 M++HIGA G IA+TVL+PGDPLRAK+ AET+L++ C NEVRGM GFTGT+ G ++++ Sbjct: 1 MTIHIGAAPGDIAETVLMPGDPLRAKWAAETFLDDPVCVNEVRGMLGFTGTWCGHRVTIH 60 Query: 61 GTGMGVPSISIYVNELIQSYDVQNLIRVGSCGAIRKDVKVRDVILAMTSSTDSQMNRVAF 120 G+GMG+PS+SIY NELI Y Q LIR+GS GA++ V +RDVILAMT S+ S + F Sbjct: 61 GSGMGMPSLSIYANELITEYGAQTLIRIGSTGAMQNHVALRDVILAMTCSSISTPSSGIF 120 Query: 121 GSVDFAPCADFELLKNAYDAAKDKGVPVTVGSVFTADQFYNDDSQI-EKLAKYGVLGVEM 179 ++FAPCAD+ LLK A AA KG VG ++++D FY++ + E++ ++GVLGVEM Sbjct: 121 CELNFAPCADWGLLKAAEAAAGAKGTKTHVGGIYSSDVFYDERPDLTEQMIRHGVLGVEM 180 Query: 180 ETTALYTLAAKHGRKALSILTVSDHVLTGEETTAEERQTTFHDMIEVALHS 230 E LYTLAA+HGR+AL++LTVSDH+LT + + ERQ++F DM+E+AL + Sbjct: 181 EAAELYTLAARHGRRALAVLTVSDHLLTHDALPSAERQSSFGDMVEIALEA 231 Lambda K H 0.317 0.133 0.370 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: 180 Number of extensions: 3 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: 233 Length of database: 234 Length adjustment: 23 Effective length of query: 210 Effective length of database: 211 Effective search space: 44310 Effective search space used: 44310 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: 46 (22.3 bits)
Align candidate 3609474 Dshi_2858 (purine nucleoside phosphorylase (RefSeq))
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.21826.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-93 296.6 0.0 6.7e-93 296.5 0.0 1.0 1 lcl|FitnessBrowser__Dino:3609474 Dshi_2858 purine nucleoside phos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609474 Dshi_2858 purine nucleoside phosphorylase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 296.5 0.0 6.7e-93 6.7e-93 1 229 [. 4 232 .. 4 234 .] 0.99 Alignments for each domain: == domain 1 score: 296.5 bits; conditional E-value: 6.7e-93 TIGR00107 1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiyskelikey 77 hi+a gdia++vl+pGdPlrak+ ae+fl+d+ +vnevrgmlgftG++ g+++++ G GmG+ps+siy++eli+ey lcl|FitnessBrowser__Dino:3609474 4 HIGAAPGDIAETVLMPGDPLRAKWAAETFLDDPVCVNEVRGMLGFTGTWCGHRVTIHGSGMGMPSLSIYANELITEY 80 9**************************************************************************** PP TIGR00107 78 evkkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaakkkgldvkvGnvfsad 154 + +++ir+Gs Ga++++v l+dvi+a+++s+ s + f e ++a++ad l+k+a aa +kg + +vG ++s+d lcl|FitnessBrowser__Dino:3609474 81 GAQTLIRIGSTGAMQNHVALRDVILAMTCSSISTPSSGIFCELNFAPCADWGLLKAAEAAAGAKGTKTHVGGIYSSD 157 ***************************************************************************** PP TIGR00107 155 lfystdkevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthealtaeerqktfkdmielalesv 229 +fy+++ + + + ++gvl+vemeaa ly++aa++g++al++ltvsdhl+th+al+++erq++f dm+e+ale++ lcl|FitnessBrowser__Dino:3609474 158 VFYDERPDLTEQMIRHGVLGVEMEAAELYTLAARHGRRALAVLTVSDHLLTHDALPSAERQSSFGDMVEIALEAA 232 ************************************************************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (232 nodes) Target sequences: 1 (234 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: 6.72 // [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