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 WP_022601312.1 NSB1T_RS23310 purine-nucleoside phosphorylase
Query= SwissProt::P77834 (274 letters) >NCBI__GCF_000473955.1:WP_022601312.1 Length = 270 Score = 275 bits (703), Expect = 8e-79 Identities = 134/263 (50%), Positives = 186/263 (70%) Query: 6 IEQAAQFLKEKFPTSPQIGLILGSGLGVLADEIEQAIKIPYSDIPNFPVSTVEGHAGQLV 65 I++ A F+KE+FP P+ +ILG+GLG L + I ++ Y DIPNFP+STVEGH+G+L+ Sbjct: 5 IKETAAFIKERFPIIPETAIILGTGLGELVNHITNQKELAYKDIPNFPISTVEGHSGKLI 64 Query: 66 YGQLEGATVVVMQGRFHYYEGYSFDKVTFPVRVMKALGVEQLIVTNAAGGVNESFEPGDL 125 +G+L ++ MQGRFH+YEGY +VTFPVRVMK LGV+ L V+NAAGG+N +F+ GDL Sbjct: 65 FGKLGTKDIMAMQGRFHFYEGYDMKQVTFPVRVMKQLGVKTLFVSNAAGGMNPTFKVGDL 124 Query: 126 MIISDHINNMGGNPLIGPNDSALGVRFPDMSEAYSKRLRQLAKDVANDIGLRVREGVYVA 185 M+I DHIN +PL G N + LG RFPDMSEAYSKRL + A ++A + +++GVYV Sbjct: 125 MVIRDHINLFPEHPLHGKNYNELGPRFPDMSEAYSKRLIKKAFEIAEKNNIYLQQGVYVG 184 Query: 186 NTGPAYETPAEIRMIRVMGGDAVGMSTVPEVIVARHAGMEVLGISCISNMAAGILDQPLT 245 GP +ETPAE + +++GGDAVGMSTVPEVIVARH+ MEV IS I+++ + + + Sbjct: 185 TQGPTFETPAEYKYFKIIGGDAVGMSTVPEVIVARHSDMEVFAISVITDLGVEGIVEKAS 244 Query: 246 HDEVIETTEKVKADFLRFVKAIV 268 H+EV + + +K +V Sbjct: 245 HEEVQKAAALAQPKMTLIMKELV 267 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: 250 Number of extensions: 4 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: 270 Length adjustment: 25 Effective length of query: 249 Effective length of database: 245 Effective search space: 61005 Effective search space used: 61005 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 WP_022601312.1 NSB1T_RS23310 (purine-nucleoside phosphorylase)
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.975633.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-109 349.8 1.2 4.8e-109 349.6 1.2 1.0 1 NCBI__GCF_000473955.1:WP_022601312.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000473955.1:WP_022601312.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 349.6 1.2 4.8e-109 4.8e-109 2 248 .. 22 267 .. 21 268 .. 0.98 Alignments for each domain: == domain 1 score: 349.6 bits; conditional E-value: 4.8e-109 TIGR01700 2 iaiilGsGlGelaekvedavildyseiPefpestveGhkGklvfGklegkkvvilqGrfhlyegydlakvtfP 74 +aiilG+GlGel++++++++ l y++iP+fp stveGh+Gkl+fGkl+ k ++++qGrfh+yegyd+++vtfP NCBI__GCF_000473955.1:WP_022601312.1 22 TAIILGTGLGELVNHITNQKELAYKDIPNFPISTVEGHSGKLIFGKLGTKDIMAMQGRFHFYEGYDMKQVTFP 94 79*********************************************************************** PP TIGR01700 75 vrvlkllGvealvvtnaaGgintefkvGdlmlikdhinllalnPliGpneekfGarfpdmsdaydkelrqkak 147 vrv+k+lGv++l+v+naaGg+n++fkvGdlm+i+dhinl + Pl G n +++G+rfpdms+ay k l++ka NCBI__GCF_000473955.1:WP_022601312.1 95 VRVMKQLGVKTLFVSNAAGGMNPTFKVGDLMVIRDHINLFPEHPLHGKNYNELGPRFPDMSEAYSKRLIKKAF 167 ************************************************************************* PP TIGR01700 148 eiakelditlkeGvyvavtGPsyetpaevrllkklGadavGmstvpevivarhcGlrvlglslitnkaagild 220 eia++ +i l++Gvyv+ +GP +etpae++ +k +G+davGmstvpevivarh+ + v+++s+it+ +++ + NCBI__GCF_000473955.1:WP_022601312.1 168 EIAEKNNIYLQQGVYVGTQGPTFETPAEYKYFKIIGGDAVGMSTVPEVIVARHSDMEVFAISVITDLGVEGIV 240 *******************************************************************998777 PP TIGR01700 221 aelsdheevlevakkakekleklvsalv 248 +++s heev ++a a+ k++ ++++lv NCBI__GCF_000473955.1:WP_022601312.1 241 EKAS-HEEVQKAAALAQPKMTLIMKELV 267 8888.9*****************99998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (249 nodes) Target sequences: 1 (270 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: 17.33 // [ok]
This GapMind analysis is from Sep 24 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