Align Purine nucleoside phosphorylase 2; Inosine-guanosine phosphorylase; Purine nucleoside phosphorylase II; PNP II; Xanthosine phosphorylase; EC 2.4.2.1 (characterized)
to candidate 16506 b2407 purine nucleoside phosphorylase (NCBI)
Query= SwissProt::P45563 (277 letters) >FitnessBrowser__Keio:16506 Length = 277 Score = 553 bits (1425), Expect = e-162 Identities = 277/277 (100%), Positives = 277/277 (100%) Query: 1 MSQVQFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVS 60 MSQVQFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVS Sbjct: 1 MSQVQFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVS 60 Query: 61 TVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGS 120 TVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGS Sbjct: 61 TVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGS 120 Query: 121 LRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEG 180 LRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEG Sbjct: 121 LRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEG 180 Query: 181 FPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNM 240 FPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNM Sbjct: 181 FPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNM 240 Query: 241 AEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277 AEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA Sbjct: 241 AEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277 Lambda K H 0.323 0.139 0.410 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: 443 Number of extensions: 7 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: 277 Length of database: 277 Length adjustment: 25 Effective length of query: 252 Effective length of database: 252 Effective search space: 63504 Effective search space used: 63504 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
Align candidate 16506 b2407 (purine nucleoside phosphorylase (NCBI))
to HMM TIGR01699 (xapA: xanthosine 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/TIGR01699.hmm # target sequence database: /tmp/gapView.6881.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01699 [M=248] Accession: TIGR01699 Description: XAPA: xanthosine 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-168 541.9 1.0 1.1e-167 541.7 1.0 1.0 1 lcl|FitnessBrowser__Keio:16506 b2407 purine nucleoside phosphor Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:16506 b2407 purine nucleoside phosphorylase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 541.7 1.0 1.1e-167 1.1e-167 1 248 [] 27 274 .. 27 274 .. 1.00 Alignments for each domain: == domain 1 score: 541.7 bits; conditional E-value: 1.1e-167 TIGR01699 1 rvafilgsglgdlvdqiendvaisyedlpgfpvssvhghagelvlgdlqgvpvvcmkgrghfyegkgmsimtdavrtfk 79 rvafilgsglg+l+dqien+vaisye+lpgfpvs+vhghagelvlg+lqgvpvvcmkgrghfyeg+gm+imtda+rtfk lcl|FitnessBrowser__Keio:16506 27 RVAFILGSGLGALADQIENAVAISYEKLPGFPVSTVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFK 105 79***************************************************************************** PP TIGR01699 80 llgcellfctnaagslrpevlagslvalkdhintmpgtplvglnddrfgerffslanaydkelradlakvakeediplt 158 llgcellfctnaagslrpev+agslvalkdhintmpgtp+vglnddrfgerffslanayd+e+ra+l+kvakee++plt lcl|FitnessBrowser__Keio:16506 106 LLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEGFPLT 184 ******************************************************************************* PP TIGR01699 159 egvfvsylgpnfetaaeirmmqiiggdvvgmsvvpevlsaahcdlkvvalsaitnlaeglsdvklsheqtlkaaklakv 237 egvfvsy+gpnfetaaeirmmqiiggdvvgmsvvpev+sa+hcdlkvva+saitn+aeglsdvklsh+qtl+aa+l+k+ lcl|FitnessBrowser__Keio:16506 185 EGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNMAEGLSDVKLSHAQTLAAAELSKQ 263 ******************************************************************************* PP TIGR01699 238 nfiklieaflk 248 nfi+li++fl+ lcl|FitnessBrowser__Keio:16506 264 NFINLICGFLR 274 *********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (277 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: 11.21 // [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